diff --git a/buildscripts/build_manuals_mcstas b/buildscripts/build_manuals_mcstas index f3209b13b3..c4327feb6e 100755 --- a/buildscripts/build_manuals_mcstas +++ b/buildscripts/build_manuals_mcstas @@ -14,6 +14,7 @@ echo echo LaTeX build of McStas manuals v $1 done! echo cp dist/mcstas-manuals-$1-noarch-not-packaged.work/*pdf docpkg/manuals/mcstas +cp dist/mcstas-manuals-$1-noarch-not-packaged.work/*-html.tgz docpkg/manuals/mcstas 2>/dev/null || echo "(no HTML manual .tgz archives found -- htlatex/tex4ht not available during this build?)" echo -echo Consider doing a git commit for the PDF files in docpkg/manuals/mcstas, as these have now been updated: +echo Consider doing a git commit for the PDF and HTML-manual files in docpkg/manuals/mcstas, as these have now been updated: git status docpkg/manuals/mcstas diff --git a/buildscripts/build_manuals_mcxtrace b/buildscripts/build_manuals_mcxtrace index 25b61e3c4d..ba0d80cee7 100755 --- a/buildscripts/build_manuals_mcxtrace +++ b/buildscripts/build_manuals_mcxtrace @@ -14,6 +14,7 @@ echo echo LaTeX build of McXtrace manuals v $1 done! echo cp dist/mcxtrace-manuals-$1-noarch-not-packaged.work/*pdf docpkg/manuals/mcxtrace +cp dist/mcxtrace-manuals-$1-noarch-not-packaged.work/*-html.tgz docpkg/manuals/mcxtrace 2>/dev/null || echo "(no HTML manual .tgz archives found -- htlatex/tex4ht not available during this build?)" echo -echo Consider doing a git commit for the PDF files in docpkg/manuals/mcxtrace, as these have now been updated: +echo Consider doing a git commit for the PDF and HTML-manual files in docpkg/manuals/mcxtrace, as these have now been updated: git status docpkg/manuals/mcxtrace diff --git a/docpkg/manuals/mcstas/CMakeLists.txt b/docpkg/manuals/mcstas/CMakeLists.txt index 73815283cf..fdc171ba47 100644 --- a/docpkg/manuals/mcstas/CMakeLists.txt +++ b/docpkg/manuals/mcstas/CMakeLists.txt @@ -54,3 +54,31 @@ install(FILES "${PROJECT_SOURCE_DIR}/Component_manual.pdf" DESTINATION "${MANDEST}" RENAME "${CMANUAL}" ) + +# --- HTML manuals: ship the .tgz archives alongside the PDFs, and extract +# each into its own subdirectory under ${DEST_DATADIR_DOC} at install time. +install(FILES "${PROJECT_SOURCE_DIR}/manual-html.tgz" + DESTINATION "${MANDEST}" +) + +install(FILES "${PROJECT_SOURCE_DIR}/Component_manual-html.tgz" + DESTINATION "${MANDEST}" +) + +install(CODE " + set(_extract_dir \"\$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/${MANDEST}/${FLAVOR}-manual\") + file(MAKE_DIRECTORY \"\${_extract_dir}\") + execute_process( + COMMAND \"${CMAKE_COMMAND}\" -E tar xzf \"${PROJECT_SOURCE_DIR}/manual-html.tgz\" + WORKING_DIRECTORY \"\${_extract_dir}\" + ) +") + +install(CODE " + set(_extract_dir \"\$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/${MANDEST}/${FLAVOR}-components\") + file(MAKE_DIRECTORY \"\${_extract_dir}\") + execute_process( + COMMAND \"${CMAKE_COMMAND}\" -E tar xzf \"${PROJECT_SOURCE_DIR}/Component_manual-html.tgz\" + WORKING_DIRECTORY \"\${_extract_dir}\" + ) +") diff --git a/docpkg/manuals/mcstas/Component_manual-html.tgz b/docpkg/manuals/mcstas/Component_manual-html.tgz new file mode 100644 index 0000000000..67a524c8f7 Binary files /dev/null and b/docpkg/manuals/mcstas/Component_manual-html.tgz differ diff --git a/docpkg/manuals/mcstas/Component_manual.pdf b/docpkg/manuals/mcstas/Component_manual.pdf index 90b93e70e0..855b63b292 100644 Binary files a/docpkg/manuals/mcstas/Component_manual.pdf and b/docpkg/manuals/mcstas/Component_manual.pdf differ diff --git a/docpkg/manuals/mcstas/manual-html.tgz b/docpkg/manuals/mcstas/manual-html.tgz new file mode 100644 index 0000000000..ee62b743f4 Binary files /dev/null and b/docpkg/manuals/mcstas/manual-html.tgz differ diff --git a/docpkg/manuals/mcstas/manual.pdf b/docpkg/manuals/mcstas/manual.pdf index 95e3d9713d..be9e3e5124 100644 Binary files a/docpkg/manuals/mcstas/manual.pdf and b/docpkg/manuals/mcstas/manual.pdf differ diff --git a/docpkg/manuals/mcxtrace/CMakeLists.txt b/docpkg/manuals/mcxtrace/CMakeLists.txt index 0c677c5076..3388d1920a 100644 --- a/docpkg/manuals/mcxtrace/CMakeLists.txt +++ b/docpkg/manuals/mcxtrace/CMakeLists.txt @@ -54,3 +54,31 @@ install(FILES "${PROJECT_SOURCE_DIR}/Component_manual.pdf" DESTINATION "${MANDEST}" RENAME "${CMANUAL}" ) + +# --- HTML manuals: ship the .tgz archives alongside the PDFs, and extract +# each into its own subdirectory under ${DEST_DATADIR_DOC} at install time. +install(FILES "${PROJECT_SOURCE_DIR}/manual-html.tgz" + DESTINATION "${MANDEST}" +) + +install(FILES "${PROJECT_SOURCE_DIR}/Component_manual-html.tgz" + DESTINATION "${MANDEST}" +) + +install(CODE " + set(_extract_dir \"\$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/${MANDEST}/${FLAVOR}-manual\") + file(MAKE_DIRECTORY \"\${_extract_dir}\") + execute_process( + COMMAND \"${CMAKE_COMMAND}\" -E tar xzf \"${PROJECT_SOURCE_DIR}/manual-html.tgz\" + WORKING_DIRECTORY \"\${_extract_dir}\" + ) +") + +install(CODE " + set(_extract_dir \"\$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/${MANDEST}/${FLAVOR}-components\") + file(MAKE_DIRECTORY \"\${_extract_dir}\") + execute_process( + COMMAND \"${CMAKE_COMMAND}\" -E tar xzf \"${PROJECT_SOURCE_DIR}/Component_manual-html.tgz\" + WORKING_DIRECTORY \"\${_extract_dir}\" + ) +") diff --git a/docpkg/manuals/mcxtrace/Component_manual-html.tgz b/docpkg/manuals/mcxtrace/Component_manual-html.tgz new file mode 100644 index 0000000000..21bf3448a8 Binary files /dev/null and b/docpkg/manuals/mcxtrace/Component_manual-html.tgz differ diff --git a/docpkg/manuals/mcxtrace/Component_manual.pdf b/docpkg/manuals/mcxtrace/Component_manual.pdf index c3f576a80b..1f9e63b691 100644 Binary files a/docpkg/manuals/mcxtrace/Component_manual.pdf and b/docpkg/manuals/mcxtrace/Component_manual.pdf differ diff --git a/docpkg/manuals/mcxtrace/manual-html.tgz b/docpkg/manuals/mcxtrace/manual-html.tgz new file mode 100644 index 0000000000..60af7588af Binary files /dev/null and b/docpkg/manuals/mcxtrace/manual-html.tgz differ diff --git a/docpkg/manuals/mcxtrace/manual.pdf b/docpkg/manuals/mcxtrace/manual.pdf index c09ba4caf2..eb69cebff3 100644 Binary files a/docpkg/manuals/mcxtrace/manual.pdf and b/docpkg/manuals/mcxtrace/manual.pdf differ diff --git a/docs/GRAMMAR/Component/COMPONENT_Grammar.html b/docs/GRAMMAR/Component/COMPONENT_Grammar.html index 772ddf7bf7..fe24b82882 100644 --- a/docs/GRAMMAR/Component/COMPONENT_Grammar.html +++ b/docs/GRAMMAR/Component/COMPONENT_Grammar.html @@ -6,7 +6,7 @@ McStas / McXtrace COMPONENT grammar +""" + +def find_toc_source(doc): + """Return (filename, toc_html) for whichever generated page contains + the actual \\tableofcontents output -- tex4ht wraps it in +
...
(the literal word 'Contents' + inside it is just the first entry's link text, not a heading tag).""" + for fn in sorted(glob.glob(f"{doc}*.html")): + with open(fn, encoding="utf-8", errors="ignore") as f: + content = f.read() + m = re.search( + r'(
.*?
)', + content, re.IGNORECASE | re.DOTALL) + if m: + return fn, m.group(1) + return None, None + +def find_title(master_fn): + """Extract the manual's title as plain text from the master page. + Prefer the clean

...

that \\maketitle + produces; fall back to the tag (which may be duplicated due + to how tex4ht records TITLE metadata) if that class isn't found.""" + with open(master_fn, encoding="utf-8", errors="ignore") as f: + content = f.read() + m = re.search(r'<h2 class="titleHead">(.*?)</h2>', content, re.IGNORECASE | re.DOTALL) + if not m: + m = re.search(r'<title>(.*?)', content, re.IGNORECASE | re.DOTALL) + if not m: + return None + text = re.sub(r'<[^>]+>', ' ', m.group(1)) # strip any inline tags + text = re.sub(r'\s+', ' ', text).strip() + # crude de-duplication for the -tag fallback case, where the + # same title can appear twice separated by a comma-space + half = len(text) // 2 + if len(text) > 20 and text[:half].strip().rstrip(',') == text[half:].strip().lstrip(', '): + text = text[:half].strip().rstrip(',') + return text + +LOGO_FILENAMES = {"DTU_logo.png", "DTU_logo", "DTU_logo-.png", "DTU_logo-", + "mcstas_logo_reflection.png", "mcstas_logo_reflection", + "mcxtrace_logo", "mcxtrace_logo.png"} + +def mark_content_figures(content): + """Tag every <img> tag with class="mccode-content-figure", except the + known front-page logos (matched by filename, so this works regardless + of which page an image appears on) -- lets CSS grow content figures + without also blowing up the small, intentionally-sized logos.""" + def replacer(m): + img_tag = m.group(0) + src_match = re.search(r'src="([^"]+)"', img_tag) + if not src_match: + return img_tag + basename = src_match.group(1).rsplit('/', 1)[-1] + if basename in LOGO_FILENAMES: + return img_tag + if 'class="' in img_tag: + return re.sub(r'class="', 'class="mccode-content-figure ', img_tag, count=1) + return img_tag[:4] + ' class="mccode-content-figure"' + img_tag[4:] + return re.sub(r'<img\b[^>]*>', replacer, content, flags=re.IGNORECASE) + +# Every custom (non-standard) LaTeX macro found to be used inside math mode +# anywhere across the manuals (verified empirically against the actual +# generated output, not just recalled from memory) -- tex4ht's MathJax mode +# passes math source through un-expanded, so MathJax needs to be told about +# each of these directly; a few are flavour/chapter-specific but harmless to +# register everywhere (an unused macro registration is a no-op). +MATHJAX_MACROS = { + "PB": r"\mathbf{P}", "tP": r"\hat{\mathbf{P}}", "SB": r"\mathbf{S}", + "sB": r"\mathbf{s}", "BB": r"\mathbf{B}", "nB": r"\mathbf{n}", + "muB": r"\boldsymbol{\mu}", "muno": r"\hat{\boldsymbol{\mu}}", + "tauB": r"\boldsymbol{\sigma}", "dB": r"\mathbf{d}", "lB": r"\mathbf{l}", + "RB": r"\mathbf{R}", "Io": r"\hat{\mathbf{I}}", "so": r"\hat{\mathbf{s}}", + "sigmao": r"\boldsymbol{\hat\sigma}", "sigmaH": r"\hat\sigma", + "rhoo": r"\hat\rho", "alphao": r"\boldsymbol{\alpha}", + "betao": r"\boldsymbol{\beta}", "Q": r"\mathbf{Q}", + "tQ": r"\hat{\mathbf{Q}}", "tN": r"\hat{\mathbf{N}}", "FN": r"F_N", + "FM": r"F_M", "Ru": r"R_\uparrow", "Rd": r"R_\downarrow", + "nup": r"n^\uparrow", "nd": r"n^\downarrow", "Pu": r"P^\uparrow", + "Pd": r"P^\downarrow", "chiU": r"\chi_\uparrow", "chiD": r"\chi_\downarrow", + "madsq": r"\overline{|F_N(\mathbf{Q})|^2}", + "sqmad": r"\left|\overline{F_N(\mathbf{Q})}\right|^2", + "bd": r"\overline{|B_{ld}|^2}", "kappaB": r"\boldsymbol{\kappa}", + "etaB": r"\boldsymbol{\eta}", "alphaB": r"\boldsymbol{\alpha}", + "sigmaB": r"\boldsymbol{\sigma}", "Ombold": r"\boldsymbol{\Omega}", +} + +def inject_mathjax_macros(content): + """Replace tex4ht's default window.MathJax config (just tex.tags) with + an extended one that also registers MATHJAX_MACROS, so custom LaTeX + macros used in equations actually render instead of showing as raw + source text. No-op (returns content unchanged) if this page has no + MathJax config block at all (i.e. no math on the page).""" + new_config = ('<script>window.MathJax = { tex: { tags: "ams", macros: ' + + json.dumps(MATHJAX_MACROS) + ' } }; </script>') + content, n = re.subn(r'<script>window\.MathJax\s*=.*?</script>', + lambda m: new_config, content, count=1, flags=re.DOTALL) + return content + +def linkify_images(content): + """Wrap every <img> tag in <a href="SAME_SRC" target="_blank">, so + clicking any figure opens the raw image standalone in a new tab.""" + def replacer(m): + img_tag = m.group(0) + src_match = re.search(r'src="([^"]+)"', img_tag) + if not src_match: + return img_tag + return f'<a href="{src_match.group(1)}" target="_blank">{img_tag}</a>' + return re.sub(r'<img\b[^>]*>', replacer, content, flags=re.IGNORECASE) + +def inject(doc, toc_html, header_html): + sidebar = f'<nav id="mccode-toc-sidebar">{toc_html}</nav>' + files = sorted(glob.glob(f"{doc}*.html")) + changed = 0 + for fn in files: + with open(fn, encoding="utf-8", errors="ignore") as f: + content = f.read() + if 'id="mccode-toc-sidebar"' in content: + continue # already injected (re-run safety) + content = linkify_images(content) + content = mark_content_figures(content) + content = inject_mathjax_macros(content) + # Insert CSS + sidebar right after <body ...>, then the header bar, + # then open the content div; close it right before </body>. + content, n1 = re.subn( + r'(<body[^>]*>)', + r'\1' + SIDEBAR_CSS + sidebar + header_html + '<div id="mccode-page-content">', + content, count=1, flags=re.IGNORECASE) + content, n2 = re.subn( + r'(</body>)', + r'</div>\1', + content, count=1, flags=re.IGNORECASE) + if n1 and n2: + with open(fn, "w", encoding="utf-8") as f: + f.write(content) + changed += 1 + return changed + +if __name__ == "__main__": + if len(sys.argv) != 2: + sys.exit(f"Usage: {sys.argv[0]} <DOC>") + doc = sys.argv[1] + src_fn, toc_html = find_toc_source(doc) + if not toc_html: + print(f"[inject-toc-sidebar] WARNING: could not find a table of " + f"contents in any {doc}*.html file -- skipping sidebar/header " + f"injection (pages left unmodified).", file=sys.stderr) + sys.exit(0) # non-fatal: don't break the build over this + title = find_title(src_fn) + base_page = os.path.basename(src_fn) + if title: + header_html = (f'<div id="mccode-page-header">' + f'<a href="{base_page}">{title}</a></div>') + else: + print(f"[inject-toc-sidebar] WARNING: could not extract a title " + f"from {src_fn} -- injecting sidebar without a header bar.", + file=sys.stderr) + header_html = '' + n = inject(doc, toc_html, header_html) + print(f"[inject-toc-sidebar] TOC/title sourced from {src_fn}; " + f"sidebar{'+header' if title else ''} injected into {n} page(s).") diff --git a/docs/manuals/mcstas/instrum.tex b/docs/manuals/mcstas/instrum.tex index 2a482ad6d1..658946d3a1 100644 --- a/docs/manuals/mcstas/instrum.tex +++ b/docs/manuals/mcstas/instrum.tex @@ -6,7 +6,7 @@ \chapter{Instrument examples} In this section, we present a few typical instruments from the \MCS example library. We then give a longer description of three selected worked examples: a simple sample test instrument (\ref{s:V-instr}), the historical -Ris\o\ triple-axis spectrometer TAS1 (\ref{s:TAS1}), and the ISIS +Risø triple-axis spectrometer TAS1 (\ref{s:TAS1}), and the ISIS time-of-flight spectrometer PRISMA (\ref{s:PRISMA}). These instrument files are included in the \MCS distribution in the @@ -46,7 +46,7 @@ \subsection{Templates} \subsection{Risoe} -Historical Ris\o\ National Laboratory instruments, including the TAS1 +Historical Risø National Laboratory instruments, including the TAS1 triple-axis spectrometer family described in detail in section \ref{s:TAS1} below. TAS1 was decommissioned along with the DR3 reactor, but its detailed McStas model remains one of the most thoroughly @@ -121,7 +121,7 @@ \subsection{Tests\_* categories} \subsection{Other facility categories} -Further contributed instrument models exist for BNL, DTU, FZ\_J\"ulich, HZB, +Further contributed instrument models exist for BNL, DTU, FZ\_Jülich, HZB, HighNESS, LLB, Necsa, PSI, SINE2020, SNS, TRIGA and TU~Delft, alongside a \texttt{Mantid} category (instruments paired with Mantid IDF export via \texttt{mcdisplay-mantid\_xml}, see section~\ref{s:mcdisplay}) and a @@ -185,7 +185,7 @@ \section{The triple axis spectrometer TAS1} With this instrument definition, we have tried to create a very detailed model of the conventional cold-source triple-axis spectrometer TAS1 at the now closed neutron source DR3 of -Ris\o\ National Laboratory. +Risø National Laboratory. Except for the cold source itself, all components used have quite realistic properties. Furthermore, the overall geometry of the instrument has been adapted from diff --git a/docs/manuals/mcstas/intro.tex b/docs/manuals/mcstas/intro.tex index 0155c997a7..be01ee7175 100644 --- a/docs/manuals/mcstas/intro.tex +++ b/docs/manuals/mcstas/intro.tex @@ -53,7 +53,7 @@ \section{Development of Monte Carlo neutron simulation} to users for training, experiment planning, diagnostics, and data analysis. -In the late 90'ies at Ris\o\ National Laboratory, +In the late 90'ies at Risø National Laboratory, simulation tools were urgently needed, not only to better utilize existing instruments ({\em e.g.} RITA-1 and RITA-2~\cite{cjp_73_697,pb_241_50,pb_283_343}), @@ -76,7 +76,7 @@ \section{Development of Monte Carlo neutron simulation} several systematic comparative studies of the European instrument Monte Carlo codes. Hence, PSI has also become a part of the core \MCS team. -Since year 2001 Ris\o\ was no longer a neutron source, and the authors +Since year 2001 Risø was no longer a neutron source, and the authors from that site have moved on to positions at University of Copenhagen (NBI) and Technical University of Denmark (DTU Physics), hence these two partners have joined the core \MCS team. @@ -341,7 +341,7 @@ \section{Overview} %\paragraph{The kernel.} Here are located some geometrical tools %({\em e.g.} intersection between a line and various surfaces) %and other elemental tools ({\em e.g.} creation and annihilation -%of a neutron). The kernel is maintained by the Ris\o\ group. +%of a neutron). The kernel is maintained by the Risø group. %\paragraph{The components.} Here resides the code for simulation % of the individual spectrometer components @@ -351,7 +351,7 @@ \section{Overview} % Interested users are encouraged to modify existing components and to % design new ones. % A library of general and well documented components -% is being maintained by the Ris\o\ group. +% is being maintained by the Risø group. %\paragraph{The instruments.} An instrument definition is written % in the \MCS meta-language, which is a means of positioning @@ -360,7 +360,7 @@ \section{Overview} % $(\omega,2\theta)$ pairs of a standard triple-axis spectrometer. % For each specific instrument, a new instrument definition % should be written. This will usually be done by the users, -% possibly in collaboration with the Ris\o\ group. +% possibly in collaboration with the Risø group. %\paragraph{The instrument control interface.} % Here, the setting parameters of the @@ -369,7 +369,7 @@ \section{Overview} % In the present version 1.0, the control interface % consists of a very preliminary MATLAB program, % but we expect soon to implement a simulation version of the -% Ris\o\ spectrometer control software TASCOM. +% Risø spectrometer control software TASCOM. % By using the preprogrammed scans or the TASCOM programming features, % the user will then be able easily to perform the desired simulations. % Later, interfaces to other control software may be implemented. @@ -382,4 +382,4 @@ \section{Overview} % This enables the user to choose between various analysis packages % for the output side. % Both ASCII and TASCOM files may be analysed and plotted through -% the Ris\o\ MATLAB package MVIEW/MFIT \cite{mview}. +% the Risø MATLAB package MVIEW/MFIT \cite{mview}. diff --git a/docs/manuals/mcstas/intro_comp.tex b/docs/manuals/mcstas/intro_comp.tex index 6c3e1fc1d6..512959c283 100644 --- a/docs/manuals/mcstas/intro_comp.tex +++ b/docs/manuals/mcstas/intro_comp.tex @@ -20,7 +20,7 @@ \chapter{Introduction to \MCS} The \MCS package is written in ISO-C and is freely available for down-load from the \MCS web-page~\cite{mcstas_webpage}. The package is actively -being developed and supported by Ris\o\ National Laboratory +being developed and supported by Risø National Laboratory and the Institut Laue Langevin (ILL). The system is well tested and is supplied with several examples and with an extensive documentation. @@ -29,7 +29,7 @@ \chapter{Introduction to \MCS} \section{Background} -In the late 90'ies at Ris\o\ National Laboratory, +In the late 90'ies at Risø National Laboratory, simulation tools were urgently needed, not only to better utilize existing instruments ({\em e.g.} RITA-1 and RITA-2~\cite{cjp_73_697,pb_241_50,pb_283_343}), @@ -206,7 +206,7 @@ \section{Overview} %\paragraph{The kernel.} Here are located some geometrical tools %({\em e.g.} intersection between a line and various surfaces) %and other elemental tools ({\em e.g.} creation and annihilation -%of a neutron). The kernel is maintained by the Ris\o\ group. +%of a neutron). The kernel is maintained by the Risø group. %\paragraph{The components.} Here resides the code for simulation % of the individual spectrometer components @@ -216,7 +216,7 @@ \section{Overview} % Interested users are encouraged to modify existing components and to % design new ones. % A library of general and well documented components -% is being maintained by the Ris\o\ group. +% is being maintained by the Risø group. %\paragraph{The instruments.} An instrument definition is written % in the \MCS meta-language, which is a means of positioning @@ -225,7 +225,7 @@ \section{Overview} % $(\omega,2\theta)$ pairs of a standard triple-axis spectrometer. % For each specific instrument, a new instrument definition % should be written. This will usually be done by the users, -% possibly in collaboration with the Ris\o\ group. +% possibly in collaboration with the Risø group. %\paragraph{The instrument control interface.} % Here, the setting parameters of the @@ -234,7 +234,7 @@ \section{Overview} % In the present version 1.0, the control interface % consists of a very preliminary MATLAB program, % but we expect soon to implement a simulation version of the -% Ris\o\ spectrometer control software TASCOM. +% Risø spectrometer control software TASCOM. % By using the preprogrammed scans or the TASCOM programming features, % the user will then be able easily to perform the desired simulations. % Later, interfaces to other control software may be implemented. @@ -247,4 +247,4 @@ \section{Overview} % This enables the user to choose between various analysis packages % for the output side. % Both ASCII and TASCOM files may be analysed and plotted through -% the Ris\o\ MATLAB package MVIEW/MFIT \cite{mview}. +% the Risø MATLAB package MVIEW/MFIT \cite{mview}. diff --git a/docs/manuals/mcstas/mcstas.bib b/docs/manuals/mcstas/mcstas.bib index 4b3a95fd8b..a535d4cf27 100644 --- a/docs/manuals/mcstas/mcstas.bib +++ b/docs/manuals/mcstas/mcstas.bib @@ -488,7 +488,7 @@ @MISC{dev_cpp_webpage } @MISC{ess_webpage, - note = {See \url{http://www.ess-europe.de}} + note = {See \url{https://www.ess.eu}} } @MISC{Fullprof, diff --git a/docs/manuals/mcstas/misc/Annulus.tex b/docs/manuals/mcstas/misc/Annulus.tex index 181f4937eb..5c7ed5a432 100644 --- a/docs/manuals/mcstas/misc/Annulus.tex +++ b/docs/manuals/mcstas/misc/Annulus.tex @@ -3,19 +3,15 @@ \section{The \texttt{Annulus} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} June 23rd 2009 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An inactive geometrical shape (annulus), for drawing purposes only. -Derived from the <b><a href="Shape.html">Shape</a></b> component +An inactive geometrical shape (annulus), for drawing purposes only. Derived from the \textbf{\htmladdnormallink{Shape}{Shape.html}} component Example: Annulus(radius=0.05, yheight=0.1) -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,7 +32,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/Annulus.comp}{Source code} for \texttt{Annulus.comp}. - \item mcdoc page of \textless{}a href="Shape.html"\textgreater{}Shape\textless{}/a\textgreater{}\textless{}/b\textgreater{} component + \item Component source code found in file \texttt{Annulus.comp}. + \item mcdoc page of \htmladdnormallink{Shape}{Shape.html}} component \end{itemize} -\IfFileExists{Annulus_static.tex}{\input{Annulus_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/Annulus_static.tex}{\input{misc/Annulus_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/Circle.tex b/docs/manuals/mcstas/misc/Circle.tex index 0ac4998b0a..013c20f3ee 100644 --- a/docs/manuals/mcstas/misc/Circle.tex +++ b/docs/manuals/mcstas/misc/Circle.tex @@ -3,19 +3,15 @@ \section{The \texttt{Circle} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} June 23rd 2009 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An inactive geometrical shape (circle), for drawing purposes only. -Derived from the <b><a href="Shape.html">Shape</a></b> component +An inactive geometrical shape (circle), for drawing purposes only. Derived from the \textbf{\htmladdnormallink{Shape}{Shape.html}} component Example: Circle(radius=0.05, yheight=0.1) -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -34,7 +30,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/Circle.comp}{Source code} for \texttt{Circle.comp}. - \item mcdoc page of \textless{}a href="Shape.html"\textgreater{}Shape\textless{}/a\textgreater{}\textless{}/b\textgreater{} component + \item Component source code found in file \texttt{Circle.comp}. + \item mcdoc page of \htmladdnormallink{Shape}{Shape.html}} component \end{itemize} -\IfFileExists{Circle_static.tex}{\input{Circle_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/Circle_static.tex}{\input{misc/Circle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/Cone.tex b/docs/manuals/mcstas/misc/Cone.tex index 6cdf6f5cdd..fa64b35baf 100644 --- a/docs/manuals/mcstas/misc/Cone.tex +++ b/docs/manuals/mcstas/misc/Cone.tex @@ -6,16 +6,13 @@ \section{The \texttt{Cone} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} June 23rd 2009 \end{itemize} \subsection*{Description} -\begin{lstlisting} -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -34,7 +31,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/Cone.comp}{Source code} for \texttt{Cone.comp}. - \item mcdoc page of \textless{}a href="Shape.html"\textgreater{}Shape\textless{}/a\textgreater{}\textless{}/b\textgreater{} component + \item Component source code found in file \texttt{Cone.comp}. + \item mcdoc page of \htmladdnormallink{Shape}{Shape.html}} component \end{itemize} -\IfFileExists{Cone_static.tex}{\input{Cone_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/Cone_static.tex}{\input{misc/Cone_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/Disc.tex b/docs/manuals/mcstas/misc/Disc.tex index 7857615e2b..465c57b7f6 100644 --- a/docs/manuals/mcstas/misc/Disc.tex +++ b/docs/manuals/mcstas/misc/Disc.tex @@ -3,19 +3,15 @@ \section{The \texttt{Disc} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} June 23rd 2009 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An inactive geometrical shape (annulus), for drawing purposes only. -Derived from the <b><a href="Shape.html">Shape</a></b> component +An inactive geometrical shape (annulus), for drawing purposes only. Derived from the \textbf{\htmladdnormallink{Shape}{Shape.html}} component Example: Annulus(radius=0.05, yheight=0.1) -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -37,7 +33,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/Disc.comp}{Source code} for \texttt{Disc.comp}. - \item mcdoc page of \textless{}a href="Shape.html"\textgreater{}Shape\textless{}/a\textgreater{}\textless{}/b\textgreater{} component + \item Component source code found in file \texttt{Disc.comp}. + \item mcdoc page of \htmladdnormallink{Shape}{Shape.html}} component \end{itemize} -\IfFileExists{Disc_static.tex}{\input{Disc_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/Disc_static.tex}{\input{misc/Disc_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/File.tex b/docs/manuals/mcstas/misc/File.tex index 09304e5c0a..ca243bbf83 100644 --- a/docs/manuals/mcstas/misc/File.tex +++ b/docs/manuals/mcstas/misc/File.tex @@ -4,17 +4,13 @@ \section{The \texttt{File} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Greg Tucker \item \textbf{Origin:} ESS \item \textbf{Date:} 2024 \end{itemize} \subsection*{Description} -\begin{lstlisting} -File.comp - allows to generate instrument/component input-files -from METADATA blocks - see test_File.instr for an example. -\end{lstlisting} +File.comp - allows to generate instrument/component input-files from METADATA blocks - see test\_File.instr for an example. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -32,6 +28,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/File.comp}{Source code} for \texttt{File.comp}. + \item Component source code found in file \texttt{File.comp}. \end{itemize} -\IfFileExists{File_static.tex}{\input{File_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/File_static.tex}{\input{misc/File_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/KDSource.tex b/docs/manuals/mcstas/misc/KDSource.tex new file mode 100644 index 0000000000..f2bd1acb20 --- /dev/null +++ b/docs/manuals/mcstas/misc/KDSource.tex @@ -0,0 +1,44 @@ +\section{The \texttt{KDSource} McStas Component} +Distributional source, based on a MCPL-format particle list, on which +the Kernel Density Estimation (KDE) method is applied. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} O.I.Abbate, N.S.Schmidt, updates for McStas by T.Kittelmann and P.Willendrup + \item \textbf{Origin:} Instituto Balseiro + \item \textbf{Date:} Dec 2022 / May 2026 +\end{itemize} + +\subsection*{Description} +Distributional source, based on a MCPL-format particle list, on which the Kernel Density Estimation (KDE) method is applied. + +It allows sampling more particles than the number present in a virtual, previously generated virtual source, without repeating samples, controlled via the nloop input parameter. + +To function, this component requires a KDSource installation v.2.0.2 or later, as distributed on conda-forge and pypi and included with (conda-based) McStas 3.7.0 or later. + +As inputs the component needs access to all of: \textless{}ol\textgreater{} \textless{}li\textgreater{}The original MPCL file \textless{}li\textgreater{}Outputs of a KDSource-analyzed / optimized KDE source: \textless{}ul\textgreater{} \textless{}li\textgreater{}An XML parameter-file containing the needed configuration \textless{}li\textgreater{}A "bandwidth" file (source\_bws) \textless{}/ul\textgreater{} \textless{}/ol\textgreater{} For information on performing KDSource analysis, please refer to the KDSource example notebooks and the KDSource online documentation (links below). + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +filename & str & Name of the XML parameters file containing KDSource definition. & 0 \\ +Emin & meV & Lower energy bound. Particles found in the MCPL-file below the limit are skipped. & 0 \\ +Emax & meV & Upper energy bound. Particles found in the MCPL-file above the limit are skipped. & FLT\_MAX \\ +nloop & int & Number of times to loop through the file. & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{KDSource.comp}. + \item N.S. Schmidt et. al \htmladdnormallink{Annals of Nuclear Energy, Volume 177, 2022, 109309}{https://doi.org/10.1016/j.anucene.2022.109309} + \item \htmladdnormallink{Test\_KDSource example instrument}{../examples/Tests\_MCPL\_etc/Test\_KDSource/Test\_KDSource.html} + \item \htmladdnormallink{KDSource online documentation}{https://kdsource.readthedocs.io/en/latest/} (not fully updated) + \item \htmladdnormallink{KDSource verification notebooks}{https://github.com/KDSource/KDSource/tree/develop/docs/examples} +\end{itemize} +\IfFileExists{misc/KDSource_static.tex}{\input{misc/KDSource_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/Legacy_circle.tex b/docs/manuals/mcstas/misc/Legacy_circle.tex index 95269feabd..07aa0de49e 100644 --- a/docs/manuals/mcstas/misc/Legacy_circle.tex +++ b/docs/manuals/mcstas/misc/Legacy_circle.tex @@ -3,38 +3,35 @@ \section{The \texttt{Legacy\_circle} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} June 23rd 2009 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An inactive geometrical shape, for drawing purposes only. -It does not propagate neutron, nor interact. -<b>Shape:</b> -Geometric shape may be a cylinder, a sphere, a box or any other shape +An inactive geometrical shape, for drawing purposes only. It does not propagate neutron, nor interact. \textbf{Shape:} Geometric shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} box/plate: xwidth x yheight x zdepth (thickness=0) -hollow box/plate:xwidth x yheight x zdepth and thickness>0 +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} cylinder: radius x yheight (thickness=0) -hollow cylinder: radius x yheight and thickness>0 +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} sphere: radius (yheight=0 thickness=0) hollow sphere: radius and thickness>0 (yheight=0) any shape: geometry=OFF file +\end{verbatim} -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using qhull/powercrust, and -viewed with geomview -The default size of the object depends of the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using qhull/powercrust, and viewed with geomview The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. -Example: Shape(radius=0.05, yheight=0.1) -Shape(geometry="socket.off") -\end{lstlisting} +Example: Shape(radius=0.05, yheight=0.1) Shape(geometry="socket.off") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -50,8 +47,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/Legacy_circle.comp}{Source code} for \texttt{Legacy\_circle.comp}. + \item Component source code found in file \texttt{Legacy\_circle.comp}. \item Geomview and Object File Format (OFF) \textless{}http|://www.geomview.org\textgreater{} \item Powercrust/qhull \textless{}http://www.cs.utexas.edu/users/amenta/powercrust\textgreater{} \end{itemize} -\IfFileExists{Legacy_circle_static.tex}{\input{Legacy_circle_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/Legacy_circle_static.tex}{\input{misc/Legacy_circle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/MCPL_input.tex b/docs/manuals/mcstas/misc/MCPL_input.tex index ae22ec4bc5..7e500ff9e4 100644 --- a/docs/manuals/mcstas/misc/MCPL_input.tex +++ b/docs/manuals/mcstas/misc/MCPL_input.tex @@ -3,24 +3,19 @@ \section{The \texttt{MCPL\_input} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen \item \textbf{Origin:} DTU Physics \item \textbf{Date:} Mar 2016 \end{itemize} \subsection*{Description} -\begin{lstlisting} Source-like component that reads neutron state parameters from a binary mcpl-file. -MCPL is short for Monte Carlo Particle List, and is a new format for sharing events -between e.g. MCNP(X), Geant4 and McStas. +MCPL is short for Monte Carlo Particle List, and is a new format for sharing events between e.g. MCNP(X), Geant4 and McStas. -When used with MPI, the --ncount given on the commandline is overwritten by -#MPI nodes x #events in the file. +When used with MPI, the --ncount given on the commandline is overwritten by \#MPI nodes x \#events in the file. -Example: MCPL_input(filename=voutput,verbose=1,repeat_count=1,v_smear=0.1,pos_smear=0.001,dir_smear=0.01) -\end{lstlisting} +Example: MCPL\_input(filename=voutput,verbose=1,repeat\_count=1,v\_smear=0.1,pos\_smear=0.001,dir\_smear=0.01) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -45,6 +40,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/MCPL_input.comp}{Source code} for \texttt{MCPL\_input.comp}. + \item Component source code found in file \texttt{MCPL\_input.comp}. \end{itemize} -\IfFileExists{MCPL_input_static.tex}{\input{MCPL_input_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/MCPL_input_static.tex}{\input{misc/MCPL_input_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/MCPL_input_once.tex b/docs/manuals/mcstas/misc/MCPL_input_once.tex index 956f9bb1f8..a4c8535e8c 100644 --- a/docs/manuals/mcstas/misc/MCPL_input_once.tex +++ b/docs/manuals/mcstas/misc/MCPL_input_once.tex @@ -3,24 +3,19 @@ \section{The \texttt{MCPL\_input\_once} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Gregory S Tucker \item \textbf{Origin:} European Spallation Source ERIC \item \textbf{Date:} Sep 2024 \end{itemize} \subsection*{Description} -\begin{lstlisting} Source-like component that reads neutron state parameters from a MCPL-file one time. -MCPL is short for Monte Carlo Particle List, and is a format for sharing events -between e.g. MCNP(X), Geant4 and McStas. +MCPL is short for Monte Carlo Particle List, and is a format for sharing events between e.g. MCNP(X), Geant4 and McStas. -When used with MPI, the file contents are shared between workers with each accessing -approximately (#events in the file) / (#MPI nodes) +When used with MPI, the file contents are shared between workers with each accessing approximately (\#events in the file) / (\#MPI nodes) -%BUGS -\end{lstlisting} +\%BUGS \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -45,6 +40,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/MCPL_input_once.comp}{Source code} for \texttt{MCPL\_input\_once.comp}. + \item Component source code found in file \texttt{MCPL\_input\_once.comp}. \end{itemize} -\IfFileExists{MCPL_input_once_static.tex}{\input{MCPL_input_once_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/MCPL_input_once_static.tex}{\input{misc/MCPL_input_once_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/MCPL_output.tex b/docs/manuals/mcstas/misc/MCPL_output.tex index ba34516758..6a4174eebf 100644 --- a/docs/manuals/mcstas/misc/MCPL_output.tex +++ b/docs/manuals/mcstas/misc/MCPL_output.tex @@ -4,34 +4,23 @@ \section{The \texttt{MCPL\_output} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen \item \textbf{Origin:} DTU Physics \item \textbf{Date:} Mar 2016 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Detector-like component that writes neutron state parameters into an mcpl-format -binary, virtual-source neutron file. +Detector-like component that writes neutron state parameters into an mcpl-format binary, virtual-source neutron file. -MCPL is short for Monte Carlo Particle List, and is a new format for sharing events -between e.g. MCNP(X), Geant4 and McStas. +MCPL is short for Monte Carlo Particle List, and is a new format for sharing events between e.g. MCNP(X), Geant4 and McStas. -When used with MPI, the component will output #MPI nodes individual MCPL files that -can be merged using the mcpltool. +When used with MPI, the component will output \#MPI nodes individual MCPL files that can be merged using the mcpltool. -MCPL_output allows a few flags to tweak the output files: -1. If use_polarisation is unset (default) the polarisation vector will not be stored (saving space) -2. If doubleprec is unset (default) data will be stored as 32 bit floating points, effectively cutting the output file size in half. -3. Extra information may be attached to each ray in the form of a userflag, a user-defined variable wich is packed into 32 bits. If -the user variable does not fit in 32 bits the value will be truncated and likely garbage. If more than one variable is to be attached to -each neutron this must be packed into the 32 bits. +MCPL\_output allows a few flags to tweak the output files: 1. If use\_polarisation is unset (default) the polarisation vector will not be stored (saving space) 2. If doubleprec is unset (default) data will be stored as 32 bit floating points, effectively cutting the output file size in half. 3. Extra information may be attached to each ray in the form of a userflag, a user-defined variable wich is packed into 32 bits. If the user variable does not fit in 32 bits the value will be truncated and likely garbage. If more than one variable is to be attached to each neutron this must be packed into the 32 bits. These features are set this way to keep file sizes as manageable as possible. -Example: MCPL_output( filename="voutput", verbose=1, userflag="flag", userflagcomment="Neutron Id" ) -\end{lstlisting} +Example: MCPL\_output( filename="voutput", verbose=1, userflag="flag", userflagcomment="Neutron Id" ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -54,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/MCPL_output.comp}{Source code} for \texttt{MCPL\_output.comp}. + \item Component source code found in file \texttt{MCPL\_output.comp}. \end{itemize} -\IfFileExists{MCPL_output_static.tex}{\input{MCPL_output_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/MCPL_output_static.tex}{\input{misc/MCPL_output_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/MCPL_output_noacc.tex b/docs/manuals/mcstas/misc/MCPL_output_noacc.tex index 36747c51bc..108b85a753 100644 --- a/docs/manuals/mcstas/misc/MCPL_output_noacc.tex +++ b/docs/manuals/mcstas/misc/MCPL_output_noacc.tex @@ -4,34 +4,23 @@ \section{The \texttt{MCPL\_output\_noacc} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen \item \textbf{Origin:} DTU Physics \item \textbf{Date:} Mar 2016 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Detector-like component that writes neutron state parameters into an mcpl-format -binary, virtual-source neutron file. +Detector-like component that writes neutron state parameters into an mcpl-format binary, virtual-source neutron file. -MCPL is short for Monte Carlo Particle List, and is a new format for sharing events -between e.g. MCNP(X), Geant4 and McStas. +MCPL is short for Monte Carlo Particle List, and is a new format for sharing events between e.g. MCNP(X), Geant4 and McStas. -When used with MPI, the component will output #MPI nodes individual MCPL files that -can be merged using the mcpltool. +When used with MPI, the component will output \#MPI nodes individual MCPL files that can be merged using the mcpltool. -MCPL_output allows a few flags to tweak the output files: -1. If use_polarisation is unset (default) the polarisation vector will not be stored (saving space) -2. If doubleprec is unset (default) data will be stored as 32 bit floating points, effectively cutting the output file size in half. -3. Extra information may be attached to each ray in the form of a userflag, a user-defined variable wich is packed into 32 bits. If -the user variable does not fit in 32 bits the value will be truncated and likely garbage. If more than one variable is to be attached to -each neutron this must be packed into the 32 bits. +MCPL\_output allows a few flags to tweak the output files: 1. If use\_polarisation is unset (default) the polarisation vector will not be stored (saving space) 2. If doubleprec is unset (default) data will be stored as 32 bit floating points, effectively cutting the output file size in half. 3. Extra information may be attached to each ray in the form of a userflag, a user-defined variable wich is packed into 32 bits. If the user variable does not fit in 32 bits the value will be truncated and likely garbage. If more than one variable is to be attached to each neutron this must be packed into the 32 bits. These features are set this way to keep file sizes as manageable as possible. -%BUGS -\end{lstlisting} +\%BUGS \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -54,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/MCPL_output_noacc.comp}{Source code} for \texttt{MCPL\_output\_noacc.comp}. + \item Component source code found in file \texttt{MCPL\_output\_noacc.comp}. \end{itemize} -\IfFileExists{MCPL_output_noacc_static.tex}{\input{MCPL_output_noacc_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/MCPL_output_noacc_static.tex}{\input{misc/MCPL_output_noacc_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/Progress_bar.tex b/docs/manuals/mcstas/misc/Progress_bar.tex index a61c4d44bf..8beae800c9 100644 --- a/docs/manuals/mcstas/misc/Progress_bar.tex +++ b/docs/manuals/mcstas/misc/Progress_bar.tex @@ -3,23 +3,15 @@ \section{The \texttt{Progress\_bar} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Emmanuel Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} 2002 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An indicator of the progress of the simulation, monitoring -the Init, Trace with the achieved percentage, and the Finally section. -Intermediate savings (e.g. triggered by USR2 signal) are also shown. -This component should be positioned at the very begining of the instrument -The profile option will save the intensity and number of events for each -component It may be used to evaluate the simulation efficiency. +An indicator of the progress of the simulation, monitoring the Init, Trace with the achieved percentage, and the Finally section. Intermediate savings (e.g. triggered by USR2 signal) are also shown. This component should be positioned at the very begining of the instrument The profile option will save the intensity and number of events for each component It may be used to evaluate the simulation efficiency. -Example: Progress_bar(percent=10,flag_save=1) AT (0,0,0) -\end{lstlisting} +Example: Progress\_bar(percent=10,flag\_save=1) AT (0,0,0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -38,6 +30,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/Progress_bar.comp}{Source code} for \texttt{Progress\_bar.comp}. + \item Component source code found in file \texttt{Progress\_bar.comp}. \end{itemize} -\IfFileExists{Progress_bar_static.tex}{\input{Progress_bar_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/Progress_bar_static.tex}{\input{misc/Progress_bar_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/Shape.tex b/docs/manuals/mcstas/misc/Shape.tex index 7a4eeb8b07..668e53c2be 100644 --- a/docs/manuals/mcstas/misc/Shape.tex +++ b/docs/manuals/mcstas/misc/Shape.tex @@ -3,38 +3,35 @@ \section{The \texttt{Shape} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} June 23rd 2009 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An inactive geometrical shape, for drawing purposes only. -It does not propagate neutron, nor interact. -<b>Shape:</b> -Geometric shape may be a cylinder, a sphere, a box or any other shape +An inactive geometrical shape, for drawing purposes only. It does not propagate neutron, nor interact. \textbf{Shape:} Geometric shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} box/plate: xwidth x yheight x zdepth (thickness=0) -hollow box/plate:xwidth x yheight x zdepth and thickness>0 +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} cylinder: radius x yheight (thickness=0) -hollow cylinder: radius x yheight and thickness>0 +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} sphere: radius (yheight=0 thickness=0) hollow sphere: radius and thickness>0 (yheight=0) any shape: geometry=OFF file +\end{verbatim} -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using qhull/powercrust, and -viewed with geomview -The default size of the object depends of the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using qhull/powercrust, and viewed with geomview The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. -Example: Shape(radius=0.05, yheight=0.1) -Shape(geometry="socket.off") -\end{lstlisting} +Example: Shape(radius=0.05, yheight=0.1) Shape(geometry="socket.off") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -59,8 +56,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/Shape.comp}{Source code} for \texttt{Shape.comp}. + \item Component source code found in file \texttt{Shape.comp}. \item Geomview and Object File Format (OFF) \textless{}http|://www.geomview.org\textgreater{} \item Powercrust/qhull \textless{}http://www.cs.utexas.edu/users/amenta/powercrust\textgreater{} \end{itemize} -\IfFileExists{Shape_static.tex}{\input{Shape_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/Shape_static.tex}{\input{misc/Shape_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/misc/Shape_simple.tex b/docs/manuals/mcstas/misc/Shape_simple.tex index cc3e3d76e5..57c6d44515 100644 --- a/docs/manuals/mcstas/misc/Shape_simple.tex +++ b/docs/manuals/mcstas/misc/Shape_simple.tex @@ -3,38 +3,35 @@ \section{The \texttt{Shape\_simple} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} June 23rd 2009 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An inactive geometrical shape, for drawing purposes only. -It does not propagate neutron, nor interact. -<b>Shape:</b> -Geometric shape may be a cylinder, a sphere, a box or any other shape +An inactive geometrical shape, for drawing purposes only. It does not propagate neutron, nor interact. \textbf{Shape:} Geometric shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} box/plate: xwidth x yheight x zdepth (thickness=0) -hollow box/plate:xwidth x yheight x zdepth and thickness>0 +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} cylinder: radius x yheight (thickness=0) -hollow cylinder: radius x yheight and thickness>0 +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} sphere: radius (yheight=0 thickness=0) hollow sphere: radius and thickness>0 (yheight=0) any shape: geometry=OFF file +\end{verbatim} -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using qhull/powercrust, and -viewed with geomview -The default size of the object depends of the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using qhull/powercrust, and viewed with geomview The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. -Example: Shape(radius=0.05, yheight=0.1) -Shape(geometry="socket.off") -\end{lstlisting} +Example: Shape(radius=0.05, yheight=0.1) Shape(geometry="socket.off") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -56,8 +53,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/misc/Shape_simple.comp}{Source code} for \texttt{Shape\_simple.comp}. + \item Component source code found in file \texttt{Shape\_simple.comp}. \item Geomview and Object File Format (OFF) \textless{}http|://www.geomview.org\textgreater{} \item Powercrust/qhull \textless{}http://www.cs.utexas.edu/users/amenta/powercrust\textgreater{} \end{itemize} -\IfFileExists{Shape_simple_static.tex}{\input{Shape_simple_static.tex}}{} \ No newline at end of file +\IfFileExists{misc/Shape_simple_static.tex}{\input{misc/Shape_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Brilliance_monitor.tex b/docs/manuals/mcstas/monitors/Brilliance_monitor.tex index 4bfc1a9af7..57d86b9f53 100644 --- a/docs/manuals/mcstas/monitors/Brilliance_monitor.tex +++ b/docs/manuals/mcstas/monitors/Brilliance_monitor.tex @@ -3,38 +3,28 @@ \section{The \texttt{Brilliance\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup, derived from TOF\_lambda\_monitor.comp \item \textbf{Origin:} DTU Physics \item \textbf{Date:} May 23, 2012 \end{itemize} \subsection*{Description} -\begin{lstlisting} -If used in the right setting, will output "instantaneous" and "mean" brilliances in units of Neutrons/cm^2/ster/AA/s. Conditions for proper units: -<ul> -<li>Use a with a source of area 1x1cm -<li>The source must illuminate/focus to an area of 1x1cm a 1m distance -<li>Parametrise the Brilliance_monitor with the frequency of the source -<li>To not change the source TOF distribution, place the Brilliance monitor close to the source! -</ul> +If used in the right setting, will output "instantaneous" and "mean" brilliances in units of Neutrons/cm\textasciicircum{}2/ster/\AA{}/s. Conditions for proper units: \textless{}ul\textgreater{} \textless{}li\textgreater{}Use a with a source of area 1x1cm \textless{}li\textgreater{}The source must illuminate/focus to an area of 1x1cm a 1m distance \textless{}li\textgreater{}Parametrise the Brilliance\_monitor with the frequency of the source \textless{}li\textgreater{}To not change the source TOF distribution, place the Brilliance monitor close to the source! \textless{}/ul\textgreater{} -with a source of area 1x1cm illuminating/focusing to an area of 1x1cm a 1m distance, this monitor will output "instantaneous" and "mean" brilliances in units of Neutrons/cm^2/ster/AA/s +with a source of area 1x1cm illuminating/focusing to an area of 1x1cm a 1m distance, this monitor will output "instantaneous" and "mean" brilliances in units of Neutrons/cm\textasciicircum{}2/ster/\AA{}/s Here is an example of the use of the component. Note how the mentioned Unit conditions are implemented in instrument code. -COMPONENT Source = ESS_moderator_long( -l_low = lambdamin, l_high = lambdamax, dist = 1, xw = 0.01, yh = 0.01, +COMPONENT Source = ESS\_moderator\_long( l\_low = lambdamin, l\_high = lambdamax, dist = 1, xw = 0.01, yh = 0.01, + +\begin{verbatim} freq = 14, T=50, tau=287e-6, tau1=0, tau2=20e-6, n=20, n2=5, d=0.00286, chi2=0.9, I0=6.9e11, I2=27.6e10, -branch1=0, branch2=0.5, twopulses=0, size=0.01) -AT (0, 0, 0) RELATIVE Origin +\end{verbatim} + +branch1=0, branch2=0.5, twopulses=0, size=0.01) AT (0, 0, 0) RELATIVE Origin -COMPONENT BRIL = Brilliance_monitor(nlam=196,nt=401,filename="bril.sim", -t_0=0,t_1=4000,lambda_0=lambdamin, -lambda_1=lambdamax, Freq=14) -AT (0,0,0.000001) RELATIVE Source -\end{lstlisting} +COMPONENT BRIL = Brilliance\_monitor(nlam=196,nt=401,filename="bril.sim", t\_0=0,t\_1=4000,lambda\_0=lambdamin, lambda\_1=lambdamax, Freq=14) AT (0,0,0.000001) RELATIVE Source \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -47,8 +37,8 @@ \subsection*{Input parameters} nlam & 1 & Number of bins in wavelength & 101 \\ nt & 1 & Number of bins in TOF & 1001 \\ nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ -lambda\_0 & AA & Minimum wavelength detected & 0 \\ -lambda\_1 & AA & Maximum wavelength detected & 20 \\ +lambda\_0 & \AA{} & Minimum wavelength detected & 0 \\ +lambda\_1 & \AA{} & Maximum wavelength detected & 20 \\ restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ \textbf{Freq} & Hz & Source frequency. Use freq=1 for reactor source & \\ tofcuts & 1 & Flag to generate TOF-distributions as function of wavelength & 0 \\ @@ -59,12 +49,12 @@ \subsection*{Input parameters} filename & string & Defines filenames for the detector images. Stored as:\textless{}br\textgreater{}Peak\_\<filename\> and Mean\_\<filename\> & 0 \\ t\_0 & us & Minimum time & 0 \\ t\_1 & us & Maximum time & 20000 \\ -srcarea & cm\textasciicircum{}2 & Source area & 1 \\ +srcarea & cm$^{2}$ & Source area & 1 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Brilliance_monitor.comp}{Source code} for \texttt{Brilliance\_monitor.comp}. + \item Component source code found in file \texttt{Brilliance\_monitor.comp}. \end{itemize} -\IfFileExists{Brilliance_monitor_static.tex}{\input{Brilliance_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Brilliance_monitor_static.tex}{\input{monitors/Brilliance_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Cyl_monitor.tex b/docs/manuals/mcstas/monitors/Cyl_monitor.tex index 72bf7fdd4e..0c0a2ebc66 100644 --- a/docs/manuals/mcstas/monitors/Cyl_monitor.tex +++ b/docs/manuals/mcstas/monitors/Cyl_monitor.tex @@ -4,19 +4,15 @@ \section{The \texttt{Cyl\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} October 26, 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel PSD monitor with cylinder shape, -vertical axis, centered at (0,0,0). +An (n times m) pixel PSD monitor with cylinder shape, vertical axis, centered at (0,0,0). -Example: PSDcyl_monitor(nr=20, ny=20, filename="Output.cyl", yheight=0.2, radius=0.1) -\end{lstlisting} +Example: PSDcyl\_monitor(nr=20, ny=20, filename="Output.cyl", yheight=0.2, radius=0.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -39,6 +35,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Cyl_monitor.comp}{Source code} for \texttt{Cyl\_monitor.comp}. + \item Component source code found in file \texttt{Cyl\_monitor.comp}. \end{itemize} -\IfFileExists{Cyl_monitor_static.tex}{\input{Cyl_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Cyl_monitor_static.tex}{\input{monitors/Cyl_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Cyl_monitor_PSD.tex b/docs/manuals/mcstas/monitors/Cyl_monitor_PSD.tex index d12ebd952b..5fcc41572d 100644 --- a/docs/manuals/mcstas/monitors/Cyl_monitor_PSD.tex +++ b/docs/manuals/mcstas/monitors/Cyl_monitor_PSD.tex @@ -4,19 +4,15 @@ \section{The \texttt{Cyl\_monitor\_PSD} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} October 26, 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel PSD monitor with cylinder shape, -vertical axis, centered at (0,0,0). +An (n times m) pixel PSD monitor with cylinder shape, vertical axis, centered at (0,0,0). -Example: PSDcyl_monitor(nr=20, ny=20, filename="Output.cyl", yheight=0.2, radius=0.1) -\end{lstlisting} +Example: PSDcyl\_monitor(nr=20, ny=20, filename="Output.cyl", yheight=0.2, radius=0.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,6 +36,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Cyl_monitor_PSD.comp}{Source code} for \texttt{Cyl\_monitor\_PSD.comp}. + \item Component source code found in file \texttt{Cyl\_monitor\_PSD.comp}. \end{itemize} -\IfFileExists{Cyl_monitor_PSD_static.tex}{\input{Cyl_monitor_PSD_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Cyl_monitor_PSD_static.tex}{\input{monitors/Cyl_monitor_PSD_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Cyl_monitor_TOF.tex b/docs/manuals/mcstas/monitors/Cyl_monitor_TOF.tex index 887e4fe327..05a0ac3a19 100644 --- a/docs/manuals/mcstas/monitors/Cyl_monitor_TOF.tex +++ b/docs/manuals/mcstas/monitors/Cyl_monitor_TOF.tex @@ -4,19 +4,15 @@ \section{The \texttt{Cyl\_monitor\_TOF} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} October 26, 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel PSD monitor with cylinder shape, -vertical axis, centered at (0,0,0). +An (n times m) pixel PSD monitor with cylinder shape, vertical axis, centered at (0,0,0). -Example: PSDcyl_monitor(nr=20, ny=20, filename="Output.cyl", yheight=0.2, radius=0.1) -\end{lstlisting} +Example: PSDcyl\_monitor(nr=20, ny=20, filename="Output.cyl", yheight=0.2, radius=0.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +38,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Cyl_monitor_TOF.comp}{Source code} for \texttt{Cyl\_monitor\_TOF.comp}. + \item Component source code found in file \texttt{Cyl\_monitor\_TOF.comp}. \end{itemize} -\IfFileExists{Cyl_monitor_TOF_static.tex}{\input{Cyl_monitor_TOF_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Cyl_monitor_TOF_static.tex}{\input{monitors/Cyl_monitor_TOF_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Div1D_monitor.tex b/docs/manuals/mcstas/monitors/Div1D_monitor.tex index 30d0a5ca60..7b64c4b98b 100644 --- a/docs/manuals/mcstas/monitors/Div1D_monitor.tex +++ b/docs/manuals/mcstas/monitors/Div1D_monitor.tex @@ -3,19 +3,15 @@ \section{The \texttt{Div1D\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} KL, \item \textbf{Origin:} Risoe \item \textbf{Date:} Nov. 11, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A divergence sensitive monitor. The counts are distributed in -ndiv pixels along either the horizontal axis x (default) or the vertical y. +A divergence sensitive monitor. The counts are distributed in ndiv pixels along either the horizontal axis x (default) or the vertical y. -Example: Div1D_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, ndiv=20, filename="Output.hd", maxdiv=2) -\end{lstlisting} +Example: Div1D\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, ndiv=20, filename="Output.hd", maxdiv=2) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +38,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Div1D_monitor.comp}{Source code} for \texttt{Div1D\_monitor.comp}. + \item Component source code found in file \texttt{Div1D\_monitor.comp}. \end{itemize} -\IfFileExists{Div1D_monitor_static.tex}{\input{Div1D_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Div1D_monitor_static.tex}{\input{monitors/Div1D_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/DivLambda_monitor.tex b/docs/manuals/mcstas/monitors/DivLambda_monitor.tex index e26018bc19..ad69b90cd9 100644 --- a/docs/manuals/mcstas/monitors/DivLambda_monitor.tex +++ b/docs/manuals/mcstas/monitors/DivLambda_monitor.tex @@ -3,21 +3,21 @@ \section{The \texttt{DivLambda\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -2D detector for intensity as a function of both horizontal divergence -and wavelength. +2D detector for intensity as a function of both horizontal divergence and wavelength. -Example: DivLambda_monitor(nL=20, nh=20, filename="Output.div", +Example: DivLambda\_monitor(nL=20, nh=20, filename="Output.div", + +\begin{verbatim} xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, -maxdiv_h=2, Lmin=2, Lmax=10) -\end{lstlisting} +\end{verbatim} + +maxdiv\_h=2, Lmin=2, Lmax=10) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -38,8 +38,8 @@ \subsection*{Input parameters} xwidth & m & Width of detector. Overrides xmin,xmax. & 0 \\ yheight & m & Height of detector. Overrides ymin,ymax. & 0 \\ maxdiv\_h & degrees & Maximal horizontal divergence detected & 2 \\ -\textbf{Lmin} & AA & Minimum wavelength detected & \\ -\textbf{Lmax} & AA & Maximum wavelength detected & \\ +\textbf{Lmin} & \AA{} & Minimum wavelength detected & \\ +\textbf{Lmax} & \AA{} & Maximum wavelength detected & \\ restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ nx & 1 & & 0 \\ ny & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane. & 0 \\ @@ -49,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/DivLambda_monitor.comp}{Source code} for \texttt{DivLambda\_monitor.comp}. + \item Component source code found in file \texttt{DivLambda\_monitor.comp}. \end{itemize} -\IfFileExists{DivLambda_monitor_static.tex}{\input{DivLambda_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/DivLambda_monitor_static.tex}{\input{monitors/DivLambda_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/DivPos_monitor.tex b/docs/manuals/mcstas/monitors/DivPos_monitor.tex index 5ccabee52d..c20371c89d 100644 --- a/docs/manuals/mcstas/monitors/DivPos_monitor.tex +++ b/docs/manuals/mcstas/monitors/DivPos_monitor.tex @@ -3,22 +3,15 @@ \section{The \texttt{DivPos\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -2D detector for intensity as a function of position -and divergence, either horizontally or vertically (depending on the flag vertical). -This gives information similar to an aceptance diagram used -eg. to investigate beam profiles in neutron guides. +2D detector for intensity as a function of position and divergence, either horizontally or vertically (depending on the flag vertical). This gives information similar to an aceptance diagram used eg. to investigate beam profiles in neutron guides. -Example: DivPos_monitor(nh=20, ndiv=20, filename="Output.dip", -xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, maxdiv_h=2) -\end{lstlisting} +Example: DivPos\_monitor(nh=20, ndiv=20, filename="Output.dip", xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, maxdiv\_h=2) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -49,6 +42,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/DivPos_monitor.comp}{Source code} for \texttt{DivPos\_monitor.comp}. + \item Component source code found in file \texttt{DivPos\_monitor.comp}. \end{itemize} -\IfFileExists{DivPos_monitor_static.tex}{\input{DivPos_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/DivPos_monitor_static.tex}{\input{monitors/DivPos_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Divergence_monitor.tex b/docs/manuals/mcstas/monitors/Divergence_monitor.tex index d6b9a1b9fd..c680ed6763 100644 --- a/docs/manuals/mcstas/monitors/Divergence_monitor.tex +++ b/docs/manuals/mcstas/monitors/Divergence_monitor.tex @@ -3,21 +3,21 @@ \section{The \texttt{Divergence\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} Nov. 11, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A divergence sensitive monitor. The counts are distributed in -(n times m) pixels. +A divergence sensitive monitor. The counts are distributed in (n times m) pixels. -Example: Divergence_monitor(nh=20, nv=20, filename="Output.pos", +Example: Divergence\_monitor(nh=20, nv=20, filename="Output.pos", + +\begin{verbatim} xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, -maxdiv_h=2, maxdiv_v=2) -\end{lstlisting} +\end{verbatim} + +maxdiv\_h=2, maxdiv\_v=2) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -48,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Divergence_monitor.comp}{Source code} for \texttt{Divergence\_monitor.comp}. + \item Component source code found in file \texttt{Divergence\_monitor.comp}. \end{itemize} -\IfFileExists{Divergence_monitor_static.tex}{\input{Divergence_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Divergence_monitor_static.tex}{\input{monitors/Divergence_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/EPSD_monitor.tex b/docs/manuals/mcstas/monitors/EPSD_monitor.tex index aef1da781d..f295ed0934 100644 --- a/docs/manuals/mcstas/monitors/EPSD_monitor.tex +++ b/docs/manuals/mcstas/monitors/EPSD_monitor.tex @@ -3,19 +3,15 @@ \section{The \texttt{EPSD\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} 16.4.00 \end{itemize} \subsection*{Description} -\begin{lstlisting} A monitor measuring neutron intensity vs. position, x, and neutron energy, E -Example: EPSD_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, -Emin=1, Emax=50, nx=20, nE=20, filename="Output.poe") -\end{lstlisting} +Example: EPSD\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, Emin=1, Emax=50, nx=20, nE=20, filename="Output.poe") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -43,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/EPSD_monitor.comp}{Source code} for \texttt{EPSD\_monitor.comp}. + \item Component source code found in file \texttt{EPSD\_monitor.comp}. \end{itemize} -\IfFileExists{EPSD_monitor_static.tex}{\input{EPSD_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/EPSD_monitor_static.tex}{\input{monitors/EPSD_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/E_monitor.tex b/docs/manuals/mcstas/monitors/E_monitor.tex index 6341948117..5ca6d43304 100644 --- a/docs/manuals/mcstas/monitors/E_monitor.tex +++ b/docs/manuals/mcstas/monitors/E_monitor.tex @@ -3,19 +3,15 @@ \section{The \texttt{E\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen and Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} April 20, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} A square single monitor that measures the energy of the incoming neutrons. -Example: E_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, -Emin=1, Emax=50, nE=20, filename="Output.nrj") -\end{lstlisting} +Example: E\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, Emin=1, Emax=50, nE=20, filename="Output.nrj") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +38,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/E_monitor.comp}{Source code} for \texttt{E\_monitor.comp}. + \item Component source code found in file \texttt{E\_monitor.comp}. \end{itemize} -\IfFileExists{E_monitor_static.tex}{\input{E_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/E_monitor_static.tex}{\input{monitors/E_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Event_monitor_simple.tex b/docs/manuals/mcstas/monitors/Event_monitor_simple.tex index 2fe275b21e..df66be50e5 100644 --- a/docs/manuals/mcstas/monitors/Event_monitor_simple.tex +++ b/docs/manuals/mcstas/monitors/Event_monitor_simple.tex @@ -3,18 +3,13 @@ \section{The \texttt{Event\_monitor\_simple} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} DTU \item \textbf{Date:} Oct 3rd, 2020 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Simple, low-key event-monitor for debugging purposes. No propagation, -no MPI support. Simply prints the event list to a log file in the SAVE section. -The filename is "comp-instance".log -\end{lstlisting} +Simple, low-key event-monitor for debugging purposes. No propagation, no MPI support. Simply prints the event list to a log file in the SAVE section. The filename is "comp-instance".log \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,6 +25,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Event_monitor_simple.comp}{Source code} for \texttt{Event\_monitor\_simple.comp}. + \item Component source code found in file \texttt{Event\_monitor\_simple.comp}. \end{itemize} -\IfFileExists{Event_monitor_simple_static.tex}{\input{Event_monitor_simple_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Event_monitor_simple_static.tex}{\input{monitors/Event_monitor_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Flex_monitor_1D.tex b/docs/manuals/mcstas/monitors/Flex_monitor_1D.tex index 8e07c2dd64..ca03527ce1 100644 --- a/docs/manuals/mcstas/monitors/Flex_monitor_1D.tex +++ b/docs/manuals/mcstas/monitors/Flex_monitor_1D.tex @@ -3,18 +3,15 @@ \section{The \texttt{Flex\_monitor\_1D} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen \& Peter Willendrup \item \textbf{Origin:} DTU Physics \item \textbf{Date:} Oct '20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A square 1D single monitor that measures intensity (or something else) as a function of some variable or parameter. +Non-propagating monitor that measures intensity (or something else) as a function of some variable or parameter. -Example: Flex_monitor_1D(nU=20, filename="Output", ustring="x", Umin=-.1, Umax=.1) -\end{lstlisting} +Example: Flex\_monitor\_1D(nU=20, filename="Output", ustring="x", Umin=-.1, Umax=.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,8 +26,7 @@ \subsection*{Input parameters} \textbf{Umin} & & Minimum U to detect & \\ \textbf{Umax} & & Maximum U to detect & \\ uid & 1 & Integer index of uservar to be monitored. Overrides ustring. & -1 \\ -ustring & string & Name of variable (user or neutron state parameter as a string) to be monitored. & "" \\ -restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ +ustring & string & Name of variable (user or particle state parameter as a string) to be monitored. & "" \\ signal & string & Name of variable to be used as an additive signal to be monitored. Default is intensity. & "p" \\ nowritefile & 1 & Flag to indicate if monitor should not save any data. & 0 \\ \bottomrule @@ -38,6 +34,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Flex_monitor_1D.comp}{Source code} for \texttt{Flex\_monitor\_1D.comp}. + \item Component source code found in file \texttt{Flex\_monitor\_1D.comp}. \end{itemize} -\IfFileExists{Flex_monitor_1D_static.tex}{\input{Flex_monitor_1D_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Flex_monitor_1D_static.tex}{\input{monitors/Flex_monitor_1D_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Flex_monitor_2D.tex b/docs/manuals/mcstas/monitors/Flex_monitor_2D.tex index a2bc196c88..6c914db73a 100644 --- a/docs/manuals/mcstas/monitors/Flex_monitor_2D.tex +++ b/docs/manuals/mcstas/monitors/Flex_monitor_2D.tex @@ -3,18 +3,15 @@ \section{The \texttt{Flex\_monitor\_2D} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen \& Peter Willendrup \item \textbf{Origin:} DTU Physics \item \textbf{Date:} Oct '20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A square 2D single monitor that measures intensity (or something else) as a function of two selectable variables or parameters. +Non-propagating 2D monitor that measures intensity (or something else) as a function of two selectable variables or parameters. -Example: Flex_monitor_2D(nU1=20, nU2=20, filename="Output", ustring1="x", ustring2="y", Umin1=-.1, Umax1=.1, Umin2=-.1, Umax2=.1) -\end{lstlisting} +Example: Flex\_monitor\_2D(nU1=20, nU2=20, filename="Output", ustring1="x", ustring2="y", Umin1=-.1, Umax1=.1, Umin2=-.1, Umax2=.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,12 +27,11 @@ \subsection*{Input parameters} \textbf{Umin1} & & Minimum U1 to detect & \\ \textbf{Umax1} & & Maximum U1 to detect & \\ uid1 & 1 & Integer index of uservar to be monitored. Overrides ustring1. & -1 \\ -ustring1 & string & Name of variable U1 (user or neutron state parameter as a string) to be monitored. & "" \\ +ustring1 & string & Name of variable U1 (user or particle state parameter as a string) to be monitored. & "" \\ \textbf{Umin2} & & Minimum U1 to detect & \\ \textbf{Umax2} & & Maximum U1 to detect & \\ uid2 & 1 & Integer index of uservar to be monitored. Overrides ustring2. & -1 \\ -ustring2 & string & Name of variable U2 (user or neutron state parameter as a string) to be monitored. & "" \\ -restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ +ustring2 & string & Name of variable U2 (user or particle state parameter as a string) to be monitored. & "" \\ signal & string & Name of variable to be used as an additive signal to be monitored. Default is intensity. & "p" \\ nowritefile & 1 & Flag to indicate if monitor should not save any data. & 0 \\ \bottomrule @@ -43,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Flex_monitor_2D.comp}{Source code} for \texttt{Flex\_monitor\_2D.comp}. + \item Component source code found in file \texttt{Flex\_monitor\_2D.comp}. \end{itemize} -\IfFileExists{Flex_monitor_2D_static.tex}{\input{Flex_monitor_2D_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Flex_monitor_2D_static.tex}{\input{monitors/Flex_monitor_2D_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Flex_monitor_3D.tex b/docs/manuals/mcstas/monitors/Flex_monitor_3D.tex index 20c6cc5016..e9ea54d9fc 100644 --- a/docs/manuals/mcstas/monitors/Flex_monitor_3D.tex +++ b/docs/manuals/mcstas/monitors/Flex_monitor_3D.tex @@ -3,18 +3,15 @@ \section{The \texttt{Flex\_monitor\_3D} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen \& Peter Willendrup \item \textbf{Origin:} DTU Physics \item \textbf{Date:} Oct '20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A square 3D single monitor that measures intensity (or something else) as a function of two selectable variables or parameters. +Non-propagating 3D monitor that measures intensity (or something else) as a function of three selectable variables or parameters. The 3D data is saved as a series of 2D datasets, which names are filename\_index -Example: Flex_monitor_3D(nU1=20, nU2=20, nU3=20, filename="Output", ustring1="x", ustring2="y", ustring1="z", Umin1=-.1, Umax1=.1, Umin2=-.1, Umax2=.1, Umin3=-.1, Umax3=.1) -\end{lstlisting} +Example: Flex\_monitor\_3D(nU1=20, nU2=20, nU3=20, filename="Output", ustring1="x", ustring2="y", ustring1="z", Umin1=-.1, Umax1=.1, Umin2=-.1, Umax2=.1, Umin3=-.1, Umax3=.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -31,16 +28,15 @@ \subsection*{Input parameters} \textbf{Umin1} & & Minimum U1 to detect & \\ \textbf{Umax1} & & Maximum U1 to detect & \\ uid1 & 1 & Integer index of uservar to be monitored. Overrides ustring1. & -1 \\ -ustring1 & string & Name of variable U1 (user or neutron state parameter as a string) to be monitored. & "" \\ +ustring1 & string & Name of variable U1 (user or particle state parameter as a string) to be monitored. & "" \\ \textbf{Umin2} & & Minimum U1 to detect & \\ \textbf{Umax2} & & Maximum U1 to detect & \\ uid2 & 1 & Integer index of uservar to be monitored. Overrides ustring2. & -1 \\ -ustring2 & string & Name of variable U2 (user or neutron state parameter as a string) to be monitored. & "" \\ +ustring2 & string & Name of variable U2 (user or particle state parameter as a string) to be monitored. & "" \\ \textbf{Umin3} & & Minimum U3 to detect & \\ \textbf{Umax3} & & Maximum U3 to detect & \\ uid3 & 1 & Integer index of uservar to be monitored. Overrides ustring3. & -1 \\ -ustring3 & string & Name of variable U3 (user or neutron state parameter as a string) to be monitored. & "" \\ -restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ +ustring3 & string & Name of variable U3 (user or particle state parameter as a string) to be monitored. & "" \\ signal & string & Name of variable to be used as an additive signal to be monitored. Default is intensity. & "p" \\ nowritefile & 1 & Flag to indicate if monitor should not save any data. & 0 \\ \bottomrule @@ -48,6 +44,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Flex_monitor_3D.comp}{Source code} for \texttt{Flex\_monitor\_3D.comp}. + \item Component source code found in file \texttt{Flex\_monitor\_3D.comp}. \end{itemize} -\IfFileExists{Flex_monitor_3D_static.tex}{\input{Flex_monitor_3D_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Flex_monitor_3D_static.tex}{\input{monitors/Flex_monitor_3D_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/L_monitor.tex b/docs/manuals/mcstas/monitors/L_monitor.tex index 537f237ba1..1128d02208 100644 --- a/docs/manuals/mcstas/monitors/L_monitor.tex +++ b/docs/manuals/mcstas/monitors/L_monitor.tex @@ -3,19 +3,15 @@ \section{The \texttt{L\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen and Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} April 20, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A square single monitor that measures the wavelength of the incoming -neutrons. +A square single monitor that measures the wavelength of the incoming neutrons. -Example: L_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nL=20, filename="Output.L", Lmin=2, Lmax=10) -\end{lstlisting} +Example: L\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nL=20, filename="Output.L", Lmin=2, Lmax=10) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -34,14 +30,14 @@ \subsection*{Input parameters} ymax & m & Upper y bound of detector opening & 0.05 \\ xwidth & m & Width of detector. Overrides xmin, xmax. & 0 \\ yheight & m & Height of detector. Overrides ymin, ymax. & 0 \\ -\textbf{Lmin} & AA & Minimum wavelength to detect & \\ -\textbf{Lmax} & AA & Maximum wavelength to detect & \\ +\textbf{Lmin} & \AA{} & Minimum wavelength to detect & \\ +\textbf{Lmax} & \AA{} & Maximum wavelength to detect & \\ restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/L_monitor.comp}{Source code} for \texttt{L\_monitor.comp}. + \item Component source code found in file \texttt{L\_monitor.comp}. \end{itemize} -\IfFileExists{L_monitor_static.tex}{\input{L_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/L_monitor_static.tex}{\input{monitors/L_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/MeanPolLambda_monitor.tex b/docs/manuals/mcstas/monitors/MeanPolLambda_monitor.tex index 6c0a0b4596..936fbfaa5c 100644 --- a/docs/manuals/mcstas/monitors/MeanPolLambda_monitor.tex +++ b/docs/manuals/mcstas/monitors/MeanPolLambda_monitor.tex @@ -3,20 +3,15 @@ \section{The \texttt{MeanPolLambda\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Christiansen \item \textbf{Origin:} Risoe \item \textbf{Date:} July 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A square single monitor that measures the MEAN projection of the -polarisation along a given normalized m-vector (mx, my, mz) as a -function of wavelength. +A square single monitor that measures the MEAN projection of the polarisation along a given normalized m-vector (mx, my, mz) as a function of wavelength. -Example: MeanPollambda_monitor(xwidth=0.1, yheight=0.1, npol=11, my=1, filename="meanpollambdaMon.data") -\end{lstlisting} +Example: MeanPollambda\_monitor(xwidth=0.1, yheight=0.1, npol=11, my=1, filename="meanpollambdaMon.data") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -35,13 +30,13 @@ \subsection*{Input parameters} mx & 1 & X-component of monitor vector (can be negative) & 0 \\ my & 1 & Y-component of monitor vector (can be negative) & 0 \\ mz & 1 & Z-component of monitor vector (can be negative) & 0 \\ -\textbf{Lmin} & AA & Minimum wavelength detected & \\ -\textbf{Lmax} & AA & Maximum wavelength detected & \\ +\textbf{Lmin} & \AA{} & Minimum wavelength detected & \\ +\textbf{Lmax} & \AA{} & Maximum wavelength detected & \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/MeanPolLambda_monitor.comp}{Source code} for \texttt{MeanPolLambda\_monitor.comp}. + \item Component source code found in file \texttt{MeanPolLambda\_monitor.comp}. \end{itemize} -\IfFileExists{MeanPolLambda_monitor_static.tex}{\input{MeanPolLambda_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/MeanPolLambda_monitor_static.tex}{\input{monitors/MeanPolLambda_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Monitor.tex b/docs/manuals/mcstas/monitors/Monitor.tex index b6ec51ab56..a0fa6ba470 100644 --- a/docs/manuals/mcstas/monitors/Monitor.tex +++ b/docs/manuals/mcstas/monitors/Monitor.tex @@ -3,19 +3,15 @@ \section{The \texttt{Monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} October 4, 1997 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Sums neutrons (0th, 1st, and 2nd moment of p) flying through -the rectangular monitor opening. May also be used as detector. +Sums neutrons (0th, 1st, and 2nd moment of p) flying through the rectangular monitor opening. May also be used as detector. Example: Monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1) -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -37,6 +33,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Monitor.comp}{Source code} for \texttt{Monitor.comp}. + \item Component source code found in file \texttt{Monitor.comp}. \end{itemize} -\IfFileExists{Monitor_static.tex}{\input{Monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Monitor_static.tex}{\input{monitors/Monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Monitor_4PI.tex b/docs/manuals/mcstas/monitors/Monitor_4PI.tex index a5012c332b..2808613fe5 100644 --- a/docs/manuals/mcstas/monitors/Monitor_4PI.tex +++ b/docs/manuals/mcstas/monitors/Monitor_4PI.tex @@ -7,17 +7,13 @@ \section{The \texttt{Monitor\_4PI} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann and Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} April 17, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Counts ALL neutrons that propagate this far in the instrument, regardless -of origin or direction. Mostly used for test purposes. -\end{lstlisting} +Counts ALL neutrons that propagate this far in the instrument, regardless of origin or direction. Mostly used for test purposes. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -32,6 +28,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Monitor_4PI.comp}{Source code} for \texttt{Monitor\_4PI.comp}. + \item Component source code found in file \texttt{Monitor\_4PI.comp}. \end{itemize} -\IfFileExists{Monitor_4PI_static.tex}{\input{Monitor_4PI_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Monitor_4PI_static.tex}{\input{monitors/Monitor_4PI_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Monitor_nD.tex b/docs/manuals/mcstas/monitors/Monitor_nD.tex index ddb60d52b9..6f27701b34 100644 --- a/docs/manuals/mcstas/monitors/Monitor_nD.tex +++ b/docs/manuals/mcstas/monitors/Monitor_nD.tex @@ -7,66 +7,44 @@ \section{The \texttt{Monitor\_nD} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:farhi@ill.fr"\textgreater{}Emmanuel Farhi\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} 14th Feb 2000. \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component is a general Monitor that can output 0/1/2D signals -It can produce many 1D signals (one for any variable specified in -option list), or a single 2D output (two variables correlation). -Also, an additional 'list' of neutron events can be produced. -By default, monitor is square (in x/y plane). A disk shape is also possible -The 'cylinder' and 'banana' option will change that for a banana shape -The 'sphere' option simulates spherical detector. The 'box' is a box. -The cylinder, sphere and banana should be centered on the scattering point. -The monitored flux may be per monitor unit area, and weighted by -a lambda/lambda(2200m/s) factor to obtain standard integrated capture flux. -In normal configuration, the Monitor_nD measures the current parameters -of the neutron that is beeing detected. But a PreMonitor_nD component can -be used in order to study correlations between a neutron being detected in -a Monitor_nD place, and given parameters that are monitored elsewhere -(at <b>PreMonitor_nD</b>). -The monitor can also act as a 3He gas detector, taking into account the -detection efficiency. - -The 'bins' and 'limits' modifiers are to be used after each variable, -and 'auto','log' and 'abs' come before it. (eg: auto abs log hdiv bins=10 -limits=[-5 5]) When placed after all variables, these two latter modifiers -apply to the signal (e.g. intensity). Unknown keywords are ignored. -If no limits are specified for a given observable, reasonable defaults will be -applied. Note that these implicit limits are <b>even</b> applied in list mode. - -<b>Implicit limits for typical variables:</b> -(consult monitor_nd-lib.c if you don't find your variable here) -x, y, z: Derived from detection-object geometry +This component is a general Monitor that can output 0/1/2D signals It can produce many 1D signals (one for any variable specified in option list), or a single 2D output (two variables correlation). Also, an additional 'list' of neutron events can be produced. By default, monitor is square (in x/y plane). A disk shape is also possible The 'cylinder' and 'banana' option will change that for a banana shape The 'sphere' option simulates spherical detector. The 'box' is a box. The cylinder, sphere and banana should be centered on the scattering point. The monitored flux may be per monitor unit area, and weighted by a lambda/lambda(2200m/s) factor to obtain standard integrated capture flux. In normal configuration, the Monitor\_nD measures the current parameters of the neutron that is beeing detected. USERVARS may be used in order to study correlations between a neutron being detected in a Monitor\_nD place, and given parameters that are monitored elsewhere (at the point of initialisation of the USERVARS). The monitor can also act as a 3He gas detector, taking into account the detection efficiency. + +The 'bins' and 'limits' modifiers are to be used after each variable, and 'auto','log' and 'abs' come before it. (eg: auto abs log hdiv bins=10 limits=[-5 5]) When placed after all variables, these two latter modifiers apply to the signal (e.g. intensity). Unknown keywords are ignored. If no limits are specified for a given observable, reasonable defaults will be applied. Note that these implicit limits are \textbf{even} applied in list mode. + +\textbf{Implicit limits for typical variables:} (consult monitor\_nd-lib.c if you don't find your variable here) x, y, z: Derived from detection-object geometry + +\begin{verbatim} k: [0 10] Angs-1 v: [0 1e6] m/s t: [0 1] s -p: [0 FLT_MAX] in intensity-units +\end{verbatim} + +p: [0 FLT\_MAX] in intensity-units + +\begin{verbatim} vx, vy: [-1000 1000] m/s vz: [0 10000] m/s kx, ky: [-1 1] Angs-1 kz: [-10 10] Angs-1 -energy, omega: [0 100] meV -lambda,wavelength: [0 100] Angs -sx, sy, sz: [-1 1] in polarisation-units -angle: [-50 50] deg -divergence, vdiv, hdiv, xdiv, ydiv: [-5 5] deg -longitude, lattitude: [-180 180] deg -neutron: [0 simulaton_ncount] -id, pixel id: [0 FLT_MAX] -uservars u1,u2,u3: [-1e10 1e10] - -In the case of multiple components at the same position, the 'parallel' -keyword must be used in each instance instead of defining a GROUP. - -<b>Possible options are</b> -Variables to record: -kx ky kz k wavevector [Angs-1] Wavevector on x,y,z and norm +\end{verbatim} + +energy, omega: [0 100] meV lambda,wavelength: [0 100] \AA{} sx, sy, sz: [-1 1] in polarisation-units angle: [-50 50] deg divergence, vdiv, hdiv, xdiv, ydiv: [-5 5] deg longitude, lattitude: [-180 180] deg neutron: [0 simulaton\_ncount] id, pixel id: [0 FLT\_MAX] + +\begin{verbatim} +uservars u0,u1,u2,u3,u4,u5,u6,u7,u8,u9: [-1e10 1e10] +\end{verbatim} + +In the case of multiple components at the same position, the 'parallel' keyword must be used in each instance instead of defining a GROUP. + +\textbf{Possible options are} Variables to record: kx ky kz k wavevector [\AA{}-1] Wavevector on x,y,z and norm + +\begin{verbatim} vx vy vz v [m/s] Velocity on x,y,z and norm x y z radius [m] Distance, Position and norm xy, yz, xz [m] Radial position in xy, yz and xz plane @@ -81,15 +59,28 @@ \subsection*{Description} angle [deg] divergence from <z> direction theta longitude [deg] longitude (x/z) for sphere and cylinder phi lattitude [deg] lattitude (y/z) for sphere and cylinder +\end{verbatim} -user user1 will monitor the [Mon_Name]_Vars.UserVariable{1|2|3} +\begin{verbatim} +user0 user1 will monitor the [Mon_Name]_Vars.UserVariable{0|1|2|3|4|5} user2 user3 to be assigned in an other component (see below) +\end{verbatim} + +user4 user5 user6 user7 user8 user9 + +\begin{verbatim} +Premonitoring: Please use uservars in place of the former PreMonitor_nD. +\end{verbatim} +\begin{verbatim} p intensity flux [n/s or n/cm^2/s] ncounts n neutron [1] neutron ID, i.e current event index pixel id [1] pixelID in histogram made of preceeding vars, e.g. 'theta y'. To set an offset PixelID use the 'min=value' keyword. Sets event mode. +\end{verbatim} -<b>Other options keywords are:</b> +\textbf{Other options keywords are:} + +\begin{verbatim} abs Will monitor the abs of the following variable or of the signal (if used after all variables) auto Automatically set detector limits for one/all all {limits|bins|auto} To set all limits or bins values or auto mode @@ -100,25 +91,36 @@ \subsection*{Description} file=string Detector image file name. default is component name, plus date and variable extension. incoming Monitor incoming beam in non flat det limits=[min max] Lower/Upper limits for axes (see up for the variable unit) +\end{verbatim} + list=[counts=1000] or all For a long file of neutron characteristics with [counts] or all events + +\begin{verbatim} log Will monitor the log of the following variable or of the signal (if used after all variables) min=[min_value] Same as limits, but only sets the min or max -max=[max_value] +\end{verbatim} + +max=[max\_value] + +\begin{verbatim} multiple Create multiple independant 1D monitors files no or not Revert next option outgoing Monitor outgoing beam (default) parallel Use this option when the next component is at the same position (parallel components) per cm2 Intensity will be per cm^2 (detector area). Displays beam section. per steradian Displays beam solid angle in steradian -premonitor Will monitor neutron parameters stored previously with <b>PreMonitor_nD</b>. signal=[var] Will monitor [var] instead of usual intensity slit or absorb Absorb neutrons that are out detector source The monitor will save neutron states inactivate To inactivate detector (0D detector) verbose To display additional informations -3He_pressure=[3 in bars] The 3He gas pressure in detector. 3He_pressure=0 is perfect detector (default) +\end{verbatim} + +3He\_pressure=[3 in bars] The 3He gas pressure in detector. 3He\_pressure=0 is perfect detector (default) Detector shape options (specified as xwidth,yheight,zdepth or x/y/z/min/max) + +\begin{verbatim} box Box of size xwidth, yheight, zdepth. cylinder To get a cylindrical monitor (diameter is xwidth or set radius, height is yheight). banana Same as cylinder, without top/bottom, on restricted angular area; use theta variable with limits to define arc. (diameter is xwidth or set radius, height is yheight). @@ -126,57 +128,41 @@ \subsection*{Description} sphere To get a spherical monitor (e.g. a 4PI) (diameter is xwidth or set radius). square Square flat xy monitor (xwidth, yheight). previous The monitor uses PREVIOUS component as detector surface. Or use 'geometry' parameter to specify any PLY/OFF geometry file. +\end{verbatim} + +\textbf{EXAMPLES:} \textless{}ul\textgreater{} \textless{}li\textgreater{}MyMon = Monitor\_nD(xwidth = 0.1, yheight = 0.1, zdepth = 0, \ \ options = "intensity per cm2 angle,limits=[-5 5] bins=10,with \ \ borders, file = mon1"); will monitor neutron angle from [z] axis, between -5 and 5 degrees, in 10 bins, into "mon1.A" output 1D file -<b>EXAMPLES:</b> -<ul> -<li>MyMon = Monitor_nD(xwidth = 0.1, yheight = 0.1, zdepth = 0, -  options = "intensity per cm2 angle,limits=[-5 5] bins=10,with -  borders, file = mon1"); -will monitor neutron angle from [z] axis, between -5 -and 5 degrees, in 10 bins, into "mon1.A" output 1D file +\textless{}li\textgreater{} options = "sphere theta phi outgoing" for a sphere PSD detector (out beam) and saves into file "MyMon\_[Date\_ID].th\_ph" -<li> options = "sphere theta phi outgoing" -for a sphere PSD detector (out beam) and saves into file "MyMon_[Date_ID].th_ph" +\textless{}li\textgreater{} options = "banana, theta limits=[10,130], bins=120, y" a theta/height banana detector -<li> options = "banana, theta limits=[10,130], bins=120, y" -a theta/height banana detector +\textless{}li\textgreater{} options = "angle radius all auto" is a 2D monitor with automatic limits -<li> options = "angle radius all auto" -is a 2D monitor with automatic limits +\textless{}li\textgreater{} options = "list=1000 kx ky kz energy" records 1000 neutron event in a file -<li> options = "list=1000 kx ky kz energy" -records 1000 neutron event in a file +\textless{}li\textgreater{} options = "multiple kx ky kz, auto abs log t, and list all neutrons" makes 4 output 1D files and produces a complete list for all neutrons and monitor log(abs(tof)) within automatic limits (for t) -<li> options = "multiple kx ky kz, auto abs log t, and list all neutrons" -makes 4 output 1D files and produces a complete list for all neutrons -and monitor log(abs(tof)) within automatic limits (for t) +\textless{}li\textgreater{} options = "theta y, sphere, pixel min=100" a 4pi detector which outputs an event list with pixelID from the actual detector surface, starting from index 100. -<li> options = "theta y, sphere, pixel min=100" -a 4pi detector which outputs an event list with pixelID from the actual -detector surface, starting from index 100. +\textless{}/ul\textgreater{} To dynamically define a number of bins, or limits: -</ul> -To dynamically define a number of bins, or limits: +\begin{verbatim} Use in DECLARE: char op[256]; -Use in INITIALIZE: sprintf(op, "lambda limits=[%g %g], bins=%i", lmin, lmax, lbin); +\end{verbatim} + +Use in INITIALIZE: sprintf(op, "lambda limits=[\%g \%g], bins=\%i", lmin, lmax, lbin); + +\begin{verbatim} Use in TRACE: Monitor_nD(... options=op ...) +\end{verbatim} -<b>How to monitor any instrument/component variable into a Monitor_nD</b> -Suppose you want to monitor a variable 'age' which you assign somwhere in -the instrument: -COMPONENT MyMonitor = Monitor_nD( -xwidth = 0.1, yheight = 0.1, -user1="age", username1="Age of the Captain [years]", -options="user1, auto") -AT ... +\textbf{How to monitor any instrument/component variable into a Monitor\_nD} Suppose you want to monitor a variable 'age' which you assign somwhere in the instrument: COMPONENT MyMonitor = Monitor\_nD( xwidth = 0.1, yheight = 0.1, user1="age", username1="Age of the Captain [years]", options="user1, auto") -See also the example in <a href="PreMonitor_nD.html">PreMonitor_nD</a> to -monitor neutron parameters cross-correlations. +\begin{verbatim} +AT ... +\end{verbatim} -%BUGS -The 'auto' option for guessing optimal variable bounds should NOT be used with MPI -as each process may use different limits. -\end{lstlisting} +\%BUGS The 'auto' option for guessing optimal variable bounds should NOT be used with MPI as each process may use different limits. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -186,9 +172,16 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead +user0 & str & Variable name of USERVAR to be monitored by user0. & "" \\ user1 & str & Variable name of USERVAR to be monitored by user1. & "" \\ user2 & str & Variable name of USERVAR to be monitored by user2. & "" \\ user3 & str & Variable name of USERVAR to be monitored by user3. & "" \\ +user4 & str & Variable name of USERVAR to be monitored by user4. & "" \\ +user5 & str & Variable name of USERVAR to be monitored by user5. & "" \\ +user6 & str & Variable name of USERVAR to be monitored by user6. & "" \\ +user7 & str & Variable name of USERVAR to be monitored by user7. & "" \\ +user8 & str & Variable name of USERVAR to be monitored by user8. & "" \\ +user9 & str & Variable name of USERVAR to be monitored by user9. & "" \\ xwidth & m & Width of detector. & 0 \\ yheight & m & Height of detector. & 0 \\ zdepth & m & Thickness of detector (z). & 0 \\ @@ -208,50 +201,21 @@ \subsection*{Input parameters} geometry & str & Name of an OFF file to specify a complex geometry detector & "NULL" \\ nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ nexus\_bins & 1 & NeXus mode only: store component BIN information \textless{}br\textgreater{}(-1 disable, 0 enable for list mode monitor, 1 enable for any montor) & 0 \\ +username0 & str & Name assigned to User0 & "NULL" \\ username1 & str & Name assigned to User1 & "NULL" \\ username2 & str & Name assigned to User2 & "NULL" \\ username3 & str & Name assigned to User3 & "NULL" \\ +username4 & str & Name assigned to User4 & "NULL" \\ +username5 & str & Name assigned to User5 & "NULL" \\ +username6 & str & Name assigned to User6 & "NULL" \\ +username7 & str & Name assigned to User7 & "NULL" \\ +username8 & str & Name assigned to User8 & "NULL" \\ +username9 & str & Name assigned to User9 & "NULL" \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Monitor_nD.comp}{Source code} for \texttt{Monitor\_nD.comp}. - \item \textless{}a href="PreMonitor\_nD.html"\textgreater{}PreMonitor\_nD\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Monitor\_nD.comp}. \end{itemize} -\IfFileExists{Monitor_nD_static.tex}{\input{Monitor_nD_static.tex}}{} -\subsection{Monitoring neutron parameter correlations via USERVARS} - -The first imediate usage of the Monitor\_nD component is when one requires to identify cross-correlations between some neutron parameters, e.g. position and divergence (\textit{aka} phase-space diagram). -\begin{lstlisting} -options="x dx, auto", bins=30 -\end{lstlisting} -This example records the correlation between position and divergence of neutrons at a given instrument location. - -But it is also possible to search for cross-correlation between two part of the instrument simulation. One example is the acceptance phase-diagram, which shows the neutron caracteristics at the input required to reach the end of the simulation. This \emph{spatial} correlation may be revealed using \index{Monitors!Neutron parameter correlations, USERVARS}\ref{s:monnd:user} initialised in an \textbf{EXTEND} block of an earlier component. \textbf{USERVARS} may store neutron parameters at a given instrument location, to be used with a later Monitor\_nD location for monitoring: - -\begin{lstlisting} -USERVARS \%{ - double x_in; - double xdiv_in; -\%} - -TRACE - -COMPONENT CorrelationLocation = Arm() -AT (...) -EXTEND \%{ - x_in=x; - // Calculate divergence wrt. z - xdiv_in = RAD2DEG * atan2 (vx, vz); -\%} - - (... e.g. a guide system ) - - COMPONENT CorrelationMonitor = Monitor_nD( - user1=''x_in'', user2=''xdiv_in'', - username1=''Upstream pos'', username2=''Upstream div'' - options="user1 user2, auto, all bins=30") -AT (...) -\end{lstlisting} -which performs the same monitoring as the previous example, but with a spatial correlation constrain. Indeed, it records the position \textit{vs} the divergence of neutrons at the correlation location, but only if they reach the monitoring position. +\IfFileExists{monitors/Monitor_nD_static.tex}{\input{monitors/Monitor_nD_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Monitor_nD_noacc.tex b/docs/manuals/mcstas/monitors/Monitor_nD_noacc.tex index 6449560e06..fba64e5a22 100644 --- a/docs/manuals/mcstas/monitors/Monitor_nD_noacc.tex +++ b/docs/manuals/mcstas/monitors/Monitor_nD_noacc.tex @@ -7,66 +7,44 @@ \section{The \texttt{Monitor\_nD\_noacc} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:farhi@ill.fr"\textgreater{}Emmanuel Farhi\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} 14th Feb 2000. \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component is a general Monitor that can output 0/1/2D signals -It can produce many 1D signals (one for any variable specified in -option list), or a single 2D output (two variables correlation). -Also, an additional 'list' of neutron events can be produced. -By default, monitor is square (in x/y plane). A disk shape is also possible -The 'cylinder' and 'banana' option will change that for a banana shape -The 'sphere' option simulates spherical detector. The 'box' is a box. -The cylinder, sphere and banana should be centered on the scattering point. -The monitored flux may be per monitor unit area, and weighted by -a lambda/lambda(2200m/s) factor to obtain standard integrated capture flux. -In normal configuration, the Monitor_nD measures the current parameters -of the neutron that is beeing detected. But a PreMonitor_nD component can -be used in order to study correlations between a neutron being detected in -a Monitor_nD place, and given parameters that are monitored elsewhere -(at <b>PreMonitor_nD</b>). -The monitor can also act as a 3He gas detector, taking into account the -detection efficiency. - -The 'bins' and 'limits' modifiers are to be used after each variable, -and 'auto','log' and 'abs' come before it. (eg: auto abs log hdiv bins=10 -limits=[-5 5]) When placed after all variables, these two latter modifiers -apply to the signal (e.g. intensity). Unknown keywords are ignored. -If no limits are specified for a given observable, reasonable defaults will be -applied. Note that these implicit limits are <b>even</b> applied in list mode. - -<b>Implicit limits for typical variables:</b> -(consult monitor_nd-lib.c if you don't find your variable here) -x, y, z: Derived from detection-object geometry +This component is a general Monitor that can output 0/1/2D signals It can produce many 1D signals (one for any variable specified in option list), or a single 2D output (two variables correlation). Also, an additional 'list' of neutron events can be produced. By default, monitor is square (in x/y plane). A disk shape is also possible The 'cylinder' and 'banana' option will change that for a banana shape The 'sphere' option simulates spherical detector. The 'box' is a box. The cylinder, sphere and banana should be centered on the scattering point. The monitored flux may be per monitor unit area, and weighted by a lambda/lambda(2200m/s) factor to obtain standard integrated capture flux. In normal configuration, the Monitor\_nD measures the current parameters of the neutron that is beeing detected. USERVARS can be used in order to study correlations between a neutron being detected in a Monitor\_nD place, and given parameters that are monitored elsewhere (at the point of initialisation of the USERVARS). The monitor can also act as a 3He gas detector, taking into account the detection efficiency. + +The 'bins' and 'limits' modifiers are to be used after each variable, and 'auto','log' and 'abs' come before it. (eg: auto abs log hdiv bins=10 limits=[-5 5]) When placed after all variables, these two latter modifiers apply to the signal (e.g. intensity). Unknown keywords are ignored. If no limits are specified for a given observable, reasonable defaults will be applied. Note that these implicit limits are \textbf{even} applied in list mode. + +\textbf{Implicit limits for typical variables:} (consult monitor\_nd-lib.c if you don't find your variable here) x, y, z: Derived from detection-object geometry + +\begin{verbatim} k: [0 10] Angs-1 v: [0 1e6] m/s t: [0 1] s -p: [0 FLT_MAX] in intensity-units +\end{verbatim} + +p: [0 FLT\_MAX] in intensity-units + +\begin{verbatim} vx, vy: [-1000 1000] m/s vz: [0 10000] m/s kx, ky: [-1 1] Angs-1 kz: [-10 10] Angs-1 -energy, omega: [0 100] meV -lambda,wavelength: [0 100] Angs -sx, sy, sz: [-1 1] in polarisation-units -angle: [-50 50] deg -divergence, vdiv, hdiv, xdiv, ydiv: [-5 5] deg -longitude, lattitude: [-180 180] deg -neutron: [0 simulaton_ncount] -id, pixel id: [0 FLT_MAX] -uservars u1,u2,u3: [-1e10 1e10] - -In the case of multiple components at the same position, the 'parallel' -keyword must be used in each instance instead of defining a GROUP. - -<b>Possible options are</b> -Variables to record: -kx ky kz k wavevector [Angs-1] Wavevector on x,y,z and norm +\end{verbatim} + +energy, omega: [0 100] meV lambda,wavelength: [0 100] \AA{} sx, sy, sz: [-1 1] in polarisation-units angle: [-50 50] deg divergence, vdiv, hdiv, xdiv, ydiv: [-5 5] deg longitude, lattitude: [-180 180] deg neutron: [0 simulaton\_ncount] id, pixel id: [0 FLT\_MAX] + +\begin{verbatim} +uservars u0,u1,u2,u3,u4,u5,u6,u7,u8,u9: [-1e10 1e10] +\end{verbatim} + +In the case of multiple components at the same position, the 'parallel' keyword must be used in each instance instead of defining a GROUP. + +\textbf{Possible options are} Variables to record: kx ky kz k wavevector [\AA{}-1] Wavevector on x,y,z and norm + +\begin{verbatim} vx vy vz v [m/s] Velocity on x,y,z and norm x y z radius [m] Distance, Position and norm xy, yz, xz [m] Radial position in xy, yz and xz plane @@ -81,15 +59,28 @@ \subsection*{Description} angle [deg] divergence from <z> direction theta longitude [deg] longitude (x/z) for sphere and cylinder phi lattitude [deg] lattitude (y/z) for sphere and cylinder +\end{verbatim} -user user1 will monitor the [Mon_Name]_Vars.UserVariable{1|2|3} +\begin{verbatim} +user0 user1 will monitor the [Mon_Name]_Vars.UserVariable{0|1|2|3|4|5} user2 user3 to be assigned in an other component (see below) +\end{verbatim} + +user4 user5 user6 user7 user8 user9 + +\begin{verbatim} +Premonitoring: Please use uservars in place of the former PreMonitor_nD. +\end{verbatim} +\begin{verbatim} p intensity flux [n/s or n/cm^2/s] ncounts n neutron [1] neutron ID, i.e current event index pixel id [1] pixelID in histogram made of preceeding vars, e.g. 'theta y'. To set an offset PixelID use the 'min=value' keyword. Sets event mode. +\end{verbatim} -<b>Other options keywords are:</b> +\textbf{Other options keywords are:} + +\begin{verbatim} abs Will monitor the abs of the following variable or of the signal (if used after all variables) auto Automatically set detector limits for one/all all {limits|bins|auto} To set all limits or bins values or auto mode @@ -100,25 +91,36 @@ \subsection*{Description} file=string Detector image file name. default is component name, plus date and variable extension. incoming Monitor incoming beam in non flat det limits=[min max] Lower/Upper limits for axes (see up for the variable unit) +\end{verbatim} + list=[counts=1000] or all For a long file of neutron characteristics with [counts] or all events + +\begin{verbatim} log Will monitor the log of the following variable or of the signal (if used after all variables) min=[min_value] Same as limits, but only sets the min or max -max=[max_value] +\end{verbatim} + +max=[max\_value] + +\begin{verbatim} multiple Create multiple independant 1D monitors files no or not Revert next option outgoing Monitor outgoing beam (default) parallel Use this option when the next component is at the same position (parallel components) per cm2 Intensity will be per cm^2 (detector area). Displays beam section. per steradian Displays beam solid angle in steradian -premonitor Will monitor neutron parameters stored previously with <b>PreMonitor_nD</b>. signal=[var] Will monitor [var] instead of usual intensity slit or absorb Absorb neutrons that are out detector source The monitor will save neutron states inactivate To inactivate detector (0D detector) verbose To display additional informations -3He_pressure=[3 in bars] The 3He gas pressure in detector. 3He_pressure=0 is perfect detector (default) +\end{verbatim} + +3He\_pressure=[3 in bars] The 3He gas pressure in detector. 3He\_pressure=0 is perfect detector (default) Detector shape options (specified as xwidth,yheight,zdepth or x/y/z/min/max) + +\begin{verbatim} box Box of size xwidth, yheight, zdepth. cylinder To get a cylindrical monitor (diameter is xwidth or set radius, height is yheight). banana Same as cylinder, without top/bottom, on restricted angular area; use theta variable with limits to define arc. (diameter is xwidth or set radius, height is yheight). @@ -126,57 +128,41 @@ \subsection*{Description} sphere To get a spherical monitor (e.g. a 4PI) (diameter is xwidth or set radius). square Square flat xy monitor (xwidth, yheight). previous The monitor uses PREVIOUS component as detector surface. Or use 'geometry' parameter to specify any PLY/OFF geometry file. +\end{verbatim} + +\textbf{EXAMPLES:} \textless{}ul\textgreater{} \textless{}li\textgreater{}MyMon = Monitor\_nD(xwidth = 0.1, yheight = 0.1, zdepth = 0, \ \ options = "intensity per cm2 angle,limits=[-5 5] bins=10,with \ \ borders, file = mon1"); will monitor neutron angle from [z] axis, between -5 and 5 degrees, in 10 bins, into "mon1.A" output 1D file -<b>EXAMPLES:</b> -<ul> -<li>MyMon = Monitor_nD(xwidth = 0.1, yheight = 0.1, zdepth = 0, -  options = "intensity per cm2 angle,limits=[-5 5] bins=10,with -  borders, file = mon1"); -will monitor neutron angle from [z] axis, between -5 -and 5 degrees, in 10 bins, into "mon1.A" output 1D file +\textless{}li\textgreater{} options = "sphere theta phi outgoing" for a sphere PSD detector (out beam) and saves into file "MyMon\_[Date\_ID].th\_ph" -<li> options = "sphere theta phi outgoing" -for a sphere PSD detector (out beam) and saves into file "MyMon_[Date_ID].th_ph" +\textless{}li\textgreater{} options = "banana, theta limits=[10,130], bins=120, y" a theta/height banana detector -<li> options = "banana, theta limits=[10,130], bins=120, y" -a theta/height banana detector +\textless{}li\textgreater{} options = "angle radius all auto" is a 2D monitor with automatic limits -<li> options = "angle radius all auto" -is a 2D monitor with automatic limits +\textless{}li\textgreater{} options = "list=1000 kx ky kz energy" records 1000 neutron event in a file -<li> options = "list=1000 kx ky kz energy" -records 1000 neutron event in a file +\textless{}li\textgreater{} options = "multiple kx ky kz, auto abs log t, and list all neutrons" makes 4 output 1D files and produces a complete list for all neutrons and monitor log(abs(tof)) within automatic limits (for t) -<li> options = "multiple kx ky kz, auto abs log t, and list all neutrons" -makes 4 output 1D files and produces a complete list for all neutrons -and monitor log(abs(tof)) within automatic limits (for t) +\textless{}li\textgreater{} options = "theta y, sphere, pixel min=100" a 4pi detector which outputs an event list with pixelID from the actual detector surface, starting from index 100. -<li> options = "theta y, sphere, pixel min=100" -a 4pi detector which outputs an event list with pixelID from the actual -detector surface, starting from index 100. +\textless{}/ul\textgreater{} To dynamically define a number of bins, or limits: -</ul> -To dynamically define a number of bins, or limits: +\begin{verbatim} Use in DECLARE: char op[256]; -Use in INITIALIZE: sprintf(op, "lambda limits=[%g %g], bins=%i", lmin, lmax, lbin); +\end{verbatim} + +Use in INITIALIZE: sprintf(op, "lambda limits=[\%g \%g], bins=\%i", lmin, lmax, lbin); + +\begin{verbatim} Use in TRACE: Monitor_nD(... options=op ...) +\end{verbatim} -<b>How to monitor any instrument/component variable into a Monitor_nD</b> -Suppose you want to monitor a variable 'age' which you assign somwhere in -the instrument: -COMPONENT MyMonitor = Monitor_nD( -xwidth = 0.1, yheight = 0.1, -user1="age", username1="Age of the Captain [years]", -options="user1, auto") -AT ... +\textbf{How to monitor any instrument/component variable into a Monitor\_nD} Suppose you want to monitor a variable 'age' which you assign somwhere in the instrument: COMPONENT MyMonitor = Monitor\_nD( xwidth = 0.1, yheight = 0.1, user1="age", username1="Age of the Captain [years]", options="user1, auto") -See also the example in <a href="PreMonitor_nD.html">PreMonitor_nD</a> to -monitor neutron parameters cross-correlations. +\begin{verbatim} +AT ... +\end{verbatim} -%BUGS -The 'auto' option for guessing optimal variable bounds should NOT be used with MPI -as each process may use different limits. -\end{lstlisting} +\%BUGS The 'auto' option for guessing optimal variable bounds should NOT be used with MPI as each process may use different limits. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -186,9 +172,16 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead +user0 & str & Variable name of USERVAR to be monitored by user0. & "" \\ user1 & str & Variable name of USERVAR to be monitored by user1. & "" \\ user2 & str & Variable name of USERVAR to be monitored by user2. & "" \\ user3 & str & Variable name of USERVAR to be monitored by user3. & "" \\ +user4 & str & Variable name of USERVAR to be monitored by user4. & "" \\ +user5 & str & Variable name of USERVAR to be monitored by user5. & "" \\ +user6 & str & Variable name of USERVAR to be monitored by user6. & "" \\ +user7 & str & Variable name of USERVAR to be monitored by user7. & "" \\ +user8 & str & Variable name of USERVAR to be monitored by user8. & "" \\ +user9 & str & Variable name of USERVAR to be monitored by user9. & "" \\ xwidth & m & Width of detector. & 0 \\ yheight & m & Height of detector. & 0 \\ zdepth & m & Thickness of detector (z). & 0 \\ @@ -208,15 +201,21 @@ \subsection*{Input parameters} geometry & str & Name of an OFF file to specify a complex geometry detector & "NULL" \\ nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ nexus\_bins & 1 & NeXus mode only: store component BIN information \textless{}br\textgreater{}(-1 disable, 0 enable for list mode monitor, 1 enable for any montor) & 0 \\ +username0 & str & Name assigned to User0 & "NULL" \\ username1 & str & Name assigned to User1 & "NULL" \\ username2 & str & Name assigned to User2 & "NULL" \\ username3 & str & Name assigned to User3 & "NULL" \\ +username4 & str & Name assigned to User4 & "NULL" \\ +username5 & str & Name assigned to User5 & "NULL" \\ +username6 & str & Name assigned to User6 & "NULL" \\ +username7 & str & Name assigned to User7 & "NULL" \\ +username8 & str & Name assigned to User8 & "NULL" \\ +username9 & str & Name assigned to User9 & "NULL" \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Monitor_nD_noacc.comp}{Source code} for \texttt{Monitor\_nD\_noacc.comp}. - \item \textless{}a href="PreMonitor\_nD.html"\textgreater{}PreMonitor\_nD\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Monitor\_nD\_noacc.comp}. \end{itemize} -\IfFileExists{Monitor_nD_noacc_static.tex}{\input{Monitor_nD_noacc_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Monitor_nD_noacc_static.tex}{\input{monitors/Monitor_nD_noacc_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSD_TOF_monitor.tex b/docs/manuals/mcstas/monitors/PSD_TOF_monitor.tex index 980109f9d0..ca52961218 100644 --- a/docs/manuals/mcstas/monitors/PSD_TOF_monitor.tex +++ b/docs/manuals/mcstas/monitors/PSD_TOF_monitor.tex @@ -3,20 +3,17 @@ \section{The \texttt{PSD\_TOF\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup, derived from PSD\_monitor by Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} Feb 3, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} An (nx times ny) pixel PSD monitor with nt time bins pr pixel. Will output nt PSD images plus 1 integrated image. -Example: PSD_TOF_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, tmin=4000, tmax=7000, nt=3, filename="Output") -\end{lstlisting} +Example: PSD\_TOF\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, tmin=4000, tmax=7000, nt=3, filename="Output") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -45,6 +42,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSD_TOF_monitor.comp}{Source code} for \texttt{PSD\_TOF\_monitor.comp}. + \item Component source code found in file \texttt{PSD\_TOF\_monitor.comp}. \end{itemize} -\IfFileExists{PSD_TOF_monitor_static.tex}{\input{PSD_TOF_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSD_TOF_monitor_static.tex}{\input{monitors/PSD_TOF_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSD_monitor.tex b/docs/manuals/mcstas/monitors/PSD_monitor.tex index dfd09583c3..c33abb8b69 100644 --- a/docs/manuals/mcstas/monitors/PSD_monitor.tex +++ b/docs/manuals/mcstas/monitors/PSD_monitor.tex @@ -3,19 +3,15 @@ \section{The \texttt{PSD\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} Feb 3, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel PSD monitor. This component may also be used as a beam -detector. +An (n times m) pixel PSD monitor. This component may also be used as a beam detector. -Example: PSD_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, filename="Output.psd") -\end{lstlisting} +Example: PSD\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, filename="Output.psd") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -41,6 +37,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSD_monitor.comp}{Source code} for \texttt{PSD\_monitor.comp}. + \item Component source code found in file \texttt{PSD\_monitor.comp}. \end{itemize} -\IfFileExists{PSD_monitor_static.tex}{\input{PSD_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSD_monitor_static.tex}{\input{monitors/PSD_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSD_monitor_4PI.tex b/docs/manuals/mcstas/monitors/PSD_monitor_4PI.tex index 65dd2395ff..37fb47a190 100644 --- a/docs/manuals/mcstas/monitors/PSD_monitor_4PI.tex +++ b/docs/manuals/mcstas/monitors/PSD_monitor_4PI.tex @@ -3,19 +3,15 @@ \section{The \texttt{PSD\_monitor\_4PI} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann and Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} April 17, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel spherical PSD monitor using a cylindrical projection. -Mostly for test and debugging purposes. +An (n times m) pixel spherical PSD monitor using a cylindrical projection. Mostly for test and debugging purposes. -Example: PSD_monitor_4PI(radius=0.1, nx=90, ny=90, filename="Output.psd") -\end{lstlisting} +Example: PSD\_monitor\_4PI(radius=0.1, nx=90, ny=90, filename="Output.psd") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,8 +32,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSD_monitor_4PI.comp}{Source code} for \texttt{PSD\_monitor\_4PI.comp}. + \item Component source code found in file \texttt{PSD\_monitor\_4PI.comp}. \item \textless{}A HREF="http://neutron.risoe.dk/mcstas/components/tests/powder/"\textgreater{}Test \item results\textless{}/A\textgreater{} (not up-to-date). \end{itemize} -\IfFileExists{PSD_monitor_4PI_static.tex}{\input{PSD_monitor_4PI_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSD_monitor_4PI_static.tex}{\input{monitors/PSD_monitor_4PI_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSD_monitor_4PI_spin.tex b/docs/manuals/mcstas/monitors/PSD_monitor_4PI_spin.tex index 40a3df043b..c9815be127 100644 --- a/docs/manuals/mcstas/monitors/PSD_monitor_4PI_spin.tex +++ b/docs/manuals/mcstas/monitors/PSD_monitor_4PI_spin.tex @@ -3,20 +3,15 @@ \section{The \texttt{PSD\_monitor\_4PI\_spin} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen \item \textbf{Origin:} DTU \item \textbf{Date:} April 17, 2010 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel spherical PSD monitor using a cylindrical projection. -Mostly for test and debugging purposes. +An (n times m) pixel spherical PSD monitor using a cylindrical projection. Mostly for test and debugging purposes. -Example: PSD_monitor_4PI(radius=0.1, -nx=90, ny=90, filename="Output.psd") -\end{lstlisting} +Example: PSD\_monitor\_4PI(radius=0.1, nx=90, ny=90, filename="Output.psd") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -39,6 +34,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSD_monitor_4PI_spin.comp}{Source code} for \texttt{PSD\_monitor\_4PI\_spin.comp}. + \item Component source code found in file \texttt{PSD\_monitor\_4PI\_spin.comp}. \end{itemize} -\IfFileExists{PSD_monitor_4PI_spin_static.tex}{\input{PSD_monitor_4PI_spin_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSD_monitor_4PI_spin_static.tex}{\input{monitors/PSD_monitor_4PI_spin_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSD_monitor_TOF.tex b/docs/manuals/mcstas/monitors/PSD_monitor_TOF.tex index 8294cdad0f..a15bfea7da 100644 --- a/docs/manuals/mcstas/monitors/PSD_monitor_TOF.tex +++ b/docs/manuals/mcstas/monitors/PSD_monitor_TOF.tex @@ -3,20 +3,17 @@ \section{The \texttt{PSD\_monitor\_TOF} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup, derived from PSD\_monitor by Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} Feb 3, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} An (nx times ny) pixel PSD monitor with nt time bins pr pixel. Will output 1 integrated PSD images plus an nt time bin TOF signal pr pixel. -Example: PSD_monitor_TOF(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, tmin=4000, tmax=7000, nt=1000, filename="Output") -\end{lstlisting} +Example: PSD\_monitor\_TOF(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, tmin=4000, tmax=7000, nt=1000, filename="Output") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -45,6 +42,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSD_monitor_TOF.comp}{Source code} for \texttt{PSD\_monitor\_TOF.comp}. + \item Component source code found in file \texttt{PSD\_monitor\_TOF.comp}. \end{itemize} -\IfFileExists{PSD_monitor_TOF_static.tex}{\input{PSD_monitor_TOF_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSD_monitor_TOF_static.tex}{\input{monitors/PSD_monitor_TOF_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSD_monitor_psf.tex b/docs/manuals/mcstas/monitors/PSD_monitor_psf.tex index c181ff13bb..10993abcb3 100644 --- a/docs/manuals/mcstas/monitors/PSD_monitor_psf.tex +++ b/docs/manuals/mcstas/monitors/PSD_monitor_psf.tex @@ -3,19 +3,15 @@ \section{The \texttt{PSD\_monitor\_psf} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann, Linda Udby \item \textbf{Origin:} Risoe \item \textbf{Date:} Feb 3, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel PSD monitor. This component may also be used as a beam -detector. +An (n times m) pixel PSD monitor. This component may also be used as a beam detector. -Example: PSD_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, filename="Output.psd") -\end{lstlisting} +Example: PSD\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, filename="Output.psd") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +38,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSD_monitor_psf.comp}{Source code} for \texttt{PSD\_monitor\_psf.comp}. + \item Component source code found in file \texttt{PSD\_monitor\_psf.comp}. \end{itemize} -\IfFileExists{PSD_monitor_psf_static.tex}{\input{PSD_monitor_psf_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSD_monitor_psf_static.tex}{\input{monitors/PSD_monitor_psf_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSD_monitor_psf_eff.tex b/docs/manuals/mcstas/monitors/PSD_monitor_psf_eff.tex index c791263e06..dea4b3b290 100644 --- a/docs/manuals/mcstas/monitors/PSD_monitor_psf_eff.tex +++ b/docs/manuals/mcstas/monitors/PSD_monitor_psf_eff.tex @@ -3,19 +3,15 @@ \section{The \texttt{PSD\_monitor\_psf\_eff} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann, Linda Udby \item \textbf{Origin:} Risoe \item \textbf{Date:} Feb 3, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel PSD monitor. This component may also be used as a beam -detector. Models 1/k behaviour and efficiency, based on user defined k0 and eff parameters. +An (n times m) pixel PSD monitor. This component may also be used as a beam detector. Models 1/k behaviour and efficiency, based on user defined k0 and eff parameters. -Example: PSD_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, filename="Output.psd") -\end{lstlisting} +Example: PSD\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, nx=90, ny=90, filename="Output.psd") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,7 +32,7 @@ \subsection*{Input parameters} xwidth & m & Width/diameter of detector (x). Overrides xmin, xmax & 0 \\ yheight & m & Height of detector (y). Overrides ymin, ymax & 0 \\ psf & m & Point spread function, ray (x,y) coordinate randomized by gaussion of sigma psf & 0 \\ -k0 & AA\textasciicircum{}-1 & Numerator in k0/k weighting & 1 \\ +k0 & \AA{}$^{-1}$ & Numerator in k0/k weighting & 1 \\ eff & 1 & Detector efficiency & 1 \\ restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ \bottomrule @@ -44,6 +40,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSD_monitor_psf_eff.comp}{Source code} for \texttt{PSD\_monitor\_psf\_eff.comp}. + \item Component source code found in file \texttt{PSD\_monitor\_psf\_eff.comp}. \end{itemize} -\IfFileExists{PSD_monitor_psf_eff_static.tex}{\input{PSD_monitor_psf_eff_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSD_monitor_psf_eff_static.tex}{\input{monitors/PSD_monitor_psf_eff_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSDcyl_monitor.tex b/docs/manuals/mcstas/monitors/PSDcyl_monitor.tex index f156354c01..77a5eb7d34 100644 --- a/docs/manuals/mcstas/monitors/PSDcyl_monitor.tex +++ b/docs/manuals/mcstas/monitors/PSDcyl_monitor.tex @@ -4,19 +4,15 @@ \section{The \texttt{PSDcyl\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} October 26, 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An (n times m) pixel PSD monitor with cylinder shape, -vertical axis, centered at (0,0,0). +An (n times m) pixel PSD monitor with cylinder shape, vertical axis, centered at (0,0,0). -Example: PSDcyl_monitor(nr=20, ny=20, filename="Output.cyl", yheight=0.2, radius=0.1) -\end{lstlisting} +Example: PSDcyl\_monitor(nr=20, ny=20, filename="Output.cyl", yheight=0.2, radius=0.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,6 +36,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSDcyl_monitor.comp}{Source code} for \texttt{PSDcyl\_monitor.comp}. + \item Component source code found in file \texttt{PSDcyl\_monitor.comp}. \end{itemize} -\IfFileExists{PSDcyl_monitor_static.tex}{\input{PSDcyl_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSDcyl_monitor_static.tex}{\input{monitors/PSDcyl_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSDlin_diff_monitor.tex b/docs/manuals/mcstas/monitors/PSDlin_diff_monitor.tex index 7b5fcc80d0..9cd4fb393b 100644 --- a/docs/manuals/mcstas/monitors/PSDlin_diff_monitor.tex +++ b/docs/manuals/mcstas/monitors/PSDlin_diff_monitor.tex @@ -4,17 +4,17 @@ \section{The \texttt{PSDlin\_diff\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann, Peter Willendrup, Linda Udby \item \textbf{Origin:} Risoe \item \textbf{Date:} May 7, 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Example: PSDlin_diff_monitor(nx=20, filename="Output.x", +Example: PSDlin\_diff\_monitor(nx=20, filename="Output.x", + +\begin{verbatim} xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1) -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -39,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSDlin_diff_monitor.comp}{Source code} for \texttt{PSDlin\_diff\_monitor.comp}. + \item Component source code found in file \texttt{PSDlin\_diff\_monitor.comp}. \end{itemize} -\IfFileExists{PSDlin_diff_monitor_static.tex}{\input{PSDlin_diff_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSDlin_diff_monitor_static.tex}{\input{monitors/PSDlin_diff_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PSDlin_monitor.tex b/docs/manuals/mcstas/monitors/PSDlin_monitor.tex index a8d76f5113..3f483ae038 100644 --- a/docs/manuals/mcstas/monitors/PSDlin_monitor.tex +++ b/docs/manuals/mcstas/monitors/PSDlin_monitor.tex @@ -3,20 +3,15 @@ \section{The \texttt{PSDlin\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} May 7, 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A 1-dimensional PSD measuring intensity along either the horizontal axis x (default) or -the vertical axis y. +A 1-dimensional PSD measuring intensity along either the horizontal axis x (default) or the vertical axis y. - -Example: PSDlin_monitor(nbins=20, filename="Output.x", xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1) -\end{lstlisting} +Example: PSDlin\_monitor(nbins=20, filename="Output.x", xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +37,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PSDlin_monitor.comp}{Source code} for \texttt{PSDlin\_monitor.comp}. + \item Component source code found in file \texttt{PSDlin\_monitor.comp}. \end{itemize} -\IfFileExists{PSDlin_monitor_static.tex}{\input{PSDlin_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PSDlin_monitor_static.tex}{\input{monitors/PSDlin_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/PolLambda_monitor.tex b/docs/manuals/mcstas/monitors/PolLambda_monitor.tex index ed023b9dc3..831bafdf46 100644 --- a/docs/manuals/mcstas/monitors/PolLambda_monitor.tex +++ b/docs/manuals/mcstas/monitors/PolLambda_monitor.tex @@ -3,20 +3,15 @@ \section{The \texttt{PolLambda\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Christiansen \item \textbf{Origin:} Risoe \item \textbf{Date:} July 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A square single monitor that measures the projection of the -polarisation along a given normalized m-vector (mx, my, mz) as a -function of wavelength. +A square single monitor that measures the projection of the polarisation along a given normalized m-vector (mx, my, mz) as a function of wavelength. -Example: Pollambda_monitor(Lmin=1, Lmax=20, nL=20, xwidth=0.1, yheight=0.1, npol=11, mx=0, my=1, mz=0, filename="pollambdaMon.data") -\end{lstlisting} +Example: Pollambda\_monitor(Lmin=1, Lmax=20, nL=20, xwidth=0.1, yheight=0.1, npol=11, mx=0, my=1, mz=0, filename="pollambdaMon.data") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,13 +31,13 @@ \subsection*{Input parameters} mx & 1 & X-component of monitor vector (can be negative) & 0 \\ my & 1 & Y-component of monitor vector (can be negative) & 0 \\ mz & 1 & Z-component of monitor vector (can be negative) & 0 \\ -\textbf{Lmin} & AA & Minimum wavelength detected & \\ -\textbf{Lmax} & AA & Maximum wavelength detected & \\ +\textbf{Lmin} & \AA{} & Minimum wavelength detected & \\ +\textbf{Lmax} & \AA{} & Maximum wavelength detected & \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/PolLambda_monitor.comp}{Source code} for \texttt{PolLambda\_monitor.comp}. + \item Component source code found in file \texttt{PolLambda\_monitor.comp}. \end{itemize} -\IfFileExists{PolLambda_monitor_static.tex}{\input{PolLambda_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/PolLambda_monitor_static.tex}{\input{monitors/PolLambda_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Pol_monitor.tex b/docs/manuals/mcstas/monitors/Pol_monitor.tex index c128326fb1..744245c31c 100644 --- a/docs/manuals/mcstas/monitors/Pol_monitor.tex +++ b/docs/manuals/mcstas/monitors/Pol_monitor.tex @@ -3,20 +3,15 @@ \section{The \texttt{Pol\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Christiansen \item \textbf{Origin:} Risoe \item \textbf{Date:} July 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A square single monitor that measures the projection of the -polarisation along a given normalized m-vector (mx, my, mz). -The measured quantity is: sx*mx+sy*my+mz*sz +A square single monitor that measures the projection of the polarisation along a given normalized m-vector (mx, my, mz). The measured quantity is: sx*mx+sy*my+mz*sz -Example: Pol_monitor(xwidth=0.1, yheight=0.1, nchan=11, mx=0, my=1, mz=0) -\end{lstlisting} +Example: Pol\_monitor(xwidth=0.1, yheight=0.1, nchan=11, mx=0, my=1, mz=0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -38,6 +33,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Pol_monitor.comp}{Source code} for \texttt{Pol\_monitor.comp}. + \item Component source code found in file \texttt{Pol\_monitor.comp}. \end{itemize} -\IfFileExists{Pol_monitor_static.tex}{\input{Pol_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Pol_monitor_static.tex}{\input{monitors/Pol_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Res_monitor.tex b/docs/manuals/mcstas/monitors/Res_monitor.tex index 41f0dd3161..6a8f3b5d3b 100644 --- a/docs/manuals/mcstas/monitors/Res_monitor.tex +++ b/docs/manuals/mcstas/monitors/Res_monitor.tex @@ -1,53 +1,58 @@ -\section{Res\_monitor: The monitor for resolution calculation} -\label{s:res_monitor} -\index{Monitors!Resolution monitor|see{Samples/Resolution function}} - -The component \textbf{Res\_monitor} is used for calculating the -resolution function of a particular instrument with detector of the -given shape, size, and position. -The shape of \textbf{Res\_monitor} is by default rectangular, -but can be a box, a sphere, a disk, or a cylinder, -depending on the parameter ``options''. -The component works like a normal monitor, but -also records all scattering events and stores -them to a file that can later be read by -the \MCS frontend tool \verb+mcresplot+. - -For time-of-flight (TOF) instruments, {Res\_monitor} should be understood -as giving the resolution of one time bin of the TOF-detector only; -the bin properties being specified in the preceding \textbf{TOF\_Res\_sample}. - -As described in section~\ref{s:res_sample}, -the \textbf{Res\_monitor} should be used in connection with one of the -components \textbf{Res\_sample} or \textbf{TOF\_Res\_sample}, -the name of which should be passed as an -input parameter to \textbf{Res\_monitor}. For example -\begin{lstlisting} - COMPONENT mysample = Res_sample( ... ) - ... - COMPONENT det = Res_monitor(res_sample_comp = mysample, ...) - ... -\end{lstlisting} - -The output file is in ASCII format, one line per scattering event, with -the following columns: +\section{The \texttt{Res\_monitor} McStas Component} +Monitor for resolution calculations + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Kristian Nielsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} 1999 +\end{itemize} + +\subsection*{Description} +A single detector/monitor, used together with the Res\_sample component to compute instrument resolution functions. Outputs a list of neutron scattering events in the sample along with their intensities in the detector. The output file may be analyzed with the mcresplot front-end. + +Example: Res\_monitor(filename="Output.res", res\_sample\_comp="RSample", xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1) + +Setting the monitor geometry. The optional parameter 'options' may be set as a string with the following keywords. Default is rectangular ('square'): + +\begin{verbatim} +box Box of size xwidth, yheight, zdepth +cylinder To get a cylindrical monitor (diameter is xwidth, height is yheight). +banana Same as cylinder, without top/bottom, on restricted angular area +disk Disk flat xy monitor. diameter is xwidth. +sphrere To get a spherical monitor (e.g. a 4PI) (diameter is xwidth). +square Square flat xy monitor (xwidth, yheight) +\end{verbatim} + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{res\_sample\_comp} & WITH quotes & Name of Res\_sample component in the instrument definition & \\ +filename & string & Name of output file. If unset, use automatic name & 0 \\ +options & str & String that specifies the geometry of the monitor & 0 \\ +xwidth & m & Width/diameter of detector & .1 \\ +yheight & m & Height of detector & .1 \\ +zdepth & m & Thichness of detector & 0 \\ +radius & m & Radius of sphere/cylinder monitor & 0 \\ +xmin & m & Lower x bound of detector opening & 0 \\ +xmax & m & Upper x bound of detector opening & 0 \\ +ymin & m & Lower y bound of detector opening & 0 \\ +ymax & m & Upper y bound of detector opening & 0 \\ +zmin & m & Lower z bound of detector opening & 0 \\ +zmax & m & Upper z bound of detector opening & 0 \\ +bufsize & 1 & Number of events to store. Use 0 to store all & 0 \\ +restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ +live\_calc & 1 & If set, the monitor directly outputs the resolution matrix & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} \begin{itemize} -\item $\textbf{k}_\textrm{i}$, the three components of the initial wave vector. -\item $\textbf{k}_\textrm{f}$, the three components of the final wave vector. -\item $\textbf{r}$, the three components of the position of the scattering - event in the sample. -\item $p_\textrm{i}$, the neutron weight just after the scattering event. -\item $p_\textrm{f}$, the relative neutron weight adjustment from sample to - detector (so the total weight in the detector is $p_\textrm{i}p_\textrm{f}$). + \item Component source code found in file \texttt{Res\_monitor.comp}. \end{itemize} -From $\textbf{k}_\textrm{i}$ and $\textbf{k}_\textrm{f}$, we may compute -the scattering parameters -$\kappa = \textbf{k}_\textrm{i} - \textbf{k}_\textrm{f}$ and -$\hbar \omega = \hbar^2/(2 m_\textrm{n})(\textbf{k}_\textrm{i}^2 - \textbf{k}_\textrm{f}^2)$. -The vectors are given in the local coordinate system of the resolution -sample component. The wave vectors are in units of $\mbox{\AA}^{-1}$, the -energy transfer in meV. - -The output parameters from \textbf{Res\_monitor} -are the three count numbers, \textit{Nsum}, \textit{psum}, -and \textit{p2sum}, and the handle \textit{file} of the output file. +\IfFileExists{monitors/Res_monitor_static.tex}{\input{monitors/Res_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Sqq_w_monitor.tex b/docs/manuals/mcstas/monitors/Sqq_w_monitor.tex index a69a855313..294067ab2d 100644 --- a/docs/manuals/mcstas/monitors/Sqq_w_monitor.tex +++ b/docs/manuals/mcstas/monitors/Sqq_w_monitor.tex @@ -4,26 +4,19 @@ \section{The \texttt{Sqq\_w\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} DTU \item \textbf{Date:} June-July, 2018 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Cylindrical monitor on the x-z plane outputting a series of energy-planes in a subset of reciprocal -space, spanned by scattering vectors qa(x,z) and qb(x,z). +Cylindrical monitor on the x-z plane outputting a series of energy-planes in a subset of reciprocal space, spanned by scattering vectors qa(x,z) and qb(x,z). -The radius and yheight parameters are not used for propagation, but only to define the outgoing divergence -limit considered when estimating k_f +The radius and yheight parameters are not used for propagation, but only to define the outgoing divergence limit considered when estimating k\_f -The assumption is that the "current" neutron represents the final state, whereas the incoming state -is found by restoring the neutron state "index" components earlier. +The assumption is that the "current" neutron represents the final state, whereas the incoming state is found by restoring the neutron state "index" components earlier. -Example: Sqq_w_monitor(filename="output",radius=1, yheight=0.05, Emin=0,Emax=5,nE=11,nqa=100,nqb=100,qamin=1,qamax=10,qbmin=1qbmax=10, vix="vix", viy="viy", viz="viz") -AT (0,0,0) RELATIVE sample -\end{lstlisting} +Example: Sqq\_w\_monitor(filename="output",radius=1, yheight=0.05, Emin=0,Emax=5,nE=11,nqa=100,nqb=100,qamin=1,qamax=10,qbmin=1qbmax=10, vix="vix", viy="viy", viz="viz") AT (0,0,0) RELATIVE sample \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -39,10 +32,10 @@ \subsection*{Input parameters} qaz & 1 & z-component of 1st q-vector & 0 \\ qbx & 1 & x-component of 2nd q-vector & 0 \\ qbz & 1 & z-component of 2nd q-vector & 1 \\ -qamin & AA\textasciicircum{}-1 & Defines interval (qamin,qamax) where monitor measures in nqa bins & 0 \\ -qamax & AA\textasciicircum{}-1 & Defines interval (qamin,qamax) where monitor measures in nqa bins & 2 \\ -qbmin & AA\textasciicircum{}-1 & Defines interval (qbmin,qbmax) where monitor measures in nqb bins & 0 \\ -qbmax & AA\textasciicircum{}-1 & Defines interval (qbmin,qbmax) where monitor measures in nqb bins & 2 \\ +qamin & \AA{}$^{-1}$ & Defines interval (qamin,qamax) where monitor measures in nqa bins & 0 \\ +qamax & \AA{}$^{-1}$ & Defines interval (qamin,qamax) where monitor measures in nqa bins & 2 \\ +qbmin & \AA{}$^{-1}$ & Defines interval (qbmin,qbmax) where monitor measures in nqb bins & 0 \\ +qbmax & \AA{}$^{-1}$ & Defines interval (qbmin,qbmax) where monitor measures in nqb bins & 2 \\ Emin & meV & Defines the energy-transfer [Emin,Emax] window to monitor in nE bins & 0 \\ Emax & meV & Defines the energy-transfer [Emax,Emax] window to monitor in nE bins & 5 \\ nqa & int & Number of bins along qa direction & 90 \\ @@ -59,6 +52,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Sqq_w_monitor.comp}{Source code} for \texttt{Sqq\_w\_monitor.comp}. + \item Component source code found in file \texttt{Sqq\_w\_monitor.comp}. \end{itemize} -\IfFileExists{Sqq_w_monitor_static.tex}{\input{Sqq_w_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Sqq_w_monitor_static.tex}{\input{monitors/Sqq_w_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/Sqw_monitor.tex b/docs/manuals/mcstas/monitors/Sqw_monitor.tex index 7782a62519..a023163cb6 100644 --- a/docs/manuals/mcstas/monitors/Sqw_monitor.tex +++ b/docs/manuals/mcstas/monitors/Sqw_monitor.tex @@ -3,20 +3,15 @@ \section{The \texttt{Sqw\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} DTU \item \textbf{Date:} November, 2020 \end{itemize} \subsection*{Description} -\begin{lstlisting} -The assumption is that the "current" neutron represents the final state, whereas the incoming state -is found by restoring the neutron state "index" components earlier. +The assumption is that the "current" neutron represents the final state, whereas the incoming state is found by restoring the neutron state "index" components earlier. -Example: Sqw_monitor(filename="output", Emin=0,Emax=5,nE=11,nq=100,nqb=100,qmin=0,qmax=1,index=-2) -AT (0,0,0) RELATIVE sample -\end{lstlisting} +Example: Sqw\_monitor(filename="output", Emin=0,Emax=5,nE=11,nq=100,nqb=100,qmin=0,qmax=1,index=-2) AT (0,0,0) RELATIVE sample \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -26,8 +21,8 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -qmin & AA\textasciicircum{}-1 & Defines interval (qmin,qmax) where monitor measures in nq bins & 0 \\ -qmax & AA\textasciicircum{}-1 & Defines interval (qmin,qmax) where monitor measures in nq bins & 2 \\ +qmin & \AA{}$^{-1}$ & Defines interval (qmin,qmax) where monitor measures in nq bins & 0 \\ +qmax & \AA{}$^{-1}$ & Defines interval (qmin,qmax) where monitor measures in nq bins & 2 \\ Emin & meV & Defines the energy-transfer [Emin,Emax] window to monitor in nE bins & 0 \\ Emax & meV & Defines the energy-transfer [Emax,Emax] window to monitor in nE bins & 5 \\ nq & int & Number of bins in q & 90 \\ @@ -44,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/Sqw_monitor.comp}{Source code} for \texttt{Sqw\_monitor.comp}. + \item Component source code found in file \texttt{Sqw\_monitor.comp}. \end{itemize} -\IfFileExists{Sqw_monitor_static.tex}{\input{Sqw_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/Sqw_monitor_static.tex}{\input{monitors/Sqw_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/TOF2E_monitor.tex b/docs/manuals/mcstas/monitors/TOF2E_monitor.tex index bd38265353..24cca0ef7b 100644 --- a/docs/manuals/mcstas/monitors/TOF2E_monitor.tex +++ b/docs/manuals/mcstas/monitors/TOF2E_monitor.tex @@ -3,19 +3,15 @@ \section{The \texttt{TOF2E\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann and Helmuth Schoeber \item \textbf{Origin:} Risoe \item \textbf{Date:} Sept. 13, 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A square single monitor that measures the energy of the incoming neutrons -from their time-of-flight +A square single monitor that measures the energy of the incoming neutrons from their time-of-flight -Example: TOF2E_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, Emin=1, Emax=50, nE=20, filename="Output.nrj", L_flight=20, T_zero=0) -\end{lstlisting} +Example: TOF2E\_monitor(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, Emin=1, Emax=50, nE=20, filename="Output.nrj", L\_flight=20, T\_zero=0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -44,6 +40,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/TOF2E_monitor.comp}{Source code} for \texttt{TOF2E\_monitor.comp}. + \item Component source code found in file \texttt{TOF2E\_monitor.comp}. \end{itemize} -\IfFileExists{TOF2E_monitor_static.tex}{\input{TOF2E_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/TOF2E_monitor_static.tex}{\input{monitors/TOF2E_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/TOF2Q_cylPSD_monitor.tex b/docs/manuals/mcstas/monitors/TOF2Q_cylPSD_monitor.tex index 9f4a871718..405bf2e84a 100644 --- a/docs/manuals/mcstas/monitors/TOF2Q_cylPSD_monitor.tex +++ b/docs/manuals/mcstas/monitors/TOF2Q_cylPSD_monitor.tex @@ -6,16 +6,13 @@ \section{The \texttt{TOF2Q\_cylPSD\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Anette Vickery, derived from Lefmann TOF\_cylPSD \item \textbf{Origin:} Risoe \item \textbf{Date:} October 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -31,8 +28,8 @@ \subsection*{Input parameters} nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ \textbf{radius} & m & Cylinder radius & \\ \textbf{yheight} & m & Cylinder height & \\ -\textbf{Qmin} & AA\textasciicircum{}-1 & Beginning of Q-range & \\ -\textbf{Qmax} & AA\textasciicircum{}-1 & End of Q-range & \\ +\textbf{Qmin} & \AA{}$^{-1}$ & Beginning of Q-range & \\ +\textbf{Qmax} & \AA{}$^{-1}$ & End of Q-range & \\ ymin & m & Minimum value of y monitored & 0 \\ ymax & m & Maximum value of y monitored & 0 \\ \textbf{T\_zero} & s & Beginning of time window & \\ @@ -44,6 +41,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/TOF2Q_cylPSD_monitor.comp}{Source code} for \texttt{TOF2Q\_cylPSD\_monitor.comp}. + \item Component source code found in file \texttt{TOF2Q\_cylPSD\_monitor.comp}. \end{itemize} -\IfFileExists{TOF2Q_cylPSD_monitor_static.tex}{\input{TOF2Q_cylPSD_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/TOF2Q_cylPSD_monitor_static.tex}{\input{monitors/TOF2Q_cylPSD_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/TOFLambda_monitor.tex b/docs/manuals/mcstas/monitors/TOFLambda_monitor.tex index a961cb4f9d..e92a856635 100644 --- a/docs/manuals/mcstas/monitors/TOFLambda_monitor.tex +++ b/docs/manuals/mcstas/monitors/TOFLambda_monitor.tex @@ -3,17 +3,13 @@ \section{The \texttt{TOFLambda\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} KL \item \textbf{Origin:} Risoe \item \textbf{Date:} September 28, 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -2D detector for intensity as a function of both time-of-flight -and wavelength. -\end{lstlisting} +2D detector for intensity as a function of both time-of-flight and wavelength. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -35,14 +31,14 @@ \subsection*{Input parameters} ymax & m & Upper y bound of detector opening & 0.05 \\ xwidth & m & Width/diameter of detector (x). Overrides xmin, xmax & 0 \\ yheight & m & Height of detector (y). Overrides ymin, ymax & 0 \\ -\textbf{Lmin} & AA & Minimum wavelength detected & \\ -\textbf{Lmax} & AA & Maximum wavelength detected & \\ +\textbf{Lmin} & \AA{} & Minimum wavelength detected & \\ +\textbf{Lmax} & \AA{} & Maximum wavelength detected & \\ restore\_neutron & 1 & If set, the monitor does not influence the neutron state & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/TOFLambda_monitor.comp}{Source code} for \texttt{TOFLambda\_monitor.comp}. + \item Component source code found in file \texttt{TOFLambda\_monitor.comp}. \end{itemize} -\IfFileExists{TOFLambda_monitor_static.tex}{\input{TOFLambda_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/TOFLambda_monitor_static.tex}{\input{monitors/TOFLambda_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/TOFRes_monitor.tex b/docs/manuals/mcstas/monitors/TOFRes_monitor.tex index f00d04116e..a70a50cb7e 100644 --- a/docs/manuals/mcstas/monitors/TOFRes_monitor.tex +++ b/docs/manuals/mcstas/monitors/TOFRes_monitor.tex @@ -3,31 +3,26 @@ \section{The \texttt{TOFRes\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A single detector/monitor, used together with the TOFRes_sample component to -compute instrument resolution functions. Outputs a list of neutron -scattering events in the sample along with their intensities in the -detector. The output file may be analyzed with the mcresplot front-end. +A single detector/monitor, used together with the TOFRes\_sample component to compute instrument resolution functions. Outputs a list of neutron scattering events in the sample along with their intensities in the detector. The output file may be analyzed with the mcresplot front-end. -Example: TOFRes_monitor(filename="Output.res", res_sample_comp="RSample", xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1) +Example: TOFRes\_monitor(filename="Output.res", res\_sample\_comp="RSample", xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1) -Setting the monitor geometry. -The optional parameter 'options' may be set as a string with the -following keywords. Default is rectangular ('square'): +Setting the monitor geometry. The optional parameter 'options' may be set as a string with the following keywords. Default is rectangular ('square'): + +\begin{verbatim} box Box of size xwidth, yheight, zdepth cylinder To get a cylindrical monitor (diameter is xwidth, height is yheight). banana Same as cylinder, without top/bottom, on restricted angular area disk Disk flat xy monitor. diameter is xwidth. sphrere To get a spherical monitor (e.g. a 4PI) (diameter is xwidth). square Square flat xy monitor (xwidth, yheight) -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -58,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/TOFRes_monitor.comp}{Source code} for \texttt{TOFRes\_monitor.comp}. + \item Component source code found in file \texttt{TOFRes\_monitor.comp}. \end{itemize} -\IfFileExists{TOFRes_monitor_static.tex}{\input{TOFRes_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/TOFRes_monitor_static.tex}{\input{monitors/TOFRes_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/TOF_PSD_monitor_rad.tex b/docs/manuals/mcstas/monitors/TOF_PSD_monitor_rad.tex index afc4360110..cb73176b98 100644 --- a/docs/manuals/mcstas/monitors/TOF_PSD_monitor_rad.tex +++ b/docs/manuals/mcstas/monitors/TOF_PSD_monitor_rad.tex @@ -3,21 +3,15 @@ \section{The \texttt{TOF\_PSD\_monitor\_rad} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} UCPH \item \textbf{Date:} March 2012 \end{itemize} \subsection*{Description} -\begin{lstlisting} -TOF monitor that performs radial averaging. -Comment: The intensity is given as two 2D files: -1) a radial sum vs. TOF -2) a radial average (i.e. intensity per area) vs. TOF +TOF monitor that performs radial averaging. Comment: The intensity is given as two 2D files: 1) a radial sum vs. TOF 2) a radial average (i.e. intensity per area) vs. TOF -Example: TOF_PSD_monitor_rad(rmax=0.2, nr=100, filename="Output.psd", filename_av="Output_av.psd") -\end{lstlisting} +Example: TOF\_PSD\_monitor\_rad(rmax=0.2, nr=100, filename="Output.psd", filename\_av="Output\_av.psd") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -41,6 +35,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/TOF_PSD_monitor_rad.comp}{Source code} for \texttt{TOF\_PSD\_monitor\_rad.comp}. + \item Component source code found in file \texttt{TOF\_PSD\_monitor\_rad.comp}. \end{itemize} -\IfFileExists{TOF_PSD_monitor_rad_static.tex}{\input{TOF_PSD_monitor_rad_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/TOF_PSD_monitor_rad_static.tex}{\input{monitors/TOF_PSD_monitor_rad_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/TOF_cylPSD_monitor.tex b/docs/manuals/mcstas/monitors/TOF_cylPSD_monitor.tex index 0d3ea0efa4..e6bb986ce8 100644 --- a/docs/manuals/mcstas/monitors/TOF_cylPSD_monitor.tex +++ b/docs/manuals/mcstas/monitors/TOF_cylPSD_monitor.tex @@ -3,16 +3,13 @@ \section{The \texttt{TOF\_cylPSD\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} October 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,6 +33,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/TOF_cylPSD_monitor.comp}{Source code} for \texttt{TOF\_cylPSD\_monitor.comp}. + \item Component source code found in file \texttt{TOF\_cylPSD\_monitor.comp}. \end{itemize} -\IfFileExists{TOF_cylPSD_monitor_static.tex}{\input{TOF_cylPSD_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/TOF_cylPSD_monitor_static.tex}{\input{monitors/TOF_cylPSD_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/TOF_monitor.tex b/docs/manuals/mcstas/monitors/TOF_monitor.tex index f927b2dc4d..a8a4c9a801 100644 --- a/docs/manuals/mcstas/monitors/TOF_monitor.tex +++ b/docs/manuals/mcstas/monitors/TOF_monitor.tex @@ -3,16 +3,13 @@ \section{The \texttt{TOF\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} KN, M. Hagen \item \textbf{Origin:} Risoe \item \textbf{Date:} August 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,6 +37,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/TOF_monitor.comp}{Source code} for \texttt{TOF\_monitor.comp}. + \item Component source code found in file \texttt{TOF\_monitor.comp}. \end{itemize} -\IfFileExists{TOF_monitor_static.tex}{\input{TOF_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/TOF_monitor_static.tex}{\input{monitors/TOF_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/monitors/TOFlog_monitor.tex b/docs/manuals/mcstas/monitors/TOFlog_monitor.tex index 1a3d792090..4080ad1470 100644 --- a/docs/manuals/mcstas/monitors/TOFlog_monitor.tex +++ b/docs/manuals/mcstas/monitors/TOFlog_monitor.tex @@ -3,17 +3,13 @@ \section{The \texttt{TOFlog\_monitor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} October 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A rectangular time-of-flight monitor with logarithmic time binning. -(The neutron intensity is NOT given logarithmically) -\end{lstlisting} +A rectangular time-of-flight monitor with logarithmic time binning. (The neutron intensity is NOT given logarithmically) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,6 +36,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/monitors/TOFlog_monitor.comp}{Source code} for \texttt{TOFlog\_monitor.comp}. + \item Component source code found in file \texttt{TOFlog\_monitor.comp}. \end{itemize} -\IfFileExists{TOFlog_monitor_static.tex}{\input{TOFlog_monitor_static.tex}}{} \ No newline at end of file +\IfFileExists{monitors/TOFlog_monitor_static.tex}{\input{monitors/TOFlog_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Beam_spy.tex b/docs/manuals/mcstas/obsolete/Beam_spy.tex index 384a085e8b..7c112e7418 100644 --- a/docs/manuals/mcstas/obsolete/Beam_spy.tex +++ b/docs/manuals/mcstas/obsolete/Beam_spy.tex @@ -3,20 +3,13 @@ \section{The \texttt{Beam\_spy} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} Risoe \item \textbf{Date:} Nov 2005 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component displays informations about the beam at the previous component -position. No data file is produced. -It behaves as the Monitor component, but No propagation to the Beam_spy is -performed, and all events are analyzed. -The component should be located at the same position as the previous one. -\end{lstlisting} +This component displays informations about the beam at the previous component position. No data file is produced. It behaves as the Monitor component, but No propagation to the Beam\_spy is performed, and all events are analyzed. The component should be located at the same position as the previous one. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -31,7 +24,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Beam_spy.comp}{Source code} for \texttt{Beam\_spy.comp}. + \item Component source code found in file \texttt{Beam\_spy.comp}. \item Monitor component \end{itemize} -\IfFileExists{Beam_spy_static.tex}{\input{Beam_spy_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Beam_spy_static.tex}{\input{obsolete/Beam_spy_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/ESS_moderator_short.tex b/docs/manuals/mcstas/obsolete/ESS_moderator_short.tex index 71271a5f88..c132003742 100644 --- a/docs/manuals/mcstas/obsolete/ESS_moderator_short.tex +++ b/docs/manuals/mcstas/obsolete/ESS_moderator_short.tex @@ -3,59 +3,61 @@ \section{The \texttt{ESS\_moderator\_short} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} KL, February 2001 \item \textbf{Origin:} Risoe \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -Produces a time-of-flight spectrum, from the ESS parameters -Chooses evenly in lambda, exponentially decaying in time . -Adapted from Moderator by: KN, M.Hagen, August 1998 - -Units of flux: n/cm^2/s/AA/ster -(McStas units are in general neutrons/second) - -Example general parameters (general): -size=0.12 Lmin=0.1 Lmax=10 dist=2 focus_xw=0.06 yh=0.12 nu=50 -branchframe=0.5 - -Example moderator specific parameters -(From F. Mezei, "ESS reference moderator characteristics for ...", 4/12/00: -Defining the normalised Maxwelian -M(lam,T) = 2 a^2 lam^-5 exp(-a/lam^2); a=949/T; lam in AA; T in K, -and the normalised pulse shape function -F(t,tau,n) = ( exp(-t/tau) - exp(-nt/tau) ) n/(n-1)/tau, -the flux distribution is given as -Phi(t,lam) = I0 M(lam,T) F(t,tau,n) -+ I2/(1+exp(chi2 lam-2.2))/lam*F(t,tau2*lam,n2) ) +Produces a time-of-flight spectrum, from the ESS parameters Chooses evenly in lambda, exponentially decaying in time . Adapted from Moderator by: KN, M.Hagen, August 1998 + +Units of flux: n/cm\textasciicircum{}2/s/\AA{}/ster (McStas units are in general neutrons/second) + +Example general parameters (general): size=0.12 Lmin=0.1 Lmax=10 dist=2 focus\_xw=0.06 yh=0.12 nu=50 branchframe=0.5 + +Example moderator specific parameters (From F. Mezei, "ESS reference moderator characteristics for ...", 4/12/00: Defining the normalised Maxwelian M(lam,T) = 2 a\textasciicircum{}2 lam\textasciicircum{}-5 exp(-a/lam\textasciicircum{}2); a=949/T; lam in \AA{}; T in K, and the normalised pulse shape function F(t,tau,n) = ( exp(-t/tau) - exp(-nt/tau) ) n/(n-1)/tau, the flux distribution is given as Phi(t,lam) = I0 M(lam,T) F(t,tau,n) + I2/(1+exp(chi2 lam-2.2))/lam*F(t,tau2*lam,n2) ) a1: Ambient H20, short pulse, decoupled poisoned + +\begin{verbatim} T=325 tau=22e-6 tau1=0 tau2=7e-6 n=5 n2=5 chi2=2.5 I0=9e10 I2=4.6e10 branch1=0 branch2=0.5 +\end{verbatim} a2: Ambient H20, short pulse, decoupled un-poisoned + +\begin{verbatim} T=325 tau=35e-6 tau1=0 tau2=12e-6 n=5 n2=5 chi2=2.5 I0=1.8e11 I2=9.2e10 branch1=0 branch2=0.5 +\end{verbatim} a3: Ambient H20, short pulse, coupled + +\begin{verbatim} T=325 tau=80e-6 tau1=400e-6 tau2=12e-6 n=20 n2=5 chi2=2.5 I0=4.5e11 I2=9.2e10 branch1=0.5 branch2=0.5 +\end{verbatim} b1: Liquid H2, short pulse, decoupled poisoned + +\begin{verbatim} T=50 tau=49e-6 tau1=0 tau2=7e-6 n=5 n2=5 chi2=0.9 I0=2.7e10 I2=4.6e10 branch1=0 branch2=0.5 +\end{verbatim} b2: Liquid H2, short pulse, decoupled un-poisoned + +\begin{verbatim} T=50 tau=78e-6 tau1=0 tau2=12e-6 n=5 n2=5 chi2=0.9 I0=5.4e10 I2=9.2e10 branch1=0 branch2=0.5 +\end{verbatim} b3: Liquid H2, short pulse, coupled + +\begin{verbatim} T=50 tau=287e-6 tau1=0 tau2=12e-6 n=20 n2=5 chi2=0.9 I0=2.3e11 I2=9.2e10 branch1=0 branch2=0.5 -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -66,8 +68,8 @@ \subsection*{Input parameters} \midrule \endhead \textbf{size} & m & Edge of cube shaped source & \\ -\textbf{Lmin} & AA & Lower edge of wavelength distribution & \\ -\textbf{Lmax} & AA & Upper edge of wavelength distribution & \\ +\textbf{Lmin} & \AA{} & Lower edge of wavelength distribution & \\ +\textbf{Lmax} & \AA{} & Upper edge of wavelength distribution & \\ \textbf{dist} & m & Distance from source to focusing rectangle; at (0,0,dist) & \\ \textbf{focus\_xw} & m & Width of focusing rectangle & \\ \textbf{focus\_yh} & m & Height of focusing rectangle & \\ @@ -75,12 +77,12 @@ \subsection*{Input parameters} T & K & Temperature of source & 325 \\ tau & s & long time decay constant for pulse, 1a & 22e-6 \\ tau1 & s & long time decay constant for pulse, 1b (only for coupled water, else 0) & 0 \\ -tau2 & s/AA & long time decay constant for pulse, 2 & 7e-6 \\ +tau2 & s/\AA{} & long time decay constant for pulse, 2 & 7e-6 \\ n & 1 & pulse shape parameter 1 & 5 \\ n2 & 1 & pulse shape parameter 2 & 5 \\ -chi2 & 1/AA & lambda-distribution parameter in pulse 2 & 2.5 \\ +chi2 & 1/\AA{} & lambda-distribution parameter in pulse 2 & 2.5 \\ I0 & flux & integrated flux 1 (in flux units, see above) (default 9e10) & 9e10 \\ -I2 & flux*AA & integrated flux 2 (default 4.6e10) & 4.6e10 \\ +I2 & flux*\AA{} & integrated flux 2 (default 4.6e10) & 4.6e10 \\ branch1 & 1 & limit for switching between distribution 1 and 2. (has effect only for coupled water, tau1\textgreater{}0) & 0 \\ branch2 & 1 & limit for switching between distribution 1 and 2. (default value 0.5) & 0.5 \\ branchframe & 1 & limit for switching between 1st and 2nd pulse (if only one pulse wanted: 1) & 0 \\ @@ -90,6 +92,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/ESS_moderator_short.comp}{Source code} for \texttt{ESS\_moderator\_short.comp}. + \item Component source code found in file \texttt{ESS\_moderator\_short.comp}. \end{itemize} -\IfFileExists{ESS_moderator_short_static.tex}{\input{ESS_moderator_short_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/ESS_moderator_short_static.tex}{\input{obsolete/ESS_moderator_short_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/SasView_model.tex b/docs/manuals/mcstas/obsolete/SasView_model.tex new file mode 100644 index 0000000000..5fb89d6b5c --- /dev/null +++ b/docs/manuals/mcstas/obsolete/SasView_model.tex @@ -0,0 +1,753 @@ +\section{The \texttt{SasView\_model} McStas Component} +This SANS sample exposes \textless{}a href="http://www.sasview.org"\textgreater{}SasView's\textless{}/a\textgreater{} scattering kernels to McStas. In this way SasView's monodisperse scattering kernels can be call from McStas. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jakob Garde, Torben Nielsen, Peter Willendrup + \item \textbf{Origin:} SasView, DTU, European Spallation Source ERIC + \item \textbf{Date:} 03.02.2016 +\end{itemize} + +\subsection*{Description} +\textbf{OBSOLETE} - we recommend using individual component models form the \textless{}pre\textgreater{}sasmodels\textless{}/pre\textgreater{} selection. If you keep using this component, be aware that the URLs listed in the table below are broken, please refer to the new revamped \htmladdnormallink{SasView model page}{https://www.sasview.org/docs/user/models/capped\_cylinder.html}. + +Sample for use in SANS instruments. The models describe mono disperse particles in thin solution. The sample geometry may have the shape: + +\begin{verbatim} +Shape: - A filled box with dimensions xwidth, yheight and zdepth. +\end{verbatim} + +- A cylinder with dimensions radius and yheight. - A filled sphere given by radius. + +These parameters are mutually exclusive. + +Example using spheres in thin solution, with radius=200 \AA{} and a delta\_sld=0.6 fm/\AA{}\textasciicircum{}3: SasView\_model(model\_index=47, model\_scale=1.0, model\_pars=\{1, 7, 200\}, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005,) + +The algorithm of this component requires use of the ISO C standard c99, standard from McStas 2.7 and 3.0. + +The list of scattering models in SasView is called sasmodels. The list of McStas available \htmladdnormallink{SasView sasmodels}{http://www.sasview.org/sasview/user/models/model\_functions.html\#model} are found in the table below. + +A few models may require manual documentation lookup using the above link to the SasView site. + +McStas does currently not support multiplication of formfactor models with structure factor models. + +The 2D scattering scattering kernels are denoted by modelname\_xy. I.e. to evalulate scattering from aligned cylinders use model\_index=10 to use cylinder\_xy. + +MDOC + +\textless{}table border=1\textgreater{}\textless{}tr\textgreater{}\textless{}td\textgreater{}\textbf{Model no.}\textless{}/td\textgreater{}\textless{}td\textgreater{}\textbf{SasView name}\textless{}/td\textgreater{}\textless{}td\textgreater{}\textbf{Parameters}\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 0\textless{}/td\textgreater{}\textless{}td\textgreater{}None\textless{}/td\textgreater{}\textless{}td\textgreater{}None\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 1\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{barbell}{http://www.sasview.org/sasview/user/models/model\_functions.html\#barbellmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, bell\_radius, radius, length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 2\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{barbell\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#barbellmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, bell\_radius, radius, length, theta, phi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 3\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{bcc\_paracrystal}{http://www.sasview.org/sasview/user/models/model\_functions.html\#bccparacrystalmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(dnn, d\_factor, radius, sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 4\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{bcc\_paracrystal\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#bcc\_paracrystalmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(dnn, d\_factor, radius, sld, solvent\_sld, theta, phi, psi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 5\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{capped\_cylinder}{http://www.sasview.org/sasview/user/models/model\_functions.html\#cappedcylindermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, radius, cap\_radius, length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 6\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{capped\_cylinder\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#capped\_cylindermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, radius, cap\_radius, length, theta, phi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 7\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{core\_shell\_cylinder}{http://www.sasview.org/sasview/user/models/model\_functions.html\#coreshellcylindermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(core\_sld, shell\_sld, solvent\_sld, radius, thickness, length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 8\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{core\_shell\_cylinder\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#core\_shell\_cylindermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(core\_sld, shell\_sld, solvent\_sld, radius, thickness, length, theta, phi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{} 9\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{cylinder}{http://www.sasview.org/sasview/user/models/model\_functions.html\#cylindermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, radius, length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}10\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{cylinder\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#cylindermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, radius, length, theta, phi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}11\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{dab}{http://www.sasview.org/sasview/user/models/model\_functions.html\#dabmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}12\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{dab\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#dabmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}13\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{ellipsoid}{http://www.sasview.org/sasview/user/models/model\_functions.html\#ellipsoidmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, rpolar, requatorial)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}14\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{ellipsoid\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#ellipsoidmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, rpolar, requatorial, theta, phi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}15\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{fcc\_paracrystal}{http://www.sasview.org/sasview/user/models/model\_functions.html\#fccparacrystalmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(dnn, d\_factor, radius, sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}16\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{fcc\_paracrystal\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#fcc\_paracrystalmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(dnn, d\_factor, radius, sld, solvent\_sld, theta, phi, psi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}17\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{flexible\_cylinder\_ex}{http://www.sasview.org/sasview/user/models/model\_functions.html\#flexiblecylinderexmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(length, kuhn\_length, radius, axis\_ratio, sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}18\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{flexible\_cylinder\_ex\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#flexible\_cylinder\_exmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(length, kuhn\_length, radius, axis\_ratio, sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}19\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{gaussian\_peak}{http://www.sasview.org/sasview/user/models/model\_functions.html\#gaussianpeakmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(q0, sigma)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}20\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{gaussian\_peak\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#gaussian\_peakmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(q0, sigma)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}21\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{guinier}{http://www.sasview.org/sasview/user/models/model\_functions.html\#guiniermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(rg)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}22\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{guinier\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#guiniermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(rg)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}23\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{hardsphere}{http://www.sasview.org/sasview/user/models/model\_functions.html\#hardspheremodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(effect\_radius, volfraction)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}24\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{hardsphere\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#hardspheremodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(effect\_radius, volfraction)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}25\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{HayterMSAsq}{http://www.sasview.org/sasview/user/models/model\_functions.html\#HayterMSAsqmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(effect\_radius, zz, VolFrac, Temp, csalt, dialec)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}26\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{HayterMSAsq\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#HayterMSAsqmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(effect\_radius, charge, volfraction, temperature, saltconc, dielectconst)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}27\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{hollow\_cylinder}{http://www.sasview.org/sasview/user/models/model\_functions.html\#hollowcylindermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(radius, core\_radius, length, sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}28\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{hollow\_cylinder\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#hollow\_cylindermodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(radius, core\_radius, length, sld, solvent\_sld, theta, phi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}29\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lamellar}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lamellarmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, thickness)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}30\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lamellar\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lamellarmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, thickness)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}31\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lamellar\_FFHG}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lamellarFFHGmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(tail\_length, head\_length, sld, head\_sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}32\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lamellar\_FFHG\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lamellar\_FFHGmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(tail\_length, head\_length, sld, head\_sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}33\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lamellarCailleHG}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lamellarCailleHGmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(tail\_length, head\_length, Nlayers, dd, Cp, tail\_sld, head\_sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}34\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lamellarCailleHG\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lamellarCailleHGmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(tail\_length, head\_length, Nlayers, spacing, Caille\_parameter, sld, head\_sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}35\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lamellarPC}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lamellarPCmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(th, Nlayers, davg, pd, sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} 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\textless{}tr\textgreater{}\textless{}td\textgreater{}38\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lamellarPS\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lamellarPSmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(thickness, Nlayers, spacing, Caille\_parameter, sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}39\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{linear\_pearls}{http://www.sasview.org/sasview/user/models/model\_functions.html\#linearpearlsmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(radius, edge\_sep, num\_pearls, pearl\_sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}40\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{linear\_pearls\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#linear\_pearlsmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(radius, edge\_sep, num\_pearls, pearl\_sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}41\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lorentz}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lorentzmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(cor\_length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}42\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{lorentz\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#lorentzmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(cor\_length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}43\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{mass\_fractal}{http://www.sasview.org/sasview/user/models/model\_functions.html\#massfractalmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(radius, mass\_dim, cutoff\_length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}44\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{mass\_fractal\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#mass\_fractalmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(radius, mass\_dim, cutoff\_length)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}45\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{mass\_surface\_fractal}{http://www.sasview.org/sasview/user/models/model\_functions.html\#masssurfacefractalmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(mass\_dim, surface\_dim, cluster\_rg, primary\_rg)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}46\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{mass\_surface\_fractal\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#mass\_surface\_fractalmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(mass\_dim, surface\_dim, cluster\_rg, primary\_rg)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}47\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{parallelepiped}{http://www.sasview.org/sasview/user/models/model\_functions.html\#parallelepipedmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, a\_side, b\_side, c\_side)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}48\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{parallelepiped\_xy}{http://www.sasview.org/sasview/user/models/model\_functions.html\#parallelepipedmodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(sld, solvent\_sld, a\_side, b\_side, c\_side, theta, phi, psi)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} \textless{}tr\textgreater{}\textless{}td\textgreater{}49\textless{}/td\textgreater{}\textless{}td\textgreater{}\htmladdnormallink{pearl\_necklace}{http://www.sasview.org/sasview/user/models/model\_functions.html\#pearlnecklacemodel}\textless{}/td\textgreater{}\textless{}td\textgreater{}(radius, edge\_separation, string\_thickness, number\_of\_pearls, sld, string\_sld, solvent\_sld)\textless{}/td\textgreater{}\textless{}/tr\textgreater{} 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\textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}Parameters:\textless{}/td\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}effective radius of hard sphere\textless{}/td\textgreater{} \textless{}td\textgreater{}\AA{}\textless{}/td\textgreater{} \textless{}td\textgreater{}[0, inf]\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}volume fraction of hard spheres\textless{}/td\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} 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\textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}Parameters:\textless{}/td\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}Ellipsoid scattering length density\textless{}/td\textgreater{} \textless{}td\textgreater{}1e-6/\AA{}\textasciicircum{}2\textless{}/td\textgreater{} \textless{}td\textgreater{}[-inf, inf]\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}\ \textless{}/td\textgreater{} \textless{}td\textgreater{}Solvent scattering length 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\textless{}td\textgreater{}CappedCylinder\textless{}/td\textgreater{} \textless{}td\textgreater{}capped\_cylinder \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}CoreShellCylinder\textless{}/td\textgreater{} \textless{}td\textgreater{}core\_shell\_cylinder \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}Cylinder\textless{}/td\textgreater{} \textless{}td\textgreater{}cylinder \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + 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\textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}FlexCylEllipX\textless{}/td\textgreater{} \textless{}td\textgreater{}flexible\_cylinder\_ex \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}PeakGauss\textless{}/td\textgreater{} \textless{}td\textgreater{}gaussian\_peak \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}Guinier\textless{}/td\textgreater{} \textless{}td\textgreater{}guinier \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}HardsphereStructure\textless{}/td\textgreater{} \textless{}td\textgreater{}hardsphere \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +\end{verbatim} + +\textless{}td\textgreater{} Y \textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}HayterMSAStructure\textless{}/td\textgreater{} \textless{}td\textgreater{}HayterMSAsq \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +\end{verbatim} + +\textless{}td\textgreater{} Y \textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}HollowCylinder\textless{}/td\textgreater{} \textless{}td\textgreater{}hollow\_cylinder \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}Lamellar\textless{}/td\textgreater{} \textless{}td\textgreater{}lamellar \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}LamellarPS\textless{}/td\textgreater{} \textless{}td\textgreater{}lamellarCaille \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}LamellarPSHG\textless{}/td\textgreater{} \textless{}td\textgreater{}lamellarCailleHG \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}LamellarFFHG\textless{}/td\textgreater{} \textless{}td\textgreater{}lamellarFFHG \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}LamellarPCrystal\textless{}/td\textgreater{} \textless{}td\textgreater{}lamellarPC \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}LinearPearls\textless{}/td\textgreater{} \textless{}td\textgreater{}linear\_pearls \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}Lorentz\textless{}/td\textgreater{} \textless{}td\textgreater{}lorentz \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}MassFractal\textless{}/td\textgreater{} \textless{}td\textgreater{}mass\_fractal \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}MassSurfaceFractal\textless{}/td\textgreater{} \textless{}td\textgreater{}mass\_surface\_fractal \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}Parallelepiped\textless{}/td\textgreater{} \textless{}td\textgreater{}parallelepiped \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}PearlNecklace\textless{}/td\textgreater{} \textless{}td\textgreater{}pearl\_necklace \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}Sphere\textless{}/td\textgreater{} \textless{}td\textgreater{}sphere \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}StarPolymer\textless{}/td\textgreater{} \textless{}td\textgreater{}star\_polymer \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}StickyHSStructure\textless{}/td\textgreater{} \textless{}td\textgreater{}stickyhardsphere \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +\end{verbatim} + +\textless{}td\textgreater{} Y \textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}tr\textgreater{} \textless{}td\textgreater{}TriaxialEllipsoid\textless{}/td\textgreater{} \textless{}td\textgreater{}triaxial\_ellipsoid \textless{}/td\textgreater{} + +\begin{verbatim} +<td>- </td> +<td> - </td> +\end{verbatim} + +\textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}td\textgreater{}-\textless{}/td\textgreater{} \textless{}/tr\textgreater{} \textless{}/table\textgreater{} \textless{}/body\textgreater{} \textless{}/html\textgreater{} MDOC\_END + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +model\_index & & Index of the applied sasview model. Recompile instrument for changes to take effect. & 21 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_pars & & Model parameters are given as a set of comma-separated values enclosed by \{\}, e.g. \{60\} for the model index 21 (the guinier model). Consult the sasview docs for further info. & \{60,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\} \\ +model\_abs & 1/m & Absorption cross section density at 2200 m/s & 0.5 \\ +xwidth & m & horiz. dimension of sample, as a width & 0 \\ +yheight & m & vert . dimension of sample, as a height for cylinder/box & 0 \\ +zdepth & m & depth of sample & 0 \\ +radius & m & Outer radius of sample in (x,z) plane for cylinder/sphere & 0 \\ +target\_x & m & relative focus target position & 0 \\ +target\_y & m & relative focus target position & 0 \\ +target\_z & m & relative focus target position & 6 \\ +target\_index & 1 & Relative index of component to focus at, e.g. next is +1 & 0 \\ +focus\_xw & m & horiz. dimension of a rectangular area & 0 \\ +focus\_yh & m & vert. dimension of a rectangular area & 0 \\ +focus\_aw & deg & horiz. angular dimension of a rectangular area & 0 \\ +focus\_ah & deg & vert. angular dimension of a rectangular area & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_model.comp}. + \item http://www.sasview.org/sasview/user/models/model\_functions.html +\end{itemize} +\IfFileExists{obsolete/SasView_model_static.tex}{\input{obsolete/SasView_model_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/V_sample.tex b/docs/manuals/mcstas/obsolete/V_sample.tex index c89255ef25..0125269eb0 100644 --- a/docs/manuals/mcstas/obsolete/V_sample.tex +++ b/docs/manuals/mcstas/obsolete/V_sample.tex @@ -3,31 +3,15 @@ \section{The \texttt{V\_sample} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann and Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 15.4.98 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A Double-cylinder shaped incoherent scatterer (a V-sample) -with both elastic and quasielastic (Lorentzian) components. -No multiple scattering. Absorbtion included. -The shape of the sample may be a box with dimensions xwidth, yheight, zthick. -The area to scatter to is a disk of radius 'focus_r' situated at the target. -This target area may also be rectangular if specified focus_xw and focus_yh -or focus_aw and focus_ah, respectively in meters and degrees. -The target itself is either situated according to given coordinates (x,y,z), -or defined with the relative target_index of the component to focus -to (next is +1). -This target position will be set to its AT position. When targeting to -centered components, such as spheres or cylinders, define an Arm component -where to focus to. +A Double-cylinder shaped incoherent scatterer (a V-sample) with both elastic and quasielastic (Lorentzian) components. No multiple scattering. Absorbtion included. The shape of the sample may be a box with dimensions xwidth, yheight, zthick. The area to scatter to is a disk of radius 'focus\_r' situated at the target. This target area may also be rectangular if specified focus\_xw and focus\_yh or focus\_aw and focus\_ah, respectively in meters and degrees. The target itself is either situated according to given coordinates (x,y,z), or defined with the relative target\_index of the component to focus to (next is +1). This target position will be set to its AT position. When targeting to centered components, such as spheres or cylinders, define an Arm component where to focus to. -Example: V_sample(radius_i=0.001,radius_o=0.01,h=0.02,focus_r=0.035,pack=1, -target_index=1) -\end{lstlisting} +Example: V\_sample(radius\_i=0.001,radius\_o=0.01,h=0.02,focus\_r=0.035,pack=1, target\_index=1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,7 +24,7 @@ \subsection*{Input parameters} radius & m & Outer radius of sample in (x,z) plane & 0 \\ thickness & m & Thickness of outer wall & 0 \\ zdepth & m & depth of box sample & 0 \\ -Vc & & Unit cell volume [AA\textasciicircum{}3] & 13.827 \\ +Vc & & Unit cell volume [\AA{}\textasciicircum{}3] & 13.827 \\ sigma\_abs & barns & Absorbtion cross section pr. unit cell & 5.08 \\ sigma\_inc & barns & Incoherent scattering cross section pr. unit cell & 5.08 \\ radius\_i & m & radius-thickness & 0 \\ @@ -64,7 +48,7 @@ \subsection*{Input parameters} rad\_sphere & m & Radius for a spherical sample & 0 \\ sig\_a & barns & Same as sigma\_abs & 0 \\ sig\_i & barns & Same as sigma\_inc & 0 \\ -V0 & & Same as Vc [AA\textasciicircum{}3] & 0 \\ +V0 & & Same as Vc [\AA{}\textasciicircum{}3] & 0 \\ target\_index & 1 & relative index of component to focus at, e.g. next is +1 & 0 \\ multiples & 1 & Apply crude estimate for multiple scattering & 1 \\ \bottomrule @@ -72,10 +56,10 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/V_sample.comp}{Source code} for \texttt{V\_sample.comp}. + \item Component source code found in file \texttt{V\_sample.comp}. \item \textless{}A HREF="http://neutron.risoe.dk/mcstas/components/tests/v\_sample/"\textgreater{}Test \item results\textless{}/A\textgreater{} (not up-to-date). - \item The test/example instrument \textless{}a href="../examples/vanadium\_example.instr"\textgreater{}vanadium\_example.instr\textless{}/a\textgreater{}. - \item The test/example instrument \textless{}a href="../examples/QENS\_test.instr"\textgreater{}QENS\_test.instr\textless{}/a\textgreater{}. + \item The test/example instrument \htmladdnormallink{vanadium\_example.instr}{../examples/vanadium\_example.instr}. + \item The test/example instrument \htmladdnormallink{QENS\_test.instr}{../examples/QENS\_test.instr}. \end{itemize} -\IfFileExists{V_sample_static.tex}{\input{V_sample_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/V_sample_static.tex}{\input{obsolete/V_sample_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_input.tex b/docs/manuals/mcstas/obsolete/Virtual_input.tex index da1efc084f..a202ffa8ba 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_input.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_input.tex @@ -4,44 +4,19 @@ \section{The \texttt{Virtual\_input} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:farhi@ill.fr"\textgreater{}E. Farhi\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} Sep 28th, 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component reads neutron events stored from a file, and sends them into -the instrument. It thus replaces a Source component, using a previously -computed neutron set. The 'source' file type is an ascii text file with the -format listed below. The number of neutron events for the -simulation is set to the length of the 'source' file times the -repetition parameter 'repeat_count' (1 by default). -It is particularly useful to generate a virtual source at a point that few -neutron reach. A long simulation will then only be performed once, to create -the 'source' filename. Further simulations are much faster if they start from -this low flux position with the 'source' filename. +This component reads neutron events stored from a file, and sends them into the instrument. It thus replaces a Source component, using a previously computed neutron set. The 'source' file type is an ascii text file with the format listed below. The number of neutron events for the simulation is set to the length of the 'source' file times the repetition parameter 'repeat\_count' (1 by default). It is particularly useful to generate a virtual source at a point that few neutron reach. A long simulation will then only be performed once, to create the 'source' filename. Further simulations are much faster if they start from this low flux position with the 'source' filename. -The input file format is: -text column formatted with lines containing 11 values in the order: -p x y z vx vy vz t sx sy sz stored into about 83 bytes/n. +The input file format is: text column formatted with lines containing 11 values in the order: p x y z vx vy vz t sx sy sz stored into about 83 bytes/n. -%BUGS -We recommend NOT to use parallel execution (MPI) with this component. If you -need to, set parameter 'smooth=1'. +\%BUGS We recommend NOT to use parallel execution (MPI) with this component. If you need to, set parameter 'smooth=1'. -EXAMPLE: -To create a 'source' file collecting all neutron states, use: -COMPONENT MySourceCreator = Virtual_output(filename = "MySource.list") -at the position where will be the Virtual_input. -Then inactivate the part of the simulation description before (and including) -the component MySourceCreator. Put the new instrument source: -COMPONENT Source = Virtual_input(filename="MySource.list") -at the same position as 'MySourceCreator'. -A Vitess filename may be obtained from the 'Vitess_output' component or from a -Vitess simulation (104 bytes per neutron) and read with Vitess_input. -\end{lstlisting} +EXAMPLE: To create a 'source' file collecting all neutron states, use: COMPONENT MySourceCreator = Virtual\_output(filename = "MySource.list") at the position where will be the Virtual\_input. Then inactivate the part of the simulation description before (and including) the component MySourceCreator. Put the new instrument source: COMPONENT Source = Virtual\_input(filename="MySource.list") at the same position as 'MySourceCreator'. A Vitess filename may be obtained from the 'Vitess\_output' component or from a Vitess simulation (104 bytes per neutron) and read with Vitess\_input. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -60,6 +35,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_input.comp}{Source code} for \texttt{Virtual\_input.comp}. + \item Component source code found in file \texttt{Virtual\_input.comp}. \end{itemize} -\IfFileExists{Virtual_input_static.tex}{\input{Virtual_input_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_input_static.tex}{\input{obsolete/Virtual_input_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_mcnp_input.tex b/docs/manuals/mcstas/obsolete/Virtual_mcnp_input.tex index 504bec53a7..d4e8794994 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_mcnp_input.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_mcnp_input.tex @@ -4,53 +4,38 @@ \section{The \texttt{Virtual\_mcnp\_input} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:hennanec@ensimag.fr"\textgreater{}Chama Hennane\textless{}/a\textgreater{} and E. Farhi \item \textbf{Origin:} \textless{}a href="http://www.ill.fr/"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} June 28th, 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component generates neutron events from a filename created using the -MCNP Monte Carlo code for nuclear reactors. It is used to -calculate flux exiting from hot or cold neutron sources. -Neutron position and velocity is set from the filename. The neutron time is -left at zero. +This component generates neutron events from a filename created using the MCNP Monte Carlo code for nuclear reactors. It is used to calculate flux exiting from hot or cold neutron sources. Neutron position and velocity is set from the filename. The neutron time is left at zero. -Note that axes orientation may be different between MCNP and McStas. -The component has the ability to center and orient the neutron beam to the Z-axis. -It also may change the coordinate system from the MCNP frame to the McStas one. -The verbose mode is highly recommended as it displays lots of useful informations. -To obtain absolute intensity, set 'intensity' and 'nps' parameters. -The source total intensity is 1.054e18 for LLB/Saclay (14 MW) and 4.28e18 for -ILL/Grenoble (58 MW). +Note that axes orientation may be different between MCNP and McStas. The component has the ability to center and orient the neutron beam to the Z-axis. It also may change the coordinate system from the MCNP frame to the McStas one. The verbose mode is highly recommended as it displays lots of useful informations. To obtain absolute intensity, set 'intensity' and 'nps' parameters. The source total intensity is 1.054e18 for LLB/Saclay (14 MW) and 4.28e18 for ILL/Grenoble (58 MW). Format of MCNP events are : -position_X position_Y position_Z dir_X dir_Y dir_Z Energy Weight Time +position\_X position\_Y position\_Z dir\_X dir\_Y dir\_Z Energy Weight Time -energy is in Mega eV, time in shakes (1e-8 s), -positions are in cm and the direction vector is normalized to 1. +energy is in Mega eV, time in shakes (1e-8 s), positions are in cm and the direction vector is normalized to 1. -%BUGS -We recommend NOT to use parallel execution (MPI) with this component. If you -need to, set parameter 'smooth=1'. +\%BUGS We recommend NOT to use parallel execution (MPI) with this component. If you need to, set parameter 'smooth=1'. -EXAMPLE: -To generate PTRAC files using MCNP/MCNPX, add at the end of your input file: +EXAMPLE: To generate PTRAC files using MCNP/MCNPX, add at the end of your input file: + +\begin{verbatim} f1:n 2001 // tally +\end{verbatim} + (...) + +\begin{verbatim} ptrac filename = asc max = -1000000 // number of neutrons to generate and stop -write = all -event = sur -filter = 2001,jsu // surface tally id -To create a 'source' from a MCNP simulation event file for the ILL: -COMPONENT source = Virtual_mcnp_input( -filename = "H10p", intensity=4.28e18, nps=11328982, -verbose = 1, autocenter="translate rotate rescale") -\end{lstlisting} +\end{verbatim} + +write = all event = sur filter = 2001,jsu // surface tally id To create a 'source' from a MCNP simulation event file for the ILL: COMPONENT source = Virtual\_mcnp\_input( filename = "H10p", intensity=4.28e18, nps=11328982, verbose = 1, autocenter="translate rotate rescale") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -74,8 +59,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_mcnp_input.comp}{Source code} for \texttt{Virtual\_mcnp\_input.comp}. - \item \textless{}a href="http://mcnp-green.lanl.gov/index.html"\textgreater{}MCNP\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Virtual\_mcnp\_input.comp}. + \item \htmladdnormallink{MCNP}{http://mcnp-green.lanl.gov/index.html} \item MCNP -- A General Monte Carlo N-Particle Transport Code, Version 5, Volume II: User's Guide, p177 \end{itemize} -\IfFileExists{Virtual_mcnp_input_static.tex}{\input{Virtual_mcnp_input_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_mcnp_input_static.tex}{\input{obsolete/Virtual_mcnp_input_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_mcnp_output.tex b/docs/manuals/mcstas/obsolete/Virtual_mcnp_output.tex index d55202011d..d283bd0cb1 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_mcnp_output.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_mcnp_output.tex @@ -4,34 +4,21 @@ \section{The \texttt{Virtual\_mcnp\_output} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto hennanec@ensimag.fr"\textgreater{}Chama Hennane\textless{}/a\textgreater{} and E. Farhi \item \textbf{Origin:} \textless{}a href="http://www.ill.fr/"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} July 7th, 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Detector-like component writing neutron state parameters to a -virtual source neutron file with MCNP/PTRAC format. -The component geometry is the full plane, and saves the neutron state as -it exits from the previous component. -Format is the one used by MCNP 5 files : +Detector-like component writing neutron state parameters to a virtual source neutron file with MCNP/PTRAC format. The component geometry is the full plane, and saves the neutron state as it exits from the previous component. Format is the one used by MCNP 5 files : -position_X position_Y position_Z dir_X dir_Y dir_Z energy weight time +position\_X position\_Y position\_Z dir\_X dir\_Y dir\_Z energy weight time -energy is in Mega eV -positions are in cm and the direction vector is normalized to 1. +energy is in Mega eV positions are in cm and the direction vector is normalized to 1. -%BUGS -This component will NOT work with parallel execution (MPI). +\%BUGS This component will NOT work with parallel execution (MPI). -EXAMPLE: -To create a file collecting all neutron states with MCNP5 format -COMPONENT fichier_sortie = Virtual_mcnp_output( -filename = "exit_guide_result.dat") -at the position where will be the Virtual_mcnp_input. -\end{lstlisting} +EXAMPLE: To create a file collecting all neutron states with MCNP5 format COMPONENT fichier\_sortie = Virtual\_mcnp\_output( filename = "exit\_guide\_result.dat") at the position where will be the Virtual\_mcnp\_input. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -47,8 +34,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_mcnp_output.comp}{Source code} for \texttt{Virtual\_mcnp\_output.comp}. - \item \textless{}a href="http://mcnp-green.lanl.gov/index.html"\textgreater{}MCNP\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Virtual\_mcnp\_output.comp}. + \item \htmladdnormallink{MCNP}{http://mcnp-green.lanl.gov/index.html} \item MCNP -- A General Monte Carlo N-Particle Transport Code, Version 5, Volume II: User's Guide, p177 \end{itemize} -\IfFileExists{Virtual_mcnp_output_static.tex}{\input{Virtual_mcnp_output_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_mcnp_output_static.tex}{\input{obsolete/Virtual_mcnp_output_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_Guide.tex b/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_Guide.tex index 8627b2aaa7..efc8a9fbf4 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_Guide.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_Guide.tex @@ -3,44 +3,29 @@ \section{The \texttt{Virtual\_mcnp\_ss\_Guide} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Esben klinkby and Peter Willendrup \item \textbf{Origin:} Risoe-DTU \item \textbf{Date:} Marts 2012 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Based on Kristian Nielsens Guide.comp -Models a rectangular guide tube centered on the Z axis. The entrance lies -in the X-Y plane. -The component must be initiated after Virtual_mcnp_ss_input.comp, -and replaces Virtual_mcnp_ss_output.comp - see examples/Test_SSR_SSW_Guide.instr. -The basic idea is, that rather than discarding unreflected (i.e. absorbed) -neutrons at the guide mirrors, these neutron states are stored on disk. -Thus, after the McStas simulation a MCNP simulation can be performed based -on the un-reflected neutrons - intended for shielding studies. -(details: we don't deal with actual neutrons, so what is transferred between -simulations suites is neutron state parameters: pos,mom,time,weight. The latter is -whatever remains after reflection. +Based on Kristian Nielsens Guide.comp Models a rectangular guide tube centered on the Z axis. The entrance lies in the X-Y plane. The component must be initiated after Virtual\_mcnp\_ss\_input.comp, and replaces Virtual\_mcnp\_ss\_output.comp - see examples/Test\_SSR\_SSW\_Guide.instr. The basic idea is, that rather than discarding unreflected (i.e. absorbed) neutrons at the guide mirrors, these neutron states are stored on disk. Thus, after the McStas simulation a MCNP simulation can be performed based on the un-reflected neutrons - intended for shielding studies. (details: we don't deal with actual neutrons, so what is transferred between simulations suites is neutron state parameters: pos,mom,time,weight. The latter is whatever remains after reflection. -For details on the geometry calculation see the description in the McStas -reference manual. -The reflectivity profile may either use an analytical mode (see Component -Manual) or a 2-columns reflectivity free text file with format +For details on the geometry calculation see the description in the McStas reference manual. The reflectivity profile may either use an analytical mode (see Component Manual) or a 2-columns reflectivity free text file with format + +\begin{verbatim} [q(Angs-1) R(0-1)]. +\end{verbatim} + +Example: Virtual\_mcnp\_ss\_Guide(w1=0.1, h1=0.1, w2=0.1, h2=0.1, l=2.0, -Example: Virtual_mcnp_ss_Guide(w1=0.1, h1=0.1, w2=0.1, h2=0.1, l=2.0, +\begin{verbatim} R0=0.99, Qc=0.021, alpha=6.07, m=2, W=0.003 +\end{verbatim} -%VALIDATION -Upcomming in 2012 based on ESS shielding -Validated by: D. Ene & E. Klinkby +\%VALIDATION Upcomming in 2012 based on ESS shielding Validated by: D. Ene \& E. Klinkby -%BUGS -This component does not work with gravitation on. Use component Guide_gravity then -(doesn't work with SSR/SSW unfortunately) -\end{lstlisting} +\%BUGS This component does not work with gravitation on. Use component Guide\_gravity then (doesn't work with SSR/SSW unfortunately) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -50,22 +35,22 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -reflect & str & Reflectivity file name. Format \textless{}q(Angs-1) R(0-1)\textgreater{} & 0 \\ +reflect & str & Reflectivity file name. Format \textless{}q(\AA{}-1) R(0-1)\textgreater{} & 0 \\ \textbf{w1} & m & Width at the guide entry & \\ \textbf{h1} & m & Height at the guide entry & \\ \textbf{w2} & m & Width at the guide exit & \\ \textbf{h2} & m & Height at the guide exit & \\ \textbf{l} & m & length of guide & \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qc & AA-1 & Critical scattering vector & 0.0219 \\ -alpha & AA & Slope of reflectivity & 6.07 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0219 \\ +alpha & \AA{} & Slope of reflectivity & 6.07 \\ m & 1 & m-value of material. Zero means completely absorbing. & 2 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_mcnp_ss_Guide.comp}{Source code} for \texttt{Virtual\_mcnp\_ss\_Guide.comp}. + \item Component source code found in file \texttt{Virtual\_mcnp\_ss\_Guide.comp}. \end{itemize} -\IfFileExists{Virtual_mcnp_ss_Guide_static.tex}{\input{Virtual_mcnp_ss_Guide_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_mcnp_ss_Guide_static.tex}{\input{obsolete/Virtual_mcnp_ss_Guide_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_input.tex b/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_input.tex index cd90ce31f3..11e341891c 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_input.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_input.tex @@ -4,52 +4,27 @@ \section{The \texttt{Virtual\_mcnp\_ss\_input} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:esbe@dtu.dk"\textgreater{}Esben Klinkby\textless{}/a\textgreater{} and \textless{}a href="mailto:pkwi@dtu.dk"\textgreater{}Peter Willendrup\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.risoe.dtu.dk/"\textgreater{}DTU\textless{}/a\textgreater{} \item \textbf{Date:} January, 2012 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component draws neutron events from a Source Surface file created using the -MCNP Monte Carlo code and converts them to make them suitable for a McStas simulation +This component draws neutron events from a Source Surface file created using the MCNP Monte Carlo code and converts them to make them suitable for a McStas simulation -Note that axes orientation may be different between MCNP and McStas! -Note also that the conversion of between McStas and MCNP units and parameters -is done automatically by this component - but the user must ensure that -geometry description matches between the two Monte Carlo codes. +Note that axes orientation may be different between MCNP and McStas! Note also that the conversion of between McStas and MCNP units and parameters is done automatically by this component - but the user must ensure that geometry description matches between the two Monte Carlo codes. The verbose mode is highly recommended as it displays lots of useful informations. -This interface uses the MCNP Source Surface Read/Write format (SSW/SSR). -Infomation transfer from(to) SSW files proceeds via a set of Fortran modules -and subroutines collected in "subs.f" -For succesful compilation, it is required that these subroutines are compiled -and linked to the instrument file: +This interface uses the MCNP Source Surface Read/Write format (SSW/SSR). Infomation transfer from(to) SSW files proceeds via a set of Fortran modules and subroutines collected in "subs.f" For succesful compilation, it is required that these subroutines are compiled and linked to the instrument file: -mcstas dummy.instr -> generates dummy.c -gfortran -c subs.f -> generates subs.f -gcc -o runme.out dummy.c subs.o -lm -lgfortran -> generates runme.out +mcstas dummy.instr -\textgreater{} generates dummy.c gfortran -c subs.f -\textgreater{} generates subs.f gcc -o runme.out dummy.c subs.o -lm -lgfortran -\textgreater{} generates runme.out Note that this requires a fortran compiler (here gfortran) and gcc. -%BUGS -None known bugs so far. But surely this will change... -Caveat: when writing the header for the output wssa file, the number of histories and tracks are assumed to be that of the -input MNCP run. This is generally not the case, due to losses in the McStas simulation step. -In case of losses any subsequel MCNP run based on the McStas output, can be confused by inconsistency between -header and file content. To resolve, either ensure that NPS is lower than the actual number of events in the McStas output. -Or hardcode values of nhis & ntrk in either subs.f or Virtual_mcnp_ss_output.comp. +\%BUGS None known bugs so far. But surely this will change... Caveat: when writing the header for the output wssa file, the number of histories and tracks are assumed to be that of the input MNCP run. This is generally not the case, due to losses in the McStas simulation step. In case of losses any subsequel MCNP run based on the McStas output, can be confused by inconsistency between header and file content. To resolve, either ensure that NPS is lower than the actual number of events in the McStas output. Or hardcode values of nhis \& ntrk in either subs.f or Virtual\_mcnp\_ss\_output.comp. -EXAMPLE of usage: -first a MCNP simulation is run -and at a relevant surface, a Source Surface Write card is given (e.g. for MCNP surface #1, add the line: -SSW 1 -to the end of the input file. -By this a ".w" file is produced, which then serves as input to the McStas simulation. -Present version: rename *.w to rssa, and make sure to put it in the dir from which McStas is run -\end{lstlisting} +EXAMPLE of usage: first a MCNP simulation is run and at a relevant surface, a Source Surface Write card is given (e.g. for MCNP surface \#1, add the line: SSW 1 to the end of the input file. By this a ".w" file is produced, which then serves as input to the McStas simulation. Present version: rename *.w to rssa, and make sure to put it in the dir from which McStas is run \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -66,8 +41,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_mcnp_ss_input.comp}{Source code} for \texttt{Virtual\_mcnp\_ss\_input.comp}. - \item \textless{}a href="http://mcnp-green.lanl.gov/index.html"\textgreater{}MCNP\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Virtual\_mcnp\_ss\_input.comp}. + \item \htmladdnormallink{MCNP}{http://mcnp-green.lanl.gov/index.html} \item MCNP -- A General Monte Carlo N-Particle Transport Code, Version 5, Volume II: User's Guide, p177 \end{itemize} -\IfFileExists{Virtual_mcnp_ss_input_static.tex}{\input{Virtual_mcnp_ss_input_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_mcnp_ss_input_static.tex}{\input{obsolete/Virtual_mcnp_ss_input_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_output.tex b/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_output.tex index 1bbceb41ae..c3b87ab81a 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_output.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_mcnp_ss_output.tex @@ -4,52 +4,27 @@ \section{The \texttt{Virtual\_mcnp\_ss\_output} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:esbe@dtu.dk"\textgreater{}Esben Klinkby\textless{}/a\textgreater{} and \textless{}a href="mailto:pkwi@dtu.dk"\textgreater{}Peter Willendrup\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.risoe.dtu.dk/"\textgreater{}DTU\textless{}/a\textgreater{} \item \textbf{Date:} January, 2012 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component draws neutron events from a Source Surface file created using the -MCNP Monte Carlo code and converts them to make them suitable for a McStas simulation +This component draws neutron events from a Source Surface file created using the MCNP Monte Carlo code and converts them to make them suitable for a McStas simulation -Note that axes orientation may be different between MCNP and McStas! -Note also that the conversion of between McStas and MCNP units and parameters -is done automatically by this component - but the user must ensure that -geometry description matches between the two Monte Carlo codes. +Note that axes orientation may be different between MCNP and McStas! Note also that the conversion of between McStas and MCNP units and parameters is done automatically by this component - but the user must ensure that geometry description matches between the two Monte Carlo codes. The verbose mode is highly recommended as it displays lots of useful informations. -This interface uses the MCNP Source Surface Read/Write format (SSW/SSR). -Infomation transfer from(to) SSW files proceeds via a set of Fortran modules -and subroutines collected in "subs.f" -For succesful compilation, it is required that these subroutines are compiled -and linked to the instrument file: +This interface uses the MCNP Source Surface Read/Write format (SSW/SSR). Infomation transfer from(to) SSW files proceeds via a set of Fortran modules and subroutines collected in "subs.f" For succesful compilation, it is required that these subroutines are compiled and linked to the instrument file: -mcstas dummy.instr -> generates dummy.c -gfortran -c subs.f -> generates subs.f -gcc -o runme.out dummy.c subs.o -lm -lgfortran -> generates runme.out +mcstas dummy.instr -\textgreater{} generates dummy.c gfortran -c subs.f -\textgreater{} generates subs.f gcc -o runme.out dummy.c subs.o -lm -lgfortran -\textgreater{} generates runme.out Note that this requires a fortran compiler (here gfortran) and gcc. -%BUGS -None known bugs so far. But surely this will change... -Caveat: when writing the header for the output wssa file, the number of histories and tracks are assumed to be that of the -input MNCP run. This is generally not the case, due to losses in the McStas simulation step. -In case of losses any subsequel MCNP run based on the McStas output, can be confused by inconsistency between -header and file content. To resolve, either ensure that NPS is lower than the actual number of events in the McStas output. -Or hardcode values of nhis & ntrk in either subs.f or Virtual_mcnp_ss_output.comp. +\%BUGS None known bugs so far. But surely this will change... Caveat: when writing the header for the output wssa file, the number of histories and tracks are assumed to be that of the input MNCP run. This is generally not the case, due to losses in the McStas simulation step. In case of losses any subsequel MCNP run based on the McStas output, can be confused by inconsistency between header and file content. To resolve, either ensure that NPS is lower than the actual number of events in the McStas output. Or hardcode values of nhis \& ntrk in either subs.f or Virtual\_mcnp\_ss\_output.comp. -EXAMPLE of usage: -first a MCNP simulation is run -and at a relevant surface, a Source Surface Write card is given (e.g. for MCNP surface #1, add the line: -SSW 1 -to the end of the input file. -By this a ".w" file is produced, which then serves as input to the McStas simulation. -Present version: rename *.w to rssa, and make sure to put it in the dir from which McStas is run (or use symbolic links) -\end{lstlisting} +EXAMPLE of usage: first a MCNP simulation is run and at a relevant surface, a Source Surface Write card is given (e.g. for MCNP surface \#1, add the line: SSW 1 to the end of the input file. By this a ".w" file is produced, which then serves as input to the McStas simulation. Present version: rename *.w to rssa, and make sure to put it in the dir from which McStas is run (or use symbolic links) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -66,8 +41,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_mcnp_ss_output.comp}{Source code} for \texttt{Virtual\_mcnp\_ss\_output.comp}. - \item \textless{}a href="http://mcnp-green.lanl.gov/index.html"\textgreater{}MCNP\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Virtual\_mcnp\_ss\_output.comp}. + \item \htmladdnormallink{MCNP}{http://mcnp-green.lanl.gov/index.html} \item MCNP -- A General Monte Carlo N-Particle Transport Code, Version 5, Volume II: User's Guide, p177 \end{itemize} -\IfFileExists{Virtual_mcnp_ss_output_static.tex}{\input{Virtual_mcnp_ss_output_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_mcnp_ss_output_static.tex}{\input{obsolete/Virtual_mcnp_ss_output_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_output.tex b/docs/manuals/mcstas/obsolete/Virtual_output.tex index c9f2bc132c..87930990de 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_output.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_output.tex @@ -4,44 +4,25 @@ \section{The \texttt{Virtual\_output} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:farhi@ill.fr"\textgreater{}E. Farhi\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} Dec 17th, 2002 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Detector-like component writing neutron state parameters to a -virtual source neutron filename. The component geometry is the full -plane, and saves the neutron state as it exits from the previous -component. - -It is particularly useful to generate a virtual source at a point that few -neutron reach. A long simulation will then only be performed once, to create -the upstream 'source' file. Further simulations are much faster if they start -from this low flux position with the 'source' filename. - -The output file format is: -text column formatted with lines containing 11 values in the order: -p x y z vx vy vz t sx sy sz stored into about 83 bytes/n. - -Beware the size of generated files ! When saving all events (bufsize=0) the -required memory has been optimized and remains very small. On the other hand -using large bufsize values (not recommended) requires huge storage memory. -Moreover, using the 'bufsize' parameter will often lead to wrong intensities. -Both methods will generate huge files. - -A Vitess file may be obtained from the 'Vitess_output' component or from a -Vitess simulation (104 bytes per neutron) and read with Vitess_input. - -Example: Virtual_output(filename="MySource.dat") -will generate a 9 Mo text file for 1e5 events stored. - -%BUGS -Using bufsize non-zero may generate a virtual source with wrong intensity. This -component works with MPI (parallel execution mode). -\end{lstlisting} +Detector-like component writing neutron state parameters to a virtual source neutron filename. The component geometry is the full plane, and saves the neutron state as it exits from the previous component. + +It is particularly useful to generate a virtual source at a point that few neutron reach. A long simulation will then only be performed once, to create the upstream 'source' file. Further simulations are much faster if they start from this low flux position with the 'source' filename. + +The output file format is: text column formatted with lines containing 11 values in the order: p x y z vx vy vz t sx sy sz stored into about 83 bytes/n. + +Beware the size of generated files ! When saving all events (bufsize=0) the required memory has been optimized and remains very small. On the other hand using large bufsize values (not recommended) requires huge storage memory. Moreover, using the 'bufsize' parameter will often lead to wrong intensities. Both methods will generate huge files. + +A Vitess file may be obtained from the 'Vitess\_output' component or from a Vitess simulation (104 bytes per neutron) and read with Vitess\_input. + +Example: Virtual\_output(filename="MySource.dat") will generate a 9 Mo text file for 1e5 events stored. + +\%BUGS Using bufsize non-zero may generate a virtual source with wrong intensity. This component works with MPI (parallel execution mode). \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -58,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_output.comp}{Source code} for \texttt{Virtual\_output.comp}. + \item Component source code found in file \texttt{Virtual\_output.comp}. \end{itemize} -\IfFileExists{Virtual_output_static.tex}{\input{Virtual_output_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_output_static.tex}{\input{obsolete/Virtual_output_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_tripoli4_input.tex b/docs/manuals/mcstas/obsolete/Virtual_tripoli4_input.tex index 244259baa7..93c54a9195 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_tripoli4_input.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_tripoli4_input.tex @@ -4,49 +4,25 @@ \section{The \texttt{Virtual\_tripoli4\_input} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:guillaume.campioni@cea.fr"\textgreater{}Guillaume Campioni\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.serma.cea.fr/"\textgreater{}SERMA\textless{}/a\textgreater{} \item \textbf{Date:} Sep 28th, 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component generates neutron events from a file created using the -TRIPOLI4 Monte Carlo code for nuclear reactors (as MCNP). It is used to -calculate flux exiting from hot or cold neutron sources. -Neutron position and velocity is set from the file. The neutron time is -left at zero. -Storage files from TRIPOLI4.4 contain several batches of particules, all -of them having the same statictical weight. +This component generates neutron events from a file created using the TRIPOLI4 Monte Carlo code for nuclear reactors (as MCNP). It is used to calculate flux exiting from hot or cold neutron sources. Neutron position and velocity is set from the file. The neutron time is left at zero. Storage files from TRIPOLI4.4 contain several batches of particules, all of them having the same statictical weight. -Note that axes orientation may be different between TRIPOLI4.4 and McStas. -The component has the ability to center and orient the neutron beam to the Z-axis. -It also changes the coordinate system from the Tripoli frame to the McStas one. -The verbose mode is highly recommended as it displays lots of useful informations, -including the absolute intensity normalisation factor. All neutron fluxes in the -instrument should be multiplied by this factor. Such a renormalization is done -when 'autocenter' contains the word 'rescale'. -The source total intensity is 1.054e18 for LLB/Saclay (14 MW) and 4.28e18 for -ILL/Grenoble (58 MW). +Note that axes orientation may be different between TRIPOLI4.4 and McStas. The component has the ability to center and orient the neutron beam to the Z-axis. It also changes the coordinate system from the Tripoli frame to the McStas one. The verbose mode is highly recommended as it displays lots of useful informations, including the absolute intensity normalisation factor. All neutron fluxes in the instrument should be multiplied by this factor. Such a renormalization is done when 'autocenter' contains the word 'rescale'. The source total intensity is 1.054e18 for LLB/Saclay (14 MW) and 4.28e18 for ILL/Grenoble (58 MW). Format of TRIPOLI4.4 event files is : -NEUTRON energy position_X position_Y position_Z dir_X dir_Y dir_Z weight +NEUTRON energy position\_X position\_Y position\_Z dir\_X dir\_Y dir\_Z weight -energy is in Mega eV -positions are in cm and the direction vector is normalized to 1. +energy is in Mega eV positions are in cm and the direction vector is normalized to 1. -%BUGS -We recommend NOT to use parallel execution (MPI) with this component. If you -need to, set parameter 'smooth=1'. +\%BUGS We recommend NOT to use parallel execution (MPI) with this component. If you need to, set parameter 'smooth=1'. -EXAMPLE: -To create a 'source' from a Tripoli4 simulation event file for the ILL: -COMPONENT source = Virtual_tripoli4_input( -filename = "ILL_SFH.dat", intensity=4.28e18, -verbose = 1, autocenter="translate rotate rescale") -\end{lstlisting} +EXAMPLE: To create a 'source' from a Tripoli4 simulation event file for the ILL: COMPONENT source = Virtual\_tripoli4\_input( filename = "ILL\_SFH.dat", intensity=4.28e18, verbose = 1, autocenter="translate rotate rescale") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -71,9 +47,9 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_tripoli4_input.comp}{Source code} for \texttt{Virtual\_tripoli4\_input.comp}. - \item \textless{}a href="http://www.nea.fr/html/dbprog/tripoli-abs.html"\textgreater{}Tripoli\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Virtual\_tripoli4\_input.comp}. + \item \htmladdnormallink{Tripoli}{http://www.nea.fr/html/dbprog/tripoli-abs.html} \item Virtual\_tripoli4\_output \item CAMPIONI Guillaume, Etude et Modelisation des Sources Froides de Neutrons, These de Doctorat, CEA Saclay/UJF (2004) \end{itemize} -\IfFileExists{Virtual_tripoli4_input_static.tex}{\input{Virtual_tripoli4_input_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_tripoli4_input_static.tex}{\input{obsolete/Virtual_tripoli4_input_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Virtual_tripoli4_output.tex b/docs/manuals/mcstas/obsolete/Virtual_tripoli4_output.tex index 2daf90ef4d..a72556d915 100644 --- a/docs/manuals/mcstas/obsolete/Virtual_tripoli4_output.tex +++ b/docs/manuals/mcstas/obsolete/Virtual_tripoli4_output.tex @@ -5,35 +5,21 @@ \section{The \texttt{Virtual\_tripoli4\_output} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailtoguillaume.campioni@cea.fr"\textgreater{}Guillaume Campioni\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.cea-llb.fr"\textgreater{}LLB\textless{}/a\textgreater{} \item \textbf{Date:} Sep 28th, 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Detector-like component writing neutron state parameters to a -virtual source neutron file when neutron are coming from a -Virtual_tripoli4_input.comp. -The component geometry is the full plane, and saves the neutron state as -it exits from the previous component. -Format is the one used by TRIPOLI4.4 stock files : +Detector-like component writing neutron state parameters to a virtual source neutron file when neutron are coming from a Virtual\_tripoli4\_input.comp. The component geometry is the full plane, and saves the neutron state as it exits from the previous component. Format is the one used by TRIPOLI4.4 stock files : -NEUTRON energy position_X position_Y position_Z dir_X dir_Y dir_Z weight +NEUTRON energy position\_X position\_Y position\_Z dir\_X dir\_Y dir\_Z weight -energy is in [Mega eV] -positions are in [cm] and the direction vector is normalized to 1. +energy is in [Mega eV] positions are in [cm] and the direction vector is normalized to 1. -%BUGS -This component will NOT work with parallel execution (MPI/GPU). +\%BUGS This component will NOT work with parallel execution (MPI/GPU). -EXAMPLE: -To create a file collecting all neutron states with TRIPOLI4 format -COMPONENT T4output = Virtual_tripoli4_output( -filename = "exit_guide_result.dat", batch = 1 ) -at the position where will be the Virtual_tripoli4_input when reading the file. -\end{lstlisting} +EXAMPLE: To create a file collecting all neutron states with TRIPOLI4 format COMPONENT T4output = Virtual\_tripoli4\_output( filename = "exit\_guide\_result.dat", batch = 1 ) at the position where will be the Virtual\_tripoli4\_input when reading the file. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -50,8 +36,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Virtual_tripoli4_output.comp}{Source code} for \texttt{Virtual\_tripoli4\_output.comp}. - \item \textless{}a href="http://www.nea.fr/html/dbprog/tripoli-abs.html"\textgreater{}Tripoli\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Virtual\_tripoli4\_output.comp}. + \item \htmladdnormallink{Tripoli}{http://www.nea.fr/html/dbprog/tripoli-abs.html} \item Virtual\_tripoli4\_input \end{itemize} -\IfFileExists{Virtual_tripoli4_output_static.tex}{\input{Virtual_tripoli4_output_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Virtual_tripoli4_output_static.tex}{\input{obsolete/Virtual_tripoli4_output_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Vitess_input.tex b/docs/manuals/mcstas/obsolete/Vitess_input.tex index c2217c9496..e2873175d1 100644 --- a/docs/manuals/mcstas/obsolete/Vitess_input.tex +++ b/docs/manuals/mcstas/obsolete/Vitess_input.tex @@ -3,23 +3,17 @@ \section{The \texttt{Vitess\_input} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe/ILL \item \textbf{Date:} June 6, 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Source-like component reading neutron state parameters from a -VITESS neutron filename. Used to interface McStas components or -simulations into VITESS. Each neutron is 104 bytes. +Source-like component reading neutron state parameters from a VITESS neutron filename. Used to interface McStas components or simulations into VITESS. Each neutron is 104 bytes. -Example: Vitess_input(filename="MySource.vit", bufsize = 10000, repeat_count = 2) +Example: Vitess\_input(filename="MySource.vit", bufsize = 10000, repeat\_count = 2) -%BUGS -We recommend NOT to use parallel execution (MPI) with this component. -\end{lstlisting} +\%BUGS We recommend NOT to use parallel execution (MPI) with this component. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -37,6 +31,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Vitess_input.comp}{Source code} for \texttt{Vitess\_input.comp}. + \item Component source code found in file \texttt{Vitess\_input.comp}. \end{itemize} -\IfFileExists{Vitess_input_static.tex}{\input{Vitess_input_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Vitess_input_static.tex}{\input{obsolete/Vitess_input_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/obsolete/Vitess_output.tex b/docs/manuals/mcstas/obsolete/Vitess_output.tex index fb73b24aae..903daf3d60 100644 --- a/docs/manuals/mcstas/obsolete/Vitess_output.tex +++ b/docs/manuals/mcstas/obsolete/Vitess_output.tex @@ -3,28 +3,19 @@ \section{The \texttt{Vitess\_output} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe/ILL \item \textbf{Date:} June 6, 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Detector-like component writing neutron state parameters to a -VITESS neutron filename. Used to interface McStas components or -simulations into VITESS. Each neutron is 104 bytes. +Detector-like component writing neutron state parameters to a VITESS neutron filename. Used to interface McStas components or simulations into VITESS. Each neutron is 104 bytes. -Note that when standard output is used, as is the default, no -monitors or other components that produce terminal output must be -used, or the neutron output from this component will become -corrupted. +Note that when standard output is used, as is the default, no monitors or other components that produce terminal output must be used, or the neutron output from this component will become corrupted. -Example: Vitess_output(filename="MySource.vit", bufsize = 10000, progress = 1) +Example: Vitess\_output(filename="MySource.vit", bufsize = 10000, progress = 1) -%BUGS -This component will NOT work with parallel execution (MPI). -\end{lstlisting} +\%BUGS This component will NOT work with parallel execution (MPI). \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +33,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/obsolete/Vitess_output.comp}{Source code} for \texttt{Vitess\_output.comp}. + \item Component source code found in file \texttt{Vitess\_output.comp}. \end{itemize} -\IfFileExists{Vitess_output_static.tex}{\input{Vitess_output_static.tex}}{} \ No newline at end of file +\IfFileExists{obsolete/Vitess_output_static.tex}{\input{obsolete/Vitess_output_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Absorber.tex b/docs/manuals/mcstas/optics/Absorber.tex index 07b54117d4..c3f067759c 100644 --- a/docs/manuals/mcstas/optics/Absorber.tex +++ b/docs/manuals/mcstas/optics/Absorber.tex @@ -3,18 +3,15 @@ \section{The \texttt{Absorber} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} Risoe \item \textbf{Date:} November 2008 \end{itemize} \subsection*{Description} -\begin{lstlisting} Infinitely absorbing slab of material. Example: Absorber(xmin=-0.01, xmax=0.01, ymin=-0.05, ymax=0.05, zmin=-0.2, zmax=0) -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -35,6 +32,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Absorber.comp}{Source code} for \texttt{Absorber.comp}. + \item Component source code found in file \texttt{Absorber.comp}. \end{itemize} -\IfFileExists{Absorber_static.tex}{\input{Absorber_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Absorber_static.tex}{\input{optics/Absorber_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Arm.tex b/docs/manuals/mcstas/optics/Arm.tex index a37b4250f1..31eafd47d8 100644 --- a/docs/manuals/mcstas/optics/Arm.tex +++ b/docs/manuals/mcstas/optics/Arm.tex @@ -3,19 +3,15 @@ \section{The \texttt{Arm} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann and Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} September 1997 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An arm does not actually do anything, it is just there to set -up a new coordinate system. +An arm does not actually do anything, it is just there to set up a new coordinate system. Example: Arm() -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,6 +26,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Arm.comp}{Source code} for \texttt{Arm.comp}. + \item Component source code found in file \texttt{Arm.comp}. \end{itemize} -\IfFileExists{Arm_static.tex}{\input{Arm_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Arm_static.tex}{\input{optics/Arm_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Beamstop.tex b/docs/manuals/mcstas/optics/Beamstop.tex index 668f099d52..aff18cb48d 100644 --- a/docs/manuals/mcstas/optics/Beamstop.tex +++ b/docs/manuals/mcstas/optics/Beamstop.tex @@ -3,22 +3,15 @@ \section{The \texttt{Beamstop} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} January 2000 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A simple rectangular or circular beam stop. -Infinitely thin and infinitely absorbing. -The beam stop is by default rectangular. You may either -specify the radius (circular shape), or the rectangular bounds. +A simple rectangular or circular beam stop. Infinitely thin and infinitely absorbing. The beam stop is by default rectangular. You may either specify the radius (circular shape), or the rectangular bounds. -Example: Beamstop(xmin=-0.05, xmax=0.05, ymin=-0.05, ymax=0.05) -Beamstop(radius=0.1) -\end{lstlisting} +Example: Beamstop(xmin=-0.05, xmax=0.05, ymin=-0.05, ymax=0.05) Beamstop(radius=0.1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,6 +33,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Beamstop.comp}{Source code} for \texttt{Beamstop.comp}. + \item Component source code found in file \texttt{Beamstop.comp}. \end{itemize} -\IfFileExists{Beamstop_static.tex}{\input{Beamstop_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Beamstop_static.tex}{\input{optics/Beamstop_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Bender.tex b/docs/manuals/mcstas/optics/Bender.tex index e80dfc0d02..26ad8f3b09 100644 --- a/docs/manuals/mcstas/optics/Bender.tex +++ b/docs/manuals/mcstas/optics/Bender.tex @@ -3,48 +3,28 @@ \section{The \texttt{Bender} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Philipp Bernhardt \item \textbf{Origin:} Uni. Erlangen (Germany) \item \textbf{Date:} Februar 7 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} Models a curved neutron guide with cylindrical walls. -Bender radius, entrance width and height are necessary input data. To define -the bender, you may either enter the deviation angle 'Win' or the length 'l'. -The bender may consist of 'k' vertical channels, separated by partitioning walls -of thickness 'd'. Three different reflectivity profiles can be given: for outer -walls, for inner walls and for the top and bottom walls. The partitioning walls -have the same coating as the exterior walls. +Bender radius, entrance width and height are necessary input data. To define the bender, you may either enter the deviation angle 'Win' or the length 'l'. The bender may consist of 'k' vertical channels, separated by partitioning walls of thickness 'd'. Three different reflectivity profiles can be given: for outer walls, for inner walls and for the top and bottom walls. The partitioning walls have the same coating as the exterior walls. -The entrance lies in the X-Y plane, centered on the Z axis. The neutrons will -also leave the bender in the X-Y plane at the z-value l=r*Win, i.e. they are -centred on (0,0,r*Win); they have an (average) flight direction along the z-axis. -Therefore, the following component is adjacent, if positioned AT (0,0,r*Win) -<b>without</b> rotation. -So, seen from outside, it behaves like a straight guide along the Z axis. As a -consequence, it is shown straight in 'mcdisplay'. -This behaviour results from a co-ordinate transformation inside the component. -It is done to facilitate its use. Neither rotation nor shift along the x-axis -need to be calculated; a new arm is not necessary. Internally, the bender is -bent to the negative X axis; +The entrance lies in the X-Y plane, centered on the Z axis. The neutrons will also leave the bender in the X-Y plane at the z-value l=r*Win, i.e. they are centred on (0,0,r*Win); they have an (average) flight direction along the z-axis. Therefore, the following component is adjacent, if positioned AT (0,0,r*Win) \textbf{without} rotation. So, seen from outside, it behaves like a straight guide along the Z axis. As a consequence, it is shown straight in 'mcdisplay'. This behaviour results from a co-ordinate transformation inside the component. It is done to facilitate its use. Neither rotation nor shift along the x-axis need to be calculated; a new arm is not necessary. Internally, the bender is bent to the negative X axis; -Example: -Bender of 120 mm height, 50 mm width, 250 m radius and 0.04 rad (or 2.292 deg) curvature -not channeled, with a standard m=2 coating on +Example: Bender of 120 mm height, 50 mm width, 250 m radius and 0.04 rad (or 2.292 deg) curvature not channeled, with a standard m=2 coating on +\begin{verbatim} Bender(w=0.05,h=0.12,r=250,Win=0.04, R0a=0.99,Qca=0.021,alphaa=6.07,ma=2,Wa=0.003, R0i=0.99,Qci=0.021,alphai=6.07,mi=2,Wi=0.003, R0s=0.99,Qcs=0.021,alphas=6.07,ms=2,Ws=0.003) +\end{verbatim} -%BUGS -Some users have reported potentially strange behaviours with this component. -This component does not work with gravitation on. -\end{lstlisting} +\%BUGS Some users have reported potentially strange behaviours with this component. This component does not work with gravitation on. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -62,27 +42,27 @@ \subsection*{Input parameters} d & m & Thickness of one blade separating the channels & 0.001 \\ l & m & length of bender l=r*Win & 0 \\ R0a & 1 & Low-angle reflectivity at the \textless{}b\textgreater{}outer\textless{}/b\textgreater{} side of the bender & 0.99 \\ -Qca & AA-1 & Critical scattering vector & 0.021 \\ -alphaa & AA & Slope of reflectivity & 6.07 \\ +Qca & \AA{}$^{-1}$ & Critical scattering vector & 0.021 \\ +alphaa & \AA{} & Slope of reflectivity & 6.07 \\ ma & 1 & m-value of material & 2 \\ -Wa & AA-1 & Width of supermirror cut-off & 0.003 \\ +Wa & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ R0i & 1 & Low-angle reflectivity at the \textless{}b\textgreater{}inner\textless{}/b\textgreater{} side of the bender & 0.99 \\ -Qci & AA-1 & Critical scattering vector & 0.021 \\ -alphai & AA & Slope of reflectivity & 6.07 \\ +Qci & \AA{}$^{-1}$ & Critical scattering vector & 0.021 \\ +alphai & \AA{} & Slope of reflectivity & 6.07 \\ mi & 1 & m-value of material & 2 \\ -Wi & AA-1 & Width of supermirror cut-off & 0.003 \\ +Wi & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ R0s & 1 & Low-angle reflectivity at the \textless{}b\textgreater{}top and bottom\textless{}/b\textgreater{} side of the bender & 0.99 \\ -Qcs & AA-1 & Critical scattering vector & 0.021 \\ -alphas & AA & Slope of reflectivity & 6.07 \\ +Qcs & \AA{}$^{-1}$ & Critical scattering vector & 0.021 \\ +alphas & \AA{} & Slope of reflectivity & 6.07 \\ ms & 1 & m-value of material & 2 \\ -Ws & AA-1 & Width of supermirror cut-off & 0.003 \\ +Ws & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Bender.comp}{Source code} for \texttt{Bender.comp}. - \item \textless{}a href="../contrib/Guide\_curved.comp.html\textgreater{}Guide\_curved\textless{}/a\textgreater{} (contributed) - \item See also \textless{}a href="http://mailman.risoe.dk/pipermail/neutron-mc/1999q1/000052.html"\textgreater{}Additional note\textless{}/a\textgreater{} from \textless{}a href="mailto:philipp.bernhardt@siemens.com"\textgreater{}Philipp Bernhardt\textless{}/a\textgreater{}. + \item Component source code found in file \texttt{Bender.comp}. + \item \htmladdnormallink{Guide\_curved}{} (contributed) + \item See also \htmladdnormallink{Additional note}{http://mailman.risoe.dk/pipermail/neutron-mc/1999q1/000052.html} from \htmladdnormallink{Philipp Bernhardt}{mailto:philipp.bernhardt@siemens.com}. \end{itemize} -\IfFileExists{Bender_static.tex}{\input{Bender_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Bender_static.tex}{\input{optics/Bender_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Collimator_linear.tex b/docs/manuals/mcstas/optics/Collimator_linear.tex index ee97cd5449..1770ea8f23 100644 --- a/docs/manuals/mcstas/optics/Collimator_linear.tex +++ b/docs/manuals/mcstas/optics/Collimator_linear.tex @@ -3,21 +3,15 @@ \section{The \texttt{Collimator\_linear} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} August 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Soller collimator with rectangular opening and specified length. The -transmission function is an average and does not utilize knowledge of the -actual neutron trajectory. A zero divergence disables collimation (then the -component works as a double slit). +Soller collimator with rectangular opening and specified length. The transmission function is an average and does not utilize knowledge of the actual neutron trajectory. A zero divergence disables collimation (then the component works as a double slit). -Example: Collimator_linear(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, length=0.25, divergence=40,transmission=0.7) -\end{lstlisting} +Example: Collimator\_linear(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, length=0.25, divergence=40,transmission=0.7) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +36,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Collimator_linear.comp}{Source code} for \texttt{Collimator\_linear.comp}. + \item Component source code found in file \texttt{Collimator\_linear.comp}. \end{itemize} -\IfFileExists{Collimator_linear_static.tex}{\input{Collimator_linear_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Collimator_linear_static.tex}{\input{optics/Collimator_linear_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Collimator_radial.tex b/docs/manuals/mcstas/optics/Collimator_radial.tex index 6d4410c162..b814edba0e 100644 --- a/docs/manuals/mcstas/optics/Collimator_radial.tex +++ b/docs/manuals/mcstas/optics/Collimator_radial.tex @@ -3,43 +3,25 @@ \section{The \texttt{Collimator\_radial} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Emmanuel Farhi \textless{}farhi@ill.fr\textgreater{} \item \textbf{Origin:} ILL \item \textbf{Date:} July 2005 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Radial Soller collimator with rectangular opening and specified length. -The collimator is made of many rectangular channels stacked radially. -Each channel is a set of transmitting layers (nslit), separated by an absorbing -material (infinitely thin), the whole stuff is inside an absorbing housing. +Radial Soller collimator with rectangular opening and specified length. The collimator is made of many rectangular channels stacked radially. Each channel is a set of transmitting layers (nslit), separated by an absorbing material (infinitely thin), the whole stuff is inside an absorbing housing. -When specifying the number of channels (nchan), each channel has a total -entrance width=radius*fabs(theta_max-theta_min)/nchan, but only the central -portion 'xwidth' accepts neutrons. When xwidth=0, it is set to the full -apperture so that all neutrons enter the channels (all walls are infinitely thin). +When specifying the number of channels (nchan), each channel has a total entrance width=radius*fabs(theta\_max-theta\_min)/nchan, but only the central portion 'xwidth' accepts neutrons. When xwidth=0, it is set to the full apperture so that all neutrons enter the channels (all walls are infinitely thin). -When using zero as the number of channels (nchan), the collimator is continuous, -whithout shadowing effect. +When using zero as the number of channels (nchan), the collimator is continuous, whithout shadowing effect. -The component should be positioned at the radius center. -The component can be made oscillating (usual on diffractometers and TOF -machines) with the 'roc' parameter. -The neutron beam outside the collimator angular area is transmitted unaffected. +The component should be positioned at the radius center. The component can be made oscillating (usual on diffractometers and TOF machines) with the 'roc' parameter. The neutron beam outside the collimator angular area is transmitted unaffected. When used as a focusing collimator, the focusing parameter should be set to 1. -An example of a instrument that uses this collimator can be found in the SALSA instrument, -in the example folder +An example of a instrument that uses this collimator can be found in the SALSA instrument, in the example folder -Example: -Channelled radial collimator with shadow parts -Collimator_radial(xwidth=0.015, yheight=.3, length=.35, divergence=40,transmission=1, theta_min=5, theta_max=165, nchan=128, radius=0.9) -A continuous radial collimator -Collimator_radial(yheight=.3, length=.35, divergence=40,transmission=1, theta_min=5, theta_max=165, radius=0.9) -\end{lstlisting} +Example: Channelled radial collimator with shadow parts Collimator\_radial(xwidth=0.015, yheight=.3, length=.35, divergence=40,transmission=1, theta\_min=5, theta\_max=165, nchan=128, radius=0.9) A continuous radial collimator Collimator\_radial(yheight=.3, length=.35, divergence=40,transmission=1, theta\_min=5, theta\_max=165, radius=0.9) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -69,6 +51,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Collimator_radial.comp}{Source code} for \texttt{Collimator\_radial.comp}. + \item Component source code found in file \texttt{Collimator\_radial.comp}. \end{itemize} -\IfFileExists{Collimator_radial_static.tex}{\input{Collimator_radial_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Collimator_radial_static.tex}{\input{optics/Collimator_radial_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Derotator.tex b/docs/manuals/mcstas/optics/Derotator.tex index 17831e9fd5..3775c45e92 100644 --- a/docs/manuals/mcstas/optics/Derotator.tex +++ b/docs/manuals/mcstas/optics/Derotator.tex @@ -3,24 +3,15 @@ \section{The \texttt{Derotator} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Emmanuel Farhi \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} June 20th 2013 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A component which stops the rotative frame set by the Rotator component. -Its position should better coincide with the Rotator instance. -Components preceding the Derotator are rotating, all following are steady. +A component which stops the rotative frame set by the Rotator component. Its position should better coincide with the Rotator instance. Components preceding the Derotator are rotating, all following are steady. -Example: -R=Rotator(nu=14, phase=0) -... -DR=Derotator(rotator="R") -AT (0,0,0) RELATIVE R -\end{lstlisting} +Example: R=Rotator(nu=14, phase=0) ... DR=Derotator(rotator="R") AT (0,0,0) RELATIVE R \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,6 +27,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Derotator.comp}{Source code} for \texttt{Derotator.comp}. + \item Component source code found in file \texttt{Derotator.comp}. \end{itemize} -\IfFileExists{Derotator_static.tex}{\input{Derotator_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Derotator_static.tex}{\input{optics/Derotator_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Diaphragm.tex b/docs/manuals/mcstas/optics/Diaphragm.tex index dcd1d7b991..6303a86f0e 100644 --- a/docs/manuals/mcstas/optics/Diaphragm.tex +++ b/docs/manuals/mcstas/optics/Diaphragm.tex @@ -3,24 +3,17 @@ \section{The \texttt{Diaphragm} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} DTU \item \textbf{Date:} February 2016 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A simple rectangular or circular diaphragm. You may either -specify the radius (circular shape), or the rectangular bounds. -No transmission around the diaphragm is allowed. +A simple rectangular or circular diaphragm. You may either specify the radius (circular shape), or the rectangular bounds. No transmission around the diaphragm is allowed. -Example: Diaphragm(xmin=-0.01, xmax=0.01, ymin=-0.01, ymax=0.01) -Diaphragm(radius=0.01) +Example: Diaphragm(xmin=-0.01, xmax=0.01, ymin=-0.01, ymax=0.01) Diaphragm(radius=0.01) - -For <B>INPUT PARAMETERS</B> - please consult <a href="Slit.html">Slit.comp</a> as Diaphragm is a copy of that component. -\end{lstlisting} +For \textbf{INPUT PARAMETERS} - please consult \htmladdnormallink{Slit.comp}{Slit.html} as Diaphragm is a copy of that component. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -35,6 +28,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Diaphragm.comp}{Source code} for \texttt{Diaphragm.comp}. + \item Component source code found in file \texttt{Diaphragm.comp}. \end{itemize} -\IfFileExists{Diaphragm_static.tex}{\input{Diaphragm_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Diaphragm_static.tex}{\input{optics/Diaphragm_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/DiskChopper.tex b/docs/manuals/mcstas/optics/DiskChopper.tex index 81ffb9ea50..68a7062677 100644 --- a/docs/manuals/mcstas/optics/DiskChopper.tex +++ b/docs/manuals/mcstas/optics/DiskChopper.tex @@ -4,39 +4,23 @@ \section{The \texttt{DiskChopper} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} Risoe \item \textbf{Date:} March 9 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a disc chopper with nslit identical slits, which are symmetrically distributed -on the disc. At time t=0, the centre of the first slit opening will be situated at the -vertical axis when phase=0, assuming the chopper centre of rotation is placed <b>BELOW</b> the beam axis. -If you want to place the chopper <b>ABOVE</b> the beam axis, please use a 180 degree rotation around Z -(otherwise unexpected beam splitting can occur in combination with the isfirst=1 setting, see -<a href="https://github.com/mccode-dev/McCode/issues/650">related bug on GitHub</a>) +Models a disc chopper with nslit identical slits, which are symmetrically distributed on the disc. At time t=0, the centre of the first slit opening will be situated at the vertical axis when phase=0, assuming the chopper centre of rotation is placed \textbf{BELOW} the beam axis. If you want to place the chopper \textbf{ABOVE} the beam axis, please use a 180 degree rotation around Z (otherwise unexpected beam splitting can occur in combination with the isfirst=1 setting, see \htmladdnormallink{related bug on GitHub}{https://github.com/mccode-dev/McCode/issues/650}) For more complicated gemometries, see component manual example of DiskChopper GROUPing. -If the chopper is the 1st chopper of a continuous source instrument, you should use the "isfirst" parameter. -This parameter SETS the neutron time to match the passage of the chooper slit(s), taking into account the -chopper timing and phasing (thus conserving your simulated statistics). +If the chopper is the 1st chopper of a continuous source instrument, you should use the "isfirst" parameter. This parameter SETS the neutron time to match the passage of the chooper slit(s), taking into account the chopper timing and phasing (thus conserving your simulated statistics). The isfirst parameter is ONLY relevant for use in continuous source settings. -Example: DiskChopper(radius=0.2, theta_0=10, nu=41.7, nslit=3, delay=0, isfirst=1) First chopper -DiskChopper(radius=0.2, theta_0=10, nu=41.7, nslit=3, delay=0, isfirst=0) +Example: DiskChopper(radius=0.2, theta\_0=10, nu=41.7, nslit=3, delay=0, isfirst=1) First chopper DiskChopper(radius=0.2, theta\_0=10, nu=41.7, nslit=3, delay=0, isfirst=0) -NOTA BENE wrt. GROUPing and isfirst: -When setting up a GROUP of DiskChoppers for a steady-state / reactor source, you will need -to set up -1) An initial chopper with isfirst=1, NOT part of the GROUP - and using a "big" chopper opening -that spans the full angular extent of the openings of the subsequent GROUP -2) Add your DiskChopper GROUP setting isfirst=0 -\end{lstlisting} +NOTA BENE wrt. GROUPing and isfirst: When setting up a GROUP of DiskChoppers for a steady-state / reactor source, you will need to set up 1) An initial chopper with isfirst=1, NOT part of the GROUP - and using a "big" chopper opening that spans the full angular extent of the openings of the subsequent GROUP 2) Add your DiskChopper GROUP setting isfirst=0 \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -64,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/DiskChopper.comp}{Source code} for \texttt{DiskChopper.comp}. + \item Component source code found in file \texttt{DiskChopper.comp}. \end{itemize} -\IfFileExists{DiskChopper_static.tex}{\input{DiskChopper_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/DiskChopper_static.tex}{\input{optics/DiskChopper_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/DiskChopper_static.tex b/docs/manuals/mcstas/optics/DiskChopper_static.tex index 1c2d683c59..70cb4b8558 100644 --- a/docs/manuals/mcstas/optics/DiskChopper_static.tex +++ b/docs/manuals/mcstas/optics/DiskChopper_static.tex @@ -4,12 +4,6 @@ \subsection*{The disc chopper} \label{s:chopper} \index{Optics!Disc chopper} -%\component{DiskChopper}{Peter Willendrup, Ris\o\ (System)}{$\theta_0$, -% $R$, $h$, $\omega$, $n$, $t_0$, $\phi_0$}{IsFirst, - % $n_\textrm{pulse}$}{Based on Chopper by P Bernhardt, extensions K - %Hewitt Klen\o\ and R Bewey} -%\mcdoccomp{optics/DiskChopper.parms} - To cut a continuous neutron beam into short pulses, or to control the pulse shape (in time) from a pulsed source, one can use a disc chopper (see figure~\ref{f:chopper1}). This is a fast rotating disc with the diff --git a/docs/manuals/mcstas/optics/Elliptic_guide_gravity.tex b/docs/manuals/mcstas/optics/Elliptic_guide_gravity.tex index befead3594..b3e24d5660 100644 --- a/docs/manuals/mcstas/optics/Elliptic_guide_gravity.tex +++ b/docs/manuals/mcstas/optics/Elliptic_guide_gravity.tex @@ -5,73 +5,59 @@ \section{The \texttt{Elliptic\_guide\_gravity} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Henrik Bo Hoffmann Carlsen and Mads Bertelsen \item \textbf{Origin:} NBI \item \textbf{Date:} 27 Aug 2012 \end{itemize} \subsection*{Description} -\begin{lstlisting} -The perfect elliptic guide is centered along the z-axis with the entrance -and exit in the xy-plane. The horizontal and vertical ellipses defining -the guide geometry is by default set by two focal points. -These are placed a distance away from the guide openings along the z-axis; -if distance given is positive, when the focal point is outside the guide. - -Multiple options for defining these ellipse exist including approximation of -parabolas and half ellipses (mid point of the ellipse or one of the guide openings) - -The guide coating parameters can be set for each side of the guide. -Furthermore the m-value can be specified for user defined segments -of the guide. - -<b>Example 1, Elliptical definition using focal points:</b> - -Elliptic_guide_gravity( -l=50, -linxw=5,linyh=5,loutxw=10,loutyh=10, -xwidth=0.05,yheight=0.05, +The perfect elliptic guide is centered along the z-axis with the entrance and exit in the xy-plane. The horizontal and vertical ellipses defining the guide geometry is by default set by two focal points. These are placed a distance away from the guide openings along the z-axis; if distance given is positive, when the focal point is outside the guide. + +Multiple options for defining these ellipse exist including approximation of parabolas and half ellipses (mid point of the ellipse or one of the guide openings) + +The guide coating parameters can be set for each side of the guide. Furthermore the m-value can be specified for user defined segments of the guide. + +\textbf{Example 1, Elliptical definition using focal points:} + +Elliptic\_guide\_gravity( l=50, linxw=5,linyh=5,loutxw=10,loutyh=10, xwidth=0.05,yheight=0.05, + +\begin{verbatim} R0=0.99,Qc=0.0219,alpha=6.07,m=1.0,W=0.003 +\end{verbatim} + ) -<b>Example 2: Half elliptical definition:</b> +\textbf{Example 2: Half elliptical definition:} -Elliptic_guide_gravity( -l=50, -linxw=5,linyh=5,loutxw=10,loutyh=10, -xwidth=0.1,yheight=0.1, +Elliptic\_guide\_gravity( l=50, linxw=5,linyh=5,loutxw=10,loutyh=10, xwidth=0.1,yheight=0.1, + +\begin{verbatim} R0=0.99,Qc=0.0219,alpha=6.07,m=1.0,W=0.003, -option = "halfEllipse", -dimensionsAt = "entrance" -) +\end{verbatim} -<b>Example 3: Parabolic approximation:</b> +option = "halfEllipse", dimensionsAt = "entrance" ) -Elliptic_guide_gravity( -l=50, -linxw=5,linyh=5,loutxw=1e6,loutyh=1e6, // values larger than 1e8 may cause erroneous results -xwidth=0.1,yheight=0.1, +\textbf{Example 3: Parabolic approximation:} + +Elliptic\_guide\_gravity( l=50, linxw=5,linyh=5,loutxw=1e6,loutyh=1e6, // values larger than 1e8 may cause erroneous results xwidth=0.1,yheight=0.1, + +\begin{verbatim} R0 = 0.99,Qc=0.0219,alpha=6.07,m=1.0,W=0.003, -dimensionsAt = "exit" -) +\end{verbatim} + +dimensionsAt = "exit" ) -<b>Example 4: Elliptical definition with varying m-values:</b> +\textbf{Example 4: Elliptical definition with varying m-values:} -Elliptic_guide_gravity( -l=50, -linxw=5,linyh=5,loutxw=10,loutyh=10, -xwidth=0.1,yheight=0.1, +Elliptic\_guide\_gravity( l=50, linxw=5,linyh=5,loutxw=10,loutyh=10, xwidth=0.1,yheight=0.1, + +\begin{verbatim} R0 = 0.99,Qc=0.0219,alpha=6.07,m=1.0,W=0.003, -mvaluesright=marray,mvaluesleft=marray,mvaluestop=marray,mvaluesbottom=marray -) +\end{verbatim} + +mvaluesright=marray,mvaluesleft=marray,mvaluestop=marray,mvaluesbottom=marray ) -where marray is initialized as -for(iter=0; iter < 50; iter++){ marray[iter] = 2; } -And Declared as -double mValues[50]; -If you are using the array-based coating-specification, you **must** give nSegments a compatible value. -\end{lstlisting} +where marray is initialized as for(iter=0; iter \textless{} 50; iter++)\{ marray[iter] = 2; \} And Declared as double mValues[50]; If you are using the array-based coating-specification, you **must** give nSegments a compatible value. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -97,17 +83,17 @@ \subsection*{Input parameters} dimensionsAt & string & define whether xwidth and yheight sets the size of the opening, minor axis or the end of the guide. & "entrance" \\ option & string & options are 'ellipse' and 'halfEllipse'. Ellipse is defined by both the focal points, while halfEllipse locked the center of the ellipse either the entrance or exit of the guide, and use the focal point of the other end to define the ellipse & "ellipse" \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qc & AA-1 & Critical scattering vector & 0.0218 \\ -alpha & AA & Slope of reflectivity & 6.07 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0218 \\ +alpha & \AA{} & Slope of reflectivity & 6.07 \\ m & 1 & m-value of material for all mirrors, zero means complete absorption. & 2 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ -alpharight & AA & Slope of reflectivity for right vertical mirror & -1 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ +alpharight & \AA{} & Slope of reflectivity for right vertical mirror & -1 \\ mright & 1 & m-value of material for right vertical mirror & -1 \\ -alphaleft & AA & Slope of reflectivity for left vertical mirror & -1 \\ +alphaleft & \AA{} & Slope of reflectivity for left vertical mirror & -1 \\ mleft & 1 & m-value of material for left vertical mirror & -1 \\ -alphatop & AA & Slope of reflectivity for top horizontal mirror, overwrites alpha & -1 \\ +alphatop & \AA{} & Slope of reflectivity for top horizontal mirror, overwrites alpha & -1 \\ mtop & 1 & m-value of material for top horizontal mirror, overwrites m & -1 \\ -alphabottom & AA & Slope of reflectivity for bottom horizontal mirror & -1 \\ +alphabottom & \AA{} & Slope of reflectivity for bottom horizontal mirror & -1 \\ mbottom & 1 & m-value of material for bottom horizontal mirror & -1 \\ verbose & bool & Give extra information about calculations & "on" \\ enableGravity & m & Flag to select propagation with gravity. & 1.0 \\ @@ -123,6 +109,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Elliptic_guide_gravity.comp}{Source code} for \texttt{Elliptic\_guide\_gravity.comp}. + \item Component source code found in file \texttt{Elliptic\_guide\_gravity.comp}. \end{itemize} -\IfFileExists{Elliptic_guide_gravity_static.tex}{\input{Elliptic_guide_gravity_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Elliptic_guide_gravity_static.tex}{\input{optics/Elliptic_guide_gravity_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/FZP_simple.tex b/docs/manuals/mcstas/optics/FZP_simple.tex index 7972d2e10a..81de3586c0 100644 --- a/docs/manuals/mcstas/optics/FZP_simple.tex +++ b/docs/manuals/mcstas/optics/FZP_simple.tex @@ -3,21 +3,13 @@ \section{The \texttt{FZP\_simple} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} A Komar Ravn, and Erik B Knudsen \item \textbf{Origin:} NBI/DTU \item \textbf{Date:} Aug, 2015 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A simple phenomenological thin-object approximation of a Fresnel Zone Plate. -This component was adapted for neutrons from the original component -written for helium scattering. -The focal length of the Zone Plate is determined by the formula: -\[f = 2*r*dr/(lambda)\] -If a diffraction order other than 1 is wanted the focal distance is scaled accordingly. -\end{lstlisting} +A simple phenomenological thin-object approximation of a Fresnel Zone Plate. This component was adapted for neutrons from the original component written for helium scattering. The focal length of the Zone Plate is determined by the formula: \textbackslash{}[f = 2*r*dr/(lambda)\textbackslash{}] If a diffraction order other than 1 is wanted the focal distance is scaled accordingly. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -35,7 +27,7 @@ \subsection*{Input parameters} sigma\_abs & barn & 2200 m/s absorption cross section. & 0 \\ sigma\_inc & barn & Incoherent scattering cross section. & 0 \\ sigma\_coh & barn & Coherent scattering cross section. & 0 \\ -rho & g/cm3 & Density of Zone plate material - used merely for absorption estimation. & 1 \\ +rho & g/cm$^{3}$ & Density of Zone plate material - used merely for absorption estimation. & 1 \\ thickness & m & Thickness of the FZP. Note that the FZP still is modelled as a thin object. The thickness is used in conjunction with the sigma\_x cross sections. & 0 \\ gamma & & Duty cycle of the Zone plate - used merely for absorption estimation. & 0.5 \\ \bottomrule @@ -43,6 +35,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/FZP_simple.comp}{Source code} for \texttt{FZP\_simple.comp}. + \item Component source code found in file \texttt{FZP\_simple.comp}. \end{itemize} -\IfFileExists{FZP_simple_static.tex}{\input{FZP_simple_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/FZP_simple_static.tex}{\input{optics/FZP_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/FermiChopper.tex b/docs/manuals/mcstas/optics/FermiChopper.tex index 9e45e76f67..357cd3cae3 100644 --- a/docs/manuals/mcstas/optics/FermiChopper.tex +++ b/docs/manuals/mcstas/optics/FermiChopper.tex @@ -3,34 +3,23 @@ \section{The \texttt{FermiChopper} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} M. Poehlmann, C. Carbogno, H. Schober, E. Farhi \item \textbf{Origin:} ILL Grenoble / TU Muenchen \item \textbf{Date:} May 2002 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a fermi chopper with optional supermirror coated blades -supermirror facilities may be disabled by setting m = 0, R0=0 -Slit packages are straight. Chopper slits are separated by an infinitely -thin absorbing material. The effective transmission (resulting from fraction -of the transparent material and its transmission) may be specified. -The chopper slit package width may be specified through the total width 'xwidth' -of the full package or the width 'w' of each single slit. The other parameter -is calculated by: xwidth = nslit*w. The slit package may be made curved and use -super-mirror coating. +Models a fermi chopper with optional supermirror coated blades supermirror facilities may be disabled by setting m = 0, R0=0 Slit packages are straight. Chopper slits are separated by an infinitely thin absorbing material. The effective transmission (resulting from fraction of the transparent material and its transmission) may be specified. The chopper slit package width may be specified through the total width 'xwidth' of the full package or the width 'w' of each single slit. The other parameter is calculated by: xwidth = nslit*w. The slit package may be made curved and use super-mirror coating. Example: + +\begin{verbatim} FermiChopper(phase=-50.0, radius=0.04, nu=100, yheight=0.08, w=0.00022475, nslit=200.0, R0=0.0, Qc=0.02176, alpha=2.33, m=0.0, length=0.012, eff=0.95) +\end{verbatim} -%VALIDATION -Apr 2005: extensive external test, most problems solved (cf. 'Bugs') -Validated by: K. Lieutenant, E. Farhi +\%VALIDATION Apr 2005: extensive external test, most problems solved (cf. 'Bugs') Validated by: K. Lieutenant, E. Farhi -limitations: -no absorbing blade width used -\end{lstlisting} +limitations: no absorbing blade width used \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -46,25 +35,25 @@ \subsection*{Input parameters} w & m & width of one chopper slit & 0.00022475 \\ nslit & 1 & number of chopper slits & 200 \\ R0 & 1 & low-angle reflectivity & 0.0 \\ -Qc & AA-1 & critical scattering vector & 0.02176 \\ -alpha & AA & slope of reflectivity & 2.33 \\ +Qc & \AA{}$^{-1}$ & critical scattering vector & 0.02176 \\ +alpha & \AA{} & slope of reflectivity & 2.33 \\ m & 1 & m-value of material. Zero means completely absorbing. & 0.0 \\ -W & AA-1 & width of supermirror cut-off & 2e-3 \\ +W & \AA{}$^{-1}$ & width of supermirror cut-off & 2e-3 \\ length & m & channel length of the Fermi chopper & 0.012 \\ eff & 1 & efficiency = transmission x fraction of transparent material & 0.95 \\ zero\_time & 1 & set time to zero: 0=no, 1=once per half cycle, 2=auto adjust phase & 0 \\ xwidth & m & optional total width of slit package & 0 \\ verbose & 1 & set to 1,2 or 3 gives debugging information & 0 \\ yheight & m & height of slit package & 0.08 \\ -curvature & m-1 & Curvature of slits (1/radius of curvature). & 0 \\ +curvature & m$^{-1}$ & Curvature of slits (1/radius of curvature). & 0 \\ delay & s & sets phase so that transmision is centered on 'delay' & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/FermiChopper.comp}{Source code} for \texttt{FermiChopper.comp}. - \item \textless{}a href="Vitess\_ChopperFermi.html"\textgreater{}Vitess\_ChopperFermi\textless{}/a\textgreater{} component by + \item Component source code found in file \texttt{FermiChopper.comp}. + \item \htmladdnormallink{Vitess\_ChopperFermi}{Vitess\_ChopperFermi.html} component by \item G. Zsigmond, imported from Vitess by K. Lieutenant. \end{itemize} -\IfFileExists{FermiChopper_static.tex}{\input{FermiChopper_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/FermiChopper_static.tex}{\input{optics/FermiChopper_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Filter_gen.tex b/docs/manuals/mcstas/optics/Filter_gen.tex index 312ac55ba1..6cef1ad620 100644 --- a/docs/manuals/mcstas/optics/Filter_gen.tex +++ b/docs/manuals/mcstas/optics/Filter_gen.tex @@ -6,51 +6,25 @@ \section{The \texttt{Filter\_gen} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} Dec, 15th, 2002 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component changes the neutron flux (weight) in order to match -a reference table in a filename. -Typically you may set the neutron flux (source-like), or multiply it -using a transmission table (filter-like). -The component may be placed after a source, in order to e.g. -simulate a real source from a reference table, or used as a filter (BeO) -or as a window (Al). The behaviour of the component is -specified using the 'options' parameter, or from the filename itself (see below) -If the thickness for the transmission data filename D was t0, and a different -thickness t1 would be required, then the resulting transmission is: +This component changes the neutron flux (weight) in order to match a reference table in a filename. Typically you may set the neutron flux (source-like), or multiply it using a transmission table (filter-like). The component may be placed after a source, in order to e.g. simulate a real source from a reference table, or used as a filter (BeO) or as a window (Al). The behaviour of the component is specified using the 'options' parameter, or from the filename itself (see below) If the thickness for the transmission data filename D was t0, and a different thickness t1 would be required, then the resulting transmission is: + +\begin{verbatim} D^(t1/t0). +\end{verbatim} + You may use the 'thickness' and 'scaling' parameter for that purpose. -<b>File format:</b> -This filename may be of any 2-columns free format (k[Angs-1],p), (omega[meV],p) -and (lambda[Angs],p) where p is the weight. The type of the filename may be -written explicitely in the filename, as a comment, or using the 'options' -parameter. -Non mumerical content in filename is treated as comment (e.g. lines starting -with '#' character). -A table rebinning and linear interpolation are performed. +\textbf{File format:} This filename may be of any 2-columns free format (k[\AA{}-1],p), (omega[meV],p) and (lambda[\AA{}],p) where p is the weight. The type of the filename may be written explicitely in the filename, as a comment, or using the 'options' parameter. Non mumerical content in filename is treated as comment (e.g. lines starting with '\#' character). A table rebinning and linear interpolation are performed. -EXAMPLE : in order to simulate a PG filter, using the lib/data/HOPG.trm file -Filter_gen(xwidth=.1 yheight=.1, filename="HOPG.trm") -A Sapphire filter, using the lib/data/Al2O3_sapphire.trm file -Filter_gen(xwidth=.1 yheight=.1, filename="Al2O3_sapphire.trm") -A Berylium filter, using the lib/data/Be.trm file -Filter_gen(xwidth=.1 yheight=.1, filename="Be.trm") -an other possibility to simulate a Be filter is to use the PowderN component: -PowderN(xwidth=.1, yheight=.1, zdepth=.1, reflections="Be.laz", p_inc=1e-4) +EXAMPLE : in order to simulate a PG filter, using the lib/data/HOPG.trm file Filter\_gen(xwidth=.1 yheight=.1, filename="HOPG.trm") A Sapphire filter, using the lib/data/Al2O3\_sapphire.trm file Filter\_gen(xwidth=.1 yheight=.1, filename="Al2O3\_sapphire.trm") A Berylium filter, using the lib/data/Be.trm file Filter\_gen(xwidth=.1 yheight=.1, filename="Be.trm") an other possibility to simulate a Be filter is to use the PowderN component: PowderN(xwidth=.1, yheight=.1, zdepth=.1, reflections="Be.laz", p\_inc=1e-4) -in this filename, the comment line -# wavevector multiply -sets the behaviour of the component. One may as well have used -options="wavevector multiply" -in the component instance parameters. -\end{lstlisting} +in this filename, the comment line \# wavevector multiply sets the behaviour of the component. One may as well have used options="wavevector multiply" in the component instance parameters. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -76,7 +50,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Filter_gen.comp}{Source code} for \texttt{Filter\_gen.comp}. - \item \textless{}a href="../data/HOPG.trm"\textgreater{}HOPG.trm\textless{}/a\textgreater{} filename as an example. + \item Component source code found in file \texttt{Filter\_gen.comp}. + \item \htmladdnormallink{HOPG.trm}{../data/HOPG.trm} filename as an example. \end{itemize} -\IfFileExists{Filter_gen_static.tex}{\input{Filter_gen_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Filter_gen_static.tex}{\input{optics/Filter_gen_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Guide.tex b/docs/manuals/mcstas/optics/Guide.tex index 6d2102f9dd..f8c18845b3 100644 --- a/docs/manuals/mcstas/optics/Guide.tex +++ b/docs/manuals/mcstas/optics/Guide.tex @@ -3,31 +3,25 @@ \section{The \texttt{Guide} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} September 2 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a rectangular guide tube centered on the Z axis. The entrance lies -in the X-Y plane. -For details on the geometry calculation see the description in the McStas -reference manual. -The reflectivity profile may either use an analytical mode (see Component -Manual) or a 2-columns reflectivity free text file with format +Models a rectangular guide tube centered on the Z axis. The entrance lies in the X-Y plane. For details on the geometry calculation see the description in the McStas reference manual. The reflectivity profile may either use an analytical mode (see Component Manual) or a 2-columns reflectivity free text file with format + +\begin{verbatim} [q(Angs-1) R(0-1)]. +\end{verbatim} +\begin{verbatim} Example: Guide(w1=0.1, h1=0.1, w2=0.1, h2=0.1, l=2.0, R0=0.99, Qc=0.021, alpha=6.07, m=2, W=0.003 +\end{verbatim} -%VALIDATION -May 2005: extensive internal test, no bugs found -Validated by: K. Lieutenant +\%VALIDATION May 2005: extensive internal test, no bugs found Validated by: K. Lieutenant -%BUGS -This component does not work with gravitation on. Use component Guide_gravity then. -\end{lstlisting} +\%BUGS This component does not work with gravitation on. Use component Guide\_gravity then. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -37,22 +31,22 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -reflect & str & Reflectivity file name. Format \textless{}q(Angs-1) R(0-1)\textgreater{} & 0 \\ +reflect & str & Reflectivity file name. Format \textless{}q(\AA{}-1) R(0-1)\textgreater{} & 0 \\ \textbf{w1} & m & Width at the guide entry & \\ \textbf{h1} & m & Height at the guide entry & \\ w2 & m & Width at the guide exit & 0 \\ h2 & m & Height at the guide exit & 0 \\ \textbf{l} & m & length of guide & \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qc & AA-1 & Critical scattering vector & 0.0219 \\ -alpha & AA & Slope of reflectivity & 6.07 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0219 \\ +alpha & \AA{} & Slope of reflectivity & 6.07 \\ m & 1 & m-value of material. Zero means completely absorbing. glass/SiO2 Si Ni Ni58 supermirror Be Diamond m= 0.65 0.47 1 1.18 2-6 1.01 1.12 & 2 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Guide.comp}{Source code} for \texttt{Guide.comp}. + \item Component source code found in file \texttt{Guide.comp}. \end{itemize} -\IfFileExists{Guide_static.tex}{\input{Guide_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Guide_static.tex}{\input{optics/Guide_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Guide_anyshape.tex b/docs/manuals/mcstas/optics/Guide_anyshape.tex index 7f1921a9bd..db59597be6 100644 --- a/docs/manuals/mcstas/optics/Guide_anyshape.tex +++ b/docs/manuals/mcstas/optics/Guide_anyshape.tex @@ -3,35 +3,17 @@ \section{The \texttt{Guide\_anyshape} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Emmanuel Farhi \item \textbf{Origin:} ILL \item \textbf{Date:} August 4th 2010 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This is a reflecting object component. Its shape is defined from an OFF file, -given with its file name. The object size is set as given from the file, where -dimensions should be in meters. The bounding box may be re-scaled by specifying -xwidth,yheight,zdepth parameters. The object may optionally be centered when -using 'center=1'. +This is a reflecting object component. Its shape is defined from an OFF file, given with its file name. The object size is set as given from the file, where dimensions should be in meters. The bounding box may be re-scaled by specifying xwidth,yheight,zdepth parameters. The object may optionally be centered when using 'center=1'. -The reflectivity is specified either from the usual parametric description -R0,Qc,alpha,W,m, or from a reflectivity file 'reflect' with a 2 column -format [q(Angs-1) R(0-1)]. +The reflectivity is specified either from the usual parametric description R0,Qc,alpha,W,m, or from a reflectivity file 'reflect' with a 2 column format [q(\AA{}-1) R(0-1)]. -The complex OFF/PLY geometry option handles any closed non-convex polyhedra. -It supports the OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using: -qhull < coordinates.xyz Qx Qv Tv o > geomview.off -or -powercrust coordinates.xyz -and viewed with geomview or java -jar jroff.jar (see below). -The default size of the object depends of the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. -PLY geometry files are also supported. -\end{lstlisting} +The complex OFF/PLY geometry option handles any closed non-convex polyhedra. It supports the OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. PLY geometry files are also supported. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -47,21 +29,21 @@ \subsection*{Input parameters} center & 1 & When set to 1, the object will be centered w.r.t. the local coordinate frame & 0 \\ transmit & 1 & When true, non reflected neutrons are transmitted through the surfaces, instead of being absorbed. No material absorption is taken into account though & 0 \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qc & AA-1 & Critical scattering vector & 0.0219 \\ -alpha & AA & Slope of reflectivity & 3 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0219 \\ +alpha & \AA{} & Slope of reflectivity & 3 \\ m & 1 & m-value of material. Zero means completely absorbing. & 2 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ -reflect & q(Angs-1) R(0-1) & (str) Reflectivity file name. Format & 0 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ +reflect & q(\AA{}$^{-1}$ R(0-1) & (str) Reflectivity file name. Format & 0 \\ geometry & str & Name of the OFF/PLY file describing the guide geometry & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Guide_anyshape.comp}{Source code} for \texttt{Guide\_anyshape.comp}. - \item \textless{}a href="http://www.geomview.org"\textgreater{}Geomview and Object File Format (OFF)\textless{}/a\textgreater{} - \item Java version of Geomview (display only) \textless{}a href="http://www.holmes3d.net/graphics/roffview/"\textgreater{}jroff.jar\textless{}/a\textgreater{} - \item \textless{}a href="http://qhull.org"\textgreater{}qhull\textless{}/a\textgreater{} - \item \textless{}a href="http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html"\textgreater{}powercrust\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Guide\_anyshape.comp}. + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} + \item Java version of Geomview (display only) \htmladdnormallink{jroff.jar}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{qhull}{http://qhull.org} + \item \htmladdnormallink{powercrust}{http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} \end{itemize} -\IfFileExists{Guide_anyshape_static.tex}{\input{Guide_anyshape_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Guide_anyshape_static.tex}{\input{optics/Guide_anyshape_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Guide_channeled.tex b/docs/manuals/mcstas/optics/Guide_channeled.tex index 654175dbc7..b5ebcd57a2 100644 --- a/docs/manuals/mcstas/optics/Guide_channeled.tex +++ b/docs/manuals/mcstas/optics/Guide_channeled.tex @@ -3,34 +3,24 @@ \section{The \texttt{Guide\_channeled} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Christian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a rectangular guide tube centered on the Z axis. The entrance lies -in the X-Y plane. -The guide may be tapered, and may have vertical subdivisions (used for -bender devices). +Models a rectangular guide tube centered on the Z axis. The entrance lies in the X-Y plane. The guide may be tapered, and may have vertical subdivisions (used for bender devices). -There is a special rotating mode in order to approximate a Fermi Chopper -behaviour, in the case the neutron trajectory is nearly linear inside the -chopper slits, i.e. the neutrons are fast w/r/ to the chopper speed. -Slits are straight, but may be super-mirror coated. In this case, the -component is NOT centered, but located at its entry window. It should then -be shifted by -l/2. +There is a special rotating mode in order to approximate a Fermi Chopper behaviour, in the case the neutron trajectory is nearly linear inside the chopper slits, i.e. the neutrons are fast w/r/ to the chopper speed. Slits are straight, but may be super-mirror coated. In this case, the component is NOT centered, but located at its entry window. It should then be shifted by -l/2. -Example: Guide_channeled(w1=0.1, h1=0.1, w2=0.1, h2=0.1, l=2.0, +Example: Guide\_channeled(w1=0.1, h1=0.1, w2=0.1, h2=0.1, l=2.0, + +\begin{verbatim} R0=0.99, Qcx=0.0219, Qcy=0.0219, alphax=6.07, alphay=6.07, W=0.003, nslit=1, d=0.0005, mx=1, my=1) +\end{verbatim} -%BUGS -This component does not work with gravitation on. Use Guide_gravity. -This component does not work in multichannel focusing geometry. -\end{lstlisting} +\%BUGS This component does not work with gravitation on. Use Guide\_gravity. This component does not work in multichannel focusing geometry. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -46,16 +36,16 @@ \subsection*{Input parameters} h2 & m & Height at the guide exit & 0 \\ \textbf{l} & m & Length of guide & \\ R0 & 1 & Low-angle reflectivity & 0.995 \\ -Qc & AA-1 & Critical scattering vector & 0 \\ -alpha & AA & Slope of reflectivity & 0 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0 \\ +alpha & \AA{} & Slope of reflectivity & 0 \\ m & 1 & m-value of material. Zero means completely absorbing. & 0 \\ nslit & 1 & Number of channels in the guide (\textgreater{}= 1) & 1 \\ d & m & Thickness of subdividing absorbing walls & 0.0005 \\ -Qcx & AA-1 & Critical scattering vector for left and right vertical mirrors in each channel & 0.0218 \\ -Qcy & AA-1 & Critical scattering vector for top and bottom mirrors & 0.0218 \\ -alphax & AA & Slope of reflectivity for left and right vertical mirrors in each channel & 4.38 \\ -alphay & AA & Slope of reflectivity for top and bottom mirrors & 4.38 \\ -W & AA-1 & Width of supermirror cut-off for all mirrors & 0.003 \\ +Qcx & \AA{}$^{-1}$ & Critical scattering vector for left and right vertical mirrors in each channel & 0.0218 \\ +Qcy & \AA{}$^{-1}$ & Critical scattering vector for top and bottom mirrors & 0.0218 \\ +alphax & \AA{} & Slope of reflectivity for left and right vertical mirrors in each channel & 4.38 \\ +alphay & \AA{} & Slope of reflectivity for top and bottom mirrors & 4.38 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off for all mirrors & 0.003 \\ mx & 1 & m-value of material for left and right vertical mirrors in each channel. Zero means completely absorbing. & 1 \\ my & 1 & m-value of material for top and bottom mirrors. Zero means completely absorbing. & 1 \\ nu & Hz & Rotation frequency (round/s) for Fermi Chopper approximation & 0 \\ @@ -65,6 +55,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Guide_channeled.comp}{Source code} for \texttt{Guide\_channeled.comp}. + \item Component source code found in file \texttt{Guide\_channeled.comp}. \end{itemize} -\IfFileExists{Guide_channeled_static.tex}{\input{Guide_channeled_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Guide_channeled_static.tex}{\input{optics/Guide_channeled_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Guide_gravity.tex b/docs/manuals/mcstas/optics/Guide_gravity.tex index ca6affd427..3723196c6c 100644 --- a/docs/manuals/mcstas/optics/Guide_gravity.tex +++ b/docs/manuals/mcstas/optics/Guide_gravity.tex @@ -4,46 +4,27 @@ \section{The \texttt{Guide\_gravity} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:farhi@ill.fr"\textgreater{}Emmanuel Farhi\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL (France)\textless{}/a\textgreater{}. \item \textbf{Date:} Aug 03 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a rectangular straight guide tube centered on the Z axis, with -gravitation handling. The entrance lies in the X-Y plane. -The guide can be channeled (nslit,d,nhslit parameters). The guide coating -specifications may be entered via different ways (global, or for -each wall m-value). +Models a rectangular straight guide tube centered on the Z axis, with gravitation handling. The entrance lies in the X-Y plane. The guide can be channeled (nslit,d,nhslit parameters). The guide coating specifications may be entered via different ways (global, or for each wall m-value). -Waviness (random) may be specified either globally or for each mirror type. -Side chamfers (due to substrate processing) may be specified the same way. -In order to model a realistic straight guide assembly, a long guide of -length 'l' may be splitted into 'nelements' between which chamfers/gaps are -positioned. +Waviness (random) may be specified either globally or for each mirror type. Side chamfers (due to substrate processing) may be specified the same way. In order to model a realistic straight guide assembly, a long guide of length 'l' may be splitted into 'nelements' between which chamfers/gaps are positioned. -The reflectivity may be specified either using an analytical mode (see -Component manual) or as a text file in free format, with 1st -column as q[Angs-1] and 2nd column as the reflectivity R in [0-1]. -For details on the geometry calculation see the description in the McStas -component manual. +The reflectivity may be specified either using an analytical mode (see Component manual) or as a text file in free format, with 1st column as q[\AA{}-1] and 2nd column as the reflectivity R in [0-1]. For details on the geometry calculation see the description in the McStas component manual. -There is a special rotating mode in order to approximate a Fermi Chopper -behaviour, in the case the neutron trajectory is nearly linear inside the -chopper slits, i.e. the neutrons are fast w/r/ to the chopper speed. -Slits are straight, but may be super-mirror coated. In this case, the -component is NOT centered, but located at its entry window. It should then -be shifted by -l/2. +There is a special rotating mode in order to approximate a Fermi Chopper behaviour, in the case the neutron trajectory is nearly linear inside the chopper slits, i.e. the neutrons are fast w/r/ to the chopper speed. Slits are straight, but may be super-mirror coated. In this case, the component is NOT centered, but located at its entry window. It should then be shifted by -l/2. -Example: Guide_gravity(w1=0.1, h1=0.1, w2=0.1, h2=0.1, l=12, +Example: Guide\_gravity(w1=0.1, h1=0.1, w2=0.1, h2=0.1, l=12, + +\begin{verbatim} R0=0.99, Qc=0.0219, alpha=6.07, m=1.0, W=0.003) +\end{verbatim} -%VALIDATION -May 2005: extensive internal test, all problems solved -Validated by: nslit. Lieutenant -\end{lstlisting} +\%VALIDATION May 2005: extensive internal test, all problems solved Validated by: nslit. Lieutenant \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -59,10 +40,10 @@ \subsection*{Input parameters} h2 & m & Height at the guide exit. If 0, use h1. & 0 \\ \textbf{l} & m & length of guide & \\ R0 & 1 & Low-angle reflectivity & 0.995 \\ -Qc & AA-1 & Critical scattering vector & 0.0218 \\ -alpha & AA & Slope of reflectivity & 4.38 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0218 \\ +alpha & \AA{} & Slope of reflectivity & 4.38 \\ m & 1 & m-value of material. Zero means completely absorbing. m=0.65 glass/SiO2 Si Ni Ni58 supermirror Be Diamond m= 0.65 0.47 1 1.18 2-6 1.01 1.12 for glass/SiO2, m=1 for Ni, 1.2 for Ni58, m=2-6 for supermirror. m=0.47 for Si & 1.0 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ nslit & 1 & Number of vertical channels in the guide (\textgreater{}= 1) (nslit-1 vertical dividing walls). & 1 \\ d & m & Thickness of subdividing walls & 0.0005 \\ mleft & 1 & m-value of material for left. vert. mirror & -1 \\ @@ -70,7 +51,7 @@ \subsection*{Input parameters} mtop & 1 & m-value of material for top. horz. mirror & -1 \\ mbottom & 1 & m-value of material for bottom. horz. mirror & -1 \\ nhslit & 1 & Number of horizontal channels in the guide (\textgreater{}= 1). (nhslit-1 horizontal dividing walls). this enables to have nslit*nhslit rectangular channels & 1 \\ -G & m/s2 & Gravitation norm. 0 value disables G effects. & 0 \\ +G & m/s$^{2}$ & Gravitation norm. 0 value disables G effects. & 0 \\ aleft & 1 & alpha-value of left vert. mirror & -1 \\ aright & 1 & alpha-value of right vert. mirror & -1 \\ atop & 1 & alpha-value of top horz. mirror & -1 \\ @@ -86,12 +67,12 @@ \subsection*{Input parameters} nelements & 1 & Number of sections in the guide (length l/nelements). & 1 \\ nu & Hz & Rotation frequency (round/s) for Fermi Chopper approximation & 0 \\ phase & deg & Phase shift for the Fermi Chopper approximation & 0 \\ -reflect & str & Reflectivity file name. Format \textless{}q(Angs-1) R(0-1)\textgreater{} & "NULL" \\ +reflect & str & Reflectivity file name. Format \textless{}q(\AA{}-1) R(0-1)\textgreater{} & "NULL" \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Guide_gravity.comp}{Source code} for \texttt{Guide\_gravity.comp}. + \item Component source code found in file \texttt{Guide\_gravity.comp}. \end{itemize} -\IfFileExists{Guide_gravity_static.tex}{\input{Guide_gravity_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Guide_gravity_static.tex}{\input{optics/Guide_gravity_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Guide_simple.tex b/docs/manuals/mcstas/optics/Guide_simple.tex index fc4704216c..94c372aa26 100644 --- a/docs/manuals/mcstas/optics/Guide_simple.tex +++ b/docs/manuals/mcstas/optics/Guide_simple.tex @@ -3,31 +3,25 @@ \section{The \texttt{Guide\_simple} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} September 2 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a rectangular guide tube centered on the Z axis. The entrance lies -in the X-Y plane. -For details on the geometry calculation see the description in the McStas -reference manual. -The reflectivity profile may either use an analytical mode (see Component -Manual) or a 2-columns reflectivity free text file with format +Models a rectangular guide tube centered on the Z axis. The entrance lies in the X-Y plane. For details on the geometry calculation see the description in the McStas reference manual. The reflectivity profile may either use an analytical mode (see Component Manual) or a 2-columns reflectivity free text file with format + +\begin{verbatim} [q(Angs-1) R(0-1)]. +\end{verbatim} +\begin{verbatim} Example: Guide(w1=0.1, h1=0.1, w2=0.1, h2=0.1, l=2.0, R0=0.99, Qc=0.021, alpha=6.07, m=2, W=0.003 +\end{verbatim} -%VALIDATION -May 2005: extensive internal test, no bugs found -Validated by: K. Lieutenant +\%VALIDATION May 2005: extensive internal test, no bugs found Validated by: K. Lieutenant -%BUGS -This component does not work with gravitation on. Use component Guide_gravity then. -\end{lstlisting} +\%BUGS This component does not work with gravitation on. Use component Guide\_gravity then. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -43,15 +37,15 @@ \subsection*{Input parameters} h2 & m & Height at the guide exit & 0 \\ \textbf{l} & m & length of guide & \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qc & AA-1 & Critical scattering vector & 0.0219 \\ -alpha & AA & Slope of reflectivity & 6.07 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0219 \\ +alpha & \AA{} & Slope of reflectivity & 6.07 \\ m & 1 & m-value of material. Zero means completely absorbing. glass/SiO2 Si Ni Ni58 supermirror Be Diamond m= 0.65 0.47 1 1.18 2-6 1.01 1.12 & 2 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Guide_simple.comp}{Source code} for \texttt{Guide\_simple.comp}. + \item Component source code found in file \texttt{Guide\_simple.comp}. \end{itemize} -\IfFileExists{Guide_simple_static.tex}{\input{Guide_simple_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Guide_simple_static.tex}{\input{optics/Guide_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Guide_tapering.tex b/docs/manuals/mcstas/optics/Guide_tapering.tex index a6cbbd832a..d6caf2e031 100644 --- a/docs/manuals/mcstas/optics/Guide_tapering.tex +++ b/docs/manuals/mcstas/optics/Guide_tapering.tex @@ -3,34 +3,21 @@ \section{The \texttt{Guide\_tapering} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Uwe Filges \item \textbf{Origin:} PSI \item \textbf{Date:} 22/10/2003 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a rectangular guide tube centered on the Z axis. The entrance lies -in the X-Y plane. -The guide may be tapered. +Models a rectangular guide tube centered on the Z axis. The entrance lies in the X-Y plane. The guide may be tapered. -The component includes a feature to read in self-defined functions for -guide tapering. Under the parameter 'option' the KEYWORD 'file=' offers -the possibility to read in parameters from an ASC-file. The file structure -is shown below in the example. It is important to know that the first -3 lines will be interpreted as comments. -Afterwards the dimension of each guide segment must be defined. The -length of each segment is constant l(i)=l/segments . The number of -segments is defined through the number of lines minus the first 3 -lines taken from the Input-File. -The guide can be made curved both horizontally and vertically (not shown in 3d -view), and m-coating, when set negative, is varied in 1/width. +The component includes a feature to read in self-defined functions for guide tapering. Under the parameter 'option' the KEYWORD 'file=' offers the possibility to read in parameters from an ASC-file. The file structure is shown below in the example. It is important to know that the first 3 lines will be interpreted as comments. Afterwards the dimension of each guide segment must be defined. The length of each segment is constant l(i)=l/segments . The number of segments is defined through the number of lines minus the first 3 lines taken from the Input-File. The guide can be made curved both horizontally and vertically (not shown in 3d view), and m-coating, when set negative, is varied in 1/width. Example Input-File: -c Guide_tapering.comp -c i = 0 - 199 segments +c Guide\_tapering.comp c i = 0 - 199 segments + +\begin{verbatim} c h1(i) h2(i) w1(i) w2(i) 0.120000 0.119850 0.020000 0.020000 0.119850 0.119700 0.020000 0.020000 @@ -38,15 +25,15 @@ \subsection*{Description} 0.119550 0.119400 0.020000 0.020000 0.119400 0.119250 0.020000 0.020000 0.119250 0.119100 0.020000 0.020000 +\end{verbatim} + ... -Example1: Guide_tapering(w1=0.1, h1=0.18, linw=0.1, loutw=0.1, linh=0.1, louth=0.1, l=1.5, option="elliptical", R0=0.99, Qcx=0.021, Qcy=0.021, alphax=6.07, alphay=6.07, W=0.003, mx=1, my=1, segno=800) +Example1: Guide\_tapering(w1=0.1, h1=0.18, linw=0.1, loutw=0.1, linh=0.1, louth=0.1, l=1.5, option="elliptical", R0=0.99, Qcx=0.021, Qcy=0.021, alphax=6.07, alphay=6.07, W=0.003, mx=1, my=1, segno=800) -Example2: Guide_tapering(w1=0, h1=0, linw=0, loutw=0, linh=0, louth=0, l=1.5, option="file=ownfunction.txt", R0=0.99, Qcx=0.021, Qcy=0.021, alphax=6.07, alphay=6.07, W=0.003, mx=1, my=1) +Example2: Guide\_tapering(w1=0, h1=0, linw=0, loutw=0, linh=0, louth=0, l=1.5, option="file=ownfunction.txt", R0=0.99, Qcx=0.021, Qcy=0.021, alphax=6.07, alphay=6.07, W=0.003, mx=1, my=1) -%BUGS -This component does not work with gravitation on. Use component Guide_gravity then. -\end{lstlisting} +\%BUGS This component does not work with gravitation on. Use component Guide\_gravity then. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -65,11 +52,11 @@ \subsection*{Input parameters} linh & m & distance from 1st focal point to real guide entry - top and bottom vertical mirrors & 0 \\ louth & m & distance from real guide exit to 2nd focal point - top and bottom vertical mirrors & 0 \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qcx & AA-1 & Critical scattering vector for left and right vertical mirrors in each channel & 0.021 \\ -Qcy & AA-1 & Critical scattering vector for top and bottom mirrors & 0.021 \\ -alphax & AA & Slope of reflectivity for left and right vertical mirrors in each channel & 6.07 \\ -alphay & AA & Slope of reflectivity for top and bottom mirrors & 6.07 \\ -W & AA-1 & Width of supermirror cut-off for all mirrors & 0.003 \\ +Qcx & \AA{}$^{-1}$ & Critical scattering vector for left and right vertical mirrors in each channel & 0.021 \\ +Qcy & \AA{}$^{-1}$ & Critical scattering vector for top and bottom mirrors & 0.021 \\ +alphax & \AA{} & Slope of reflectivity for left and right vertical mirrors in each channel & 6.07 \\ +alphay & \AA{} & Slope of reflectivity for top and bottom mirrors & 6.07 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off for all mirrors & 0.003 \\ mx & 1 & m-value of material for left and right vertical mirrors in each channel. Zero means completely absorbing. Negative value will adapt coating as e.g. m=mx*w1/w & 1 \\ my & 1 & m-value of material for top and bottom mirrors. Zero means completely absorbing. Negative value will adapt coating as e.g. m=my*h1/h & 1 \\ segno & 1 & number of segments (z-axis) for cutting the tube & 800 \\ @@ -80,6 +67,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Guide_tapering.comp}{Source code} for \texttt{Guide\_tapering.comp}. + \item Component source code found in file \texttt{Guide\_tapering.comp}. \end{itemize} -\IfFileExists{Guide_tapering_static.tex}{\input{Guide_tapering_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Guide_tapering_static.tex}{\input{optics/Guide_tapering_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Guide_wavy.tex b/docs/manuals/mcstas/optics/Guide_wavy.tex index c9b12f3212..708eefe0f1 100644 --- a/docs/manuals/mcstas/optics/Guide_wavy.tex +++ b/docs/manuals/mcstas/optics/Guide_wavy.tex @@ -3,24 +3,17 @@ \section{The \texttt{Guide\_wavy} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a rectangular guide tube centered on the Z axis. The entrance lies -in the X-Y plane. -For details on the geometry calculation see the description in the McStas -reference manual. +Models a rectangular guide tube centered on the Z axis. The entrance lies in the X-Y plane. For details on the geometry calculation see the description in the McStas reference manual. Example: m=2 Qc=0.0218 (nat. Ni) W=1/300 alpha=4.38 R0=0.995 (given by Daniel Clemens, PSI) -%BUGS -This component does not work with gravitation on. Use component Guide_gravity then. -\end{lstlisting} +\%BUGS This component does not work with gravitation on. Use component Guide\_gravity then. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,22 +29,22 @@ \subsection*{Input parameters} h2 & m & Height at the guide exit & 0 \\ \textbf{l} & m & length of guide & \\ R0 & 1 & Low-angle reflectivity & 0.995 \\ -Qc & AA-1 & Critical scattering vector & 0.0218 \\ -alpha & AA & Slope of reflectivity & 0 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0218 \\ +alpha & \AA{} & Slope of reflectivity & 0 \\ m & 1 & m-value of material. Zero means completely absorbing. & 0 \\ -W & AA-1 & Width of supermirror cut-off for all mirrors & 0 \\ -alpha1 & AA & Slope of reflectivity left & 4.38 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off for all mirrors & 0 \\ +alpha1 & \AA{} & Slope of reflectivity left & 4.38 \\ m1 & 1 & m-value of material, left & 2 \\ -W1 & AA-1 & Width of supermirror cut-off left & 0.003 \\ -alpha2 & AA & Slope of reflectivity right & 4.38 \\ +W1 & \AA{}$^{-1}$ & Width of supermirror cut-off left & 0.003 \\ +alpha2 & \AA{} & Slope of reflectivity right & 4.38 \\ m2 & 1 & m-value of material, right. & 2 \\ -W2 & AA-1 & Width of supermirror cut-off right & 0.003 \\ -alpha3 & AA & Slope of reflectivity top & 4.38 \\ +W2 & \AA{}$^{-1}$ & Width of supermirror cut-off right & 0.003 \\ +alpha3 & \AA{} & Slope of reflectivity top & 4.38 \\ m3 & 1 & m-value of material, top. & 2 \\ -W3 & AA-1 & Width of supermirror cut-off top & 0.003 \\ -alpha4 & AA & Slope of reflectivity bottom & 4.38 \\ +W3 & \AA{}$^{-1}$ & Width of supermirror cut-off top & 0.003 \\ +alpha4 & \AA{} & Slope of reflectivity bottom & 4.38 \\ m4 & 1 & m-value of material, bottom. & 2 \\ -W4 & AA-1 & Width of supermirror cut-off bottom & 0.003 \\ +W4 & \AA{}$^{-1}$ & Width of supermirror cut-off bottom & 0.003 \\ wavy\_z & deg & Waviness in the z-(flight-)direction & 0 \\ wavy\_xy & deg & Waviness in the transverse direction & 0 \\ \bottomrule @@ -59,6 +52,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Guide_wavy.comp}{Source code} for \texttt{Guide\_wavy.comp}. + \item Component source code found in file \texttt{Guide\_wavy.comp}. \end{itemize} -\IfFileExists{Guide_wavy_static.tex}{\input{Guide_wavy_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Guide_wavy_static.tex}{\input{optics/Guide_wavy_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/He3_cell.tex b/docs/manuals/mcstas/optics/He3_cell.tex index 2e4828e555..f9109aa063 100644 --- a/docs/manuals/mcstas/optics/He3_cell.tex +++ b/docs/manuals/mcstas/optics/He3_cell.tex @@ -5,23 +5,17 @@ \section{The \texttt{He3\_cell} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Trefor Roberts \& Erik B Knudsen \item \textbf{Origin:} ILL/DTU Physics \item \textbf{Date:} March 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Simple polarised 3He neutron spin filter cell, defaults to a cylindrical geometry but may be -used with a sphere or box geometry also. -The glass container for the cell is not included in the model. +Simple polarised 3He neutron spin filter cell, defaults to a cylindrical geometry but may be used with a sphere or box geometry also. The glass container for the cell is not included in the model. -This component has been validated against: -Batz, M, Baessler, S, Heil, W, et al., J Res Natl Inst Stand Technol. 2005;110(3):293–298. +This component has been validated against: Batz, M, Baessler, S, Heil, W, et al., J Res Natl Inst Stand Technol. 2005;110(3):293–298. -Example: He3_cell(radius=0.1,length=.2,pressure=3,p3he=0.7,bx=0,by=1e-3,bz=0) -\end{lstlisting} +Example: He3\_cell(radius=0.1,length=.2,pressure=3,p3he=0.7,bx=0,by=1e-3,bz=0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -45,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/He3_cell.comp}{Source code} for \texttt{He3\_cell.comp}. + \item Component source code found in file \texttt{He3\_cell.comp}. \end{itemize} -\IfFileExists{He3_cell_static.tex}{\input{He3_cell_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/He3_cell_static.tex}{\input{optics/He3_cell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Mask.tex b/docs/manuals/mcstas/optics/Mask.tex index bd12090fdc..67fdff7960 100644 --- a/docs/manuals/mcstas/optics/Mask.tex +++ b/docs/manuals/mcstas/optics/Mask.tex @@ -3,36 +3,27 @@ \section{The \texttt{Mask} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik Knudsen \item \textbf{Origin:} DTU Physics \item \textbf{Date:} March 2014 \end{itemize} \subsection*{Description} -\begin{lstlisting} -The Mask component takes an image as input either as an standard image file in png or pnm format, or as an ascii file (see below for format), -and uses the image as a mask. For instance as a manner of measuring resolution for imaging applications. -If the image is supplied as a png or pnm file, they interpretation of the pixels varies depending on the file. If the image is grayscale the pixel values are directly mapped -to opacity (or transparency if invert is set) values in the range [0..1]. If the image has RGB channels the R channel is considered most significant, the B channel least significant. -The resulting number, e.g. R*255^2 + G*255 + B, is then mapped to a real valued opacity. -Additionally png images may have an alpha channel - which is then considered the least significant channel. Palette mapped pngs are as of yet _not_ supported. -A regular ascii file may be supplied - in which case the file is like the one below -#any initial line starting with a hash is silently ignored +The Mask component takes an image as input either as an standard image file in png or pnm format, or as an ascii file (see below for format), and uses the image as a mask. For instance as a manner of measuring resolution for imaging applications. If the image is supplied as a png or pnm file, they interpretation of the pixels varies depending on the file. If the image is grayscale the pixel values are directly mapped to opacity (or transparency if invert is set) values in the range [0..1]. If the image has RGB channels the R channel is considered most significant, the B channel least significant. The resulting number, e.g. R*255\textasciicircum{}2 + G*255 + B, is then mapped to a real valued opacity. Additionally png images may have an alpha channel - which is then considered the least significant channel. Palette mapped pngs are as of yet \_not\_ supported. A regular ascii file may be supplied - in which case the file is like the one below \#any initial line starting with a hash is silently ignored + +\begin{verbatim} 0.0 1.0 0.0 1.0 0.0 0.5 0.0 0.5 0.0 0.5 0.0 0.25 0.0 0.25 0.0 0.75 0.0 0.75 0.0 0.75 1.0 0.0 1.0 0.0 1.0 +\end{verbatim} ...which defines a 5x5 mask with a kind of checkerboard pattern- -N.b. If you want to use the png-option of the component you must have libpng installed _and_ link your compiled instrument to it. Assuming libpng is installed you may do this -by adding "-DUSE_PNG=1 -lpng" to 1) the MCXTRACE_CFLAGS environment variable or 2) to the compiler flags textbox in the GUI. Open File->Configuration and edit the textbox. +N.b. If you want to use the png-option of the component you must have libpng installed \_and\_ link your compiled instrument to it. Assuming libpng is installed you may do this by adding "-DUSE\_PNG=1 -lpng" to 1) the MCXTRACE\_CFLAGS environment variable or 2) to the compiler flags textbox in the GUI. Open File-\textgreater{}Configuration and edit the textbox. -The virtual option of the Mask, is intended as a help to use a png-image as a grayscale distribution. If the virtual flag is set, rays are porpagated to the mask plane -and the pixel value at the intersection point is read, but the rays reamin unaffected. By extracting the output parameter masking it can subsequently be used. -\end{lstlisting} +The virtual option of the Mask, is intended as a help to use a png-image as a grayscale distribution. If the virtual flag is set, rays are porpagated to the mask plane and the pixel value at the intersection point is read, but the rays reamin unaffected. By extracting the output parameter masking it can subsequently be used. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -52,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Mask.comp}{Source code} for \texttt{Mask.comp}. + \item Component source code found in file \texttt{Mask.comp}. \end{itemize} -\IfFileExists{Mask_static.tex}{\input{Mask_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Mask_static.tex}{\input{optics/Mask_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Mirror.tex b/docs/manuals/mcstas/optics/Mirror.tex index ec291ff2bd..f3ee3288eb 100644 --- a/docs/manuals/mcstas/optics/Mirror.tex +++ b/docs/manuals/mcstas/optics/Mirror.tex @@ -3,30 +3,15 @@ \section{The \texttt{Mirror} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} August 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Single mirror plate (used to build guides in compound components). -The component Mirror models a single rectangular neutron mirror plate. -It can be used as a sample component or to e.g. assemble a complete neutron -guide by putting multiple mirror components at appropriate locations and -orientations in the instrument definition, much like a real guide is build -from individual mirrors. -Additionally, it may be centered in order to be used as a sample or -monochromator plate, else it starts from AT position. -Reflectivity is either defined by an analytical model (see Component Manual) -or from a two-columns file with q [Angs-1] as first and R [0-1] as second. -In the local coordinate system, the mirror lies in the first quadrant of the -x-y plane, with one corner at (0, 0, 0). Plane is thus perpendicular to the -incoming beam, and should usually be rotated. +Single mirror plate (used to build guides in compound components). The component Mirror models a single rectangular neutron mirror plate. It can be used as a sample component or to e.g. assemble a complete neutron guide by putting multiple mirror components at appropriate locations and orientations in the instrument definition, much like a real guide is build from individual mirrors. Additionally, it may be centered in order to be used as a sample or monochromator plate, else it starts from AT position. Reflectivity is either defined by an analytical model (see Component Manual) or from a two-columns file with q [\AA{}-1] as first and R [0-1] as second. In the local coordinate system, the mirror lies in the first quadrant of the x-y plane, with one corner at (0, 0, 0). Plane is thus perpendicular to the incoming beam, and should usually be rotated. Example: Mirror(xwidth=.1, yheight=.1,R0=0.99,Qc=0.021,alpha=6.1,m=2,W=0.003) -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,14 +21,14 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -reflect & str & Name of reflectivity file. Format q(Angs-1) R(0-1) & 0 \\ +reflect & str & Name of reflectivity file. Format q(\AA{}-1) R(0-1) & 0 \\ \textbf{xwidth} & m & width of mirror plate & \\ \textbf{yheight} & m & height of mirror plate & \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qc & AA-1 & Critical scattering vector & 0.021 \\ -alpha & AA & Slope of reflectivity & 6.07 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.021 \\ +alpha & \AA{} & Slope of reflectivity & 6.07 \\ m & 1 & m-value of material. Zero means completely absorbing. & 2 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ center & 1 & if true (1), the Mirror is centered arount AT position. & 0 \\ transmit & 1 & When true, non reflected neutrons are transmitted through the mirror, instead of being absorbed. & 0 \\ \bottomrule @@ -51,6 +36,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Mirror.comp}{Source code} for \texttt{Mirror.comp}. + \item Component source code found in file \texttt{Mirror.comp}. \end{itemize} -\IfFileExists{Mirror_static.tex}{\input{Mirror_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Mirror_static.tex}{\input{optics/Mirror_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Monochromator_curved.tex b/docs/manuals/mcstas/optics/Monochromator_curved.tex index b2ff10bbde..e6c82dd228 100644 --- a/docs/manuals/mcstas/optics/Monochromator_curved.tex +++ b/docs/manuals/mcstas/optics/Monochromator_curved.tex @@ -3,38 +3,28 @@ \section{The \texttt{Monochromator\_curved} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Emmanuel Farhi, Kim, Lefmann, Peter Link \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} Aug. 24th 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Double bent infinitely thin mosaic crystal, useful as a monochromator or -analyzer. which uses a small-mosaicity approximation and taking into account -higher order scattering. The mosaic is anisotropic gaussian, with different -FWHMs in the Y and Z directions. The scattering vector is perpendicular to the -surface. For an unrotated monochromator component, the crystal plane lies in -the y-z plane (ie. parallel to the beam). The component works in reflection, but -also transmits the non-diffracted beam. Reflectivity and transmission files may -be used. The slabs are positioned in the vertical plane (not on a -cylinder/sphere), and are rotated according to the curvature radius. -When curvatures are set to 0, the monochromator is flat. -The curvatures approximation for parallel beam focusing to distance L, with -monochromator rotation angle A1 are: -RV = 2*L*sin(DEG2RAD*A1); -RH = 2*L/sin(DEG2RAD*A1); +Double bent infinitely thin mosaic crystal, useful as a monochromator or analyzer. which uses a small-mosaicity approximation and taking into account higher order scattering. The mosaic is anisotropic gaussian, with different FWHMs in the Y and Z directions. The scattering vector is perpendicular to the surface. For an unrotated monochromator component, the crystal plane lies in the y-z plane (ie. parallel to the beam). The component works in reflection, but also transmits the non-diffracted beam. Reflectivity and transmission files may be used. The slabs are positioned in the vertical plane (not on a cylinder/sphere), and are rotated according to the curvature radius. When curvatures are set to 0, the monochromator is flat. The curvatures approximation for parallel beam focusing to distance L, with monochromator rotation angle A1 are: RV = 2*L*sin(DEG2RAD*A1); RH = 2*L/sin(DEG2RAD*A1); -When you rotate the component by A1 = asin(Q/2/Ki)*RAD2DEG, do not forget to -rotate the following components by A2=2*A1 (for 1st order) ! +When you rotate the component by A1 = asin(Q/2/Ki)*RAD2DEG, do not forget to rotate the following components by A2=2*A1 (for 1st order) ! -Example: Monochromator_curved(zwidth=0.01, yheight=0.01, gap=0.0005, NH=11, NV=11, mosaich=30.0, mosaicv=30.0, r0=0.7, Q=1.8734) +Example: Monochromator\_curved(zwidth=0.01, yheight=0.01, gap=0.0005, NH=11, NV=11, mosaich=30.0, mosaicv=30.0, r0=0.7, Q=1.8734) Monochromator lattice parameter + +\begin{verbatim} PG 002 DM=3.355 AA (Highly Oriented Pyrolythic Graphite) PG 004 DM=1.677 AA -Heusler 111 DM=3.362 AA (Cu2MnAl) +\end{verbatim} + +Heusler 111 DM=3.362 \AA{} (Cu2MnAl) + +\begin{verbatim} CoFe DM=1.771 AA (Co0.92Fe0.08) Ge 111 DM=3.266 AA Ge 311 DM=1.714 AA @@ -45,7 +35,7 @@ \subsection*{Description} Cu 002 DM=1.807 AA Cu 220 DM=1.278 AA Cu 111 DM=2.095 AA -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -66,10 +56,10 @@ \subsection*{Input parameters} mosaicv & arc minutes & Vertical mosaic FWHM & 30.0 \\ r0 & 1 & Maximum reflectivity. O unactivates component & 0.7 \\ t0 & 1 & transmission efficiency & 1.0 \\ -Q & AA-1 & Scattering vector & 1.8734 \\ +Q & \AA{}$^{-1}$ & Scattering vector & 1.8734 \\ RV & m & radius of vertical focussing. flat for 0 & 0 \\ RH & m & radius of horizontal focussing. flat for 0 & 0 \\ -DM & AA & monochromator d-spacing instead of Q=2*pi/DM & 0 \\ +DM & \AA{} & monochromator d-spacing instead of Q=2*pi/DM & 0 \\ mosaic & arc minutes & sets mosaich=mosaicv & 0 \\ width & m & total width of monochromator, along Z & 0 \\ height & m & total height of monochromator, along Y & 0 \\ @@ -80,9 +70,9 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Monochromator_curved.comp}{Source code} for \texttt{Monochromator\_curved.comp}. - \item \textless{}a href="http://mcstas.risoe.dk/pipermail/neutron-mc/1999q1/000133.html"\textgreater{}Additional note\textless{}/a\textgreater{} from Peter Link. + \item Component source code found in file \texttt{Monochromator\_curved.comp}. + \item \htmladdnormallink{Additional note}{http://mcstas.risoe.dk/pipermail/neutron-mc/1999q1/000133.html} from Peter Link. \item Obsolete Mosaic\_anisotropic by Kristian Nielsen \item Contributed Monochromator\_2foc by Peter Link \end{itemize} -\IfFileExists{Monochromator_curved_static.tex}{\input{Monochromator_curved_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Monochromator_curved_static.tex}{\input{optics/Monochromator_curved_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Monochromator_flat.tex b/docs/manuals/mcstas/optics/Monochromator_flat.tex index c68039ed43..9f2300603b 100644 --- a/docs/manuals/mcstas/optics/Monochromator_flat.tex +++ b/docs/manuals/mcstas/optics/Monochromator_flat.tex @@ -3,26 +3,26 @@ \section{The \texttt{Monochromator\_flat} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Flat, infinitely thin mosaic crystal, useful as a monochromator or analyzer. -For an unrotated monochromator component, the crystal surface lies in the Y-Z -plane (ie. parallel to the beam). -The mosaic is anisotropic gaussian, with different FWHMs in the Y and Z -directions. The scattering vector is perpendicular to the surface. +Flat, infinitely thin mosaic crystal, useful as a monochromator or analyzer. For an unrotated monochromator component, the crystal surface lies in the Y-Z plane (ie. parallel to the beam). The mosaic is anisotropic gaussian, with different FWHMs in the Y and Z directions. The scattering vector is perpendicular to the surface. -Example: Monochromator_flat(zmin=-0.1, zmax=0.1, ymin=-0.1, ymax=0.1, mosaich=30.0, mosaicv=30.0, r0=0.7, Q=1.8734) +Example: Monochromator\_flat(zmin=-0.1, zmax=0.1, ymin=-0.1, ymax=0.1, mosaich=30.0, mosaicv=30.0, r0=0.7, Q=1.8734) Monochromator lattice parameter + +\begin{verbatim} PG 002 DM=3.355 AA (Highly Oriented Pyrolythic Graphite) PG 004 DM=1.677 AA -Heusler 111 DM=3.362 AA (Cu2MnAl) +\end{verbatim} + +Heusler 111 DM=3.362 \AA{} (Cu2MnAl) + +\begin{verbatim} CoFe DM=1.771 AA (Co0.92Fe0.08) Ge 111 DM=3.266 AA Ge 311 DM=1.714 AA @@ -33,7 +33,7 @@ \subsection*{Description} Cu 002 DM=1.807 AA Cu 220 DM=1.278 AA Cu 111 DM=2.095 AA -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -53,12 +53,12 @@ \subsection*{Input parameters} mosaicv & arc minutes & Vertical mosaic (in y direction) (FWHM) & 30.0 \\ r0 & 1 & Maximum reflectivity & 0.7 \\ Q & 1/angstrom & Magnitude of scattering vector & 1.8734 \\ -DM & AA & monochromator d-spacing, instead of Q = 2*pi/DM & 0 \\ +DM & \AA{} & monochromator d-spacing, instead of Q = 2*pi/DM & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Monochromator_flat.comp}{Source code} for \texttt{Monochromator\_flat.comp}. + \item Component source code found in file \texttt{Monochromator\_flat.comp}. \end{itemize} -\IfFileExists{Monochromator_flat_static.tex}{\input{Monochromator_flat_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Monochromator_flat_static.tex}{\input{optics/Monochromator_flat_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Monochromator_pol.tex b/docs/manuals/mcstas/optics/Monochromator_pol.tex index f9e1bec6e5..da7204097b 100644 --- a/docs/manuals/mcstas/optics/Monochromator_pol.tex +++ b/docs/manuals/mcstas/optics/Monochromator_pol.tex @@ -3,52 +3,36 @@ \section{The \texttt{Monochromator\_pol} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Christiansen \item \textbf{Origin:} RISOE \item \textbf{Date:} 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Based on Monochromator_flat. -Flat, infinitely thin mosaic crystal, useful as a monochromator or analyzer. -For an unrotated monochromator component, the crystal surface lies in the Y-Z -plane (ie. parallel to the beam). -The mosaic and d-spread distributions are both Gaussian. -Neutrons are just reflected (billard ball like). No correction is done for -mosaicity of reflecting crystal. -The crystal is assumed to be a ferromagnet with spin pointing up -eta-tilde = (0, 1, 0) (along y-axis), so that the magnetic field is -pointing opposite (0, -|B|, 0). +Based on Monochromator\_flat. Flat, infinitely thin mosaic crystal, useful as a monochromator or analyzer. For an unrotated monochromator component, the crystal surface lies in the Y-Z plane (ie. parallel to the beam). The mosaic and d-spread distributions are both Gaussian. Neutrons are just reflected (billard ball like). No correction is done for mosaicity of reflecting crystal. The crystal is assumed to be a ferromagnet with spin pointing up eta-tilde = (0, 1, 0) (along y-axis), so that the magnetic field is pointing opposite (0, -|B|, 0). -The polarisation is done by defining the reflectivity for spin up -(Rup) and spin down (Rdown) (which can be negative, see now!) and -based on this the nuclear and magnetic structure factors are -calculated: -FM = sign(Rup)*sqrt(|Rup|) + sign(Rdown)*sqrt(|Rdown|) -FN = sign(Rup)*sqrt(|Rup|) - sign(Rdown)*sqrt(|Rdown|) -and the physics is calculated as -Pol in = (sx_in, sy_in, sz_in) -Reflectivity R0 = FN*FN + 2*FN*FM*sy_in + FM*FM -(= |Rup| + |Rdown| (for sy_in=0)) -Pol out: -sx = (FN*FN - FM*FM)*sx_in/R0; -sy = ((FN*FN - FM*FM)*sy_in + 2*FN*FM + FM*FM*sy_in)/R0; -sz = (FN*FN - FM*FM)*sz_in/R0; +The polarisation is done by defining the reflectivity for spin up (Rup) and spin down (Rdown) (which can be negative, see now!) and based on this the nuclear and magnetic structure factors are calculated: FM = sign(Rup)*sqrt(|Rup|) + sign(Rdown)*sqrt(|Rdown|) FN = sign(Rup)*sqrt(|Rup|) - sign(Rdown)*sqrt(|Rdown|) and the physics is calculated as Pol in = (sx\_in, sy\_in, sz\_in) Reflectivity R0 = FN*FN + 2*FN*FM*sy\_in + FM*FM (= |Rup| + |Rdown| (for sy\_in=0)) Pol out: sx = (FN*FN - FM*FM)*sx\_in/R0; sy = ((FN*FN - FM*FM)*sy\_in + 2*FN*FM + FM*FM*sy\_in)/R0; sz = (FN*FN - FM*FM)*sz\_in/R0; -These equations are taken from: -Lovesey: "Theory of neutron scattering from condensed matter, Volume +These equations are taken from: Lovesey: "Theory of neutron scattering from condensed matter, Volume + +\begin{verbatim} 2", Eq. 10.96 and Eq. 10.110 +\end{verbatim} -This component works with gravity (uses PROP_X0). +This component works with gravity (uses PROP\_X0). -Example: Monochromator_pol(zwidth=0.2, yheight=0.2, mosaic=30.0, dspread=0.0025, Rup=1.0, Rdown=0.0, Q=1.8734) +Example: Monochromator\_pol(zwidth=0.2, yheight=0.2, mosaic=30.0, dspread=0.0025, Rup=1.0, Rdown=0.0, Q=1.8734) Monochromator lattice parameter + +\begin{verbatim} PG 002 DM=3.355 AA (Highly Oriented Pyrolythic Graphite) PG 004 DM=1.677 AA -Heusler 111 DM=3.362 AA (Cu2MnAl) +\end{verbatim} + +Heusler 111 DM=3.362 \AA{} (Cu2MnAl) + +\begin{verbatim} CoFe DM=1.771 AA (Co0.92Fe0.08) Ge 111 DM=3.266 AA Ge 311 DM=1.714 AA @@ -59,7 +43,7 @@ \subsection*{Description} Cu 002 DM=1.807 AA Cu 220 DM=1.278 AA Cu 111 DM=2.095 AA -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -73,8 +57,8 @@ \subsection*{Input parameters} yheight & m & Height of crystal & 0.1 \\ mosaic & & Mosaicity (FWHM) [arc minutes] & 30.0 \\ dspread & 1 & Relative d-spread (FWHM) & 0 \\ -Q & AA-1 & Magnitude of scattering vector & 1.8734 \\ -DM & AA & monochromator d-spacing instead of Q = 2*pi/DM & 0 \\ +Q & \AA{}$^{-1}$ & Magnitude of scattering vector & 1.8734 \\ +DM & \AA{} & monochromator d-spacing instead of Q = 2*pi/DM & 0 \\ pThreshold & & if probability\textgreater{}pThreshold then accept and weight else random & 0 \\ Rup & 1 & Reflectivity of neutrons with polarization up & 1 \\ Rdown & 1 & Reflectivity of neutrons with polarization down & 1 \\ @@ -84,6 +68,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Monochromator_pol.comp}{Source code} for \texttt{Monochromator\_pol.comp}. + \item Component source code found in file \texttt{Monochromator\_pol.comp}. \end{itemize} -\IfFileExists{Monochromator_pol_static.tex}{\input{Monochromator_pol_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Monochromator_pol_static.tex}{\input{optics/Monochromator_pol_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Place.tex b/docs/manuals/mcstas/optics/Place.tex index d0f0a5534d..d21012382a 100644 --- a/docs/manuals/mcstas/optics/Place.tex +++ b/docs/manuals/mcstas/optics/Place.tex @@ -3,19 +3,15 @@ \section{The \texttt{Place} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} DTU \item \textbf{Date:} June 2025 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Just like Arm, Place does not actually do anything, it is just there to set -up a new coordinate system. +Just like Arm, Place does not actually do anything, it is just there to set up a new coordinate system. Example: Place() -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,6 +26,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Place.comp}{Source code} for \texttt{Place.comp}. + \item Component source code found in file \texttt{Place.comp}. \end{itemize} -\IfFileExists{Place_static.tex}{\input{Place_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Place_static.tex}{\input{optics/Place_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/PolAnalyser_ideal.tex b/docs/manuals/mcstas/optics/PolAnalyser_ideal.tex index 068ca9f57e..e72cd8e5b8 100644 --- a/docs/manuals/mcstas/optics/PolAnalyser_ideal.tex +++ b/docs/manuals/mcstas/optics/PolAnalyser_ideal.tex @@ -3,20 +3,15 @@ \section{The \texttt{PolAnalyser\_ideal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik Knudsen \item \textbf{Origin:} Risoe \item \textbf{Date:} June 2010 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This is an ideal model of a polarization analyser device. Given a polarization vector -it "lets through" a scaled neutron weight. An imperfect analyzer could be modelled by an -analysis vector M with |M|<1. +This is an ideal model of a polarization analyser device. Given a polarization vector it "lets through" a scaled neutron weight. An imperfect analyzer could be modelled by an analysis vector M with |M|\textless{}1. -Example: PolAnalyser_ideal(mx=0, my=1, mz=0) -\end{lstlisting} +Example: PolAnalyser\_ideal(mx=0, my=1, mz=0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -34,6 +29,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/PolAnalyser_ideal.comp}{Source code} for \texttt{PolAnalyser\_ideal.comp}. + \item Component source code found in file \texttt{PolAnalyser\_ideal.comp}. \end{itemize} -\IfFileExists{PolAnalyser_ideal_static.tex}{\input{PolAnalyser_ideal_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/PolAnalyser_ideal_static.tex}{\input{optics/PolAnalyser_ideal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_Bfield.tex b/docs/manuals/mcstas/optics/Pol_Bfield.tex index 564f83651c..24d99d61bd 100644 --- a/docs/manuals/mcstas/optics/Pol_Bfield.tex +++ b/docs/manuals/mcstas/optics/Pol_Bfield.tex @@ -3,61 +3,29 @@ \section{The \texttt{Pol\_Bfield} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen, Peter Christiansen and Peter Willendrup \item \textbf{Origin:} RISOE \item \textbf{Date:} July 2011 \end{itemize} \subsection*{Description} -\begin{lstlisting} Region with a definable magnetic field. -The component is nestable if the concentric flag is set (the default). This means that it may have a -construction like the following: -// START MAGNETIC FIELD -COMPONENT msf = -Pol_Bfield(xwidth=0.08, yheight=0.08, zdepth=0.2, Bx=0, By=-0.678332e-4, Bz=0) -AT (0, 0, 0) RELATIVE armMSF +The component is nestable if the concentric flag is set (the default). This means that it may have a construction like the following: // START MAGNETIC FIELD COMPONENT msf = Pol\_Bfield(xwidth=0.08, yheight=0.08, zdepth=0.2, Bx=0, By=-0.678332e-4, Bz=0) AT (0, 0, 0) RELATIVE armMSF // OTHER COMPONENTS INSIDE THE MAGNETIC FIELD CAN BE PLACED HERE -// STOP MAGNETIC FIELD -COMPONENT msf_stop = Pol_simpleBfield_stop(magnet_comp_stop=msf) -AT (0, 0, 0) RELATIVE armMSF +// STOP MAGNETIC FIELD COMPONENT msf\_stop = Pol\_simpleBfield\_stop(magnet\_comp\_stop=msf) AT (0, 0, 0) RELATIVE armMSF -Note that if you have objects within the magnetic field that extend outside it you may get -wrong results, because propagation within the field will then possibly extend outside, e.g. -when using a tabled field. The evaluated field will then use the nearest defined field point -_also_ outside the defintion area. If these outside-points have a non-zero field precession will -continue - even after the neutron has left the field region. +Note that if you have objects within the magnetic field that extend outside it you may get wrong results, because propagation within the field will then possibly extend outside, e.g. when using a tabled field. The evaluated field will then use the nearest defined field point \_also\_ outside the defintion area. If these outside-points have a non-zero field precession will continue - even after the neutron has left the field region. -In between the two component instances the propagation routine -PROP_DT also handles spin propagation. -The current algorithm used for spin propagation is: -SimpleNumMagnetPrecession -in pol-lib. +In between the two component instances the propagation routine PROP\_DT also handles spin propagation. The current algorithm used for spin propagation is: SimpleNumMagnetPrecession in pol-lib. -Example: Pol_Bfield(xwidth=0.1, yheight=0.1, zdepth=0.2, Bx=0, By=1, Bz=0) -Pol_Bfield(xwidth=0.1, yheight=0.1, zdepth=0.2, field_type=1) +Example: Pol\_Bfield(xwidth=0.1, yheight=0.1, zdepth=0.2, Bx=0, By=1, Bz=0) Pol\_Bfield(xwidth=0.1, yheight=0.1, zdepth=0.2, field\_type=1) -Functions supplied by the system are (the number is the ID of the function to be given as the field_type parameter: -1. Constant magnetic field: Constant field (Bx,By,Bz) within the region -2. Rotating magnetic_field: Field is initially (0,By,0) but after a length of zdepth -has rotated to (By,0,0) -3. Majorana magnetic_field: Field is initially (Bx,By,0) with By<<Bx, then linearly transforms to -(-Bx,By,0) at z=zdepth. -4. MSF field: -5. RF field: A radio frequency field is modeled by an implcit use of a roating frame. -6. Gradient field: Similar to Majorana by without an x-component to the field. I.e. it (0,By,0) at z=0, and -becomes (0,-By,0) AT z=zdepth. +Functions supplied by the system are (the number is the ID of the function to be given as the field\_type parameter: 1. Constant magnetic field: Constant field (Bx,By,Bz) within the region 2. Rotating magnetic\_field: Field is initially (0,By,0) but after a length of zdepth has rotated to (By,0,0) 3. Majorana magnetic\_field: Field is initially (Bx,By,0) with By\textless{}\textless{}Bx, then linearly transforms to (-Bx,By,0) at z=zdepth. 4. MSF field: 5. RF field: A radio frequency field is modeled by an implcit use of a roating frame. 6. Gradient field: Similar to Majorana by without an x-component to the field. I.e. it (0,By,0) at z=0, and becomes (0,-By,0) AT z=zdepth. -If the concentric parameter is set to 1 the magnetic field is turned on by an -instance of this component, and turned off by an instance of Pol_simpleBfield_stop. -Anything in between is considered inside the field. -If concentric is zero the field is considered a closed component - neutrons are propagated -through the field region, and no other components are permitted inside the field. -\end{lstlisting} +If the concentric parameter is set to 1 the magnetic field is turned on by an instance of this component, and turned off by an instance of Pol\_simpleBfield\_stop. Anything in between is considered inside the field. If concentric is zero the field is considered a closed component - neutrons are propagated through the field region, and no other components are permitted inside the field. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -81,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_Bfield.comp}{Source code} for \texttt{Pol\_Bfield.comp}. + \item Component source code found in file \texttt{Pol\_Bfield.comp}. \end{itemize} -\IfFileExists{Pol_Bfield_static.tex}{\input{Pol_Bfield_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_Bfield_static.tex}{\input{optics/Pol_Bfield_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_Bfield_stop.tex b/docs/manuals/mcstas/optics/Pol_Bfield_stop.tex index 9d663898dd..714368fba2 100644 --- a/docs/manuals/mcstas/optics/Pol_Bfield_stop.tex +++ b/docs/manuals/mcstas/optics/Pol_Bfield_stop.tex @@ -3,41 +3,33 @@ \section{The \texttt{Pol\_Bfield\_stop} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen, Peter Christiansen, and Peter Willendrup \item \textbf{Origin:} RISOE \item \textbf{Date:} August 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -End of magnetic field region defined by the latest preceeding Pol_Bfield component. +End of magnetic field region defined by the latest preceeding Pol\_Bfield component. The component is concentric. It means that it requires a -// START MAGNETIC FIELD -COMPONENT msf = +// START MAGNETIC FIELD COMPONENT msf = + +\begin{verbatim} Pol_Bfield(xw=0.08, yh=0.08, length=0.2, Bx=0, By=-0.678332e-4, Bz=0) +\end{verbatim} + AT (0, 0, 0) RELATIVE armMSF // HERE CAN BE OTHER COMPONENTS INSIDE THE MAGNETIC FIELD -// STOP MAGNETIC FIELD -COMPONENT msfCp = Pol_Bfield_stop() -AT ("SOMEWHERE") RELATIVE armMSF +// STOP MAGNETIC FIELD COMPONENT msfCp = Pol\_Bfield\_stop() AT ("SOMEWHERE") RELATIVE armMSF -In between the two components the propagation routine -PROP_DT also handles the spin propagation. -The current algorithm used for spin propagation is: -SimpleNumMagnetPrecession -in pol-lib. -and does not handle gravity. +In between the two components the propagation routine PROP\_DT also handles the spin propagation. The current algorithm used for spin propagation is: SimpleNumMagnetPrecession in pol-lib. and does not handle gravity. -GRAVITY: NO -POLARISATION: YES +GRAVITY: NO POLARISATION: YES -Example: Pol_Bfield_stop() -\end{lstlisting} +Example: Pol\_Bfield\_stop() \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_Bfield_stop.comp}{Source code} for \texttt{Pol\_Bfield\_stop.comp}. + \item Component source code found in file \texttt{Pol\_Bfield\_stop.comp}. \end{itemize} -\IfFileExists{Pol_Bfield_stop_static.tex}{\input{Pol_Bfield_stop_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_Bfield_stop_static.tex}{\input{optics/Pol_Bfield_stop_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_FieldBox.tex b/docs/manuals/mcstas/optics/Pol_FieldBox.tex index c920cdcf8c..0c04a746a7 100644 --- a/docs/manuals/mcstas/optics/Pol_FieldBox.tex +++ b/docs/manuals/mcstas/optics/Pol_FieldBox.tex @@ -3,16 +3,13 @@ \section{The \texttt{Pol\_FieldBox} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen and P Willendrup \item \textbf{Origin:} Risoe \item \textbf{Date:} 2013 \end{itemize} \subsection*{Description} -\begin{lstlisting} -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -33,6 +30,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_FieldBox.comp}{Source code} for \texttt{Pol\_FieldBox.comp}. + \item Component source code found in file \texttt{Pol\_FieldBox.comp}. \end{itemize} -\IfFileExists{Pol_FieldBox_static.tex}{\input{Pol_FieldBox_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_FieldBox_static.tex}{\input{optics/Pol_FieldBox_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_SF_ideal.tex b/docs/manuals/mcstas/optics/Pol_SF_ideal.tex index a94ec7cd36..d14c43ddc4 100644 --- a/docs/manuals/mcstas/optics/Pol_SF_ideal.tex +++ b/docs/manuals/mcstas/optics/Pol_SF_ideal.tex @@ -3,19 +3,13 @@ \section{The \texttt{Pol\_SF\_ideal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \item \textbf{Origin:} \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component simply mirrors the polarization vector of the neutron -ray in the plane through (0,0,0) with normal nx,ny,nz. -The flipper is surrounded by a perfectly absorbing box. Neutron rays not hitting -the box are left untouched. -\end{lstlisting} +This component simply mirrors the polarization vector of the neutron ray in the plane through (0,0,0) with normal nx,ny,nz. The flipper is surrounded by a perfectly absorbing box. Neutron rays not hitting the box are left untouched. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,6 +30,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_SF_ideal.comp}{Source code} for \texttt{Pol\_SF\_ideal.comp}. + \item Component source code found in file \texttt{Pol\_SF\_ideal.comp}. \end{itemize} -\IfFileExists{Pol_SF_ideal_static.tex}{\input{Pol_SF_ideal_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_SF_ideal_static.tex}{\input{optics/Pol_SF_ideal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_bender.tex b/docs/manuals/mcstas/optics/Pol_bender.tex index 9a82b1fe67..9faecd755b 100644 --- a/docs/manuals/mcstas/optics/Pol_bender.tex +++ b/docs/manuals/mcstas/optics/Pol_bender.tex @@ -3,52 +3,38 @@ \section{The \texttt{Pol\_bender} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Christiansen \item \textbf{Origin:} RISOE \item \textbf{Date:} August 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Based on Guide_curved written by Ross Stewart. -Models a rectangular curved guide tube with entrance centered on the Z axis. -The entrance lies in the X-Y plane. Draws a true depiction -of the guide with multiple slits (but without spacers), and trajectories. -It relies on similar physics as the Monochromator_pol. -The reflec function and parameters are passed to this component to -give a bigger freedom. -The up direction is hardcoded to be along the y-axis (0, 1, 0) +Based on Guide\_curved written by Ross Stewart. Models a rectangular curved guide tube with entrance centered on the Z axis. The entrance lies in the X-Y plane. Draws a true depiction of the guide with multiple slits (but without spacers), and trajectories. It relies on similar physics as the Monochromator\_pol. The reflec function and parameters are passed to this component to give a bigger freedom. The up direction is hardcoded to be along the y-axis (0, 1, 0) -The guide is asummed to have half a spacer on each side: -slit1 slit2 slit3 +The guide is asummed to have half a spacer on each side: slit1 slit2 slit3 + +\begin{verbatim} |+ ++ ++ +| |+ ++ ++ +| <---------------------> xwidth -<------> xwidth/nslit (nslit=3) -<> d +\end{verbatim} + +\textless{}------\textgreater{} xwidth/nslit (nslit=3) \textless{}\textgreater{} d + +The reflection functions and parameters defaults as follows: Bot defaults to Top, Left defaults to Top, Right defaults to left. Down defaults to down and up defaults to up for all functions and Top(Up and Down) defaults to StdReflecFunc and \{0.99,0.0219,6.07,2.0,0.003\} which stands for \{R0, Qc, alpha, m, W\}. -The reflection functions and parameters defaults as follows: -Bot defaults to Top, Left defaults to Top, Right defaults to left. -Down defaults to down and up defaults to up for all functions and -Top(Up and Down) defaults to StdReflecFunc and {0.99,0.0219,6.07,2.0,0.003} -which stands for {R0, Qc, alpha, m, W}. +Example: Pol\_bender(xwidth = 0.08, yheight = 0.08, length = 1.0, radius= 10.0, nslit=5, d=0.0, endFlat=0, drawOption=2, -Example: -Pol_bender(xwidth = 0.08, yheight = 0.08, length = 1.0, radius= 10.0, -nslit=5, d=0.0, endFlat=0, drawOption=2, +\begin{verbatim} rTopUpPar={0.99, 0.0219, 6.07, 3.0, 0.003}, rTopDownPar={0.99, 0.0219, 6.07, 1.0, 0.003}) +\end{verbatim} -See also the example instruments Test_Pol_Bender and -Test_Pol_Bender_Vs_Guide_Curved (under tests). +See also the example instruments Test\_Pol\_Bender and Test\_Pol\_Bender\_Vs\_Guide\_Curved (under tests). -%BUGS -This component has been against tested Guide_curved and found to -give the same intensities. Gravity option has not been tested. +\%BUGS This component has been against tested Guide\_curved and found to give the same intensities. Gravity option has not been tested. GRAVITY: YES (when gravity is along y-axis) -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -62,7 +48,7 @@ \subsection*{Input parameters} \textbf{yheight} & m & Height at the guide entry & \\ \textbf{length} & m & length of guide along center & \\ \textbf{radius} & m & Radius of curvature of the guide (+:curve left/-:right) & \\ -G & m/s\textasciicircum{}2 & Gravitational constant & 9.8 \\ +G & m/s$^{2}$ & Gravitational constant & 9.8 \\ nslit & 1 & Number of slits & 1 \\ d & m & Width of spacers (subdividing absorbing walls) & 0.0 \\ debug & 1 & if debug \textgreater{} 0 print out some internal parameters & 0 \\ @@ -88,6 +74,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_bender.comp}{Source code} for \texttt{Pol\_bender.comp}. + \item Component source code found in file \texttt{Pol\_bender.comp}. \end{itemize} -\IfFileExists{Pol_bender_static.tex}{\input{Pol_bender_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_bender_static.tex}{\input{optics/Pol_bender_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_constBfield.tex b/docs/manuals/mcstas/optics/Pol_constBfield.tex index 7a5ada2d78..0705ff2c95 100644 --- a/docs/manuals/mcstas/optics/Pol_constBfield.tex +++ b/docs/manuals/mcstas/optics/Pol_constBfield.tex @@ -3,21 +3,15 @@ \section{The \texttt{Pol\_constBfield} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Christiansen \item \textbf{Origin:} RISOE \item \textbf{Date:} July 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Rectangular box with constant B field along y-axis (up). The -component can be rotated to make either a guide field or a spin -flipper. A neutron hitting outside the box opening or the box sides -is absorbed. +Rectangular box with constant B field along y-axis (up). The component can be rotated to make either a guide field or a spin flipper. A neutron hitting outside the box opening or the box sides is absorbed. -Example: Pol_constBfield(xwidth=0.1, yheight=0.1, zdepth=0.2, fliplambda=5.0) -\end{lstlisting} +Example: Pol\_constBfield(xwidth=0.1, yheight=0.1, zdepth=0.2, fliplambda=5.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -31,13 +25,13 @@ \subsection*{Input parameters} \textbf{yheight} & m & Height of opening & \\ \textbf{zdepth} & m & Length of field & \\ B & Gauss & Magnetic field along y-direction & 0 \\ -fliplambda & AA & lambda for calculating B field & 0 \\ +fliplambda & \AA{} & lambda for calculating B field & 0 \\ flipangle & deg & Angle flipped for lambda = fliplambda fliplambda and flipangle overrides B so a neutron with s= (1, 0, 0) and v = (0, 0, v(fliplambda)) will have s =(cos(flipangle), sin(flipangle), 0) after the section. & 180 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_constBfield.comp}{Source code} for \texttt{Pol\_constBfield.comp}. + \item Component source code found in file \texttt{Pol\_constBfield.comp}. \end{itemize} -\IfFileExists{Pol_constBfield_static.tex}{\input{Pol_constBfield_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_constBfield_static.tex}{\input{optics/Pol_constBfield_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_guide_mirror.tex b/docs/manuals/mcstas/optics/Pol_guide_mirror.tex index eab18fa16a..bb17bd2087 100644 --- a/docs/manuals/mcstas/optics/Pol_guide_mirror.tex +++ b/docs/manuals/mcstas/optics/Pol_guide_mirror.tex @@ -3,41 +3,21 @@ \section{The \texttt{Pol\_guide\_mirror} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen \item \textbf{Origin:} DTU Physics \item \textbf{Date:} July 2018 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Based on Pol_guide_vmirror by P. Christiansen. -Models a rectangular guide with entrance centered on the Z axis and -with one supermirror sitting on the diagonal inside. -The entrance lies in the X-Y plane. Draws a true depiction -of the guide with mirror and trajectories. -The polarisation is handled similar to in Monochromator_pol. -The reflec functions are handled similar to Pol_mirror. -The up direction is hardcoded to be along the y-axis (0, 1, 0) +Based on Pol\_guide\_vmirror by P. Christiansen. Models a rectangular guide with entrance centered on the Z axis and with one supermirror sitting on the diagonal inside. The entrance lies in the X-Y plane. Draws a true depiction of the guide with mirror and trajectories. The polarisation is handled similar to in Monochromator\_pol. The reflec functions are handled similar to Pol\_mirror. The up direction is hardcoded to be along the y-axis (0, 1, 0) -Note that this component can also be used as a frame overlap-mirror -if the up and down reflectivities are set equal. In this case the wall -reflectivity (rPar) should probably be set to 0. +Note that this component can also be used as a frame overlap-mirror if the up and down reflectivities are set equal. In this case the wall reflectivity (rPar) should probably be set to 0. -Reflectivity values can either come from datafiles or from -sets of parameters to the standard analytic reflectivity function commonly -used for neutron guides: -R=R0; q<qc, R=(1-tanh((q-m qc)/W))(1-alpha(q-qc)). -If a filename is specified for e.g. rData -the datafile table overrides the analytic function. +Reflectivity values can either come from datafiles or from sets of parameters to the standard analytic reflectivity function commonly used for neutron guides: R=R0; q\textless{}qc, R=(1-tanh((q-m qc)/W))(1-alpha(q-qc)). If a filename is specified for e.g. rData the datafile table overrides the analytic function. GRAVITY: YES -%BUGS -No absorption by mirror. -The reflectivity parameters must be given as literal constants. Using variables -will result in undefined behaviour. -\end{lstlisting} +\%BUGS No absorption by mirror. The reflectivity parameters must be given as literal constants. Using variables will result in undefined behaviour. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -61,6 +41,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_guide_mirror.comp}{Source code} for \texttt{Pol\_guide\_mirror.comp}. + \item Component source code found in file \texttt{Pol\_guide\_mirror.comp}. \end{itemize} -\IfFileExists{Pol_guide_mirror_static.tex}{\input{Pol_guide_mirror_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_guide_mirror_static.tex}{\input{optics/Pol_guide_mirror_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_guide_vmirror.tex b/docs/manuals/mcstas/optics/Pol_guide_vmirror.tex index 3d73de9833..81a8c58351 100644 --- a/docs/manuals/mcstas/optics/Pol_guide_vmirror.tex +++ b/docs/manuals/mcstas/optics/Pol_guide_vmirror.tex @@ -4,35 +4,19 @@ \section{The \texttt{Pol\_guide\_vmirror} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} DTU \item \textbf{Date:} June 2022 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Models a rectangular guide with entrance centered on the Z axis and -with nvs x two supermirrors sitting in v-shapes inside. -The entrance lies in the X-Y plane. Draws a true depiction -of the guide with mirrors, and trajectories. -The polarisation is handled similar to in Monochromator_pol. -The reflec functions are handled similar to Pol_mirror. -The up direction is hardcoded to be along the y-axis (0, 1, 0) +Models a rectangular guide with entrance centered on the Z axis and with nvs x two supermirrors sitting in v-shapes inside. The entrance lies in the X-Y plane. Draws a true depiction of the guide with mirrors, and trajectories. The polarisation is handled similar to in Monochromator\_pol. The reflec functions are handled similar to Pol\_mirror. The up direction is hardcoded to be along the y-axis (0, 1, 0) -The reflectivity parameters can be -1. double pointer initializations with 5 parameters (e.g. {R0, Qc, alpha, m, W} AND inputType=0), or -2. double pointer initializations with 6 parameters (e.g. {R0, Qc, alpha, m, W, beta} AND inputType=0), or -3. table names (e.g."supermirror_m2.rfl" AND inputType=1), or -4. individually assigned values (e.g. rR0=1.0, rQc=0.0217, ... etc AND inputType=2). -NB! This might cause warnings by the compiler that can be ignored. -Note that the reflectivity functions that use with values and those that use tables are different. +The reflectivity parameters can be 1. double pointer initializations with 5 parameters (e.g. \{R0, Qc, alpha, m, W\} AND inputType=0), or 2. double pointer initializations with 6 parameters (e.g. \{R0, Qc, alpha, m, W, beta\} AND inputType=0), or 3. table names (e.g."supermirror\_m2.rfl" AND inputType=1), or 4. individually assigned values (e.g. rR0=1.0, rQc=0.0217, ... etc AND inputType=2). NB! This might cause warnings by the compiler that can be ignored. Note that the reflectivity functions that use with values and those that use tables are different. GRAVITY: YES -%BUGS -No absorption by mirror. -\end{lstlisting} +\%BUGS No absorption by mirror. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -47,23 +31,23 @@ \subsection*{Input parameters} yheight & m & Height at the guide entry & 0.1 \\ length & m & length of guide & 0.5 \\ rR0 & 1 & Cavity wall reflectivity below critical scattering vector, use with inputType = 2 & 1.0 \\ -rQc & AA-1 & Cavity wall reflectivity critical scattering vector, use natural Ni (m=1 definition) value of 0.0217, use with inputType = 2 & 0.0217 \\ -ralpha & AA & Cavity wall slope of reflectivity, use with inputType = 2 & 6.5 \\ +rQc & \AA{}$^{-1}$ & Cavity wall reflectivity critical scattering vector, use natural Ni (m=1 definition) value of 0.0217, use with inputType = 2 & 0.0217 \\ +ralpha & \AA{} & Cavity wall slope of reflectivity, use with inputType = 2 & 6.5 \\ rmSM & 1 & Cavity wall m-value of material. Zero means completely absorbing. Use with inputType = 2 & 2 \\ -rW & AA-1 & Cavity wall width of reflectivity cut-off, use with inputType = 2 & 0.00157 \\ -rbeta & AA2 & Cavity wall curvature of reflectivity, use with inputType = 2 & 80 \\ +rW & \AA{}$^{-1}$ & Cavity wall width of reflectivity cut-off, use with inputType = 2 & 0.00157 \\ +rbeta & \AA{}$^{2}$ & Cavity wall curvature of reflectivity, use with inputType = 2 & 80 \\ rUpR0 & 1 & Mirror spin up reflectivity below critical scattering vector, use with inputType = 2 & 1.0 \\ -rUpQc & AA-1 & Mirror spin up reflectivity critical scattering vector, use natural Ni (m=1 definition) value of 0.0217, use with inputType = 2 & 0.0217 \\ -rUpalpha & AA & Mirror spin up slope of reflectivity, use with inputType = 2 & 2.47 \\ +rUpQc & \AA{}$^{-1}$ & Mirror spin up reflectivity critical scattering vector, use natural Ni (m=1 definition) value of 0.0217, use with inputType = 2 & 0.0217 \\ +rUpalpha & \AA{} & Mirror spin up slope of reflectivity, use with inputType = 2 & 2.47 \\ rUpmSM & 1 & Mirror spin up m-value of material. Zero means completely absorbing. Use with inputType = 2 & 4 \\ -rUpW & AA-1 & Mirror spin up width of reflectivity cut-off, use with inputType = 2 & 0.0014 \\ -rUpbeta & AA2 & Mirror spin up curvature of reflectivity, use with inputType = 2 & 0 \\ +rUpW & \AA{}$^{-1}$ & Mirror spin up width of reflectivity cut-off, use with inputType = 2 & 0.0014 \\ +rUpbeta & \AA{}$^{2}$ & Mirror spin up curvature of reflectivity, use with inputType = 2 & 0 \\ rDownR0 & 1 & Mirror spin down reflectivity below critical scattering vector, use with inputType = 2 & 1.0 \\ -rDownQc & AA-1 & Mirror spin down reflectivity critical scattering vector, use natural Ni (m=1 definition) value of 0.0217, use with inputType = 2 & 0.0217 \\ -rDownalpha & AA & Mirror spin down slope of reflectivity, use with inputType = 2 & 1 \\ +rDownQc & \AA{}$^{-1}$ & Mirror spin down reflectivity critical scattering vector, use natural Ni (m=1 definition) value of 0.0217, use with inputType = 2 & 0.0217 \\ +rDownalpha & \AA{} & Mirror spin down slope of reflectivity, use with inputType = 2 & 1 \\ rDownmSM & 1 & Mirror spin down m-value of material. Zero means completely absorbing. Use with inputType = 2 & 0.65 \\ -rDownW & AA-1 & Mirror spin down width of reflectivity cut-off, use with inputType = 2 & 0.003 \\ -rDownbeta & AA2 & Mirror spin down curvature of reflectivity, use with inputType = 2 & 0 \\ +rDownW & \AA{}$^{-1}$ & Mirror spin down width of reflectivity cut-off, use with inputType = 2 & 0.003 \\ +rDownbeta & \AA{}$^{2}$ & Mirror spin down curvature of reflectivity, use with inputType = 2 & 0 \\ debug & 1 & if debug \textgreater{} 0 print out some internal runtime parameters & 0 \\ allow\_inside\_start & 1 & Allow neutron to start inside cavity (no propagation to entry plane) & 0 \\ rPar & 1 & Cavity wall parameters array for rFunc, use with inputType = 0 & \{1.0, 0.0217, 6.5, 2, 0.00157, 80\} \\ @@ -77,6 +61,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_guide_vmirror.comp}{Source code} for \texttt{Pol\_guide\_vmirror.comp}. + \item Component source code found in file \texttt{Pol\_guide\_vmirror.comp}. \end{itemize} -\IfFileExists{Pol_guide_vmirror_static.tex}{\input{Pol_guide_vmirror_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_guide_vmirror_static.tex}{\input{optics/Pol_guide_vmirror_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_mirror.tex b/docs/manuals/mcstas/optics/Pol_mirror.tex index 7077c0ab95..0bea8d7a3e 100644 --- a/docs/manuals/mcstas/optics/Pol_mirror.tex +++ b/docs/manuals/mcstas/optics/Pol_mirror.tex @@ -3,55 +3,29 @@ \section{The \texttt{Pol\_mirror} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Christiansen \item \textbf{Origin:} RISOE \item \textbf{Date:} July 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component models a rectangular infinitely thin mirror. -For an unrotated component, the mirror surface lies in the Y-Z -plane (ie. parallel to the beam). -It relies on similar physics as the Monochromator_pol. -The reflectivity function (see e.g. share/ref-lib for examples) and parameters -are passed to this component to give a bigger freedom. -The up direction is hardcoded to be along the y-axis (0, 1, 0) -IMPORTANT: At present the component only works correctly for polarization along the up/down -direction and for completely unpolarized beams, i.e. sx=sy=sz=0 for all rays. +This component models a rectangular infinitely thin mirror. For an unrotated component, the mirror surface lies in the Y-Z plane (ie. parallel to the beam). It relies on similar physics as the Monochromator\_pol. The reflectivity function (see e.g. share/ref-lib for examples) and parameters are passed to this component to give a bigger freedom. The up direction is hardcoded to be along the y-axis (0, 1, 0) IMPORTANT: At present the component only works correctly for polarization along the up/down direction and for completely unpolarized beams, i.e. sx=sy=sz=0 for all rays. -For now we assume: -P(Transmit|Q) = 1 - P(Reflect|Q) -i.e. NO ABSORPTION! +For now we assume: P(Transmit|Q) = 1 - P(Reflect|Q) i.e. NO ABSORPTION! +The component can both reflect and transmit neutrons with a respective proportion depending on the p\_reflect parameter: p\_reflect=-1 Reflect and transmit (proportions given from reflectivity) [default] p\_reflect=1 Only handle reflected events p\_reflect=0 Only handle transmitted events (reduce weight) p\_reflect=0-1 Both transmit and reflect with fixed statistics proportions -The component can both reflect and transmit neutrons with a respective proportion -depending on the p_reflect parameter: -p_reflect=-1 Reflect and transmit (proportions given from reflectivity) [default] -p_reflect=1 Only handle reflected events -p_reflect=0 Only handle transmitted events (reduce weight) -p_reflect=0-1 Both transmit and reflect with fixed statistics proportions +The parameters can either be double pointer initializations (e.g. \{R0, Qc, alpha, m, W\}) or table names (e.g."supermirror\_m2.rfl" AND useTables=1). NB! This might cause warnings by the compiler that can be ignored. -The parameters can either be -double pointer initializations (e.g. {R0, Qc, alpha, m, W}) -or table names (e.g."supermirror_m2.rfl" AND useTables=1). -NB! This might cause warnings by the compiler that can be ignored. +Examples: Reflection function parametrization Pol\_mirror(zwidth = 0.40, yheight = 0.40, rUpFunc=StdReflecFunc, rUpPar=\{1.0, 0.0219, 6.07, 2.0, 0.003\}) -Examples: -Reflection function parametrization -Pol_mirror(zwidth = 0.40, yheight = 0.40, rUpFunc=StdReflecFunc, rUpPar={1.0, 0.0219, 6.07, 2.0, 0.003}) +Table function Pol\_mirror(zwidth = 0.40, yheight = 0.40, rUpFunc=TableReflecFunc, rUpPar="supermirror\_m2.rfl", rDownFunc=TableReflecFunc, rDownPar="supermirror\_m3.rfl", useTables=1) -Table function -Pol_mirror(zwidth = 0.40, yheight = 0.40, rUpFunc=TableReflecFunc, rUpPar="supermirror_m2.rfl", rDownFunc=TableReflecFunc, rDownPar="supermirror_m3.rfl", useTables=1) - -See also the example instrument Test_Pol_Mirror (under tests). +See also the example instrument Test\_Pol\_Mirror (under tests). GRAVITY: YES -%BUGS -NO ABSORPTION -\end{lstlisting} +\%BUGS NO ABSORPTION \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -72,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_mirror.comp}{Source code} for \texttt{Pol\_mirror.comp}. + \item Component source code found in file \texttt{Pol\_mirror.comp}. \end{itemize} -\IfFileExists{Pol_mirror_static.tex}{\input{Pol_mirror_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_mirror_static.tex}{\input{optics/Pol_mirror_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Pol_tabled_field.tex b/docs/manuals/mcstas/optics/Pol_tabled_field.tex index 294bda5101..18f7b21015 100644 --- a/docs/manuals/mcstas/optics/Pol_tabled_field.tex +++ b/docs/manuals/mcstas/optics/Pol_tabled_field.tex @@ -3,23 +3,13 @@ \section{The \texttt{Pol\_tabled\_field} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen, Peter Christiansen and Peter Willendrup \item \textbf{Origin:} RISOE \item \textbf{Date:} July 2011 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Region with a tabled magnetic field read from file. -The magnetic field is read from a text file where it is -specified as a point cloud with N rows of 6 columns: -x y z Bx By Bz -the B field map is resampled with Stepx*Stepy*Stepz points. -Use Stepx=Stepy=Stepz=0 to skip resampling and use the table as is. -The regions itself may be either a 3D rectangular block, a cylinder with axis along y, -or spherical. Interpolation is done between data-points. -\end{lstlisting} +Region with a tabled magnetic field read from file. The magnetic field is read from a text file where it is specified as a point cloud with N rows of 6 columns: x y z Bx By Bz the B field map is resampled with Stepx*Stepy*Stepz points. Use Stepx=Stepy=Stepz=0 to skip resampling and use the table as is. The regions itself may be either a 3D rectangular block, a cylinder with axis along y, or spherical. Interpolation is done between data-points. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -41,6 +31,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Pol_tabled_field.comp}{Source code} for \texttt{Pol\_tabled\_field.comp}. + \item Component source code found in file \texttt{Pol\_tabled\_field.comp}. \end{itemize} -\IfFileExists{Pol_tabled_field_static.tex}{\input{Pol_tabled_field_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Pol_tabled_field_static.tex}{\input{optics/Pol_tabled_field_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Refractor.tex b/docs/manuals/mcstas/optics/Refractor.tex index 05215c826c..baf85da206 100644 --- a/docs/manuals/mcstas/optics/Refractor.tex +++ b/docs/manuals/mcstas/optics/Refractor.tex @@ -3,65 +3,55 @@ \section{The \texttt{Refractor} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi, B. Cubitt \item \textbf{Origin:} ILL \item \textbf{Date:} Oct 2014 \end{itemize} \subsection*{Description} -\begin{lstlisting} Single bulk material shape that can be used as a prism or lens. -NEUTRON INTERACTION PROCESSES: -The bulk material can reflect, refract, scatter and absorb neutrons, depending -on the material cross sections and incident angles. +NEUTRON INTERACTION PROCESSES: The bulk material can reflect, refract, scatter and absorb neutrons, depending on the material cross sections and incident angles. -The refracting material is specified from its molar weight, density, coherent -scattering cross section. The refractive index is computed as: +The refracting material is specified from its molar weight, density, coherent scattering cross section. The refractive index is computed as: + +\begin{verbatim} n = sqrt(1-(lambda*lambda*rho*bc/PI)) is the refraction index +\end{verbatim} + +The surface can be coated when specifying a critical wavevector Qc, with e.g. Qc=m*0.0219 for a super mirror coating. The mirror coating can be suppressed by setting Qc=0. The critical wavevector is then set to -The surface can be coated when specifying a critical wavevector Qc, with e.g. -Qc=m*0.0219 for a super mirror coating. The mirror coating can be suppressed -by setting Qc=0. The critical wavevector is then set to +\begin{verbatim} Qc = 4*sqrt(PI*rho*bc); with -rho= density*6.02214179*1e23*1e-24/weight; -bc = sqrt(fabs(sigma_coh)*100/4/PI)*1e-5; +\end{verbatim} + +rho= density*6.02214179*1e23*1e-24/weight; bc = sqrt(fabs(sigma\_coh)*100/4/PI)*1e-5; + +COMPONENT GEOMETRY: The component shape can be a sphere, box, cylinder, biconcave spherical lens or any other shape defined from an external OFF/PLY file. -COMPONENT GEOMETRY: -The component shape can be a sphere, box, cylinder, biconcave spherical lens -or any other shape defined from an external OFF/PLY file. +\begin{verbatim} sphere: radius cylinder: radius, yheight box: xwidth, yheight, zdepth OFF/PLY: geometry="filename.off or ply", xwidth, yheight, zdepth (bounding box) lens_sphere: geometry="lens_sphere", radius, zdepth (thickness) +\end{verbatim} + +The lens\_sphere geometry is composed of two concave half spheres of same radius, separated with a minimal thickness zdepth along the Z axis. + +Optionally, you can specify the 'geometry' parameter as a OFF/PLY file name. The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the PLY, OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). + +All geometries are centred. The bulk material fills the shape, but can be set 'outside' when density is given a negative value. In this case, the material outside the bulk is void (vacuum). -The lens_sphere geometry is composed of two concave half spheres of same radius, -separated with a minimal thickness zdepth along the Z axis. - -Optionally, you can specify the 'geometry' parameter as a OFF/PLY file name. -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the PLY, OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using: -qhull < coordinates.xyz Qx Qv Tv o > geomview.off -or -powercrust coordinates.xyz -and viewed with geomview or java -jar jroff.jar (see below). - -All geometries are centred. The bulk material fills the shape, but can be -set 'outside' when density is given a negative value. In this case, the material -outside the bulk is void (vacuum). - -Usually, you should stack more than one of these to get a significant effect -on the neutron beam, so-called 'compound refractive lens'. -The focal length for N lenses with focal 'f' is f/N, where f=R/(1-n) +Usually, you should stack more than one of these to get a significant effect on the neutron beam, so-called 'compound refractive lens'. The focal length for N lenses with focal 'f' is f/N, where f=R/(1-n) + +\begin{verbatim} and R = r/2 for a spherical lens with curvature radius 'r' +\end{verbatim} + +COMMON MATERIALS: Should have high coherent, and low incoherent and absorption cross sections -COMMON MATERIALS: -Should have high coherent, and low incoherent and absorption cross sections +\begin{verbatim} Be: density=1.85, weight=9.0121, sigma_coh=7.63, sigma_inc=0.0018,sigma_abs=0.0076 Pb: density=11.115,weight=207.2, sigma_coh=11.115,sigma_inc=0.003, sigma_abs=0.171 Pb206: sigma_coh=10.68, sigma_inc=0 , sigma_abs=0.03 @@ -73,17 +63,26 @@ \subsection*{Description} Mg: density=1.738, weight=24.3, sigma_coh=3.631, sigma_inc=0.08, sigma_abs=0.063 MgF2: density=3.148, weight=62.3018,sigma_coh=11.74, sigma_inc=0.0816,sigma_abs=0.0822 diamond: density=3.52, weight=12.01, sigma_coh=5.551, sigma_inc=0.001, sigma_abs=0.0035 -Quartz/silica: density=2.53, weight=60.08, sigma_coh=10.625,sigma_inc=0.0056,sigma_abs=0.1714 +\end{verbatim} + +Quartz/silica: density=2.53, weight=60.08, sigma\_coh=10.625,sigma\_inc=0.0056,sigma\_abs=0.1714 + +\begin{verbatim} Si: density=2.329, weight=28.0855,sigma_coh=2.1633,sigma_inc=0.004, sigma_abs=0.171 Al: density=2.7, weight=26.98, sigma_coh=1.495, sigma_inc=0.0082,sigma_abs=0.231 Ni: density=8.908, weight=58.69, sigma_coh=13.3, sigma_inc=5.2, sigma_abs=4.49 Mn: (bc < 0) density=7.21, weight=54.94, sigma_coh=-1.75, sigma_inc=0.4, sigma_abs=13.3 +\end{verbatim} + perfluoropolymer(PTFE/Teflon/CF2): + +\begin{verbatim} density=2.2, weight=50.007, sigma_coh=13.584,sigma_inc=0.0026,sigma_abs=0.0227 +\end{verbatim} + Organic molecules with C,O,H,F Among the most commonly available and machinable materials are MgF2, SiO2, Si, and Al. -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -100,13 +99,13 @@ \subsection*{Input parameters} geometry & str & OFF/PLY geometry file name, or NULL to use simple shape A spherical bi-concave lens can be obtained with geometry="lens\_sphere" and given radius and zdepth & "NULL" \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ sigma\_coh & barn & coherent cross section of refracting material. Use negative value to indicate a negative coherent scattering length & 11.74 \\ -density & g/cm3 & density of the refracting material. density \textless{} 0 means the material is outside/before the shape. & 3.148 \\ +density & g/cm$^{3}$ & density of the refracting material. density \textless{} 0 means the material is outside/before the shape. & 3.148 \\ weight & g/mol & molar mass of the refracting material & 62.3018 \\ sigma\_inc & barn & incoherent cross section & 0 \\ sigma\_abs & barn & thermal absorption cross section & 0 \\ -Qc & Angs-1 & critical scattering vector, e.g. Qc=0.0219 for Ni coating. Set Qc=0 to use the bulk critical grazing angles. & 0 \\ +Qc & \AA{}$^{-1}$ & critical scattering vector, e.g. Qc=0.0219 for Ni coating. Set Qc=0 to use the bulk critical grazing angles. & 0 \\ p\_interact & 1 & MC Probability for scattering the ray; otherwise transmit. Use 0 to compute true probability, or specify it as e.g. 0.05 & 0.05 \\ -RMS & Angs & root mean square wavyness of the surface & 0 \\ +RMS & \AA{} & root mean square wavyness of the surface & 0 \\ focus\_scatter & deg & angle in which to scatter in bulk, with probability 'p\_interact' & 10 \\ verbose & 1 & flag to display detailed component behaviour & 0 \\ p\_scatter & 1 & flag to allow scattering in the refractor bulk & 1 \\ @@ -117,15 +116,15 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Refractor.comp}{Source code} for \texttt{Refractor.comp}. + \item Component source code found in file \texttt{Refractor.comp}. \item M. L. Goldberger et al, Phys. Rev. 71, 294 - 310 (1947) \item Sears V.F. Neutron optics. An introduction to the theory of neutron optical phenomena and their applications. Oxford University Press, 1989. \item H. Park et al. Measured operational neutron energies of compound refractive lenses. Nuclear Instruments and Methods B, 251:507-511, 2006. \item J. Feinstein and R. H. Pantell. Characteristics of the thick, compound refractive lens. Applied Optics, 42 No. 4:719-723, 2001. - \item \textless{}a href="http://www.geomview.org"\textgreater{}Geomview and Object File Format (OFF)\textless{}/a\textgreater{} - \item Java version of Geomview (display only) \textless{}a href="http://www.holmes3d.net/graphics/roffview/"\textgreater{}jroff.jar\textless{}/a\textgreater{} - \item \textless{}a hrefp="http://meshlab.sourceforge.net/"\textgreater{}Meshlab\textless{}/a\textgreater{} can view OFF and PLY files - \item \textless{}a href="http://qhull.org"\textgreater{}qhull\textless{}/a\textgreater{} for points to OFF conversion - \item \textless{}a href="http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html"\textgreater{}powercrust\textless{}/a\textgreater{} for points to OFF conversion + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} + \item Java version of Geomview (display only) \htmladdnormallink{jroff.jar}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{Meshlab}{} can view OFF and PLY files + \item \htmladdnormallink{qhull}{http://qhull.org} for points to OFF conversion + \item \htmladdnormallink{powercrust}{http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} for points to OFF conversion \end{itemize} -\IfFileExists{Refractor_static.tex}{\input{Refractor_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Refractor_static.tex}{\input{optics/Refractor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Rotator.tex b/docs/manuals/mcstas/optics/Rotator.tex index 449d9ccac6..b1648f884f 100644 --- a/docs/manuals/mcstas/optics/Rotator.tex +++ b/docs/manuals/mcstas/optics/Rotator.tex @@ -3,27 +3,17 @@ \section{The \texttt{Rotator} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Emmanuel Farhi \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL\textless{}/a\textgreater{} \item \textbf{Date:} June 20th 2013 \end{itemize} \subsection*{Description} -\begin{lstlisting} -All components positioned after this one are rotating at frequency 'nu' with -phase 'phase'. Use the Derotator component to put back the model steady. -The rotation is performed w.r.t. the position of the component, along a chosen -main axis (use directon=1 for x, direction=2 for y, direction=3 for z). +All components positioned after this one are rotating at frequency 'nu' with phase 'phase'. Use the Derotator component to put back the model steady. The rotation is performed w.r.t. the position of the component, along a chosen main axis (use directon=1 for x, direction=2 for y, direction=3 for z). Default rotation axis is vertical axis / 'y'. -Example: -R=Rotator(nu=14, phase=0) -... -DR=Derotator(rotator=R) -AT (0,0,0) RELATIVE R -\end{lstlisting} +Example: R=Rotator(nu=14, phase=0) ... DR=Derotator(rotator=R) AT (0,0,0) RELATIVE R \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -41,6 +31,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Rotator.comp}{Source code} for \texttt{Rotator.comp}. + \item Component source code found in file \texttt{Rotator.comp}. \end{itemize} -\IfFileExists{Rotator_static.tex}{\input{Rotator_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Rotator_static.tex}{\input{optics/Rotator_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Selector.tex b/docs/manuals/mcstas/optics/Selector.tex index 65ce1c9928..ed2e097f36 100644 --- a/docs/manuals/mcstas/optics/Selector.tex +++ b/docs/manuals/mcstas/optics/Selector.tex @@ -3,31 +3,25 @@ \section{The \texttt{Selector} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Link, \textless{}a href="mailto:Andreas.Ostermann@frm2.tum.de"\textgreater{}Andreas Ostermann\textless{}/a\textgreater{} \item \textbf{Origin:} Uni. Gottingen (Germany) \item \textbf{Date:} MARCH 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Velocity selector consisting of rotating Soller-like blades -defining a helically twisted passage. -Geometry is defined by two identical apertures at 12 o'clock position, -The origin is at the ENTRANCE of the selector. +Velocity selector consisting of rotating Soller-like blades defining a helically twisted passage. Geometry is defined by two identical apertures at 12 o'clock position, The origin is at the ENTRANCE of the selector. -Example: Selector(xmin=-0.015, xmax=0.015, ymin=-0.025, ymax=0.025, length=0.25, +Example: Selector(xmin=-0.015, xmax=0.015, ymin=-0.025, ymax=0.025, length=0.25, + +\begin{verbatim} nslit=72,d=0.0004, radius=0.12, alpha=48.298, nu=500) +\end{verbatim} + These are values for the D11@ILL Dornier 'Dolores' Velocity Selector (NVS 023) -%VALIDATION -Jun 2005: extensive external test, one minor problem -Jan 2006: problem solved (for McStas-1.9.1) -Validated by: K. Lieutenant +\%VALIDATION Jun 2005: extensive external test, one minor problem Jan 2006: problem solved (for McStas-1.9.1) Validated by: K. Lieutenant -%BUGS -for transmission calculation, each neutron is supposed to be in the guide centre -\end{lstlisting} +\%BUGS for transmission calculation, each neutron is supposed to be in the guide centre \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -54,7 +48,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Selector.comp}{Source code} for \texttt{Selector.comp}. - \item See also Additional notes \textless{}a href="http://mcstas.risoe.dk/pipermail/neutron-mc/1999q1/000134.html"\textgreater{}March 1999\textless{}/a\textgreater{} and \textless{}a href="http://mcstas.risoe.dk/pipermail/neutron-mc/1999q2/000136.html"\textgreater{}Jan 2000\textless{}/a\textgreater{}. + \item Component source code found in file \texttt{Selector.comp}. + \item See also Additional notes \htmladdnormallink{March 1999}{http://mcstas.risoe.dk/pipermail/neutron-mc/1999q1/000134.html} and \htmladdnormallink{Jan 2000}{http://mcstas.risoe.dk/pipermail/neutron-mc/1999q2/000136.html}. \end{itemize} -\IfFileExists{Selector_static.tex}{\input{Selector_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Selector_static.tex}{\input{optics/Selector_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Set_pol.tex b/docs/manuals/mcstas/optics/Set_pol.tex index ef185ae3e5..8046347eee 100644 --- a/docs/manuals/mcstas/optics/Set_pol.tex +++ b/docs/manuals/mcstas/optics/Set_pol.tex @@ -3,22 +3,13 @@ \section{The \texttt{Set\_pol} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Christiansen \item \textbf{Origin:} Risoe \item \textbf{Date:} August 2006 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component has no physical size (like Arm - also drawn that -way), but is used to set the polarisation in one of four ways: -1) (randomOn=0, normalize=0) Hardcode the polarisation to the vector (px, py, pz) -2) (randomOn!=0, normalize!=0) Set the polarisation to a random vector on the unit sphere -3) (randomOn!=0, normalize=0) Set the polarisation to a radnom vector within the unit sphere -4) (randomOn=0, normalize!=0) Hardcode the polarisation to point in the direction of (px,py,pz) but with polarization=1. -Example: Set_pol(px=0, py=-1, pz=0) -\end{lstlisting} +This component has no physical size (like Arm - also drawn that way), but is used to set the polarisation in one of four ways: 1) (randomOn=0, normalize=0) Hardcode the polarisation to the vector (px, py, pz) 2) (randomOn!=0, normalize!=0) Set the polarisation to a random vector on the unit sphere 3) (randomOn!=0, normalize=0) Set the polarisation to a radnom vector within the unit sphere 4) (randomOn=0, normalize!=0) Hardcode the polarisation to point in the direction of (px,py,pz) but with polarization=1. Example: Set\_pol(px=0, py=-1, pz=0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -38,6 +29,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Set_pol.comp}{Source code} for \texttt{Set\_pol.comp}. + \item Component source code found in file \texttt{Set\_pol.comp}. \end{itemize} -\IfFileExists{Set_pol_static.tex}{\input{Set_pol_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Set_pol_static.tex}{\input{optics/Set_pol_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Slit.tex b/docs/manuals/mcstas/optics/Slit.tex index 120cd35d30..4d47286000 100644 --- a/docs/manuals/mcstas/optics/Slit.tex +++ b/docs/manuals/mcstas/optics/Slit.tex @@ -3,24 +3,17 @@ \section{The \texttt{Slit} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann and Henrik M. Roennow \item \textbf{Origin:} Risoe \item \textbf{Date:} June 16, 1997 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A simple rectangular or circular slit. You may either -specify the radius (circular shape), or the rectangular bounds. -No transmission around the slit is allowed. +A simple rectangular or circular slit. You may either specify the radius (circular shape), or the rectangular bounds. No transmission around the slit is allowed. -Example: Slit(xmin=-0.01, xmax=0.01, ymin=-0.01, ymax=0.01) -Slit(xwidth=0.02, yheight=0.02) -Slit(radius=0.01) +Example: Slit(xmin=-0.01, xmax=0.01, ymin=-0.01, ymax=0.01) Slit(xwidth=0.02, yheight=0.02) Slit(radius=0.01) The Slit will issue a warning if run as "closed" -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +35,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Slit.comp}{Source code} for \texttt{Slit.comp}. + \item Component source code found in file \texttt{Slit.comp}. \end{itemize} -\IfFileExists{Slit_static.tex}{\input{Slit_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Slit_static.tex}{\input{optics/Slit_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/V_selector.tex b/docs/manuals/mcstas/optics/V_selector.tex index 319eb46f47..5dcd2ac79a 100644 --- a/docs/manuals/mcstas/optics/V_selector.tex +++ b/docs/manuals/mcstas/optics/V_selector.tex @@ -3,27 +3,17 @@ \section{The \texttt{V\_selector} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} Nov 25, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Velocity selector consisting of rotating Soller-like blades -defining a helically twisted passage. -Geometry defined by two identical, centered apertures at 12 o'clock -position, Origo is at the centre of the selector (input is at -zdepth/2). -Transmission is analytical assuming a continuous source. +Velocity selector consisting of rotating Soller-like blades defining a helically twisted passage. Geometry defined by two identical, centered apertures at 12 o'clock position, Origo is at the centre of the selector (input is at -zdepth/2). Transmission is analytical assuming a continuous source. -Example: V_selector(xwidth=0.03, yheight=0.05, zdepth=0.30, radius=0.12, alpha=48.298, length=0.25, d=0.0004, nu=20000, nslit=72) -These are values for the D11@ILL Dornier 'Dolores' Velocity Selector (NVS 023) +Example: V\_selector(xwidth=0.03, yheight=0.05, zdepth=0.30, radius=0.12, alpha=48.298, length=0.25, d=0.0004, nu=20000, nslit=72) These are values for the D11@ILL Dornier 'Dolores' Velocity Selector (NVS 023) -%VALIDATION -Jun 2005: extensive external test, no problems found -Validated by: K. Lieutenant -\end{lstlisting} +\%VALIDATION Jun 2005: extensive external test, no problems found Validated by: K. Lieutenant \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -47,6 +37,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/V_selector.comp}{Source code} for \texttt{V\_selector.comp}. + \item Component source code found in file \texttt{V\_selector.comp}. \end{itemize} -\IfFileExists{V_selector_static.tex}{\input{V_selector_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/V_selector_static.tex}{\input{optics/V_selector_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/optics/Vitess_ChopperFermi.tex b/docs/manuals/mcstas/optics/Vitess_ChopperFermi.tex index 36b6462742..d282f633bc 100644 --- a/docs/manuals/mcstas/optics/Vitess_ChopperFermi.tex +++ b/docs/manuals/mcstas/optics/Vitess_ChopperFermi.tex @@ -3,66 +3,48 @@ \section{The \texttt{Vitess\_ChopperFermi} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Geza Zsigmond \item \textbf{Origin:} VITESS module 'chopper\_fermi' \item \textbf{Date:} Sep 2004 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This component simulates a Fermi chopper with absorbing walls. The rotation axis is -vertical (y-axis), i.e. the path length through the channels is given by the length -'depth' along the z-axis. -The shape of the channels can be straight, curved with circular, or curved with ideal -(i.e. close to a parabolic) shape. This is determined by the parameter 'GeomOption'. - -Geometry for straight and circular channels: -The geometry of the chopper consists of a rectangular shaped object with a channel -system. In transmission position, there are 'Nchannels' slits along the x-axis, -separated by absorbing walls of thickness 'wallwidth' giving a total width 'width'. -The rectangular channel system is surrounded by a so-called shadowing cylinder -(cf component manual). - -Geometry for parabolic channels: -In this case, the Fermi chopper is supposed to be a full cylinder, i.e. the central -channels are longer than those on the edges (cf. figure in the component manual). -The other features are the same as for the other options. - -Apart from the frequency of rotation, the phase of the chopper at t=0 has to be given; -phase = 0 means transmission orientation. - -The option 'zerotime' may be used to reset the time at the chopper position. The -consequence is that only 1 pulse is generated instead of several. - -NOTE: This component must NOT be located at the same position as the previous one. -This also stands for monitors and Arms. A non zero distance must be defined. - -Examples: -straight Fermi chopper, 18000 rpm, 20 channels a 0.9 mm separated by 0.1 mm walls, -16 mm channel length, minimal shadowing cylinder, phased to be open at 1 ms, -generation of only 1 pulse, normal precision (for short wavelength neutrons) -Vitess_ChopperFermi(GeomOption=0, zerotime=1, Nchannels=20, Ngates=4, +This component simulates a Fermi chopper with absorbing walls. The rotation axis is vertical (y-axis), i.e. the path length through the channels is given by the length 'depth' along the z-axis. The shape of the channels can be straight, curved with circular, or curved with ideal (i.e. close to a parabolic) shape. This is determined by the parameter 'GeomOption'. + +Geometry for straight and circular channels: The geometry of the chopper consists of a rectangular shaped object with a channel system. In transmission position, there are 'Nchannels' slits along the x-axis, separated by absorbing walls of thickness 'wallwidth' giving a total width 'width'. The rectangular channel system is surrounded by a so-called shadowing cylinder (cf component manual). + +Geometry for parabolic channels: In this case, the Fermi chopper is supposed to be a full cylinder, i.e. the central channels are longer than those on the edges (cf. figure in the component manual). The other features are the same as for the other options. + +Apart from the frequency of rotation, the phase of the chopper at t=0 has to be given; phase = 0 means transmission orientation. + +The option 'zerotime' may be used to reset the time at the chopper position. The consequence is that only 1 pulse is generated instead of several. + +NOTE: This component must NOT be located at the same position as the previous one. This also stands for monitors and Arms. A non zero distance must be defined. + +Examples: straight Fermi chopper, 18000 rpm, 20 channels a 0.9 mm separated by 0.1 mm walls, 16 mm channel length, minimal shadowing cylinder, phased to be open at 1 ms, generation of only 1 pulse, normal precision (for short wavelength neutrons) Vitess\_ChopperFermi(GeomOption=0, zerotime=1, Nchannels=20, Ngates=4, + +\begin{verbatim} freq=300.0, height=0.06, width=0.0201, depth=0.016, r_curv=0.0, diameter=0.025691, Phase=-108.0, -wallwidth=0.0001, sGeomFileName="FC_geom_str.dat") +\end{verbatim} + +wallwidth=0.0001, sGeomFileName="FC\_geom\_str.dat") -Fermi chopper with circular channels, 12000 rpm, optimized for 6 Ang, several pulses, -highest accuracy (because of long wavelength neutrons used), rest as above +Fermi chopper with circular channels, 12000 rpm, optimized for 6 \AA{}, several pulses, highest accuracy (because of long wavelength neutrons used), rest as above + +\begin{verbatim} Vitess_ChopperFermi(GeomOption=2, zerotime=0, Nchannels=20, Ngates=8, freq=200.0, height=0.06, width=0.0201, depth=0.016, r_curv=0.2623, diameter=0.025691, Phase=-72.0, -wallwidth=0.0001, sGeomFileName="FC_geom_circ.dat") +\end{verbatim} + +wallwidth=0.0001, sGeomFileName="FC\_geom\_circ.dat") -%VALIDATION -Apr 2005: extensive external test, most problems solved (cf. 'Bugs' and source header) -Validated by: K. Lieutenant +\%VALIDATION Apr 2005: extensive external test, most problems solved (cf. 'Bugs' and source header) Validated by: K. Lieutenant limitations: slow (10 times slower than FermiChopper), especially for a high number of channels -%BUGS -reduction of transmission by a large shadowing cylinder underestimated -\end{lstlisting} +\%BUGS reduction of transmission by a large shadowing cylinder underestimated \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -90,8 +72,8 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/optics/Vitess_ChopperFermi.comp}{Source code} for \texttt{Vitess\_ChopperFermi.comp}. - \item \textless{}a href="http://www.hmi.de/projects/ess/vitess/DOC/chopper\_fermi\_str.html"\textgreater{}straight VITESS Fermi chopper\textless{}/a\textgreater{} - \item \textless{}a href="http://www.hmi.de/projects/ess/vitess/DOC/chopper\_fermi\_cur.html"\textgreater{}curved VITESS Fermi chopper\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Vitess\_ChopperFermi.comp}. + \item \htmladdnormallink{straight VITESS Fermi chopper}{http://www.hmi.de/projects/ess/vitess/DOC/chopper\_fermi\_str.html} + \item \htmladdnormallink{curved VITESS Fermi chopper}{http://www.hmi.de/projects/ess/vitess/DOC/chopper\_fermi\_cur.html} \end{itemize} -\IfFileExists{Vitess_ChopperFermi_static.tex}{\input{Vitess_ChopperFermi_static.tex}}{} \ No newline at end of file +\IfFileExists{optics/Vitess_ChopperFermi_static.tex}{\input{optics/Vitess_ChopperFermi_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/preamble_common.tex b/docs/manuals/mcstas/preamble_common.tex.in similarity index 96% rename from docs/manuals/mcstas/preamble_common.tex rename to docs/manuals/mcstas/preamble_common.tex.in index 3191bf91d4..529aa70034 100644 --- a/docs/manuals/mcstas/preamble_common.tex +++ b/docs/manuals/mcstas/preamble_common.tex.in @@ -16,7 +16,7 @@ % A few macros: \newcommand{\MCS}{McStas\xspace} \newcommand{\mcs}{\texttt{mcstas}\xspace} -\newcommand{\version}{3.8.5\xspace} +\newcommand{\version}{@MCCODE_VERSION@\xspace} \newcommand{\reldate}{September, 2026} % Unused: @@ -53,6 +53,7 @@ \newcommand{\indexMCCH}[2]{\index{#1 (C macro mccode-r.h)@\texttt{#1} (C macro, mccode-r.h)|#2}} \newcommand{\indexRTLC}[2]{\index{#1 (C function read\_table-lib.c)@\texttt{#1} (C function, read\_table-lib.c)|#2}} \makeindex % enable index generation +\providecommand{\hyperindexformat}[2]{#1{#2}} \usepackage{color} \usepackage{xcolor} diff --git a/docs/manuals/mcstas/preamble_comp.tex b/docs/manuals/mcstas/preamble_comp.tex index 78c69a763a..2b3f1bca30 100644 --- a/docs/manuals/mcstas/preamble_comp.tex +++ b/docs/manuals/mcstas/preamble_comp.tex @@ -4,12 +4,12 @@ \newcommand{\component}[5]{\begin{tabular}{|lp{0.7\textwidth}|}\hline \textbf{Name:} & #1 \\ \hline \textbf{Author:} & #2 \\ \hline \textbf{Input parameters} & #3 \\ \hline \textbf{Optional parameters} & #4 \\ \hline \textbf{Notes} & #5 \\ \hline \end{tabular} \\ \noindent } \newcommand{\mcdoccomp}[1]{\input{#1}} -\newcommand{\kappaB}{\mbox{\boldmath $\kappa$}} -\newcommand{\etaB}{\mbox{\boldmath $\eta$}} -\newcommand{\alphaB}{\mbox{\boldmath $\alpha$}} -\newcommand{\sigmaB}{\mbox{\boldmath $\sigma$}} -\newcommand{\tauB}{\mbox{\boldmath $\sigma$}} -\newcommand{\muB}{\mbox{\boldmath $\mu$}} +\newcommand{\kappaB}{\boldsymbol{\kappa}} +\newcommand{\etaB}{\boldsymbol{\eta}} +\newcommand{\alphaB}{\boldsymbol{\alpha}} +\newcommand{\sigmaB}{\boldsymbol{\sigma}} +\newcommand{\tauB}{\boldsymbol{\sigma}} +\newcommand{\muB}{\boldsymbol{\mu}} \def\nup{n_\uparrow} \def\nd{n_\downarrow} @@ -87,3 +87,4 @@ \makeindex % enable index generation +\providecommand{\hyperindexformat}[2]{#1{#2}} diff --git a/docs/manuals/mcstas/preface_comp.tex b/docs/manuals/mcstas/preface_comp.tex index ad821867ce..4876970700 100644 --- a/docs/manuals/mcstas/preface_comp.tex +++ b/docs/manuals/mcstas/preface_comp.tex @@ -23,9 +23,9 @@ \chapter*{Preface and acknowledgements} It is a pleasure to thank Dir.~Kurt N.~Clausen, PSI, for his continuous support to \MCS and for having initiated the project. Continuous support to \MCS has also come from Prof.~Robert McGreevy, ISIS. -Apart from the authors of this manual, also Per-Olof \AA strand, NTNU Trondheim, +Apart from the authors of this manual, also Per-Olof Åstrand, NTNU Trondheim, has contributed to the development of the \MCS system. -%Both he and our other collaborators, Henrik M.\ R\o nnow and Mark +%Both he and our other collaborators, Henrik M.\ Rønnow and Mark %Hagen have made major contributions to the project. Also the %contributions from our test users, the students Asger Abrahamsen, Niels %Bech Christensen, and Erik Lauridsen, are gratefully acknowledged; they diff --git a/docs/manuals/mcstas/risoe-rep-title.tex b/docs/manuals/mcstas/risoe-rep-title.tex index 20d40e3d54..586546d332 100644 --- a/docs/manuals/mcstas/risoe-rep-title.tex +++ b/docs/manuals/mcstas/risoe-rep-title.tex @@ -34,7 +34,7 @@ \includegraphics[width=0.95\textwidth]{figures/frontpage.pdf} \end{flushright} \par \vfill \baselineskip 12dd - \frtnbf\noindent Ris{\o} DTU, Roskilde, Denmark \par + \frtnbf\noindent Risø DTU, Roskilde, Denmark \par \vskip 4dd \noindent\ifcase\month\or January\or February\or March\or April\or May\or June\or July\or August\or September\or October\or November\or December\fi diff --git a/docs/manuals/mcstas/risoe-rep_comp-title.tex b/docs/manuals/mcstas/risoe-rep_comp-title.tex index 6c1f9d28c5..137f2484db 100644 --- a/docs/manuals/mcstas/risoe-rep_comp-title.tex +++ b/docs/manuals/mcstas/risoe-rep_comp-title.tex @@ -33,7 +33,7 @@ \includegraphics[width=\textwidth]{figures/sqw.eps} \end{center} \par \vfill \baselineskip 12dd - \frtnbf\noindent Ris{\o} DTU, Roskilde, Denmark \par + \frtnbf\noindent Risø DTU, Roskilde, Denmark \par \vskip 4dd \noindent\ifcase\month\or January\or February\or March\or April\or May\or June\or July\or August\or September\or October\or November\or December\fi @@ -45,6 +45,6 @@ \title{Component~Manual~for~\rlap{the}\\ % Avoid overfull message. Neutron~Ray-Tracing~Package\\ \MCS, Version \version\ } -\author{Peter Kj\ae r Willendrup, Erik Knudsen, Kim Lefmann and\\Emmanuel Farhi} +\author{Peter Kjær Willendrup, Erik Knudsen, Kim Lefmann and\\Emmanuel Farhi} \maketitle \endgroup diff --git a/docs/manuals/mcstas/samples/Incoherent.tex b/docs/manuals/mcstas/samples/Incoherent.tex index 5348393100..2a0758bce8 100644 --- a/docs/manuals/mcstas/samples/Incoherent.tex +++ b/docs/manuals/mcstas/samples/Incoherent.tex @@ -3,52 +3,35 @@ \section{The \texttt{Incoherent} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann and Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 15.4.98 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A Double-cylinder shaped incoherent scatterer (like Vanadium) -with both elastic and quasielastic (Lorentzian) components. -No multiple scattering (but approximation available). Absorption included. -<b>Sample focusing:</b> -The area to scatter to is a disk of radius 'focus_r' situated at the target. -This target area may also be rectangular if specified focus_xw and focus_yh -or focus_aw and focus_ah, respectively in meters and degrees. -The target itself is either situated according to given coordinates (x,y,z), -or defined with the relative target_index of the component to focus -to (next is +1). -This target position will be set to its AT position. When targeting to -centered components, such as spheres or cylinders, define an Arm component -where to focus to. -<b>Sample shape:</b> -Sample shape may be a cylinder, a sphere, a box or any other shape +A Double-cylinder shaped incoherent scatterer (like Vanadium) with both elastic and quasielastic (Lorentzian) components. No multiple scattering (but approximation available). Absorption included. \textbf{Sample focusing:} The area to scatter to is a disk of radius 'focus\_r' situated at the target. This target area may also be rectangular if specified focus\_xw and focus\_yh or focus\_aw and focus\_ah, respectively in meters and degrees. The target itself is either situated according to given coordinates (x,y,z), or defined with the relative target\_index of the component to focus to (next is +1). This target position will be set to its AT position. When targeting to centered components, such as spheres or cylinders, define an Arm component where to focus to. \textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} box/plate: xwidth x yheight x zdepth (thickness=0) -hollow box/plate:xwidth x yheight x zdepth and thickness>0 +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} cylinder: radius x yheight (thickness=0) -hollow cylinder: radius x yheight and thickness>0 +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} sphere: radius (yheight=0 thickness=0) hollow sphere: radius and thickness>0 (yheight=0) any shape: geometry=OFF file +\end{verbatim} -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the PLY, OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using: -qhull < coordinates.xyz Qx Qv Tv o > geomview.off -or -powercrust coordinates.xyz -and viewed with geomview or java -jar jroff.jar (see below). -The default size of the object depends of the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the PLY, OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. -Example: Incoherent(radius=0.05,focus_r=0.035, pack=1, target_index=1) -Incoherent(geometry="socket.off",focus_r=0.035, pack=1, target_index=1) -\end{lstlisting} +Example: Incoherent(radius=0.05,focus\_r=0.035, pack=1, target\_index=1) Incoherent(geometry="socket.off",focus\_r=0.035, pack=1, target\_index=1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -81,7 +64,7 @@ \subsection*{Input parameters} deltaE & meV & Width in energy around Etrans, for use in inelastic settings & 0 \\ sigma\_abs & barns & Absorption cross section pr. unit cell at 2200 m/s & 5.08 \\ sigma\_inc & barns & Incoherent scattering cross section pr. unit cell & 5.08 \\ -Vc & AA\textasciicircum{}3 & Unit cell volume & 13.827 \\ +Vc & \AA{}$^{3}$ & Unit cell volume & 13.827 \\ concentric & 1 & Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere) & 0 \\ order & 1 & Limit multiple scattering up to given order 0 means all (default), 1 means single, 2 means double, ... & 0 \\ \bottomrule @@ -89,17 +72,17 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Incoherent.comp}{Source code} for \texttt{Incoherent.comp}. - \item \textless{}a href="http://www.ncnr.nist.gov/resources/n-lengths/"\textgreater{}Cross sections for single elements\textless{}/a\textgreater{} - \item \textless{}a href="http://www.ncnr.nist.gov/resources/sldcalc.html\textgreater{}Cross sections for compounds\textless{}/a\textgreater{} - \item \textless{}a href="http://www.webelements.com/"\textgreater{}Web Elements\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Incoherent.comp}. + \item \htmladdnormallink{Cross sections for single elements}{http://www.ncnr.nist.gov/resources/n-lengths/} + \item \htmladdnormallink{Cross sections for compounds}{} + \item \htmladdnormallink{Web Elements}{http://www.webelements.com/} \item \textless{}A HREF="http://neutron.risoe.dk/mcstas/components/tests/Incoherent/"\textgreater{}Test \item results\textless{}/A\textgreater{} (not up-to-date). - \item The test/example instrument \textless{}a href="../examples/vanadium\_example.instr"\textgreater{}vanadium\_example.instr\textless{}/a\textgreater{}. - \item The test/example instrument \textless{}a href="../examples/QENS\_test.instr"\textgreater{}QENS\_test.instr\textless{}/a\textgreater{}. - \item \textless{}a href="http://www.geomview.org"\textgreater{}Geomview and Object File Format (OFF)\textless{}/a\textgreater{} - \item Java version of Geomview (display only) \textless{}a href="http://www.holmes3d.net/graphics/roffview/"\textgreater{}jroff.jar\textless{}/a\textgreater{} - \item \textless{}a href="http://qhull.org"\textgreater{}qhull\textless{}/a\textgreater{} - \item \textless{}a href="http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html"\textgreater{}powercrust\textless{}/a\textgreater{} + \item The test/example instrument \htmladdnormallink{vanadium\_example.instr}{../examples/vanadium\_example.instr}. + \item The test/example instrument \htmladdnormallink{QENS\_test.instr}{../examples/QENS\_test.instr}. + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} + \item Java version of Geomview (display only) \htmladdnormallink{jroff.jar}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{qhull}{http://qhull.org} + \item \htmladdnormallink{powercrust}{http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} \end{itemize} -\IfFileExists{Incoherent_static.tex}{\input{Incoherent_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Incoherent_static.tex}{\input{samples/Incoherent_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Isotropic_Sqw.tex b/docs/manuals/mcstas/samples/Isotropic_Sqw.tex index 82207461bd..ca02bd5f12 100644 --- a/docs/manuals/mcstas/samples/Isotropic_Sqw.tex +++ b/docs/manuals/mcstas/samples/Isotropic_Sqw.tex @@ -4,181 +4,129 @@ \section{The \texttt{Isotropic\_Sqw} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E. Farhi, V. Hugouvieux \item \textbf{Origin:} ILL \item \textbf{Date:} August 2003 \end{itemize} \subsection*{Description} -\begin{lstlisting} -An isotropic sample handling multiple scattering and including as input the -dynamic structure factor of the chosen sample (e.g. from Molecular -Dynamics). Handles elastic/inelastic, coherent and incoherent scattering - -depending on the input S(q,w) - with multiple scattering and absorption. -Only the norm of q is handled (not the vector), and thus suitable for -liquids, gazes, amorphous and powder samples. - -If incoherent/self S(q,w) file is specified as empty (0 or "") then the -scattering is constant isotropic (Vanadium like). -In case you only have one S(q,w) data containing both coherent and -incoherent contributions you should e.g. use 'Sqw_coh' and set 'sigma_coh' -to the total scattering cross section. Set sigma_coh and sigma_inc to -1 to inactivate. - -The implementation will automatically nornalise S(q,w) so that S(q) -> 1 at -large q (parameter norm=-1). Alternatively, the S(q,w) data will be multiplied -by 'norm' for positive values. Use norm=0 or 1 to use the raw data as input. - -The material temperature can be defined in the S(q,w) data files (see below) -or set manually as parameter T. Setting T=-1 disables detailed balance. -Setting T=-2 attempts to guess the temperature from the input S(q,w) data -which must then be non-classical and extend on both energy sides (+/-). -To use the S(q,w) data as is, without temperature effect, set T=-1 and norm=1. - -Both non symmetric (quantum) and classical S(q,w) data sets can be given by mean -of the 'classical' parameter (see below). - -Additionally, for single order scattering (order=1), you may restrict the -vertical spreading of the scattering area using d_phi parameter. - -An important option to enhance statistics is to set 'p_interact' to, say, -30 percent (0.3) in order to force a fraction of the beam to scatter. This -will result on a larger number of scattered events, retaining intensity. - -If you use this component and produce valuable scientific results, please -cite authors with references bellow (in <a href="#links">Links</a>). -E. Farhi et al, J Comp Phys 228 (2009) 5251 - -<b>Sample shape:</b> -Sample shape may be a cylinder, a sphere, a box or any other shape +An isotropic sample handling multiple scattering and including as input the dynamic structure factor of the chosen sample (e.g. from Molecular Dynamics). Handles elastic/inelastic, coherent and incoherent scattering - depending on the input S(q,w) - with multiple scattering and absorption. Only the norm of q is handled (not the vector), and thus suitable for liquids, gazes, amorphous and powder samples. + +If incoherent/self S(q,w) file is specified as empty (0 or "") then the scattering is constant isotropic (Vanadium like). In case you only have one S(q,w) data containing both coherent and incoherent contributions you should e.g. use 'Sqw\_coh' and set 'sigma\_coh' to the total scattering cross section. Set sigma\_coh and sigma\_inc to -1 to inactivate. + +The implementation will automatically nornalise S(q,w) so that S(q) -\textgreater{} 1 at large q (parameter norm=-1). Alternatively, the S(q,w) data will be multiplied by 'norm' for positive values. Use norm=0 or 1 to use the raw data as input. + +The material temperature can be defined in the S(q,w) data files (see below) or set manually as parameter T. Setting T=-1 disables detailed balance. Setting T=-2 attempts to guess the temperature from the input S(q,w) data which must then be non-classical and extend on both energy sides (+/-). To use the S(q,w) data as is, without temperature effect, set T=-1 and norm=1. + +Both non symmetric (quantum) and classical S(q,w) data sets can be given by mean of the 'classical' parameter (see below). + +Additionally, for single order scattering (order=1), you may restrict the vertical spreading of the scattering area using d\_phi parameter. + +An important option to enhance statistics is to set 'p\_interact' to, say, 30 percent (0.3) in order to force a fraction of the beam to scatter. This will result on a larger number of scattered events, retaining intensity. + +If you use this component and produce valuable scientific results, please cite authors with references bellow (in \htmladdnormallink{Links}{\#links}). E. Farhi et al, J Comp Phys 228 (2009) 5251 + +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} box/plate: xwidth x yheight x zdepth (thickness=0) -hollow box/plate:xwidth x yheight x zdepth and thickness>0 +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} cylinder: radius x yheight (thickness=0) -hollow cylinder: radius x yheight and thickness>0 +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} sphere: radius (yheight=0 thickness=0) hollow sphere: radius and thickness>0 (yheight=0) any shape: geometry=OFF file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF, PLY and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +\textbf{Concentric components:} This component has the ability to contain other components when used in hollow cylinder geometry (namely sample environment, e.g. cryostat and furnace structure). Such component 'shells' should be split into input and output side surrounding the 'inside' components. First part must then use 'concentric=1' flag to enter the inside part. The component itself must be repeated to mark the end of the concentric zone. The number of concentric shells and number of components inside is not limited. + +COMPONENT S\_in = Isotropic\_Sqw(Sqw\_coh="Al.laz", concentric=1, ...) AT (0,0,0) RELATIVE sample\_position -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the OFF, PLY and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using: -qhull < coordinates.xyz Qx Qv Tv o > geomview.off -or -powercrust coordinates.xyz -and viewed with geomview or java -jar jroff.jar (see below). -The default size of the object depends of the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. - -<b>Concentric components:</b> -This component has the ability to contain other components when used in -hollow cylinder geometry (namely sample environment, e.g. cryostat and -furnace structure). Such component 'shells' should be split into input and -output side surrounding the 'inside' components. First part must then use -'concentric=1' flag to enter the inside part. The component itself must be -repeated to mark the end of the concentric zone. The number of concentric -shells and number of components inside is not limited. - -COMPONENT S_in = Isotropic_Sqw(Sqw_coh="Al.laz", concentric=1, ...) -AT (0,0,0) RELATIVE sample_position - -COMPONENT something_inside ... // e.g. the sample itself or other materials - -COMPONENT S_out = COPY(S_in)(concentric=0) -AT (0,0,0) RELATIVE sample_position - -<b>Sqw file format:</b> -File format for S(Q,w) (coherent and incoherent) should contain 3 numerical -blocks, defining q axis values (vector), then energy axis values (vector), -then a matrix with one line per q axis value, containing Sqw values for -each energy axis value. Comments (starting with '#') and non numerical lines -are ignored and used to separate blocks. Sampling must be regular. -Some parameters can be specified in comment lines, namely (00 is a numerical value): +COMPONENT something\_inside ... // e.g. the sample itself or other materials +COMPONENT S\_out = COPY(S\_in)(concentric=0) AT (0,0,0) RELATIVE sample\_position + +\textbf{Sqw file format:} File format for S(Q,w) (coherent and incoherent) should contain 3 numerical blocks, defining q axis values (vector), then energy axis values (vector), then a matrix with one line per q axis value, containing Sqw values for each energy axis value. Comments (starting with '\#') and non numerical lines are ignored and used to separate blocks. Sampling must be regular. Some parameters can be specified in comment lines, namely (00 is a numerical value): + +\begin{verbatim} # sigma_abs 00 absorption scattering cross section in [barn] # sigma_inc 00 coherent scattering cross section in [barn] # sigma_coh 00 incoherent scattering cross section in [barn] -# Temperature 00 in [K] +\end{verbatim} + +\# Temperature 00 in [K] + +\begin{verbatim} # V_rho 00 atom density per Angs^3 # density 00 in [g/cm^3] # weight 00 in [g/mol] # classical 00 [0=contains Bose factor (measurement) ; 1=classical symmetric] +\end{verbatim} -Example: -# q axis values -# vector of m values in Angstroem-1 +Example: \# q axis values \# vector of m values in Angstroem-1 + +\begin{verbatim} 0.001000 .... 3.591000 -# w axis values -# vector of n values in meV +\end{verbatim} + +\# w axis values \# vector of n values in meV + +\begin{verbatim} 0.001391 ... 1.681391 -# sqw values (one line per q axis value) -# matrix of S(q,w) values (m rows x n values), one line per q value, +\end{verbatim} + +\# sqw values (one line per q axis value) \# matrix of S(q,w) values (m rows x n values), one line per q value, + +\begin{verbatim} 9.721422 10.599145 ... 0.000000 10.054191 11.025244 ... 0.000000 +\end{verbatim} + ... + +\begin{verbatim} 0.000000 ... 3.860253 +\end{verbatim} + +See for instance file He4\_liq\_coh.sqw. Such files may be obtained from e.g. INX, Nathan, Lamp and IDA softwares, as well as Molecular Dynamics (nMoldyn). When the provided S(q,w) data is obtained from the classical correlation function G(r,t), which is real and symmetric in time, the 'classical=1' parameter should be set in order to multiply the file data with exp(hw/2kT). Otherwise, the S(q,w) is NOT symmetrised (classical). If the S(q,w) data set includes both negative and positive energy values, setting 'classical=-1' will attempt to guess what type of S(q,w) it is. The temperature can also be determined this way. In case you do not know if the data is classical or quantum, assume it is usually classical at high temperatures, and quantum otherwise (T \textless{} typical mode excitations). The positive energy values correspond to Stokes processes, i.e. material gains energy, and neutrons loose energy. The energy range is symmetrized to allow up and down scattering, taking into account detailed balance exp(-hw/2kT). + +You may also generate such S(q,w) 2D files using \htmladdnormallink{iFit}{http://ifit.mccode.org/McStas.html\#mozTocId297488} + +\textbf{Powder file format:} Files for coherent elastic powder scattering may also be used. Format specification follows the same principle as in the PowderN component, with parameters: + +powder\_format= Crystallographica: \{ 4,5,7,0,0,0,0, 0,0 \} -See for instance file He4_liq_coh.sqw. Such files may be obtained from e.g. INX, -Nathan, Lamp and IDA softwares, as well as Molecular Dynamics (nMoldyn). -When the provided S(q,w) data is obtained from the classical correlation function -G(r,t), which is real and symmetric in time, the 'classical=1' parameter -should be set in order to multiply the file data with exp(hw/2kT). Otherwise, -the S(q,w) is NOT symmetrised (classical). If the S(q,w) data set includes both -negative and positive energy values, setting 'classical=-1' will attempt to -guess what type of S(q,w) it is. The temperature can also be determined this way. -In case you do not know if the data is classical or quantum, assume it is usually classical -at high temperatures, and quantum otherwise (T < typical mode excitations). -The positive energy values correspond to Stokes processes, i.e. material gains -energy, and neutrons loose energy. The energy range is symmetrized to allow up -and down scattering, taking into account detailed balance exp(-hw/2kT). - -You may also generate such S(q,w) 2D files using <a href="http://ifit.mccode.org/McStas.html#mozTocId297488">iFit </a> - -<b>Powder file format:</b> -Files for coherent elastic powder scattering may also be used. -Format specification follows the same principle as in the PowderN -component, with parameters: - -powder_format= -Crystallographica: { 4,5,7,0,0,0,0, 0,0 } +\begin{verbatim} Fullprof: { 4,0,8,0,0,5,0, 0,0 } Undefined: { 0,0,0,0,0,0,0, 0,0 } Lazy: {17,6,0,0,0,0,0,13,0 } qSq: {-1,0,0,0,0,0,1, 0,0 } // special case for [q,Sq] table or: {j,d,F2,DW,Delta_d/d,1/2d,q,F,strain} +\end{verbatim} -or column indexes (starting from 1) given as comments in the file header -(e.g. '#column_j 4'). Refer to the PowderN component for more details. -Delta_d/d and Debye-Waller factor may be specified for all lines with the -'powder_Dd' and 'powder_DW' parameters. -The reflection list should be ordered by decreasing d-spacing values. +or column indexes (starting from 1) given as comments in the file header (e.g. '\#column\_j 4'). Refer to the PowderN component for more details. Delta\_d/d and Debye-Waller factor may be specified for all lines with the 'powder\_Dd' and 'powder\_DW' parameters. The reflection list should be ordered by decreasing d-spacing values. -Additionally a special [q,Sq] format is also defined with: -powder_format=qSq -for which column 1 is 'q' and column 2 is 'S(q)'. +Additionally a special [q,Sq] format is also defined with: powder\_format=qSq for which column 1 is 'q' and column 2 is 'S(q)'. -<b>Examples:</b> -1- Vanadium-like incoherent elastic scattering -Isotropic_Sqw(radius=0.005, yheight=0.01, V_rho=1/13.827, -sigma_abs=5.08, sigma_inc=4.935, sigma_coh=0) +\textbf{Examples:} 1- Vanadium-like incoherent elastic scattering Isotropic\_Sqw(radius=0.005, yheight=0.01, V\_rho=1/13.827, sigma\_abs=5.08, sigma\_inc=4.935, sigma\_coh=0) -2- liq-4He parameters -Isotropic_Sqw(..., Sqw_coh="He4_liq_coh.sqw", T=10, p_interact=0.3) +2- liq-4He parameters Isotropic\_Sqw(..., Sqw\_coh="He4\_liq\_coh.sqw", T=10, p\_interact=0.3) -3- powder sample -Isotropic_Sqw(..., Sqw_coh="Al.laz") +3- powder sample Isotropic\_Sqw(..., Sqw\_coh="Al.laz") -%BUGS: -When used in concentric mode, multiple bouncing scattering -(traversing the hollow part) is not taken into account. +\%BUGS: When used in concentric mode, multiple bouncing scattering (traversing the hollow part) is not taken into account. -%VALIDATION -For Vanadium incoherent scattering mode, V_sample, PowderN, Single_crystal -and Isotropic_Sqw produce equivalent results, eventhough the two later are -more accurate (geometry, multiple scattering). Isotropic_Sqw gives same -powder patterns as PowderN, with an intensity within 20 %. -\end{lstlisting} +\%VALIDATION For Vanadium incoherent scattering mode, V\_sample, PowderN, Single\_crystal and Isotropic\_Sqw produce equivalent results, eventhough the two later are more accurate (geometry, multiple scattering). Isotropic\_Sqw gives same powder patterns as PowderN, with an intensity within 20 \%. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -189,7 +137,7 @@ \subsection*{Input parameters} \midrule \endhead powder\_format & no quotes & name or definition of column indexes in file & \{0,0,0,0,0,0,0,0,0\} \\ -Sqw\_coh & str & Name of the file containing the values of Q, w and S(Q,w) Coherent part; Q in Angs-1, E in meV, S(q,w) in meV-1. Use 0, NULL or "" to disable. & 0 \\ +Sqw\_coh & str & Name of the file containing the values of Q, w and S(Q,w) Coherent part; Q in \AA{}-1, E in meV, S(q,w) in meV-1. Use 0, NULL or "" to disable. & 0 \\ Sqw\_inc & str & Name of the file containing the values of Q, w and S(Q,w). Incoherent (self) part. Use 0, NULL or "" to scatter isotropically (V-like). & 0 \\ geometry & str & Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust & 0 \\ radius & m & Outer radius of sample in (x,z) plane. cylinder/sphere. & 0 \\ @@ -203,15 +151,15 @@ \subsection*{Input parameters} verbose & 1 & Verbosity level (0:silent, 1:normal, 2:verbose, 3:debug). A verbosity\textgreater{}1 also computes dispersions and S(q,w) analysis. & 1 \\ d\_phi & deg & scattering vertical angular spreading (usually the height of the next component/detector). Use 0 for full space. This is only relevant for single scattering (order=1). & 0 \\ concentric & 1 & Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere) [1] & 0 \\ -rho & AA-3 & Density of scattering elements (nb atoms/unit cell V\_0). & 0 \\ +rho & \AA{}$^{-3}$ & Density of scattering elements (nb atoms/unit cell V\_0). & 0 \\ sigma\_abs & barns & Absorption cross-section at 2200 m/s. Use -1 to inactivate. & 0 \\ sigma\_coh & barns & Coherent Scattering cross-section. Use -1 to inactivate. & 0 \\ sigma\_inc & barns & Incoherent Scattering cross-section. Use -1 to inactivate. & 0 \\ classical & 1 & Assumes the S(q,w) data from the files is a classical S(q,w), and multiply that data by exp(hw/2kT) on up/down energy sides. Use 0 when obtained from raw experiments, 1 from molecular dynamics. Use -1 to guess from a data set including both energy sides. & -1 \\ powder\_Dd & 1 & global Delta\_d/d spreading, or 0 if ideal. & 0 \\ powder\_DW & 1 & global Debey-Waller factor, if not in |F2| or 1. & 0 \\ -powder\_Vc & AA\textasciicircum{}3 & volume of the unit cell & 0 \\ -density & g/cm\textasciicircum{}3 & density of material. V\_rho=density/weight/1e24*N\_A & 0 \\ +powder\_Vc & \AA{}$^{3}$ & volume of the unit cell & 0 \\ +density & g/cm$^{3}$ & density of material. V\_rho=density/weight/1e24*N\_A & 0 \\ weight & g/mol & atomic/molecular weight of material & 0 \\ p\_interact & 1 & Force a given fraction of the beam to scatter, keeping intensity right, to enhance small signals (-1 inactivate). & -1 \\ norm & 1 & Normalize S(q,w) when -1 (default). Use raw data when 1, multiplier for S(q,w) when norm\textgreater{}0. & -1 \\ @@ -221,7 +169,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Isotropic_Sqw.comp}{Source code} for \texttt{Isotropic\_Sqw.comp}. + \item Component source code found in file \texttt{Isotropic\_Sqw.comp}. \item E. Farhi, V. Hugouvieux, M.R. Johnson, and W. Kob, Journal of Computational Physics 228 (2009) 5251-5261 "Virtual experiments: Combining realistic neutron scattering instrument and sample simulations" \item Hugouvieux V, Farhi E, Johnson MR, Physica B, 350 (2004) 151 "Virtual neutron scattering experiments" \item Hugouvieux V, PhD, University of Montpellier II, France (2004). @@ -229,17 +177,17 @@ \subsection*{Links} \item H.E. Fischer, A.C. Barnes, and P.S. Salmon. Rep. Prog. Phys., 69 (2006) 233 \item P.A. Egelstaff, An Introduction to the Liquid State, 2nd Ed., Oxford Science Pub., Clarendon Press (1992). \item S. W. Lovesey, Theory of Neutron Scattering from Condensed Matter, Vol1, Oxford Science Pub., Clarendon Press (1984). - \item \textless{}a href="http://www.ncnr.nist.gov/resources/n-lengths/"\textgreater{}Cross sections for single elements\textless{}/a\textgreater{} - \item \textless{}a href="http://www.ncnr.nist.gov/resources/sldcalc.html\textgreater{}Cross sections for compounds\textless{}/a\textgreater{} - \item \textless{}a href="http://www.webelements.com/"\textgreater{}Web Elements\textless{}/a\textgreater{} - \item \textless{}a href="http://www.ill.eu/sites/fullprof/index.html"\textgreater{}Fullprof\textless{}/a\textgreater{} powder refinement - \item \textless{}a href="http://www.crystallographica.com/"\textgreater{}Crystallographica\textless{}/a\textgreater{} software - \item Example data file \textless{}a href="../data/He4\_liq\_coh.sqw"\textgreater{}He4\_liq\_coh.sqw\textless{}/a\textgreater{} - \item The \textless{}a href="PowderN.html"\textgreater{}PowderN\textless{}/a\textgreater{} component. - \item The test/example instrument \textless{}a href="../examples/Test\_Isotropic\_Sqw.instr"\textgreater{}Test\_Isotropic\_Sqw.instr\textless{}/a\textgreater{}. - \item \textless{}a href="http://www.geomview.org"\textgreater{}Geomview and Object File Format (OFF)\textless{}/a\textgreater{} - \item Java version of Geomview (display only) \textless{}a href="http://www.holmes3d.net/graphics/roffview/"\textgreater{}jroff.jar\textless{}/a\textgreater{} - \item \textless{}a href="http://qhull.org"\textgreater{}qhull\textless{}/a\textgreater{} - \item \textless{}a href="http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html"\textgreater{}powercrust\textless{}/a\textgreater{} + \item \htmladdnormallink{Cross sections for single elements}{http://www.ncnr.nist.gov/resources/n-lengths/} + \item \htmladdnormallink{Cross sections for compounds}{} + \item \htmladdnormallink{Web Elements}{http://www.webelements.com/} + \item \htmladdnormallink{Fullprof}{http://www.ill.eu/sites/fullprof/index.html} powder refinement + \item \htmladdnormallink{Crystallographica}{http://www.crystallographica.com/} software + \item Example data file \htmladdnormallink{He4\_liq\_coh.sqw}{../data/He4\_liq\_coh.sqw} + \item The \htmladdnormallink{PowderN}{PowderN.html} component. + \item The test/example instrument \htmladdnormallink{Test\_Isotropic\_Sqw.instr}{../examples/Test\_Isotropic\_Sqw.instr}. + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} + \item Java version of Geomview (display only) \htmladdnormallink{jroff.jar}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{qhull}{http://qhull.org} + \item \htmladdnormallink{powercrust}{http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} \end{itemize} -\IfFileExists{Isotropic_Sqw_static.tex}{\input{Isotropic_Sqw_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Isotropic_Sqw_static.tex}{\input{samples/Isotropic_Sqw_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Magnon_bcc.tex b/docs/manuals/mcstas/samples/Magnon_bcc.tex index f5289885bb..69d203a71e 100644 --- a/docs/manuals/mcstas/samples/Magnon_bcc.tex +++ b/docs/manuals/mcstas/samples/Magnon_bcc.tex @@ -4,39 +4,17 @@ \section{The \texttt{Magnon\_bcc} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} KU \item \textbf{Date:} 23.10.08 - 24.07.18 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Single-cylinder shape. -Absorption included. -No multiple scattering. -No incoherent scattering emitted. -No attenuation from coherent scattering. No Bragg scattering. -bcc crystal n.n. and n.n.n. interactions only -Can do either FM or AFM order upon a flag -Assume J>0 for both FM and AFM. MUST BE CHANGED FOR CONSISTENCY -If AFM, the order is two-sublattice, e.g. the AFM Bragg ordering vectors are Q = (1 0 0) and equivalent. -One magnon branch only -Assume spin along z -Possible easy axis anisotropy along z -No external field +Single-cylinder shape. Absorption included. No multiple scattering. No incoherent scattering emitted. No attenuation from coherent scattering. No Bragg scattering. bcc crystal n.n. and n.n.n. interactions only Can do either FM or AFM order upon a flag Assume J\textgreater{}0 for both FM and AFM. MUST BE CHANGED FOR CONSISTENCY If AFM, the order is two-sublattice, e.g. the AFM Bragg ordering vectors are Q = (1 0 0) and equivalent. One magnon branch only Assume spin along z Possible easy axis anisotropy along z No external field -KNOWN BUGS: -Gives zero scattering for too large J values (for AFM J=0.362, h approx 1). Probably this is a malfunction of zridd or call thereof -The value of the absolute scattered intensity is clearly too high. This is probably due to unit confusion. The relative intensity scaling seems about right. +KNOWN BUGS: Gives zero scattering for too large J values (for AFM J=0.362, h approx 1). Probably this is a malfunction of zridd or call thereof The value of the absolute scattered intensity is clearly too high. This is probably due to unit confusion. The relative intensity scaling seems about right. -Algorithm: -0. Always perform the scattering if possible (otherwise ABSORB) -1. Choose direction within a focusing solid angle -2. Calculate the zeros of (E_i-E_f-hbar omega(kappa)) as a function of k_f -3. Choose one value of k_f (always at least one is possible!) -4. Perform the correct weight transformation -\end{lstlisting} +Algorithm: 0. Always perform the scattering if possible (otherwise ABSORB) 1. Choose direction within a focusing solid angle 2. Calculate the zeros of (E\_i-E\_f-hbar omega(kappa)) as a function of k\_f 3. Choose one value of k\_f (always at least one is possible!) 4. Perform the correct weight transformation \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -50,7 +28,7 @@ \subsection*{Input parameters} \textbf{yheight} & m & Height of sample in y direction & \\ \textbf{sigma\_abs} & barns & Absorption cross section at 2200 m/s per atom & \\ \textbf{sigma\_inc} & barns & Incoherent scattering cross section per atom & \\ -\textbf{a} & AA & bcc Lattice constant & \\ +\textbf{a} & \AA{} & bcc Lattice constant & \\ FM & 1 & Flag for whether the order if FM (0 means AFM) & 0 \\ \textbf{J1} & meV & spin-spin interaction 1 (nn) & \\ \textbf{J2} & meV & spin-spin interaction 2 (nnn) & \\ @@ -74,7 +52,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Magnon_bcc.comp}{Source code} for \texttt{Magnon\_bcc.comp}. - \item The test/example instrument \textless{}a href="../examples/Test\_Magnon.instr"\textgreater{}Test\_Magnon.instr\textless{}/a\textgreater{}. + \item Component source code found in file \texttt{Magnon\_bcc.comp}. + \item The test/example instrument \htmladdnormallink{Test\_Magnon.instr}{../examples/Test\_Magnon.instr}. \end{itemize} -\IfFileExists{Magnon_bcc_static.tex}{\input{Magnon_bcc_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Magnon_bcc_static.tex}{\input{samples/Magnon_bcc_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/NCrystal_sample.tex b/docs/manuals/mcstas/samples/NCrystal_sample.tex index 0ea4838c68..f9e05ed08f 100644 --- a/docs/manuals/mcstas/samples/NCrystal_sample.tex +++ b/docs/manuals/mcstas/samples/NCrystal_sample.tex @@ -4,32 +4,21 @@ \section{The \texttt{NCrystal\_sample} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} NCrystal developers \item \textbf{Origin:} NCrystal Developers (European Spallation Source ERIC and DTU Nutech) \item \textbf{Date:} 2015 \end{itemize} \subsection*{Description} -\begin{lstlisting} -McStas sample component using the NCrystal library for thermal neutron -transport in a single bulk material filling a single simple convex volume -(box, sphere or cylinder). +McStas sample component using the NCrystal library for thermal neutron transport in a single bulk material filling a single simple convex volume (box, sphere or cylinder). -The geometrical layout of the volume is determined via the xwidth, yheight, -zdepth, and radius parameters, and the material being modelled is determined -via an NCrystal configuration string ("cfg-string"). +The geometrical layout of the volume is determined via the xwidth, yheight, zdepth, and radius parameters, and the material being modelled is determined via an NCrystal configuration string ("cfg-string"). -For more information about NCrystal and cfg-strings, refer to the <a href="https://github.com/mctools/ncrystal/wiki">NCrystal wiki</a>. -In particular, browse the available datafiles at <a href="https://github.com/mctools/ncrystal/wiki/Data-library">Data-library</a> and read about the -format of the cfg-string expected in the "cfg" parameter at <a href="https://github.com/mctools/ncrystal/wiki/Using-NCrystal">Using-NCrystal</a>. +For more information about NCrystal and cfg-strings, refer to the \htmladdnormallink{NCrystal wiki}{https://github.com/mctools/ncrystal/wiki}. In particular, browse the available datafiles at \htmladdnormallink{Data-library}{https://github.com/mctools/ncrystal/wiki/Data-library} and read about the format of the cfg-string expected in the "cfg" parameter at \htmladdnormallink{Using-NCrystal}{https://github.com/mctools/ncrystal/wiki/Using-NCrystal}. -For more complicated geometries, it might be desirable to use NCrystal via the -McStas Union components instead. +For more complicated geometries, it might be desirable to use NCrystal via the McStas Union components instead. -Note that the physics backend of this component will be whichever NCrystal -installation is available and associated with the "ncrystal-config" command. -\end{lstlisting} +Note that the physics backend of this component will be whichever NCrystal installation is available and associated with the "ncrystal-config" command. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -51,7 +40,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/NCrystal_sample.comp}{Source code} for \texttt{NCrystal\_sample.comp}. - \item The NCrystal wiki at \textless{}a href="https://github.com/mctools/ncrystal/wiki"\textgreater{}https://github.com/mctools/ncrystal/wiki\textless{}/a\textgreater{}. + \item Component source code found in file \texttt{NCrystal\_sample.comp}. + \item The NCrystal wiki at \htmladdnormallink{https://github.com/mctools/ncrystal/wiki}{https://github.com/mctools/ncrystal/wiki}. \end{itemize} -\IfFileExists{NCrystal_sample_static.tex}{\input{NCrystal_sample_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/NCrystal_sample_static.tex}{\input{samples/NCrystal_sample_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Phonon_simple.tex b/docs/manuals/mcstas/samples/Phonon_simple.tex index f29808d2c0..0acbfbc609 100644 --- a/docs/manuals/mcstas/samples/Phonon_simple.tex +++ b/docs/manuals/mcstas/samples/Phonon_simple.tex @@ -4,30 +4,15 @@ \section{The \texttt{Phonon\_simple} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} 04.02.04 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Single-cylinder shape. -Absorption included. -No multiple scattering. -No incoherent scattering emitted. -No attenuation from coherent scattering. No Bragg scattering. -fcc crystal n.n. interactions only -One phonon branch only -> phonon polarization not accounted for. -Bravais lattice only. (i.e. just one atom per unit cell) +Single-cylinder shape. Absorption included. No multiple scattering. No incoherent scattering emitted. No attenuation from coherent scattering. No Bragg scattering. fcc crystal n.n. interactions only One phonon branch only -\textgreater{} phonon polarization not accounted for. Bravais lattice only. (i.e. just one atom per unit cell) -Algorithm: -0. Always perform the scattering if possible (otherwise ABSORB) -1. Choose direction within a focusing solid angle -2. Calculate the zeros of (E_i-E_f-hbar omega(kappa)) as a function of k_f -3. Choose one value of k_f (always at least one is possible!) -4. Perform the correct weight transformation -\end{lstlisting} +Algorithm: 0. Always perform the scattering if possible (otherwise ABSORB) 1. Choose direction within a focusing solid angle 2. Calculate the zeros of (E\_i-E\_f-hbar omega(kappa)) as a function of k\_f 3. Choose one value of k\_f (always at least one is possible!) 4. Perform the correct weight transformation \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -41,10 +26,10 @@ \subsection*{Input parameters} \textbf{yheight} & m & Height of sample in y direction & \\ \textbf{sigma\_abs} & barns & Absorption cross section at 2200 m/s per atom & \\ \textbf{sigma\_inc} & barns & Incoherent scattering cross section per atom & \\ -\textbf{a} & AA & fcc Lattice constant & \\ +\textbf{a} & \AA{} & fcc Lattice constant & \\ \textbf{b} & fm & Scattering length & \\ \textbf{M} & a.u. & Atomic mass & \\ -\textbf{c} & meV/AA\textasciicircum{}(-1) & Velocity of sound & \\ +\textbf{c} & meV/\AA{}$^{-1}$ & Velocity of sound & \\ \textbf{DW} & 1 & Debye-Waller factor & \\ \textbf{T} & K & Temperature & \\ target\_x & m & position of target to focus at . Transverse coordinate & 0 \\ @@ -64,7 +49,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Phonon_simple.comp}{Source code} for \texttt{Phonon\_simple.comp}. - \item The test/example instrument \textless{}a href="../examples/Test\_Phonon.instr"\textgreater{}Test\_Phonon.instr\textless{}/a\textgreater{}. + \item Component source code found in file \texttt{Phonon\_simple.comp}. + \item The test/example instrument \htmladdnormallink{Test\_Phonon.instr}{../examples/Test\_Phonon.instr}. \end{itemize} -\IfFileExists{Phonon_simple_static.tex}{\input{Phonon_simple_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Phonon_simple_static.tex}{\input{samples/Phonon_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Phonon_simple_static.tex b/docs/manuals/mcstas/samples/Phonon_simple_static.tex index ab244e7756..798efd0608 100644 --- a/docs/manuals/mcstas/samples/Phonon_simple_static.tex +++ b/docs/manuals/mcstas/samples/Phonon_simple_static.tex @@ -3,7 +3,7 @@ \subsection*{A simple phonon sample} \index{Samples!Phonon scattering} \index{Inelastic scattering} -%\component{Phonon\_simple}{Kim Lefmann, Ris\o\ National Laboratory}{ $r_\textrm{o}$, $h$, $r_\textrm{foc}$, $x_\textrm{target}$, $y_\textrm{target}$, $z_\textrm{target}$, $\sigma_\textrm{abs}$, $\sigma_\textrm{inc}$, $a$, $b$, $c$, $M$, $DW$, $T$}{$w_x$, $h_y$, $t_z$, $w_\textrm{focus}, h_\textrm{focus}$, $w_\textrm{foc, angle}$, $h_\textrm{foc, angle}$, target\_index}{only validated qualitatively} +%\component{Phonon\_simple}{Kim Lefmann, Risø National Laboratory}{ $r_\textrm{o}$, $h$, $r_\textrm{foc}$, $x_\textrm{target}$, $y_\textrm{target}$, $z_\textrm{target}$, $\sigma_\textrm{abs}$, $\sigma_\textrm{inc}$, $a$, $b$, $c$, $M$, $DW$, $T$}{$w_x$, $h_y$, $t_z$, $w_\textrm{focus}, h_\textrm{focus}$, $w_\textrm{foc, angle}$, $h_\textrm{foc, angle}$, target\_index}{only validated qualitatively} %\mcdoccomp{samples/Phonon_simple.parms} This component models a simple phonon signal from a single crystal of @@ -36,7 +36,7 @@ \subsection{The phonon cross section} % This is modified from the paper version \frac{d^2\sigma'}{d\Omega dE_\textrm{f}} &=& b^2 \frac{k_\textrm{f}}{k_\textrm{i}} \frac{(2\pi)^3}{V_0}\frac{1}{2M} \exp(-2W) \nonumber \\ &\times& - \sum_{\tau,q,p} \frac{(\mbox{\boldmath $\kappa$} \cdot \textbf{e}_{q,p})^2} + \sum_{\tau,q,p} \frac{(\boldsymbol{\kappa} \cdot \textbf{e}_{q,p})^2} {\omega_{q,p}} \left\langle n_{q,p} + \frac{1}{2} \mp \frac{1}{2} \right\rangle \delta(\omega\pm\omega_{q,p}) \delta(\kappa\pm\textbf{q}-\tau) , @@ -58,7 +58,7 @@ \subsection{The phonon cross section} % This is modified from the paper version We have simplified this expression by assuming no polarization dependence of the dispersion, giving -$\sum_{p} (\mbox{\boldmath $\kappa$} \cdot \textbf{e}_{q,p})^2 = \kappa^2$. +$\sum_{p} (\boldsymbol{\kappa} \cdot \textbf{e}_{q,p})^2 = \kappa^2$. We assume that the inter-atomic interaction is nearest-neighbour-only so that the phonon dispersion becomes: \begin{equation} @@ -75,16 +75,16 @@ \subsection{The phonon cross section} % This is modified from the paper version To calculate $d\sigma/d\Omega$ we need to transform the \textbf{q} sum into an integral over the Brillouin zone by $\sum_q \rightarrow N V_\textrm{c} (2\pi)^{-3} \int_\textrm{BZ} d^3\textbf{q}$. -The $\mbox{\boldmath $\kappa$}$ sum can now be removed by +The $\boldsymbol{\kappa}$ sum can now be removed by expanding the \textbf{q} integral to infinity. All in all, the partial differential cross section reads \begin{eqnarray} \frac{d^2\sigma'}{d\Omega dE_\textrm{f}} - (\mbox{\boldmath $\kappa$},\omega) &=& + (\boldsymbol{\kappa},\omega) &=& N b^2 \frac{k_\textrm{f}}{k_\textrm{i}} \frac{1}{2M} \int \frac{\hbar \kappa^2}{\hbar \omega_q} \left\langle n_{q}+\frac{1}{2}\mp\frac{1}{2} \right\rangle - \delta(\omega\pm\omega_{q}) \delta(\mbox{\boldmath $\kappa$}\pm\textbf{q}) + \delta(\omega\pm\omega_{q}) \delta(\boldsymbol{\kappa}\pm\textbf{q}) d^3\textbf{q} \nonumber \\ &=& N b^2 \frac{k_\textrm{f}}{k_\textrm{i}} \frac{\hbar^2 \kappa^2}{2M \hbar \omega_q} diff --git a/docs/manuals/mcstas/samples/Powder1.tex b/docs/manuals/mcstas/samples/Powder1.tex index 5085e88971..f052ab831a 100644 --- a/docs/manuals/mcstas/samples/Powder1.tex +++ b/docs/manuals/mcstas/samples/Powder1.tex @@ -3,25 +3,19 @@ \section{The \texttt{Powder1} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} E.M.Lauridsen, N.B.Christensen, A.B.Abrahamsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 4.2.98 \end{itemize} \subsection*{Description} -\begin{lstlisting} -General powder sample with a single scattering vector. No multiple , -scattering, no incoherent scattering, no secondary extinction. -The shape of the sample may be a cylinder of given radius or a box with -dimensions xwidth, yheight, zdepth. -The efficient is highly improved when restricting the vertical scattering -range on the Debye-Scherrer cone (with 'd_phi'). -You may use PowderN to use N scattering lines defined in a file. +General powder sample with a single scattering vector. No multiple , scattering, no incoherent scattering, no secondary extinction. The shape of the sample may be a cylinder of given radius or a box with dimensions xwidth, yheight, zdepth. The efficient is highly improved when restricting the vertical scattering range on the Debye-Scherrer cone (with 'd\_phi'). You may use PowderN to use N scattering lines defined in a file. -Example: Powder1(radius=0.015,yheight=0.05,q =1.8049,d_phi=0.07,pack=1, +Example: Powder1(radius=0.015,yheight=0.05,q =1.8049,d\_phi=0.07,pack=1, + +\begin{verbatim} j=6,DW=1,F2=56.8,Vc=85.0054,sigma_abs=0.463) -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -35,23 +29,23 @@ \subsection*{Input parameters} yheight & m & Height of sample y direction & 0.05 \\ xwidth & m & horiz. dimension of sample, as a width & 0 \\ zdepth & m & depth of box sample & 0 \\ -q & AA\textasciicircum{}-1 & Scattering vector of reflection & 1.8049 \\ -d & AA & d-spacing for sample, overrides 'q' & 0 \\ +q & \AA{}$^{-1}$ & Scattering vector of reflection & 1.8049 \\ +d & \AA{} & d-spacing for sample, overrides 'q' & 0 \\ d\_phi & deg,0-180 & Angle corresponding to the vertical angular range to focus to, e.g. detector height. 0 for no focusing & 0 \\ pack & 1 & Packing factor & 1 \\ j & 1 & Multiplicity of reflection & 6 \\ DW & 1 & Debye-Waller factor of reflection & 1 \\ F2 & barns & Structure factor of reflection & 56.8 \\ -Vc & AA\textasciicircum{}3 & Volume of unit cell & 85.0054 \\ +Vc & \AA{}$^{3}$ & Volume of unit cell & 85.0054 \\ sigma\_abs & barns & Absorption cross section per unit cell at 2200 m/s & 0.463 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Powder1.comp}{Source code} for \texttt{Powder1.comp}. + \item Component source code found in file \texttt{Powder1.comp}. \item \textless{}A HREF="http://neutron.risoe.dk/mcstas/components/tests/powder/"\textgreater{} \item Test results\textless{}/A\textgreater{} (not up-to-date). \item See also: Powder1, Powder2 and PowderN \end{itemize} -\IfFileExists{Powder1_static.tex}{\input{Powder1_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Powder1_static.tex}{\input{samples/Powder1_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/PowderN.tex b/docs/manuals/mcstas/samples/PowderN.tex index f92d73f1b1..a8d0aeaa66 100644 --- a/docs/manuals/mcstas/samples/PowderN.tex +++ b/docs/manuals/mcstas/samples/PowderN.tex @@ -3,127 +3,107 @@ \section{The \texttt{PowderN} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} P. Willendrup, L. Chapon, K. Lefmann, A.B.Abrahamsen, N.B.Christensen, E.M.Lauridsen. \item \textbf{Origin:} McStas release \item \textbf{Date:} 4.2.98 \end{itemize} \subsection*{Description} -\begin{lstlisting} -General powder sample with -many scattering vectors -possibility for intrinsic line broadening -incoherent elastic background ratio is specified by user -No multiple scattering. No secondary extinction. - -Based on Powder1/Powder2/Single_crystal. -Geometry is a powder filled cylinder, sphere, box or any shape from an OFF file. -Incoherent scattering is only provided here to account for a background. -The efficient is highly improved when restricting the vertical scattering -range on the Debye-Scherrer cone (with 'd_phi' and 'focus_flip'). -The unit cell volume Vc may also be computed when giving the density, -the atomic/molecular weight and the number of atoms per unit cell. -A simple strain handling is available by mean of either a global Strain parameter, -or a column with a strain value per Bragg reflection. The strain values are -specified in ppm (1e-6). -The Single_crystal component can also handle a powder mode, as well as an -approximated texture. - -<b>Sample shape:</b> -Sample shape may be a cylinder, a sphere, a box or any other shape. +General powder sample with many scattering vectors possibility for intrinsic line broadening incoherent elastic background ratio is specified by user No multiple scattering. No secondary extinction. + +Based on Powder1/Powder2/Single\_crystal. Geometry is a powder filled cylinder, sphere, box or any shape from an OFF file. Incoherent scattering is only provided here to account for a background. The efficient is highly improved when restricting the vertical scattering range on the Debye-Scherrer cone (with 'd\_phi' and 'focus\_flip'). The unit cell volume Vc may also be computed when giving the density, the atomic/molecular weight and the number of atoms per unit cell. A simple strain handling is available by mean of either a global Strain parameter, or a column with a strain value per Bragg reflection. The strain values are specified in ppm (1e-6). The Single\_crystal component can also handle a powder mode, as well as an approximated texture. + +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape. + +\begin{verbatim} box/plate: xwidth x yheight x zdepth (thickness=0) -hollow box/plate:xwidth x yheight x zdepth and thickness>0 +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} cylinder: radius x yheight (thickness=0) -hollow cylinder: radius x yheight and thickness>0 +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} sphere: radius (yheight=0 thickness=0) hollow sphere: radius and thickness>0 (yheight=0) any shape: geometry=OFF_file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the PLY, OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +If you use this component and produce valuable scientific results, please cite authors with references bellow (in \htmladdnormallink{Links}{\#links}). + +Example: PowderN(reflections = "c60.lau", d\_phi = 15 , radius = 0.01, yheight = 0.05, Vc = 1076.89, sigma\_abs = 0, delta\_d\_d=0, DW=1)) + +\textbf{Powder definition file format} Powder structure is specified with an ascii data file 'reflections'. The powder data are free-text column based files. The reflection list should be ordered by decreasing d-spacing values. -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the PLY, OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using: -qhull < coordinates.xyz Qx Qv Tv o > geomview.off -or -powercrust coordinates.xyz -and viewed with geomview or java -jar jroff.jar (see below). -The default size of the object depends of the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. - -If you use this component and produce valuable scientific results, please -cite authors with references bellow (in <a href="#links">Links</a>). - -Example: PowderN(reflections = "c60.lau", d_phi = 15 , radius = 0.01, -yheight = 0.05, Vc = 1076.89, sigma_abs = 0, delta_d_d=0, DW=1)) - -<b>Powder definition file format</b> -Powder structure is specified with an ascii data file 'reflections'. -The powder data are free-text column based files. -The reflection list should be ordered by decreasing d-spacing values. +\begin{verbatim} ... d ... F2 -Lines begining by '#' are read as comments (ignored) but they may contain -the following keywords (in the header): +\end{verbatim} + +Lines begining by '\#' are read as comments (ignored) but they may contain the following keywords (in the header): + +\begin{verbatim} #Vc <value of unit cell volume Vc [Angs^3]> #sigma_abs <value of Absorption cross section [barns]> #sigma_inc <value of Incoherent cross section [barns]> -#Debye_Waller <value of Debye-Waller factor DW> +\end{verbatim} + +\#Debye\_Waller \textless{}value of Debye-Waller factor DW\textgreater{} + +\begin{verbatim} #delta_d_d/d <value of delta_d_d/d width for all lines> +\end{verbatim} + These values are not read if entered as component parameters (Vc=...) -The signification of the columns in the numerical block may be -set using the 'format' parameter, by defining signification of the -columns as a vector of indexes in the order -format={j,d,F2,DW,delta_d_d/d,1/2d,q,F,Strain} +The signification of the columns in the numerical block may be set using the 'format' parameter, by defining signification of the columns as a vector of indexes in the order format=\{j,d,F2,DW,delta\_d\_d/d,1/2d,q,F,Strain\} -Signification of the symbols is given below. Indices start at 1. -Indices with zero means that the column are not present, so that: -Crystallographica={ 4,5,7,0,0,0,0,0,0 } +Signification of the symbols is given below. Indices start at 1. Indices with zero means that the column are not present, so that: Crystallographica=\{ 4,5,7,0,0,0,0,0,0 \} + +\begin{verbatim} Fullprof ={ 4,0,8,0,0,5,0,0,0 } Lazy ={17,6,0,0,0,0,0,13,0} +\end{verbatim} + +At last, the format may be overridden by direct definition of the column indexes in the file itself by using the following keywords in the header (e.g. '\#column\_j 4'): -At last, the format may be overridden by direct definition of the -column indexes in the file itself by using the following keywords -in the header (e.g. '#column_j 4'): +\begin{verbatim} #column_j <index of the multiplicity 'j' column> #column_d <index of the d-spacing 'd' column [Angs]> #column_F2 <index of the squared str. factor '|F|^2' column [b]> #column_F <index of the structure factor norm '|F|' column> #column_DW <index of the Debye-Waller factor 'DW' column> #column_Dd <index of the relative line width delta_d_d/d broadening 'Dd' column> -#column_inv2d <index of the 1/2d=sin(theta)/lambda 'inv2d' column> -#column_q <index of the scattering wavevector 'q' column [Angs-1]> -#column_strain <index of the strain line shift Delta/d [ppm]> +\end{verbatim} -Last, CIF, FullProf and ShelX files can be read, and converted to F2(hkl) lists -if 'cif2hkl' is installed. The CIF2HKL env variable can be used to point to a -proper executable, else the McCode, then the system installed versions are used. +\#column\_inv2d \textless{}index of the 1/2d=sin(theta)/lambda 'inv2d' column\textgreater{} + +\begin{verbatim} +#column_q <index of the scattering wavevector 'q' column [Angs-1]> +\end{verbatim} -<b>Concentricity</b> +\#column\_strain \textless{}index of the strain line shift Delta/d [ppm]\textgreater{} -PowderN assumes 'concentric' shape, i.e. can contain other components inside its -optional inner hollow. Example, Sample in Al cryostat: +Last, CIF, FullProf and ShelX files can be read, and converted to F2(hkl) lists if 'cif2hkl' is installed. The CIF2HKL env variable can be used to point to a proper executable, else the McCode, then the system installed versions are used. +\textbf{Concentricity} -COMPONENT Cryo = PowderN(reflections="Al.laz", radius = 0.01, thickness = 0.001, -concentric = 1, p_interact=0.1) -AT (0,0,0) RELATIVE Somewhere +PowderN assumes 'concentric' shape, i.e. can contain other components inside its optional inner hollow. Example, Sample in Al cryostat: -COMPONENT Sample = some_other_component(with geometry FULLY enclosed in the hollow) -AT (0,0,0) RELATIVE Somewhere +COMPONENT Cryo = PowderN(reflections="Al.laz", radius = 0.01, thickness = 0.001, concentric = 1, p\_interact=0.1) AT (0,0,0) RELATIVE Somewhere -COMPONENT Cryo2 = COPY(Cryo)(concentric = 0) -AT (0,0,0) RELATIVE Somewhere +COMPONENT Sample = some\_other\_component(with geometry FULLY enclosed in the hollow) AT (0,0,0) RELATIVE Somewhere +COMPONENT Cryo2 = COPY(Cryo)(concentric = 0) AT (0,0,0) RELATIVE Somewhere -(The second instance of the cryostat component can also be written out completely -using PowderN(...). In both cases, this second instance needs concentric = 0.) -The concentric arrangment can not be used with OFF geometry specification. +(The second instance of the cryostat component can also be written out completely using PowderN(...). In both cases, this second instance needs concentric = 0.) The concentric arrangment can not be used with OFF geometry specification. -This sample component can advantageously benefit from the SPLIT feature, e.g. -SPLIT COMPONENT pow = PowderN(...) -\end{lstlisting} +This sample component can advantageously benefit from the SPLIT feature, e.g. SPLIT COMPONENT pow = PowderN(...) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -133,7 +113,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -reflections & string & Input file for reflections (LAZ LAU CIF, FullProf, ShelX). Use only incoherent scattering if NULL or "" & "NULL" \\ +reflections & string & Input file for reflections (LAZ LAU CIF, FullProf, ShelX, NCrystal). Use only incoherent scattering if NULL or "" & "NULL" \\ geometry & str & Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust. & "NULL" \\ format & no quotes & Name of the format, or list of column indexes (see Description). & \{0, 0, 0, 0, 0, 0, 0, 0, 0\} \\ radius & m & Outer radius of sample in (x,z) plane & 0 \\ @@ -142,7 +122,7 @@ \subsection*{Input parameters} zdepth & m & Depth of box sample & 0 \\ thickness & m & Thickness of hollow sample. Negative value extends the hollow volume outside of the box/cylinder. & 0 \\ pack & 1 & Packing factor. & 1 \\ -Vc & AA\textasciicircum{}3 & Volume of unit cell=nb atoms per cell/density of atoms. & 0 \\ +Vc & \AA{}$^{3}$ & Volume of unit cell=nb atoms per cell/density of atoms. & 0 \\ sigma\_abs & barns & Absorption cross section per unit cell at 2200 m/s. Use a negative value to inactivate it. & 0 \\ sigma\_inc & barns & Incoherent cross section per unit cell. Use a negative value to inactivate it. & 0 \\ delta\_d\_d & 0/1 & Global relative delta\_d\_d/d broadening when the 'w' column is not available. Use 0 if ideal. & 0 \\ @@ -155,29 +135,28 @@ \subsection*{Input parameters} tth\_sign & 1 & Sign of the scattering angle. If 0, the sign is chosen randomly (left and right). ONLY functional in combination with d\_phi and ONLY applies to bragg lines. & 0 \\ p\_interact & 1 & Fraction of events interacting coherently with sample. & 0.8 \\ concentric & 1 & Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere). & 0 \\ -density & g/cm\textasciicircum{}3 & Density of material. rho=density/weight/1e24*N\_A. & 0 \\ +density & g/cm$^{3}$ & Density of material. rho=density/weight/1e24*N\_A. & 0 \\ weight & g/mol & Atomic/molecular weight of material. & 0 \\ barns & 1 & Flag to indicate if |F|\textasciicircum{}2 from 'reflections' is in barns or fm\textasciicircum{}2 (barns=1 for laz, barns=0 for lau type files). & 1 \\ Strain & ppm & Global relative delta\_d\_d/d shift when the 'Strain' column is not available. Use 0 if ideal. & 0 \\ focus\_flip & 1 & Controls the sense of d\_phi. If 0 d\_phi is measured against the xz-plane. If !=0 d\_phi is measured against zy-plane. & 0 \\ -target\_index & 1 & Relative index of component to focus incoherent scattering at, e.g. next is +1 & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/PowderN.comp}{Source code} for \texttt{PowderN.comp}. + \item Component source code found in file \texttt{PowderN.comp}. \item "Validation of a realistic powder sample using data from DMC at PSI" Willendrup P, Filges U, Keller L, Farhi E, Lefmann K, Physica B-Cond Matt 385 (2006) 1032. \item See also: Powder1, Single\_crystal - \item See \textless{}a href="http://icsd.ill.fr"\textgreater{}ICSD\textless{}/a\textgreater{} Inorganic Crystal Structure Database - \item \textless{}a href="http://www.ncnr.nist.gov/resources/n-lengths/"\textgreater{}Cross sections for single elements\textless{}/a\textgreater{} - \item \textless{}a href="http://www.ncnr.nist.gov/resources/sldcalc.html\textgreater{}Cross sections for compounds\textless{}/a\textgreater{} - \item \textless{}a href="http://www.webelements.com/"\textgreater{}Web Elements\textless{}/a\textgreater{} - \item \textless{}a href="http://www.ill.eu/sites/fullprof/index.html"\textgreater{}Fullprof\textless{}/a\textgreater{} powder refinement - \item \textless{}a href="http://www.crystallographica.com/"\textgreater{}Crystallographica\textless{}/a\textgreater{} software (free license) - \item \textless{}a href="http://www.geomview.org"\textgreater{}Geomview and Object File Format (OFF)\textless{}/a\textgreater{} - \item Java version of Geomview (display only) \textless{}a href="http://www.holmes3d.net/graphics/roffview/"\textgreater{}jroff.jar\textless{}/a\textgreater{} - \item \textless{}a href="http://qhull.org"\textgreater{}qhull\textless{}/a\textgreater{} - \item \textless{}a href="http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html"\textgreater{}powercrust\textless{}/a\textgreater{} + \item See \htmladdnormallink{ICSD}{http://icsd.ill.fr} Inorganic Crystal Structure Database + \item \htmladdnormallink{Cross sections for single elements}{http://www.ncnr.nist.gov/resources/n-lengths/} + \item \htmladdnormallink{Cross sections for compounds}{} + \item \htmladdnormallink{Web Elements}{http://www.webelements.com/} + \item \htmladdnormallink{Fullprof}{http://www.ill.eu/sites/fullprof/index.html} powder refinement + \item \htmladdnormallink{Crystallographica}{http://www.crystallographica.com/} software (free license) + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} + \item Java version of Geomview (display only) \htmladdnormallink{jroff.jar}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{qhull}{http://qhull.org} + \item \htmladdnormallink{powercrust}{http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} \end{itemize} -\IfFileExists{PowderN_static.tex}{\input{PowderN_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/PowderN_static.tex}{\input{samples/PowderN_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Res_sample.tex b/docs/manuals/mcstas/samples/Res_sample.tex index 7ee724ddd2..04dea66f01 100644 --- a/docs/manuals/mcstas/samples/Res_sample.tex +++ b/docs/manuals/mcstas/samples/Res_sample.tex @@ -1,54 +1,51 @@ -\section{Res\_sample: A sample-like component for resolution calculation} -\label{s:res_sample} -\index{Samples!Resolution function, sample for} - -The component \textbf{Res\_sample} scatters neutron rays isotropically -in direction and uniformly in energy. -Regardless of the state of the incoming neutron ray, -all directions and energies for the scattered ray have the same probability, -within specified intervals. - -The component is meant -for computation of the resolution function, but may also be used -for test and debugging purposes. For actual calculations of the resolution -function, \textbf{Res\_sample} should be used -together with \textbf{Res\_monitor}, described in -section~\ref{s:res_monitor}. - -The shape of \textrm{Res\_sample} is either a hollow cylinder -or a rectangular box. -The hollow cylinder shape is -specified with the outer radius, $r$ and thickness, -respectively, and the height, $h$. -If these parameters are unspecified, -the shape is instead a box of dimensions $x_w$, $y_h$, and $z_d$. - -The component only propagates neutron rays that are scattered; -other rays are absorbed. The scattering probability is proportional to the neutron -flight path length inside the sample, to make a true volume weighting -of the sample. The reason for this is that the resolution -function of an instrument is independent of any sample properties -such as scattering and absorbtion cross sections but will in general -depend on sample size and shape. - -The point of scattering inside the sample is chosen uniformly -along the neutron flight path inside the sample, and the scattered -neutron ray is given a random energy and direction. This energy is selected in -the interval $[E_0-\Delta E; E_0+\Delta E]$ which hence must be -chosen large enough to cover all interesting neutron energies. -Similarly, the scattered -direction is chosen in a user-specified range, -either within a sphere of radius $r_\textrm{focus}$, within a rectangular -target with measures $(x_\textrm{focus}, y_\textrm{focus})$ -or in the specified angular range. This target is positioned at the $x_{target}$, $y_{target}$, $z_{target}$ point in space, or using the target\_index for which e.g. 1 is the further component, -1 is the previous, etc... - -A special feature, used when computing resolution functions, is that the -component stores complete information about the scattering event in the -output parameter \textit{res\_struct}. The information includes initial -and final wave vectors, the coordinates of the scattering point, and the -neutron weight after the scattering event. From this information the -scattering parameters $(\textbf{Q}, \omega)$ can be recorded -for every scattering event and used to compute the resolution function. -For an example of using the -information in the output parameter, see the description of the -\textbf{Res\_monitor} component in section~\ref{s:res_monitor}. +\section{The \texttt{Res\_sample} McStas Component} +Sample for resolution function calculation. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Kristian Nielsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} 1999 +\end{itemize} + +\subsection*{Description} +An inelastic sample with completely uniform scattering in both Q and energy. This sample is used together with the Res\_monitor component and (optionally) the mcresplot front-end to compute the resolution function of triple-axis or inverse-geometry time-of-flight instruments. + +The shape of the sample is either a hollow cylinder or a rectangular box. The hollow cylinder shape is specified with an inner and outer radius. The box is specified with dimensions xwidth, yheight, zdepth. + +The scattered neutrons will have directions towards a given disk and energies betweed E0-dE and E0+dE. This target area may also be rectangular if specified focus\_xw and focus\_yh or focus\_aw and focus\_ah, respectively in meters and degrees. The target itself is either situated according to given coordinates (x,y,z), or setting the relative target\_index of the component to focus at (next is +1). This target position will be set to its AT position. When targeting to centered components, such as spheres or cylinders, define an Arm component where to focus at. + +Example: Res\_sample(thickness=0.001,radius=0.02,yheight=0.4,focus\_r=0.05, E0=14.6,dE=2, target\_x=0, target\_y=0, target\_z=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +thickness & m & Thickness of hollow cylinder in (x,z) plane & 0 \\ +radius & m & Outer radius of hollow cylinder & 0.01 \\ +focus\_r & m & Radius of sphere containing target. & 0.05 \\ +E0 & meV & Center of scattered energy range & 14 \\ +dE & meV & half width of scattered energy range & 2 \\ +target\_x & m & X-position of target to focus at [m] & 0 \\ +target\_y & m & Y-position of target to focus at & 0 \\ +target\_z & m & Z-position of target to focus at [m] & .5 \\ +focus\_xw & m & horiz. dimension of a rectangular area & 0 \\ +focus\_yh & m & vert. dimension of a rectangular area & 0 \\ +focus\_aw & deg & horiz. angular dimension of a rectangular area & 0 \\ +focus\_ah & deg & vert. angular dimension of a rectangular area & 0 \\ +xwidth & m & horiz. dimension of sample, as a width & 0 \\ +yheight & m & vert. dimension of sample, as a height & 0.05 \\ +zdepth & m & depth of sample & 0 \\ +target\_index & 1 & relative index of component to focus at, e.g. next is +1 & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Res\_sample.comp}. +\end{itemize} +\IfFileExists{samples/Res_sample_static.tex}{\input{samples/Res_sample_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/SANS_spheres2.tex b/docs/manuals/mcstas/samples/SANS_spheres2.tex index 59ebf67266..cf40810b0b 100644 --- a/docs/manuals/mcstas/samples/SANS_spheres2.tex +++ b/docs/manuals/mcstas/samples/SANS_spheres2.tex @@ -3,28 +3,21 @@ \section{The \texttt{SANS\_spheres2} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} P. Willendrup, derived from H. Frielinghaus SANS\_benchmark2 \item \textbf{Origin:} DTU \item \textbf{Date:} 16.12.2019 \end{itemize} \subsection*{Description} -\begin{lstlisting} Sample for Small Angle Neutron Scattering - hard spheres in thin solution, mono disperse. -For the scattering simulation a high fraction of neutron paths is directed to the scattering (exact fraction is sc_aim). -The remaining paths are used for the transmitted beams. The absolute intensities are treated accordingly, and the p-parameter is set accordingly. +For the scattering simulation a high fraction of neutron paths is directed to the scattering (exact fraction is sc\_aim). The remaining paths are used for the transmitted beams. The absolute intensities are treated accordingly, and the p-parameter is set accordingly. -For the scattering probability, the integral of the scattering function between Q = 0.0001 and 1.0 AA-1 is calculated. -This is used in terms of transmisson, and of course for the scattering probability. -In this way, multiple scattering processes could be treated as well. +For the scattering probability, the integral of the scattering function between Q = 0.0001 and 1.0 \AA{}-1 is calculated. This is used in terms of transmisson, and of course for the scattering probability. In this way, multiple scattering processes could be treated as well. -The typical SANS range was considered to be between 0.0001 and 1.0 AA-1. -This means that the scattered neutrons are equally distributed in this range on logarithmic Q-scales. +The typical SANS range was considered to be between 0.0001 and 1.0 \AA{}-1. This means that the scattered neutrons are equally distributed in this range on logarithmic Q-scales. -Example: SANS_spheres2(xwidth=0.01, yheight=0.01, zthick=0.001, model=1.0, dsdw_inc=0.02, sc_aim=0.97, sans_aim=0.95, R-150) -\end{lstlisting} +Example: SANS\_spheres2(xwidth=0.01, yheight=0.01, zthick=0.001, model=1.0, dsdw\_inc=0.02, sc\_aim=0.97, sans\_aim=0.95, R-150) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -37,20 +30,20 @@ \subsection*{Input parameters} xwidth & m & Width of sample volume & 0.01 \\ yheight & m & Height of sample volume & 0.01 \\ zthick & m & Thickness of sample volume & 0.001 \\ -dsdw\_inc & cm\textasciicircum{}-1 & The incoherent background from the overall sample, should read ca. 1.0 for water, 0.5 for half D2O, half H2O, and ca. 0.02 for D2O & 0.02 \\ +dsdw\_inc & cm$^{-1}$ & The incoherent background from the overall sample, should read ca. 1.0 for water, 0.5 for half D2O, half H2O, and ca. 0.02 for D2O & 0.02 \\ sc\_aim & 1 & The fraction of neutron paths used to represent the scattered neutrons (including everything: incoherent and coherent). rest is transmission. & 0.97 \\ sans\_aim & 1 & The fraction of neutron paths used to represent the scattered neutrons in the sans-range (up to 1.0AA-1). rest is incoherent with Q\textgreater{}1AA-1. & 0.95 \\ -R & AA & Radius of dilute, monodisperse spheres & 150 \\ +R & \AA{} & Radius of dilute, monodisperse spheres & 150 \\ phi & 1 & Volume-ratio of the spheres wrt. solution & 1e-3 \\ -drho & cm\textasciicircum{}-2 & Scattering length density & 6e10 \\ +drho & cm$^{-2}$ & Scattering length density & 6e10 \\ singlesp & 1 & Switches between multiple scattering (parameter zero 0.0) and single scattering (parameter 1.0). The sc\_aim directs a fraction of paths to the first scattering process accordingly. The no. of paths for the second scattering process is derived from the real probability. Up to 10 scattering processes are considered. & 1 \\ -Qmind & AA\textasciicircum{}-1 & Lower limit of "SANS" scattering & 0.0001 \\ -Qmaxd & AA\textasciicircum{}-1 & Upper limit of "SANS" scattering & 2.1544346900319 \\ +Qmind & \AA{}$^{-1}$ & Lower limit of "SANS" scattering & 0.0001 \\ +Qmaxd & \AA{}$^{-1}$ & Upper limit of "SANS" scattering & 2.1544346900319 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/SANS_spheres2.comp}{Source code} for \texttt{SANS\_spheres2.comp}. + \item Component source code found in file \texttt{SANS\_spheres2.comp}. \end{itemize} -\IfFileExists{SANS_spheres2_static.tex}{\input{SANS_spheres2_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/SANS_spheres2_static.tex}{\input{samples/SANS_spheres2_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Sans_spheres.tex b/docs/manuals/mcstas/samples/Sans_spheres.tex index 778e553cd8..a43b803cd5 100644 --- a/docs/manuals/mcstas/samples/Sans_spheres.tex +++ b/docs/manuals/mcstas/samples/Sans_spheres.tex @@ -3,21 +3,15 @@ \section{The \texttt{Sans\_spheres} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} P. Willendrup, K. Lefmann, L. Arleth \item \textbf{Origin:} Risoe \item \textbf{Date:} 19.12.2003 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Sample for use in a SANS instrument, models hard, mono disperse spheres in thin solution. -The shape of the sample may be a filled box with dimensions -xwidth, yheight, zdepth, a cylinder with dimensions radius and yheight, -a filled sphere with radius. +Sample for use in a SANS instrument, models hard, mono disperse spheres in thin solution. The shape of the sample may be a filled box with dimensions xwidth, yheight, zdepth, a cylinder with dimensions radius and yheight, a filled sphere with radius. -Example: Sans_spheres(R = 100, Phi = 1e-3, Delta_rho = 0.6, sigma_abs = 50, xwidth=0.01, yheight=0.01, zdepth=0.005) -\end{lstlisting} +Example: Sans\_spheres(R = 100, Phi = 1e-3, Delta\_rho = 0.6, sigma\_abs = 50, xwidth=0.01, yheight=0.01, zdepth=0.005) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -27,10 +21,10 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -R & AA & Radius of scattering hard spheres & 100 \\ +R & \AA{} & Radius of scattering hard spheres & 100 \\ Phi & 1 & Particle volume fraction & 1e-3 \\ -Delta\_rho & fm/AA\textasciicircum{}3 & Excess scattering length density & 0.6 \\ -sigma\_abs & m\textasciicircum{}-1 & Absorption cross section density at 2200 m/s & 0.05 \\ +Delta\_rho & fm/\AA{}$^{3}$ & Excess scattering length density & 0.6 \\ +sigma\_abs & m$^{-1}$ & Absorption cross section density at 2200 m/s & 0.05 \\ xwidth & m & horiz. dimension of sample, as a width & 0 \\ yheight & m & vert . dimension of sample, as a height for cylinder/box & 0 \\ zdepth & m & depth of sample & 0 \\ @@ -49,7 +43,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Sans_spheres.comp}{Source code} for \texttt{Sans\_spheres.comp}. - \item The test/example instrument \textless{}a href="../examples/SANS.instr"\textgreater{}SANS.instr\textless{}/a\textgreater{}. + \item Component source code found in file \texttt{Sans\_spheres.comp}. + \item The test/example instrument \htmladdnormallink{SANS.instr}{../examples/SANS.instr}. \end{itemize} -\IfFileExists{Sans_spheres_static.tex}{\input{Sans_spheres_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Sans_spheres_static.tex}{\input{samples/Sans_spheres_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Single_crystal.tex b/docs/manuals/mcstas/samples/Single_crystal.tex index f166e8c35d..c59ef55693 100644 --- a/docs/manuals/mcstas/samples/Single_crystal.tex +++ b/docs/manuals/mcstas/samples/Single_crystal.tex @@ -4,145 +4,70 @@ \section{The \texttt{Single\_crystal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} December 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Single crystal with mosaic. Delta-D/D option for finite-size effects. -Rectangular geometry. Multiple scattering and secondary extinction included. -The mosaic may EITHER be specified isotropic by setting the mosaic input -parameter, OR anisotropic by setting the mosaic_a, mosaic_b, and mosaic_c -parameters. -The crystal lattice can be bent locally, keeping the external geometry unchanged. -Curvature is spherical along vertical and horizontal axes. - -<b>Speed/stat optimisation using SPLIT</b> -In order to dramatically improve the simulation efficiency, we recommend to -use a SPLIT keyword on this component (or prior to it), as well as to disable -the multiple scattering handling by setting order=1. This is especially powerful -for large reflection lists such as with macromolecular proteins. When an incoming -particle is identical to the preceeding, reciprocal space initialisation is -skipped, and a Monte Carlo choice is done on available reflections from the last -repciprocal space calculation! To assist the user in choosing a "relevant" value -of the SPLIT, a rolling average of the number of available reflections is -calculated and presented in the component output. - -<b>Mosacitiy modes:</b> -The component features three independent ways of parametrising mosaicity: -a) The original algorithm where mosaicity is implemented by extending each -reflection by a Gaussian "cigar" in reciprocal space, characterised by -the parameters mosaic and delta_d_d. -(Also known as "isotropic mosaicity".) -b) A similar mode where mosaicities can be non-isotropic and given as the -parameters mosaic_a, mosaic_b and mosaic_c, around the unit cell axes. -(Also known as "anisotropic mosaicity".) -c) Given two "macroscopically"/experimentally measured width/mosaicities -of two independent reflections, parametrised by the list -mosaic_AB = {mos_a, mos_b, a_h, a_k, a_l, b_h, b_k, b_l}, a set of -microscopic mosaicities as in b) are estimated (internally) and applied. -(Also known as "phenomenological mosaicity".) - -<b>Powder- and PG-mode</b> -When these two modes are used (powder=1 or PG=1), a randomised transformation -of the particle direction is made before and after scattering, thereby letting -the single crystal behave as a crystallite of either a powder (crystallite -orientation fully randomised) or pyrolytic graphite (crystallite randomised around -the c-axis). - -<b>Curved crystal mode</b> -The component features a method to curve the lattice planes slightly with respect -to the outer geometry of the crystal. The method is implemented as a transformation -on the particle direction vector, and should be used only in cases where -a) The reflection lattice vector is ~ orthogonal to the crystal surface -b) The modelled curvarture is "small" with respect to the crystal surface - -<b>Sample shape:</b> -Sample shape may be a cylinder, a sphere, a box or any other shape +Single crystal with mosaic. Delta-D/D option for finite-size effects. Rectangular geometry. Multiple scattering and secondary extinction included. The mosaic may EITHER be specified isotropic by setting the mosaic input parameter, OR anisotropic by setting the mosaic\_a, mosaic\_b, and mosaic\_c parameters. The crystal lattice can be bent locally, keeping the external geometry unchanged. Curvature is spherical along vertical and horizontal axes. + +\textbf{Speed/stat optimisation using SPLIT} In order to dramatically improve the simulation efficiency, we recommend to use a SPLIT keyword on this component (or prior to it), as well as to disable the multiple scattering handling by setting order=1. This is especially powerful for large reflection lists such as with macromolecular proteins. When an incoming particle is identical to the preceeding, reciprocal space initialisation is skipped, and a Monte Carlo choice is done on available reflections from the last repciprocal space calculation! To assist the user in choosing a "relevant" value of the SPLIT, a rolling average of the number of available reflections is calculated and presented in the component output. + +\textbf{Mosacitiy modes:} The component features three independent ways of parametrising mosaicity: a) The original algorithm where mosaicity is implemented by extending each reflection by a Gaussian "cigar" in reciprocal space, characterised by the parameters mosaic and delta\_d\_d. (Also known as "isotropic mosaicity".) b) A similar mode where mosaicities can be non-isotropic and given as the parameters mosaic\_a, mosaic\_b and mosaic\_c, around the unit cell axes. (Also known as "anisotropic mosaicity".) c) Given two "macroscopically"/experimentally measured width/mosaicities of two independent reflections, parametrised by the list mosaic\_AB = \{mos\_a, mos\_b, a\_h, a\_k, a\_l, b\_h, b\_k, b\_l\}, a set of microscopic mosaicities as in b) are estimated (internally) and applied. (Also known as "phenomenological mosaicity".) + +\textbf{Powder- and PG-mode} When these two modes are used (powder=1 or PG=1), a randomised transformation of the particle direction is made before and after scattering, thereby letting the single crystal behave as a crystallite of either a powder (crystallite orientation fully randomised) or pyrolytic graphite (crystallite randomised around the c-axis). + +\textbf{Curved crystal mode} The component features a method to curve the lattice planes slightly with respect to the outer geometry of the crystal. The method is implemented as a transformation on the particle direction vector, and should be used only in cases where a) The reflection lattice vector is \textasciitilde{} orthogonal to the crystal surface b) The modelled curvarture is "small" with respect to the crystal surface + +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} box/plate: xwidth x yheight x zdepth cylinder: radius x yheight sphere: radius (yheight=0) any shape: geometry=OFF file +\end{verbatim} -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the PLY, OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using: -qhull < coordinates.xyz Qx Qv Tv o > geomview.off -or -powercrust coordinates.xyz -and viewed with geomview or java -jar jroff.jar (see below). -The default size of the object depends on the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. - -<b>Crystal definition file format</b> -Crystal structure is specified with an ascii data file. Each line contains -4 or more numbers, separated by white spaces: +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the PLY, OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends on the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. +\textbf{Crystal definition file format} Crystal structure is specified with an ascii data file. Each line contains 4 or more numbers, separated by white spaces: + +\begin{verbatim} h k l ... F2 +\end{verbatim} + +The first three numbers are the (h,k,l) indices of the reciprocal lattice point, and the 7-th number is the value of the structure factor |F|**2, in barns. The rest of the numbers are not used; the file is in the format output by the Crystallographica program. The reflection list should be ordered by decreasing d-spacing values. Lines begining by '\#' are read as comments (ignored). Most sample parameters may be defined from the data file header, following the same mechanism as PowderN. + +Current data file header keywords include, for data format specification: \#column\_h \textless{}index of the Bragg Qh column\textgreater{} \#column\_k \textless{}index of the Bragg Qk column\textgreater{} \#column\_l \textless{}index of the Bragg Ql column\textgreater{} \#column\_F2 \textless{}index of the squared str. factor '|F|\textasciicircum{}2' column [b]\textgreater{} \#column\_F \textless{}index of the structure factor norm '|F|' column\textgreater{} and for material specification: \#sigma\_abs \textless{}value of absorption cross section [barns]\textgreater{} \#sigma\_inc \textless{}value of incoherent cross section [barns]\textgreater{} \#Delta\_d/d \textless{}value of Detla\_d/d width for all lines\textgreater{} \#lattice\_a \textless{}value of the a lattice parameter [\AA{}]\textgreater{} \#lattice\_b \textless{}value of the b lattice parameter [\AA{}]\textgreater{} \#lattice\_c \textless{}value of the c lattice parameter [\AA{}]\textgreater{} \#lattice\_aa \textless{}value of the alpha lattice angle [deg]\textgreater{} \#lattice\_bb \textless{}value of the beta lattice angle [deg]\textgreater{} \#lattice\_cc \textless{}value of the gamma lattice angle [deg]\textgreater{} -The first three numbers are the (h,k,l) indices of the reciprocal lattice -point, and the 7-th number is the value of the structure factor |F|**2, in -barns. The rest of the numbers are not used; the file is in the format -output by the Crystallographica program. -The reflection list should be ordered by decreasing d-spacing values. -Lines begining by '#' are read as comments (ignored). Most sample parameters -may be defined from the data file header, following the same mechanism as -PowderN. - -Current data file header keywords include, for data format specification: -#column_h <index of the Bragg Qh column> -#column_k <index of the Bragg Qk column> -#column_l <index of the Bragg Ql column> -#column_F2 <index of the squared str. factor '|F|^2' column [b]> -#column_F <index of the structure factor norm '|F|' column> -and for material specification: -#sigma_abs <value of absorption cross section [barns]> -#sigma_inc <value of incoherent cross section [barns]> -#Delta_d/d <value of Detla_d/d width for all lines> -#lattice_a <value of the a lattice parameter [Angs]> -#lattice_b <value of the b lattice parameter [Angs]> -#lattice_c <value of the c lattice parameter [Angs]> -#lattice_aa <value of the alpha lattice angle [deg]> -#lattice_bb <value of the beta lattice angle [deg]> -#lattice_cc <value of the gamma lattice angle [deg]> - -Last, CIF, FullProf and ShelX files can be read, and converted to F2(hkl) lists -if 'cif2hkl' is installed. The CIF2HKL env variable can be used to point to a -proper executable, else the McCode, then the system installed versions are used. +Last, CIF, FullProf and ShelX files can be read, and converted to F2(hkl) lists if 'cif2hkl' is installed. The CIF2HKL env variable can be used to point to a proper executable, else the McCode, then the system installed versions are used. See the Component Manual for more defails. -Example: Single_crystal(xwidth=0.01, yheight=0.01, zdepth=0.01, mosaic = 5, reflections="YBaCuO.lau") +Example: Single\_crystal(xwidth=0.01, yheight=0.01, zdepth=0.01, mosaic = 5, reflections="YBaCuO.lau") -A PG graphite crystal plate, cut for (002) reflections -Single_crystal(xwidth = 0.002, yheight = 0.1, zdepth = 0.1, -mosaic = 30, reflections = "C_graphite.lau", +A PG graphite crystal plate, cut for (002) reflections Single\_crystal(xwidth = 0.002, yheight = 0.1, zdepth = 0.1, mosaic = 30, reflections = "C\_graphite.lau", + +\begin{verbatim} ax=0, ay=2.14, az=-1.24, bx = 0, by = 0, bz = 2.47, cx = 6.71, cy = 0, cz = 0) +\end{verbatim} + +A leucine protein, without multiple scattering Single\_crystal(xwidth=0.005, yheight=0.005, zdepth=0.005, mosaic = 5, reflections="leucine.lau", order=1) -A leucine protein, without multiple scattering -Single_crystal(xwidth=0.005, yheight=0.005, zdepth=0.005, -mosaic = 5, reflections="leucine.lau", order=1) +A Vanadium incoherent elastic scattering with multiple scattering Single\_crystal(xwidth=0.01, yheight=0.01, zdepth=0.01, reflections="", sigma\_abs=5.08, sigma\_inc=4.935, -A Vanadium incoherent elastic scattering with multiple scattering -Single_crystal(xwidth=0.01, yheight=0.01, zdepth=0.01, -reflections="", sigma_abs=5.08, sigma_inc=4.935, +\begin{verbatim} ax=3.0282, by=3.0282, cz=3.0282/2) +\end{verbatim} -Also, always use a non-zero value of delta_d_d. +Also, always use a non-zero value of delta\_d\_d. -%VALIDATION: -This component has been validated. +\%VALIDATION: This component has been validated. -This sample component can advantageously benefit from the SPLIT feature, e.g. -SPLIT COMPONENT sx = Single_crystal(...) -\end{lstlisting} +This sample component can advantageously benefit from the SPLIT feature, e.g. SPLIT COMPONENT sx = Single\_crystal(...) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -166,13 +91,13 @@ \subsection*{Input parameters} mosaic\_c & arc minutes & Out-of-plane (Rotation around lattice vector c) mosaic (anisotropic), gaussian RMS & -1 \\ recip\_cell & 1 & Choice of direct/reciprocal (0/1) unit cell definition & 0 \\ barns & 1 & Flag to indicate if |F|\textasciicircum{}2 from 'reflections' is in barns or fm\textasciicircum{}2. barns=1 for laz and isotropic constant elastic scattering (reflections=NULL), barns=0 for lau type files & 0 \\ -ax & AA or AA\textasciicircum{}-1 & Coordinates of first (direct/recip) unit cell vector & 0 \\ +ax & \AA{} or \AA{}$^{-1}$ & Coordinates of first (direct/recip) unit cell vector & 0 \\ ay & & a on y axis & 0 \\ az & & a on z axis & 0 \\ -bx & AA or AA\textasciicircum{}-1 & Coordinates of second (direct/recip) unit cell vector & 0 \\ +bx & \AA{} or \AA{}$^{-1}$ & Coordinates of second (direct/recip) unit cell vector & 0 \\ by & & b on y axis & 0 \\ bz & & b on z axis & 0 \\ -cx & AA or AA\textasciicircum{}-1 & Coordinates of third (direct/recip) unit cell vector & 0 \\ +cx & \AA{} or \AA{}$^{-1}$ & Coordinates of third (direct/recip) unit cell vector & 0 \\ cy & & c on y axis & 0 \\ cz & & c on z axis & 0 \\ p\_transmit & 1 & Monte Carlo probability for neutrons to be transmitted without any scattering. Used to improve statistics from weak reflections & 0.001 \\ @@ -192,16 +117,16 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Single_crystal.comp}{Source code} for \texttt{Single\_crystal.comp}. - \item See \textless{}a href="http://icsd.ill.fr"\textgreater{}ICSD\textless{}/a\textgreater{} Inorganic Crystal Structure Database - \item \textless{}a href="http://www.ncnr.nist.gov/resources/n-lengths/"\textgreater{}Cross sections for single elements\textless{}/a\textgreater{} - \item \textless{}a href="http://www.ncnr.nist.gov/resources/sldcalc.html\textgreater{}Cross sections for compounds\textless{}/a\textgreater{} - \item \textless{}a href="http://www.webelements.com/"\textgreater{}Web Elements\textless{}/a\textgreater{} - \item \textless{}a href="http://www.ill.eu/sites/fullprof/index.html"\textgreater{}Fullprof\textless{}/a\textgreater{} powder refinement - \item \textless{}a href="http://www.crystallographica.com/"\textgreater{}Crystallographica\textless{}/a\textgreater{} software - \item \textless{}a href="http://www.geomview.org"\textgreater{}Geomview and Object File Format (OFF)\textless{}/a\textgreater{} - \item Java version of Geomview (display only) \textless{}a href="http://www.holmes3d.net/graphics/roffview/"\textgreater{}jroff.jar\textless{}/a\textgreater{} - \item \textless{}a href="http://qhull.org"\textgreater{}qhull\textless{}/a\textgreater{} - \item \textless{}a href="http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html"\textgreater{}powercrust\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Single\_crystal.comp}. + \item See \htmladdnormallink{ICSD}{http://icsd.ill.fr} Inorganic Crystal Structure Database + \item \htmladdnormallink{Cross sections for single elements}{http://www.ncnr.nist.gov/resources/n-lengths/} + \item \htmladdnormallink{Cross sections for compounds}{} + \item \htmladdnormallink{Web Elements}{http://www.webelements.com/} + \item \htmladdnormallink{Fullprof}{http://www.ill.eu/sites/fullprof/index.html} powder refinement + \item \htmladdnormallink{Crystallographica}{http://www.crystallographica.com/} software + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} + \item Java version of Geomview (display only) \htmladdnormallink{jroff.jar}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{qhull}{http://qhull.org} + \item \htmladdnormallink{powercrust}{http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} \end{itemize} -\IfFileExists{Single_crystal_static.tex}{\input{Single_crystal_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Single_crystal_static.tex}{\input{samples/Single_crystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Single_crystal_static.tex b/docs/manuals/mcstas/samples/Single_crystal_static.tex index cc9792b284..67821d6b15 100644 --- a/docs/manuals/mcstas/samples/Single_crystal_static.tex +++ b/docs/manuals/mcstas/samples/Single_crystal_static.tex @@ -22,7 +22,7 @@ \subsection*{The single crystal component} $(\textit{ax}, \textit{ay}, \textit{az})$, $(\textit{bx}, \textit{by}, \textit{bz})$, and $(\textit{cx}, \textit{cy}, \textit{cz})$ to define the axes of the direct lattice of the crystal (the sides of the unit -cell) in units of {\AA}ngstr{\o}m; and \textit{reflections}, a string +cell) in units of Ångström; and \textit{reflections}, a string giving the name of the file with the list of structure factors to consider. The mosaic is specified \emph{either} isotropically as diff --git a/docs/manuals/mcstas/samples/Single_magnetic_crystal.tex b/docs/manuals/mcstas/samples/Single_magnetic_crystal.tex index 16a0a61f93..bdaf8c2cbc 100644 --- a/docs/manuals/mcstas/samples/Single_magnetic_crystal.tex +++ b/docs/manuals/mcstas/samples/Single_magnetic_crystal.tex @@ -5,47 +5,30 @@ \section{The \texttt{Single\_magnetic\_crystal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Erik B Knudsen and Linda Udby \item \textbf{Origin:} DTU Physics \item \textbf{Date:} Jan 2020 \end{itemize} \subsection*{Description} -\begin{lstlisting} WARNING: This is an experimental component - no experimental validation has yet been done -Single magnetic crystal with mosaic. Delta-D/D option for finite-size effects. -Multiple scattering and secondary extinction included. -The mosaic may EITHER be specified isotropic by setting the mosaic input -parameter, OR anisotropic by setting the mosaic_h, mosaic_v, and mosaic_n -parameters. +Single magnetic crystal with mosaic. Delta-D/D option for finite-size effects. Multiple scattering and secondary extinction included. The mosaic may EITHER be specified isotropic by setting the mosaic input parameter, OR anisotropic by setting the mosaic\_h, mosaic\_v, and mosaic\_n parameters. -The scattering is computed solely in an spin up-down configuration. That is the -scattering is considered in relation to the externally defined vector (mx,my,mz), where it -can be either SF or NSF. -Simplifications and comments : -Lande splitting factor is assumed to be g=2 -Magnetic form factors are set =1 +The scattering is computed solely in an spin up-down configuration. That is the scattering is considered in relation to the externally defined vector (mx,my,mz), where it can be either SF or NSF. Simplifications and comments : Lande splitting factor is assumed to be g=2 Magnetic form factors are set =1 -<b>Sample shape:</b> -Sample shape may be a cylinder, a sphere, a box or any other shape +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} box/plate: xwidth x yheight x zdepth cylinder: radius x yheight sphere: radius (yheight=0) any shape: geometry=OFF file +\end{verbatim} -The complex geometry option handles any closed non-convex polyhedra. -It computes the intersection points of the neutron ray with the object -transparently, so that it can be used like a regular sample object. -It supports the OFF and NOFF file format but not COFF (colored faces). -Such files may be generated from XYZ data using qhull/powercrust, and -viewed with geomview -The default size of the object depends of the OFF file data, but its -bounding box may be resized using xwidth,yheight and zdepth. +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using qhull/powercrust, and viewed with geomview The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. -Also, always use a non-zero value of delta_d_d. -\end{lstlisting} +Also, always use a non-zero value of delta\_d\_d. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -67,23 +50,23 @@ \subsection*{Input parameters} mosaic\_v & arcmin & Vertical (rotation around Z) mosaic (anisotropic), gaussian RMS & -1 \\ mosaic\_n & arcmin & Out-of-plane (Rotation around X) mosaic (anisotropic), gaussian RMS & -1 \\ recip\_cell & 1 & Choice of direct/reciprocal (0/1) unit cell definition & 0 \\ -q\_min & AA\textasciicircum{}-1 & lower boundary of momentum transfer range to generate hkls in & 0 \\ -q\_max & AA\textasciicircum{}-1 & upper boundary of momentum transfer range to generate hkls in & -1 \\ +q\_min & \AA{}$^{-1}$ & lower boundary of momentum transfer range to generate hkls in & 0 \\ +q\_max & \AA{}$^{-1}$ & upper boundary of momentum transfer range to generate hkls in & -1 \\ mx & 1 & & 0 \\ my & 1 & Coordinates of vector defining the SF/NSF direction & 1 \\ mz & 1 & & 0 \\ na & 1 & & 1 \\ nb & 1 & Unit cell multipliers. The specified unit cell vectors are scaled by these factors. Note that the mulitpliers are applied directly to the raw input data. I.e. if recip. cell vectors are given, multipliers should be \textless{}1 (= 1/n). F.i. used to specify a magnetic unit cell which is larger than the chemical unit cell. & 1 \\ nc & 1 & & 1 \\ -ax & AA or AA\textasciicircum{}-1 & & 0 \\ -ay & AA or AA\textasciicircum{}-1 & Coordinates of first (direct/recip) unit cell vector & 0 \\ -az & AA or AA\textasciicircum{}-1 & & 0 \\ -bx & AA or AA\textasciicircum{}-1 & & 0 \\ -by & AA or AA\textasciicircum{}-1 & Coordinates of second (direct/recip) unit cell vector & 0 \\ -bz & AA or AA\textasciicircum{}-1 & & 0 \\ -cx & AA or AA\textasciicircum{}-1 & & 0 \\ -cy & AA or AA\textasciicircum{}-1 & Coordinates of third (direct/recip) unit cell vector & 0 \\ -cz & AA or AA\textasciicircum{}-1 & & 0 \\ +ax & \AA{} or \AA{}$^{-1}$ & & 0 \\ +ay & \AA{} or \AA{}$^{-1}$ & Coordinates of first (direct/recip) unit cell vector & 0 \\ +az & \AA{} or \AA{}$^{-1}$ & & 0 \\ +bx & \AA{} or \AA{}$^{-1}$ & & 0 \\ +by & \AA{} or \AA{}$^{-1}$ & Coordinates of second (direct/recip) unit cell vector & 0 \\ +bz & \AA{} or \AA{}$^{-1}$ & & 0 \\ +cx & \AA{} or \AA{}$^{-1}$ & & 0 \\ +cy & \AA{} or \AA{}$^{-1}$ & Coordinates of third (direct/recip) unit cell vector & 0 \\ +cz & \AA{} or \AA{}$^{-1}$ & & 0 \\ p\_transmit & 1 & Monte Carlo probability for neutrons to be transmitted without any scattering. Used to improve statistics from weak reflections & -1 \\ sigma\_abs & barns & absorption cross-section per unit cell at 2200 m/s & 0 \\ sigma\_inc & barns & incoherent scattering cross-section per unit cell & 0 \\ @@ -93,6 +76,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Single_magnetic_crystal.comp}{Source code} for \texttt{Single\_magnetic\_crystal.comp}. + \item Component source code found in file \texttt{Single\_magnetic\_crystal.comp}. \end{itemize} -\IfFileExists{Single_magnetic_crystal_static.tex}{\input{Single_magnetic_crystal_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Single_magnetic_crystal_static.tex}{\input{samples/Single_magnetic_crystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/TOFRes_sample.tex b/docs/manuals/mcstas/samples/TOFRes_sample.tex index 00df0b53dd..eb4232c6a0 100644 --- a/docs/manuals/mcstas/samples/TOFRes_sample.tex +++ b/docs/manuals/mcstas/samples/TOFRes_sample.tex @@ -1,40 +1,54 @@ -% Emacs settings: -*-mode: latex; TeX-master: "manual.tex"; -*- - -\section{TOF\_Res\_sample: A sample-like component for TOF resolution calculation} -\label{s:tof_res_sample} - -The component \textbf{TOF\_Res\_sample} scatters neutron rays isotropically -in position within a specified angular range. -As for \textbf{Res\_sample}, this component is meant -for computation of the resolution function, but in this case for one time bin in a -time-of-flight (TOF) instrument. The component selects uniformly the neutron -energy so that neutron arrival time at the TOF detector lies within one time bin, -specified by $t_0$ and $\Delta t$. -For actual calculations of the resolution -function, \textbf{TOF\_Res\_sample} should be used -together with \textbf{Res\_monitor}, described in -section~\ref{s:res_monitor}. - -The shape of \textbf{TOF\_Res\_sample} is either a hollow cylinder -or a rectangular box. -The hollow cylinder shape is -specified with the inner and outer radius, $r_\textrm{i}$ and $r_\textrm{o}$, -respectively, and the height, $h$. -If these parameters are unspecified, -the shape is instead a box of dimensions $x_w$, $y_h$, and $z_t$. - -The component only propagates neutron rays that are scattered; -other rays are absorbed. -As for \textbf{Res\_sample}, the scattering probability is proportional to the neutron -flight path length inside the sample. -The point of scattering in the sample is chosen uniformly -along the neutron flight path inside the sample, and the scattered -direction is chosen in a user-specified range, -either within a sphere of radius $r_\textrm{foc}$, within a rectangular -target with measures $(x_\textrm{focus}, y_\textrm{focus})$ -or in the specified angular range. -This target is positioned at the $x_{target}$, $y_{target}$, $z_{target}$ -point in space, or using target\_index. - -This component stores complete information about the scattering event in the -output parameter \textit{res\_struct}, see \textbf{Res\_Sample}. +\section{The \texttt{TOFRes\_sample} McStas Component} +Sample for TOF resolution function calculation. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} KL, 10 October 2004 + \item \textbf{Origin:} Risoe + \item \textbf{Date:} 1999 +\end{itemize} + +\subsection*{Description} +An inelastic sample with completely uniform scattering in both solid angle and energy. This sample is used together with the TOFRes\_monitor component and (optionally) the mcresplot front-end to compute the resolution function of all time-of-flight instruments. The method of time focusing is used to optimize the simulations. + +The shape of the sample is either: 1. Hollow cylinder (Please note that the cylinder **must** be specified with both a radius and a wall-thickness!) 2. A massive, rectangular box specified with dimensions xwidth, yheight, zdepth. (i.e. **withouht** a thickness) + +hollow cylinder shape **must** be specified with both a radius and a wall-thickness. The box is + +The scattered neutrons will have directions towards a given target and detector arrival time in an interval of time\_width centered on time\_bin. This target area is default disk shaped, but may also be rectangular if specified focus\_xw and focus\_yh or focus\_aw and focus\_ah, respectively in meters and degrees. The target itself is either situated according to given coordinates (x,y,z), or setting the relative target\_index of the component to focus at (next is +1). This target position will be set to its AT position. When targeting to centered components, such as spheres or cylinders, define an Arm component where to focus at. + +Example: TOFRes\_sample(thickness=0.001, radius=0.01, yheight=0.04, focus\_xw=0.025, focus\_yh=0.025, time\_bin=3e4, time\_width=200, target\_x=0, target\_y=0, target\_z=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +thickness & m & Thickness of hollow cylinder in (x,z) plane & 0 \\ +radius & m & Outer radius of hollow cylinder & 0.01 \\ +yheight & m & vert. dimension of sample, as a height & 0.05 \\ +focus\_r & m & Radius of sphere containing target & 0.05 \\ +time\_bin & us & position of time bin & 20000 \\ +time\_width & us & width of time bin & 10 \\ +f & 1 & Adaptive time-shortening factor & 50 \\ +target\_x & & & 0 \\ +target\_y & m & position of target to focus at & 0 \\ +target\_z & & & .5 \\ +focus\_xw & m & horiz. dimension of a rectangular area & 0 \\ +focus\_yh & m & vert. dimension of a rectangular area & 0 \\ +focus\_aw & deg & horiz. angular dimension of a rectangular area & 0 \\ +focus\_ah & deg & vert. angular dimension of a rectangular area & 0 \\ +xwidth & m & horiz. dimension of sample, as a width & 0 \\ +zdepth & m & depth of sample & 0 \\ +target\_index & 1 & relative index of component to focus at, e.g. next is +1 & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{TOFRes\_sample.comp}. +\end{itemize} +\IfFileExists{samples/TOFRes_sample_static.tex}{\input{samples/TOFRes_sample_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/samples/Tunneling_sample.tex b/docs/manuals/mcstas/samples/Tunneling_sample.tex index 8095a03cdc..d7a9ba04a0 100644 --- a/docs/manuals/mcstas/samples/Tunneling_sample.tex +++ b/docs/manuals/mcstas/samples/Tunneling_sample.tex @@ -5,35 +5,23 @@ \section{The \texttt{Tunneling\_sample} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} 10.05.07 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A Double-cylinder shaped all-incoherent scatterer -with both elastic, quasielastic (Lorentzian), and tunneling (sharp) -components. No multiple scattering. Absorbtion included. -The shape of the sample may be a box with dimensions xwidth, yheight, zdepth. -The area to scatter to is a disk of radius 'focus_r' situated at the target. -This target area may also be rectangular if specified focus_xw and focus_yh -or focus_aw and focus_ah, respectively in meters and degrees. -The target itself is either situated according to given coordinates (x,y,z), -or defined with the relative target_index of the component to focus -to (next is +1). -This target position will be set to its AT position. When targeting to -centered components, such as spheres or cylinders, define an Arm component -where to focus to. +A Double-cylinder shaped all-incoherent scatterer with both elastic, quasielastic (Lorentzian), and tunneling (sharp) components. No multiple scattering. Absorbtion included. The shape of the sample may be a box with dimensions xwidth, yheight, zdepth. The area to scatter to is a disk of radius 'focus\_r' situated at the target. This target area may also be rectangular if specified focus\_xw and focus\_yh or focus\_aw and focus\_ah, respectively in meters and degrees. The target itself is either situated according to given coordinates (x,y,z), or defined with the relative target\_index of the component to focus to (next is +1). This target position will be set to its AT position. When targeting to centered components, such as spheres or cylinders, define an Arm component where to focus to. The outgoing polarization is calculated as for nuclear spin incoherence: + +\begin{verbatim} P' = 1/3*P-2/3P = -1/3P +\end{verbatim} + As above multiple scattering is ignored . -Example: Tunneling_sample(thickness=0.001,radius=0.01,yheight=0.02,focus_r=0.035, -target_index=1) -\end{lstlisting} +Example: Tunneling\_sample(thickness=0.001,radius=0.01,yheight=0.02,focus\_r=0.035, target\_index=1) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -63,15 +51,15 @@ \subsection*{Input parameters} zdepth & m & depth of sample & 0 \\ sigma\_abs & barns & Absorbtion cross section pr. unit cell & 5.08 \\ sigma\_inc & barns & Total incoherent scattering cross section pr. unit cell & 4.935 \\ -Vc & AA\textasciicircum{}3 & Unit cell volume & 13.827 \\ +Vc & \AA{}$^{3}$ & Unit cell volume & 13.827 \\ target\_index & 1 & relative index of component to focus at, e.g. next is +1 & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/samples/Tunneling_sample.comp}{Source code} for \texttt{Tunneling\_sample.comp}. + \item Component source code found in file \texttt{Tunneling\_sample.comp}. \item \textless{}A HREF="http://neutron.risoe.dk/mcstas/components/tests/v\_sample/"\textgreater{}Test \item results\textless{}/A\textgreater{} (not up-to-date). \end{itemize} -\IfFileExists{Tunneling_sample_static.tex}{\input{Tunneling_sample_static.tex}}{} \ No newline at end of file +\IfFileExists{samples/Tunneling_sample_static.tex}{\input{samples/Tunneling_sample_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_adsorbed_layer.tex b/docs/manuals/mcstas/sasmodels/SasView_adsorbed_layer.tex index 11e4d129f4..1814d3bcd7 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_adsorbed_layer.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_adsorbed_layer.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_adsorbed\_layer} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_adsorbed_layer component, generated from adsorbed_layer.c in sasmodels. +SasView\_adsorbed\_layer component, generated from adsorbed\_layer.c in sasmodels. -Example: -SasView_adsorbed_layer(second_moment, adsorbed_amount, density_shell, radius, volfraction, sld_shell, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0) -\end{lstlisting} +Example: SasView\_adsorbed\_layer(second\_moment, adsorbed\_amount, density\_shell, radius, volfraction, sld\_shell, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,13 +21,13 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -second\_moment & Ang & ([0.0, inf]) Second moment of polymer distribution. & 23.0 \\ -adsorbed\_amount & mg/m\textasciicircum{}2 & ([0.0, inf]) Adsorbed amount of polymer. & 1.9 \\ -density\_shell & g/cm\textasciicircum{}3 & ([0.0, inf]) Bulk density of polymer in the shell. & 0.7 \\ -radius & Ang & ([0.0, inf]) Core particle radius. & 500.0 \\ +second\_moment & \AA{} & ([0.0, inf]) Second moment of polymer distribution. & 23.0 \\ +adsorbed\_amount & mg/m$^{2}$ & ([0.0, inf]) Adsorbed amount of polymer. & 1.9 \\ +density\_shell & g/cm$^{3}$ & ([0.0, inf]) Bulk density of polymer in the shell. & 0.7 \\ +radius & \AA{} & ([0.0, inf]) Core particle radius. & 500.0 \\ volfraction & None & ([0.0, inf]) Core particle volume fraction. & 0.14 \\ -sld\_shell & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Polymer shell SLD. & 1.5 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent SLD. & 6.3 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Polymer shell SLD. & 1.5 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent SLD. & 6.3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_adsorbed_layer.comp}{Source code} for \texttt{SasView\_adsorbed\_layer.comp}. + \item Component source code found in file \texttt{SasView\_adsorbed\_layer.comp}. \end{itemize} -\IfFileExists{SasView_adsorbed_layer_static.tex}{\input{SasView_adsorbed_layer_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_adsorbed_layer_static.tex}{\input{sasmodels/SasView_adsorbed_layer_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_barbell.tex b/docs/manuals/mcstas/sasmodels/SasView_barbell.tex index d62ca8d0b1..224b07671b 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_barbell.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_barbell.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_barbell} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_barbell component, generated from barbell.c in sasmodels. +SasView\_barbell component, generated from barbell.c in sasmodels. -Example: -SasView_barbell(sld, sld_solvent, radius_bell, radius, length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_bell=0.0, pd_radius=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_barbell(sld, sld\_solvent, radius\_bell, radius, length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_bell=0.0, pd\_radius=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Barbell scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius\_bell & Ang & ([0, inf]) Spherical bell radius. & 40 \\ -radius & Ang & ([0, inf]) Cylindrical bar radius. & 20 \\ -length & Ang & ([0, inf]) Cylinder bar length. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Barbell scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_bell & \AA{} & ([0, inf]) Spherical bell radius. & 40 \\ +radius & \AA{} & ([0, inf]) Cylindrical bar radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder bar length. & 400 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_barbell.comp}{Source code} for \texttt{SasView\_barbell.comp}. + \item Component source code found in file \texttt{SasView\_barbell.comp}. \end{itemize} -\IfFileExists{SasView_barbell_static.tex}{\input{SasView_barbell_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_barbell_static.tex}{\input{sasmodels/SasView_barbell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_barbell_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_barbell_aniso.tex index f10355638d..731260e16e 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_barbell_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_barbell_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_barbell\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_barbell component, generated from barbell.c in sasmodels. +SasView\_barbell component, generated from barbell.c in sasmodels. -Example: -SasView_barbell_aniso(sld, sld_solvent, radius_bell, radius, length, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_bell=0.0, pd_radius=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_barbell\_aniso(sld, sld\_solvent, radius\_bell, radius, length, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_bell=0.0, pd\_radius=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Barbell scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius\_bell & Ang & ([0, inf]) Spherical bell radius. & 40 \\ -radius & Ang & ([0, inf]) Cylindrical bar radius. & 20 \\ -length & Ang & ([0, inf]) Cylinder bar length. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Barbell scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_bell & \AA{} & ([0, inf]) Spherical bell radius. & 40 \\ +radius & \AA{} & ([0, inf]) Cylindrical bar radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder bar length. & 400 \\ theta & & & 60 \\ phi & & & 60 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_barbell_aniso.comp}{Source code} for \texttt{SasView\_barbell\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_barbell\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_barbell_aniso_static.tex}{\input{SasView_barbell_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_barbell_aniso_static.tex}{\input{sasmodels/SasView_barbell_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_bcc_paracrystal.tex b/docs/manuals/mcstas/sasmodels/SasView_bcc_paracrystal.tex index b3695cba3b..9142a7a3b4 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_bcc_paracrystal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_bcc_paracrystal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_bcc\_paracrystal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_bcc_paracrystal component, generated from bcc_paracrystal.c in sasmodels. +SasView\_bcc\_paracrystal component, generated from bcc\_paracrystal.c in sasmodels. -Example: -SasView_bcc_paracrystal(dnn, d_factor, radius, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0) -\end{lstlisting} +Example: SasView\_bcc\_paracrystal(dnn, d\_factor, radius, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -dnn & Ang & ([-inf, inf]) Nearest neighbour distance. & 220 \\ +dnn & \AA{} & ([-inf, inf]) Nearest neighbour distance. & 220 \\ d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ -radius & Ang & ([0, inf]) Particle radius. & 40 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Particle scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 40 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_bcc_paracrystal.comp}{Source code} for \texttt{SasView\_bcc\_paracrystal.comp}. + \item Component source code found in file \texttt{SasView\_bcc\_paracrystal.comp}. \end{itemize} -\IfFileExists{SasView_bcc_paracrystal_static.tex}{\input{SasView_bcc_paracrystal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_bcc_paracrystal_static.tex}{\input{sasmodels/SasView_bcc_paracrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_bcc_paracrystal_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_bcc_paracrystal_aniso.tex index 6f84b4f07b..58e66d63cd 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_bcc_paracrystal_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_bcc_paracrystal_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_bcc\_paracrystal\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_bcc_paracrystal component, generated from bcc_paracrystal.c in sasmodels. +SasView\_bcc\_paracrystal component, generated from bcc\_paracrystal.c in sasmodels. -Example: -SasView_bcc_paracrystal_aniso(dnn, d_factor, radius, sld, sld_solvent, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_bcc\_paracrystal\_aniso(dnn, d\_factor, radius, sld, sld\_solvent, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -dnn & Ang & ([-inf, inf]) Nearest neighbour distance. & 220 \\ +dnn & \AA{} & ([-inf, inf]) Nearest neighbour distance. & 220 \\ d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ -radius & Ang & ([0, inf]) Particle radius. & 40 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Particle scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 40 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ theta & & & 60 \\ phi & & & 60 \\ Psi & & & 60 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_bcc_paracrystal_aniso.comp}{Source code} for \texttt{SasView\_bcc\_paracrystal\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_bcc\_paracrystal\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_bcc_paracrystal_aniso_static.tex}{\input{SasView_bcc_paracrystal_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_bcc_paracrystal_aniso_static.tex}{\input{sasmodels/SasView_bcc_paracrystal_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_binary_hard_sphere.tex b/docs/manuals/mcstas/sasmodels/SasView_binary_hard_sphere.tex index 7c932a70f8..06c0d2b904 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_binary_hard_sphere.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_binary_hard_sphere.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_binary\_hard\_sphere} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_binary_hard_sphere component, generated from binary_hard_sphere.c in sasmodels. +SasView\_binary\_hard\_sphere component, generated from binary\_hard\_sphere.c in sasmodels. -Example: -SasView_binary_hard_sphere(radius_lg, radius_sm, volfraction_lg, volfraction_sm, sld_lg, sld_sm, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_lg=0.0, pd_radius_sm=0.0) -\end{lstlisting} +Example: SasView\_binary\_hard\_sphere(radius\_lg, radius\_sm, volfraction\_lg, volfraction\_sm, sld\_lg, sld\_sm, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_lg=0.0, pd\_radius\_sm=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,13 +21,13 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_lg & Ang & ([0, inf]) radius of large particle. & 100 \\ -radius\_sm & Ang & ([0, inf]) radius of small particle. & 25 \\ +radius\_lg & \AA{} & ([0, inf]) radius of large particle. & 100 \\ +radius\_sm & \AA{} & ([0, inf]) radius of small particle. & 25 \\ volfraction\_lg & & ([0, 1]) volume fraction of large particle. & 0.1 \\ volfraction\_sm & & ([0, 1]) volume fraction of small particle. & 0.2 \\ -sld\_lg & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) scattering length density of large particle. & 3.5 \\ -sld\_sm & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) scattering length density of small particle. & 0.5 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6.36 \\ +sld\_lg & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) scattering length density of large particle. & 3.5 \\ +sld\_sm & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) scattering length density of small particle. & 0.5 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.36 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -58,6 +50,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_binary_hard_sphere.comp}{Source code} for \texttt{SasView\_binary\_hard\_sphere.comp}. + \item Component source code found in file \texttt{SasView\_binary\_hard\_sphere.comp}. \end{itemize} -\IfFileExists{SasView_binary_hard_sphere_static.tex}{\input{SasView_binary_hard_sphere_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_binary_hard_sphere_static.tex}{\input{sasmodels/SasView_binary_hard_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_broad_peak.tex b/docs/manuals/mcstas/sasmodels/SasView_broad_peak.tex index 157915cfa3..219ba05939 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_broad_peak.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_broad_peak.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_broad\_peak} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_broad_peak component, generated from broad_peak.c in sasmodels. +SasView\_broad\_peak component, generated from broad\_peak.c in sasmodels. -Example: -SasView_broad_peak(porod_scale, porod_exp, peak_scale, correlation_length, peak_pos, width_exp, shape_exp, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_correlation_length=0.0) -\end{lstlisting} +Example: SasView\_broad\_peak(porod\_scale, porod\_exp, peak\_scale, correlation\_length, peak\_pos, width\_exp, shape\_exp, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_correlation\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -32,8 +24,8 @@ \subsection*{Input parameters} porod\_scale & & ([-inf, inf]) Power law scale factor. & 1e-05 \\ porod\_exp & & ([-inf, inf]) Exponent of power law. & 3.0 \\ peak\_scale & & ([-inf, inf]) Scale factor for broad peak. & 10.0 \\ -correlation\_length & Ang & ([-inf, inf]) screening length. & 50.0 \\ -peak\_pos & 1/Ang & ([-inf, inf]) Peak position in q. & 0.1 \\ +correlation\_length & \AA{} & ([-inf, inf]) screening length. & 50.0 \\ +peak\_pos & 1/\AA{} & ([-inf, inf]) Peak position in q. & 0.1 \\ width\_exp & & ([-inf, inf]) Exponent of peak width. & 2.0 \\ shape\_exp & & ([-inf, inf]) Exponent of peak shape. & 1.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_broad_peak.comp}{Source code} for \texttt{SasView\_broad\_peak.comp}. + \item Component source code found in file \texttt{SasView\_broad\_peak.comp}. \end{itemize} -\IfFileExists{SasView_broad_peak_static.tex}{\input{SasView_broad_peak_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_broad_peak_static.tex}{\input{sasmodels/SasView_broad_peak_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_capped_cylinder.tex b/docs/manuals/mcstas/sasmodels/SasView_capped_cylinder.tex index 17d5f70122..21624be906 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_capped_cylinder.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_capped_cylinder.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_capped\_cylinder} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_capped_cylinder component, generated from capped_cylinder.c in sasmodels. +SasView\_capped\_cylinder component, generated from capped\_cylinder.c in sasmodels. -Example: -SasView_capped_cylinder(sld, sld_solvent, radius, radius_cap, length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_radius_cap=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_capped\_cylinder(sld, sld\_solvent, radius, radius\_cap, length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_radius\_cap=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius & Ang & ([0, inf]) Cylinder radius. & 20 \\ -radius\_cap & Ang & ([0, inf]) Cap radius. & 20 \\ -length & Ang & ([0, inf]) Cylinder length. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder radius. & 20 \\ +radius\_cap & \AA{} & ([0, inf]) Cap radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_capped_cylinder.comp}{Source code} for \texttt{SasView\_capped\_cylinder.comp}. + \item Component source code found in file \texttt{SasView\_capped\_cylinder.comp}. \end{itemize} -\IfFileExists{SasView_capped_cylinder_static.tex}{\input{SasView_capped_cylinder_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_capped_cylinder_static.tex}{\input{sasmodels/SasView_capped_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_capped_cylinder_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_capped_cylinder_aniso.tex index daadb89483..8441657600 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_capped_cylinder_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_capped_cylinder_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_capped\_cylinder\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_capped_cylinder component, generated from capped_cylinder.c in sasmodels. +SasView\_capped\_cylinder component, generated from capped\_cylinder.c in sasmodels. -Example: -SasView_capped_cylinder_aniso(sld, sld_solvent, radius, radius_cap, length, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_radius_cap=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_capped\_cylinder\_aniso(sld, sld\_solvent, radius, radius\_cap, length, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_radius\_cap=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius & Ang & ([0, inf]) Cylinder radius. & 20 \\ -radius\_cap & Ang & ([0, inf]) Cap radius. & 20 \\ -length & Ang & ([0, inf]) Cylinder length. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder radius. & 20 \\ +radius\_cap & \AA{} & ([0, inf]) Cap radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ theta & & & 60 \\ phi & & & 60 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_capped_cylinder_aniso.comp}{Source code} for \texttt{SasView\_capped\_cylinder\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_capped\_cylinder\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_capped_cylinder_aniso_static.tex}{\input{SasView_capped_cylinder_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_capped_cylinder_aniso_static.tex}{\input{sasmodels/SasView_capped_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_multi_shell.tex b/docs/manuals/mcstas/sasmodels/SasView_core_multi_shell.tex index 021698f385..8f762c439e 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_multi_shell.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_multi_shell.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_multi\_shell} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_multi_shell component, generated from core_multi_shell.c in sasmodels. +SasView\_core\_multi\_shell component, generated from core\_multi\_shell.c in sasmodels. -Example: -SasView_core_multi_shell(sld_core, radius, sld_solvent, n, sld[n], thickness[n], -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness[n]=0.0) -\end{lstlisting} +Example: SasView\_core\_multi\_shell(sld\_core, radius, sld\_solvent, n, sld[n], thickness[n], model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness[n]=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -34,6 +26,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_multi_shell.comp}{Source code} for \texttt{SasView\_core\_multi\_shell.comp}. + \item Component source code found in file \texttt{SasView\_core\_multi\_shell.comp}. \end{itemize} -\IfFileExists{SasView_core_multi_shell_static.tex}{\input{SasView_core_multi_shell_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_multi_shell_static.tex}{\input{sasmodels/SasView_core_multi_shell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle.tex index ab2a27e2ce..f551f3a81c 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_bicelle} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_bicelle component, generated from core_shell_bicelle.c in sasmodels. +SasView\_core\_shell\_bicelle component, generated from core\_shell\_bicelle.c in sasmodels. -Example: -SasView_core_shell_bicelle(radius, thick_rim, thick_face, length, sld_core, sld_face, sld_rim, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thick_rim=0.0, pd_thick_face=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_bicelle(radius, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,14 +21,14 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Cylinder core radius. & 80 \\ -thick\_rim & Ang & ([0, inf]) Rim shell thickness. & 10 \\ -thick\_face & Ang & ([0, inf]) Cylinder face thickness. & 10 \\ -length & Ang & ([0, inf]) Cylinder length. & 50 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder core scattering length density. & 1 \\ -sld\_face & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder face scattering length density. & 4 \\ -sld\_rim & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder rim scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius. & 80 \\ +thick\_rim & \AA{} & ([0, inf]) Rim shell thickness. & 10 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 10 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 1 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 4 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_bicelle.comp}{Source code} for \texttt{SasView\_core\_shell\_bicelle.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_bicelle_static.tex}{\input{SasView_core_shell_bicelle_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_bicelle_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_aniso.tex index 1742267638..904a580079 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_bicelle\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_bicelle component, generated from core_shell_bicelle.c in sasmodels. +SasView\_core\_shell\_bicelle component, generated from core\_shell\_bicelle.c in sasmodels. -Example: -SasView_core_shell_bicelle_aniso(radius, thick_rim, thick_face, length, sld_core, sld_face, sld_rim, sld_solvent, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thick_rim=0.0, pd_thick_face=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_bicelle\_aniso(radius, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,14 +21,14 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Cylinder core radius. & 80 \\ -thick\_rim & Ang & ([0, inf]) Rim shell thickness. & 10 \\ -thick\_face & Ang & ([0, inf]) Cylinder face thickness. & 10 \\ -length & Ang & ([0, inf]) Cylinder length. & 50 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder core scattering length density. & 1 \\ -sld\_face & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder face scattering length density. & 4 \\ -sld\_rim & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder rim scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius. & 80 \\ +thick\_rim & \AA{} & ([0, inf]) Rim shell thickness. & 10 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 10 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 1 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 4 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ theta & & & 90 \\ phi & & & 0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -65,6 +57,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_bicelle_aniso.comp}{Source code} for \texttt{SasView\_core\_shell\_bicelle\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_bicelle_aniso_static.tex}{\input{SasView_core_shell_bicelle_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_bicelle_aniso_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical.tex index a66d58b9b9..a4777b1235 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_bicelle\_elliptical} McStas Component \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_bicelle_elliptical component, generated from core_shell_bicelle_elliptical.c in sasmodels. +SasView\_core\_shell\_bicelle\_elliptical component, generated from core\_shell\_bicelle\_elliptical.c in sasmodels. -Example: -SasView_core_shell_bicelle_elliptical(radius, x_core, thick_rim, thick_face, length, sld_core, sld_face, sld_rim, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thick_rim=0.0, pd_thick_face=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_bicelle\_elliptical(radius, x\_core, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,15 +21,15 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ x\_core & None & ([0, inf]) Axial ratio of core, X = r\_major/r\_minor. & 3 \\ -thick\_rim & Ang & ([0, inf]) Rim shell thickness. & 8 \\ -thick\_face & Ang & ([0, inf]) Cylinder face thickness. & 14 \\ -length & Ang & ([0, inf]) Cylinder length. & 50 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ -sld\_face & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ -sld\_rim & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ +thick\_rim & \AA{} & ([0, inf]) Rim shell thickness. & 8 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 14 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -62,6 +54,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_bicelle_elliptical.comp}{Source code} for \texttt{SasView\_core\_shell\_bicelle\_elliptical.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_elliptical.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_bicelle_elliptical_static.tex}{\input{SasView_core_shell_bicelle_elliptical_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_bicelle_elliptical_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_elliptical_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_aniso.tex index eb93065937..4237777dcc 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_bicelle\_elliptical\_aniso} McStas Co \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_bicelle_elliptical component, generated from core_shell_bicelle_elliptical.c in sasmodels. +SasView\_core\_shell\_bicelle\_elliptical component, generated from core\_shell\_bicelle\_elliptical.c in sasmodels. -Example: -SasView_core_shell_bicelle_elliptical_aniso(radius, x_core, thick_rim, thick_face, length, sld_core, sld_face, sld_rim, sld_solvent, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thick_rim=0.0, pd_thick_face=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_bicelle\_elliptical\_aniso(radius, x\_core, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,15 +21,15 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ x\_core & None & ([0, inf]) Axial ratio of core, X = r\_major/r\_minor. & 3 \\ -thick\_rim & Ang & ([0, inf]) Rim shell thickness. & 8 \\ -thick\_face & Ang & ([0, inf]) Cylinder face thickness. & 14 \\ -length & Ang & ([0, inf]) Cylinder length. & 50 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ -sld\_face & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ -sld\_rim & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ +thick\_rim & \AA{} & ([0, inf]) Rim shell thickness. & 8 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 14 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ theta & & & 90.0 \\ phi & & & 0 \\ Psi & & & 0 \\ @@ -68,6 +60,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_bicelle_elliptical_aniso.comp}{Source code} for \texttt{SasView\_core\_shell\_bicelle\_elliptical\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_elliptical\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_bicelle_elliptical_aniso_static.tex}{\input{SasView_core_shell_bicelle_elliptical_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_bicelle_elliptical_aniso_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_elliptical_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough.tex index a7a983fa86..bff15ff8ac 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough} McS \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_bicelle_elliptical_belt_rough component, generated from core_shell_bicelle_elliptical_belt_rough.c in sasmodels. +SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough component, generated from core\_shell\_bicelle\_elliptical\_belt\_rough.c in sasmodels. -Example: -SasView_core_shell_bicelle_elliptical_belt_rough(radius, x_core, thick_rim, thick_face, length, sld_core, sld_face, sld_rim, sld_solvent, sigma, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thick_rim=0.0, pd_thick_face=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough(radius, x\_core, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, sigma, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,16 +21,16 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ x\_core & None & ([0, inf]) Axial ratio of core, X = r\_major/r\_minor. & 3 \\ -thick\_rim & Ang & ([0, inf]) Rim or belt shell thickness. & 8 \\ -thick\_face & Ang & ([0, inf]) Cylinder face thickness. & 14 \\ -length & Ang & ([0, inf]) Cylinder length. & 50 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ -sld\_face & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ -sld\_rim & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ -sigma & Ang & ([0, inf]) Interfacial roughness. & 0 \\ +thick\_rim & \AA{} & ([0, inf]) Rim or belt shell thickness. & 8 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 14 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +sigma & \AA{} & ([0, inf]) Interfacial roughness. & 0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -63,6 +55,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough.comp}{Source code} for \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_bicelle_elliptical_belt_rough_static.tex}{\input{SasView_core_shell_bicelle_elliptical_belt_rough_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso.tex index 8204ff86a2..cf5de1c53e 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough\_ani \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_bicelle_elliptical_belt_rough component, generated from core_shell_bicelle_elliptical_belt_rough.c in sasmodels. +SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough component, generated from core\_shell\_bicelle\_elliptical\_belt\_rough.c in sasmodels. -Example: -SasView_core_shell_bicelle_elliptical_belt_rough_aniso(radius, x_core, thick_rim, thick_face, length, sld_core, sld_face, sld_rim, sld_solvent, sigma, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thick_rim=0.0, pd_thick_face=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough\_aniso(radius, x\_core, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, sigma, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,16 +21,16 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ x\_core & None & ([0, inf]) Axial ratio of core, X = r\_major/r\_minor. & 3 \\ -thick\_rim & Ang & ([0, inf]) Rim or belt shell thickness. & 8 \\ -thick\_face & Ang & ([0, inf]) Cylinder face thickness. & 14 \\ -length & Ang & ([0, inf]) Cylinder length. & 50 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ -sld\_face & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ -sld\_rim & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ -sigma & Ang & ([0, inf]) Interfacial roughness. & 0 \\ +thick\_rim & \AA{} & ([0, inf]) Rim or belt shell thickness. & 8 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 14 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +sigma & \AA{} & ([0, inf]) Interfacial roughness. & 0 \\ theta & & & 90.0 \\ phi & & & 0 \\ Psi & & & 0 \\ @@ -69,6 +61,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso.comp}{Source code} for \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_bicelle_elliptical_belt_rough_aniso_static.tex}{\input{SasView_core_shell_bicelle_elliptical_belt_rough_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_cylinder.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_cylinder.tex index ae9411e761..c623cc4734 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_cylinder.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_cylinder.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_cylinder} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_cylinder component, generated from core_shell_cylinder.c in sasmodels. +SasView\_core\_shell\_cylinder component, generated from core\_shell\_cylinder.c in sasmodels. -Example: -SasView_core_shell_cylinder(sld_core, sld_shell, sld_solvent, radius, thickness, length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_cylinder(sld\_core, sld\_shell, sld\_solvent, radius, thickness, length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,12 +21,12 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ -sld\_shell & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder shell scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius & Ang & ([0, inf]) Cylinder core radius. & 20 \\ -thickness & Ang & ([0, inf]) Cylinder shell thickness. & 20 \\ -length & Ang & ([0, inf]) Cylinder length. & 400 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder shell scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius. & 20 \\ +thickness & \AA{} & ([0, inf]) Cylinder shell thickness. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -58,6 +50,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_cylinder.comp}{Source code} for \texttt{SasView\_core\_shell\_cylinder.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_cylinder.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_cylinder_static.tex}{\input{SasView_core_shell_cylinder_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_cylinder_static.tex}{\input{sasmodels/SasView_core_shell_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_cylinder_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_cylinder_aniso.tex index edb556a245..19e425d33e 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_cylinder_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_cylinder_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_cylinder\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_cylinder component, generated from core_shell_cylinder.c in sasmodels. +SasView\_core\_shell\_cylinder component, generated from core\_shell\_cylinder.c in sasmodels. -Example: -SasView_core_shell_cylinder_aniso(sld_core, sld_shell, sld_solvent, radius, thickness, length, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_cylinder\_aniso(sld\_core, sld\_shell, sld\_solvent, radius, thickness, length, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,12 +21,12 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ -sld\_shell & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder shell scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius & Ang & ([0, inf]) Cylinder core radius. & 20 \\ -thickness & Ang & ([0, inf]) Cylinder shell thickness. & 20 \\ -length & Ang & ([0, inf]) Cylinder length. & 400 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder shell scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius. & 20 \\ +thickness & \AA{} & ([0, inf]) Cylinder shell thickness. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ theta & & & 60 \\ phi & & & 60 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -62,6 +54,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_cylinder_aniso.comp}{Source code} for \texttt{SasView\_core\_shell\_cylinder\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_cylinder\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_cylinder_aniso_static.tex}{\input{SasView_core_shell_cylinder_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_cylinder_aniso_static.tex}{\input{sasmodels/SasView_core_shell_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_ellipsoid.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_ellipsoid.tex index 035654ba1c..bbc6b3c1e5 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_ellipsoid.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_ellipsoid.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_ellipsoid} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_ellipsoid component, generated from core_shell_ellipsoid.c in sasmodels. +SasView\_core\_shell\_ellipsoid component, generated from core\_shell\_ellipsoid.c in sasmodels. -Example: -SasView_core_shell_ellipsoid(radius_equat_core, x_core, thick_shell, x_polar_shell, sld_core, sld_shell, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_equat_core=0.0, pd_thick_shell=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_ellipsoid(radius\_equat\_core, x\_core, thick\_shell, x\_polar\_shell, sld\_core, sld\_shell, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_equat\_core=0.0, pd\_thick\_shell=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,13 +21,13 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_equat\_core & Ang & ([0, inf]) Equatorial radius of core. & 20 \\ +radius\_equat\_core & \AA{} & ([0, inf]) Equatorial radius of core. & 20 \\ x\_core & None & ([0, inf]) axial ratio of core, X = r\_polar/r\_equatorial. & 3 \\ -thick\_shell & Ang & ([0, inf]) thickness of shell at equator. & 30 \\ +thick\_shell & \AA{} & ([0, inf]) thickness of shell at equator. & 30 \\ x\_polar\_shell & & ([0, inf]) ratio of thickness of shell at pole to that at equator. & 1 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Core scattering length density. & 2 \\ -sld\_shell & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Shell scattering length density. & 1 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Core scattering length density. & 2 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Shell scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -58,6 +50,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_ellipsoid.comp}{Source code} for \texttt{SasView\_core\_shell\_ellipsoid.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_ellipsoid.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_ellipsoid_static.tex}{\input{SasView_core_shell_ellipsoid_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_ellipsoid_static.tex}{\input{sasmodels/SasView_core_shell_ellipsoid_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_ellipsoid_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_ellipsoid_aniso.tex index d96000d421..995d7d906d 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_ellipsoid_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_ellipsoid_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_ellipsoid\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_ellipsoid component, generated from core_shell_ellipsoid.c in sasmodels. +SasView\_core\_shell\_ellipsoid component, generated from core\_shell\_ellipsoid.c in sasmodels. -Example: -SasView_core_shell_ellipsoid_aniso(radius_equat_core, x_core, thick_shell, x_polar_shell, sld_core, sld_shell, sld_solvent, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_equat_core=0.0, pd_thick_shell=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_ellipsoid\_aniso(radius\_equat\_core, x\_core, thick\_shell, x\_polar\_shell, sld\_core, sld\_shell, sld\_solvent, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_equat\_core=0.0, pd\_thick\_shell=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,13 +21,13 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_equat\_core & Ang & ([0, inf]) Equatorial radius of core. & 20 \\ +radius\_equat\_core & \AA{} & ([0, inf]) Equatorial radius of core. & 20 \\ x\_core & None & ([0, inf]) axial ratio of core, X = r\_polar/r\_equatorial. & 3 \\ -thick\_shell & Ang & ([0, inf]) thickness of shell at equator. & 30 \\ +thick\_shell & \AA{} & ([0, inf]) thickness of shell at equator. & 30 \\ x\_polar\_shell & & ([0, inf]) ratio of thickness of shell at pole to that at equator. & 1 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Core scattering length density. & 2 \\ -sld\_shell & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Shell scattering length density. & 1 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Core scattering length density. & 2 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Shell scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ theta & & & 0 \\ phi & & & 0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -62,6 +54,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_ellipsoid_aniso.comp}{Source code} for \texttt{SasView\_core\_shell\_ellipsoid\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_ellipsoid\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_ellipsoid_aniso_static.tex}{\input{SasView_core_shell_ellipsoid_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_ellipsoid_aniso_static.tex}{\input{sasmodels/SasView_core_shell_ellipsoid_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_parallelepiped.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_parallelepiped.tex index e46098466b..f7e8294b62 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_parallelepiped.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_parallelepiped.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_parallelepiped} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_parallelepiped component, generated from core_shell_parallelepiped.c in sasmodels. +SasView\_core\_shell\_parallelepiped component, generated from core\_shell\_parallelepiped.c in sasmodels. -Example: -SasView_core_shell_parallelepiped(sld_core, sld_a, sld_b, sld_c, sld_solvent, length_a, length_b, length_c, thick_rim_a, thick_rim_b, thick_rim_c, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0, pd_length_b=0.0, pd_length_c=0.0, pd_thick_rim_a=0.0, pd_thick_rim_b=0.0, pd_thick_rim_c=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_parallelepiped(sld\_core, sld\_a, sld\_b, sld\_c, sld\_solvent, length\_a, length\_b, length\_c, thick\_rim\_a, thick\_rim\_b, thick\_rim\_c, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_length\_b=0.0, pd\_length\_c=0.0, pd\_thick\_rim\_a=0.0, pd\_thick\_rim\_b=0.0, pd\_thick\_rim\_c=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,17 +21,17 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped core scattering length density. & 1 \\ -sld\_a & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped A rim scattering length density. & 2 \\ -sld\_b & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped B rim scattering length density. & 4 \\ -sld\_c & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped C rim scattering length density. & 2 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ -length\_a & Ang & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ -length\_b & Ang & ([0, inf]) Second side of the parallelepiped. & 75 \\ -length\_c & Ang & ([0, inf]) Larger side of the parallelepiped. & 400 \\ -thick\_rim\_a & Ang & ([0, inf]) Thickness of A rim. & 10 \\ -thick\_rim\_b & Ang & ([0, inf]) Thickness of B rim. & 10 \\ -thick\_rim\_c & Ang & ([0, inf]) Thickness of C rim. & 10 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped core scattering length density. & 1 \\ +sld\_a & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped A rim scattering length density. & 2 \\ +sld\_b & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped B rim scattering length density. & 4 \\ +sld\_c & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped C rim scattering length density. & 2 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +length\_b & \AA{} & ([0, inf]) Second side of the parallelepiped. & 75 \\ +length\_c & \AA{} & ([0, inf]) Larger side of the parallelepiped. & 400 \\ +thick\_rim\_a & \AA{} & ([0, inf]) Thickness of A rim. & 10 \\ +thick\_rim\_b & \AA{} & ([0, inf]) Thickness of B rim. & 10 \\ +thick\_rim\_c & \AA{} & ([0, inf]) Thickness of C rim. & 10 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -66,6 +58,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_parallelepiped.comp}{Source code} for \texttt{SasView\_core\_shell\_parallelepiped.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_parallelepiped.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_parallelepiped_static.tex}{\input{SasView_core_shell_parallelepiped_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_parallelepiped_static.tex}{\input{sasmodels/SasView_core_shell_parallelepiped_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_parallelepiped_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_parallelepiped_aniso.tex index 43e949ce7a..3c2e7e4f0c 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_parallelepiped_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_parallelepiped_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_parallelepiped\_aniso} McStas Compone \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_parallelepiped component, generated from core_shell_parallelepiped.c in sasmodels. +SasView\_core\_shell\_parallelepiped component, generated from core\_shell\_parallelepiped.c in sasmodels. -Example: -SasView_core_shell_parallelepiped_aniso(sld_core, sld_a, sld_b, sld_c, sld_solvent, length_a, length_b, length_c, thick_rim_a, thick_rim_b, thick_rim_c, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0, pd_length_b=0.0, pd_length_c=0.0, pd_thick_rim_a=0.0, pd_thick_rim_b=0.0, pd_thick_rim_c=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_parallelepiped\_aniso(sld\_core, sld\_a, sld\_b, sld\_c, sld\_solvent, length\_a, length\_b, length\_c, thick\_rim\_a, thick\_rim\_b, thick\_rim\_c, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_length\_b=0.0, pd\_length\_c=0.0, pd\_thick\_rim\_a=0.0, pd\_thick\_rim\_b=0.0, pd\_thick\_rim\_c=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,17 +21,17 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped core scattering length density. & 1 \\ -sld\_a & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped A rim scattering length density. & 2 \\ -sld\_b & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped B rim scattering length density. & 4 \\ -sld\_c & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped C rim scattering length density. & 2 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ -length\_a & Ang & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ -length\_b & Ang & ([0, inf]) Second side of the parallelepiped. & 75 \\ -length\_c & Ang & ([0, inf]) Larger side of the parallelepiped. & 400 \\ -thick\_rim\_a & Ang & ([0, inf]) Thickness of A rim. & 10 \\ -thick\_rim\_b & Ang & ([0, inf]) Thickness of B rim. & 10 \\ -thick\_rim\_c & Ang & ([0, inf]) Thickness of C rim. & 10 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped core scattering length density. & 1 \\ +sld\_a & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped A rim scattering length density. & 2 \\ +sld\_b & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped B rim scattering length density. & 4 \\ +sld\_c & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped C rim scattering length density. & 2 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +length\_b & \AA{} & ([0, inf]) Second side of the parallelepiped. & 75 \\ +length\_c & \AA{} & ([0, inf]) Larger side of the parallelepiped. & 400 \\ +thick\_rim\_a & \AA{} & ([0, inf]) Thickness of A rim. & 10 \\ +thick\_rim\_b & \AA{} & ([0, inf]) Thickness of B rim. & 10 \\ +thick\_rim\_c & \AA{} & ([0, inf]) Thickness of C rim. & 10 \\ theta & & & 0 \\ phi & & & 0 \\ Psi & & & 0 \\ @@ -72,6 +64,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_parallelepiped_aniso.comp}{Source code} for \texttt{SasView\_core\_shell\_parallelepiped\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_parallelepiped\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_parallelepiped_aniso_static.tex}{\input{SasView_core_shell_parallelepiped_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_parallelepiped_aniso_static.tex}{\input{sasmodels/SasView_core_shell_parallelepiped_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_core_shell_sphere.tex b/docs/manuals/mcstas/sasmodels/SasView_core_shell_sphere.tex index 75b6ee3bb4..bb0772630b 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_core_shell_sphere.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_core_shell_sphere.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_core\_shell\_sphere} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_core_shell_sphere component, generated from core_shell_sphere.c in sasmodels. +SasView\_core\_shell\_sphere component, generated from core\_shell\_sphere.c in sasmodels. -Example: -SasView_core_shell_sphere(radius, thickness, sld_core, sld_shell, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness=0.0) -\end{lstlisting} +Example: SasView\_core\_shell\_sphere(radius, thickness, sld\_core, sld\_shell, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Sphere core radius. & 60.0 \\ -thickness & Ang & ([0, inf]) Sphere shell thickness. & 10.0 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) core scattering length density. & 1.0 \\ -sld\_shell & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) shell scattering length density. & 2.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 3.0 \\ +radius & \AA{} & ([0, inf]) Sphere core radius. & 60.0 \\ +thickness & \AA{} & ([0, inf]) Sphere shell thickness. & 10.0 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) core scattering length density. & 1.0 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) shell scattering length density. & 2.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 3.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -56,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_core_shell_sphere.comp}{Source code} for \texttt{SasView\_core\_shell\_sphere.comp}. + \item Component source code found in file \texttt{SasView\_core\_shell\_sphere.comp}. \end{itemize} -\IfFileExists{SasView_core_shell_sphere_static.tex}{\input{SasView_core_shell_sphere_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_core_shell_sphere_static.tex}{\input{sasmodels/SasView_core_shell_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_correlation_length.tex b/docs/manuals/mcstas/sasmodels/SasView_correlation_length.tex index f53cdf3aea..f2dd1639de 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_correlation_length.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_correlation_length.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_correlation\_length} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_correlation_length component, generated from correlation_length.c in sasmodels. +SasView\_correlation\_length component, generated from correlation\_length.c in sasmodels. -Example: -SasView_correlation_length(lorentz_scale, porod_scale, cor_length, porod_exp, lorentz_exp, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_cor_length=0.0) -\end{lstlisting} +Example: SasView\_correlation\_length(lorentz\_scale, porod\_scale, cor\_length, porod\_exp, lorentz\_exp, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_cor\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -31,7 +23,7 @@ \subsection*{Input parameters} \endhead lorentz\_scale & & ([0, inf]) Lorentzian Scaling Factor. & 10.0 \\ porod\_scale & & ([0, inf]) Porod Scaling Factor. & 1e-06 \\ -cor\_length & Ang & ([0, inf]) Correlation length, xi, in Lorentzian. & 50.0 \\ +cor\_length & \AA{} & ([0, inf]) Correlation length, xi, in Lorentzian. & 50.0 \\ porod\_exp & & ([0, inf]) Porod Exponent, n, in q\textasciicircum{}-n. & 3.0 \\ lorentz\_exp & & ([0, inf]) Lorentzian Exponent, m, in 1/( 1 + (q.xi)\textasciicircum{}m). & 2.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_correlation_length.comp}{Source code} for \texttt{SasView\_correlation\_length.comp}. + \item Component source code found in file \texttt{SasView\_correlation\_length.comp}. \end{itemize} -\IfFileExists{SasView_correlation_length_static.tex}{\input{SasView_correlation_length_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_correlation_length_static.tex}{\input{sasmodels/SasView_correlation_length_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_cylinder.tex b/docs/manuals/mcstas/sasmodels/SasView_cylinder.tex index 3664a116a5..7d9068fd93 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_cylinder.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_cylinder.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_cylinder} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_cylinder component, generated from cylinder.c in sasmodels. +SasView\_cylinder component, generated from cylinder.c in sasmodels. -Example: -SasView_cylinder(sld, sld_solvent, radius, length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_cylinder(sld, sld\_solvent, radius, length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,10 +21,10 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius & Ang & ([0, inf]) Cylinder radius. & 20 \\ -length & Ang & ([0, inf]) Cylinder length. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_cylinder.comp}{Source code} for \texttt{SasView\_cylinder.comp}. + \item Component source code found in file \texttt{SasView\_cylinder.comp}. \end{itemize} -\IfFileExists{SasView_cylinder_static.tex}{\input{SasView_cylinder_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_cylinder_static.tex}{\input{sasmodels/SasView_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_cylinder_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_cylinder_aniso.tex index 5bb3fffc8a..b3a18bca3c 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_cylinder_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_cylinder_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_cylinder\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_cylinder component, generated from cylinder.c in sasmodels. +SasView\_cylinder component, generated from cylinder.c in sasmodels. -Example: -SasView_cylinder_aniso(sld, sld_solvent, radius, length, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_cylinder\_aniso(sld, sld\_solvent, radius, length, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,10 +21,10 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius & Ang & ([0, inf]) Cylinder radius. & 20 \\ -length & Ang & ([0, inf]) Cylinder length. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ theta & & & 60 \\ phi & & & 60 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -59,6 +51,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_cylinder_aniso.comp}{Source code} for \texttt{SasView\_cylinder\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_cylinder\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_cylinder_aniso_static.tex}{\input{SasView_cylinder_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_cylinder_aniso_static.tex}{\input{sasmodels/SasView_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_dab.tex b/docs/manuals/mcstas/sasmodels/SasView_dab.tex index 3c5a7cbdbb..eabcca1de5 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_dab.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_dab.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_dab} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_dab component, generated from dab.c in sasmodels. +SasView\_dab component, generated from dab.c in sasmodels. -Example: -SasView_dab(cor_length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_cor_length=0.0) -\end{lstlisting} +Example: SasView\_dab(cor\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_cor\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -cor\_length & Ang & ([0, inf]) correlation length. & 50.0 \\ +cor\_length & \AA{} & ([0, inf]) correlation length. & 50.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -51,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_dab.comp}{Source code} for \texttt{SasView\_dab.comp}. + \item Component source code found in file \texttt{SasView\_dab.comp}. \end{itemize} -\IfFileExists{SasView_dab_static.tex}{\input{SasView_dab_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_dab_static.tex}{\input{sasmodels/SasView_dab_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_ellipsoid.tex b/docs/manuals/mcstas/sasmodels/SasView_ellipsoid.tex index b7c5ed0a05..3c95090fc9 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_ellipsoid.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_ellipsoid.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_ellipsoid} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_ellipsoid component, generated from ellipsoid.c in sasmodels. +SasView\_ellipsoid component, generated from ellipsoid.c in sasmodels. -Example: -SasView_ellipsoid(sld, sld_solvent, radius_polar, radius_equatorial, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_polar=0.0, pd_radius_equatorial=0.0) -\end{lstlisting} +Example: SasView\_ellipsoid(sld, sld\_solvent, radius\_polar, radius\_equatorial, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_polar=0.0, pd\_radius\_equatorial=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,10 +21,10 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius\_polar & Ang & ([0, inf]) Polar radius. & 20 \\ -radius\_equatorial & Ang & ([0, inf]) Equatorial radius. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_polar & \AA{} & ([0, inf]) Polar radius. & 20 \\ +radius\_equatorial & \AA{} & ([0, inf]) Equatorial radius. & 400 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_ellipsoid.comp}{Source code} for \texttt{SasView\_ellipsoid.comp}. + \item Component source code found in file \texttt{SasView\_ellipsoid.comp}. \end{itemize} -\IfFileExists{SasView_ellipsoid_static.tex}{\input{SasView_ellipsoid_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_ellipsoid_static.tex}{\input{sasmodels/SasView_ellipsoid_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_ellipsoid_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_ellipsoid_aniso.tex index 309995c0a8..86d5be964b 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_ellipsoid_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_ellipsoid_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_ellipsoid\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_ellipsoid component, generated from ellipsoid.c in sasmodels. +SasView\_ellipsoid component, generated from ellipsoid.c in sasmodels. -Example: -SasView_ellipsoid_aniso(sld, sld_solvent, radius_polar, radius_equatorial, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_polar=0.0, pd_radius_equatorial=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_ellipsoid\_aniso(sld, sld\_solvent, radius\_polar, radius\_equatorial, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_polar=0.0, pd\_radius\_equatorial=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,10 +21,10 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius\_polar & Ang & ([0, inf]) Polar radius. & 20 \\ -radius\_equatorial & Ang & ([0, inf]) Equatorial radius. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_polar & \AA{} & ([0, inf]) Polar radius. & 20 \\ +radius\_equatorial & \AA{} & ([0, inf]) Equatorial radius. & 400 \\ theta & & & 60 \\ phi & & & 60 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -59,6 +51,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_ellipsoid_aniso.comp}{Source code} for \texttt{SasView\_ellipsoid\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_ellipsoid\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_ellipsoid_aniso_static.tex}{\input{SasView_ellipsoid_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_ellipsoid_aniso_static.tex}{\input{sasmodels/SasView_ellipsoid_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_elliptical_cylinder.tex b/docs/manuals/mcstas/sasmodels/SasView_elliptical_cylinder.tex index 9d083d095e..ce06f5e1b2 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_elliptical_cylinder.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_elliptical_cylinder.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_elliptical\_cylinder} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_elliptical_cylinder component, generated from elliptical_cylinder.c in sasmodels. +SasView\_elliptical\_cylinder component, generated from elliptical\_cylinder.c in sasmodels. -Example: -SasView_elliptical_cylinder(radius_minor, r_ratio, length, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_minor=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_elliptical\_cylinder(radius\_minor, r\_ratio, length, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_minor=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_minor & Ang & ([0, inf]) Ellipse minor radius. & 20.0 \\ +radius\_minor & \AA{} & ([0, inf]) Ellipse minor radius. & 20.0 \\ r\_ratio & & ([1, inf]) Ratio of major radius over minor radius. & 1.5 \\ -length & Ang & ([1, inf]) Length of the cylinder. & 400.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder scattering length density. & 4.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ +length & \AA{} & ([1, inf]) Length of the cylinder. & 400.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -56,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_elliptical_cylinder.comp}{Source code} for \texttt{SasView\_elliptical\_cylinder.comp}. + \item Component source code found in file \texttt{SasView\_elliptical\_cylinder.comp}. \end{itemize} -\IfFileExists{SasView_elliptical_cylinder_static.tex}{\input{SasView_elliptical_cylinder_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_elliptical_cylinder_static.tex}{\input{sasmodels/SasView_elliptical_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_elliptical_cylinder_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_elliptical_cylinder_aniso.tex index 9726ceb7de..57cdba3803 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_elliptical_cylinder_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_elliptical_cylinder_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_elliptical\_cylinder\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_elliptical_cylinder component, generated from elliptical_cylinder.c in sasmodels. +SasView\_elliptical\_cylinder component, generated from elliptical\_cylinder.c in sasmodels. -Example: -SasView_elliptical_cylinder_aniso(radius_minor, r_ratio, length, sld, sld_solvent, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_minor=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_elliptical\_cylinder\_aniso(radius\_minor, r\_ratio, length, sld, sld\_solvent, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_minor=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_minor & Ang & ([0, inf]) Ellipse minor radius. & 20.0 \\ +radius\_minor & \AA{} & ([0, inf]) Ellipse minor radius. & 20.0 \\ r\_ratio & & ([1, inf]) Ratio of major radius over minor radius. & 1.5 \\ -length & Ang & ([1, inf]) Length of the cylinder. & 400.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder scattering length density. & 4.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ +length & \AA{} & ([1, inf]) Length of the cylinder. & 400.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ theta & & & 90.0 \\ phi & & & 0 \\ Psi & & & 0 \\ @@ -62,6 +54,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_elliptical_cylinder_aniso.comp}{Source code} for \texttt{SasView\_elliptical\_cylinder\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_elliptical\_cylinder\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_elliptical_cylinder_aniso_static.tex}{\input{SasView_elliptical_cylinder_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_elliptical_cylinder_aniso_static.tex}{\input{sasmodels/SasView_elliptical_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_fcc_paracrystal.tex b/docs/manuals/mcstas/sasmodels/SasView_fcc_paracrystal.tex index 85e9aa40f9..d0488b8618 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_fcc_paracrystal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_fcc_paracrystal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_fcc\_paracrystal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_fcc_paracrystal component, generated from fcc_paracrystal.c in sasmodels. +SasView\_fcc\_paracrystal component, generated from fcc\_paracrystal.c in sasmodels. -Example: -SasView_fcc_paracrystal(dnn, d_factor, radius, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0) -\end{lstlisting} +Example: SasView\_fcc\_paracrystal(dnn, d\_factor, radius, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -dnn & Ang & ([-inf, inf]) Nearest neighbour distance. & 220 \\ +dnn & \AA{} & ([-inf, inf]) Nearest neighbour distance. & 220 \\ d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ -radius & Ang & ([0, inf]) Particle radius. & 40 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Particle scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 40 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_fcc_paracrystal.comp}{Source code} for \texttt{SasView\_fcc\_paracrystal.comp}. + \item Component source code found in file \texttt{SasView\_fcc\_paracrystal.comp}. \end{itemize} -\IfFileExists{SasView_fcc_paracrystal_static.tex}{\input{SasView_fcc_paracrystal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_fcc_paracrystal_static.tex}{\input{sasmodels/SasView_fcc_paracrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_fcc_paracrystal_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_fcc_paracrystal_aniso.tex index 8cc901025f..a031ed7876 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_fcc_paracrystal_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_fcc_paracrystal_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_fcc\_paracrystal\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_fcc_paracrystal component, generated from fcc_paracrystal.c in sasmodels. +SasView\_fcc\_paracrystal component, generated from fcc\_paracrystal.c in sasmodels. -Example: -SasView_fcc_paracrystal_aniso(dnn, d_factor, radius, sld, sld_solvent, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_fcc\_paracrystal\_aniso(dnn, d\_factor, radius, sld, sld\_solvent, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -dnn & Ang & ([-inf, inf]) Nearest neighbour distance. & 220 \\ +dnn & \AA{} & ([-inf, inf]) Nearest neighbour distance. & 220 \\ d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ -radius & Ang & ([0, inf]) Particle radius. & 40 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Particle scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 40 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ theta & & & 60 \\ phi & & & 60 \\ Psi & & & 60 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_fcc_paracrystal_aniso.comp}{Source code} for \texttt{SasView\_fcc\_paracrystal\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_fcc\_paracrystal\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_fcc_paracrystal_aniso_static.tex}{\input{SasView_fcc_paracrystal_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_fcc_paracrystal_aniso_static.tex}{\input{sasmodels/SasView_fcc_paracrystal_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_flexible_cylinder.tex b/docs/manuals/mcstas/sasmodels/SasView_flexible_cylinder.tex index eb2fbbb460..358231baa3 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_flexible_cylinder.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_flexible_cylinder.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_flexible\_cylinder} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_flexible_cylinder component, generated from flexible_cylinder.c in sasmodels. +SasView\_flexible\_cylinder component, generated from flexible\_cylinder.c in sasmodels. -Example: -SasView_flexible_cylinder(length, kuhn_length, radius, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length=0.0, pd_kuhn_length=0.0, pd_radius=0.0) -\end{lstlisting} +Example: SasView\_flexible\_cylinder(length, kuhn\_length, radius, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length=0.0, pd\_kuhn\_length=0.0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -length & Ang & ([0, inf]) Length of the flexible cylinder. & 1000.0 \\ -kuhn\_length & Ang & ([0, inf]) Kuhn length of the flexible cylinder. & 100.0 \\ -radius & Ang & ([0, inf]) Radius of the flexible cylinder. & 20.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder scattering length density. & 1.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ +length & \AA{} & ([0, inf]) Length of the flexible cylinder. & 1000.0 \\ +kuhn\_length & \AA{} & ([0, inf]) Kuhn length of the flexible cylinder. & 100.0 \\ +radius & \AA{} & ([0, inf]) Radius of the flexible cylinder. & 20.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_flexible_cylinder.comp}{Source code} for \texttt{SasView\_flexible\_cylinder.comp}. + \item Component source code found in file \texttt{SasView\_flexible\_cylinder.comp}. \end{itemize} -\IfFileExists{SasView_flexible_cylinder_static.tex}{\input{SasView_flexible_cylinder_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_flexible_cylinder_static.tex}{\input{sasmodels/SasView_flexible_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_flexible_cylinder_elliptical.tex b/docs/manuals/mcstas/sasmodels/SasView_flexible_cylinder_elliptical.tex index 44596fbb6c..3203626c3c 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_flexible_cylinder_elliptical.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_flexible_cylinder_elliptical.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_flexible\_cylinder\_elliptical} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_flexible_cylinder_elliptical component, generated from flexible_cylinder_elliptical.c in sasmodels. +SasView\_flexible\_cylinder\_elliptical component, generated from flexible\_cylinder\_elliptical.c in sasmodels. -Example: -SasView_flexible_cylinder_elliptical(length, kuhn_length, radius, axis_ratio, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length=0.0, pd_kuhn_length=0.0, pd_radius=0.0) -\end{lstlisting} +Example: SasView\_flexible\_cylinder\_elliptical(length, kuhn\_length, radius, axis\_ratio, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length=0.0, pd\_kuhn\_length=0.0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,12 +21,12 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -length & Ang & ([0, inf]) Length of the flexible cylinder. & 1000.0 \\ -kuhn\_length & Ang & ([0, inf]) Kuhn length of the flexible cylinder. & 100.0 \\ -radius & Ang & ([1, inf]) Radius of the flexible cylinder. & 20.0 \\ +length & \AA{} & ([0, inf]) Length of the flexible cylinder. & 1000.0 \\ +kuhn\_length & \AA{} & ([0, inf]) Kuhn length of the flexible cylinder. & 100.0 \\ +radius & \AA{} & ([1, inf]) Radius of the flexible cylinder. & 20.0 \\ axis\_ratio & & ([0, inf]) Axis\_ratio (major\_radius/minor\_radius. & 1.5 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder scattering length density. & 1.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -58,6 +50,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_flexible_cylinder_elliptical.comp}{Source code} for \texttt{SasView\_flexible\_cylinder\_elliptical.comp}. + \item Component source code found in file \texttt{SasView\_flexible\_cylinder\_elliptical.comp}. \end{itemize} -\IfFileExists{SasView_flexible_cylinder_elliptical_static.tex}{\input{SasView_flexible_cylinder_elliptical_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_flexible_cylinder_elliptical_static.tex}{\input{sasmodels/SasView_flexible_cylinder_elliptical_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_fractal.tex b/docs/manuals/mcstas/sasmodels/SasView_fractal.tex index 1ad2216281..5285b80ba3 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_fractal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_fractal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_fractal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_fractal component, generated from fractal.c in sasmodels. +SasView\_fractal component, generated from fractal.c in sasmodels. -Example: -SasView_fractal(volfraction, radius, fractal_dim, cor_length, sld_block, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_cor_length=0.0) -\end{lstlisting} +Example: SasView\_fractal(volfraction, radius, fractal\_dim, cor\_length, sld\_block, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_cor\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,11 +22,11 @@ \subsection*{Input parameters} \midrule \endhead volfraction & & ([0.0, 1]) volume fraction of blocks. & 0.05 \\ -radius & Ang & ([0.0, inf]) radius of particles. & 5.0 \\ +radius & \AA{} & ([0.0, inf]) radius of particles. & 5.0 \\ fractal\_dim & & ([0.0, 6.0]) fractal dimension. & 2.0 \\ -cor\_length & Ang & ([0.0, inf]) cluster correlation length. & 100.0 \\ -sld\_block & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) scattering length density of particles. & 2.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) scattering length density of solvent. & 6.4 \\ +cor\_length & \AA{} & ([0.0, inf]) cluster correlation length. & 100.0 \\ +sld\_block & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) scattering length density of particles. & 2.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) scattering length density of solvent. & 6.4 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_fractal.comp}{Source code} for \texttt{SasView\_fractal.comp}. + \item Component source code found in file \texttt{SasView\_fractal.comp}. \end{itemize} -\IfFileExists{SasView_fractal_static.tex}{\input{SasView_fractal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_fractal_static.tex}{\input{sasmodels/SasView_fractal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_fractal_core_shell.tex b/docs/manuals/mcstas/sasmodels/SasView_fractal_core_shell.tex index 5e21a096c9..0693d699ea 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_fractal_core_shell.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_fractal_core_shell.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_fractal\_core\_shell} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_fractal_core_shell component, generated from fractal_core_shell.c in sasmodels. +SasView\_fractal\_core\_shell component, generated from fractal\_core\_shell.c in sasmodels. -Example: -SasView_fractal_core_shell(radius, thickness, sld_core, sld_shell, sld_solvent, volfraction, fractal_dim, cor_length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness=0.0, pd_cor_length=0.0) -\end{lstlisting} +Example: SasView\_fractal\_core\_shell(radius, thickness, sld\_core, sld\_shell, sld\_solvent, volfraction, fractal\_dim, cor\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_cor\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,14 +21,14 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0.0, inf]) Sphere core radius. & 60.0 \\ -thickness & Ang & ([0.0, inf]) Sphere shell thickness. & 10.0 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Sphere core scattering length density. & 1.0 \\ -sld\_shell & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Sphere shell scattering length density. & 2.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 3.0 \\ +radius & \AA{} & ([0.0, inf]) Sphere core radius. & 60.0 \\ +thickness & \AA{} & ([0.0, inf]) Sphere shell thickness. & 10.0 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Sphere core scattering length density. & 1.0 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Sphere shell scattering length density. & 2.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 3.0 \\ volfraction & & ([0.0, inf]) Volume fraction of building block spheres. & 0.05 \\ fractal\_dim & & ([0.0, 6.0]) Fractal dimension. & 2.0 \\ -cor\_length & Ang & ([0.0, inf]) Correlation length of fractal-like aggregates. & 100.0 \\ +cor\_length & \AA{} & ([0.0, inf]) Correlation length of fractal-like aggregates. & 100.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -60,6 +52,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_fractal_core_shell.comp}{Source code} for \texttt{SasView\_fractal\_core\_shell.comp}. + \item Component source code found in file \texttt{SasView\_fractal\_core\_shell.comp}. \end{itemize} -\IfFileExists{SasView_fractal_core_shell_static.tex}{\input{SasView_fractal_core_shell_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_fractal_core_shell_static.tex}{\input{sasmodels/SasView_fractal_core_shell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_fuzzy_sphere.tex b/docs/manuals/mcstas/sasmodels/SasView_fuzzy_sphere.tex index 0c7deabe89..09e818be16 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_fuzzy_sphere.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_fuzzy_sphere.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_fuzzy\_sphere} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_fuzzy_sphere component, generated from fuzzy_sphere.c in sasmodels. +SasView\_fuzzy\_sphere component, generated from fuzzy\_sphere.c in sasmodels. -Example: -SasView_fuzzy_sphere(sld, sld_solvent, radius, fuzziness, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0) -\end{lstlisting} +Example: SasView\_fuzzy\_sphere(sld, sld\_solvent, radius, fuzziness, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,10 +21,10 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Particle scattering length density. & 1 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 3 \\ -radius & Ang & ([0, inf]) Sphere radius. & 60 \\ -fuzziness & Ang & ([0, inf]) std deviation of Gaussian convolution for interface (must be \textless{}\textless{} radius). & 10 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 3 \\ +radius & \AA{} & ([0, inf]) Sphere radius. & 60 \\ +fuzziness & \AA{} & ([0, inf]) std deviation of Gaussian convolution for interface (must be \textless{}\textless{} radius). & 10 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -54,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_fuzzy_sphere.comp}{Source code} for \texttt{SasView\_fuzzy\_sphere.comp}. + \item Component source code found in file \texttt{SasView\_fuzzy\_sphere.comp}. \end{itemize} -\IfFileExists{SasView_fuzzy_sphere_static.tex}{\input{SasView_fuzzy_sphere_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_fuzzy_sphere_static.tex}{\input{sasmodels/SasView_fuzzy_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_gauss_lorentz_gel.tex b/docs/manuals/mcstas/sasmodels/SasView_gauss_lorentz_gel.tex index 3cf7bea1a1..b6cad14942 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_gauss_lorentz_gel.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_gauss_lorentz_gel.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_gauss\_lorentz\_gel} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_gauss_lorentz_gel component, generated from gauss_lorentz_gel.c in sasmodels. +SasView\_gauss\_lorentz\_gel component, generated from gauss\_lorentz\_gel.c in sasmodels. -Example: -SasView_gauss_lorentz_gel(gauss_scale, cor_length_static, lorentz_scale, cor_length_dynamic, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_cor_length_static=0.0, pd_cor_length_dynamic=0.0) -\end{lstlisting} +Example: SasView\_gauss\_lorentz\_gel(gauss\_scale, cor\_length\_static, lorentz\_scale, cor\_length\_dynamic, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_cor\_length\_static=0.0, pd\_cor\_length\_dynamic=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,9 +22,9 @@ \subsection*{Input parameters} \midrule \endhead gauss\_scale & & ([-inf, inf]) Gauss scale factor. & 100.0 \\ -cor\_length\_static & Ang & ([0, inf]) Static correlation length. & 100.0 \\ +cor\_length\_static & \AA{} & ([0, inf]) Static correlation length. & 100.0 \\ lorentz\_scale & & ([-inf, inf]) Lorentzian scale factor. & 50.0 \\ -cor\_length\_dynamic & Ang & ([0, inf]) Dynamic correlation length. & 20.0 \\ +cor\_length\_dynamic & \AA{} & ([0, inf]) Dynamic correlation length. & 20.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_gauss_lorentz_gel.comp}{Source code} for \texttt{SasView\_gauss\_lorentz\_gel.comp}. + \item Component source code found in file \texttt{SasView\_gauss\_lorentz\_gel.comp}. \end{itemize} -\IfFileExists{SasView_gauss_lorentz_gel_static.tex}{\input{SasView_gauss_lorentz_gel_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_gauss_lorentz_gel_static.tex}{\input{sasmodels/SasView_gauss_lorentz_gel_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_gaussian_peak.tex b/docs/manuals/mcstas/sasmodels/SasView_gaussian_peak.tex index 9f4b50b238..8854632154 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_gaussian_peak.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_gaussian_peak.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_gaussian\_peak} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_gaussian_peak component, generated from gaussian_peak.c in sasmodels. +SasView\_gaussian\_peak component, generated from gaussian\_peak.c in sasmodels. -Example: -SasView_gaussian_peak(peak_pos, sigma, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +Example: SasView\_gaussian\_peak(peak\_pos, sigma, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,8 +21,8 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -peak\_pos & 1/Ang & ([-inf, inf]) Peak position. & 0.05 \\ -sigma & 1/Ang & ([0, inf]) Peak width (standard deviation). & 0.005 \\ +peak\_pos & 1/\AA{} & ([-inf, inf]) Peak position. & 0.05 \\ +sigma & 1/\AA{} & ([0, inf]) Peak width (standard deviation). & 0.005 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -51,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_gaussian_peak.comp}{Source code} for \texttt{SasView\_gaussian\_peak.comp}. + \item Component source code found in file \texttt{SasView\_gaussian\_peak.comp}. \end{itemize} -\IfFileExists{SasView_gaussian_peak_static.tex}{\input{SasView_gaussian_peak_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_gaussian_peak_static.tex}{\input{sasmodels/SasView_gaussian_peak_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_gel_fit.tex b/docs/manuals/mcstas/sasmodels/SasView_gel_fit.tex index b059da3d35..340ec7ddcf 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_gel_fit.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_gel_fit.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_gel\_fit} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_gel_fit component, generated from gel_fit.c in sasmodels. +SasView\_gel\_fit component, generated from gel\_fit.c in sasmodels. -Example: -SasView_gel_fit(guinier_scale, lorentz_scale, rg, fractal_dim, cor_length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_rg=0.0, pd_cor_length=0.0) -\end{lstlisting} +Example: SasView\_gel\_fit(guinier\_scale, lorentz\_scale, rg, fractal\_dim, cor\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0, pd\_cor\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -guinier\_scale & cm\textasciicircum{}-1 & ([-inf, inf]) Guinier term scale. & 1.7 \\ -lorentz\_scale & cm\textasciicircum{}-1 & ([-inf, inf]) Lorentz term scale. & 3.5 \\ -rg & Ang & ([2, inf]) Radius of gyration. & 104.0 \\ +guinier\_scale & cm$^{-1}$ & ([-inf, inf]) Guinier term scale. & 1.7 \\ +lorentz\_scale & cm$^{-1}$ & ([-inf, inf]) Lorentz term scale. & 3.5 \\ +rg & \AA{} & ([2, inf]) Radius of gyration. & 104.0 \\ fractal\_dim & & ([0, inf]) Fractal exponent. & 2.0 \\ -cor\_length & Ang & ([0, inf]) Correlation length. & 16.0 \\ +cor\_length & \AA{} & ([0, inf]) Correlation length. & 16.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -56,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_gel_fit.comp}{Source code} for \texttt{SasView\_gel\_fit.comp}. + \item Component source code found in file \texttt{SasView\_gel\_fit.comp}. \end{itemize} -\IfFileExists{SasView_gel_fit_static.tex}{\input{SasView_gel_fit_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_gel_fit_static.tex}{\input{sasmodels/SasView_gel_fit_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_guinier.tex b/docs/manuals/mcstas/sasmodels/SasView_guinier.tex index d79b945c1a..f76b8a6723 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_guinier.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_guinier.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_guinier} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_guinier component, generated from guinier.c in sasmodels. +SasView\_guinier component, generated from guinier.c in sasmodels. -Example: -SasView_guinier(rg, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_rg=0.0) -\end{lstlisting} +Example: SasView\_guinier(rg, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -rg & Ang & ([-inf, inf]) Radius of Gyration. & 60.0 \\ +rg & \AA{} & ([-inf, inf]) Radius of Gyration. & 60.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -51,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_guinier.comp}{Source code} for \texttt{SasView\_guinier.comp}. + \item Component source code found in file \texttt{SasView\_guinier.comp}. \end{itemize} -\IfFileExists{SasView_guinier_static.tex}{\input{SasView_guinier_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_guinier_static.tex}{\input{sasmodels/SasView_guinier_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_guinier_porod.tex b/docs/manuals/mcstas/sasmodels/SasView_guinier_porod.tex index 42bca66b8e..8a8995f3ca 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_guinier_porod.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_guinier_porod.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_guinier\_porod} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_guinier_porod component, generated from guinier_porod.c in sasmodels. +SasView\_guinier\_porod component, generated from guinier\_porod.c in sasmodels. -Example: -SasView_guinier_porod(rg, s, porod_exp, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_rg=0.0) -\end{lstlisting} +Example: SasView\_guinier\_porod(rg, s, porod\_exp, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -rg & Ang & ([0, inf]) Radius of gyration. & 60.0 \\ +rg & \AA{} & ([0, inf]) Radius of gyration. & 60.0 \\ s & & ([0, inf]) Dimension variable. & 1.0 \\ porod\_exp & & ([0, inf]) Porod exponent. & 3.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -53,6 +45,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_guinier_porod.comp}{Source code} for \texttt{SasView\_guinier\_porod.comp}. + \item Component source code found in file \texttt{SasView\_guinier\_porod.comp}. \end{itemize} -\IfFileExists{SasView_guinier_porod_static.tex}{\input{SasView_guinier_porod_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_guinier_porod_static.tex}{\input{sasmodels/SasView_guinier_porod_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_hardsphere.tex b/docs/manuals/mcstas/sasmodels/SasView_hardsphere.tex index 29d8fe35b7..e79cac4075 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_hardsphere.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_hardsphere.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_hardsphere} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_hardsphere component, generated from hardsphere.c in sasmodels. +SasView\_hardsphere component, generated from hardsphere.c in sasmodels. -Example: -SasView_hardsphere(radius_effective, volfraction, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_effective=0.0) -\end{lstlisting} +Example: SasView\_hardsphere(radius\_effective, volfraction, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_effective=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_effective & Ang & ([0, inf]) effective radius of hard sphere. & 50.0 \\ +radius\_effective & \AA{} & ([0, inf]) effective radius of hard sphere. & 50.0 \\ volfraction & & ([0, 0.74]) volume fraction of hard spheres. & 0.2 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ @@ -52,6 +44,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_hardsphere.comp}{Source code} for \texttt{SasView\_hardsphere.comp}. + \item Component source code found in file \texttt{SasView\_hardsphere.comp}. \end{itemize} -\IfFileExists{SasView_hardsphere_static.tex}{\input{SasView_hardsphere_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_hardsphere_static.tex}{\input{sasmodels/SasView_hardsphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_hayter_msa.tex b/docs/manuals/mcstas/sasmodels/SasView_hayter_msa.tex index 114687bd4b..96e1be7644 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_hayter_msa.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_hayter_msa.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_hayter\_msa} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_hayter_msa component, generated from hayter_msa.c in sasmodels. +SasView\_hayter\_msa component, generated from hayter\_msa.c in sasmodels. -Example: -SasView_hayter_msa(radius_effective, volfraction, charge, temperature, concentration_salt, dielectconst, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_effective=0.0, pd_charge=0.0) -\end{lstlisting} +Example: SasView\_hayter\_msa(radius\_effective, volfraction, charge, temperature, concentration\_salt, dielectconst, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_effective=0.0, pd\_charge=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_effective & Ang & ([0, inf]) effective radius of charged sphere. & 20.75 \\ +radius\_effective & \AA{} & ([0, inf]) effective radius of charged sphere. & 20.75 \\ volfraction & None & ([0, 0.74]) volume fraction of spheres. & 0.0192 \\ charge & e & ([1e-06, 200]) charge on sphere (in electrons). & 19.0 \\ temperature & K & ([0, 450]) temperature, in Kelvin, for Debye length calculation. & 318.16 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_hayter_msa.comp}{Source code} for \texttt{SasView\_hayter\_msa.comp}. + \item Component source code found in file \texttt{SasView\_hayter\_msa.comp}. \end{itemize} -\IfFileExists{SasView_hayter_msa_static.tex}{\input{SasView_hayter_msa_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_hayter_msa_static.tex}{\input{sasmodels/SasView_hayter_msa_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_hollow_cylinder.tex b/docs/manuals/mcstas/sasmodels/SasView_hollow_cylinder.tex index a059353fbb..674ac031e2 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_hollow_cylinder.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_hollow_cylinder.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_hollow\_cylinder} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_hollow_cylinder component, generated from hollow_cylinder.c in sasmodels. +SasView\_hollow\_cylinder component, generated from hollow\_cylinder.c in sasmodels. -Example: -SasView_hollow_cylinder(radius, thickness, length, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness=0.0, pd_length=0.0) -\end{lstlisting} +Example: SasView\_hollow\_cylinder(radius, thickness, length, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Cylinder core radius. & 20.0 \\ -thickness & Ang & ([0, inf]) Cylinder wall thickness. & 10.0 \\ -length & Ang & ([0, inf]) Cylinder total length. & 400.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder sld. & 6.3 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent sld. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius. & 20.0 \\ +thickness & \AA{} & ([0, inf]) Cylinder wall thickness. & 10.0 \\ +length & \AA{} & ([0, inf]) Cylinder total length. & 400.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder sld. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent sld. & 1 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_hollow_cylinder.comp}{Source code} for \texttt{SasView\_hollow\_cylinder.comp}. + \item Component source code found in file \texttt{SasView\_hollow\_cylinder.comp}. \end{itemize} -\IfFileExists{SasView_hollow_cylinder_static.tex}{\input{SasView_hollow_cylinder_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_hollow_cylinder_static.tex}{\input{sasmodels/SasView_hollow_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_hollow_cylinder_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_hollow_cylinder_aniso.tex index 1d840da2fb..fba60622e5 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_hollow_cylinder_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_hollow_cylinder_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_hollow\_cylinder\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_hollow_cylinder component, generated from hollow_cylinder.c in sasmodels. +SasView\_hollow\_cylinder component, generated from hollow\_cylinder.c in sasmodels. -Example: -SasView_hollow_cylinder_aniso(radius, thickness, length, sld, sld_solvent, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness=0.0, pd_length=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_hollow\_cylinder\_aniso(radius, thickness, length, sld, sld\_solvent, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Cylinder core radius. & 20.0 \\ -thickness & Ang & ([0, inf]) Cylinder wall thickness. & 10.0 \\ -length & Ang & ([0, inf]) Cylinder total length. & 400.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Cylinder sld. & 6.3 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent sld. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius. & 20.0 \\ +thickness & \AA{} & ([0, inf]) Cylinder wall thickness. & 10.0 \\ +length & \AA{} & ([0, inf]) Cylinder total length. & 400.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder sld. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent sld. & 1 \\ theta & & & 90 \\ phi & & & 0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_hollow_cylinder_aniso.comp}{Source code} for \texttt{SasView\_hollow\_cylinder\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_hollow\_cylinder\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_hollow_cylinder_aniso_static.tex}{\input{SasView_hollow_cylinder_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_hollow_cylinder_aniso_static.tex}{\input{sasmodels/SasView_hollow_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism.tex b/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism.tex index 6779f7d1ac..bf4776887f 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_hollow\_rectangular\_prism} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_hollow_rectangular_prism component, generated from hollow_rectangular_prism.c in sasmodels. +SasView\_hollow\_rectangular\_prism component, generated from hollow\_rectangular\_prism.c in sasmodels. -Example: -SasView_hollow_rectangular_prism(sld, sld_solvent, length_a, b2a_ratio, c2a_ratio, thickness, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0, pd_thickness=0.0) -\end{lstlisting} +Example: SasView\_hollow\_rectangular\_prism(sld, sld\_solvent, length\_a, b2a\_ratio, c2a\_ratio, thickness, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_thickness=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,12 +21,12 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -length\_a & Ang & ([0, inf]) Shortest, external, size of the parallelepiped. & 35 \\ -b2a\_ratio & Ang & ([0, inf]) Ratio sides b/a. & 1 \\ -c2a\_ratio & Ang & ([0, inf]) Ratio sides c/a. & 1 \\ -thickness & Ang & ([0, inf]) Thickness of parallelepiped. & 1 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shortest, external, size of the parallelepiped. & 35 \\ +b2a\_ratio & \AA{} & ([0, inf]) Ratio sides b/a. & 1 \\ +c2a\_ratio & \AA{} & ([0, inf]) Ratio sides c/a. & 1 \\ +thickness & \AA{} & ([0, inf]) Thickness of parallelepiped. & 1 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_hollow_rectangular_prism.comp}{Source code} for \texttt{SasView\_hollow\_rectangular\_prism.comp}. + \item Component source code found in file \texttt{SasView\_hollow\_rectangular\_prism.comp}. \end{itemize} -\IfFileExists{SasView_hollow_rectangular_prism_static.tex}{\input{SasView_hollow_rectangular_prism_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_hollow_rectangular_prism_static.tex}{\input{sasmodels/SasView_hollow_rectangular_prism_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism_aniso.tex index 61347aad4d..3c4aebb028 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_hollow\_rectangular\_prism\_aniso} McStas Componen \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_hollow_rectangular_prism component, generated from hollow_rectangular_prism.c in sasmodels. +SasView\_hollow\_rectangular\_prism component, generated from hollow\_rectangular\_prism.c in sasmodels. -Example: -SasView_hollow_rectangular_prism_aniso(sld, sld_solvent, length_a, b2a_ratio, c2a_ratio, thickness, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0, pd_thickness=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_hollow\_rectangular\_prism\_aniso(sld, sld\_solvent, length\_a, b2a\_ratio, c2a\_ratio, thickness, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_thickness=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,12 +21,12 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -length\_a & Ang & ([0, inf]) Shortest, external, size of the parallelepiped. & 35 \\ -b2a\_ratio & Ang & ([0, inf]) Ratio sides b/a. & 1 \\ -c2a\_ratio & Ang & ([0, inf]) Ratio sides c/a. & 1 \\ -thickness & Ang & ([0, inf]) Thickness of parallelepiped. & 1 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shortest, external, size of the parallelepiped. & 35 \\ +b2a\_ratio & \AA{} & ([0, inf]) Ratio sides b/a. & 1 \\ +c2a\_ratio & \AA{} & ([0, inf]) Ratio sides c/a. & 1 \\ +thickness & \AA{} & ([0, inf]) Thickness of parallelepiped. & 1 \\ theta & & & 0 \\ phi & & & 0 \\ Psi & & & 0 \\ @@ -63,6 +55,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_hollow_rectangular_prism_aniso.comp}{Source code} for \texttt{SasView\_hollow\_rectangular\_prism\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_hollow\_rectangular\_prism\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_hollow_rectangular_prism_aniso_static.tex}{\input{SasView_hollow_rectangular_prism_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_hollow_rectangular_prism_aniso_static.tex}{\input{sasmodels/SasView_hollow_rectangular_prism_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism_thin_walls.tex b/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism_thin_walls.tex index cc887b86fa..b7e1b102c1 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism_thin_walls.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_hollow_rectangular_prism_thin_walls.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_hollow\_rectangular\_prism\_thin\_walls} McStas Co \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_hollow_rectangular_prism_thin_walls component, generated from hollow_rectangular_prism_thin_walls.c in sasmodels. +SasView\_hollow\_rectangular\_prism\_thin\_walls component, generated from hollow\_rectangular\_prism\_thin\_walls.c in sasmodels. -Example: -SasView_hollow_rectangular_prism_thin_walls(sld, sld_solvent, length_a, b2a_ratio, c2a_ratio, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0) -\end{lstlisting} +Example: SasView\_hollow\_rectangular\_prism\_thin\_walls(sld, sld\_solvent, length\_a, b2a\_ratio, c2a\_ratio, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -length\_a & Ang & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ -b2a\_ratio & Ang & ([0, inf]) Ratio sides b/a. & 1 \\ -c2a\_ratio & Ang & ([0, inf]) Ratio sides c/a. & 1 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +b2a\_ratio & \AA{} & ([0, inf]) Ratio sides b/a. & 1 \\ +c2a\_ratio & \AA{} & ([0, inf]) Ratio sides c/a. & 1 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_hollow_rectangular_prism_thin_walls.comp}{Source code} for \texttt{SasView\_hollow\_rectangular\_prism\_thin\_walls.comp}. + \item Component source code found in file \texttt{SasView\_hollow\_rectangular\_prism\_thin\_walls.comp}. \end{itemize} -\IfFileExists{SasView_hollow_rectangular_prism_thin_walls_static.tex}{\input{SasView_hollow_rectangular_prism_thin_walls_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_hollow_rectangular_prism_thin_walls_static.tex}{\input{sasmodels/SasView_hollow_rectangular_prism_thin_walls_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_lamellar_hg.tex b/docs/manuals/mcstas/sasmodels/SasView_lamellar_hg.tex index 6bc7d9edd4..dc5d56484b 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_lamellar_hg.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_lamellar_hg.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_lamellar\_hg} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_lamellar_hg component, generated from lamellar_hg.c in sasmodels. +SasView\_lamellar\_hg component, generated from lamellar\_hg.c in sasmodels. -Example: -SasView_lamellar_hg(length_tail, length_head, sld, sld_head, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_tail=0.0, pd_length_head=0.0) -\end{lstlisting} +Example: SasView\_lamellar\_hg(length\_tail, length\_head, sld, sld\_head, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_tail=0.0, pd\_length\_head=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -length\_tail & Ang & ([0, inf]) Tail thickness ( total = H+T+T+H). & 15 \\ -length\_head & Ang & ([0, inf]) Head thickness. & 10 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Tail scattering length density. & 0.4 \\ -sld\_head & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Head scattering length density. & 3.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ +length\_tail & \AA{} & ([0, inf]) Tail thickness ( total = H+T+T+H). & 15 \\ +length\_head & \AA{} & ([0, inf]) Head thickness. & 10 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Tail scattering length density. & 0.4 \\ +sld\_head & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Head scattering length density. & 3.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -56,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_lamellar_hg.comp}{Source code} for \texttt{SasView\_lamellar\_hg.comp}. + \item Component source code found in file \texttt{SasView\_lamellar\_hg.comp}. \end{itemize} -\IfFileExists{SasView_lamellar_hg_static.tex}{\input{SasView_lamellar_hg_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_lamellar_hg_static.tex}{\input{sasmodels/SasView_lamellar_hg_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_lamellar_hg_stack_caille.tex b/docs/manuals/mcstas/sasmodels/SasView_lamellar_hg_stack_caille.tex index 9a365d9fe8..1c91a3cf4e 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_lamellar_hg_stack_caille.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_lamellar_hg_stack_caille.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_lamellar\_hg\_stack\_caille} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_lamellar_hg_stack_caille component, generated from lamellar_hg_stack_caille.c in sasmodels. +SasView\_lamellar\_hg\_stack\_caille component, generated from lamellar\_hg\_stack\_caille.c in sasmodels. -Example: -SasView_lamellar_hg_stack_caille(length_tail, length_head, Nlayers, d_spacing, Caille_parameter, sld, sld_head, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_tail=0.0, pd_length_head=0.0) -\end{lstlisting} +Example: SasView\_lamellar\_hg\_stack\_caille(length\_tail, length\_head, Nlayers, d\_spacing, Caille\_parameter, sld, sld\_head, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_tail=0.0, pd\_length\_head=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,14 +21,14 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -length\_tail & Ang & ([0, inf]) Tail thickness. & 10 \\ -length\_head & Ang & ([0, inf]) head thickness. & 2 \\ +length\_tail & \AA{} & ([0, inf]) Tail thickness. & 10 \\ +length\_head & \AA{} & ([0, inf]) head thickness. & 2 \\ Nlayers & & ([1, inf]) Number of layers. & 30 \\ -d\_spacing & Ang & ([0.0, inf]) lamellar d-spacing of Caille S(Q). & 40.0 \\ +d\_spacing & \AA{} & ([0.0, inf]) lamellar d-spacing of Caille S(Q). & 40.0 \\ Caille\_parameter & & ([0.0, 0.8]) Caille parameter. & 0.001 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Tail scattering length density. & 0.4 \\ -sld\_head & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Head scattering length density. & 2.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Tail scattering length density. & 0.4 \\ +sld\_head & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Head scattering length density. & 2.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -59,6 +51,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_lamellar_hg_stack_caille.comp}{Source code} for \texttt{SasView\_lamellar\_hg\_stack\_caille.comp}. + \item Component source code found in file \texttt{SasView\_lamellar\_hg\_stack\_caille.comp}. \end{itemize} -\IfFileExists{SasView_lamellar_hg_stack_caille_static.tex}{\input{SasView_lamellar_hg_stack_caille_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_lamellar_hg_stack_caille_static.tex}{\input{sasmodels/SasView_lamellar_hg_stack_caille_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_lamellar_stack_caille.tex b/docs/manuals/mcstas/sasmodels/SasView_lamellar_stack_caille.tex index 73ab758cd1..cec5039d6b 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_lamellar_stack_caille.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_lamellar_stack_caille.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_lamellar\_stack\_caille} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_lamellar_stack_caille component, generated from lamellar_stack_caille.c in sasmodels. +SasView\_lamellar\_stack\_caille component, generated from lamellar\_stack\_caille.c in sasmodels. -Example: -SasView_lamellar_stack_caille(thickness, Nlayers, d_spacing, Caille_parameter, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_thickness=0.0) -\end{lstlisting} +Example: SasView\_lamellar\_stack\_caille(thickness, Nlayers, d\_spacing, Caille\_parameter, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_thickness=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,12 +21,12 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -thickness & Ang & ([0, inf]) sheet thickness. & 30.0 \\ +thickness & \AA{} & ([0, inf]) sheet thickness. & 30.0 \\ Nlayers & & ([1, inf]) Number of layers. & 20 \\ -d\_spacing & Ang & ([0.0, inf]) lamellar d-spacing of Caille S(Q). & 400.0 \\ -Caille\_parameter & 1/Ang\textasciicircum{}2 & ([0.0, 0.8]) Caille parameter. & 0.1 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) layer scattering length density. & 6.3 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ +d\_spacing & \AA{} & ([0.0, inf]) lamellar d-spacing of Caille S(Q). & 400.0 \\ +Caille\_parameter & 1/\AA{}$^{2}$ & ([0.0, 0.8]) Caille parameter. & 0.1 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) layer scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -56,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_lamellar_stack_caille.comp}{Source code} for \texttt{SasView\_lamellar\_stack\_caille.comp}. + \item Component source code found in file \texttt{SasView\_lamellar\_stack\_caille.comp}. \end{itemize} -\IfFileExists{SasView_lamellar_stack_caille_static.tex}{\input{SasView_lamellar_stack_caille_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_lamellar_stack_caille_static.tex}{\input{sasmodels/SasView_lamellar_stack_caille_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_lamellar_stack_paracrystal.tex b/docs/manuals/mcstas/sasmodels/SasView_lamellar_stack_paracrystal.tex index 86eebb2b11..dc6a692ccb 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_lamellar_stack_paracrystal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_lamellar_stack_paracrystal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_lamellar\_stack\_paracrystal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_lamellar_stack_paracrystal component, generated from lamellar_stack_paracrystal.c in sasmodels. +SasView\_lamellar\_stack\_paracrystal component, generated from lamellar\_stack\_paracrystal.c in sasmodels. -Example: -SasView_lamellar_stack_paracrystal(thickness, Nlayers, d_spacing, sigma_d, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_thickness=0.0) -\end{lstlisting} +Example: SasView\_lamellar\_stack\_paracrystal(thickness, Nlayers, d\_spacing, sigma\_d, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_thickness=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,12 +21,12 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -thickness & Ang & ([0, inf]) sheet thickness. & 33.0 \\ +thickness & \AA{} & ([0, inf]) sheet thickness. & 33.0 \\ Nlayers & & ([1, inf]) Number of layers. & 20 \\ -d\_spacing & Ang & ([0.0, inf]) lamellar spacing of paracrystal stack. & 250.0 \\ -sigma\_d & Ang & ([0.0, inf]) Sigma (polydispersity) of the lamellar spacing. & 0.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) layer scattering length density. & 1.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6.34 \\ +d\_spacing & \AA{} & ([0.0, inf]) lamellar spacing of paracrystal stack. & 250.0 \\ +sigma\_d & \AA{} & ([0.0, inf]) Sigma (polydispersity) of the lamellar spacing. & 0.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) layer scattering length density. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.34 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -56,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_lamellar_stack_paracrystal.comp}{Source code} for \texttt{SasView\_lamellar\_stack\_paracrystal.comp}. + \item Component source code found in file \texttt{SasView\_lamellar\_stack\_paracrystal.comp}. \end{itemize} -\IfFileExists{SasView_lamellar_stack_paracrystal_static.tex}{\input{SasView_lamellar_stack_paracrystal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_lamellar_stack_paracrystal_static.tex}{\input{sasmodels/SasView_lamellar_stack_paracrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_line.tex b/docs/manuals/mcstas/sasmodels/SasView_line.tex index dd9fd1e546..c880fabc23 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_line.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_line.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_line} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_line component, generated from line.c in sasmodels. +SasView\_line component, generated from line.c in sasmodels. -Example: -SasView_line(intercept, slope, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +Example: SasView\_line(intercept, slope, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,7 +22,7 @@ \subsection*{Input parameters} \midrule \endhead intercept & 1/cm & ([-inf, inf]) intercept in linear model. & 1.0 \\ -slope & Ang/cm & ([-inf, inf]) slope in linear model. & 1.0 \\ +slope & \AA{}/cm & ([-inf, inf]) slope in linear model. & 1.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -51,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_line.comp}{Source code} for \texttt{SasView\_line.comp}. + \item Component source code found in file \texttt{SasView\_line.comp}. \end{itemize} -\IfFileExists{SasView_line_static.tex}{\input{SasView_line_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_line_static.tex}{\input{sasmodels/SasView_line_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_linear_pearls.tex b/docs/manuals/mcstas/sasmodels/SasView_linear_pearls.tex index 71066a5621..fd15b3492f 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_linear_pearls.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_linear_pearls.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_linear\_pearls} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_linear_pearls component, generated from linear_pearls.c in sasmodels. +SasView\_linear\_pearls component, generated from linear\_pearls.c in sasmodels. -Example: -SasView_linear_pearls(radius, edge_sep, num_pearls, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0) -\end{lstlisting} +Example: SasView\_linear\_pearls(radius, edge\_sep, num\_pearls, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Radius of the pearls. & 80.0 \\ -edge\_sep & Ang & ([0, inf]) Length of the string segment - surface to surface. & 350.0 \\ +radius & \AA{} & ([0, inf]) Radius of the pearls. & 80.0 \\ +edge\_sep & \AA{} & ([0, inf]) Length of the string segment - surface to surface. & 350.0 \\ num\_pearls & & ([1, inf]) Number of the pearls. & 3.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) SLD of the pearl spheres. & 1.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) SLD of the solvent. & 6.3 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) SLD of the pearl spheres. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) SLD of the solvent. & 6.3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_linear_pearls.comp}{Source code} for \texttt{SasView\_linear\_pearls.comp}. + \item Component source code found in file \texttt{SasView\_linear\_pearls.comp}. \end{itemize} -\IfFileExists{SasView_linear_pearls_static.tex}{\input{SasView_linear_pearls_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_linear_pearls_static.tex}{\input{sasmodels/SasView_linear_pearls_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_lorentz.tex b/docs/manuals/mcstas/sasmodels/SasView_lorentz.tex index 0fc9101c51..08ef3ae46d 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_lorentz.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_lorentz.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_lorentz} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_lorentz component, generated from lorentz.c in sasmodels. +SasView\_lorentz component, generated from lorentz.c in sasmodels. -Example: -SasView_lorentz(cor_length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_cor_length=0.0) -\end{lstlisting} +Example: SasView\_lorentz(cor\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_cor\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -cor\_length & Ang & ([0, inf]) Screening length. & 50.0 \\ +cor\_length & \AA{} & ([0, inf]) Screening length. & 50.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -51,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_lorentz.comp}{Source code} for \texttt{SasView\_lorentz.comp}. + \item Component source code found in file \texttt{SasView\_lorentz.comp}. \end{itemize} -\IfFileExists{SasView_lorentz_static.tex}{\input{SasView_lorentz_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_lorentz_static.tex}{\input{sasmodels/SasView_lorentz_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_mass_fractal.tex b/docs/manuals/mcstas/sasmodels/SasView_mass_fractal.tex index 4df68384f4..9df25a60c9 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_mass_fractal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_mass_fractal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_mass\_fractal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_mass_fractal component, generated from mass_fractal.c in sasmodels. +SasView\_mass\_fractal component, generated from mass\_fractal.c in sasmodels. -Example: -SasView_mass_fractal(radius, fractal_dim_mass, cutoff_length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_cutoff_length=0.0) -\end{lstlisting} +Example: SasView\_mass\_fractal(radius, fractal\_dim\_mass, cutoff\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_cutoff\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,9 +21,9 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0.0, inf]) Particle radius. & 10.0 \\ +radius & \AA{} & ([0.0, inf]) Particle radius. & 10.0 \\ fractal\_dim\_mass & & ([1.0, 6.0]) Mass fractal dimension. & 1.9 \\ -cutoff\_length & Ang & ([0.0, inf]) Cut-off length. & 100.0 \\ +cutoff\_length & \AA{} & ([0.0, inf]) Cut-off length. & 100.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -54,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_mass_fractal.comp}{Source code} for \texttt{SasView\_mass\_fractal.comp}. + \item Component source code found in file \texttt{SasView\_mass\_fractal.comp}. \end{itemize} -\IfFileExists{SasView_mass_fractal_static.tex}{\input{SasView_mass_fractal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_mass_fractal_static.tex}{\input{sasmodels/SasView_mass_fractal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_mass_surface_fractal.tex b/docs/manuals/mcstas/sasmodels/SasView_mass_surface_fractal.tex index ea750e74d1..9bf6cda5cf 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_mass_surface_fractal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_mass_surface_fractal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_mass\_surface\_fractal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_mass_surface_fractal component, generated from mass_surface_fractal.c in sasmodels. +SasView\_mass\_surface\_fractal component, generated from mass\_surface\_fractal.c in sasmodels. -Example: -SasView_mass_surface_fractal(fractal_dim_mass, fractal_dim_surf, rg_cluster, rg_primary, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_rg_cluster=0.0, pd_rg_primary=0.0) -\end{lstlisting} +Example: SasView\_mass\_surface\_fractal(fractal\_dim\_mass, fractal\_dim\_surf, rg\_cluster, rg\_primary, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg\_cluster=0.0, pd\_rg\_primary=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -31,8 +23,8 @@ \subsection*{Input parameters} \endhead fractal\_dim\_mass & & ([0.0, 6.0]) Mass fractal dimension. & 1.8 \\ fractal\_dim\_surf & & ([0.0, 6.0]) Surface fractal dimension. & 2.3 \\ -rg\_cluster & Ang & ([0.0, inf]) Cluster radius of gyration. & 4000.0 \\ -rg\_primary & Ang & ([0.0, inf]) Primary particle radius of gyration. & 86.7 \\ +rg\_cluster & \AA{} & ([0.0, inf]) Cluster radius of gyration. & 4000.0 \\ +rg\_primary & \AA{} & ([0.0, inf]) Primary particle radius of gyration. & 86.7 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_mass_surface_fractal.comp}{Source code} for \texttt{SasView\_mass\_surface\_fractal.comp}. + \item Component source code found in file \texttt{SasView\_mass\_surface\_fractal.comp}. \end{itemize} -\IfFileExists{SasView_mass_surface_fractal_static.tex}{\input{SasView_mass_surface_fractal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_mass_surface_fractal_static.tex}{\input{sasmodels/SasView_mass_surface_fractal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_mono_gauss_coil.tex b/docs/manuals/mcstas/sasmodels/SasView_mono_gauss_coil.tex index f227f627f4..87cb3fe1ee 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_mono_gauss_coil.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_mono_gauss_coil.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_mono\_gauss\_coil} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_mono_gauss_coil component, generated from mono_gauss_coil.c in sasmodels. +SasView\_mono\_gauss\_coil component, generated from mono\_gauss\_coil.c in sasmodels. -Example: -SasView_mono_gauss_coil(i_zero, rg, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_rg=0.0) -\end{lstlisting} +Example: SasView\_mono\_gauss\_coil(i\_zero, rg, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,7 +22,7 @@ \subsection*{Input parameters} \midrule \endhead i\_zero & 1/cm & ([0.0, inf]) Intensity at q=0. & 70.0 \\ -rg & Ang & ([0.0, inf]) Radius of gyration. & 75.0 \\ +rg & \AA{} & ([0.0, inf]) Radius of gyration. & 75.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -52,6 +44,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_mono_gauss_coil.comp}{Source code} for \texttt{SasView\_mono\_gauss\_coil.comp}. + \item Component source code found in file \texttt{SasView\_mono\_gauss\_coil.comp}. \end{itemize} -\IfFileExists{SasView_mono_gauss_coil_static.tex}{\input{SasView_mono_gauss_coil_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_mono_gauss_coil_static.tex}{\input{sasmodels/SasView_mono_gauss_coil_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_multilayer_vesicle.tex b/docs/manuals/mcstas/sasmodels/SasView_multilayer_vesicle.tex index 49cc92f54a..b6e5ecd28a 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_multilayer_vesicle.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_multilayer_vesicle.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_multilayer\_vesicle} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_multilayer_vesicle component, generated from multilayer_vesicle.c in sasmodels. +SasView\_multilayer\_vesicle component, generated from multilayer\_vesicle.c in sasmodels. -Example: -SasView_multilayer_vesicle(volfraction, radius, thick_shell, thick_solvent, sld_solvent, sld, n_shells, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thick_shell=0.0, pd_thick_solvent=0.0) -\end{lstlisting} +Example: SasView\_multilayer\_vesicle(volfraction, radius, thick\_shell, thick\_solvent, sld\_solvent, sld, n\_shells, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_shell=0.0, pd\_thick\_solvent=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,11 +22,11 @@ \subsection*{Input parameters} \midrule \endhead volfraction & & ([0.0, 1]) volume fraction of vesicles. & 0.05 \\ -radius & Ang & ([0.0, inf]) radius of solvent filled core. & 60.0 \\ -thick\_shell & Ang & ([0.0, inf]) thickness of one shell. & 10.0 \\ -thick\_solvent & Ang & ([0.0, inf]) solvent thickness between shells. & 10.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) solvent scattering length density. & 6.4 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Shell scattering length density. & 0.4 \\ +radius & \AA{} & ([0.0, inf]) radius of solvent filled core. & 60.0 \\ +thick\_shell & \AA{} & ([0.0, inf]) thickness of one shell. & 10.0 \\ +thick\_solvent & \AA{} & ([0.0, inf]) solvent thickness between shells. & 10.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) solvent scattering length density. & 6.4 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Shell scattering length density. & 0.4 \\ n\_shells & & ([1.0, inf]) Number of shell plus solvent layer pairs (must be integer). & 2.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ @@ -59,6 +51,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_multilayer_vesicle.comp}{Source code} for \texttt{SasView\_multilayer\_vesicle.comp}. + \item Component source code found in file \texttt{SasView\_multilayer\_vesicle.comp}. \end{itemize} -\IfFileExists{SasView_multilayer_vesicle_static.tex}{\input{SasView_multilayer_vesicle_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_multilayer_vesicle_static.tex}{\input{sasmodels/SasView_multilayer_vesicle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_onion.tex b/docs/manuals/mcstas/sasmodels/SasView_onion.tex index 757182637e..4317588325 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_onion.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_onion.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_onion} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_onion component, generated from onion.c in sasmodels. +SasView\_onion component, generated from onion.c in sasmodels. -Example: -SasView_onion(sld_core, radius_core, sld_solvent, n_shells, sld_in[n_shells], sld_out[n_shells], thickness[n_shells], A[n_shells], -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_core=0.0, pd_thickness[n_shells]=0.0) -\end{lstlisting} +Example: SasView\_onion(sld\_core, radius\_core, sld\_solvent, n\_shells, sld\_in[n\_shells], sld\_out[n\_shells], thickness[n\_shells], A[n\_shells], model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_core=0.0, pd\_thickness[n\_shells]=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -34,6 +26,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_onion.comp}{Source code} for \texttt{SasView\_onion.comp}. + \item Component source code found in file \texttt{SasView\_onion.comp}. \end{itemize} -\IfFileExists{SasView_onion_static.tex}{\input{SasView_onion_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_onion_static.tex}{\input{sasmodels/SasView_onion_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_parallelepiped.tex b/docs/manuals/mcstas/sasmodels/SasView_parallelepiped.tex index a72cc9df5b..e30c042a4b 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_parallelepiped.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_parallelepiped.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_parallelepiped} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_parallelepiped component, generated from parallelepiped.c in sasmodels. +SasView\_parallelepiped component, generated from parallelepiped.c in sasmodels. -Example: -SasView_parallelepiped(sld, sld_solvent, length_a, length_b, length_c, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0, pd_length_b=0.0, pd_length_c=0.0) -\end{lstlisting} +Example: SasView\_parallelepiped(sld, sld\_solvent, length\_a, length\_b, length\_c, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_length\_b=0.0, pd\_length\_c=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -length\_a & Ang & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ -length\_b & Ang & ([0, inf]) Second side of the parallelepiped. & 75 \\ -length\_c & Ang & ([0, inf]) Larger side of the parallelepiped. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +length\_b & \AA{} & ([0, inf]) Second side of the parallelepiped. & 75 \\ +length\_c & \AA{} & ([0, inf]) Larger side of the parallelepiped. & 400 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_parallelepiped.comp}{Source code} for \texttt{SasView\_parallelepiped.comp}. + \item Component source code found in file \texttt{SasView\_parallelepiped.comp}. \end{itemize} -\IfFileExists{SasView_parallelepiped_static.tex}{\input{SasView_parallelepiped_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_parallelepiped_static.tex}{\input{sasmodels/SasView_parallelepiped_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_parallelepiped_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_parallelepiped_aniso.tex index c37e0ca42b..90cf1a5afc 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_parallelepiped_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_parallelepiped_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_parallelepiped\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_parallelepiped component, generated from parallelepiped.c in sasmodels. +SasView\_parallelepiped component, generated from parallelepiped.c in sasmodels. -Example: -SasView_parallelepiped_aniso(sld, sld_solvent, length_a, length_b, length_c, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0, pd_length_b=0.0, pd_length_c=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_parallelepiped\_aniso(sld, sld\_solvent, length\_a, length\_b, length\_c, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_length\_b=0.0, pd\_length\_c=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -length\_a & Ang & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ -length\_b & Ang & ([0, inf]) Second side of the parallelepiped. & 75 \\ -length\_c & Ang & ([0, inf]) Larger side of the parallelepiped. & 400 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +length\_b & \AA{} & ([0, inf]) Second side of the parallelepiped. & 75 \\ +length\_c & \AA{} & ([0, inf]) Larger side of the parallelepiped. & 400 \\ theta & & & 60 \\ phi & & & 60 \\ Psi & & & 60 \\ @@ -63,6 +55,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_parallelepiped_aniso.comp}{Source code} for \texttt{SasView\_parallelepiped\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_parallelepiped\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_parallelepiped_aniso_static.tex}{\input{SasView_parallelepiped_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_parallelepiped_aniso_static.tex}{\input{sasmodels/SasView_parallelepiped_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_peak_lorentz.tex b/docs/manuals/mcstas/sasmodels/SasView_peak_lorentz.tex index 653317872c..06cc76bf7f 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_peak_lorentz.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_peak_lorentz.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_peak\_lorentz} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_peak_lorentz component, generated from peak_lorentz.c in sasmodels. +SasView\_peak\_lorentz component, generated from peak\_lorentz.c in sasmodels. -Example: -SasView_peak_lorentz(peak_pos, peak_hwhm, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +Example: SasView\_peak\_lorentz(peak\_pos, peak\_hwhm, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,8 +21,8 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -peak\_pos & 1/Ang & ([-inf, inf]) Peak postion in q. & 0.05 \\ -peak\_hwhm & 1/Ang & ([-inf, inf]) HWHM of peak. & 0.005 \\ +peak\_pos & 1/\AA{} & ([-inf, inf]) Peak postion in q. & 0.05 \\ +peak\_hwhm & 1/\AA{} & ([-inf, inf]) HWHM of peak. & 0.005 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -51,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_peak_lorentz.comp}{Source code} for \texttt{SasView\_peak\_lorentz.comp}. + \item Component source code found in file \texttt{SasView\_peak\_lorentz.comp}. \end{itemize} -\IfFileExists{SasView_peak_lorentz_static.tex}{\input{SasView_peak_lorentz_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_peak_lorentz_static.tex}{\input{sasmodels/SasView_peak_lorentz_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_pearl_necklace.tex b/docs/manuals/mcstas/sasmodels/SasView_pearl_necklace.tex index e2ca6b5c67..be124dd0be 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_pearl_necklace.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_pearl_necklace.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_pearl\_necklace} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_pearl_necklace component, generated from pearl_necklace.c in sasmodels. +SasView\_pearl\_necklace component, generated from pearl\_necklace.c in sasmodels. -Example: -SasView_pearl_necklace(radius, edge_sep, thick_string, num_pearls, sld, sld_string, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thick_string=0.0) -\end{lstlisting} +Example: SasView\_pearl\_necklace(radius, edge\_sep, thick\_string, num\_pearls, sld, sld\_string, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_string=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,13 +21,13 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Mean radius of the chained spheres. & 80.0 \\ -edge\_sep & Ang & ([0, inf]) Mean separation of chained particles. & 350.0 \\ -thick\_string & Ang & ([0, inf]) Thickness of the chain linkage. & 2.5 \\ +radius & \AA{} & ([0, inf]) Mean radius of the chained spheres. & 80.0 \\ +edge\_sep & \AA{} & ([0, inf]) Mean separation of chained particles. & 350.0 \\ +thick\_string & \AA{} & ([0, inf]) Thickness of the chain linkage. & 2.5 \\ num\_pearls & none & ([1, inf]) Number of pearls in the necklace (must be integer). & 3 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Scattering length density of the chained spheres. & 1.0 \\ -sld\_string & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Scattering length density of the chain linkage. & 1.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Scattering length density of the solvent. & 6.3 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Scattering length density of the chained spheres. & 1.0 \\ +sld\_string & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Scattering length density of the chain linkage. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Scattering length density of the solvent. & 6.3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -58,6 +50,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_pearl_necklace.comp}{Source code} for \texttt{SasView\_pearl\_necklace.comp}. + \item Component source code found in file \texttt{SasView\_pearl\_necklace.comp}. \end{itemize} -\IfFileExists{SasView_pearl_necklace_static.tex}{\input{SasView_pearl_necklace_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_pearl_necklace_static.tex}{\input{sasmodels/SasView_pearl_necklace_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_poly_gauss_coil.tex b/docs/manuals/mcstas/sasmodels/SasView_poly_gauss_coil.tex index 5946f46796..f240ae13be 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_poly_gauss_coil.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_poly_gauss_coil.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_poly\_gauss\_coil} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_poly_gauss_coil component, generated from poly_gauss_coil.c in sasmodels. +SasView\_poly\_gauss\_coil component, generated from poly\_gauss\_coil.c in sasmodels. -Example: -SasView_poly_gauss_coil(i_zero, rg, polydispersity, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_rg=0.0) -\end{lstlisting} +Example: SasView\_poly\_gauss\_coil(i\_zero, rg, polydispersity, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,7 +22,7 @@ \subsection*{Input parameters} \midrule \endhead i\_zero & 1/cm & ([0.0, inf]) Intensity at q=0. & 70.0 \\ -rg & Ang & ([0.0, inf]) Radius of gyration. & 75.0 \\ +rg & \AA{} & ([0.0, inf]) Radius of gyration. & 75.0 \\ polydispersity & None & ([1.0, inf]) Polymer Mw/Mn. & 2.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ @@ -53,6 +45,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_poly_gauss_coil.comp}{Source code} for \texttt{SasView\_poly\_gauss\_coil.comp}. + \item Component source code found in file \texttt{SasView\_poly\_gauss\_coil.comp}. \end{itemize} -\IfFileExists{SasView_poly_gauss_coil_static.tex}{\input{SasView_poly_gauss_coil_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_poly_gauss_coil_static.tex}{\input{sasmodels/SasView_poly_gauss_coil_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_polymer_excl_volume.tex b/docs/manuals/mcstas/sasmodels/SasView_polymer_excl_volume.tex index 4fb22b44c5..692c77eb28 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_polymer_excl_volume.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_polymer_excl_volume.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_polymer\_excl\_volume} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_polymer_excl_volume component, generated from polymer_excl_volume.c in sasmodels. +SasView\_polymer\_excl\_volume component, generated from polymer\_excl\_volume.c in sasmodels. -Example: -SasView_polymer_excl_volume(rg, porod_exp, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_rg=0.0) -\end{lstlisting} +Example: SasView\_polymer\_excl\_volume(rg, porod\_exp, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -rg & Ang & ([0, inf]) Radius of Gyration. & 60.0 \\ +rg & \AA{} & ([0, inf]) Radius of Gyration. & 60.0 \\ porod\_exp & & ([0, inf]) Porod exponent. & 3.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ @@ -52,6 +44,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_polymer_excl_volume.comp}{Source code} for \texttt{SasView\_polymer\_excl\_volume.comp}. + \item Component source code found in file \texttt{SasView\_polymer\_excl\_volume.comp}. \end{itemize} -\IfFileExists{SasView_polymer_excl_volume_static.tex}{\input{SasView_polymer_excl_volume_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_polymer_excl_volume_static.tex}{\input{sasmodels/SasView_polymer_excl_volume_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_polymer_micelle.tex b/docs/manuals/mcstas/sasmodels/SasView_polymer_micelle.tex index f98d10d8be..1c1c7b3f8a 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_polymer_micelle.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_polymer_micelle.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_polymer\_micelle} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_polymer_micelle component, generated from polymer_micelle.c in sasmodels. +SasView\_polymer\_micelle component, generated from polymer\_micelle.c in sasmodels. -Example: -SasView_polymer_micelle(ndensity, v_core, v_corona, sld_solvent, sld_core, sld_corona, radius_core, rg, d_penetration, n_aggreg, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_core=0.0, pd_rg=0.0) -\end{lstlisting} +Example: SasView\_polymer\_micelle(ndensity, v\_core, v\_corona, sld\_solvent, sld\_core, sld\_corona, radius\_core, rg, d\_penetration, n\_aggreg, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_core=0.0, pd\_rg=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,14 +21,14 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -ndensity & 1e15/cm\textasciicircum{}3 & ([0.0, inf]) Number density of micelles. & 8.94 \\ -v\_core & Ang\textasciicircum{}3 & ([0.0, inf]) Core volume . & 62624.0 \\ -v\_corona & Ang\textasciicircum{}3 & ([0.0, inf]) Corona volume. & 61940.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([0.0, inf]) Solvent scattering length density. & 6.4 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([0.0, inf]) Core scattering length density. & 0.34 \\ -sld\_corona & 1e-6/Ang\textasciicircum{}2 & ([0.0, inf]) Corona scattering length density. & 0.8 \\ -radius\_core & Ang & ([0.0, inf]) Radius of core ( must be \textgreater{}\textgreater{} rg ). & 45.0 \\ -rg & Ang & ([0.0, inf]) Radius of gyration of chains in corona. & 20.0 \\ +ndensity & 1e15/cm$^{3}$ & ([0.0, inf]) Number density of micelles. & 8.94 \\ +v\_core & \AA{}$^{3}$ & ([0.0, inf]) Core volume . & 62624.0 \\ +v\_corona & \AA{}$^{3}$ & ([0.0, inf]) Corona volume. & 61940.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Solvent scattering length density. & 6.4 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Core scattering length density. & 0.34 \\ +sld\_corona & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Corona scattering length density. & 0.8 \\ +radius\_core & \AA{} & ([0.0, inf]) Radius of core ( must be \textgreater{}\textgreater{} rg ). & 45.0 \\ +rg & \AA{} & ([0.0, inf]) Radius of gyration of chains in corona. & 20.0 \\ d\_penetration & & ([-inf, inf]) Factor to mimic non-penetration of Gaussian chains. & 1.0 \\ n\_aggreg & & ([-inf, inf]) Aggregation number of the micelle. & 6.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_polymer_micelle.comp}{Source code} for \texttt{SasView\_polymer\_micelle.comp}. + \item Component source code found in file \texttt{SasView\_polymer\_micelle.comp}. \end{itemize} -\IfFileExists{SasView_polymer_micelle_static.tex}{\input{SasView_polymer_micelle_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_polymer_micelle_static.tex}{\input{sasmodels/SasView_polymer_micelle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_porod.tex b/docs/manuals/mcstas/sasmodels/SasView_porod.tex index 9484e33bbd..890a96d392 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_porod.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_porod.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_porod} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_porod component, generated from porod.c in sasmodels. +SasView\_porod component, generated from porod.c in sasmodels. -Example: -SasView_porod(, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +Example: SasView\_porod(, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -49,6 +41,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_porod.comp}{Source code} for \texttt{SasView\_porod.comp}. + \item Component source code found in file \texttt{SasView\_porod.comp}. \end{itemize} -\IfFileExists{SasView_porod_static.tex}{\input{SasView_porod_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_porod_static.tex}{\input{sasmodels/SasView_porod_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_power_law.tex b/docs/manuals/mcstas/sasmodels/SasView_power_law.tex index 03dc976ecd..45b47feb60 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_power_law.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_power_law.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_power\_law} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_power_law component, generated from power_law.c in sasmodels. +SasView\_power\_law component, generated from power\_law.c in sasmodels. -Example: -SasView_power_law(power, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +Example: SasView\_power\_law(power, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -50,6 +42,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_power_law.comp}{Source code} for \texttt{SasView\_power\_law.comp}. + \item Component source code found in file \texttt{SasView\_power\_law.comp}. \end{itemize} -\IfFileExists{SasView_power_law_static.tex}{\input{SasView_power_law_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_power_law_static.tex}{\input{sasmodels/SasView_power_law_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_pringle.tex b/docs/manuals/mcstas/sasmodels/SasView_pringle.tex index c439a2f4ea..6dcf03897d 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_pringle.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_pringle.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_pringle} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_pringle component, generated from pringle.c in sasmodels. +SasView\_pringle component, generated from pringle.c in sasmodels. -Example: -SasView_pringle(radius, thickness, alpha, beta, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness=0.0) -\end{lstlisting} +Example: SasView\_pringle(radius, thickness, alpha, beta, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,12 +21,12 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Pringle radius. & 60.0 \\ -thickness & Ang & ([0, inf]) Thickness of pringle. & 10.0 \\ +radius & \AA{} & ([0, inf]) Pringle radius. & 60.0 \\ +thickness & \AA{} & ([0, inf]) Thickness of pringle. & 10.0 \\ alpha & & ([-inf, inf]) Curvature parameter alpha. & 0.001 \\ beta & & ([-inf, inf]) Curvature paramter beta. & 0.02 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Pringle sld. & 1.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent sld. & 6.3 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Pringle sld. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent sld. & 6.3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_pringle.comp}{Source code} for \texttt{SasView\_pringle.comp}. + \item Component source code found in file \texttt{SasView\_pringle.comp}. \end{itemize} -\IfFileExists{SasView_pringle_static.tex}{\input{SasView_pringle_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_pringle_static.tex}{\input{sasmodels/SasView_pringle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_raspberry.tex b/docs/manuals/mcstas/sasmodels/SasView_raspberry.tex index 09ee5dbabf..70da7563f7 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_raspberry.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_raspberry.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_raspberry} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_raspberry component, generated from raspberry.c in sasmodels. +SasView\_raspberry component, generated from raspberry.c in sasmodels. -Example: -SasView_raspberry(sld_lg, sld_sm, sld_solvent, volfraction_lg, volfraction_sm, surface_fraction, radius_lg, radius_sm, penetration, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_lg=0.0, pd_radius_sm=0.0) -\end{lstlisting} +Example: SasView\_raspberry(sld\_lg, sld\_sm, sld\_solvent, volfraction\_lg, volfraction\_sm, surface\_fraction, radius\_lg, radius\_sm, penetration, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_lg=0.0, pd\_radius\_sm=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,15 +21,15 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld\_lg & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) large particle scattering length density. & -0.4 \\ -sld\_sm & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) small particle scattering length density. & 3.5 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) solvent scattering length density. & 6.36 \\ +sld\_lg & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) large particle scattering length density. & -0.4 \\ +sld\_sm & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) small particle scattering length density. & 3.5 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) solvent scattering length density. & 6.36 \\ volfraction\_lg & & ([-inf, inf]) volume fraction of large spheres. & 0.05 \\ volfraction\_sm & & ([-inf, inf]) volume fraction of small spheres. & 0.005 \\ surface\_fraction & & ([-inf, inf]) fraction of small spheres at surface. & 0.4 \\ -radius\_lg & Ang & ([0, inf]) radius of large spheres. & 5000 \\ -radius\_sm & Ang & ([0, inf]) radius of small spheres. & 100 \\ -penetration & Ang & ([-1, 1]) fractional penetration depth of small spheres into large sphere. & 0 \\ +radius\_lg & \AA{} & ([0, inf]) radius of large spheres. & 5000 \\ +radius\_sm & \AA{} & ([0, inf]) radius of small spheres. & 100 \\ +penetration & \AA{} & ([-1, 1]) fractional penetration depth of small spheres into large sphere. & 0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -60,6 +52,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_raspberry.comp}{Source code} for \texttt{SasView\_raspberry.comp}. + \item Component source code found in file \texttt{SasView\_raspberry.comp}. \end{itemize} -\IfFileExists{SasView_raspberry_static.tex}{\input{SasView_raspberry_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_raspberry_static.tex}{\input{sasmodels/SasView_raspberry_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_rectangular_prism.tex b/docs/manuals/mcstas/sasmodels/SasView_rectangular_prism.tex index 85b0d6d2fd..1cb69ea97c 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_rectangular_prism.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_rectangular_prism.tex @@ -3,16 +3,13 @@ \section{The \texttt{SasView\_rectangular\_prism} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -48,6 +45,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_rectangular_prism.comp}{Source code} for \texttt{SasView\_rectangular\_prism.comp}. + \item Component source code found in file \texttt{SasView\_rectangular\_prism.comp}. \end{itemize} -\IfFileExists{SasView_rectangular_prism_static.tex}{\input{SasView_rectangular_prism_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_rectangular_prism_static.tex}{\input{sasmodels/SasView_rectangular_prism_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_rectangular_prism_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_rectangular_prism_aniso.tex index 0b2dc9213a..08e19507a1 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_rectangular_prism_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_rectangular_prism_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_rectangular\_prism\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_rectangular_prism component, generated from rectangular_prism.c in sasmodels. +SasView\_rectangular\_prism component, generated from rectangular\_prism.c in sasmodels. -Example: -SasView_rectangular_prism_aniso(sld, sld_solvent, length_a, b2a_ratio, c2a_ratio, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_rectangular\_prism\_aniso(sld, sld\_solvent, length\_a, b2a\_ratio, c2a\_ratio, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,9 +21,9 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -length\_a & Ang & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ b2a\_ratio & & ([0, inf]) Ratio sides b/a. & 1 \\ c2a\_ratio & & ([0, inf]) Ratio sides c/a. & 1 \\ theta & & & 0 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_rectangular_prism_aniso.comp}{Source code} for \texttt{SasView\_rectangular\_prism\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_rectangular\_prism\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_rectangular_prism_aniso_static.tex}{\input{SasView_rectangular_prism_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_rectangular_prism_aniso_static.tex}{\input{sasmodels/SasView_rectangular_prism_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_rpa.tex b/docs/manuals/mcstas/sasmodels/SasView_rpa.tex index a3a8bd9350..c284baf289 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_rpa.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_rpa.tex @@ -3,23 +3,21 @@ \section{The \texttt{SasView\_rpa} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_rpa component, generated from rpa.c in sasmodels. +SasView\_rpa component, generated from rpa.c in sasmodels. Example: + +\begin{verbatim} SasView_rpa(case_num, N[4], Phi[4], v[4], L[4], b[4], K12, K13, K14, K23, K24, K34, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +\end{verbatim} + +model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -34,6 +32,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_rpa.comp}{Source code} for \texttt{SasView\_rpa.comp}. + \item Component source code found in file \texttt{SasView\_rpa.comp}. \end{itemize} -\IfFileExists{SasView_rpa_static.tex}{\input{SasView_rpa_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_rpa_static.tex}{\input{sasmodels/SasView_rpa_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_sc_paracrystal.tex b/docs/manuals/mcstas/sasmodels/SasView_sc_paracrystal.tex index c0b52dc85b..432a560060 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_sc_paracrystal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_sc_paracrystal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_sc\_paracrystal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_sc_paracrystal component, generated from sc_paracrystal.c in sasmodels. +SasView\_sc\_paracrystal component, generated from sc\_paracrystal.c in sasmodels. -Example: -SasView_sc_paracrystal(dnn, d_factor, radius, sld, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0) -\end{lstlisting} +Example: SasView\_sc\_paracrystal(dnn, d\_factor, radius, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -dnn & Ang & ([0.0, inf]) Nearest neighbor distance. & 220.0 \\ +dnn & \AA{} & ([0.0, inf]) Nearest neighbor distance. & 220.0 \\ d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ -radius & Ang & ([0.0, inf]) Radius of sphere. & 40.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([0.0, inf]) Sphere scattering length density. & 3.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([0.0, inf]) Solvent scattering length density. & 6.3 \\ +radius & \AA{} & ([0.0, inf]) Radius of sphere. & 40.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Sphere scattering length density. & 3.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Solvent scattering length density. & 6.3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -55,6 +47,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_sc_paracrystal.comp}{Source code} for \texttt{SasView\_sc\_paracrystal.comp}. + \item Component source code found in file \texttt{SasView\_sc\_paracrystal.comp}. \end{itemize} -\IfFileExists{SasView_sc_paracrystal_static.tex}{\input{SasView_sc_paracrystal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_sc_paracrystal_static.tex}{\input{sasmodels/SasView_sc_paracrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_sc_paracrystal_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_sc_paracrystal_aniso.tex index 727f210276..dd5153808b 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_sc_paracrystal_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_sc_paracrystal_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_sc\_paracrystal\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_sc_paracrystal component, generated from sc_paracrystal.c in sasmodels. +SasView\_sc\_paracrystal component, generated from sc\_paracrystal.c in sasmodels. -Example: -SasView_sc_paracrystal_aniso(dnn, d_factor, radius, sld, sld_solvent, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_sc\_paracrystal\_aniso(dnn, d\_factor, radius, sld, sld\_solvent, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -dnn & Ang & ([0.0, inf]) Nearest neighbor distance. & 220.0 \\ +dnn & \AA{} & ([0.0, inf]) Nearest neighbor distance. & 220.0 \\ d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ -radius & Ang & ([0.0, inf]) Radius of sphere. & 40.0 \\ -sld & 1e-6/Ang\textasciicircum{}2 & ([0.0, inf]) Sphere scattering length density. & 3.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([0.0, inf]) Solvent scattering length density. & 6.3 \\ +radius & \AA{} & ([0.0, inf]) Radius of sphere. & 40.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Sphere scattering length density. & 3.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Solvent scattering length density. & 6.3 \\ theta & & & 0 \\ phi & & & 0 \\ Psi & & & 0 \\ @@ -61,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_sc_paracrystal_aniso.comp}{Source code} for \texttt{SasView\_sc\_paracrystal\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_sc\_paracrystal\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_sc_paracrystal_aniso_static.tex}{\input{SasView_sc_paracrystal_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_sc_paracrystal_aniso_static.tex}{\input{sasmodels/SasView_sc_paracrystal_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_sphere.tex b/docs/manuals/mcstas/sasmodels/SasView_sphere.tex index f33e534749..118f3b8661 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_sphere.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_sphere.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_sphere} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_sphere component, generated from sphere.c in sasmodels. +SasView\_sphere component, generated from sphere.c in sasmodels. -Example: -SasView_sphere(sld, sld_solvent, radius, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0) -\end{lstlisting} +Example: SasView\_sphere(sld, sld\_solvent, radius, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,9 +21,9 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Layer scattering length density. & 1 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 6 \\ -radius & Ang & ([0, inf]) Sphere radius. & 50 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Layer scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +radius & \AA{} & ([0, inf]) Sphere radius. & 50 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -53,6 +45,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_sphere.comp}{Source code} for \texttt{SasView\_sphere.comp}. + \item Component source code found in file \texttt{SasView\_sphere.comp}. \end{itemize} -\IfFileExists{SasView_sphere_static.tex}{\input{SasView_sphere_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_sphere_static.tex}{\input{sasmodels/SasView_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_spinodal.tex b/docs/manuals/mcstas/sasmodels/SasView_spinodal.tex index eb41be14e0..e3668d1234 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_spinodal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_spinodal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_spinodal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_spinodal component, generated from spinodal.c in sasmodels. +SasView\_spinodal component, generated from spinodal.c in sasmodels. -Example: -SasView_spinodal(gamma, q_0, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +Example: SasView\_spinodal(gamma, q\_0, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,7 +22,7 @@ \subsection*{Input parameters} \midrule \endhead gamma & & ([-inf, inf]) Exponent. & 3.0 \\ -q\_0 & 1/Ang & ([-inf, inf]) Correlation peak position. & 0.1 \\ +q\_0 & 1/\AA{} & ([-inf, inf]) Correlation peak position. & 0.1 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -51,6 +43,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_spinodal.comp}{Source code} for \texttt{SasView\_spinodal.comp}. + \item Component source code found in file \texttt{SasView\_spinodal.comp}. \end{itemize} -\IfFileExists{SasView_spinodal_static.tex}{\input{SasView_spinodal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_spinodal_static.tex}{\input{sasmodels/SasView_spinodal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_squarewell.tex b/docs/manuals/mcstas/sasmodels/SasView_squarewell.tex index 99cea12b8a..53daf54543 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_squarewell.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_squarewell.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_squarewell} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_squarewell component, generated from squarewell.c in sasmodels. +SasView\_squarewell component, generated from squarewell.c in sasmodels. -Example: -SasView_squarewell(radius_effective, volfraction, welldepth, wellwidth, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_effective=0.0) -\end{lstlisting} +Example: SasView\_squarewell(radius\_effective, volfraction, welldepth, wellwidth, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_effective=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_effective & Ang & ([0, inf]) effective radius of hard sphere. & 50.0 \\ +radius\_effective & \AA{} & ([0, inf]) effective radius of hard sphere. & 50.0 \\ volfraction & & ([0, 0.08]) volume fraction of spheres. & 0.04 \\ welldepth & kT & ([0.0, 1.5]) depth of well, epsilon. & 1.5 \\ wellwidth & diameters & ([1.0, inf]) width of well in diameters (=2R) units, must be \textgreater{} 1. & 1.2 \\ @@ -54,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_squarewell.comp}{Source code} for \texttt{SasView\_squarewell.comp}. + \item Component source code found in file \texttt{SasView\_squarewell.comp}. \end{itemize} -\IfFileExists{SasView_squarewell_static.tex}{\input{SasView_squarewell_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_squarewell_static.tex}{\input{sasmodels/SasView_squarewell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_stacked_disks.tex b/docs/manuals/mcstas/sasmodels/SasView_stacked_disks.tex index b88998bd0c..3c95ff331e 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_stacked_disks.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_stacked_disks.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_stacked\_disks} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_stacked_disks component, generated from stacked_disks.c in sasmodels. +SasView\_stacked\_disks component, generated from stacked\_disks.c in sasmodels. -Example: -SasView_stacked_disks(thick_core, thick_layer, radius, n_stacking, sigma_d, sld_core, sld_layer, sld_solvent, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_thick_core=0.0, pd_thick_layer=0.0, pd_radius=0.0) -\end{lstlisting} +Example: SasView\_stacked\_disks(thick\_core, thick\_layer, radius, n\_stacking, sigma\_d, sld\_core, sld\_layer, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_thick\_core=0.0, pd\_thick\_layer=0.0, pd\_radius=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,14 +21,14 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -thick\_core & Ang & ([0, inf]) Thickness of the core disk. & 10.0 \\ -thick\_layer & Ang & ([0, inf]) Thickness of layer each side of core. & 10.0 \\ -radius & Ang & ([0, inf]) Radius of the stacked disk. & 15.0 \\ +thick\_core & \AA{} & ([0, inf]) Thickness of the core disk. & 10.0 \\ +thick\_layer & \AA{} & ([0, inf]) Thickness of layer each side of core. & 10.0 \\ +radius & \AA{} & ([0, inf]) Radius of the stacked disk. & 15.0 \\ n\_stacking & & ([1, inf]) Number of stacked layer/core/layer disks. & 1.0 \\ -sigma\_d & Ang & ([0, inf]) Sigma of nearest neighbor spacing. & 0 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Core scattering length density. & 4 \\ -sld\_layer & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Layer scattering length density. & 0.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 5.0 \\ +sigma\_d & \AA{} & ([0, inf]) Sigma of nearest neighbor spacing. & 0 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Core scattering length density. & 4 \\ +sld\_layer & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Layer scattering length density. & 0.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 5.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -60,6 +52,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_stacked_disks.comp}{Source code} for \texttt{SasView\_stacked\_disks.comp}. + \item Component source code found in file \texttt{SasView\_stacked\_disks.comp}. \end{itemize} -\IfFileExists{SasView_stacked_disks_static.tex}{\input{SasView_stacked_disks_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_stacked_disks_static.tex}{\input{sasmodels/SasView_stacked_disks_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_stacked_disks_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_stacked_disks_aniso.tex index dabf5440c9..40fce913d1 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_stacked_disks_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_stacked_disks_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_stacked\_disks\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_stacked_disks component, generated from stacked_disks.c in sasmodels. +SasView\_stacked\_disks component, generated from stacked\_disks.c in sasmodels. -Example: -SasView_stacked_disks_aniso(thick_core, thick_layer, radius, n_stacking, sigma_d, sld_core, sld_layer, sld_solvent, theta, phi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_thick_core=0.0, pd_thick_layer=0.0, pd_radius=0.0, pd_theta=0.0, pd_phi=0.0) -\end{lstlisting} +Example: SasView\_stacked\_disks\_aniso(thick\_core, thick\_layer, radius, n\_stacking, sigma\_d, sld\_core, sld\_layer, sld\_solvent, theta, phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_thick\_core=0.0, pd\_thick\_layer=0.0, pd\_radius=0.0, pd\_theta=0.0, pd\_phi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,14 +21,14 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -thick\_core & Ang & ([0, inf]) Thickness of the core disk. & 10.0 \\ -thick\_layer & Ang & ([0, inf]) Thickness of layer each side of core. & 10.0 \\ -radius & Ang & ([0, inf]) Radius of the stacked disk. & 15.0 \\ +thick\_core & \AA{} & ([0, inf]) Thickness of the core disk. & 10.0 \\ +thick\_layer & \AA{} & ([0, inf]) Thickness of layer each side of core. & 10.0 \\ +radius & \AA{} & ([0, inf]) Radius of the stacked disk. & 15.0 \\ n\_stacking & & ([1, inf]) Number of stacked layer/core/layer disks. & 1.0 \\ -sigma\_d & Ang & ([0, inf]) Sigma of nearest neighbor spacing. & 0 \\ -sld\_core & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Core scattering length density. & 4 \\ -sld\_layer & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Layer scattering length density. & 0.0 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 5.0 \\ +sigma\_d & \AA{} & ([0, inf]) Sigma of nearest neighbor spacing. & 0 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Core scattering length density. & 4 \\ +sld\_layer & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Layer scattering length density. & 0.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 5.0 \\ theta & & & 0 \\ phi & & & 0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -64,6 +56,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_stacked_disks_aniso.comp}{Source code} for \texttt{SasView\_stacked\_disks\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_stacked\_disks\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_stacked_disks_aniso_static.tex}{\input{SasView_stacked_disks_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_stacked_disks_aniso_static.tex}{\input{sasmodels/SasView_stacked_disks_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_star_polymer.tex b/docs/manuals/mcstas/sasmodels/SasView_star_polymer.tex index 99be9c0a48..2157e2c9c5 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_star_polymer.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_star_polymer.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_star\_polymer} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_star_polymer component, generated from star_polymer.c in sasmodels. +SasView\_star\_polymer component, generated from star\_polymer.c in sasmodels. -Example: -SasView_star_polymer(rg_squared, arms, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_rg_squared=0.0) -\end{lstlisting} +Example: SasView\_star\_polymer(rg\_squared, arms, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg\_squared=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -rg\_squared & Ang\textasciicircum{}2 & ([0.0, inf]) Ensemble radius of gyration SQUARED of the full polymer. & 100.0 \\ +rg\_squared & \AA{}$^{2}$ & ([0.0, inf]) Ensemble radius of gyration SQUARED of the full polymer. & 100.0 \\ arms & & ([1.0, 6.0]) Number of arms in the model. & 3 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ @@ -52,6 +44,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_star_polymer.comp}{Source code} for \texttt{SasView\_star\_polymer.comp}. + \item Component source code found in file \texttt{SasView\_star\_polymer.comp}. \end{itemize} -\IfFileExists{SasView_star_polymer_static.tex}{\input{SasView_star_polymer_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_star_polymer_static.tex}{\input{sasmodels/SasView_star_polymer_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_stickyhardsphere.tex b/docs/manuals/mcstas/sasmodels/SasView_stickyhardsphere.tex index daf050aa22..9a56631191 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_stickyhardsphere.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_stickyhardsphere.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_stickyhardsphere} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_stickyhardsphere component, generated from stickyhardsphere.c in sasmodels. +SasView\_stickyhardsphere component, generated from stickyhardsphere.c in sasmodels. -Example: -SasView_stickyhardsphere(radius_effective, volfraction, perturb, stickiness, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_effective=0.0) -\end{lstlisting} +Example: SasView\_stickyhardsphere(radius\_effective, volfraction, perturb, stickiness, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_effective=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,7 +21,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius\_effective & Ang & ([0, inf]) effective radius of hard sphere. & 50.0 \\ +radius\_effective & \AA{} & ([0, inf]) effective radius of hard sphere. & 50.0 \\ volfraction & & ([0, 0.74]) volume fraction of hard spheres. & 0.2 \\ perturb & & ([0.01, 0.1]) perturbation parameter, tau. & 0.05 \\ stickiness & & ([-inf, inf]) stickiness, epsilon. & 0.2 \\ @@ -54,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_stickyhardsphere.comp}{Source code} for \texttt{SasView\_stickyhardsphere.comp}. + \item Component source code found in file \texttt{SasView\_stickyhardsphere.comp}. \end{itemize} -\IfFileExists{SasView_stickyhardsphere_static.tex}{\input{SasView_stickyhardsphere_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_stickyhardsphere_static.tex}{\input{sasmodels/SasView_stickyhardsphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_superball.tex b/docs/manuals/mcstas/sasmodels/SasView_superball.tex index 22930ed0e2..f0c4342ce6 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_superball.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_superball.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_superball} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_superball component, generated from superball.c in sasmodels. +SasView\_superball component, generated from superball.c in sasmodels. -Example: -SasView_superball(sld, sld_solvent, length_a, exponent_p, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0) -\end{lstlisting} +Example: SasView\_superball(sld, sld\_solvent, length\_a, exponent\_p, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,9 +21,9 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Superball scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -length\_a & Ang & ([0, inf]) Cube edge length of the superball. & 50 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Superball scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Cube edge length of the superball. & 50 \\ exponent\_p & & ([0, inf]) Exponent describing the roundness of the superball. & 2.5 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ @@ -54,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_superball.comp}{Source code} for \texttt{SasView\_superball.comp}. + \item Component source code found in file \texttt{SasView\_superball.comp}. \end{itemize} -\IfFileExists{SasView_superball_static.tex}{\input{SasView_superball_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_superball_static.tex}{\input{sasmodels/SasView_superball_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_superball_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_superball_aniso.tex index 2071200356..31b70b67a2 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_superball_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_superball_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_superball\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_superball component, generated from superball.c in sasmodels. +SasView\_superball component, generated from superball.c in sasmodels. -Example: -SasView_superball_aniso(sld, sld_solvent, length_a, exponent_p, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_length_a=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_superball\_aniso(sld, sld\_solvent, length\_a, exponent\_p, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,9 +21,9 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Superball scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -length\_a & Ang & ([0, inf]) Cube edge length of the superball. & 50 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Superball scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Cube edge length of the superball. & 50 \\ exponent\_p & & ([0, inf]) Exponent describing the roundness of the superball. & 2.5 \\ theta & & & 0 \\ phi & & & 0 \\ @@ -60,6 +52,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_superball_aniso.comp}{Source code} for \texttt{SasView\_superball\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_superball\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_superball_aniso_static.tex}{\input{SasView_superball_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_superball_aniso_static.tex}{\input{sasmodels/SasView_superball_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_surface_fractal.tex b/docs/manuals/mcstas/sasmodels/SasView_surface_fractal.tex index 5134bfbaf1..18057c538d 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_surface_fractal.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_surface_fractal.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_surface\_fractal} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_surface_fractal component, generated from surface_fractal.c in sasmodels. +SasView\_surface\_fractal component, generated from surface\_fractal.c in sasmodels. -Example: -SasView_surface_fractal(radius, fractal_dim_surf, cutoff_length, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_cutoff_length=0.0) -\end{lstlisting} +Example: SasView\_surface\_fractal(radius, fractal\_dim\_surf, cutoff\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_cutoff\_length=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,9 +21,9 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -radius & Ang & ([0, inf]) Particle radius. & 10.0 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 10.0 \\ fractal\_dim\_surf & & ([1, 3]) Surface fractal dimension. & 2.0 \\ -cutoff\_length & Ang & ([0.0, inf]) Cut-off Length. & 500.0 \\ +cutoff\_length & \AA{} & ([0.0, inf]) Cut-off Length. & 500.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -54,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_surface_fractal.comp}{Source code} for \texttt{SasView\_surface\_fractal.comp}. + \item Component source code found in file \texttt{SasView\_surface\_fractal.comp}. \end{itemize} -\IfFileExists{SasView_surface_fractal_static.tex}{\input{SasView_surface_fractal_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_surface_fractal_static.tex}{\input{sasmodels/SasView_surface_fractal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_teubner_strey.tex b/docs/manuals/mcstas/sasmodels/SasView_teubner_strey.tex index 1e7ba570bf..3bd41cd03e 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_teubner_strey.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_teubner_strey.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_teubner\_strey} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_teubner_strey component, generated from teubner_strey.c in sasmodels. +SasView\_teubner\_strey component, generated from teubner\_strey.c in sasmodels. -Example: -SasView_teubner_strey(volfraction_a, sld_a, sld_b, d, xi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +Example: SasView\_teubner\_strey(volfraction\_a, sld\_a, sld\_b, d, xi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,10 +22,10 @@ \subsection*{Input parameters} \midrule \endhead volfraction\_a & & ([0, 1.0]) Volume fraction of phase a. & 0.5 \\ -sld\_a & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) SLD of phase a. & 0.3 \\ -sld\_b & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) SLD of phase b. & 6.3 \\ -d & Ang & ([0, inf]) Domain size (periodicity). & 100.0 \\ -xi & Ang & ([0, inf]) Correlation length. & 30.0 \\ +sld\_a & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) SLD of phase a. & 0.3 \\ +sld\_b & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) SLD of phase b. & 6.3 \\ +d & \AA{} & ([0, inf]) Domain size (periodicity). & 100.0 \\ +xi & \AA{} & ([0, inf]) Correlation length. & 30.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -54,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_teubner_strey.comp}{Source code} for \texttt{SasView\_teubner\_strey.comp}. + \item Component source code found in file \texttt{SasView\_teubner\_strey.comp}. \end{itemize} -\IfFileExists{SasView_teubner_strey_static.tex}{\input{SasView_teubner_strey_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_teubner_strey_static.tex}{\input{sasmodels/SasView_teubner_strey_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_triaxial_ellipsoid.tex b/docs/manuals/mcstas/sasmodels/SasView_triaxial_ellipsoid.tex index ccf4bf58db..6ef0d0e50c 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_triaxial_ellipsoid.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_triaxial_ellipsoid.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_triaxial\_ellipsoid} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_triaxial_ellipsoid component, generated from triaxial_ellipsoid.c in sasmodels. +SasView\_triaxial\_ellipsoid component, generated from triaxial\_ellipsoid.c in sasmodels. -Example: -SasView_triaxial_ellipsoid(sld, sld_solvent, radius_equat_minor, radius_equat_major, radius_polar, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_equat_minor=0.0, pd_radius_equat_major=0.0, pd_radius_polar=0.0) -\end{lstlisting} +Example: SasView\_triaxial\_ellipsoid(sld, sld\_solvent, radius\_equat\_minor, radius\_equat\_major, radius\_polar, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_equat\_minor=0.0, pd\_radius\_equat\_major=0.0, pd\_radius\_polar=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius\_equat\_minor & Ang & ([0, inf]) Minor equatorial radius, Ra. & 20 \\ -radius\_equat\_major & Ang & ([0, inf]) Major equatorial radius, Rb. & 400 \\ -radius\_polar & Ang & ([0, inf]) Polar radius, Rc. & 10 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_equat\_minor & \AA{} & ([0, inf]) Minor equatorial radius, Ra. & 20 \\ +radius\_equat\_major & \AA{} & ([0, inf]) Major equatorial radius, Rb. & 400 \\ +radius\_polar & \AA{} & ([0, inf]) Polar radius, Rc. & 10 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_triaxial_ellipsoid.comp}{Source code} for \texttt{SasView\_triaxial\_ellipsoid.comp}. + \item Component source code found in file \texttt{SasView\_triaxial\_ellipsoid.comp}. \end{itemize} -\IfFileExists{SasView_triaxial_ellipsoid_static.tex}{\input{SasView_triaxial_ellipsoid_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_triaxial_ellipsoid_static.tex}{\input{sasmodels/SasView_triaxial_ellipsoid_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_triaxial_ellipsoid_aniso.tex b/docs/manuals/mcstas/sasmodels/SasView_triaxial_ellipsoid_aniso.tex index 3d77285551..59286b0f89 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_triaxial_ellipsoid_aniso.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_triaxial_ellipsoid_aniso.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_triaxial\_ellipsoid\_aniso} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_triaxial_ellipsoid component, generated from triaxial_ellipsoid.c in sasmodels. +SasView\_triaxial\_ellipsoid component, generated from triaxial\_ellipsoid.c in sasmodels. -Example: -SasView_triaxial_ellipsoid_aniso(sld, sld_solvent, radius_equat_minor, radius_equat_major, radius_polar, theta, phi, Psi, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius_equat_minor=0.0, pd_radius_equat_major=0.0, pd_radius_polar=0.0, pd_theta=0.0, pd_phi=0.0, pd_Psi=0.0) -\end{lstlisting} +Example: SasView\_triaxial\_ellipsoid\_aniso(sld, sld\_solvent, radius\_equat\_minor, radius\_equat\_major, radius\_polar, theta, phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_equat\_minor=0.0, pd\_radius\_equat\_major=0.0, pd\_radius\_polar=0.0, pd\_theta=0.0, pd\_phi=0.0, pd\_Psi=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) Solvent scattering length density. & 1 \\ -radius\_equat\_minor & Ang & ([0, inf]) Minor equatorial radius, Ra. & 20 \\ -radius\_equat\_major & Ang & ([0, inf]) Major equatorial radius, Rb. & 400 \\ -radius\_polar & Ang & ([0, inf]) Polar radius, Rc. & 10 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_equat\_minor & \AA{} & ([0, inf]) Minor equatorial radius, Ra. & 20 \\ +radius\_equat\_major & \AA{} & ([0, inf]) Major equatorial radius, Rb. & 400 \\ +radius\_polar & \AA{} & ([0, inf]) Polar radius, Rc. & 10 \\ theta & & & 60 \\ phi & & & 60 \\ Psi & & & 60 \\ @@ -63,6 +55,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_triaxial_ellipsoid_aniso.comp}{Source code} for \texttt{SasView\_triaxial\_ellipsoid\_aniso.comp}. + \item Component source code found in file \texttt{SasView\_triaxial\_ellipsoid\_aniso.comp}. \end{itemize} -\IfFileExists{SasView_triaxial_ellipsoid_aniso_static.tex}{\input{SasView_triaxial_ellipsoid_aniso_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_triaxial_ellipsoid_aniso_static.tex}{\input{sasmodels/SasView_triaxial_ellipsoid_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_two_lorentzian.tex b/docs/manuals/mcstas/sasmodels/SasView_two_lorentzian.tex index f75cfe8de0..7a3ae00577 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_two_lorentzian.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_two_lorentzian.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_two\_lorentzian} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_two_lorentzian component, generated from two_lorentzian.c in sasmodels. +SasView\_two\_lorentzian component, generated from two\_lorentzian.c in sasmodels. -Example: -SasView_two_lorentzian(lorentz_scale_1, lorentz_length_1, lorentz_exp_1, lorentz_scale_2, lorentz_length_2, lorentz_exp_2, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_lorentz_length_1=0.0, pd_lorentz_length_2=0.0) -\end{lstlisting} +Example: SasView\_two\_lorentzian(lorentz\_scale\_1, lorentz\_length\_1, lorentz\_exp\_1, lorentz\_scale\_2, lorentz\_length\_2, lorentz\_exp\_2, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_lorentz\_length\_1=0.0, pd\_lorentz\_length\_2=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,10 +22,10 @@ \subsection*{Input parameters} \midrule \endhead lorentz\_scale\_1 & & ([-inf, inf]) First power law scale factor. & 10.0 \\ -lorentz\_length\_1 & Ang & ([-inf, inf]) First Lorentzian screening length. & 100.0 \\ +lorentz\_length\_1 & \AA{} & ([-inf, inf]) First Lorentzian screening length. & 100.0 \\ lorentz\_exp\_1 & & ([-inf, inf]) First exponent of power law. & 3.0 \\ lorentz\_scale\_2 & & ([-inf, inf]) Second scale factor for broad Lorentzian peak. & 1.0 \\ -lorentz\_length\_2 & Ang & ([-inf, inf]) Second Lorentzian screening length. & 10.0 \\ +lorentz\_length\_2 & \AA{} & ([-inf, inf]) Second Lorentzian screening length. & 10.0 \\ lorentz\_exp\_2 & & ([-inf, inf]) Second exponent of power law. & 2.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ @@ -57,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_two_lorentzian.comp}{Source code} for \texttt{SasView\_two\_lorentzian.comp}. + \item Component source code found in file \texttt{SasView\_two\_lorentzian.comp}. \end{itemize} -\IfFileExists{SasView_two_lorentzian_static.tex}{\input{SasView_two_lorentzian_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_two_lorentzian_static.tex}{\input{sasmodels/SasView_two_lorentzian_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_two_power_law.tex b/docs/manuals/mcstas/sasmodels/SasView_two_power_law.tex index 2906aae8e7..0b3a86d908 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_two_power_law.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_two_power_law.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_two\_power\_law} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_two_power_law component, generated from two_power_law.c in sasmodels. +SasView\_two\_power\_law component, generated from two\_power\_law.c in sasmodels. -Example: -SasView_two_power_law(coefficent_1, crossover, power_1, power_2, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -) -\end{lstlisting} +Example: SasView\_two\_power\_law(coefficent\_1, crossover, power\_1, power\_2, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -30,7 +22,7 @@ \subsection*{Input parameters} \midrule \endhead coefficent\_1 & & ([-inf, inf]) coefficent A in low Q region. & 1.0 \\ -crossover & 1/Ang & ([0, inf]) crossover location. & 0.04 \\ +crossover & 1/\AA{} & ([0, inf]) crossover location. & 0.04 \\ power\_1 & & ([0, inf]) power law exponent at low Q. & 1.0 \\ power\_2 & & ([0, inf]) power law exponent at high Q. & 4.0 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ @@ -53,6 +45,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_two_power_law.comp}{Source code} for \texttt{SasView\_two\_power\_law.comp}. + \item Component source code found in file \texttt{SasView\_two\_power\_law.comp}. \end{itemize} -\IfFileExists{SasView_two_power_law_static.tex}{\input{SasView_two_power_law_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_two_power_law_static.tex}{\input{sasmodels/SasView_two_power_law_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sasmodels/SasView_vesicle.tex b/docs/manuals/mcstas/sasmodels/SasView_vesicle.tex index 23cefe933b..aea6771dc7 100644 --- a/docs/manuals/mcstas/sasmodels/SasView_vesicle.tex +++ b/docs/manuals/mcstas/sasmodels/SasView_vesicle.tex @@ -3,23 +3,15 @@ \section{The \texttt{SasView\_vesicle} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Jose Robledo \item \textbf{Origin:} FZJ / DTU / ESS DMSC \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -SasView_vesicle component, generated from vesicle.c in sasmodels. +SasView\_vesicle component, generated from vesicle.c in sasmodels. -Example: -SasView_vesicle(sld, sld_solvent, volfraction, radius, thickness, -model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, -int target_index=1, target_x=0, target_y=0, target_z=1, -focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, -pd_radius=0.0, pd_thickness=0.0) -\end{lstlisting} +Example: SasView\_vesicle(sld, sld\_solvent, volfraction, radius, thickness, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -29,11 +21,11 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -sld & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) vesicle shell scattering length density. & 0.5 \\ -sld\_solvent & 1e-6/Ang\textasciicircum{}2 & ([-inf, inf]) solvent scattering length density. & 6.36 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) vesicle shell scattering length density. & 0.5 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) solvent scattering length density. & 6.36 \\ volfraction & & ([0, 1.0]) volume fraction of shell. & 0.05 \\ -radius & Ang & ([0, inf]) vesicle core radius. & 100 \\ -thickness & Ang & ([0, inf]) vesicle shell thickness. & 30 \\ +radius & \AA{} & ([0, inf]) vesicle core radius. & 100 \\ +thickness & \AA{} & ([0, inf]) vesicle shell thickness. & 30 \\ model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ @@ -56,6 +48,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sasmodels/SasView_vesicle.comp}{Source code} for \texttt{SasView\_vesicle.comp}. + \item Component source code found in file \texttt{SasView\_vesicle.comp}. \end{itemize} -\IfFileExists{SasView_vesicle_static.tex}{\input{SasView_vesicle_static.tex}}{} \ No newline at end of file +\IfFileExists{sasmodels/SasView_vesicle_static.tex}{\input{sasmodels/SasView_vesicle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Adapt_check.tex b/docs/manuals/mcstas/sources/Adapt_check.tex index 3f36e88094..c701dc7ec7 100644 --- a/docs/manuals/mcstas/sources/Adapt_check.tex +++ b/docs/manuals/mcstas/sources/Adapt_check.tex @@ -3,24 +3,15 @@ \section{The \texttt{Adapt\_check} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This components works together with the Source_adapt component, and -is used to define the criteria for selecting which neutrons are -considered "good" in the adaptive algorithm. The name of the -associated Source_adapt component in the instrument definition is -given as parameter. The component is special in that its position -does not matter; all neutrons that have not been absorbed prior to -the component are considered "good". +This components works together with the Source\_adapt component, and is used to define the criteria for selecting which neutrons are considered "good" in the adaptive algorithm. The name of the associated Source\_adapt component in the instrument definition is given as parameter. The component is special in that its position does not matter; all neutrons that have not been absorbed prior to the component are considered "good". -Example: Adapt_check(source_comp="MySource") -\end{lstlisting} +Example: Adapt\_check(source\_comp="MySource") \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,6 +27,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Adapt_check.comp}{Source code} for \texttt{Adapt\_check.comp}. + \item Component source code found in file \texttt{Adapt\_check.comp}. \end{itemize} -\IfFileExists{Adapt_check_static.tex}{\input{Adapt_check_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Adapt_check_static.tex}{\input{sources/Adapt_check_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/ESS_butterfly.tex b/docs/manuals/mcstas/sources/ESS_butterfly.tex index a5dd3dae54..e2c71a8fc5 100644 --- a/docs/manuals/mcstas/sources/ESS_butterfly.tex +++ b/docs/manuals/mcstas/sources/ESS_butterfly.tex @@ -3,76 +3,29 @@ \section{The \texttt{ESS\_butterfly} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup and Esben Klinkby \item \textbf{Origin:} DTU \item \textbf{Date:} August-September 2016 \end{itemize} \subsection*{Description} -\begin{lstlisting} -ESS butterfly moderator with automatic choice of coordinate system, with origin -placed at relevant "Moderator Focus Coordinate System" depending on sector location. +ESS butterfly moderator with automatic choice of coordinate system, with origin placed at relevant "Moderator Focus Coordinate System" depending on sector location. To select beamport N 5 simply use -COMPONENT Source = ESS_butterfly(sector="N",beamline=5,Lmin=0.1,Lmax=20,dist=2, -cold_frac=0.5, yheight=0.03,focus_xw=0.1, focus_yh=0.1) +COMPONENT Source = ESS\_butterfly(sector="N",beamline=5,Lmin=0.1,Lmax=20,dist=2, cold\_frac=0.5, yheight=0.03,focus\_xw=0.1, focus\_yh=0.1) -<b>Geometry</b> -The geometry corresponds correctly to the latest release of the butterfly moderator, -including changes warranted by the ESS CCB in July 2016, the so called BF1 type moderator. -A set of official release documents are available with this component, see the benchmarking -website mentioned below. +\textbf{Geometry} The geometry corresponds correctly to the latest release of the butterfly moderator, including changes warranted by the ESS CCB in July 2016, the so called BF1 type moderator. A set of official release documents are available with this component, see the benchmarking website mentioned below. -<b>Brilliances, geometry adapted from earlier BF2 design</b> -The geometry and brightness data implemented in the McStas ESS source component ESS_butterfly.comp, -are released as an updated component library for McStas 2.3, as well as a stand alone archive for -use with earlier versions of McStas. +\textbf{Brilliances, geometry adapted from earlier BF2 design} The geometry and brightness data implemented in the McStas ESS source component ESS\_butterfly.comp, are released as an updated component library for McStas 2.3, as well as a stand alone archive for use with earlier versions of McStas. -The following features are worth highlighting: -<ul> -<li>The brightness data are still based on last years MCNP calculations, based on the Butterfly 2 geometry. -As a result, the spatial variation of the brightness across the moderator face should be considered to -have an uncertainty of the order of 10%. Detailed information on the reasoning behind the change to -the Butterfly 1 geometry can be found in <A HREF="http://essbutterfly.mcstas.org/PDFs/Update_to_ESS_moderators_KHA_latest.pdf">[1]</a> and detailed information on horizontal spatial brightness -variation can be found in <A HREF="http://essbutterfly.mcstas.org/PDFs/BFpaper_LZ_latest.pdf">[2]</a>. The spectral shape has been checked and has not changed significantly. -<li>A scaling factor has been introduced to in order to account for the decrease in brightness since 2015. -To accommodate the influence of the changed geometry, this scaling factor has been applied independently -for the cold and thermal contributions and is beamline dependent. It is adjusted to agree with the -spectrally-integrated 6cm width data shown in <A HREF="http://essbutterfly.mcstas.org/PDFs/Update_to_ESS_moderators_KHA_latest.pdf">[1]</a>,Figure 3. -<li>To allow future user adjustments of brilliance, the scalar parameters c_performance and t_performance -have been implemented. For now, we recommend to keep these at their default value of 1.0. -<li>The geometry has been updated to correspond within about 2 mm to the geometry described in <A HREF="http://essbutterfly.mcstas.org/PDFs/Update_to_ESS_moderators_KHA_latest.pdf">[1]</a>. This -has been done by ensuring that the position and apparent width of the moderators correspond to <A HREF="http://essbutterfly.mcstas.org/PDFs/Update_to_ESS_moderators_KHA_latest.pdf">[1]</a>,Figure 2, -which has been derived from current MCNP butterfly 1 model. -<li>The beamport is now defined directly by its sector and number (e.g. 'W' and '5'), rather than giving the angle, -as before. <A HREF="http://essbutterfly.mcstas.org/PDFs/Update_to_ESS_moderators_KHA_latest.pdf">[1]</a>,Figure 5 shows the geometry of the moderator2, beamport insert and beamline axis for beamline W5. -Since the underlying data is still from last years MCNP run, when the brightness was calculated at 10-degree -intervals, this means that the spectral curve for the nearest beamport on the grid 5,15,25,35,45,55 degrees -is used. The use of this grid has no effect on the accuracy of the geometry or brilliance because of the above- -mentioned beamline-dependent adjustments to the brilliance and geometry. See the website <A HREF="http://essbutterfly.mcstas.org/">[3]</a> for details. -</ul> -As before, the beamports all originate at the focal point of the sector. The beamline will in almost all cases be -horizontally tilted in order to view the cold or thermal moderator, which should be done using an Arm component. +The following features are worth highlighting: \textless{}ul\textgreater{} \textless{}li\textgreater{}The brightness data are still based on last years MCNP calculations, based on the Butterfly 2 geometry. As a result, the spatial variation of the brightness across the moderator face should be considered to have an uncertainty of the order of 10\%. Detailed information on the reasoning behind the change to the Butterfly 1 geometry can be found in \htmladdnormallink{[1]}{http://essbutterfly.mcstas.org/PDFs/Update\_to\_ESS\_moderators\_KHA\_latest.pdf} and detailed information on horizontal spatial brightness variation can be found in \htmladdnormallink{[2]}{http://essbutterfly.mcstas.org/PDFs/BFpaper\_LZ\_latest.pdf}. The spectral shape has been checked and has not changed significantly. \textless{}li\textgreater{}A scaling factor has been introduced to in order to account for the decrease in brightness since 2015. To accommodate the influence of the changed geometry, this scaling factor has been applied independently for the cold and thermal contributions and is beamline dependent. It is adjusted to agree with the spectrally-integrated 6cm width data shown in \htmladdnormallink{[1]}{http://essbutterfly.mcstas.org/PDFs/Update\_to\_ESS\_moderators\_KHA\_latest.pdf},Figure 3. \textless{}li\textgreater{}To allow future user adjustments of brilliance, the scalar parameters c\_performance and t\_performance have been implemented. For now, we recommend to keep these at their default value of 1.0. \textless{}li\textgreater{}The geometry has been updated to correspond within about 2 mm to the geometry described in \htmladdnormallink{[1]}{http://essbutterfly.mcstas.org/PDFs/Update\_to\_ESS\_moderators\_KHA\_latest.pdf}. This has been done by ensuring that the position and apparent width of the moderators correspond to \htmladdnormallink{[1]}{http://essbutterfly.mcstas.org/PDFs/Update\_to\_ESS\_moderators\_KHA\_latest.pdf},Figure 2, which has been derived from current MCNP butterfly 1 model. \textless{}li\textgreater{}The beamport is now defined directly by its sector and number (e.g. 'W' and '5'), rather than giving the angle, as before. \htmladdnormallink{[1]}{http://essbutterfly.mcstas.org/PDFs/Update\_to\_ESS\_moderators\_KHA\_latest.pdf},Figure 5 shows the geometry of the moderator2, beamport insert and beamline axis for beamline W5. Since the underlying data is still from last years MCNP run, when the brightness was calculated at 10-degree intervals, this means that the spectral curve for the nearest beamport on the grid 5,15,25,35,45,55 degrees is used. The use of this grid has no effect on the accuracy of the geometry or brilliance because of the above- mentioned beamline-dependent adjustments to the brilliance and geometry. See the website \htmladdnormallink{[3]}{http://essbutterfly.mcstas.org/} for details. \textless{}/ul\textgreater{} As before, the beamports all originate at the focal point of the sector. The beamline will in almost all cases be horizontally tilted in order to view the cold or thermal moderator, which should be done using an Arm component. -<p>We expect to release an MCNP-event-based source model later in 2016, and possibly also new set of brilliance -functions for ESS_butterfly.comp. These are expected to include more realistic brilliances in terms of variation -across sectors and potentially also performance losses due to engineering reality. </b> +\textless{}p\textgreater{}We expect to release an MCNP-event-based source model later in 2016, and possibly also new set of brilliance functions for ESS\_butterfly.comp. These are expected to include more realistic brilliances in terms of variation across sectors and potentially also performance losses due to engineering reality. } -<b>Engineering reality</b> -An ad-hoc method for future implementation of "engineering reality" is included, use the -"c_performance/t_performance" parameters to down-scale performance uniformly across all wavelengths. +\textbf{Engineering reality} An ad-hoc method for future implementation of "engineering reality" is included, use the "c\_performance/t\_performance" parameters to down-scale performance uniformly across all wavelengths. -<b>References:</b> -<ol> -<li><A HREF="http://essbutterfly.mcstas.org/PDFs/Update_to_ESS_moderators_KHA_latest.pdf">Release document "Update to ESS Moderators, latest version"</a> -<li><A HREF="http://essbutterfly.mcstas.org/PDFs/BFpaper_LZ_latest.pdf">Release document "Description and performance of the new baseline ESS moderators, latest version"</a> -<li><A HREF="http://essbutterfly.mcstas.org/">http://essbutterfly.mcstas.org/</a> benchmarking website with comparative McStas-MCNP figures -<li><a href="http://essbutterfly.mcstas.org/visualisation">html-based, interactive 3D model of moderators and monolith, as seen from beamline N4</a>. -<li><A HREF="https://github.com/mccode-dev/McCode/blob/master/mcstas-comps/sources/ESS_butterfly.comp">Source code</A> for <CODE>ESS_butterfly.comp</CODE> at GitHub. -</ol> -\end{lstlisting} +\textbf{References:} \textless{}ol\textgreater{} \textless{}li\textgreater{}\htmladdnormallink{Release document "Update to ESS Moderators, latest version"}{http://essbutterfly.mcstas.org/PDFs/Update\_to\_ESS\_moderators\_KHA\_latest.pdf} \textless{}li\textgreater{}\htmladdnormallink{Release document "Description and performance of the new baseline ESS moderators, latest version"}{http://essbutterfly.mcstas.org/PDFs/BFpaper\_LZ\_latest.pdf} \textless{}li\textgreater{}\htmladdnormallink{http://essbutterfly.mcstas.org/}{http://essbutterfly.mcstas.org/} benchmarking website with comparative McStas-MCNP figures \textless{}li\textgreater{}\htmladdnormallink{html-based, interactive 3D model of moderators and monolith, as seen from beamline N4}{http://essbutterfly.mcstas.org/visualisation}. \textless{}li\textgreater{}\htmladdnormallink{Source code}{https://github.com/mccode-dev/McCode/blob/master/mcstas-comps/sources/ESS\_butterfly.comp} for \texttt{ESS\_butterfly.comp} at GitHub. \textless{}/ol\textgreater{} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -92,8 +45,8 @@ \subsection*{Input parameters} focus\_yh & m & Height of focusing rectangle & 0 \\ c\_performance & 1 & Cold brilliance scalar performance multiplicator c\_performance \textgreater{} 0 & 1 \\ t\_performance & 1 & Thermal brilliance scalar performance multiplicator t\_performance \textgreater{} 0 & 1 \\ -\textbf{Lmin} & AA & Minimum wavelength simulated & \\ -\textbf{Lmax} & AA & Maximum wavelength simulated & \\ +\textbf{Lmin} & \AA{} & Minimum wavelength simulated & \\ +\textbf{Lmax} & \AA{} & Maximum wavelength simulated & \\ tmax\_multiplier & 1 & Defined maximum emission time at moderator, tmax= tmax\_multiplier * ESS\_PULSE\_DURATION. & 3 \\ n\_pulses & 1 & Number of pulses simulated. 0 and 1 creates one pulse. & 1 \\ acc\_power & MW & Accelerator power in MW & 5 \\ @@ -105,6 +58,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/ESS_butterfly.comp}{Source code} for \texttt{ESS\_butterfly.comp}. + \item Component source code found in file \texttt{ESS\_butterfly.comp}. \end{itemize} -\IfFileExists{ESS_butterfly_static.tex}{\input{ESS_butterfly_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/ESS_butterfly_static.tex}{\input{sources/ESS_butterfly_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/ESS_moderator.tex b/docs/manuals/mcstas/sources/ESS_moderator.tex index 1462624c8c..1f1080ad9d 100644 --- a/docs/manuals/mcstas/sources/ESS_moderator.tex +++ b/docs/manuals/mcstas/sources/ESS_moderator.tex @@ -3,50 +3,27 @@ \section{The \texttt{ESS\_moderator} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} P Willendrup and E Klinkby, February 2014, derived from K Lefmann ESS\_moderator\_long \item \textbf{Origin:} DTU \item \textbf{Date:} \end{itemize} \subsection*{Description} -\begin{lstlisting} -Produces a time-of-flight spectrum, from the ESS parameters -Chooses evenly in lambda, evenly/exponentially decaying in time -Adapted from ESS_moderator_long by: K Lefmann, 2001 +Produces a time-of-flight spectrum, from the ESS parameters Chooses evenly in lambda, evenly/exponentially decaying in time Adapted from ESS\_moderator\_long by: K Lefmann, 2001 -Updates and simplified interface: -<ol> -<li>The spectrum from the source(s) is defined via the sourcedef string input parameter which allows these values: -<ul> -<li>sourcedef="2001", legacy "Mezei moderators" from the original F. Mezei documents -"ESS reference moderator characteristics for generic instrument performance evaluation", but rescaled to ESS TDR frequency, pulselength and power. -<li>sourcedef="TDR", Mezei moderators, with a wavelength-dependent correction term to the cold flux, derived from -2012 MCNPX calculations by ESS neutronics group. Corrections calculated by K Lieutenant (Vitess) and -implemented here by E Klinkby. NOTE: uses the 2001 brilliance for the thermal moderator! -<li>sourcedef="2014", updated brilliance using formulation by Troels Schoenfeldt, including support for the "pancacke", i.e. flat geometry. -<li>sourcedef="2015", updated brilliance using formulation by Troels Schoenfeldt, new butterfly baseline. -</ul> -<li>The component can use target_index for focusing to a given beam port. Use an Arm() and ROTATED to position -relatively to the moderator. -<li>The component relies on the new ess_source-lib which is expected to become further enriched during design-finaliziation and construciton of the ESS. -</ol> +Updates and simplified interface: \textless{}ol\textgreater{} \textless{}li\textgreater{}The spectrum from the source(s) is defined via the sourcedef string input parameter which allows these values: \textless{}ul\textgreater{} \textless{}li\textgreater{}sourcedef="2001", legacy "Mezei moderators" from the original F. Mezei documents "ESS reference moderator characteristics for generic instrument performance evaluation", but rescaled to ESS TDR frequency, pulselength and power. \textless{}li\textgreater{}sourcedef="TDR", Mezei moderators, with a wavelength-dependent correction term to the cold flux, derived from 2012 MCNPX calculations by ESS neutronics group. Corrections calculated by K Lieutenant (Vitess) and implemented here by E Klinkby. NOTE: uses the 2001 brilliance for the thermal moderator! \textless{}li\textgreater{}sourcedef="2014", updated brilliance using formulation by Troels Schoenfeldt, including support for the "pancacke", i.e. flat geometry. \textless{}li\textgreater{}sourcedef="2015", updated brilliance using formulation by Troels Schoenfeldt, new butterfly baseline. \textless{}/ul\textgreater{} \textless{}li\textgreater{}The component can use target\_index for focusing to a given beam port. Use an Arm() and ROTATED to position relatively to the moderator. \textless{}li\textgreater{}The component relies on the new ess\_source-lib which is expected to become further enriched during design-finaliziation and construciton of the ESS. \textless{}/ol\textgreater{} -<p><b>Note that this component does not implement "engineering reality" and currently uses a coordinate system centered on the moderator assembly. An -updated moderator component which references the "Moderator focus coordinate system" will be released later during the spring of 2016.</b> +\textless{}p\textgreater{}\textbf{Note that this component does not implement "engineering reality" and currently uses a coordinate system centered on the moderator assembly. An updated moderator component which references the "Moderator focus coordinate system" will be released later during the spring of 2016.} -<p>Derived from ESS_moderator_long which was debugged intensively against Mezei note (4/12 2000) and VitESS @ Rencurel 2006. +\textless{}p\textgreater{}Derived from ESS\_moderator\_long which was debugged intensively against Mezei note (4/12 2000) and VitESS @ Rencurel 2006. +\begin{verbatim} ----------------------------------------------- -Correction by J. Saroun, NPI Rez: -1) version 2015: accepts negative port angles -2) version 2015: weight by cosine of the port angle -Warning: The negative beamport angle is not taken into acccount by mcplot +\end{verbatim} -%VALIDATION -Mezei-modererators validated against VitESS and Mezei note (4/12 2000) @ Rencurel 2006 -Benchmarked against multiple versions of ESS moderator group simulation data 2013-2015 -\end{lstlisting} +Correction by J. Saroun, NPI Rez: 1) version 2015: accepts negative port angles 2) version 2015: weight by cosine of the port angle Warning: The negative beamport angle is not taken into acccount by mcplot + +\%VALIDATION Mezei-modererators validated against VitESS and Mezei note (4/12 2000) @ Rencurel 2006 Benchmarked against multiple versions of ESS moderator group simulation data 2013-2015 \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -57,8 +34,8 @@ \subsection*{Input parameters} \midrule \endhead isleft & 1 & Fraction of thermal neutrons generated at the "left" moderator slab in case of "2013" or "2014" & 0.9 \\ -\textbf{Lmin} & AA & Lower edge of wavelength distribution & \\ -\textbf{Lmax} & AA & Upper edge of wavelength distribution & \\ +\textbf{Lmin} & \AA{} & Lower edge of wavelength distribution & \\ +\textbf{Lmax} & \AA{} & Upper edge of wavelength distribution & \\ cold\_frac & 1 & Fraction of neutron statistics from cold source. It is implicitely assumed that supermirror allows each beamline to choose the desired fraction of cold and thermal neutrons (i.e. extreme idealization). & 1.0 \\ dist & m & Distance from source to focusing rectangle; at (0,0,dist) & 0 \\ \textbf{focus\_xw} & m & Width of focusing rectangle & \\ @@ -79,6 +56,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/ESS_moderator.comp}{Source code} for \texttt{ESS\_moderator.comp}. + \item Component source code found in file \texttt{ESS\_moderator.comp}. \end{itemize} -\IfFileExists{ESS_moderator_static.tex}{\input{ESS_moderator_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/ESS_moderator_static.tex}{\input{sources/ESS_moderator_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Moderator.tex b/docs/manuals/mcstas/sources/Moderator.tex index c470db0800..fa47778a53 100644 --- a/docs/manuals/mcstas/sources/Moderator.tex +++ b/docs/manuals/mcstas/sources/Moderator.tex @@ -3,18 +3,17 @@ \section{The \texttt{Moderator} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} KN, M.Hagen \item \textbf{Origin:} Risoe \item \textbf{Date:} August 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} Produces a simple time-of-flight spectrum, with a flat energy distribution +\begin{verbatim} Example: Moderator(radius = 0.0707, dist = 9.035, focus_xw = 0.021, focus_yh = 0.021, Emin = 10, Emax = 15, Ec = 9.0, t0 = 37.15, gamma = 39.1) -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Moderator.comp}{Source code} for \texttt{Moderator.comp}. + \item Component source code found in file \texttt{Moderator.comp}. \end{itemize} -\IfFileExists{Moderator_static.tex}{\input{Moderator_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Moderator_static.tex}{\input{sources/Moderator_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Monitor_Optimizer.tex b/docs/manuals/mcstas/sources/Monitor_Optimizer.tex index 74e42f20e6..2efac490da 100644 --- a/docs/manuals/mcstas/sources/Monitor_Optimizer.tex +++ b/docs/manuals/mcstas/sources/Monitor_Optimizer.tex @@ -3,24 +3,15 @@ \section{The \texttt{Monitor\_Optimizer} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:farhi@ill.fr"\textgreater{}Emmanuel Farhi\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL (France)\textless{}/a\textgreater{} \item \textbf{Date:} 17 Sept 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A component that optimizes the neutron flux passing through the -<b>Source_Optimizer</b> in order to have the maximum flux at the -Monitor_Optimizer position(s). -<b>Source_optimizer</b> should be placed just after the source. -Monitor_Optimizer should be placed at the position to optimize. -I prefer to put one just before the sample. +A component that optimizes the neutron flux passing through the \textbf{Source\_Optimizer} in order to have the maximum flux at the Monitor\_Optimizer position(s). \textbf{Source\_optimizer} should be placed just after the source. Monitor\_Optimizer should be placed at the position to optimize. I prefer to put one just before the sample. -See <a href="Source_Optimizer.html">Source_Optimizer</a> for -usage example and additional informations. -\end{lstlisting} +See \htmladdnormallink{Source\_Optimizer}{Source\_Optimizer.html} for usage example and additional informations. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,7 +33,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Monitor_Optimizer.comp}{Source code} for \texttt{Monitor\_Optimizer.comp}. - \item \textless{}a href="Source\_Optimizer.html"\textgreater{}Source\_Optimizer\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Monitor\_Optimizer.comp}. + \item \htmladdnormallink{Source\_Optimizer}{Source\_Optimizer.html} \end{itemize} -\IfFileExists{Monitor_Optimizer_static.tex}{\input{Monitor_Optimizer_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Monitor_Optimizer_static.tex}{\input{sources/Monitor_Optimizer_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Source_4PI.tex b/docs/manuals/mcstas/sources/Source_4PI.tex index 0bd1854a2d..bd18296110 100644 --- a/docs/manuals/mcstas/sources/Source_4PI.tex +++ b/docs/manuals/mcstas/sources/Source_4PI.tex @@ -3,16 +3,13 @@ \section{The \texttt{Source\_4PI} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Peter Willendrup \item \textbf{Origin:} DTU \item \textbf{Date:} May 2024 \end{itemize} \subsection*{Description} -\begin{lstlisting} Spherical, 4PI-emitting, monochromatic source for benchmarking purposes -\end{lstlisting} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -27,13 +24,13 @@ \subsection*{Input parameters} gauss & & Flag to indicate if Energy/Wavelength distribution is gaussian & 0 \\ E0 & meV & Mean energy of neutrons. & 0 \\ dE & meV & Energy half spread of neutrons (flat or gaussian sigma). & 0 \\ -lambda0 & AA & Mean wavelength of neutrons. & 0 \\ -dlambda & AA & Wavelength half spread of neutrons. & 0 \\ +lambda0 & \AA{} & Mean wavelength of neutrons. & 0 \\ +dlambda & \AA{} & Wavelength half spread of neutrons. & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Source_4PI.comp}{Source code} for \texttt{Source\_4PI.comp}. + \item Component source code found in file \texttt{Source\_4PI.comp}. \end{itemize} -\IfFileExists{Source_4PI_static.tex}{\input{Source_4PI_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Source_4PI_static.tex}{\input{sources/Source_4PI_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Source_Maxwell_3.tex b/docs/manuals/mcstas/sources/Source_Maxwell_3.tex index 45491d4e6f..704edb92db 100644 --- a/docs/manuals/mcstas/sources/Source_Maxwell_3.tex +++ b/docs/manuals/mcstas/sources/Source_Maxwell_3.tex @@ -3,26 +3,21 @@ \section{The \texttt{Source\_Maxwell\_3} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} March 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A parametrised continuous source for modelling a (cubic) source -with (up to) 3 Maxwellian distributions. -The source produces a continuous spectrum. -The sampling of the neutrons is uniform in wavelength. +A parametrised continuous source for modelling a (cubic) source with (up to) 3 Maxwellian distributions. The source produces a continuous spectrum. The sampling of the neutrons is uniform in wavelength. -Units of flux: neutrons/cm^2/second/ster -(McStas units are in general neutrons/second) +Units of flux: neutrons/cm\textasciicircum{}2/second/ster (McStas units are in general neutrons/second) +\begin{verbatim} Example: PSI cold source T1=150.42 K / 2.51 AA I1 = 3.67 E11 T2=38.74 K / 4.95 AA I2 = 3.64 E11 T3=14.84 K / 9.5 AA I3 = 0.95 E11 -\end{lstlisting} +\end{verbatim} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -35,8 +30,8 @@ \subsection*{Input parameters} size & m & Edge of cube shaped source (for backward compatibility) & 0 \\ yheight & m & Height of rectangular source & 0 \\ xwidth & m & Width of rectangular source & 0 \\ -\textbf{Lmin} & AA & Lower edge of lambda distribution & \\ -\textbf{Lmax} & AA & Upper edge of lambda distribution & \\ +\textbf{Lmin} & \AA{} & Lower edge of lambda distribution & \\ +\textbf{Lmax} & \AA{} & Upper edge of lambda distribution & \\ \textbf{dist} & m & Distance from source to focusing rectangle; at (0,0,dist) & \\ \textbf{focus\_xw} & m & Width of focusing rectangle & \\ \textbf{focus\_yh} & m & Height of focusing rectangle & \\ @@ -47,13 +42,13 @@ \subsection*{Input parameters} I2 & 1/(cm**2*st) & flux, 2 (in flux units, see above) & 0 \\ I3 & 1/(cm**2*st) & flux, 3 - - - & 0 \\ target\_index & 1 & relative index of component to focus at, e.g. next is +1 this is used to compute 'dist' automatically. & 1 \\ -lambda0 & AA & Mean wavelength of neutrons. & 0 \\ -dlambda & AA & Wavelength spread of neutrons. & 0 \\ +lambda0 & \AA{} & Mean wavelength of neutrons. & 0 \\ +dlambda & \AA{} & Wavelength spread of neutrons. & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Source_Maxwell_3.comp}{Source code} for \texttt{Source\_Maxwell\_3.comp}. + \item Component source code found in file \texttt{Source\_Maxwell\_3.comp}. \end{itemize} -\IfFileExists{Source_Maxwell_3_static.tex}{\input{Source_Maxwell_3_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Source_Maxwell_3_static.tex}{\input{sources/Source_Maxwell_3_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Source_Optimizer.tex b/docs/manuals/mcstas/sources/Source_Optimizer.tex index 51e30fda00..6abd5833a2 100644 --- a/docs/manuals/mcstas/sources/Source_Optimizer.tex +++ b/docs/manuals/mcstas/sources/Source_Optimizer.tex @@ -5,82 +5,53 @@ \section{The \texttt{Source\_Optimizer} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} \textless{}a href="mailto:farhi@ill.fr"\textgreater{}Emmanuel Farhi\textless{}/a\textgreater{} \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL (France)\textless{}/a\textgreater{} \item \textbf{Date:} 17 Sept 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Principle: The optimizer first (step 1) computes neutron state parameter -limits passing in the Source_Optimizer, and then (step 2) records a Reference -source as well as the state (at Source_Optimizer position) of neutrons -reaching Monitor. The optimized source is defined as a fraction of the -Reference source plus the distribution of 'good' neutrons reaching the -Monitor. The optimization then starts (step 3), and focuses new neutrons on -the Monitor_Optimizer. In fact it changes 'bad' neutrons into 'good' ones -(that reach the Monitor), acting on their position, spin and divergence or -velocity. The overall Monitor flux is kept during process. The energy and -polarisation distributions are kept during optimization as far as possible -during optimisation. The optimization method considers that all neutron -parameters - (x,y), (vx,vy,vz) or (vx/v2,vy/v2,v2), (sx,sy,sz) or -(sx/s2,sy/s2,s2) - are independent. - -Options: The optimized source can be computed regularly ('continuous' -option) or only once ('not continuous'). The time spent in steps 1 and 2 can -be reduced for a shorter optimization ('auto'). The neutrons passing during -steps 1 and 2 can be smoothed for a better neutron weight distribution -('smooth' option). - -Source_optimizer can be placed at any position where you want to act on the -flux, for instance just after the source. -Monitor_Optimizer should be placed at position(s) to optimize. -I prefer to put one just before the sample. - -Default parameters bins, step, and keep are 10, 10% and 10% respectively. -The option string can be empty (""), which stands for default configuration -that works fine in usual cases: +Principle: The optimizer first (step 1) computes neutron state parameter limits passing in the Source\_Optimizer, and then (step 2) records a Reference source as well as the state (at Source\_Optimizer position) of neutrons reaching Monitor. The optimized source is defined as a fraction of the Reference source plus the distribution of 'good' neutrons reaching the Monitor. The optimization then starts (step 3), and focuses new neutrons on the Monitor\_Optimizer. In fact it changes 'bad' neutrons into 'good' ones (that reach the Monitor), acting on their position, spin and divergence or velocity. The overall Monitor flux is kept during process. The energy and polarisation distributions are kept during optimization as far as possible during optimisation. The optimization method considers that all neutron parameters - (x,y), (vx,vy,vz) or (vx/v2,vy/v2,v2), (sx,sy,sz) or (sx/s2,sy/s2,s2) - are independent. + +Options: The optimized source can be computed regularly ('continuous' option) or only once ('not continuous'). The time spent in steps 1 and 2 can be reduced for a shorter optimization ('auto'). The neutrons passing during steps 1 and 2 can be smoothed for a better neutron weight distribution ('smooth' option). + +Source\_optimizer can be placed at any position where you want to act on the flux, for instance just after the source. Monitor\_Optimizer should be placed at position(s) to optimize. I prefer to put one just before the sample. + +Default parameters bins, step, and keep are 10, 10\% and 10\% respectively. The option string can be empty (""), which stands for default configuration that works fine in usual cases: options="continuous optimization, auto mode, smooth, SetXY+SetDivV+SetDivS" -<b>Possible options are</b> +\textbf{Possible options are} + +\begin{verbatim} continuous for continuous source optimization (default). verbose displays optimization process (debug purpose). auto uses the shortest possible 'step 1' and 'step 2' and sets 'step' value as required (default). smooth remove possible spikes generated in steps 1 and 2 (default is smooth). inactivate to inactivate the Optimizer. no or not revert next option -bins=[value=10] set the Number of cells for sampling neutron states -step=[value=10] Optimizer step in % of simulation. -keep=[value=10] Percentage of initial source distribution that is kept +\end{verbatim} + +bins=[value=10] set the Number of cells for sampling neutron states step=[value=10] Optimizer step in \% of simulation. keep=[value=10] Percentage of initial source distribution that is kept + +\begin{verbatim} file=[name] Filename where to save optimized source distributions (no file is generated if not given. Default ext. is .src) SetXY Keywords to indicate what may be changed during SetV optimisation. Default is position, divergence and spin SetS direction ("SetXY+SetDivV+SetdivS"). Choosing the speed SetDivV or spin optimization (SetV or SetS) may modify the energy SetDivS or polarisation distribution (norm of V and S) as the three components are then independent. +\end{verbatim} Parameters bins, step and keep can also be entered as optional parameters. -<b>EXAMPLE</b>: I use the following settings +\textbf{EXAMPLE}: I use the following settings -optim_s = Source_Optimizer(options="please be clever") (same as empty) -(...) -Monitor_Optimizer(xmin=-0.05, xmax=0.05, ymin=-0.05, ymax=0.05, -optim_comp = "optim_s") +optim\_s = Source\_Optimizer(options="please be clever") (same as empty) (...) Monitor\_Optimizer(xmin=-0.05, xmax=0.05, ymin=-0.05, ymax=0.05, optim\_comp = "optim\_s") -A good optimization needs to record enough non optimized neutrons on Monitor -during step 2. Typical enhancement in computation speed is by a factor 20. -This component usually works well. +A good optimization needs to record enough non optimized neutrons on Monitor during step 2. Typical enhancement in computation speed is by a factor 20. This component usually works well. -<b>NOTE:</b> You must be aware that in some cases (SetV and SetS), -the optimization might sligtly afect the energy or spin distribution of the -source. The optimizer tries to do its best anyway. -Also, some 'spikes' may sometime appear in monitor signals in the course of -the optimization, coming from non-optimized neutrons with original weight. -The 'smooth' option minimises this effect (on by default). -\end{lstlisting} +\textbf{NOTE:} You must be aware that in some cases (SetV and SetS), the optimization might sligtly afect the energy or spin distribution of the source. The optimizer tries to do its best anyway. Also, some 'spikes' may sometime appear in monitor signals in the course of the optimization, coming from non-optimized neutrons with original weight. The 'smooth' option minimises this effect (on by default). \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -99,6 +70,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Source_Optimizer.comp}{Source code} for \texttt{Source\_Optimizer.comp}. + \item Component source code found in file \texttt{Source\_Optimizer.comp}. \end{itemize} -\IfFileExists{Source_Optimizer_static.tex}{\input{Source_Optimizer_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Source_Optimizer_static.tex}{\input{sources/Source_Optimizer_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Source_adapt.tex b/docs/manuals/mcstas/sources/Source_adapt.tex index 849b057e36..952b2d84d6 100644 --- a/docs/manuals/mcstas/sources/Source_adapt.tex +++ b/docs/manuals/mcstas/sources/Source_adapt.tex @@ -3,44 +3,21 @@ \section{The \texttt{Source\_adapt} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kristian Nielsen \item \textbf{Origin:} Risoe \item \textbf{Date:} 1999 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Rectangular source with flat energy or wavelength distribution that -uses adaptive importance sampling to improve simulation efficiency. -Works together with the Adapt_check component. +Rectangular source with flat energy or wavelength distribution that uses adaptive importance sampling to improve simulation efficiency. Works together with the Adapt\_check component. -The source divides the three-dimensional phase space of (energy, -horizontal position, horizontal divergence) into a number of -rectangular bins. The probability for selecting neutrons from each -bin is adjusted so that neutrons that reach the Adapt_check -component with high weights are emitted more frequently than those -with low weights. The adjustment is made so as to attemt to make -the weights at the Adapt_check components equal. +The source divides the three-dimensional phase space of (energy, horizontal position, horizontal divergence) into a number of rectangular bins. The probability for selecting neutrons from each bin is adjusted so that neutrons that reach the Adapt\_check component with high weights are emitted more frequently than those with low weights. The adjustment is made so as to attemt to make the weights at the Adapt\_check components equal. -Focusing is achieved by only emitting neutrons towards a rectangle -perpendicular to and placed at a certain distance along the Z axis. -Focusing is only approximate (for simplicity); neutrons are also -emitted to pass slightly above and below the focusing rectangle, -more so for wider focusing. +Focusing is achieved by only emitting neutrons towards a rectangle perpendicular to and placed at a certain distance along the Z axis. Focusing is only approximate (for simplicity); neutrons are also emitted to pass slightly above and below the focusing rectangle, more so for wider focusing. -In order to prevent false learning, a parameter beta sets a -fraction of the neutrons that are emitted uniformly, without regard -to the adaptive distribution. The parameter alpha sets an initial -fraction of neutrons that are emitted with low weights; this is -done to prevent early neutrons with rare initial parameters but -high weight to ruin the statistics before the component adapts its -distribution to the problem at hand. Good general-purpose values -for these parameters are alpha = beta = 0.25. +In order to prevent false learning, a parameter beta sets a fraction of the neutrons that are emitted uniformly, without regard to the adaptive distribution. The parameter alpha sets an initial fraction of neutrons that are emitted with low weights; this is done to prevent early neutrons with rare initial parameters but high weight to ruin the statistics before the component adapts its distribution to the problem at hand. Good general-purpose values for these parameters are alpha = beta = 0.25. -%VALIDATION -This component is not validated. It does not work properly with MPI. -\end{lstlisting} +\%VALIDATION This component is not validated. It does not work properly with MPI. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -65,9 +42,9 @@ \subsection*{Input parameters} focus\_yh & m & Height of target & 0.1 \\ E0 & meV & Mean energy of neutrons & 0 \\ dE & meV & Energy spread (energy range is from E0-dE to E0+dE) & 0 \\ -lambda0 & AA & Mean wavelength of neutrons (if energy not specified) & 0 \\ -dlambda & AA & Wavelength spread half width & 0 \\ -flux & & (1/(cm 2 AA st)) Absolute source flux & 1e13 \\ +lambda0 & \AA{} & Mean wavelength of neutrons (if energy not specified) & 0 \\ +dlambda & \AA{} & Wavelength spread half width & 0 \\ +flux & & (1/(cm 2 \AA{} st)) Absolute source flux & 1e13 \\ target\_index & 1 & relative index of component to focus at, e.g. next is +1 this is used to compute 'dist' automatically. & 1 \\ alpha & 1 & Learning cut-off factor (0 \textless{} alpha \textless{}= 1) & 0.25 \\ beta & 1 & Aggressiveness of adaptive algorithm (0 \textless{} beta \textless{}= 1) & 0.25 \\ @@ -76,6 +53,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Source_adapt.comp}{Source code} for \texttt{Source\_adapt.comp}. + \item Component source code found in file \texttt{Source\_adapt.comp}. \end{itemize} -\IfFileExists{Source_adapt_static.tex}{\input{Source_adapt_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Source_adapt_static.tex}{\input{sources/Source_adapt_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Source_adapt_static.tex b/docs/manuals/mcstas/sources/Source_adapt_static.tex index 9403175d04..a5b850c9fe 100644 --- a/docs/manuals/mcstas/sources/Source_adapt_static.tex +++ b/docs/manuals/mcstas/sources/Source_adapt_static.tex @@ -22,9 +22,9 @@ \subsection*{A neutron source with adaptive importance sampling} \textbf{Source\_simple} (see section~\ref{source-simple}). The source is a thin rectangle in the $x$-$y$ plane with a flat energy spectrum in a user-specified range. The flux, $\Phi$, per area per steradian per -{\AA}ngstr{\o}m per second is specified by the user. +Ångström per second is specified by the user. -The initial neutron weight is given by Eq. (\ref{proprule}) using +The initial neutron weight is given by Eq. (\ref{e:probrule}) using $\Delta\lambda$ as the total wavelength range of the source. A later version of this component will probably include a $\lambda$-dependence of the flux. @@ -80,7 +80,7 @@ \subsubsection{The adaption algorithm} Compared to a uniform sampling of the phase space (where the probability of each bin is $1/N_\textrm{bin}$), the neutron weight -must be adjusted as given by (\ref{probrule}) +must be adjusted as given by (\ref{e:probrule}) \begin{equation} \pi_1 = \frac{P_1}{f_\textrm{MC,1}} =\frac{1/N_\textrm{bin}}{P(i)} = \frac{\sum_{j=1}^{N_\textrm{bin}} w_j}{N_\textrm{bin} w_i} , diff --git a/docs/manuals/mcstas/sources/Source_div.tex b/docs/manuals/mcstas/sources/Source_div.tex index ef9faee728..c0c0da2a72 100644 --- a/docs/manuals/mcstas/sources/Source_div.tex +++ b/docs/manuals/mcstas/sources/Source_div.tex @@ -3,37 +3,25 @@ \section{The \texttt{Source\_div} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} KL \item \textbf{Origin:} Risoe \item \textbf{Date:} November 20, 1998 \end{itemize} \subsection*{Description} -\begin{lstlisting} -The routine is a rectangular neutron source, which has a gaussian or uniform -divergent output in the forward direction. -The neutron energy is distributed between lambda0-dlambda and -lambda0+dlambda or between E0-dE and E0+dE. The flux unit is specified -in n/cm2/s/st/energy unit (meV or Angs). -In the case of uniform distribution (gauss=0), angles are uniformly distributed -between -focus_aw and +focus_aw as well as -focus_ah and +focus_ah. -For Gaussian distribution (gauss=1), 'focus_aw' and 'focus_ah' define the -FWHM of a Gaussian distribution. Energy/wavelength distribution is also -Gaussian. - -Example: Source_div(xwidth=0.1, yheight=0.1, focus_aw=2, focus_ah=2, E0=14, dE=2, gauss=0) - -%VALIDATION +The routine is a rectangular neutron source, which has a gaussian or uniform divergent output in the forward direction. The neutron energy is distributed between lambda0-dlambda and lambda0+dlambda or between E0-dE and E0+dE. The flux unit is specified in n/cm2/s/st/energy unit (meV or \AA{}). In the case of uniform distribution (gauss=0), angles are uniformly distributed between -focus\_aw and +focus\_aw as well as -focus\_ah and +focus\_ah. For Gaussian distribution (gauss=1), 'focus\_aw' and 'focus\_ah' define the FWHM of a Gaussian distribution. Energy/wavelength distribution is also Gaussian. + +Example: Source\_div(xwidth=0.1, yheight=0.1, focus\_aw=2, focus\_ah=2, E0=14, dE=2, gauss=0) + +\%VALIDATION + +\begin{verbatim} Feb 2005: tested by Kim Lefmann (o.k.) -Apr 2005: energy distribution used in external tests of Fermi choppers (o.k.) -Jun 2005: wavelength distribution used in external tests of velocity selectors (o.k.) -Validated by: K. Lieutenant +\end{verbatim} + +Apr 2005: energy distribution used in external tests of Fermi choppers (o.k.) Jun 2005: wavelength distribution used in external tests of velocity selectors (o.k.) Validated by: K. Lieutenant -%BUGS -distribution is uniform in (hor. and vert.) angle (relative to moderator normal), -therefore not suited for large angles -\end{lstlisting} +\%BUGS distribution is uniform in (hor. and vert.) angle (relative to moderator normal), therefore not suited for large angles \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -49,15 +37,15 @@ \subsection*{Input parameters} \textbf{focus\_ah} & deg & FWHM (Gaussian) or maximal (uniform) vert. height divergence & \\ E0 & meV & Mean energy of neutrons. & 0.0 \\ dE & meV & Energy half spread of neutrons. & 0.0 \\ -lambda0 & Ang & Mean wavelength of neutrons (only relevant for E0=0) & 0.0 \\ -dlambda & Ang & Wavelength half spread of neutrons. & 0.0 \\ +lambda0 & \AA{} & Mean wavelength of neutrons (only relevant for E0=0) & 0.0 \\ +dlambda & \AA{} & Wavelength half spread of neutrons. & 0.0 \\ gauss & 0|1 & Criterion: 0: uniform, 1: Gaussian distributions & 0 \\ -flux & 1/(s cm 2 st energy\_unit) & flux per energy unit, Angs or meV & 1 \\ +flux & 1/(s cm 2 st energy\_unit) & flux per energy unit, \AA{} or meV & 1 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Source_div.comp}{Source code} for \texttt{Source\_div.comp}. + \item Component source code found in file \texttt{Source\_div.comp}. \end{itemize} -\IfFileExists{Source_div_static.tex}{\input{Source_div_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Source_div_static.tex}{\input{sources/Source_div_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Source_div_quasi.tex b/docs/manuals/mcstas/sources/Source_div_quasi.tex index 12ee40e160..ceff6b076d 100644 --- a/docs/manuals/mcstas/sources/Source_div_quasi.tex +++ b/docs/manuals/mcstas/sources/Source_div_quasi.tex @@ -3,31 +3,21 @@ \section{The \texttt{Source\_div\_quasi} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Carlsen and Erik Bergbäck Knudsen (erkn@fysik.dtu.dk) \item \textbf{Origin:} DTU Physics \item \textbf{Date:} Jan 22 \end{itemize} \subsection*{Description} -\begin{lstlisting} -A flat rectangular surface source with uniform or Gaussian divergence profile and focussing. -If the parametere gauss is not set (the default) the divergence profile is flat -in the range [-focus_ax,focus_ay]. If gauss is set, the focux_ax,focus_ay is considered -the standard deviation of the gaussian profile. -Currently focussing is only active for flat profile. The "focus window" is defined by focus_xw,focus_yh and dist. -The spectral intensity profile is uniformly distributed in the energy interval defined by e0+-dE/2 or -by wavelength lambda0+-dlambda/2 +A flat rectangular surface source with uniform or Gaussian divergence profile and focussing. If the parametere gauss is not set (the default) the divergence profile is flat in the range [-focus\_ax,focus\_ay]. If gauss is set, the focux\_ax,focus\_ay is considered the standard deviation of the gaussian profile. Currently focussing is only active for flat profile. The "focus window" is defined by focus\_xw,focus\_yh and dist. The spectral intensity profile is uniformly distributed in the energy interval defined by e0+-dE/2 or by wavelength lambda0+-dlambda/2 -The phase space spanned by the generated neutrons is sampled by means of Halton-sequences, instead of regular -pseudo random numbers. This ensures that samples are evenly distributed within the phase space region of interest. +The phase space spanned by the generated neutrons is sampled by means of Halton-sequences, instead of regular pseudo random numbers. This ensures that samples are evenly distributed within the phase space region of interest. -Example: Source_div_quasi(xwidth=0.1, yheight=0.1, focus_aw=2, focus_ah=2, E0=14, dE=2, gauss=0) +Example: Source\_div\_quasi(xwidth=0.1, yheight=0.1, focus\_aw=2, focus\_ah=2, E0=14, dE=2, gauss=0) -%VALIDATION +\%VALIDATION -%BUGS -\end{lstlisting} +\%BUGS \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -47,9 +37,9 @@ \subsection*{Input parameters} focus\_ah & rad & Std. dev. (Gaussian) or maximal (uniform) vert. height divergence. focus\_yh overrrides if it is more restrictive. & 0 \\ E0 & meV & Mean energy of neutrons. & 0 \\ dE & meV & Energy spread of neutrons. & 0 \\ -lambda0 & AA & Mean wavelength of neutrons (only relevant for E0=0) & 0 \\ -dlambda & AA & Wavelength half spread of neutrons. & 0 \\ -flux & 1/(s*cm**2*st*energy unit) & Flux per energy unit, Angs or meV & 0 \\ +lambda0 & \AA{} & Mean wavelength of neutrons (only relevant for E0=0) & 0 \\ +dlambda & \AA{} & Wavelength half spread of neutrons. & 0 \\ +flux & 1/(s*cm**2*st*energy unit) & Flux per energy unit, \AA{} or meV & 0 \\ gauss & 1 & Criterion: 0: uniform, 1: Gaussian distribution of energy/wavelength & 0 \\ gauss\_a & 1 & Criterion: 0: uniform, 1: Gaussian divergence distribution & 0 \\ randomphase & & When=1, the X-ray phase is randomised & 1 \\ @@ -60,6 +50,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Source_div_quasi.comp}{Source code} for \texttt{Source\_div\_quasi.comp}. + \item Component source code found in file \texttt{Source\_div\_quasi.comp}. \end{itemize} -\IfFileExists{Source_div_quasi_static.tex}{\input{Source_div_quasi_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Source_div_quasi_static.tex}{\input{sources/Source_div_quasi_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Source_gen.tex b/docs/manuals/mcstas/sources/Source_gen.tex index e96644e21f..432eded93f 100644 --- a/docs/manuals/mcstas/sources/Source_gen.tex +++ b/docs/manuals/mcstas/sources/Source_gen.tex @@ -4,55 +4,27 @@ \section{The \texttt{Source\_gen} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Emmanuel Farhi, Kim Lefmann \item \textbf{Origin:} ILL/Risoe \item \textbf{Date:} Aug 27, 2001 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This routine is a neutron source (rectangular or circular), which aims at -a square target centered at the beam (in order to improve MC-acceptance -rate). The angular divergence is then given by the dimensions of the -target. However, it may be directly set using the 'focus-aw' and 'focus_ah' -parameters. +This routine is a neutron source (rectangular or circular), which aims at a square target centered at the beam (in order to improve MC-acceptance rate). The angular divergence is then given by the dimensions of the target. However, it may be directly set using the 'focus-aw' and 'focus\_ah' parameters. -The neutron energy/wavelength is distributed uniformly in wavelength between -Emin=E0-dE and Emax=E0+dE or Lmin=lambda0-dlambda and Lmax=lambda0+dlambda. -The I1 may be either arbitrary (I1=0), or specified in neutrons per steradian -per square cm per Angstrom per s. A Maxwellian spectra may be selected if you -give the source temperatures (up to 3). +The neutron energy/wavelength is distributed uniformly in wavelength between Emin=E0-dE and Emax=E0+dE or Lmin=lambda0-dlambda and Lmax=lambda0+dlambda. The I1 may be either arbitrary (I1=0), or specified in neutrons per steradian per square cm per \AA{} per s. A Maxwellian spectra may be selected if you give the source temperatures (up to 3). -Finally, a file with the flux as a -function of the wavelength [lambda(AA) flux(n/s/cm^2/st/AA)] may be used -with the 'flux_file' parameter. Format is 2 columns free text. +Finally, a file with the flux as a function of the wavelength [lambda(\AA{}) flux(n/s/cm\textasciicircum{}2/st/\AA{})] may be used with the 'flux\_file' parameter. Format is 2 columns free text. -Additional distributions for the horizontal and vertical phase spaces -distributions (position-divergence) may be specified with the -'xdiv_file' and 'ydiv_file' parameters. Format is free text, requiring -a comment line '# xylimits: pos_min pos_max div_min div_max' to set -the axis of the distribution matrix. All these files may be generated using -standard monitors (better in McStas/PGPLOT format), e.g.: -Monitor_nD(options="auto lambda per cm2") -Monitor_nD(options="x hdiv, all auto") -Monitor_nD(options="y vdiv, all auto") +Additional distributions for the horizontal and vertical phase spaces distributions (position-divergence) may be specified with the 'xdiv\_file' and 'ydiv\_file' parameters. Format is free text, requiring a comment line '\# xylimits: pos\_min pos\_max div\_min div\_max' to set the axis of the distribution matrix. All these files may be generated using standard monitors (better in McStas/PGPLOT format), e.g.: Monitor\_nD(options="auto lambda per cm2") Monitor\_nD(options="x hdiv, all auto") Monitor\_nD(options="y vdiv, all auto") -The source shape is defined by its radius, or can alternatively be squared -if you specify non-zero yheight and xwidth parameters. -The beam is divergence uniform,. -The source may have a thickness, which will broaden the default zero time -distribution. +The source shape is defined by its radius, or can alternatively be squared if you specify non-zero yheight and xwidth parameters. The beam is divergence uniform,. The source may have a thickness, which will broaden the default zero time distribution. -Usage example: -Source_gen(radius=0.1,lambda0=2.36,dlambda=0.16,T1=20,I1=1e13,focus_xw=0.01,focus_yh=0.01) -Source_gen(yheight=0.1,xwidth=0.1,Emin=1,Emax=3,I1=1e13,verbose=1,focus_xw=0.01,focus_yh=0.01) -EXTEND -%{ -t = rand0max(1e-3); // set time from 0 to 1 ms for TOF instruments. -%} +Usage example: Source\_gen(radius=0.1,lambda0=2.36,dlambda=0.16,T1=20,I1=1e13,focus\_xw=0.01,focus\_yh=0.01) Source\_gen(yheight=0.1,xwidth=0.1,Emin=1,Emax=3,I1=1e13,verbose=1,focus\_xw=0.01,focus\_yh=0.01) EXTEND \%\{ t = rand0max(1e-3); // set time from 0 to 1 ms for TOF instruments. \%\} -<b>Some neutron facility parameters:</b> +\textbf{Some neutron facility parameters:} + +\begin{verbatim} PSI cold source T1=296.2,I1=8.5E11, T2=40.68,I2=5.2E11 ILL VCS cold source T1=216.8,I1=1.24e+13,T2=33.9,I2=1.02e+13 (H1, 58 MW) T3=16.7 ,I3=3.0423e+12 @@ -68,12 +40,9 @@ \subsection*{Description} FRM2 thermal,20MW T1=285.6,I1=3.06e13,T2=300.0,I2=1.68e12,T3=429.9,I3=6.77e12 LLB cold,14MW T1=220, I1=2.09e12,T2=60, I2=3.83e12,T3=20, I3=1.04e12 TRIGA thermal 1MW T1=300, I1=3.5e11 (scale by thermal power in MW) +\end{verbatim} -%VALIDATION -Feb 2005: output cross-checked for 3 Maxwellians against VITESS source -I(lambda), I(hor_div), I(vert_div) identical in shape and absolute values -Validated by: K. Lieutenant -\end{lstlisting} +\%VALIDATION Feb 2005: output cross-checked for 3 Maxwellians against VITESS source I(lambda), I(hor\_div), I(vert\_div) identical in shape and absolute values Validated by: K. Lieutenant \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -83,7 +52,7 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -flux\_file & str & Name of a two columns [lambda flux] text file that contains the wavelength distribution of the flux in \textless{}b\textgreater{}either\textless{}/b\textgreater{} [1/(s*cm**2*st)] \textless{}b\textgreater{}or\textless{}/b\textgreater{} [1/(s*cm**2*st*AA)] (see flux\_file\_perAA flag) Comments (\#) and further columns are ignored. Format is compatible with McStas/PGPLOT wavelength monitor files. When specified, temperature and intensity values are ignored. & "NULL" \\ +flux\_file & str & Name of a two columns [lambda flux] text file that contains the wavelength distribution of the flux in \textless{}b\textgreater{}either\textless{}/b\textgreater{} [1/(s*cm**2*st)] \textless{}b\textgreater{}or\textless{}/b\textgreater{} [1/(s*cm**2*st*\AA{})] (see flux\_file\_perAA flag) Comments (\#) and further columns are ignored. Format is compatible with McStas/PGPLOT wavelength monitor files. When specified, temperature and intensity values are ignored. & "NULL" \\ xdiv\_file & str & Name of the x-horiz. divergence distribution file, given as a free format text matrix, preceeded with a line '\# xylimits: xmin xmax xdiv\_min xdiv\_max' & "NULL" \\ ydiv\_file & str & Name of the y-vert. divergence distribution file, given as a free format text matrix, preceeded with a line '\# xylimits: ymin ymax ydiv\_min ydiv\_max' & "NULL" \\ radius & m & Radius of circle in (x,y,0) plane where neutrons are generated. You may also use 'yheight' and 'xwidth' for a square source & 0.0 \\ @@ -94,17 +63,17 @@ \subsection*{Input parameters} focus\_ah & deg & maximal (uniform) vert. height divergence & 0 \\ E0 & meV & Mean energy of neutrons. & 0 \\ dE & meV & Energy spread of neutrons, half width. & 0 \\ -lambda0 & AA & Mean wavelength of neutrons. & 0 \\ -dlambda & AA & Wavelength spread of neutrons,half width & 0 \\ -I1 & 1/(cm**2*sr) & Source flux per solid angle, area and Angstrom if I1=0, the source emits 1 in 4*PI whole space. & 1 \\ +lambda0 & \AA{} & Mean wavelength of neutrons. & 0 \\ +dlambda & \AA{} & Wavelength spread of neutrons,half width & 0 \\ +I1 & 1/(cm**2*sr) & Source flux per solid angle, area and \AA{} if I1=0, the source emits 1 in 4*PI whole space. & 1 \\ yheight & m & Source y-height, then does not use radius parameter & 0.1 \\ xwidth & m & Source x-width, then does not use radius parameter & 0.1 \\ verbose & 0/1 & display info about the source. -1 inactivate source. & 0 \\ T1 & K & Temperature of the Maxwellian source, 0=none & 0 \\ flux\_file\_perAA & 1 & When true (1), indicates that flux file data is already per Aangstroem. If false, file data is per wavelength bin. & 0 \\ flux\_file\_log & 1 & When true, will transform the flux table in log scale to improve the sampling. & 0 \\ -Lmin & AA & Minimum wavelength of neutrons & 0 \\ -Lmax & AA & Maximum wavelength of neutrons & 0 \\ +Lmin & \AA{} & Minimum wavelength of neutrons & 0 \\ +Lmax & \AA{} & Maximum wavelength of neutrons & 0 \\ Emin & meV & Minimum energy of neutrons & 0 \\ Emax & meV & Maximum energy of neutrons & 0 \\ T2 & K & Second Maxwellian source Temperature, 0=none & 0 \\ @@ -118,7 +87,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Source_gen.comp}{Source code} for \texttt{Source\_gen.comp}. + \item Component source code found in file \texttt{Source\_gen.comp}. \item P. Ageron, Nucl. Inst. Meth. A 284 (1989) 197 \end{itemize} -\IfFileExists{Source_gen_static.tex}{\input{Source_gen_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Source_gen_static.tex}{\input{sources/Source_gen_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/sources/Source_simple.tex b/docs/manuals/mcstas/sources/Source_simple.tex index 216ae68383..87244524e3 100644 --- a/docs/manuals/mcstas/sources/Source_simple.tex +++ b/docs/manuals/mcstas/sources/Source_simple.tex @@ -3,26 +3,17 @@ \section{The \texttt{Source\_simple} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Kim Lefmann \item \textbf{Origin:} Risoe \item \textbf{Date:} October 30, 1997 \end{itemize} \subsection*{Description} -\begin{lstlisting} -The routine is a circular neutron source, which aims at a square target -centered at the beam (in order to improve MC-acceptance rate). The angular -divergence is then given by the dimensions of the target. -The neutron energy is uniformly distributed between lambda0-dlambda and -lambda0+dlambda or between E0-dE and E0+dE. -The flux unit is specified in n/cm2/s/st/energy unit (meV or Angs). +The routine is a circular neutron source, which aims at a square target centered at the beam (in order to improve MC-acceptance rate). The angular divergence is then given by the dimensions of the target. The neutron energy is uniformly distributed between lambda0-dlambda and lambda0+dlambda or between E0-dE and E0+dE. The flux unit is specified in n/cm2/s/st/energy unit (meV or \AA{}). -This component replaces Source_flat, Source_flat_lambda, -Source_flux and Source_flux_lambda. +This component replaces Source\_flat, Source\_flat\_lambda, Source\_flux and Source\_flux\_lambda. -Example: Source_simple(radius=0.1, dist=2, focus_xw=.1, focus_yh=.1, E0=14, dE=2) -\end{lstlisting} +Example: Source\_simple(radius=0.1, dist=2, focus\_xw=.1, focus\_yh=.1, E0=14, dE=2) \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,9 +31,9 @@ \subsection*{Input parameters} focus\_yh & m & Height of target & .12 \\ E0 & meV & Mean energy of neutrons. & 0 \\ dE & meV & Energy half spread of neutrons (flat or gaussian sigma). & 0 \\ -lambda0 & AA & Mean wavelength of neutrons. & 0 \\ -dlambda & AA & Wavelength half spread of neutrons. & 0 \\ -flux & 1/(s*cm**2*st*energy unit) & flux per energy unit, Angs or meV if flux=0, the source emits 1 in 4*PI whole space. & 1 \\ +lambda0 & \AA{} & Mean wavelength of neutrons. & 0 \\ +dlambda & \AA{} & Wavelength half spread of neutrons. & 0 \\ +flux & 1/(s*cm**2*st*energy unit) & flux per energy unit, \AA{} or meV if flux=0, the source emits 1 in 4*PI whole space. & 1 \\ gauss & 1 & Gaussian (1) or Flat (0) energy/wavelength distribution & 0 \\ target\_index & 1 & relative index of component to focus at, e.g. next is +1 this is used to compute 'dist' automatically. & 1 \\ \bottomrule @@ -50,6 +41,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/sources/Source_simple.comp}{Source code} for \texttt{Source\_simple.comp}. + \item Component source code found in file \texttt{Source\_simple.comp}. \end{itemize} -\IfFileExists{Source_simple_static.tex}{\input{Source_simple_static.tex}}{} \ No newline at end of file +\IfFileExists{sources/Source_simple_static.tex}{\input{sources/Source_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/techniq.tex b/docs/manuals/mcstas/techniq.tex index 881375d94f..ebb73a964c 100644 --- a/docs/manuals/mcstas/techniq.tex +++ b/docs/manuals/mcstas/techniq.tex @@ -1,7 +1,7 @@ \chapter{Monte Carlo Techniques and simulation strategy} \label{s:MCtechniques}\index{Monte Carlo method} -\newcommand{\Ombold}{\mbox{\boldmath $\Omega$}} +\newcommand{\Ombold}{\boldsymbol{\Omega}} This chapter explains the simulation strategy and the Monte Carlo techniques used in \MCS. We first explain the concept of the neutron diff --git a/docs/manuals/mcstas/title.tex b/docs/manuals/mcstas/title.tex.in similarity index 74% rename from docs/manuals/mcstas/title.tex rename to docs/manuals/mcstas/title.tex.in index b39d2ee3df..2885793768 100644 --- a/docs/manuals/mcstas/title.tex +++ b/docs/manuals/mcstas/title.tex.in @@ -1,8 +1,4 @@ -\title{User and Programmers Guide to the Neutron Ray-Tracing Package \MCS ,\\ version \version\\[15mm] - \begin{center} - \includegraphics[width=50mm]{figures/mcstas_logo_reflection.png}\\[4mm] - \end{center} - } +\title{User and Programmers Guide to the Neutron Ray-Tracing Package McStas, version @MCCODE_VERSION@} \author{P. Willendrup, E. Farhi, K. Lefmann} \date{\reldate} @@ -15,6 +11,9 @@ Technical University of Denmark\\% 2800 Kongens Lyngby, Denmark \end{minipage} +\begin{minipage}{50mm} +\includegraphics[width=50mm]{figures/mcstas_logo_reflection.png} +\end{minipage} } %\subject{} %\subtitle{} diff --git a/docs/manuals/mcstas/title_comp.tex b/docs/manuals/mcstas/title_comp.tex.in similarity index 65% rename from docs/manuals/mcstas/title_comp.tex rename to docs/manuals/mcstas/title_comp.tex.in index 224e1fde2a..b5dc5bdd4f 100644 --- a/docs/manuals/mcstas/title_comp.tex +++ b/docs/manuals/mcstas/title_comp.tex.in @@ -1,8 +1,4 @@ -\title{Component Manual for the Neutron Ray-Tracing Package \MCS ,\\ version \version\\[15mm] - \begin{center} - \includegraphics[width=50mm]{figures/mcstas_logo_reflection}\\[4mm] - \end{center} - } +\title{Component Manual for the Neutron Ray-Tracing Package McStas, version @MCCODE_VERSION@} \author{P. Willendrup, E. Farhi, E. Knudsen, K. Lefmann\\ } \date{\reldate} @@ -16,6 +12,9 @@ Technical University of Denmark\\% 2800 Kongens Lyngby, Denmark \end{minipage} +\begin{minipage}{50mm} +\includegraphics[width=50mm]{figures/mcstas_logo_reflection} +\end{minipage} } %\subject{} %\subtitle{} diff --git a/docs/manuals/mcstas/union/AF_HB_1D_process.tex b/docs/manuals/mcstas/union/AF_HB_1D_process.tex index cd42531570..1fcc0e6317 100644 --- a/docs/manuals/mcstas/union/AF_HB_1D_process.tex +++ b/docs/manuals/mcstas/union/AF_HB_1D_process.tex @@ -3,34 +3,23 @@ \section{The \texttt{AF\_HB\_1D\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} 1D Antiferromagnetic Heisenberg chain -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components - -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,9 +29,9 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -atom\_distance & AA & Distance between atom's in chain & 1 \\ -number\_density & 1/AA\textasciicircum{}3 & Number of scatteres per volume & 0 \\ -unit\_cell\_volume & AA\textasciicircum{}3 & Unit cell volume (set either unit\_cell\_volume or number density) & 0 \\ +atom\_distance & \AA{} & Distance between atom's in chain & 1 \\ +number\_density & 1/\AA{}$^{3}$ & Number of scatteres per volume & 0 \\ +unit\_cell\_volume & \AA{}$^{3}$ & Unit cell volume (set either unit\_cell\_volume or number density) & 0 \\ A\_constant & unitless & Constant from M\üller paper 1981, probably somewhere between 1 and 1.5 & 1 \\ J\_interaction & meV & Exchange constant & 1 \\ packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ @@ -53,6 +42,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/AF_HB_1D_process.comp}{Source code} for \texttt{AF\_HB\_1D\_process.comp}. + \item Component source code found in file \texttt{AF\_HB\_1D\_process.comp}. \end{itemize} -\IfFileExists{AF_HB_1D_process_static.tex}{\input{AF_HB_1D_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/AF_HB_1D_process_static.tex}{\input{union/AF_HB_1D_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/IncoherentPhonon_process.tex b/docs/manuals/mcstas/union/IncoherentPhonon_process.tex index 255f081642..6f0c52c549 100644 --- a/docs/manuals/mcstas/union/IncoherentPhonon_process.tex +++ b/docs/manuals/mcstas/union/IncoherentPhonon_process.tex @@ -5,27 +5,17 @@ \section{The \texttt{IncoherentPhonon\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Victor Laliena \item \textbf{Origin:} University of Zaragoza \item \textbf{Date:} 06.11.2018 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -expects geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus expects geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above - -Algorithm: -Described elsewhere, see e.g. <a href="https://doi.org/10.3233/JNR-190117">https://doi.org/10.3233/JNR-190117</a> -\end{lstlisting} +Algorithm: Described elsewhere, see e.g. \htmladdnormallink{https://doi.org/10.3233/JNR-190117}{https://doi.org/10.3233/JNR-190117} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -36,7 +26,7 @@ \subsection*{Input parameters} \midrule \endhead T & K & Temperature & 394 \\ -density & g/cm3 & Material density & 6.0 \\ +density & g/cm$^{3}$ & Material density & 6.0 \\ M & amu & ion mass & 50.94 \\ sigmaCoh & barns & Coherent scattering cross section & 0.0184 \\ sigmaInc & barns & Incoherent scattering cross section & 5.08 \\ @@ -46,8 +36,8 @@ \subsection*{Input parameters} approx & 1 & Approximation type: 0 gaussian, 1 saddle point & 0 \\ mph\_resum & 0/1 & Resumate the remaining terms of the phonon expansion via a saddle point: 0 No, 1 Yes & 0 \\ nxs & 1 & Number of energy points at which the total cross sections are precomputed & 1000 \\ -kabsmin & A\textasciicircum{}-1 & Lower cut-off for the neutron wave-vector k & 0.1 \\ -kabsmax & A\textasciicircum{}-1 & Higher cut-off for the neutron wave-vector k & 25 \\ +kabsmin & A$^{-1}$ & Lower cut-off for the neutron wave-vector k & 0.1 \\ +kabsmax & A$^{-1}$ & Higher cut-off for the neutron wave-vector k & 25 \\ interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ \bottomrule @@ -55,7 +45,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/IncoherentPhonon_process.comp}{Source code} for \texttt{IncoherentPhonon\_process.comp}. - \item See \textless{}a href="https://doi.org/10.3233/JNR-190117"\textgreater{}https://doi.org/10.3233/JNR-190117\textless{}/a\textgreater{} + \item Component source code found in file \texttt{IncoherentPhonon\_process.comp}. + \item See \htmladdnormallink{https://doi.org/10.3233/JNR-190117}{https://doi.org/10.3233/JNR-190117} \end{itemize} -\IfFileExists{IncoherentPhonon_process_static.tex}{\input{IncoherentPhonon_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/IncoherentPhonon_process_static.tex}{\input{union/IncoherentPhonon_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Incoherent_process.tex b/docs/manuals/mcstas/union/Incoherent_process.tex index 51f2c2bd74..1c8a25cb91 100644 --- a/docs/manuals/mcstas/union/Incoherent_process.tex +++ b/docs/manuals/mcstas/union/Incoherent_process.tex @@ -3,34 +3,23 @@ \section{The \texttt{Incoherent\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This Union_process is based on the Incoherent.comp component originally written -by Kim Lefmann and Kristian Nielsen +This Union\_process is based on the Incoherent.comp component originally written by Kim Lefmann and Kristian Nielsen -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -44,7 +33,7 @@ \subsection*{Input parameters} f\_QE & 1 & Fraction of quasielastic scattering (rest is elastic) [1] & 0 \\ gamma & meV & Lorentzian width of quasielastic broadening (HWHM) [1] & 0 \\ packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ -unit\_cell\_volume & AA\textasciicircum{}3 & Unit cell volume & 13.8 \\ +unit\_cell\_volume & \AA{}$^{3}$ & Unit cell volume & 13.8 \\ interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ init & string & name of Union\_init component (typically "init", default) & "init" \\ \bottomrule @@ -52,7 +41,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Incoherent_process.comp}{Source code} for \texttt{Incoherent\_process.comp}. - \item The test/example instrument \textless{}a href="../examples/Test\_Phonon.instr"\textgreater{}Test\_Phonon.instr\textless{}/a\textgreater{}. + \item Component source code found in file \texttt{Incoherent\_process.comp}. + \item The test/example instrument \htmladdnormallink{Test\_Phonon.instr}{../examples/Test\_Phonon.instr}. \end{itemize} -\IfFileExists{Incoherent_process_static.tex}{\input{Incoherent_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Incoherent_process_static.tex}{\input{union/Incoherent_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Inhomogenous_incoherent_process.tex b/docs/manuals/mcstas/union/Inhomogenous_incoherent_process.tex new file mode 100644 index 0000000000..7a8557e03f --- /dev/null +++ b/docs/manuals/mcstas/union/Inhomogenous_incoherent_process.tex @@ -0,0 +1,97 @@ +\section{The \texttt{Inhomogenous\_incoherent\_process} McStas Component} +A sample component to separate geometry and phsysics + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Daniel Lomholt Christensen + \item \textbf{Origin:} University of Copenhagen + \item \textbf{Date:} 26/01/2026 +\end{itemize} + +\subsection*{Description} +This Union\_process is based on the Incoherent\_process.comp component originally written by Mads Bertelsen inspired by Kim Lefmann and Kristian Nielsen + +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union components + +Algorithm: The general algorithm for the Union system is described elsewhere. + +I here give a brief introduction as to what changes occur when using an inhomogenous process in your Union make material. It is expected that you understand the basic algorithm of the Union system before reading this. + +In Union, the neutron moves through a network of objects in a 3 dimensional world. When the neutron hits a material, the probability to scatter is calculated, and a Monte Carlo choice is taken, as to whether that neutron should scatter, or pass through. For a homogenous material (i.e constant attenuation coefficient \textless{}span class="latex"\textgreater{}\$\textbackslash{}mu\$\textless{}/span\textgreater{}), this probability is the Beer-Lambert law, + +\textless{}div class="latex"\textgreater{} + +\begin{verbatim} +$P_s = 1 - e^{-\mu l}$ +\end{verbatim} + +\textless{}/div\textgreater{} + +Where \textless{}span class="latex"\textgreater{}\$P\_s\$\textless{}/span\textgreater{} is the scattering probability, and \textless{}span class="latex"\textgreater{}\$l\$\textless{}/span\textgreater{} is length of the neutron path throughout the object. + +For an inhomogenous material, this Beer-Lambert law must be modified, as \textless{}span class="latex"\textgreater{}\$\textbackslash{}mu\$\textless{}/span\textgreater{} is a function of the position. Therefore the Beer-Lambert law becomes, + +\textless{}div class="latex"\textgreater{} + +\begin{verbatim} +$P_s = \int^l_0 1 - e^{-\mu(l')l'}dl'$ +\end{verbatim} + +\textless{}/div\textgreater{} + +Calculating this \textless{}span class="latex"\textgreater{}\$\textbackslash{}mu\$\textless{}/span\textgreater{} in the inhomogenous case is often trivial, but not feasible, from a software development point of view (seeing as many different functions of \textless{}span class="latex"\textgreater{}\$\textbackslash{}mu\$\textless{}/span\textgreater{} might be wanted). Instead the inhomogenous processes performs an approximate integral, by evaluating \textless{}span class="latex"\textgreater{}\$\textbackslash{}mu\$\textless{}/span\textgreater{} at a number of points along the neutron path (This number is in fact number\_of\_sample\_points). + +For this incoherent process, the linear attenuation coefficient is, + +\textless{}div class="latex"\textgreater{} \$\textbackslash{}mu = pack/V\_u * 100 * \textbackslash{}sigma\$ \textless{}/div\textgreater{} + +Where \textless{}span class="latex"\textgreater{}\$pack\$\textless{}/span\textgreater{} is the packing factor of the material (defaults to 1), \textless{}span class="latex"\textgreater{}\$V\_u\$\textless{}/span\textgreater{} is the Unit cell volume, and \textless{}span class="latex"\textgreater{}\$\textbackslash{}sigma\$\textless{}/span\textgreater{} is the scattering cross section in barns. \textless{}span class="latex"\textgreater{}\$\textbackslash{}mu\$\textless{}/span\textgreater{} therefore has units of \textless{}span class="latex"\textgreater{}\$m\textasciicircum{}\{-1\}\$\textless{}/span\textgreater{}. + +For this component each factor in the attenuation coefficient can be a "tiny expression". This means that it can be a mathematical equation such as \textless{}span class="latex"\textgreater{}\$\textbackslash{}sigma\_\{expr\} = "5.08 + 1000 * z * 2.35"\$\textless{}/span\textgreater{}. When the attenuation coefficient is calculated, then the current value of \textless{}span class="latex"\textgreater{}\$z\$\textless{}/span\textgreater{} is used to get \textless{}span class="latex"\textgreater{}\$\textbackslash{}sigma\$\textless{}/span\textgreater{}. + +The parameters that the tiny expression can rely upon are currently: The positions, \textless{}span class="latex"\textgreater{}\$x, y, z\$\textless{}/span\textgreater{} The velocities \textless{}span class="latex"\textgreater{}\$vx, vy, vz\$\textless{}/span\textgreater{} and the time \textless{}span class="latex"\textgreater{}\$t\$\textless{}/span\textgreater{} + +McStas uses a sligthly modified version of tiny expressions that evaluate exponentials from right to left instead of the standard left to right. Furthermore McStas has added two functions to tiny expressions. These are: A heavy side function hvs(variable, switch\_point, large\_val,small\_val) which returns large val if variable \textgreater{} switch\_point and small val otherwise. + +A gaussian distribution: + +gauss(A,sig,x), which evaluates to A*1/sqrt(2*PI)/sig*exp(-x\textasciicircum{}2/2/sig\textasciicircum{}2) + +An example using these can be found in the Test instrument for this component, called Test\_inhomogenous\_process.instr. Example \#9 implements a gaussian and a heavyside function. For more information on tiny expressions, see the link below. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sigma & barns & Incoherent scattering cross section & 0 \\ +sigma\_expr & string & Tiny expression to be calculated as replacement for sigma & "" \\ +packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ +packing\_factor\_expr & string & Tiny expression to be calculated as replacement for packing factor & "" \\ +unit\_cell\_volume & \AA{}$^{3}$ & Unit cell volume & 0 \\ +unit\_cell\_volume\_expr & string & Tiny expression to be calculated as replacement for the unit cell volume & "" \\ +gamma & meV & Lorentzian width of quasielastic broadening (HWHM) [1] & 0 \\ +gamma\_expr & meV & Tiny expression to be calculated as replacement for the gamma value. & "" \\ +f\_QE & 1 & Fraction of quasielastic scattering (rest is elastic) [1] & 0 \\ +number\_of\_sample\_points & 1 & Number of points that are sampled along the neutron path through a material & 20 \\ +interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ +verbose & 1 & Flag that prints out the values calculated in the cross section calculation & 0 \\ +init & string & name of Union\_init component (typically "init", default) & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Inhomogenous\_incoherent\_process.comp}. + \item For information on how to write a tiny expression, see \htmladdnormallink{their github repository}{https://github.com/codeplea/tinyexpr} +\end{itemize} +\IfFileExists{union/Inhomogenous_incoherent_process_static.tex}{\input{union/Inhomogenous_incoherent_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Mirror_surface.tex b/docs/manuals/mcstas/union/Mirror_surface.tex index c6d564c91e..458f9fd68c 100644 --- a/docs/manuals/mcstas/union/Mirror_surface.tex +++ b/docs/manuals/mcstas/union/Mirror_surface.tex @@ -3,39 +3,23 @@ \section{The \texttt{Mirror\_surface} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This is a Union surface process that describes a supermirror or other surface -that only have specular reflection. The reflectivity can be given as a file -or using the standard reflectivity inputs. To use this in a simulation an -instance of this component should be defined in the instrument file, then -attatched to one or more geometries in their surface stacks pertaining to -each face of the geometry. +This is a Union surface process that describes a supermirror or other surface that only have specular reflection. The reflectivity can be given as a file or using the standard reflectivity inputs. To use this in a simulation an instance of this component should be defined in the instrument file, then attatched to one or more geometries in their surface stacks pertaining to each face of the geometry. -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components - -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -45,18 +29,18 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -reflect & str & Name of reflectivity file. Format q(Angs-1) R(0-1) & 0 \\ +reflect & str & Name of reflectivity file. Format q(\AA{}-1) R(0-1) & 0 \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qc & AA-1 & Critical scattering vector & 0.0219 \\ -alpha & AA & Slope of reflectivity & 6.07 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0219 \\ +alpha & \AA{} & Slope of reflectivity & 6.07 \\ m & 1 & m-value of material. Zero means completely absorbing. & 2 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Mirror_surface.comp}{Source code} for \texttt{Mirror\_surface.comp}. + \item Component source code found in file \texttt{Mirror\_surface.comp}. \end{itemize} -\IfFileExists{Mirror_surface_static.tex}{\input{Mirror_surface_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Mirror_surface_static.tex}{\input{union/Mirror_surface_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/NCrystal_process.tex b/docs/manuals/mcstas/union/NCrystal_process.tex index cfe16c3f3f..94270d1e49 100644 --- a/docs/manuals/mcstas/union/NCrystal_process.tex +++ b/docs/manuals/mcstas/union/NCrystal_process.tex @@ -3,52 +3,27 @@ \section{The \texttt{NCrystal\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} NCrystal developers, converted to a Union component by Mads Bertelsen \item \textbf{Origin:} NCrystal Developers (European Spallation Source ERIC and DTU Nutech) \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This process uses the NCrystal library as a Union process, see user documentation -for the NCrystal_sample.comp component for more information. The process only -uses the physics, as the Union components has a separate geometry system. -Absorption is also handled by Union, so any absorption output from NCrystal -is ignored. +This process uses the NCrystal library as a Union process, see user documentation for the NCrystal\_sample.comp component for more information. The process only uses the physics, as the Union components has a separate geometry system. Absorption is also handled by Union, so any absorption output from NCrystal is ignored. -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components +Original header text for NCrystal\_sample.comp: McStas sample component for the NCrystal scattering library. Find more information at \htmladdnormallink{the NCrystal wiki}{https://github.com/mctools/ncrystal/wiki}. In particular, browse the available datafiles at \htmladdnormallink{Data-library}{https://github.com/mctools/ncrystal/wiki/Data-library} and read about format of the configuration string expected in the "cfg" parameter at \htmladdnormallink{Using-NCrystal}{https://github.com/mctools/ncrystal/wiki/Using-NCrystal}. -Original header text for NCrystal_sample.comp: -McStas sample component for the NCrystal scattering library. Find more -information at <a href="https://github.com/mctools/ncrystal/wiki">the NCrystal -wiki</a>. In particular, browse the available datafiles at <a -href="https://github.com/mctools/ncrystal/wiki/Data-library">Data-library</a> -and read about format of the configuration string expected in the "cfg" -parameter at <a href="https://github.com/mctools/ncrystal/wiki/Using-NCrystal">Using-NCrystal</a>. +\textless{}p/\textgreater{}NCrystal is available under the \htmladdnormallink{Apache 2.0 license}{http://www.apache.org/licenses/LICENSE-2.0}. Depending on the configuration choices, optional NCrystal modules under different licenses might be enabled - see \htmladdnormallink{About}{https://github.com/mctools/ncrystal/wiki/About} for more details. -<p/>NCrystal is available under the <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license</a>. Depending -on the configuration choices, optional NCrystal modules under different -licenses might be enabled - see <a -href="https://github.com/mctools/ncrystal/wiki/About">About</a> for more -details. - -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -59,7 +34,6 @@ \subsection*{Input parameters} \midrule \endhead cfg & str & NCrystal material configuration string (details \textless{}a href="https://github.com/mctools/ncrystal/wiki/Using-NCrystal"\textgreater{}on this page\textless{}/a\textgreater{}). & "" \\ -packing\_factor & 1 & Material packing factor & 1 \\ interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ \bottomrule @@ -67,6 +41,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/NCrystal_process.comp}{Source code} for \texttt{NCrystal\_process.comp}. + \item Component source code found in file \texttt{NCrystal\_process.comp}. \end{itemize} -\IfFileExists{NCrystal_process_static.tex}{\input{NCrystal_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/NCrystal_process_static.tex}{\input{union/NCrystal_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Non_process.tex b/docs/manuals/mcstas/union/Non_process.tex index 44a4f90bb6..03690fecae 100644 --- a/docs/manuals/mcstas/union/Non_process.tex +++ b/docs/manuals/mcstas/union/Non_process.tex @@ -3,34 +3,23 @@ \section{The \texttt{Non\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} This process dos nothing and is used for testing -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components - -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,7 +31,7 @@ \subsection*{Input parameters} \endhead sigma & barns & Scattering cross section & 5.08 \\ packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ -unit\_cell\_volume & AA\textasciicircum{}3 & Unit cell volume & 13.8 \\ +unit\_cell\_volume & \AA{}$^{3}$ & Unit cell volume & 13.8 \\ interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ init & string & name of Union\_init component (typically "init", default) & "init" \\ \bottomrule @@ -50,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Non_process.comp}{Source code} for \texttt{Non\_process.comp}. + \item Component source code found in file \texttt{Non\_process.comp}. \end{itemize} -\IfFileExists{Non_process_static.tex}{\input{Non_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Non_process_static.tex}{\input{union/Non_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/PhononSimple_process.tex b/docs/manuals/mcstas/union/PhononSimple_process.tex index d1cecf6584..9be6bd7c1a 100644 --- a/docs/manuals/mcstas/union/PhononSimple_process.tex +++ b/docs/manuals/mcstas/union/PhononSimple_process.tex @@ -3,35 +3,23 @@ \section{The \texttt{PhononSimple\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Anders Komar Ravn, based on template by Mads Bertelsen and Phonon\_Simple \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Port of the PhononSimple component from the McStas library to the Union -components. +Port of the PhononSimple component from the McStas library to the Union components. -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components - -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,10 +30,10 @@ \subsection*{Input parameters} \midrule \endhead packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ -unit\_cell\_volume & AA\textasciicircum{}3 & Unit cell volume & 13.8 \\ +unit\_cell\_volume & \AA{}$^{3}$ & Unit cell volume & 13.8 \\ interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ -a & AA & fcc lattice constant & 4.95 \\ -c & meV*AA & Velocity of sound & 10 \\ +a & \AA{} & fcc lattice constant & 4.95 \\ +c & meV*\AA{} & Velocity of sound & 10 \\ M & units & Nucleus atomic mass in units & 207.2 \\ b & fm & Scattring length & 9.4 \\ T & K & Temperature & 290 \\ @@ -58,6 +46,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/PhononSimple_process.comp}{Source code} for \texttt{PhononSimple\_process.comp}. + \item Component source code found in file \texttt{PhononSimple\_process.comp}. \end{itemize} -\IfFileExists{PhononSimple_process_static.tex}{\input{PhononSimple_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/PhononSimple_process_static.tex}{\input{union/PhononSimple_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Powder_process.tex b/docs/manuals/mcstas/union/Powder_process.tex index 6bfc076de4..f0a64c36c6 100644 --- a/docs/manuals/mcstas/union/Powder_process.tex +++ b/docs/manuals/mcstas/union/Powder_process.tex @@ -3,34 +3,21 @@ \section{The \texttt{Powder\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This Union_process is based on the PowderN.comp component originally written -by P. Willendrup, L. Chapon, K. Lefmann, A.B.Abrahamsen, N.B.Christensen, -E.M.Lauridsen. +This Union\_process is based on the PowderN.comp component originally written by P. Willendrup, L. Chapon, K. Lefmann, A.B.Abrahamsen, N.B.Christensen, E.M.Lauridsen. -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components -Algorithm: -Described elsewhere -\end{lstlisting} +There is a dedicated manual available for the Union\_components Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,12 +29,12 @@ \subsection*{Input parameters} \endhead reflections & string & Input file for reflections. No scattering if NULL or "" [string] & "NULL" \\ packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ -Vc & AA\textasciicircum{}3 & Volume of unit cell=nb atoms per cell/density of atoms. & 0 \\ +Vc & \AA{}$^{3}$ & Volume of unit cell=nb atoms per cell/density of atoms. & 0 \\ delta\_d\_d & 0/1 & Global relative delta\_d\_d/d broadening when the 'w' column is not available. Use 0 if ideal. & 0 \\ DW & 1 & Global Debye-Waller factor when the 'DW' column is not available. Use 1 if included in F2 & 0 \\ nb\_atoms & 1 & Number of sub-unit per unit cell, that is ratio of sigma for chemical formula to sigma per unit cell & 1 \\ d\_phi & deg & Angle corresponding to the vertical angular range to focus to, e.g. detector height. 0 for no focusing. & 0 \\ -density & g/cm\textasciicircum{}3 & Density of material. rho=density/weight/1e24*N\_A. & 0 \\ +density & g/cm$^{3}$ & Density of material. rho=density/weight/1e24*N\_A. & 0 \\ weight & g/mol & Atomic/molecular weight of material. & 0 \\ barns & 1 & Flag to indicate if |F|\textasciicircum{}2 from 'reflections' is in barns or fm\textasciicircum{}2 (barns=1 for laz, barns=0 for lau type files). & 1 \\ Strain & ppm & Global relative delta\_d\_d/d shift when the 'Strain' column is not available. Use 0 if ideal. & 0 \\ @@ -58,6 +45,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Powder_process.comp}{Source code} for \texttt{Powder\_process.comp}. + \item Component source code found in file \texttt{Powder\_process.comp}. \end{itemize} -\IfFileExists{Powder_process_static.tex}{\input{Powder_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Powder_process_static.tex}{\input{union/Powder_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Single_crystal_process.tex b/docs/manuals/mcstas/union/Single_crystal_process.tex index c5481c7015..63048c5d24 100644 --- a/docs/manuals/mcstas/union/Single_crystal_process.tex +++ b/docs/manuals/mcstas/union/Single_crystal_process.tex @@ -3,34 +3,23 @@ \section{The \texttt{Single\_crystal\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This Union_process is based on the Single_crystal.comp component originally -written by Kristian Nielsen +This Union\_process is based on the Single\_crystal.comp component originally written by Kristian Nielsen -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -49,15 +38,15 @@ \subsection*{Input parameters} mosaic\_AB & arc\_minutes, arc\_minutes,1, 1, 1, 1, 1, 1 & In Plane mosaic rotation and plane vectors (anisotropic), mosaic\_A, mosaic\_B, A\_h,A\_k,A\_l, B\_h,B\_k,B\_l. Puts the crystal in the in-plane mosaic state. Vectors A and B define plane in which the crystal roation is defined, and mosaic\_A, mosaic\_B, denotes the resp. mosaicities (gaussian RMS) with respect to the two reflections chosen by A and B (Miller indices). & \{0,0, 0,0,0, 0,0,0\} \\ recip\_cell & 1 & Choice of direct/reciprocal (0/1) unit cell definition & 0 \\ barns & 1 & Flag to indicate if |F|\textasciicircum{}2 from 'reflections' is in barns or fm\textasciicircum{}2. barns=1 for laz and isotropic constant elastic scattering (reflections=NULL), barns=0 for lau type files & 0 \\ -ax & AA or AA\textasciicircum{}-1 & Coordinates of first (direct/recip) unit cell vector & 0 \\ -ay & AA or AA\textasciicircum{}-1 & a on y axis & 0 \\ -az & AA or AA\textasciicircum{}-1 & a on z axis & 0 \\ -bx & AA or AA\textasciicircum{}-1 & Coordinates of second (direct/recip) unit cell vector & 0 \\ -by & AA or AA\textasciicircum{}-1 & b on y axis & 0 \\ -bz & AA or AA\textasciicircum{}-1 & b on z axis & 0 \\ -cx & AA or AA\textasciicircum{}-1 & Coordinates of third (direct/recip) unit cell vector & 0 \\ -cy & AA or AA\textasciicircum{}-1 & c on y axis & 0 \\ -cz & AA or AA\textasciicircum{}-1 & c on z axis & 0 \\ +ax & \AA{} or \AA{}$^{-1}$ & Coordinates of first (direct/recip) unit cell vector & 0 \\ +ay & \AA{} or \AA{}$^{-1}$ & a on y axis & 0 \\ +az & \AA{} or \AA{}$^{-1}$ & a on z axis & 0 \\ +bx & \AA{} or \AA{}$^{-1}$ & Coordinates of second (direct/recip) unit cell vector & 0 \\ +by & \AA{} or \AA{}$^{-1}$ & b on y axis & 0 \\ +bz & \AA{} or \AA{}$^{-1}$ & b on z axis & 0 \\ +cx & \AA{} or \AA{}$^{-1}$ & Coordinates of third (direct/recip) unit cell vector & 0 \\ +cy & \AA{} or \AA{}$^{-1}$ & c on y axis & 0 \\ +cz & \AA{} or \AA{}$^{-1}$ & c on z axis & 0 \\ aa & deg & Unit cell angles alpha, beta and gamma. Then uses norms of vectors a,b and c as lattice parameters & 0 \\ bb & deg & Beta angle & 0 \\ cc & deg & Gamma angle & 0 \\ @@ -74,6 +63,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Single_crystal_process.comp}{Source code} for \texttt{Single\_crystal\_process.comp}. + \item Component source code found in file \texttt{Single\_crystal\_process.comp}. \end{itemize} -\IfFileExists{Single_crystal_process_static.tex}{\input{Single_crystal_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Single_crystal_process_static.tex}{\input{union/Single_crystal_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Template_process.tex b/docs/manuals/mcstas/union/Template_process.tex index 57a4a00e43..154e824ff4 100644 --- a/docs/manuals/mcstas/union/Template_process.tex +++ b/docs/manuals/mcstas/union/Template_process.tex @@ -3,37 +3,23 @@ \section{The \texttt{Template\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This is a template for a new contributor to create their own physical process. -The comments in this file are meant to teach the user about creating their own -process file, rather than explaining this one. For comments on how this code works, -look in the Incoherent_process.comp. +This is a template for a new contributor to create their own physical process. The comments in this file are meant to teach the user about creating their own process file, rather than explaining this one. For comments on how this code works, look in the Incoherent\_process.comp. -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components - -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -45,7 +31,7 @@ \subsection*{Input parameters} \endhead sigma & barns & Incoherent scattering cross section & 5.08 \\ packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ -unit\_cell\_volume & AA\textasciicircum{}3 & Unit\_cell\_volume & 13.8 \\ +unit\_cell\_volume & \AA{}$^{3}$ & Unit\_cell\_volume & 13.8 \\ interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ \bottomrule @@ -53,6 +39,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Template_process.comp}{Source code} for \texttt{Template\_process.comp}. + \item Component source code found in file \texttt{Template\_process.comp}. \end{itemize} -\IfFileExists{Template_process_static.tex}{\input{Template_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Template_process_static.tex}{\input{union/Template_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Template_surface.tex b/docs/manuals/mcstas/union/Template_surface.tex index 797a0747fc..e4a8f3b139 100644 --- a/docs/manuals/mcstas/union/Template_surface.tex +++ b/docs/manuals/mcstas/union/Template_surface.tex @@ -3,41 +3,23 @@ \section{The \texttt{Template\_surface} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -This is a template for a new contributor to create their own surface process. -The comments in this file are meant to teach the user about creating their own -surface component, rather than explaining this one. For comments on how this -code works, look in the Mirror_surface.comp. -To add a new surface process, three changes are needed in other files: -Add entry in surface enum (match your process) -Add storage struct in the union-lib.c file -Add the surface function in inion-suffix.c switch +This is a template for a new contributor to create their own surface process. The comments in this file are meant to teach the user about creating their own surface component, rather than explaining this one. For comments on how this code works, look in the Mirror\_surface.comp. To add a new surface process, three changes are needed in other files: Add entry in surface enum (match your process) Add storage struct in the union-lib.c file Add the surface function in inion-suffix.c switch -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components like this one -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components - -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -47,18 +29,18 @@ \subsection*{Input parameters} \textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ \midrule \endhead -reflect & str & Name of reflectivity file. Format q(Angs-1) R(0-1) & 0 \\ +reflect & str & Name of reflectivity file. Format q(\AA{}-1) R(0-1) & 0 \\ R0 & 1 & Low-angle reflectivity & 0.99 \\ -Qc & AA-1 & Critical scattering vector & 0.0219 \\ -alpha & AA & Slope of reflectivity & 6.07 \\ +Qc & \AA{}$^{-1}$ & Critical scattering vector & 0.0219 \\ +alpha & \AA{} & Slope of reflectivity & 6.07 \\ m & 1 & m-value of material. Zero means completely absorbing. & 2 \\ -W & AA-1 & Width of supermirror cut-off & 0.003 \\ +W & \AA{}$^{-1}$ & Width of supermirror cut-off & 0.003 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Template_surface.comp}{Source code} for \texttt{Template\_surface.comp}. + \item Component source code found in file \texttt{Template\_surface.comp}. \end{itemize} -\IfFileExists{Template_surface_static.tex}{\input{Template_surface_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Template_surface_static.tex}{\input{union/Template_surface_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Texture_process.tex b/docs/manuals/mcstas/union/Texture_process.tex index a5bc3e3ad8..b352d03912 100644 --- a/docs/manuals/mcstas/union/Texture_process.tex +++ b/docs/manuals/mcstas/union/Texture_process.tex @@ -3,28 +3,17 @@ \section{The \texttt{Texture\_process} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Victor Laliena \item \textbf{Origin:} University of Zaragoza \item \textbf{Date:} 2018-2019 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -seperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus seperates geometry and physics within McStas. The use of this component requires other components to be used. -This component deals with the coherent elastic scattering on a textured material. -The texture is described through the coefficients of the generalized Fourier transform -of the Orientation Distribution Function (ODF). -The component expects as input two files, one containing the Fourier coefficients of the -ODF and another one with crystallographic and physical information. +This component deals with the coherent elastic scattering on a textured material. The texture is described through the coefficients of the generalized Fourier transform of the Orientation Distribution Function (ODF). The component expects as input two files, one containing the Fourier coefficients of the ODF and another one with crystallographic and physical information. - -Algorithm: -Described elsewhere, see e.g. <a href="https://doi.org/10.3233/JNR-190117">https://doi.org/10.3233/JNR-190117</a> -\end{lstlisting} +Algorithm: Described elsewhere, see e.g. \htmladdnormallink{https://doi.org/10.3233/JNR-190117}{https://doi.org/10.3233/JNR-190117} \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -48,7 +37,7 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Texture_process.comp}{Source code} for \texttt{Texture\_process.comp}. - \item See \textless{}a href="https://doi.org/10.3233/JNR-190117"\textgreater{}https://doi.org/10.3233/JNR-190117\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Texture\_process.comp}. + \item See \htmladdnormallink{https://doi.org/10.3233/JNR-190117}{https://doi.org/10.3233/JNR-190117} \end{itemize} -\IfFileExists{Texture_process_static.tex}{\input{Texture_process_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Texture_process_static.tex}{\input{union/Texture_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_abs_logger_1D_space.tex b/docs/manuals/mcstas/union/Union_abs_logger_1D_space.tex index 428a215c4b..b25295ed4c 100644 --- a/docs/manuals/mcstas/union/Union_abs_logger_1D_space.tex +++ b/docs/manuals/mcstas/union/Union_abs_logger_1D_space.tex @@ -3,59 +3,31 @@ \section{The \texttt{Union\_abs\_logger\_1D\_space} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 19.06.20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) Logger and conditional components can be placed which will record what happens -5) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) Logger and conditional components can be placed which will record what happens 5) A Union\_master component placed after all of the above -Only in step 5 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 5 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This component is an absorption logger, and thus placed in point 4) above. -A absorption logger will log something for each absorption event happening -in the geometry or geometries on which it is attached. These are specified -in the target_geometry string. By leaving it blank, all geometries are -logged, even the ones not defined at this point in the instrument file. -Multiple geometries are specified as a comma separated list. +A absorption logger will log something for each absorption event happening in the geometry or geometries on which it is attached. These are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. Multiple geometries are specified as a comma separated list. -This absorption logger stores the absorbed weight as a function of height -in a histogram. It is expected this abs logger will often be attached to a -cylindrical geometry, and so if the abs logger has the same position and -orientation it will measure absorption along the axis of symmetry. This -makes it easy to create simple tubes, and it is even possible to include -the detector casing and similar to improve the realism of the simulation. +This absorption logger stores the absorbed weight as a function of height in a histogram. It is expected this abs logger will often be attached to a cylindrical geometry, and so if the abs logger has the same position and orientation it will measure absorption along the axis of symmetry. This makes it easy to create simple tubes, and it is even possible to include the detector casing and similar to improve the realism of the simulation. -This absorption logger needs to be placed in space, the position is recorded in -the coordinate system of the logger component. +This absorption logger needs to be placed in space, the position is recorded in the coordinate system of the logger component. -It is possible to attach one or more conditional components to this absorption -logger. Such a conditional component would impose a condition on the state of -the neutron after the Union_master component that executes the simulation, -and the absorption logger will only record the event if this condition is true. +It is possible to attach one or more conditional components to this absorption logger. Such a conditional component would impose a condition on the state of the neutron after the Union\_master component that executes the simulation, and the absorption logger will only record the event if this condition is true. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -73,11 +45,12 @@ \subsection*{Input parameters} order\_volume & 1 & Only log rays that have scattered n times in the same geometry, -1 for all orders & -1 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then access logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_abs_logger_1D_space.comp}{Source code} for \texttt{Union\_abs\_logger\_1D\_space.comp}. + \item Component source code found in file \texttt{Union\_abs\_logger\_1D\_space.comp}. \end{itemize} -\IfFileExists{Union_abs_logger_1D_space_static.tex}{\input{Union_abs_logger_1D_space_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_abs_logger_1D_space_static.tex}{\input{union/Union_abs_logger_1D_space_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_abs_logger_1D_space_event.tex b/docs/manuals/mcstas/union/Union_abs_logger_1D_space_event.tex index 2211409774..d918e620b8 100644 --- a/docs/manuals/mcstas/union/Union_abs_logger_1D_space_event.tex +++ b/docs/manuals/mcstas/union/Union_abs_logger_1D_space_event.tex @@ -3,68 +3,31 @@ \section{The \texttt{Union\_abs\_logger\_1D\_space\_event} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 19.06.20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) Logger and conditional components can be placed which will record what happens -5) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) Logger and conditional components can be placed which will record what happens 5) A Union\_master component placed after all of the above -Only in step 5 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 5 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This component is an absorption logger, and thus placed in point 4) above. -A absorption logger will log something for each absorption event happening -in the geometry or geometries on which it is attached. These are specified -in the target_geometry string. By leaving it blank, all geometries are -logged, even the ones not defined at this point in the instrument file. -Multiple geometries are specified as a comma separated list. +A absorption logger will log something for each absorption event happening in the geometry or geometries on which it is attached. These are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. Multiple geometries are specified as a comma separated list. -This absorption logger stores the absorbed weight as an event including a -pixel_id. The pixel_id is found from the y coordinate of the event position -in the coordinate system of the absorption logger and is binned to a -pixel_id which is necessary when importing the data in Mantid. The y -coordinate corresponds to the height and is natural when attaching this -absorption logger to a cylindrical geometry, as it will record position -along the axis of symmetry, and thus behave like a detector tube. When using -several of these absorption loggers, they will internally avoid reusing the -same pixel_id, but if any other mantid detectors are used, these need to have -pixel_ids larger than the maximum used by these loggers. Each of these components -uses three times the number of bins, as it internally is a 3xn histogram where -only the center line have data, as this is much easier to import in Mantid. -The ocmponent uses Monitor_nD functions for trace and mcdisplay, and for this -reason it can write the xml file required to transfer the detector geometry -to Mantid. +This absorption logger stores the absorbed weight as an event including a pixel\_id. The pixel\_id is found from the y coordinate of the event position in the coordinate system of the absorption logger and is binned to a pixel\_id which is necessary when importing the data in Mantid. The y coordinate corresponds to the height and is natural when attaching this absorption logger to a cylindrical geometry, as it will record position along the axis of symmetry, and thus behave like a detector tube. When using several of these absorption loggers, they will internally avoid reusing the same pixel\_id, but if any other mantid detectors are used, these need to have pixel\_ids larger than the maximum used by these loggers. Each of these components uses three times the number of bins, as it internally is a 3xn histogram where only the center line have data, as this is much easier to import in Mantid. The ocmponent uses Monitor\_nD functions for trace and mcdisplay, and for this reason it can write the xml file required to transfer the detector geometry to Mantid. -This absorption logger needs to be placed in space, the position is recorded in -the coordinate system of the logger component. +This absorption logger needs to be placed in space, the position is recorded in the coordinate system of the logger component. -It is possible to attach one or more conditional components to this absorption -logger. Such a conditional component would impose a condition on the state of -the neutron after the Union_master component that executes the simulation, -and the absorption logger will only record the event if this condition is true. +It is possible to attach one or more conditional components to this absorption logger. Such a conditional component would impose a condition on the state of the neutron after the Union\_master component that executes the simulation, and the absorption logger will only record the event if this condition is true. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -83,11 +46,12 @@ \subsection*{Input parameters} order\_volume & 1 & Only log rays that have scattered n times in the same geometry, -1 for all orders & -1 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then access logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_abs_logger_1D_space_event.comp}{Source code} for \texttt{Union\_abs\_logger\_1D\_space\_event.comp}. + \item Component source code found in file \texttt{Union\_abs\_logger\_1D\_space\_event.comp}. \end{itemize} -\IfFileExists{Union_abs_logger_1D_space_event_static.tex}{\input{Union_abs_logger_1D_space_event_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_abs_logger_1D_space_event_static.tex}{\input{union/Union_abs_logger_1D_space_event_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_abs_logger_1D_space_tof.tex b/docs/manuals/mcstas/union/Union_abs_logger_1D_space_tof.tex index 17e5ce05d3..f6b5ee2594 100644 --- a/docs/manuals/mcstas/union/Union_abs_logger_1D_space_tof.tex +++ b/docs/manuals/mcstas/union/Union_abs_logger_1D_space_tof.tex @@ -3,59 +3,31 @@ \section{The \texttt{Union\_abs\_logger\_1D\_space\_tof} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 19.06.20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) Logger and conditional components can be placed which will record what happens -5) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) Logger and conditional components can be placed which will record what happens 5) A Union\_master component placed after all of the above -Only in step 5 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 5 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This component is an absorption logger, and thus placed in point 4) above. -A absorption logger will log something for each absorption event happening -in the geometry or geometries on which it is attached. These are specified -in the target_geometry string. By leaving it blank, all geometries are -logged, even the ones not defined at this point in the instrument file. -Multiple geometries are specified as a comma separated list. +A absorption logger will log something for each absorption event happening in the geometry or geometries on which it is attached. These are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. Multiple geometries are specified as a comma separated list. -This absorption logger records the absorbed intensity as a function of the -y position and time of flight. One common use could be to attach this -absorption logger to a cylindrical helium-3 volume, creating a model of -the detector volume. In such a detector, only the y position of the event -is known, and as such creates a similar dataset. +This absorption logger records the absorbed intensity as a function of the y position and time of flight. One common use could be to attach this absorption logger to a cylindrical helium-3 volume, creating a model of the detector volume. In such a detector, only the y position of the event is known, and as such creates a similar dataset. -This absorption logger needs to be placed in space, the position is recorded in -the coordinate system of the logger component. Note the detection is along the -y axis of the component, so it is natural to place it relative to a cylinder. +This absorption logger needs to be placed in space, the position is recorded in the coordinate system of the logger component. Note the detection is along the y axis of the component, so it is natural to place it relative to a cylinder. -It is possible to attach one or more conditional components to this absorption -logger. Such a conditional component would impose a condition on the state of -the neutron after the Union_master component that executes the simulation, -and the absorption logger will only record the event if this condition is true. +It is possible to attach one or more conditional components to this absorption logger. Such a conditional component would impose a condition on the state of the neutron after the Union\_master component that executes the simulation, and the absorption logger will only record the event if this condition is true. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -76,11 +48,12 @@ \subsection*{Input parameters} order\_volume & 1 & Only log rays that have scattered n times in the same geometry, -1 for all orders & -1 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then access logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_abs_logger_1D_space_tof.comp}{Source code} for \texttt{Union\_abs\_logger\_1D\_space\_tof.comp}. + \item Component source code found in file \texttt{Union\_abs\_logger\_1D\_space\_tof.comp}. \end{itemize} -\IfFileExists{Union_abs_logger_1D_space_tof_static.tex}{\input{Union_abs_logger_1D_space_tof_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_abs_logger_1D_space_tof_static.tex}{\input{union/Union_abs_logger_1D_space_tof_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_abs_logger_1D_space_tof_to_lambda.tex b/docs/manuals/mcstas/union/Union_abs_logger_1D_space_tof_to_lambda.tex index 13c7b70633..05524d7b11 100644 --- a/docs/manuals/mcstas/union/Union_abs_logger_1D_space_tof_to_lambda.tex +++ b/docs/manuals/mcstas/union/Union_abs_logger_1D_space_tof_to_lambda.tex @@ -3,78 +3,35 @@ \section{The \texttt{Union\_abs\_logger\_1D\_space\_tof\_to\_lambda} McStas Comp \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 19.06.20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) Logger and conditional components can be placed which will record what happens -5) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) Logger and conditional components can be placed which will record what happens 5) A Union\_master component placed after all of the above -Only in step 5 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 5 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This component is an absorption logger, and thus placed in point 4) above. -A absorption logger will log something for each absorption event happening -in the geometry or geometries on which it is attached. These are specified -in the target_geometry string. By leaving it blank, all geometries are -logged, even the ones not defined at this point in the instrument file. -Multiple geometries are specified as a comma separated list. - -This absorption logger records the absorbed intensity as a function of the -measured and true wavelength. The measured wavelength is calculated from -the time of flight and distance travelled. This distance is a constant from -source to sample added to the distance from the sample position to the -detector pixel in which the event is detected. The true wavelength is -calculated directly from the velocity. This information shows any error in -conversion from tof to wavelength, especially from any added travelled -distance from multiple scattering. - -The lambda_min, max and bin parameters are used to set both the range for -measured and true wavelength. If either of these, denoted lambda_m and -lambda_t respectively, is set they will overwrite the lambda setting for -that part. Sine most data will be along the line lambda_m = lambda_t, it -is possible to record lambda_m / lambda_t as a function of lambda_t, which -will be close to 1.0. This mode is selected by setting relative_measured -to 1, and then the range can be selected with relative_min, max and bins. - -This absorption logger needs to be placed in space, the position is recorded in -the coordinate system of the logger component. Note the detection is along the -y axis of the component, so it is natural to place it relative to a cylinder. - -This component works as other absorption loggers, but converts the tof and -position data to wavelength, which is then compared to the actual wavelength -calculated from the neutron state. The neutron position used to calculate -the wavelength is pixelated while the time of flight is continous. The -distance from source to sample is an input parameter, and the distance from -sample to a detector pixel is calculated using the reference component position -which should be specified with a relative component index. - -It is possible to attach one or more conditional components to this absorption -logger. Such a conditional component would impose a condition on the state of -the neutron after the Union_master component that executes the simulation, -and the absorption logger will only record the event if this condition is true. - -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +A absorption logger will log something for each absorption event happening in the geometry or geometries on which it is attached. These are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. Multiple geometries are specified as a comma separated list. + +This absorption logger records the absorbed intensity as a function of the measured and true wavelength. The measured wavelength is calculated from the time of flight and distance travelled. This distance is a constant from source to sample added to the distance from the sample position to the detector pixel in which the event is detected. The true wavelength is calculated directly from the velocity. This information shows any error in conversion from tof to wavelength, especially from any added travelled distance from multiple scattering. + +The lambda\_min, max and bin parameters are used to set both the range for measured and true wavelength. If either of these, denoted lambda\_m and lambda\_t respectively, is set they will overwrite the lambda setting for that part. Sine most data will be along the line lambda\_m = lambda\_t, it is possible to record lambda\_m / lambda\_t as a function of lambda\_t, which will be close to 1.0. This mode is selected by setting relative\_measured to 1, and then the range can be selected with relative\_min, max and bins. + +This absorption logger needs to be placed in space, the position is recorded in the coordinate system of the logger component. Note the detection is along the y axis of the component, so it is natural to place it relative to a cylinder. + +This component works as other absorption loggers, but converts the tof and position data to wavelength, which is then compared to the actual wavelength calculated from the neutron state. The neutron position used to calculate the wavelength is pixelated while the time of flight is continous. The distance from source to sample is an input parameter, and the distance from sample to a detector pixel is calculated using the reference component position which should be specified with a relative component index. + +It is possible to attach one or more conditional components to this absorption logger. Such a conditional component would impose a condition on the state of the neutron after the Union\_master component that executes the simulation, and the absorption logger will only record the event if this condition is true. + +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -89,14 +46,14 @@ \subsection*{Input parameters} \textbf{yheight} & m & Height of absorption logger & \\ \textbf{yn} & 1 & Number of bins along y axis & \\ source\_sample\_dist & m & Travel distance between source and sample position, used to calculate total travelled distance & 0.0 \\ -lambda\_min & AA & Minimum wavelength recorded (sets both lambda\_m\_min and lambda\_t\_min) & -1 \\ -lambda\_max & AA & Maximum wavelength recorded (sets both lambda\_m\_max and lambda\_t\_max) & -1 \\ +lambda\_min & \AA{} & Minimum wavelength recorded (sets both lambda\_m\_min and lambda\_t\_min) & -1 \\ +lambda\_max & \AA{} & Maximum wavelength recorded (sets both lambda\_m\_max and lambda\_t\_max) & -1 \\ lambda\_bins & 1 & Number of wavelength bins & -1 \\ -lambda\_m\_min & AA & Minimum measured wavelength recorded from tof and travelled distance (overwrites lambda\_min) & -1 \\ -lambda\_m\_max & AA & Maximum measured wavelength recorded from tof and travelled distance (overwrites lambda\_max) & -1 \\ +lambda\_m\_min & \AA{} & Minimum measured wavelength recorded from tof and travelled distance (overwrites lambda\_min) & -1 \\ +lambda\_m\_max & \AA{} & Maximum measured wavelength recorded from tof and travelled distance (overwrites lambda\_max) & -1 \\ lambda\_m\_bins & 1 & Number of measured wavelength bins & -1 \\ -lambda\_t\_min & AA & Minimum true wavelength recorded from tof and travelled distance (overwrites lambda\_min) & -1 \\ -lambda\_t\_max & AA & Maximum true wavelength recorded from tof and travelled distance (overwrites lambda\_max) & -1 \\ +lambda\_t\_min & \AA{} & Minimum true wavelength recorded from tof and travelled distance (overwrites lambda\_min) & -1 \\ +lambda\_t\_max & \AA{} & Maximum true wavelength recorded from tof and travelled distance (overwrites lambda\_max) & -1 \\ lambda\_t\_bins & 1 & Number of true wavelength bins & -1 \\ relative\_measured & 1 & Default 0, records measured as function of true wavelength, if this is enabled, records measured relative to true wavelength & 0 \\ relative\_min & 1 & Smallest value of measured / true wavelength in histogram & 0.5 \\ @@ -107,11 +64,12 @@ \subsection*{Input parameters} order\_volume & 1 & Only log rays that have scattered n times in the same geometry, -1 for all orders & -1 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then access logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_abs_logger_1D_space_tof_to_lambda.comp}{Source code} for \texttt{Union\_abs\_logger\_1D\_space\_tof\_to\_lambda.comp}. + \item Component source code found in file \texttt{Union\_abs\_logger\_1D\_space\_tof\_to\_lambda.comp}. \end{itemize} -\IfFileExists{Union_abs_logger_1D_space_tof_to_lambda_static.tex}{\input{Union_abs_logger_1D_space_tof_to_lambda_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_abs_logger_1D_space_tof_to_lambda_static.tex}{\input{union/Union_abs_logger_1D_space_tof_to_lambda_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_abs_logger_1D_time.tex b/docs/manuals/mcstas/union/Union_abs_logger_1D_time.tex index 62e43a775c..0e68405823 100644 --- a/docs/manuals/mcstas/union/Union_abs_logger_1D_time.tex +++ b/docs/manuals/mcstas/union/Union_abs_logger_1D_time.tex @@ -3,59 +3,31 @@ \section{The \texttt{Union\_abs\_logger\_1D\_time} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 19.06.20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) Logger and conditional components can be placed which will record what happens -5) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) Logger and conditional components can be placed which will record what happens 5) A Union\_master component placed after all of the above -Only in step 5 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 5 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This component is an absorption logger, and thus placed in point 4) above. -A absorption logger will log something for each absorption event happening -in the geometry or geometries on which it is attached. These are specified -in the target_geometry string. By leaving it blank, all geometries are -logged, even the ones not defined at this point in the instrument file. -Multiple geometries are specified as a comma separated list. +A absorption logger will log something for each absorption event happening in the geometry or geometries on which it is attached. These are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. Multiple geometries are specified as a comma separated list. -This absorption logger stores the absorbed weight as a function of height -in a histogram. It is expected this abs logger will often be attached to a -cylindrical geometry, and so if the abs logger has the same position and -orientation it will measure absorption along the axis of symmetry. This -makes it easy to create simple tubes, and it is even possible to include -the detector casing and similar to improve the realism of the simulation. +This absorption logger stores the absorbed weight as a function of height in a histogram. It is expected this abs logger will often be attached to a cylindrical geometry, and so if the abs logger has the same position and orientation it will measure absorption along the axis of symmetry. This makes it easy to create simple tubes, and it is even possible to include the detector casing and similar to improve the realism of the simulation. -This absorption logger needs to be placed in space, the position is recorded in -the coordinate system of the logger component. +This absorption logger needs to be placed in space, the position is recorded in the coordinate system of the logger component. -It is possible to attach one or more conditional components to this absorption -logger. Such a conditional component would impose a condition on the state of -the neutron after the Union_master component that executes the simulation, -and the absorption logger will only record the event if this condition is true. +It is possible to attach one or more conditional components to this absorption logger. Such a conditional component would impose a condition on the state of the neutron after the Union\_master component that executes the simulation, and the absorption logger will only record the event if this condition is true. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -74,11 +46,12 @@ \subsection*{Input parameters} order\_volume & 1 & Only log rays that have scattered n times in the same geometry, -1 for all orders & -1 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then access logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_abs_logger_1D_time.comp}{Source code} for \texttt{Union\_abs\_logger\_1D\_time.comp}. + \item Component source code found in file \texttt{Union\_abs\_logger\_1D\_time.comp}. \end{itemize} -\IfFileExists{Union_abs_logger_1D_time_static.tex}{\input{Union_abs_logger_1D_time_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_abs_logger_1D_time_static.tex}{\input{union/Union_abs_logger_1D_time_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_abs_logger_2D_space.tex b/docs/manuals/mcstas/union/Union_abs_logger_2D_space.tex index a539fb4548..1cb3622a0d 100644 --- a/docs/manuals/mcstas/union/Union_abs_logger_2D_space.tex +++ b/docs/manuals/mcstas/union/Union_abs_logger_2D_space.tex @@ -3,63 +3,33 @@ \section{The \texttt{Union\_abs\_logger\_2D\_space} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 19.06.20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) Logger and conditional components can be placed which will record what happens -5) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) Logger and conditional components can be placed which will record what happens 5) A Union\_master component placed after all of the above -Only in step 5 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 5 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This component is an absorption logger, and thus placed in point 4) above. -A absorption logger will log something for each absorption event happening -in the geometry or geometries on which it is attached. These are specified -in the target_geometry string. By leaving it blank, all geometries are -logged, even the ones not defined at this point in the instrument file. -Multiple geometries are specified as a comma separated list. +A absorption logger will log something for each absorption event happening in the geometry or geometries on which it is attached. These are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. Multiple geometries are specified as a comma separated list. -This absorption logger stores the absorbed weight in a histogram spanning two -spatial directions. The position of the event is projected onto this plane. -The plotted data is very useful when ensuring the simulated geometry matches -the intentions. It is not recommended to use this tool for safety concerns, -as for example to estimate activity of a sample after irradiation. +This absorption logger stores the absorbed weight in a histogram spanning two spatial directions. The position of the event is projected onto this plane. The plotted data is very useful when ensuring the simulated geometry matches the intentions. It is not recommended to use this tool for safety concerns, as for example to estimate activity of a sample after irradiation. -The spatial plane in which the histogram is performed are chosen with the -D_direction_1 and D_direction_2 parameters which can be "x", "y" or "z". -The D1_min and D1_max parameters sets the limits for the first axis, and -D2_min / D2_max likewise for the second axis. +The spatial plane in which the histogram is performed are chosen with the D\_direction\_1 and D\_direction\_2 parameters which can be "x", "y" or "z". The D1\_min and D1\_max parameters sets the limits for the first axis, and D2\_min / D2\_max likewise for the second axis. -This absorption logger needs to be placed in space, the position is recorded in -the coordinate system of the logger component. +This absorption logger needs to be placed in space, the position is recorded in the coordinate system of the logger component. -It is possible to attach one or more conditional components to this absorption -logger. Such a conditional component would impose a condition on the state of -the neutron after the Union_master component that executes the simulation, -and the absorption logger will only record the event if this condition is true. +It is possible to attach one or more conditional components to this absorption logger. Such a conditional component would impose a condition on the state of the neutron after the Union\_master component that executes the simulation, and the absorption logger will only record the event if this condition is true. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -83,11 +53,12 @@ \subsection*{Input parameters} order\_volume & 1 & Only log rays that have scattered n times in the same geometry, -1 for all orders & -1 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then access logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_abs_logger_2D_space.comp}{Source code} for \texttt{Union\_abs\_logger\_2D\_space.comp}. + \item Component source code found in file \texttt{Union\_abs\_logger\_2D\_space.comp}. \end{itemize} -\IfFileExists{Union_abs_logger_2D_space_static.tex}{\input{Union_abs_logger_2D_space_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_abs_logger_2D_space_static.tex}{\input{union/Union_abs_logger_2D_space_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_abs_logger_event.tex b/docs/manuals/mcstas/union/Union_abs_logger_event.tex index 1915177749..fced07ce64 100644 --- a/docs/manuals/mcstas/union/Union_abs_logger_event.tex +++ b/docs/manuals/mcstas/union/Union_abs_logger_event.tex @@ -3,55 +3,31 @@ \section{The \texttt{Union\_abs\_logger\_event} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 19.06.20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) Logger and conditional components can be placed which will record what happens -5) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) Logger and conditional components can be placed which will record what happens 5) A Union\_master component placed after all of the above -Only in step 5 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 5 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This component is an absorption logger, and thus placed in point 4) above. -A absorption logger will log something for each absorption event happening -in the geometry or geometries on which it is attached. These are specified -in the target_geometry string. By leaving it blank, all geometries are -logged, even the ones not defined at this point in the instrument file. -Multiple geometries are specified as a comma separated list. +A absorption logger will log something for each absorption event happening in the geometry or geometries on which it is attached. These are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. Multiple geometries are specified as a comma separated list. -This absorption logger stores absorption as events, with position, velocity, -time and weight. The Monitor_nD libraries are used to write the event files. +This absorption logger stores absorption as events, with position, velocity, time and weight. The Monitor\_nD libraries are used to write the event files. -This absorption logger needs to be placed in space, the position and velocity -is recorded in the coordinate system of the logger component. +This absorption logger needs to be placed in space, the position and velocity is recorded in the coordinate system of the logger component. -It is possible to attach one or more conditional components to this absorption -logger. Such a conditional component would impose a condition on the state of -the neutron after the Union_master component that executes the simulation, -and the absorption logger will only record the event if this condition is true. +It is possible to attach one or more conditional components to this absorption logger. Such a conditional component would impose a condition on the state of the neutron after the Union\_master component that executes the simulation, and the absorption logger will only record the event if this condition is true. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -73,11 +49,12 @@ \subsection*{Input parameters} order\_volume & 1 & Only log rays that have scattered n times in the same geometry, -1 for all orders & -1 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then access logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_abs_logger_event.comp}{Source code} for \texttt{Union\_abs\_logger\_event.comp}. + \item Component source code found in file \texttt{Union\_abs\_logger\_event.comp}. \end{itemize} -\IfFileExists{Union_abs_logger_event_static.tex}{\input{Union_abs_logger_event_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_abs_logger_event_static.tex}{\input{union/Union_abs_logger_event_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_abs_logger_nD.tex b/docs/manuals/mcstas/union/Union_abs_logger_nD.tex index 6952c51946..453f1ae9e4 100644 --- a/docs/manuals/mcstas/union/Union_abs_logger_nD.tex +++ b/docs/manuals/mcstas/union/Union_abs_logger_nD.tex @@ -3,60 +3,31 @@ \section{The \texttt{Union\_abs\_logger\_nD} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 19.06.20 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) Logger and conditional components can be placed which will record what happens -5) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) Logger and conditional components can be placed which will record what happens 5) A Union\_master component placed after all of the above -Only in step 5 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 5 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This component is an absorption logger, and thus placed in point 4) above. -An absorption logger will log something for each absorption event happening -in the geometry or geometries on which it is attached. These are specified -in the target_geometry string. By leaving it blank, all geometries are -logged, even the ones not defined at this point in the instrument file. -Multiple geometries are specified as a comma separated list. +An absorption logger will log something for each absorption event happening in the geometry or geometries on which it is attached. These are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. Multiple geometries are specified as a comma separated list. -This absorption logger stores absorption as events, with position, velocity, -time and weight. The Monitor_nD libraries are used to write the event files. -This version is a close copy of Monitor_nD, having the same interface, though -the user must be aware that no propagation happens for rays to hit the -detector pixels, instead it uses the position of absorbed. Use the previous -keyword to tell Monitor_nD that this is going on. It still needs values set -for xwidth and yheight, even though these will not be used. +This absorption logger stores absorption as events, with position, velocity, time and weight. The Monitor\_nD libraries are used to write the event files. This version is a close copy of Monitor\_nD, having the same interface, though the user must be aware that no propagation happens for rays to hit the detector pixels, instead it uses the position of absorbed. Use the previous keyword to tell Monitor\_nD that this is going on. It still needs values set for xwidth and yheight, even though these will not be used. -This absorption logger needs to be placed in space, the position and velocity -is recorded in the coordinate system of the logger component. +This absorption logger needs to be placed in space, the position and velocity is recorded in the coordinate system of the logger component. -It is possible to attach one or more conditional components to this absorption -logger. Such a conditional component would impose a condition on the state of -the neutron after the Union_master component that executes the simulation, -and the absorption logger will only record the event if this condition is true. +It is possible to attach one or more conditional components to this absorption logger. Such a conditional component would impose a condition on the state of the neutron after the Union\_master component that executes the simulation, and the absorption logger will only record the event if this condition is true. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -71,9 +42,16 @@ \subsection*{Input parameters} order\_volume & 1 & Only log rays that have scattered n times in the same geometry, -1 for all orders & -1 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then access logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +user0 & str & Variable name of USERVAR to be monitored by user0. & "" \\ user1 & str & Variable name of USERVAR to be monitored by user1. & "" \\ user2 & str & Variable name of USERVAR to be monitored by user2. & "" \\ user3 & str & Variable name of USERVAR to be monitored by user3. & "" \\ +user4 & str & Variable name of USERVAR to be monitored by user4. & "" \\ +user5 & str & Variable name of USERVAR to be monitored by user5. & "" \\ +user6 & str & Variable name of USERVAR to be monitored by user6. & "" \\ +user7 & str & Variable name of USERVAR to be monitored by user7. & "" \\ +user8 & str & Variable name of USERVAR to be monitored by user8. & "" \\ +user9 & str & Variable name of USERVAR to be monitored by user9. & "" \\ xwidth & m & Width of detector. & 0 \\ yheight & m & Height of detector. & 0 \\ zdepth & m & Thickness of detector (z). & 0 \\ @@ -91,17 +69,24 @@ \subsection*{Input parameters} options & str & String that specifies the configuration of the monitor. The general syntax is "[x] options..." (see \textless{}b\textgreater{}Descr.\textless{}/b\textgreater{}). & "NULL" \\ filename & str & Output file name (overrides file=XX option). & "NULL" \\ geometry & str & Name of an OFF file to specify a complex geometry detector & "NULL" \\ -nowritefile & 1 & Not functional for Union version & 0 \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ nexus\_bins & 1 & NeXus mode only: store component BIN information \textless{}br\textgreater{}(-1 disable, 0 enable for list mode monitor, 1 enable for any montor) & 0 \\ +username0 & str & Name assigned to User0 & "NULL" \\ username1 & str & Name assigned to User1 & "NULL" \\ username2 & str & Name assigned to User2 & "NULL" \\ username3 & str & Name assigned to User3 & "NULL" \\ +username4 & str & Name assigned to User4 & "NULL" \\ +username5 & str & Name assigned to User5 & "NULL" \\ +username6 & str & Name assigned to User6 & "NULL" \\ +username7 & str & Name assigned to User7 & "NULL" \\ +username8 & str & Name assigned to User8 & "NULL" \\ +username9 & str & Name assigned to User9 & "NULL" \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_abs_logger_nD.comp}{Source code} for \texttt{Union\_abs\_logger\_nD.comp}. - \item See also \textless{}a href="../monitors/Monitor\_nD.html"\textgreater{}the Monitor\_nD mcdoc page"\textless{}/a\textgreater{} + \item Component source code found in file \texttt{Union\_abs\_logger\_nD.comp}. + \item See also \htmladdnormallink{the Monitor\_nD mcdoc page"}{../monitors/Monitor\_nD.html} \end{itemize} -\IfFileExists{Union_abs_logger_nD_static.tex}{\input{Union_abs_logger_nD_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_abs_logger_nD_static.tex}{\input{union/Union_abs_logger_nD_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_box.tex b/docs/manuals/mcstas/union/Union_box.tex index a6a9b5931a..452758615e 100644 --- a/docs/manuals/mcstas/union/Union_box.tex +++ b/docs/manuals/mcstas/union/Union_box.tex @@ -3,37 +3,25 @@ \section{The \texttt{Union\_box} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. There is a dedicated manual available for the Union components The position of this component is the center of the box, zdepth/2 in each direction. -It is allowed to overlap components, but it is not allowed to have two -parallel planes that coincides. This will crash the code on run time. +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincides. This will crash the code on run time. - -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -78,6 +66,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_box.comp}{Source code} for \texttt{Union\_box.comp}. + \item Component source code found in file \texttt{Union\_box.comp}. \end{itemize} -\IfFileExists{Union_box_static.tex}{\input{Union_box_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_box_static.tex}{\input{union/Union_box_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_conditional_PSD.tex b/docs/manuals/mcstas/union/Union_conditional_PSD.tex index ab1b508fbc..eec03123f1 100644 --- a/docs/manuals/mcstas/union/Union_conditional_PSD.tex +++ b/docs/manuals/mcstas/union/Union_conditional_PSD.tex @@ -3,48 +3,29 @@ \section{The \texttt{Union\_conditional\_PSD} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. There is a dedicated manual available for the Union components -This is a conditional component that affects the loggers in the target_loggers -string. When a logger is affected, it will only record events if the -conditional is true at the end of the simulation of a ray in the master. -Conditionals can be used to for example limit the loggers to rays that end -within a certain energy range, time interval or similar. +This is a conditional component that affects the loggers in the target\_loggers string. When a logger is affected, it will only record events if the conditional is true at the end of the simulation of a ray in the master. Conditionals can be used to for example limit the loggers to rays that end within a certain energy range, time interval or similar. One can apply several conditionals to each logger if desired. -In the extend section of a master, the tagging conditional can be acsessed by -the variable name tagging_conditional_extend. Beware, that it only works as -long as the tagging system is active, so you may want to increase the number -of histories allowed by that master component before stopping. +In the extend section of a master, the tagging conditional can be acsessed by the variable name tagging\_conditional\_extend. Beware, that it only works as long as the tagging system is active, so you may want to increase the number of histories allowed by that master component before stopping. -This conditional is a little special, because it needs to be placed in space. -It's center location is like a psd. +This conditional is a little special, because it needs to be placed in space. It's center location is like a psd. -overwrite_logger_weight can be used to force the loggers this conditional -controls to write the final weight for each scattering event, instead of the -recorded value. -\end{lstlisting} +overwrite\_logger\_weight can be used to force the loggers this conditional controls to write the final weight for each scattering event, instead of the recorded value. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -68,6 +49,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_conditional_PSD.comp}{Source code} for \texttt{Union\_conditional\_PSD.comp}. + \item Component source code found in file \texttt{Union\_conditional\_PSD.comp}. \end{itemize} -\IfFileExists{Union_conditional_PSD_static.tex}{\input{Union_conditional_PSD_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_conditional_PSD_static.tex}{\input{union/Union_conditional_PSD_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_conditional_standard.tex b/docs/manuals/mcstas/union/Union_conditional_standard.tex index a42574fff1..8990f3ffb0 100644 --- a/docs/manuals/mcstas/union/Union_conditional_standard.tex +++ b/docs/manuals/mcstas/union/Union_conditional_standard.tex @@ -3,45 +3,27 @@ \section{The \texttt{Union\_conditional\_standard} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box / Union_cylinder, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -This is a conditional component that affects the loggers in the target_loggers -string. When a logger is affected, it will only record events if the -conditional is true at the end of the simulation of a ray in the master. -Conditionals can be used to for example limit the loggers to rays that end -within a certain energy range, time interval or similar. +This is a conditional component that affects the loggers in the target\_loggers string. When a logger is affected, it will only record events if the conditional is true at the end of the simulation of a ray in the master. Conditionals can be used to for example limit the loggers to rays that end within a certain energy range, time interval or similar. One can apply several conditionals to each logger if desired. -In the extend section of a master, the tagging conditional can be acsessed by -the variable name tagging_conditional_extend. Beware, that it only works as -long as the tagging system is active, so you may want to increase the number -of histories allowed by that master component before stopping. +In the extend section of a master, the tagging conditional can be acsessed by the variable name tagging\_conditional\_extend. Beware, that it only works as long as the tagging system is active, so you may want to increase the number of histories allowed by that master component before stopping. -overwrite_logger_weight can be used to force the loggers this conditional -controls to write the final weight for each scattering event, instead of the -recorded value. -\end{lstlisting} +overwrite\_logger\_weight can be used to force the loggers this conditional controls to write the final weight for each scattering event, instead of the recorded value. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -68,6 +50,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_conditional_standard.comp}{Source code} for \texttt{Union\_conditional\_standard.comp}. + \item Component source code found in file \texttt{Union\_conditional\_standard.comp}. \end{itemize} -\IfFileExists{Union_conditional_standard_static.tex}{\input{Union_conditional_standard_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_conditional_standard_static.tex}{\input{union/Union_conditional_standard_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_cone.tex b/docs/manuals/mcstas/union/Union_cone.tex index 84ab628941..d5d7b906c9 100644 --- a/docs/manuals/mcstas/union/Union_cone.tex +++ b/docs/manuals/mcstas/union/Union_cone.tex @@ -3,34 +3,23 @@ \section{The \texttt{Union\_cone} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Martin Olsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 17.09.18 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -The position of this component is the center of the cone, and it thus -extends yheight/2 up and down along y axis. +The position of this component is the center of the cone, and it thus extends yheight/2 up and down along y axis. -It is allowed to overlap components, but it is not allowed to have two -parallel planes that coincides. This will crash the code on run time. -\end{lstlisting} +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincides. This will crash the code on run time. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -71,6 +60,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_cone.comp}{Source code} for \texttt{Union\_cone.comp}. + \item Component source code found in file \texttt{Union\_cone.comp}. \end{itemize} -\IfFileExists{Union_cone_static.tex}{\input{Union_cone_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_cone_static.tex}{\input{union/Union_cone_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_cylinder.tex b/docs/manuals/mcstas/union/Union_cylinder.tex index c1354a15cc..6516ea7313 100644 --- a/docs/manuals/mcstas/union/Union_cylinder.tex +++ b/docs/manuals/mcstas/union/Union_cylinder.tex @@ -3,34 +3,23 @@ \section{The \texttt{Union\_cylinder} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -The position of this component is the center of the cylinder, and it thus -extends yheight/2 up and down along y axis. +The position of this component is the center of the cylinder, and it thus extends yheight/2 up and down along y axis. -It is allowed to overlap components, but it is not allowed to have two -parallel planes that coincides. This will crash the code on run time. -\end{lstlisting} +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincides. This will crash the code on run time. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -69,6 +58,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_cylinder.comp}{Source code} for \texttt{Union\_cylinder.comp}. + \item Component source code found in file \texttt{Union\_cylinder.comp}. \end{itemize} -\IfFileExists{Union_cylinder_static.tex}{\input{Union_cylinder_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_cylinder_static.tex}{\input{union/Union_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_init.tex b/docs/manuals/mcstas/union/Union_init.tex index bf91daa4df..133119cc9a 100644 --- a/docs/manuals/mcstas/union/Union_init.tex +++ b/docs/manuals/mcstas/union/Union_init.tex @@ -3,31 +3,21 @@ \section{The \texttt{Union\_init} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} ESS DMSC \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using this component -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using this component 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +32,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_init.comp}{Source code} for \texttt{Union\_init.comp}. + \item Component source code found in file \texttt{Union\_init.comp}. \end{itemize} -\IfFileExists{Union_init_static.tex}{\input{Union_init_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_init_static.tex}{\input{union/Union_init_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_logger_1D.tex b/docs/manuals/mcstas/union/Union_logger_1D.tex index ba01c65d69..4aac4bfcc9 100644 --- a/docs/manuals/mcstas/union/Union_logger_1D.tex +++ b/docs/manuals/mcstas/union/Union_logger_1D.tex @@ -3,45 +3,25 @@ \section{The \texttt{Union\_logger\_1D} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -This logger in particular is not finished. It is supposed to allow several -different variables to be histogrammed, but currently only time is supported +This logger in particular is not finished. It is supposed to allow several different variables to be histogrammed, but currently only time is supported -A logger will log something for scattering events happening to certain volumes, -which are specified in the target_geometry string. By leaving it blank, all -geometries are logged, even the ones not defined at this point in the -instrument file. If a list og target_geometries is selected, one can further -narrow the events logged by providing a list of process names in target_process -which need to correspond with names of defined Union_process components. +A logger will log something for scattering events happening to certain volumes, which are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. If a list og target\_geometries is selected, one can further narrow the events logged by providing a list of process names in target\_process which need to correspond with names of defined Union\_process components. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -56,18 +36,19 @@ \subsection*{Input parameters} \textbf{min\_value} & 1 & Histogram boundery for logged value & \\ \textbf{max\_value} & 1 & Histogram boundery for logged value & \\ n1 & 1 & Number of bins in histogram & 90 \\ -variable & string & Time for time in seconds, q for magnitude of scattering vector in 1/AA. & "time" \\ +variable & string & Time for time in seconds, q for magnitude of scattering vector in 1/\AA{}. & "time" \\ filename & string & Filename of produced data file & "NULL" \\ order\_total & 1 & Only log rays that scatter for the n'th time, 0 for all orders & 0 \\ order\_volume & 1 & Only log rays that scatter for the n'th time in the same geometry & 0 \\ order\_volume\_process & 1 & Only log rays that scatter for the n'th time in the same geometry, using the same process & 0 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then acces logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_logger_1D.comp}{Source code} for \texttt{Union\_logger\_1D.comp}. + \item Component source code found in file \texttt{Union\_logger\_1D.comp}. \end{itemize} -\IfFileExists{Union_logger_1D_static.tex}{\input{Union_logger_1D_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_logger_1D_static.tex}{\input{union/Union_logger_1D_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_logger_2DQ.tex b/docs/manuals/mcstas/union/Union_logger_2DQ.tex index 3ba7e3e3e2..9aa45da3d2 100644 --- a/docs/manuals/mcstas/union/Union_logger_2DQ.tex +++ b/docs/manuals/mcstas/union/Union_logger_2DQ.tex @@ -3,44 +3,25 @@ \section{The \texttt{Union\_logger\_2DQ} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This logger logs a 2D projection of the scattering vector, q in the lab frame. -A logger will log something for scattering events happening to certain volumes, -which are specified in the target_geometry string. By leaving it blank, all -geometries are logged, even the ones not defined at this point in the -instrument file. If a list og target_geometries is selected, one can further -narrow the events logged by providing a list of process names in target_process -which need to correspond with names of defined Union_process components. +A logger will log something for scattering events happening to certain volumes, which are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. If a list og target\_geometries is selected, one can further narrow the events logged by providing a list of process names in target\_process which need to correspond with names of defined Union\_process components. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -53,12 +34,12 @@ \subsection*{Input parameters} target\_geometry & string & Comma seperated list of geometry names that will be logged, leave empty for all volumes (even not defined yet) & "NULL" \\ target\_process & string & Comma seperated names of physical processes, if volumes are selected, one can select Union\_process names & "NULL" \\ Q\_direction\_1 & string & Q direction for first axis ("x", "y" or "z") & "x" \\ -Q1\_min & AA\textasciicircum{}-1 & Histogram boundery, min q value for first axis & -5 \\ -Q1\_max & AA\textasciicircum{}-1 & Histogram boundery, max q value for first axis & 5 \\ +Q1\_min & \AA{}$^{-1}$ & Histogram boundery, min q value for first axis & -5 \\ +Q1\_max & \AA{}$^{-1}$ & Histogram boundery, max q value for first axis & 5 \\ n1 & 1 & Number of bins for first axis & 90 \\ Q\_direction\_2 & string & Q direction for second axis ("x", "y" or "z") & "z" \\ -Q2\_min & AA\textasciicircum{}-1 & Histogram boundery, min q value for second axis & -5 \\ -Q2\_max & AA\textasciicircum{}-1 & Histogram boundery, max q value for second axis & 5 \\ +Q2\_min & \AA{}$^{-1}$ & Histogram boundery, min q value for second axis & -5 \\ +Q2\_max & \AA{}$^{-1}$ & Histogram boundery, max q value for second axis & 5 \\ n2 & 1 & Number of bins for second axis & 90 \\ filename & string & Filename of produced data file & "NULL" \\ order\_total & 1 & Only log rays that scatter for the n'th time, 0 for all orders & 0 \\ @@ -66,11 +47,12 @@ \subsection*{Input parameters} order\_volume\_process & 1 & Only log rays that scatter for the n'th time in the same geometry, uwsing the same process & 0 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then acces logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_logger_2DQ.comp}{Source code} for \texttt{Union\_logger\_2DQ.comp}. + \item Component source code found in file \texttt{Union\_logger\_2DQ.comp}. \end{itemize} -\IfFileExists{Union_logger_2DQ_static.tex}{\input{Union_logger_2DQ_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_logger_2DQ_static.tex}{\input{union/Union_logger_2DQ_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_logger_2D_kf.tex b/docs/manuals/mcstas/union/Union_logger_2D_kf.tex index 11723b88c4..cd25e42d6b 100644 --- a/docs/manuals/mcstas/union/Union_logger_2D_kf.tex +++ b/docs/manuals/mcstas/union/Union_logger_2D_kf.tex @@ -3,45 +3,25 @@ \section{The \texttt{Union\_logger\_2D\_kf} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -This logger logs a 2D projection of the final wavevector after each scattering -in the lab frame. +This logger logs a 2D projection of the final wavevector after each scattering in the lab frame. -A logger will log something for scattering events happening to certain volumes, -which are specified in the target_geometry string. By leaving it blank, all -geometries are logged, even the ones not defined at this point in the -instrument file. If a list og target_geometries is selected, one can further -narrow the events logged by providing a list of process names in target_process -which need to correspond with names of defined Union_process components. +A logger will log something for scattering events happening to certain volumes, which are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. If a list og target\_geometries is selected, one can further narrow the events logged by providing a list of process names in target\_process which need to correspond with names of defined Union\_process components. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -53,10 +33,10 @@ \subsection*{Input parameters} \endhead target\_geometry & string & Comma seperated list of geometry names that will be logged, leave empty for all volumes (even not defined yet) & "NULL" \\ target\_process & string & Comma seperated names of physical processes, if volumes are selected, one can select Union\_process names & "NULL" \\ -Q1\_min & AA\textasciicircum{}-1 & Histogram boundery, min kf value for first axis & -5 \\ -Q1\_max & AA\textasciicircum{}-1 & Histogram boundery, max kf value for first axis & 5 \\ -Q2\_min & AA\textasciicircum{}-1 & Histogram boundery, min kf value for second axis & -5 \\ -Q2\_max & AA\textasciicircum{}-1 & Histogram boundery, max kf value for second axis & 5 \\ +Q1\_min & \AA{}$^{-1}$ & Histogram boundery, min kf value for first axis & -5 \\ +Q1\_max & \AA{}$^{-1}$ & Histogram boundery, max kf value for first axis & 5 \\ +Q2\_min & \AA{}$^{-1}$ & Histogram boundery, min kf value for second axis & -5 \\ +Q2\_max & \AA{}$^{-1}$ & Histogram boundery, max kf value for second axis & 5 \\ Q\_direction\_1 & string & kf direction for first axis ("x", "y" or "z") & "x" \\ Q\_direction\_2 & string & kf direction for second axis ("x", "y" or "z") & "z" \\ filename & string & Filename of produced data file & "NULL" \\ @@ -67,11 +47,12 @@ \subsection*{Input parameters} order\_volume\_process & 1 & Only log rays that scatter for the n'th time in the same geometry, using the same process & 0 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then acces logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_logger_2D_kf.comp}{Source code} for \texttt{Union\_logger\_2D\_kf.comp}. + \item Component source code found in file \texttt{Union\_logger\_2D\_kf.comp}. \end{itemize} -\IfFileExists{Union_logger_2D_kf_static.tex}{\input{Union_logger_2D_kf_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_logger_2D_kf_static.tex}{\input{union/Union_logger_2D_kf_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_logger_2D_kf_time.tex b/docs/manuals/mcstas/union/Union_logger_2D_kf_time.tex index f8c7a7df45..3a96701411 100644 --- a/docs/manuals/mcstas/union/Union_logger_2D_kf_time.tex +++ b/docs/manuals/mcstas/union/Union_logger_2D_kf_time.tex @@ -3,46 +3,25 @@ \section{The \texttt{Union\_logger\_2D\_kf\_time} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -This logger logs a 2D projection of the final wavevector after each scattering -in the lab frame. It will do so for a number of time_bins, making it possible -to make a animation, but beware of memory / diskspace requirements. +This logger logs a 2D projection of the final wavevector after each scattering in the lab frame. It will do so for a number of time\_bins, making it possible to make a animation, but beware of memory / diskspace requirements. -A logger will log something for scattering events happening to certain volumes, -which are specified in the target_geometry string. By leaving it blank, all -geometries are logged, even the ones not defined at this point in the -instrument file. If a list og target_geometries is selected, one can further -narrow the events logged by providing a list of process names in target_process -which need to correspond with names of defined Union_process components. +A logger will log something for scattering events happening to certain volumes, which are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. If a list og target\_geometries is selected, one can further narrow the events logged by providing a list of process names in target\_process which need to correspond with names of defined Union\_process components. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -54,10 +33,10 @@ \subsection*{Input parameters} \endhead target\_geometry & string & Comma seperated list of geometry names that will be logged, leave empty for all volumes (even not defined yet) & "NULL" \\ target\_process & string & Comma seperated names of physical processes, if volumes are selected, one can select Union\_process names & "NULL" \\ -Q1\_min & A\textasciicircum{}-1 & Histogram boundery, min kf value for first axis & -5 \\ -Q1\_max & A\textasciicircum{}-1 & Histogram boundery, max kf value for first axis & 5 \\ -Q2\_min & A\textasciicircum{}-1 & Histogram boundery, min kf value for second axis & -5 \\ -Q2\_max & A\textasciicircum{}-1 & Histogram boundery, max kf value for second axis & 5 \\ +Q1\_min & A$^{-1}$ & Histogram boundery, min kf value for first axis & -5 \\ +Q1\_max & A$^{-1}$ & Histogram boundery, max kf value for first axis & 5 \\ +Q2\_min & A$^{-1}$ & Histogram boundery, min kf value for second axis & -5 \\ +Q2\_max & A$^{-1}$ & Histogram boundery, max kf value for second axis & 5 \\ time\_min & s & Minimum time & 0 \\ time\_max & s & Maximum time & 1 \\ Q\_direction\_1 & string & kf direction for first axis ("x", "y" or "z") & "x" \\ @@ -71,11 +50,12 @@ \subsection*{Input parameters} order\_volume\_process & 1 & Only log rays that scatter for the n'th time in the same geometry, using the same process & 0 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then acces logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_logger_2D_kf_time.comp}{Source code} for \texttt{Union\_logger\_2D\_kf\_time.comp}. + \item Component source code found in file \texttt{Union\_logger\_2D\_kf\_time.comp}. \end{itemize} -\IfFileExists{Union_logger_2D_kf_time_static.tex}{\input{Union_logger_2D_kf_time_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_logger_2D_kf_time_static.tex}{\input{union/Union_logger_2D_kf_time_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_logger_2D_space.tex b/docs/manuals/mcstas/union/Union_logger_2D_space.tex index b9ea78cc08..05d4718b8f 100644 --- a/docs/manuals/mcstas/union/Union_logger_2D_space.tex +++ b/docs/manuals/mcstas/union/Union_logger_2D_space.tex @@ -3,46 +3,27 @@ \section{The \texttt{Union\_logger\_2D\_space} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components This logger logs a 2D projection of the position of each scattering in the lab frame. This logger needs to be placed in space, the position is the center of the histogram. -A logger will log something for scattering events happening to certain volumes, -which are specified in the target_geometry string. By leaving it blank, all -geometries are logged, even the ones not defined at this point in the -instrument file. If a list og target_geometries is selected, one can further -narrow the events logged by providing a list of process names in target_process -which need to correspond with names of defined Union_process components. +A logger will log something for scattering events happening to certain volumes, which are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. If a list og target\_geometries is selected, one can further narrow the events logged by providing a list of process names in target\_process which need to correspond with names of defined Union\_process components. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -68,11 +49,12 @@ \subsection*{Input parameters} order\_volume\_process & 1 & Only log rays that scatter for the n'th time in the same geometry, using the same process & 0 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then acces logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_logger_2D_space.comp}{Source code} for \texttt{Union\_logger\_2D\_space.comp}. + \item Component source code found in file \texttt{Union\_logger\_2D\_space.comp}. \end{itemize} -\IfFileExists{Union_logger_2D_space_static.tex}{\input{Union_logger_2D_space_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_logger_2D_space_static.tex}{\input{union/Union_logger_2D_space_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_logger_2D_space_time.tex b/docs/manuals/mcstas/union/Union_logger_2D_space_time.tex index 88d45e88f6..c6fa885596 100644 --- a/docs/manuals/mcstas/union/Union_logger_2D_space_time.tex +++ b/docs/manuals/mcstas/union/Union_logger_2D_space_time.tex @@ -3,46 +3,25 @@ \section{The \texttt{Union\_logger\_2D\_space\_time} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -This logger logs a 2D projection of the position of each scattering in the lab -frame. Using the time_bins one can select to get this project for different -time slots, effectively making a small animation of what happens. +This logger logs a 2D projection of the position of each scattering in the lab frame. Using the time\_bins one can select to get this project for different time slots, effectively making a small animation of what happens. -A logger will log something for scattering events happening to certain volumes, -which are specified in the target_geometry string. By leaving it blank, all -geometries are logged, even the ones not defined at this point in the -instrument file. If a list og target_geometries is selected, one can further -narrow the events logged by providing a list of process names in target_process -which need to correspond with names of defined Union_process components. +A logger will log something for scattering events happening to certain volumes, which are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. If a list og target\_geometries is selected, one can further narrow the events logged by providing a list of process names in target\_process which need to correspond with names of defined Union\_process components. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -71,11 +50,12 @@ \subsection*{Input parameters} order\_volume\_process & 1 & Only log rays that scatter for the n'th time in the same geometry, using the same process & 0 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then acces logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_logger_2D_space_time.comp}{Source code} for \texttt{Union\_logger\_2D\_space\_time.comp}. + \item Component source code found in file \texttt{Union\_logger\_2D\_space\_time.comp}. \end{itemize} -\IfFileExists{Union_logger_2D_space_time_static.tex}{\input{Union_logger_2D_space_time_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_logger_2D_space_time_static.tex}{\input{union/Union_logger_2D_space_time_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_logger_3D_space.tex b/docs/manuals/mcstas/union/Union_logger_3D_space.tex index 7ac9d4d437..ed5a8a7979 100644 --- a/docs/manuals/mcstas/union/Union_logger_3D_space.tex +++ b/docs/manuals/mcstas/union/Union_logger_3D_space.tex @@ -3,46 +3,25 @@ \section{The \texttt{Union\_logger\_3D\_space} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -This logger logs a 2D projection of the position of each scattering in the lab -frame. It does this in n3 space slices, so one can get a full 3D histogram of -scattering positions. +This logger logs a 2D projection of the position of each scattering in the lab frame. It does this in n3 space slices, so one can get a full 3D histogram of scattering positions. -A logger will log something for scattering events happening to certain volumes, -which are specified in the target_geometry string. By leaving it blank, all -geometries are logged, even the ones not defined at this point in the -instrument file. If a list og target_geometries is selected, one can further -narrow the events logged by providing a list of process names in target_process -which need to correspond with names of defined Union_process components. +A logger will log something for scattering events happening to certain volumes, which are specified in the target\_geometry string. By leaving it blank, all geometries are logged, even the ones not defined at this point in the instrument file. If a list og target\_geometries is selected, one can further narrow the events logged by providing a list of process names in target\_process which need to correspond with names of defined Union\_process components. -To use the logger_conditional_extend function, set it to some integer value n -and make and extend section to the master component that runs the geometry. -In this extend function, logger_conditional_extend[n] is 1 if the conditional -stack evaluated to true, 0 if not. This way one can check what rays is logged -using regular McStas monitors. Only works if a conditional is applied to this -logger. -\end{lstlisting} +To use the logger\_conditional\_extend function, set it to some integer value n and make and extend section to the master component that runs the geometry. In this extend function, logger\_conditional\_extend[n] is 1 if the conditional stack evaluated to true, 0 if not. This way one can check what rays is logged using regular McStas monitors. Only works if a conditional is applied to this logger. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -72,11 +51,12 @@ \subsection*{Input parameters} order\_volume\_process & 1 & Only log rays that scatter for the n'th time in the same geometry, using the same process & 0 \\ logger\_conditional\_extend\_index & 1 & If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger\_conditional\_extend", and one would then acces logger\_conditional\_extend[n] if logger\_conditional\_extend\_index is set to n & -1 \\ init & string & name of Union\_init component (typically "init", default) & "init" \\ +nowritefile & 1 & If set, logger will skip writing to disk & 0 \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_logger_3D_space.comp}{Source code} for \texttt{Union\_logger\_3D\_space.comp}. + \item Component source code found in file \texttt{Union\_logger\_3D\_space.comp}. \end{itemize} -\IfFileExists{Union_logger_3D_space_static.tex}{\input{Union_logger_3D_space_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_logger_3D_space_static.tex}{\input{union/Union_logger_3D_space_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_make_material.tex b/docs/manuals/mcstas/union/Union_make_material.tex index 33f62fcf55..391c32ce98 100644 --- a/docs/manuals/mcstas/union/Union_make_material.tex +++ b/docs/manuals/mcstas/union/Union_make_material.tex @@ -3,31 +3,21 @@ \section{The \texttt{Union\_make\_material} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using this component -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using this component 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -40,16 +30,16 @@ \subsection*{Input parameters} process\_string & string & Comma seperated names of physical processes & "NULL" \\ \textbf{my\_absorption} & 1/m & Inverse penetration depth from absorption at standard energy & \\ absorber & 0/1 & Control parameter, if set to 1 the material will have no scattering processes & 0 \\ -refraction\_density & g/cm3 & Density of the refracting material. density \textless{} 0 means the material is outside/before the shape. & 0 \\ +refraction\_density & g/cm$^{3}$ & Density of the refracting material. density \textless{} 0 means the material is outside/before the shape. & 0 \\ refraction\_sigma\_coh & barn & Coherent cross section of refracting material. Use negative value to indicate a negative coherent scattering length & 0 \\ refraction\_weight & g/mol & Molar mass of the refracting material & 0 \\ -refraction\_SLD & AA\textasciicircum{}-2 & Scattering length density of material (overwrites sigma\_coh, density and weight) & -1500 \\ +refraction\_SLD & \AA{}$^{-2}$ & Scattering length density of material (overwrites sigma\_coh, density and weight) & -1500 \\ init & string & Name of Union\_init component (typically "init", default) & "init" \\ \bottomrule \end{longtable} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_make_material.comp}{Source code} for \texttt{Union\_make\_material.comp}. + \item Component source code found in file \texttt{Union\_make\_material.comp}. \end{itemize} -\IfFileExists{Union_make_material_static.tex}{\input{Union_make_material_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_make_material_static.tex}{\input{union/Union_make_material_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_master.tex b/docs/manuals/mcstas/union/Union_master.tex index 02c63793e5..e3b65c368b 100644 --- a/docs/manuals/mcstas/union/Union_master.tex +++ b/docs/manuals/mcstas/union/Union_master.tex @@ -3,31 +3,21 @@ \section{The \texttt{Union\_master} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) This master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) This master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -54,6 +44,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_master.comp}{Source code} for \texttt{Union\_master.comp}. + \item Component source code found in file \texttt{Union\_master.comp}. \end{itemize} -\IfFileExists{Union_master_static.tex}{\input{Union_master_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_master_static.tex}{\input{union/Union_master_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_master_GPU.tex b/docs/manuals/mcstas/union/Union_master_GPU.tex index 259d0d292e..8b6761237a 100644 --- a/docs/manuals/mcstas/union/Union_master_GPU.tex +++ b/docs/manuals/mcstas/union/Union_master_GPU.tex @@ -3,31 +3,21 @@ \section{The \texttt{Union\_master\_GPU} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) This master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) This master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -51,6 +41,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_master_GPU.comp}{Source code} for \texttt{Union\_master\_GPU.comp}. + \item Component source code found in file \texttt{Union\_master\_GPU.comp}. \end{itemize} -\IfFileExists{Union_master_GPU_static.tex}{\input{Union_master_GPU_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_master_GPU_static.tex}{\input{union/Union_master_GPU_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_mesh.tex b/docs/manuals/mcstas/union/Union_mesh.tex index 9f5652a43f..76768558d2 100644 --- a/docs/manuals/mcstas/union/Union_mesh.tex +++ b/docs/manuals/mcstas/union/Union_mesh.tex @@ -3,42 +3,25 @@ \section{The \texttt{Union\_mesh} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Martin Olsen, and expanded upon by Daniel Lomholt Christensen \item \textbf{Origin:} University of Copenhagen / ACTNXT project \item \textbf{Date:} 17.09.18 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -separates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus separates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere/mesh, assigned a material -4) A Union_master component placed after all the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere/mesh, assigned a material 4) A Union\_master component placed after all the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -The mesh component loads a 3D off or stl files as the geometry. -The mesh geometry that is loaded must be a watertight mesh. -In order to check this, the component implements a simple Euler Pointcare value, -To check if the given geometry is watertight. This check is sometimes too rigid, -so a user can set the skip_convex_check parameter in order to not have this -check performed. +The mesh component loads a 3D off or stl files as the geometry. The mesh geometry that is loaded must be a watertight mesh. In order to check this, the component implements a simple Euler Pointcare value, To check if the given geometry is watertight. This check is sometimes too rigid, so a user can set the skip\_convex\_check parameter in order to not have this check performed. +If you load an off file, we currently only support rank 3 polygons, i.e triangular meshes. -If you load an off file, we currently only support rank 3 polygons, i.e -triangular meshes. - -It is allowed to overlap components, but it is not allowed to have two -parallel planes that coincides. This will crash the code on run time. -\end{lstlisting} +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincides. This will crash the code on run time. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -52,8 +35,8 @@ \subsection*{Input parameters} material\_string & string & material name of this volume, defined using Union\_make\_material & 0 \\ \textbf{priority} & 1 & priotiry of the volume (can not be the same as another volume) A high priority is on top of low. & \\ visualize & 1 & set to 0 if you wish to hide this geometry in mcdisplay & 1 \\ -all\_surfaces & & & 0 \\ -cut\_surface & & & 0 \\ +all\_surfaces & string & Comma seperated string of Union surface definitions defined prior to this component & 0 \\ +cut\_surface & string & Comma seperated string of Union surface definitions defined prior to this component, applied to all internal cuts & 0 \\ target\_index & 1 & Focuses on component a component this many steps further in the component sequence & 0 \\ target\_x & m & & 0 \\ target\_y & m & Position of target to focus at & 0 \\ @@ -75,6 +58,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_mesh.comp}{Source code} for \texttt{Union\_mesh.comp}. + \item Component source code found in file \texttt{Union\_mesh.comp}. \end{itemize} -\IfFileExists{Union_mesh_static.tex}{\input{Union_mesh_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_mesh_static.tex}{\input{union/Union_mesh_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_sphere.tex b/docs/manuals/mcstas/union/Union_sphere.tex index f0f2eb61c1..2ded9786be 100644 --- a/docs/manuals/mcstas/union/Union_sphere.tex +++ b/docs/manuals/mcstas/union/Union_sphere.tex @@ -3,33 +3,23 @@ \section{The \texttt{Union\_sphere} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using Union_make_material -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before this master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. There is a dedicated manual available for the Union components The position of this component is the center of the sphere -It is allowed to overlap components, but it is not allowed to have two -parallel planes that coincides. This will crash the code on run time. -\end{lstlisting} +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincides. This will crash the code on run time. \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -64,6 +54,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_sphere.comp}{Source code} for \texttt{Union\_sphere.comp}. + \item Component source code found in file \texttt{Union\_sphere.comp}. \end{itemize} -\IfFileExists{Union_sphere_static.tex}{\input{Union_sphere_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_sphere_static.tex}{\input{union/Union_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcstas/union/Union_stop.tex b/docs/manuals/mcstas/union/Union_stop.tex index e0f37eb6a5..fe9bfb4137 100644 --- a/docs/manuals/mcstas/union/Union_stop.tex +++ b/docs/manuals/mcstas/union/Union_stop.tex @@ -3,31 +3,21 @@ \section{The \texttt{Union\_stop} McStas Component} \subsection*{Identification} \begin{itemize} - \item \textbf{Site:} \item \textbf{Author:} Mads Bertelsen \item \textbf{Origin:} University of Copenhagen \item \textbf{Date:} 20.08.15 \end{itemize} \subsection*{Description} -\begin{lstlisting} -Part of the Union components, a set of components that work together and thus -sperates geometry and physics within McStas. -The use of this component requires other components to be used. +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. -1) One specifies a number of processes using process components -2) These are gathered into material definitions using this component -3) Geometries are placed using Union_box/cylinder/sphere, assigned a material -4) A Union_master component placed after all of the above +1) One specifies a number of processes using process components 2) These are gathered into material definitions using this component 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above -Only in step 4 will any simulation happen, and per default all geometries -defined before the master, but after the previous will be simulated here. +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. -There is a dedicated manual available for the Union_components +There is a dedicated manual available for the Union\_components -Algorithm: -Described elsewhere -\end{lstlisting} +Algorithm: Described elsewhere \subsection*{Input parameters} Parameters in \textbf{boldface} are required; the others are optional. @@ -42,6 +32,6 @@ \subsection*{Input parameters} \subsection*{Links} \begin{itemize} - \item \href{run:/home/willend/willend-McCode/mcstas-comps/union/Union_stop.comp}{Source code} for \texttt{Union\_stop.comp}. + \item Component source code found in file \texttt{Union\_stop.comp}. \end{itemize} -\IfFileExists{Union_stop_static.tex}{\input{Union_stop_static.tex}}{} \ No newline at end of file +\IfFileExists{union/Union_stop_static.tex}{\input{union/Union_stop_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/CMakeLists.txt b/docs/manuals/mcxtrace/CMakeLists.txt index 85a0a77512..f2732e5b3d 100644 --- a/docs/manuals/mcxtrace/CMakeLists.txt +++ b/docs/manuals/mcxtrace/CMakeLists.txt @@ -18,6 +18,17 @@ include(UseLATEX) # set(PDFLATEX_COMPILER "/usr/bin/xelatex") message( "setup MCCODE" ) setupMCCODE("${FLAVOR}") + +# Generate title.tex / title_comp.tex from their .in templates, substituting +# the actual build version (@MCCODE_VERSION@) -- this is the version passed +# as argument 1 to build_manuals_mcxtrace, already threaded through by +# setupMCCODE() above via mkdist, with no changes needed there. Runs at +# configure time, landing in ${CMAKE_CURRENT_BINARY_DIR} (== LATEX_OUTPUT_PATH +# below), so the LaTeX build finds them there like any other input. +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/title.tex.in" "${CMAKE_CURRENT_BINARY_DIR}/title.tex" @ONLY) +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/title_comp.tex.in" "${CMAKE_CURRENT_BINARY_DIR}/title_comp.tex" @ONLY) +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/preamble.tex.in" "${CMAKE_CURRENT_BINARY_DIR}/preamble.tex" @ONLY) +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/preamble_comp.tex.in" "${CMAKE_CURRENT_BINARY_DIR}/preamble_comp.tex" @ONLY) # CPack configuration message( "CPack configuration" ) set(CPACK_PACKAGE_NAME "${FLAVOR}-manuals") @@ -57,13 +68,30 @@ message( "LaTeX configuration" ) file(GLOB LIST CONFIGURE_DEPENDS RELATIVE "${CMAKE_CURRENT_LIST_DIR}" "*.tex" "*.sty" "*.bib" "*.bst" "[a-z]*/*.tex" "[a-z]*/*.parms" "figures/*" "Semi_mirror.comp") foreach(NAME sources samples optics monitors misc union sasmodels contrib obsolete astrox) + file(GLOB ${NAME}_COMP_SOURCES CONFIGURE_DEPENDS "${CMAKE_SOURCE_DIR}/../../../mcxtrace-comps/${NAME}/*.comp") add_custom_command( OUTPUT "${NAME}.done" - COMMAND "mxdoc" "--tex" "--in-repo" "--dir=${CMAKE_SOURCE_DIR}/../../../mcxtrace-comps/${NAME}" "--outdir=${PROJECT_BINARY_DIR}" + COMMAND "mxdoc" "--tex" "--in-repo" "--dir=${CMAKE_SOURCE_DIR}/../../../mcxtrace-comps/${NAME}" "--outdir=${CMAKE_CURRENT_SOURCE_DIR}" + COMMAND "${CMAKE_COMMAND}" "-E" "touch" "${CMAKE_CURRENT_BINARY_DIR}/${NAME}.done" + DEPENDS "${CMAKE_SOURCE_DIR}/../../../tools/Python/mcdoc/mcdoc.py" ${${NAME}_COMP_SOURCES} WORKING_DIRECTORY "${PROJECT_BINARY_DIR}" + COMMENT "Regenerating ${NAME} LaTeX component/instrument doc snippets (in-place in the source tree)" ) endforeach() +# MD files +foreach(NAME sources samples optics monitors misc union sasmodels contrib obsolete astrox) + file(GLOB ${NAME}_COMP_SOURCES_MD CONFIGURE_DEPENDS "${CMAKE_SOURCE_DIR}/../../../mcstas-comps/${NAME}/*.comp") + add_custom_command( + OUTPUT "${NAME}.mddone" + COMMAND "mxdoc" "--md" "--in-repo" "--dir=${CMAKE_SOURCE_DIR}/../../../mcxtrace-comps/${NAME}" + COMMAND "${CMAKE_COMMAND}" "-E" "touch" "${CMAKE_CURRENT_BINARY_DIR}/${NAME}.mddone" + DEPENDS "${CMAKE_SOURCE_DIR}/../../../tools/Python/mcdoc/mcdoc.py" ${${NAME}_COMP_SOURCES_MD} + WORKING_DIRECTORY "${PROJECT_BINARY_DIR}" + COMMENT "Regenerating ${NAME} Markdown component/instrument doc snippets" + ) +endforeach() + set(LATEX_OUTPUT_PATH "${PROJECT_BINARY_DIR}") add_latex_document( manual.tex @@ -91,3 +119,46 @@ install(FILES "${PROJECT_BINARY_DIR}/Component_manual.pdf" DESTINATION "${MANDEST}" RENAME "${CMANUAL}" ) + +# --- HTML manual generation (tex4ht, MathJax math rendering), packaged as .tgz --- +# Multi-pass build: htlatex -> bibtex -> makeindex -> htlatex x2 (to settle +# cross-references and citations across the split HTML pages), then tar/gzip +# the resulting page set. Requires texlive-plain-generic (htlatex/tex4ht) and +# dvipng; skipped with a warning if htlatex isn't available rather than +# failing the whole manuals build. +find_program(HTLATEX_EXECUTABLE htlatex) +find_program(BASH_EXECUTABLE bash) +find_program(PYTHON3_EXECUTABLE python3) +if(HTLATEX_EXECUTABLE AND BASH_EXECUTABLE AND PYTHON3_EXECUTABLE) + foreach(DOC manual Component_manual) + add_custom_command( + OUTPUT "${PROJECT_BINARY_DIR}/${DOC}-html.tgz" + COMMAND "${BASH_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/generate-xbb-files.sh" + COMMAND "${HTLATEX_EXECUTABLE}" "${DOC}.tex" "html,3,mathjax,charset=utf-8" " -cvalidate -cunihtf -utf8" "" + COMMAND "bibtex" "${DOC}" + COMMAND "makeindex" "${DOC}.idx" + COMMAND "${HTLATEX_EXECUTABLE}" "${DOC}.tex" "html,3,mathjax,charset=utf-8" " -cvalidate -cunihtf -utf8" "" + COMMAND "${HTLATEX_EXECUTABLE}" "${DOC}.tex" "html,3,mathjax,charset=utf-8" " -cvalidate -cunihtf -utf8" "" + COMMAND "${PYTHON3_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/inject-toc-sidebar.py" "${DOC}" + COMMAND "${BASH_EXECUTABLE}" "-c" "cat '${CMAKE_CURRENT_SOURCE_DIR}/html-style-overrides.css' >> '${DOC}.css'" + COMMAND "${BASH_EXECUTABLE}" "-c" "tar czf '${DOC}-html.tgz' ${DOC}*.html ${DOC}.css figures 2>/dev/null || tar czf '${DOC}-html.tgz' ${DOC}*.html ${DOC}.css" + WORKING_DIRECTORY "${PROJECT_BINARY_DIR}" + DEPENDS "${PROJECT_BINARY_DIR}/${DOC}.pdf" "${CMAKE_CURRENT_SOURCE_DIR}/html-style-overrides.css" "${CMAKE_CURRENT_SOURCE_DIR}/generate-xbb-files.sh" "${CMAKE_CURRENT_SOURCE_DIR}/inject-toc-sidebar.py" + COMMENT "Building HTML version of ${DOC} (tex4ht/MathJax), injecting TOC sidebar, and packaging as ${DOC}-html.tgz" + VERBATIM + ) + add_custom_target("${DOC}_html" ALL DEPENDS "${PROJECT_BINARY_DIR}/${DOC}-html.tgz") + endforeach() + install(FILES "${PROJECT_BINARY_DIR}/manual-html.tgz" + DESTINATION "${MANDEST}" + RENAME "${FLAVOR}-manual-html.tgz" + OPTIONAL + ) + install(FILES "${PROJECT_BINARY_DIR}/Component_manual-html.tgz" + DESTINATION "${MANDEST}" + RENAME "${FLAVOR}-components-html.tgz" + OPTIONAL + ) +else() + message(WARNING "htlatex, bash and/or python3 not found -- skipping HTML manual generation. Install texlive-plain-generic (htlatex/tex4ht) and dvipng to enable the .tgz HTML manuals.") +endif() diff --git a/docs/manuals/mcxtrace/abstractpage.tex b/docs/manuals/mcxtrace/abstractpage.tex index a6f4df5402..e74c1b20e4 100644 --- a/docs/manuals/mcxtrace/abstractpage.tex +++ b/docs/manuals/mcxtrace/abstractpage.tex @@ -21,7 +21,7 @@ Erik B Knudsen \verb+<erkn@fysik.dtu.dk>+ \\ \DTUPHYSlong \\ -Peter Kj\ae r Willendrup \verb+<peter.willendrup@risoe.dk>+ \\ +Peter Kjær Willendrup \verb+<peter.willendrup@risoe.dk>+ \\ \DTUPHYSlong\\ Emmanuel Farhi \verb+<emmanuel.farhi@synchrotron-soleil.fr>+ \\ diff --git a/docs/manuals/mcxtrace/abstractpage_comp.tex b/docs/manuals/mcxtrace/abstractpage_comp.tex index e9a1ac4017..595fadb90c 100644 --- a/docs/manuals/mcxtrace/abstractpage_comp.tex +++ b/docs/manuals/mcxtrace/abstractpage_comp.tex @@ -18,7 +18,7 @@ \begin{quote} \label{p:authors} \vskip\baselineskip\noindent -Erik Bergb\"ack Knudsen \\ +Erik Bergbäck Knudsen \\ Physics Department, Techical Univerisity of Denmark, Kgs. Lyngby, Denmark\\ email: \verb+erkn@fysik.dtu.dk+ \vskip\baselineskip\noindent @@ -27,7 +27,7 @@ European Synchrotron Radiation Facility, Grenoble, France\\ email: \verb+aprodi@nbi.ku.dk+ \vskip\baselineskip\noindent -Peter Kj\ae r Willendrup \\ +Peter Kjær Willendrup \\ Physics Department, Techical Univerisity of Denmark, Kgs. Lyngby, Denmark\\ email: \verb+pkwi@fysik.dtu.dk+ \vskip\baselineskip\noindent diff --git a/docs/manuals/mcxtrace/astrox/MM_c.tex b/docs/manuals/mcxtrace/astrox/MM_c.tex new file mode 100644 index 0000000000..5d7236057f --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/MM_c.tex @@ -0,0 +1,51 @@ +\section{The \texttt{MM\_c} McXtrace Component} +Single Pore as part of the Silicon Pore Optics (SPO) as envisioned for the ATHENA+ space telescope. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016, Feb. 2017 +\end{itemize} + +\subsection*{Description} +A single pore is simulated, which may have thick walls. The top and bottom are curved cylindrically azimuthally, and according to the Wolter I optic lengthwise (sagitally). A parameter specifies whether this is hyperbolic or parabolic. The azimuthal curvature is defined by the parameter radius. This refers to the center of the pore. I.e the top and bottom plates have radius of curvature \textless{}radius+yheight/2\textgreater{} and \textless{}radius-yheight/2\textgreater{} respectively. + +To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{pore\_th} & & & \\ +\textbf{pore\_width} & & & \\ +\textbf{ring\_nr} & & & \\ +\textbf{radius\_m} & m & Ring radius of the upper (reflecting) plate of the pore at the optic centre. & \\ +\textbf{Z0} & m & Distance between optics centre plane and focal spot (essentially focal length). & \\ +\textbf{xwidth} & m & Width of the pore. & \\ +\textbf{pore\_height} & & & \\ +gap & m & Gap between the plate and the intersection plane with the hyperbolic section. (currently ignored) & 0 \\ +chamfer\_width & & & 0 \\ +length & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +side\_reflec & & Data file containing reflectivities of the side walls (LEFT and RIGHT). & "" \\ +size\_file & & & "" \\ +non\_specular\_file & & & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +primary & & If non-zero, the pore is considered a primary reflector, and extends towards negative z. I.e. the entry plane is behind the z=0-plane. If zero, the pore is considered secondary and extends from the z=0-plane and towards positive z. & 1 \\ +dalpha & deg & Offset to the alpha angle computed from the focal length. Useful for targeting the modified conical geometry (currently ignored). & 0 \\ +waviness & rad & Waviness of the reflecting surface. The slope error is assumed to be uniformly distributed in the interval [-waviness:waviness]. & 0 \\ +longw & & If non-zero, waviness is 1D and along the pore axis. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{MM\_c.comp}. +\end{itemize} +\IfFileExists{astrox/MM_c_static.tex}{\input{astrox/MM_c_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/MM_h.tex b/docs/manuals/mcxtrace/astrox/MM_h.tex new file mode 100644 index 0000000000..16aaefdf7a --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/MM_h.tex @@ -0,0 +1,54 @@ +\section{The \texttt{MM\_h} McXtrace Component} +Date: Feb. 2017 +Version: 1.1 +Release: McXtrace 1.2 +Origin: DTU Physics, DTU Space + +Single Pore as part of the Silicon Pore Optics (SPO) as envisioned for the ATHENA+ space telescope. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A single pore is simulated, which may have thick walls. The top and bottom are curved cylindrically azimuthally, and according to the Wolter I optic lengthwise (sagitally). This is the hyperbolic part. The azimuthal curvature is defined by the radius parameters. + +To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +Example: MM\_h( pore\_th=0, ring\_nr=1, Z0=12, pore\_width=0.83e-3, pore\_height=0.605e-3, chamfer\_width=0.17e-3, mirror\_reflec="mirror\_coating\_unity.txt", R\_d=0, size\_file="ref\_design\_breaks.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{pore\_th} & & & \\ +\textbf{ring\_nr} & & & \\ +\textbf{Z0} & m & Distance between intersection plane and the focal spot (essentially focal length). & \\ +\textbf{pore\_height} & m & Height of the pore. (Hence the inner radii are radius\_\{m,h\}-pore\_height) & \\ +\textbf{pore\_width} & & & \\ +chamfer\_width & & & 0 \\ +gap & m & Gap between intersection with parabolic section and actual plate. & 0 \\ +zdepth & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +side\_reflec & & Data file containing reflectivities of the side walls (LEFT and RIGHT). & "" \\ +size\_file & & & "" \\ +non\_specular\_file & & & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +waviness & & & 0 \\ +longw & & & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{MM\_h.comp}. +\end{itemize} +\IfFileExists{astrox/MM_h_static.tex}{\input{astrox/MM_h_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/MM_p.tex b/docs/manuals/mcxtrace/astrox/MM_p.tex new file mode 100644 index 0000000000..fef8bba476 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/MM_p.tex @@ -0,0 +1,54 @@ +\section{The \texttt{MM\_p} McXtrace Component} +Date: Feb. 2017 +Version: 1.1 +Release: McXtrace 1.2 +Origin: DTU Physics, DTU Space + +Single Pore as part of the Silicon Pore Optics (SPO) as envisioned for the ATHENA+ space telescope. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A single pore is simulated, which may have thick walls. The top and bottom are curved cylindrically azimuthally, and according to the Wolter I optic lengthwise (sagitally). A parameter specifies whether this is hyperbolic or parabolic. The azimuthal curvature is defined by the parameter radius. This refers to the center of the pore. I.e the top and bottom plates have radius of curvature \textless{}radius+pore\_height/2\textgreater{} and \textless{}radius-pore\_height/2\textgreater{} respectively. + +To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +Example: MM\_p( pore\_th=0, ring\_nr=1, Z0=12, pore\_width=0.83e-3 , pore\_height=0.605e-3, mirror\_reflec="mirror\_coating\_unity.txt", R\_d=0, size\_file="ref\_design\_breaks.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{pore\_th} & & & \\ +\textbf{ring\_nr} & & & \\ +\textbf{Z0} & m & Distance between optics centre plane and focal spot (essentially focal length). & \\ +\textbf{pore\_height} & m & Height of the pore. & \\ +\textbf{pore\_width} & & & \\ +chamfer\_width & m & Width of side walls. & 0 \\ +gap & m & Gap between the plate and the intersection plane with the hyperbolic section. & 0 \\ +zdepth & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +side\_reflec & & Data file containing reflectivities of the side walls (LEFT and RIGHT). & "" \\ +size\_file & & & "" \\ +non\_specular\_file & & & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +waviness & & & 0 \\ +longw & & & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{MM\_p.comp}. +\end{itemize} +\IfFileExists{astrox/MM_p_static.tex}{\input{astrox/MM_p_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Pore_c.tex b/docs/manuals/mcxtrace/astrox/Pore_c.tex new file mode 100644 index 0000000000..c50a967413 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Pore_c.tex @@ -0,0 +1,46 @@ +\section{The \texttt{Pore\_c} McXtrace Component} +Single Pore as part of the Silicon Pore Optics (SPO) as envisioned for the ATHENA+ space telescope. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A single pore is simulated, which may have thick walls. The top and bottom are curved cylindrically azimuthally, whereas they are straight sagitally. The primary parameter specifies whether this is a primary or secondary mirror. If primary they mirror extends backwards. The azimuthal curvature is defined by the parameter radius. This refers to the center of the pore. I.e the top and bottom plates have radius of curvature \textless{}radius+yheight/2\textgreater{} and \textless{}radius-yheight/2\textgreater{} respectively. + +To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{radius\_m} & m & Ring radius of the upper (reflecting) plate of the pore at the optic centre. & \\ +\textbf{Z0} & m & Distance between optics centre plane and focal spot (essentially focal length). & \\ +\textbf{xwidth} & m & Width of the pore. & \\ +\textbf{yheight} & m & Height of the pore. & \\ +gap & m & Gap between the plate and the intersection plane with the hyperbolic section. (currently ignored) & 0 \\ +chamferwidth & m & Width of side walls. & 0 \\ +length & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +side\_reflec & & Data file containing reflectivities of the side walls (LEFT and RIGHT). & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +primary & & If non-zero, the pore is considered a primary reflector, and extends towards negative z. I.e. the entry plane is behind the z=0-plane. If zero, the pore is considered secondary & 1 \\ +dalpha & deg & Offset to the alpha angle computed from the focal length. Useful for targeting the modified conical geometry (currently ignored). & 0 \\ +waviness & rad & Waviness of the pore reflecting surface. The slope error is assumed to be uniformly distributed in the interval [-waviness:waviness]. & 0 \\ +longw & & If non-zero, waviness is 1D and along the pore axis. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Pore\_c.comp}. +\end{itemize} +\IfFileExists{astrox/Pore_c_static.tex}{\input{astrox/Pore_c_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Pore_h.tex b/docs/manuals/mcxtrace/astrox/Pore_h.tex new file mode 100644 index 0000000000..ff40018777 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Pore_h.tex @@ -0,0 +1,47 @@ +\section{The \texttt{Pore\_h} McXtrace Component} +Single Pore as part of the Silicon Pore Optics (SPO) as envisioned for the ATHENA+ space telescope. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A single pore is simulated, which may have thick walls. The top and bottom are curved cylindrically azimuthally, and according to the Wolter I optic lengthwise (sagitally). This is the hyperbolic part. The azimuthal curvature is defined by the radius parameters. This refers to the center of the pore. I.e the top and bottom plates have radius of curvature \textless{}radius+yheight/2\textgreater{} and \textless{}radius-yheight/2\textgreater{} respectively. + +To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +Example: Pore\_h( radius\_m=0.286148, radius\_h=0.284333, zdepth=0.101504, Z0=12, xwidth=0.83e-3, yheight=0.605e-3, mirror\_reflec="mirror\_coating\_unity.txt", R\_d=0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{radius\_m} & m & Ring radius of the upper (reflecting) plate of the pore at the intersection with the parabolic section. & \\ +\textbf{radius\_h} & m & Ring radius of the upper (reflecting) plate of the pore at the edge closest to the focal point. & \\ +\textbf{Z0} & m & distance between intersection plane and the focal spot( essentially the focal length). & \\ +\textbf{xwidth} & m & Width of the pore. & \\ +\textbf{yheight} & m & Height of the pore. (Thus the inner radius is radius\_\{m,h\}-yehight. & \\ +chamferwidth & m & Width of side walls. & 0 \\ +gap & m & gap between intersection with parabolic section and actual plate. & 0 \\ +zdepth & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +side\_reflec & & Data file containing reflectivities of the side walls (LEFT and RIGHT). & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +waviness & & & 0 \\ +longw & & & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Pore\_h.comp}. +\end{itemize} +\IfFileExists{astrox/Pore_h_static.tex}{\input{astrox/Pore_h_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Pore_p.tex b/docs/manuals/mcxtrace/astrox/Pore_p.tex new file mode 100644 index 0000000000..aef9dca1ad --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Pore_p.tex @@ -0,0 +1,45 @@ +\section{The \texttt{Pore\_p} McXtrace Component} +Single Pore as part of the Silicon Pore Optics (SPO) as envisioned for the ATHENA+ space telescope. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A single pore is simulated, which may have thick walls. The top and bottom are curved cylindrically azimuthally, and according to the Wolter I optic lengthwise (sagitally). This is the parabolic part. The azimuthal curvature is defined by the radius parameters. This refers to the center of the pore. I.e the top and bottom plates have radius of curvature \textless{}radius+yheight/2\textgreater{} and \textless{}radius-yheight/2\textgreater{} respectively. + +To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{radius\_p} & m & Ring radius of the upper (reflecting) plate of the pore at the edge furthest away from the focal point. & \\ +\textbf{radius\_m} & m & Ring radius of the upper (reflecting) plate of the pore at the intersection with the hyperbolic section. & \\ +\textbf{Z0} & m & distance between intersection plane and the focal spot( essentially the focal length). & \\ +\textbf{xwidth} & m & Width of the pore. & \\ +\textbf{yheight} & m & Height of the pore. (Thus the inner radius is radius\_\{m,h\}-yehight. & \\ +gap & m & gap between intersection with parabolic section and actual plate. & 0 \\ +chamferwidth & m & Width of side walls. & 0 \\ +zdepth & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +side\_reflec & & Data file containing reflectivities of the side walls (LEFT and RIGHT). & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +waviness & & & 0 \\ +longw & & & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Pore\_p.comp}. +\end{itemize} +\IfFileExists{astrox/Pore_p_static.tex}{\input{astrox/Pore_p_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Ring_c.tex b/docs/manuals/mcxtrace/astrox/Ring_c.tex new file mode 100644 index 0000000000..e987dd4653 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Ring_c.tex @@ -0,0 +1,49 @@ +\section{The \texttt{Ring\_c} McXtrace Component} +Date: Feb. 2017 +Version: 1.1 +Release: McXtrace 1.2 +Origin: DTU Physics, DTU Space + +Stack of conical shells as part of a Wolter optic. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A stack of conical shells is simulated. To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{ring\_nr} & & & \\ +\textbf{radius\_m} & m & Ring radius of the upper (reflecting) plate of the shell at the optic centre. & \\ +\textbf{Z0} & m & Distance between optics centre plane and focal spot (essentially focal length). & \\ +\textbf{xwidth} & & & \\ +\textbf{yheight} & m & Height of the shell. & \\ +gap & m & Gap between the plate and the intersection plane with the hyperbolic section. (currently ignored) & 0 \\ +chamferwidth & m & Width of side walls. & 0 \\ +length & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +primary & & If non-zero, the shell is considered a primary reflector, and extends towards negative z. I.e. the entry plane is behind the z=0-plane. If zero, the shell is considered secondary & 1 \\ +dalpha & deg & Offset to the alpha angle computed from the focal length. Useful for targeting the modified conical geometry (currently ignored). & 0 \\ +waviness & rad & Waviness of the shell reflecting surface. The slope error is assumed to be uniformly distributed in the interval [-waviness:waviness]. & 0 \\ +longw & & If non-zero, waviness is 1D and along the shell axis. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Ring\_c.comp}. +\end{itemize} +\IfFileExists{astrox/Ring_c_static.tex}{\input{astrox/Ring_c_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Ring_h.tex b/docs/manuals/mcxtrace/astrox/Ring_h.tex new file mode 100644 index 0000000000..111e8e7e74 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Ring_h.tex @@ -0,0 +1,49 @@ +\section{The \texttt{Ring\_h} McXtrace Component} +Date: Feb. 2017 +Version: 1.1 +Release: McXtrace 1.2 +Origin: DTU Physics, DTU Space + +Stack of conical shells as part of a Wolter optic. Hyperbolic version. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A stack of conical shells is simulated. Hyperbolic version. To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +Example: Ring\_h( pore\_th=0, ring\_nr=3, Z0=12, yheight=0.83e-3, mirror\_reflec="mirror\_coating\_unity.txt", R\_d=0, size\_file="ref\_design\_breaks.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{ring\_nr} & & & \\ +\textbf{pore\_th} & & & \\ +\textbf{Z0} & m & distance between intersection plane and the focal spot( essentially the focal length). & \\ +\textbf{yheight} & m & Height of the pore. (Thus the inner radius is radius\_\{m,h\}-yheight & \\ +chamferwidth & m & Width of side walls. & 0 \\ +gap & m & gap between intersection with parabolic section and actual plate. & 0 \\ +zdepth & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +size\_file & & & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +waviness & rad & Waviness of the pore reflecting surface. The slope error is assumed to be uniformly distributed in the interval [-waviness:waviness]. & 0 \\ +longw & & If non-zero, waviness is 1D and along the pore axis. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Ring\_h.comp}. +\end{itemize} +\IfFileExists{astrox/Ring_h_static.tex}{\input{astrox/Ring_h_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Ring_p.tex b/docs/manuals/mcxtrace/astrox/Ring_p.tex new file mode 100644 index 0000000000..4681086a80 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Ring_p.tex @@ -0,0 +1,49 @@ +\section{The \texttt{Ring\_p} McXtrace Component} +Date: Feb. 2017 +Version: 1.1 +Release: McXtrace 1.2 +Origin: DTU Physics, DTU Space + +Stack of conical shells as part of a Wolter optic. Parabolic version. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A stack of conical shells is simulated. Parabolic version. To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +Example: Ring\_p( pore\_th=0, ring\_nr=3, Z0=FL, yheight=0.605e-3, mirror\_reflec="mirror\_coating\_unity.txt", R\_d=0, size\_file="ref\_design\_breaks.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{ring\_nr} & & & \\ +\textbf{pore\_th} & & & \\ +\textbf{Z0} & m & Distance between optics centre plane and focal spot (essentially focal length). & \\ +\textbf{yheight} & m & Height of the pore. & \\ +chamferwidth & m & Width of side walls. & 0 \\ +gap & m & Gap between the plate and the intersection plane with the hyperbolic section. & 0 \\ +zdepth & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +size\_file & & & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +waviness & rad & Waviness of the pore reflecting surface. The slope error is assumed to be uniformly distributed in the interval [-waviness:waviness]. & 0 \\ +longw & & If non-zero, waviness is 1D and along the pore axis. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Ring\_p.comp}. +\end{itemize} +\IfFileExists{astrox/Ring_p_static.tex}{\input{astrox/Ring_p_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Shell_c.tex b/docs/manuals/mcxtrace/astrox/Shell_c.tex new file mode 100644 index 0000000000..ca4dc9cfa4 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Shell_c.tex @@ -0,0 +1,46 @@ +\section{The \texttt{Shell\_c} McXtrace Component} +Single conical shell as part of a Wolter optic. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A single shell is simulated. The top and bottom are curved cylindrically azimuthally, whereas they are straight sagitally. The primary parameter specifies whether this is a primary or secondary mirror. The azimuthal curvature is defined by the parameter radius. This refers to the top plate of the shell. I.e the top and bottom plates have radius of curvature \textless{}radius\textgreater{} and \textless{}radius-yheight\textgreater{} respectively. + +To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +Example: Shell\_c( radius\_m=0.535532,Z0=12,yheight=1e-2,length=0.5,primary=0, R\_d=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{radius\_m} & m & Ring radius of the upper (reflecting) plate of the shell at the optic centre. & \\ +\textbf{Z0} & m & Distance between optics centre plane and focal spot (essentially focal length). & \\ +\textbf{yheight} & m & Height of the shell. & \\ +gap & m & Gap between the plate and the intersection plane with the hyperbolic section. (currently ignored) & 0 \\ +chamferwidth & m & Width of side walls. & 0 \\ +length & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +primary & & If non-zero, the shell is considered a primary reflector, and extends towards negative z. I.e. the entry plane is behind the z=0-plane. If zero, the shell is considered secondary & 1 \\ +dalpha & deg & Offset to the alpha angle computed from the focal length. Useful for targeting the modified conical geometry (currently ignored). & 0 \\ +waviness & rad & Waviness of the shell reflecting surface. The slope error is assumed to be uniformly distributed in the interval [-waviness:waviness]. & 0 \\ +longw & & If non-zero, waviness is 1D and along the shell axis. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Shell\_c.comp}. +\end{itemize} +\IfFileExists{astrox/Shell_c_static.tex}{\input{astrox/Shell_c_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Shell_h.tex b/docs/manuals/mcxtrace/astrox/Shell_h.tex new file mode 100644 index 0000000000..ca1e9e4282 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Shell_h.tex @@ -0,0 +1,67 @@ +\section{The \texttt{Shell\_h} McXtrace Component} +Single Pore as part of the Silicon Pore Optics (SPO) as envisioned for the ATHENA+ space telescope. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A single shell is simulated. The top and bottom are curved cylindrically azimuthally, and according to the Wolter I optic lengthwise (sagitally). This is the hyperbolic part. The azimuthal curvature is defined by the radius parameters. + +To intersect the Wolter I plates we take advantage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +Imperfect mirrors may be modelled using one of 4 models. In all cases the surface normal of the mirror at the ideal mirror intersection point is perturbed before the exit vector is computed. 1. Longitudinal 1D. A perturbation angle is chosen from a uniform distribution with width waviness. 2. Isotropic 2D. The surface normal is perturbed by choosing an angle on a disc with radius waviness 3. Externally measured/computed data. We interpolate in a data-file consisting of blocks of dtheta/theta with 1 block per energy. dtheta is a sampled angle offset from the nominal Fresnel grazing angle theta. 4. Double gaussian. dtheta is chosen from one of two gaussian distributions. Either specular or off-specular, where the widths (sigmas) are given by the tables in the file "wave\_file". If the off-specular case the behaviour is similar to 2D uniform case. + +In the case of 3, the format of the data file should be: \#e\_min=0.1 \#e\_max=15 \#e\_step=0.01 \#theta\_min=0.01 \#theta\_max=1.5 \#theta\_step=0.01 \#dtheta\_min=-0.02 \#dtheta\_max=0.02 \#dtheta\_step=0.001 + +\begin{verbatim} +1.0 0.9 0.8 0.75 ... +0.99 0.89 0.79 0.749 ... +\end{verbatim} + +... \#block 2 (energy data point 2) + +\begin{verbatim} +1.0 0.9 0.8 0.75 ... +0.99 0.89 0.79 0.749 ... +\end{verbatim} + +... + +I.e. one 2D data block per energy data point where rows represent the steps in nominal incident angle, and columns represent the sampled granularity of the off-specular scattering. + +Example: Shell\_h( radius\_m=0.535532, radius\_h=0.533113, zdepth=0.5, Z0=FL, yheight=1e-2, R\_d=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{radius\_m} & m & Ring radius of the upper (reflecting) plate of the pore at the intersection with the parabolic section. & \\ +\textbf{radius\_h} & m & Ring radius of the upper (reflecting) plate of the pore at the edge closest to the focal point. & \\ +\textbf{Z0} & m & distance between intersection plane and the focal spot( essentially the focal length). & \\ +\textbf{yheight} & m & Height of the pore. (Thus the inner radius is radius\_\{m,h\}-yehight & \\ +chamferwidth & m & Width of side walls. & 0 \\ +gap & m & gap between intersection with parabolic section and actual plate. & 0 \\ +zdepth & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +wave\_file & & & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +wave\_model & & Flag to choose waviness model. 1. longitudinal uniform, 2. 2D-uniform, 3. lorentzian sagittal, 4. double gaussian sagittal. See above for details. & 0 \\ +waviness & rad & Waviness of the pore reflecting surface. The slope error is assumed to be uniformly distributed in the interval [-waviness:waviness]. & 0 \\ +verbose & & If !=0 output extra info during simulation. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Shell\_h.comp}. +\end{itemize} +\IfFileExists{astrox/Shell_h_static.tex}{\input{astrox/Shell_h_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Shell_p.tex b/docs/manuals/mcxtrace/astrox/Shell_p.tex new file mode 100644 index 0000000000..d7c1851451 --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Shell_p.tex @@ -0,0 +1,67 @@ +\section{The \texttt{Shell\_p} McXtrace Component} +Single parabolic shell as part of a Wolter optic. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen and Desiree D. M. Ferreira + \item \textbf{Origin:} DTU Physics, DTU Space + \item \textbf{Date:} Feb. 2016 +\end{itemize} + +\subsection*{Description} +A single shell is simulated. The top and bottom are curved cylindrically azimuthally. The sagital profile is defined by a parabola, which passes through the radii raidus\_m at z=0, and radius\_p at zentry (\textless{}0). + +To intersect the Wolter I plates we take advatage of the azimuthal symmetry and only consider the radial component of the photon's wavevector. + +Imperfect mirrors may be modelled using one of 4 models. In all cases the surface normal of the mirror at the ideal mirror intersection point is perturbed before the exit vector is computed. 1. Longitudinal 1D. A perturbation angle is chosen from a uniform distribution with width waviness. 2. Isotropic 2D. The surface normal is perturbed by choosing an angle on a disc with radius waviness 3. Externally measured/computed data. We interpolate in a data-file consisting of blocks of dtheta/theta with 1 block per energy. dtheta is a sampled angle offset from the nominal Fresnel grazing angle theta. 4. Double gaussian. dtheta is chosen from one of two gaussian distributions. Either specular or off-specular, where the widths (sigmas) are given by the tables in the file "wave\_file". If the off-specular case the behaviour is similar to 2D uniform case. + +In the case of 3, the format of the data file should be: \#e\_min=0.1 \#e\_max=15 \#e\_step=0.01 \#theta\_min=0.01 \#theta\_max=1.5 \#theta\_step=0.01 \#dtheta\_min=-0.02 \#dtheta\_max=0.02 \#dtheta\_step=0.001 + +\begin{verbatim} +1.0 0.9 0.8 0.75 ... +0.99 0.89 0.79 0.749 ... +\end{verbatim} + +... \#block 2 (energy data point 2) + +\begin{verbatim} +1.0 0.9 0.8 0.75 ... +0.99 0.89 0.79 0.749 ... +\end{verbatim} + +... + +I.e. one 2D data block per energy data point where rows represent the steps in nominal incident angle, and columns represent the sampled granularity of the off-specular scattering. + +Example: Shell\_p( radius\_p=0.535532, radius\_m=0.533113, zdepth=0.5, Z0=12, yheight=1e-2, R\_d=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\textbf{radius\_p} & m & Ring radius of the upper (reflecting) plate of the shell at the edge furthest away from the focal point. & \\ +\textbf{radius\_m} & m & Ring radius of the upper (reflecting) plate of the shell at the intersection with the hyperbolic section. & \\ +\textbf{Z0} & m & Distance between optics centre plane and focal spot (essentially focal length). & \\ +\textbf{yheight} & m & Height of the shell. & \\ +chamferwidth & m & Width of side walls. & 0 \\ +gap & m & Gap between the plate and the intersection plane with the hyperbolic section. & 0 \\ +zdepth & & & 0 \\ +mirror\_reflec & & Data file containing reflectivities of the reflector surface (TOP). & "" \\ +bottom\_reflec & & Data file containing reflectivities of the bottom surface (BOTTOM). & "" \\ +wave\_file & & & "" \\ +R\_d & & Default reflectivity value to use if no reflectivity file is given. Useful f.i. is one surface is reflecting and the others absorbing. & 1 \\ +wave\_model & & Flag to choose waviness model. 1. longitudinal uniform, 2. 2D-uniform, 3. lorentzian sagittal, 4. double gaussian sagittal. See above for details. & 0 \\ +waviness & rad & Waviness of the pore reflecting surface. The slope error is assumed to be uniformly distributed in the interval "[-waviness:waviness]". & 0 \\ +verbose & & If !=0 output extra info during simulation. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Shell\_p.comp}. +\end{itemize} +\IfFileExists{astrox/Shell_p_static.tex}{\input{astrox/Shell_p_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/astrox/Source_extended.tex b/docs/manuals/mcxtrace/astrox/Source_extended.tex new file mode 100644 index 0000000000..189859829b --- /dev/null +++ b/docs/manuals/mcxtrace/astrox/Source_extended.tex @@ -0,0 +1,47 @@ +\section{The \texttt{Source\_extended} McXtrace Component} +Release: McXtrace 1.4 + +A plane source emitting x-rays to emulate a distant extended source, such as a +nebula or galaxy + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Arne 'S Jegers + \item \textbf{Origin:} Technical University of Denmark + \item \textbf{Date:} May 6, 2019 +\end{itemize} + +\subsection*{Description} +A rectangular x-ray source that samples ray intensity from an image, and deflects the emitted ray to reflect having been emitted from the sampled part of the extended source. Rays that are sampled from the same point on the image are collimated, but can be emitted from anywhere on the rectangular source. The image should be provided as a 2D-ascii table, whose header includes the following entries: + +w\_pixels and h\_pixels: The width and height of the image in pixels x\_ref and y\_ref: x and y reference values of the FITS image r\_max: The maximum distance from the point (x\_ref, y\_ref) to any corner of the image iCD11, iCD12, iCD21 and iCD22: The values of the FITS image's CD matrix + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +spectrum\_file & & & NULL \\ +yheight & m & Height of rectangle in (x,y,0) plane where x-rays & 0 \\ +xwidth & m & Width of rectangle in (x,y,0) plane where x-rays & 0 \\ +dist & & & 0 \\ +E0 & keV & Mean energy of xrays. & 0 \\ +dE & keV & Energy half spread of x-rays (flat or gaussian sigma). & 0 \\ +lambda0 & \AA{} & Mean wavelength of x-rays. & 0 \\ +dlambda & \AA{} & Wavelength half spread of x-rays. & 0 \\ +flux & pht/s & total flux radiated from the source & 0 \\ +gauss & 1 & Gaussian (1) or Flat (0) energy/wavelength distribution & 0 \\ +incoherent & & Source is fully incoherent & 1 \\ +phase & & Set phase to something given. & 0 \\ +image\_path & string & Path to file containing the heat map of the source & "" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_extended.comp}. +\end{itemize} +\IfFileExists{astrox/Source_extended_static.tex}{\input{astrox/Source_extended_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/Attenuating_mask.tex b/docs/manuals/mcxtrace/contrib/Attenuating_mask.tex new file mode 100644 index 0000000000..e13f5e733b --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/Attenuating_mask.tex @@ -0,0 +1,38 @@ +\section{The \texttt{Attenuating\_mask} McXtrace Component} +Attenuating\_mask + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Matteo Busi, Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} November 2017 +\end{itemize} + +\subsection*{Description} +This component models a mask of energy dependent attenuation. This consists of a rectangular grid of size "xwidth*yheight", composed of multiple disks of finite thickness "zdepth" of an attenuating material "att\_file", width "blocks\_width" and period "blocks\_dist"(i.e. distance between the center of each disk). If holed\_mask mode is turned the model of the component is the opposite, i.e. the mask is composed of an attenuating slab of finite thickness and of size "xwidth*yheight", with apertures of desired width and period. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +att\_file & ".txt" & File that contains the object information. (Default: "W.txt") & "W.txt" \\ +xwidth & m & Horizontal width of the mask. (Default: 1e-1) & 1e-1 \\ +yheight & m & Vertical height of the mask. (Default: 1e-1) & 1e-1 \\ +zdepth & m & Thickness of the absorbing mask. (Default: 3e-3) & 10e-6 \\ +blocks\_xwidth & m & Width of the absorbing blocks in the x-direction. (Default: 3e-3) & 1e-3 \\ +blocks\_xdist & m & Distance between absorbing blocks in the x-direction. (Default: 10e-3) & 2.5e-3 \\ +blocks\_yheight & m & Height of the absorbing blocks in the y-direction. (Default: 3e-3) & 1e-3 \\ +blocks\_ydist & m & Distance between absorbing blocks in the y-direction. (Default: 10e-3) & 2.5e-2 \\ +holed\_mask & 1 & Set to 1 if the mask is a holed grid. (Default: 0) & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Attenuating\_mask.comp}. +\end{itemize} +\IfFileExists{contrib/Attenuating_mask_static.tex}{\input{contrib/Attenuating_mask_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/Bragg_crystal_BC.tex b/docs/manuals/mcxtrace/contrib/Bragg_crystal_BC.tex new file mode 100644 index 0000000000..9eaba353d3 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/Bragg_crystal_BC.tex @@ -0,0 +1,65 @@ +\section{The \texttt{Bragg\_crystal\_BC} McXtrace Component} +Perfect, reflecting crystal with common cubic structures (diamond, fcc, or bcc, and others if symmetry form factor multipliers provided explicitly) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Marcus H Mendenhall, NIST \textless{}marcus.mendenhall@nist.gov\textgreater{} + \item \textbf{Origin:} NIST + \item \textbf{Date:} May, 2017 +\end{itemize} + +\subsection*{Description} +Bragg\_crystal\_BC.comp is intended to supercede Bragg\_Crystal.comp. + +For details see: The optics of focusing bent-crystal monochromators on X-ray powder diffractometers with application to lattice parameter determination and microstructure analysis, Marcus H. Mendenhall, David Black and James P. Cline, J. Appl. Cryst. (2019). 52, https://doi.org/10.1107/S1600576719010951 + +Reads atomic formfactors from a data input file. The Bragg\_Crystal code reflects ray in an ideal geometry, does not include surface imperfections or mosaicity + +The crystal code reflects ray in an ideal geometry, i.e. does not include surface imperfections or mosaicity. The crystal planes from which the reflection is made lies in the X-Z plane on the unbent crystal rotated by an angle alpha about the Y axis with respect to the crystal surface. + +The crystal itself is set in the X-Z plane positioned such that the long axis of the crystal surface coincides with the Z-axis, withs normal pointing in the poisitivce Y-direction. + +N.B. The component does not work for rays hitting the back of the monochromator. + +Bragg\_crystal\_BC.comp is written by Marcus H. Mendenhall, NIST, Gaithersburg, MD, USA It is based on the full vector math and exact solution of the dispersion relation in Batterman and Cole, Reviews of Modern Physics 36 number 3, page 681, July 1964 + +This code has been validated against both experimental data (2 channel-cut 3-bounce Si 440 crystals together in non-dispersive mode, at Cu kalpha) and against theoretical rocking rocking curves from XOP for Si220 at Sc kalpha and Si440 at Cu kalpha. + +Non-copyright notice: Contributed by the National Institute of Standards and Technology; not subject to copyright in the United States. This is not an official contribution, in that the results are in no way certified by NIST. + +Example: Bragg\_crystal\_BC( length=0.05, width=0.02, V=160.1826, h=1, k=1, l=1, alphay=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +length & m & z depth (length) of the crystal. & 0.05 \\ +width & m & x width of the crystal. & 0.02 \\ +V & \AA{}$^{3}$ & unit cell volume & 160.1826 \\ +form\_factors & & & "FormFactors.txt" \\ +material & & Si, Ge (maybe also GaAs?) & "Si.txt" \\ +alphax & & & 0.0 \\ +alphay & & & 1.0 \\ +alphaz & & & 0.0 \\ +R0 & & Reflectivity. Overrides the computed Darwin reflectivity. Probably only useful for debugging. & 0 \\ +debye\_waller\_B & \AA{}$^{2}$ & Debye-Waller temperature factor, M=B*(sin(theta)/lambda)\textasciicircum{}2*(2/3), default=silicon at room temp. & 0.4632 \\ +crystal\_type & & 1 =\textgreater{} Mx\_crystal\_explicit: provide explicit real and imaginary form factor multipliers structure\_factor\_scale\_r, structure\_factor\_scale\_i; 2 =\textgreater{} Mx\_crystal\_diamond: diamond; 3 =\textgreater{} Mx\_crystal\_fcc: fcc; 4 =\textgreater{} Mx\_crystal\_fcc: bcc & 1 \\ +h & & Miller index of reflection & 1 \\ +k & & Miller index of reflection & 1 \\ +l & & Miller index of reflection & 1 \\ +structure\_factor\_scale\_r & & & 0.0 \\ +structure\_factor\_scale\_i & & & 0.0 \\ +verbose & & if non-zero: Output more information (warnings and messages) to the console. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Bragg\_crystal\_BC.comp}. + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{contrib/Bragg_crystal_BC_static.tex}{\input{contrib/Bragg_crystal_BC_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/Bragg_crystal_bent_BC.tex b/docs/manuals/mcxtrace/contrib/Bragg_crystal_bent_BC.tex new file mode 100644 index 0000000000..117435c021 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/Bragg_crystal_bent_BC.tex @@ -0,0 +1,69 @@ +\section{The \texttt{Bragg\_crystal\_bent\_BC} McXtrace Component} +Bent, perfect crystal with common cubic structures (diamond, fcc, or bcc, and others if symmetry form factor multipliers provided explicitly) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Marcus H Mendenhall, NIST \textless{}marcus.mendenhall@nist.gov\textgreater{} + \item \textbf{Origin:} NIST + \item \textbf{Date:} Dec 2016 +\end{itemize} + +\subsection*{Description} +Bragg\_crystal\_bent\_BC.com is intended to supercede Bragg\_Crystal\_bent.comp For details see: The optics of focusing bent-crystal monochromators on X-ray powder diffractometers with application to lattice parameter determination and microstructure analysis, Marcus H. Mendenhall,* David Black and James P. Cline, J. Appl. Cryst. (2019). 52, https://doi.org/10.1107/S1600576719010951 + +Reads atomic formfactors from a data input file. The Bragg\_Crystal code reflects ray in an ideal geometry, does not include surface imperfections or mosaicity + +The crystal code reflects ray in an ideal geometry, i.e. does not include surface imperfections or mosaicity. The crystal planes from which the reflection is made lies in the X-Z plane on the unbent crystal rotated by an angle alpha about the Y axis with respect to the crystal surface. + +The crystal itself is set in the X-Z plane positioned such that the long axis of the crystal surface coincides with the Z-axis, withs normal pointing in the poisitivce Y-direction. + +The asummetry angle alpha is defined so that positive alpha reduces the Bragg angle to the plane i.e. alpha=Thetain grazes the planes. if alpha!=0, one should restrict to rays which have small kx values, since otherwise the alpha rotation is not around the diffraction axis. + +The mirror is positioned such that the a-axis of the mirror ellipsoid is on the z-axis, the b-axis is along the y-axis and the c is along the x-axis. The reference point of the mirror is the ellipsoid centre, offset by one half-axis along the y-axis. (See the component manual for a drawing). + +Notation follows Tadashi Matsushita and Hiro-O Hashizume, X-RAY MONOCHROMATORS. Handbook on Synchrotron Radiation,North-Holland Publishing Company, 1:263–274, 1983. + +NOTE: elliptical coordinate code and documentation taken from Mirror\_elliptic.comp distributed in McXtrace v1.2 written by: Erik Knudsen. However, the coordinates are rotated to be consistent with Perfect\_Crystal.comp and NIST\_Perfect\_Crystal.comp Idealized elliptic mirror with surface ellipse and lattice ellipses independent, to allow construction of Johansson optics, for example. + +Non-copyright notice: Contributed by the National Institute of Standards and Technology; not subject to copyright in the United States. This is not an official contribution, in that the results are in no way certified by NIST. + +Example: Bragg\_crystal\_bent\_BC( length=0.05, width=0.02, V=160.1826, h=1, k=1, l=1, alpha=0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +x\_a & m & 1st short half axis (along x). Commonly set to zero, which really implies infinite value, so crystal is an elliptic cylinder. & 0 \\ +y\_b & m & 2nd short half axis (along y), which is also the presumed near-normal direction, reflection near the y-z plane. & 1.0 \\ +z\_c & m & Long half axis (along z). Commonly a=0. b=c, which creates a circular cylindrical surface. & 1.0 \\ +lattice\_x\_a & m & Curvature matrix component around a for underlying lattice, for bent/ground/rebent crystals & 0 \\ +lattice\_y\_b & m & Curvature matrix component around b for underlying lattice, for bent/ground/rebent crystals & 1.0 \\ +lattice\_z\_c & m & curvature matrix component around c for underlying lattice, for bent/ground/rebent crystals THERE HAS BEEN NO TESTING for the case in which lattice\_x\_a != x\_a. & 1.0 \\ +length & m & z depth (length) of the crystal. & 0.05 \\ +width & m & x width of the crystal. & 0.02 \\ +V & \AA{}$^{3}$ & unit cell volume & 160.1826 \\ +form\_factors & & & "FormFactors.txt" \\ +material & & Si, Ge (maybe also GaAs?) & "Si.txt" \\ +alpha & rad & Asymmetry angle (alpha=0 for symmetric reflection, i.e. the Bragg planes are parallel to the crystal surface) & 0.0 \\ +R0 & & Reflectivity. Overrides the computed Darwin reflectivity. Probably only useful for debugging. & 0 \\ +debye\_waller\_B & \AA{}$^{2}$ & Debye-Waller temperature factor, M=B*(sin(theta)/lambda)\textasciicircum{}2*(2/3), default=silicon at room temp. & 0.4632 \\ +crystal\_type & & 1 =\textgreater{} Mx\_crystal\_explicit: provide explicit real and imaginary form factor multipliers structure\_factor\_scale\_r, structure\_factor\_scale\_i; 2 =\textgreater{} Mx\_crystal\_diamond: diamond; 3 =\textgreater{} Mx\_crystal\_fcc: fcc; 4 =\textgreater{} Mx\_crystal\_fcc: bcc & 1 \\ +h & & Miller index of reflection & 1 \\ +k & & Miller index of reflection & 1 \\ +l & & Miller index of reflection & 1 \\ +structure\_factor\_scale\_r & & & 0.0 \\ +structure\_factor\_scale\_i & & & 0.0 \\ +verbose & & if non-zero: Output more information (warnings and messages) to the console. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Bragg\_crystal\_bent\_BC.comp}. + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{contrib/Bragg_crystal_bent_BC_static.tex}{\input{contrib/Bragg_crystal_bent_BC_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/Bragg_crystal_simple.tex b/docs/manuals/mcxtrace/contrib/Bragg_crystal_simple.tex new file mode 100644 index 0000000000..dde5d5511f --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/Bragg_crystal_simple.tex @@ -0,0 +1,40 @@ +\section{The \texttt{Bragg\_crystal\_simple} McXtrace Component} +Perfect Bragg reflecting slab + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose I. Robledo + \item \textbf{Origin:} FaMAF - UNC, Argentina + \item \textbf{Date:} February 2016 +\end{itemize} + +\subsection*{Description} +Rectangle of matter perfectly reflecting the incident X-ray beam that fulfills Bragg's law for a set of scattering vectors in the vicinity of the theoretical Q given a d-spacing. The rectangle is in the x-y plane. + +Example: Bragg\_crystal\_simple( yheight=0.05, xwidth=0.02, DM=3.1356, err\_Q= 0.000075, r0=1.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +xmin & & & 1.0 \\ +xmax & & & 1.0 \\ +ymin & & & 1.0 \\ +ymax & & & 1.0 \\ +xwidth & m & Width in the x direction & 0.0 \\ +yheight & m & Height in the y direction & 0.0 \\ +r0 & & Maximum reflectivity & 1 \\ +DM & \AA{}$^{-1}$ & d-spacing of the crystal & 0 \\ +err\_Q & & dQ/Q relative error of the modulus of Q vector. Approximates the Darwin width of the crystal. & 0.0001 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Bragg\_crystal\_simple.comp}. +\end{itemize} +\IfFileExists{contrib/Bragg_crystal_simple_static.tex}{\input{contrib/Bragg_crystal_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/Detector_pn.tex b/docs/manuals/mcxtrace/contrib/Detector_pn.tex new file mode 100644 index 0000000000..118f1c4fdf --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/Detector_pn.tex @@ -0,0 +1,42 @@ +\section{The \texttt{Detector\_pn} McXtrace Component} +Version: McXtrace 1.2 + +Block of a attenuating material + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Maria Thomsen (mariath@fys.ku.dk) + \item \textbf{Origin:} NBI, KU + \item \textbf{Date:} Jan 24, 2011 +\end{itemize} + +\subsection*{Description} +A scintillator detector model taking photoabsorption efficiency into account. As such it consitututes a more physical version of the PSD\_monitor. Only direct absorption is taken into account. + +Example: Detector\_pn(restore\_xray=restore\_flag,filename="detector\_Si", material\_datafile="Si.txt", xwidth=1e-2, yheight=1e-2,zdepth=1e-5) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_datafile & str & File where the material parameters for the scintillator may be found. Format is similar to what may be found off the NIST website. & "Be.txt" \\ +nx & m & Number of pixel columns. & 90 \\ +ny & m & Number of pixel rows. & 90 \\ +filename & str & Name of file in which to store the detector image. & "" \\ +restore\_xray & & If set, the monitor does not influence the xray state. & 0 \\ +xwidth & m & Width of block. & 1e-2 \\ +yheight & m & Height of block. & 1e-2 \\ +zdepth & m & Thickness of block. & 1e-6 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Detector\_pn.comp}. + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{contrib/Detector_pn_static.tex}{\input{contrib/Detector_pn_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/Laue_crystal_BC.tex b/docs/manuals/mcxtrace/contrib/Laue_crystal_BC.tex new file mode 100644 index 0000000000..0e14905f2f --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/Laue_crystal_BC.tex @@ -0,0 +1,57 @@ +\section{The \texttt{Laue\_crystal\_BC} McXtrace Component} +Perfect, Laue crystal with common cubic structures (diamond, fcc, or bcc, and others if symmetry form factor multipliers provided explicitly) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Marcus H Mendenhall, NIST \textless{}marcus.mendenhall@nist.gov\textgreater{} + \item \textbf{Origin:} NIST + \item \textbf{Date:} June, 2017 +\end{itemize} + +\subsection*{Description} +NIST\_Laue\_crystal\_BC.comp is written by Marcus H. Mendenhall, NIST, Gaithersburg, MD, USA It is based on the full vector math and exact solution of the dispersion relation in Batterman and Cole, Reviews of Modern Physics 36 number 3, page 681, July 1964 Perfect crystal with common cubic structures (diamond, fcc, or bcc, and others if symmetry form factor multipliers provided explicitly) + +Reads atomic form factors from a data input file. The Laue\_Crystal code reflects rays in an ideal geometry, does not include surface imperfections or mosaicity. + +The crystal is positioned such that the long axis of the crystal surface coincides with z-axis and the outer normal to the crystal surface is along +y. + +The ratio of the transmitted beam and forward-diffracted Borrman-effect beam is a hack. The sum of the two is exactly right, but the actual ratio depends critically on geometry, and I just put in a wild estimate to allow one to demonstrate what the Borrmann effect looks like. If this is turned on, the displacement of the transmitted beam and forward diffracted beam at the back side of the crystal will be correctly computed. This displacement is only exact for symmetrical Laue; asymmetrical computation requires more effort, and is probably not worth it. The sampling of these processes are controlled by the 3 variables transmission\_sampling, forward\_diffraction\_sampling, and Laue\_sampling. Since 99\% of uses of this will have the transmitted beam turned off, and use Laue diffraction mode, the values should be just 0,0,1. If the general behavior of the transmitted beams is interesting, use 1,1,1 which samples all beams equally. Results weights are adjusted for this, so computed intensities won't be affected. + +Non-copyright notice: Contributed by the National Institute of Standards and Technology; not subject to copyright in the United States. This is not an official contribution, in that the results are in no way certified by NIST. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +length & m & zdepth (length) of the crystal. & 0.05 \\ +width & m & width of the crystal. & 0.02 \\ +thickness & m & thickness of crystal (along y-axis, the surface normal) & 1e-4 \\ +V & \AA{}$^{3}$ & unit cell volume & 160.1826 \\ +form\_factors & & "FormFactors.txt" from McXtrace install, usually & "FormFactors.txt" \\ +material & & Si ("Si.txt"), Ge ("Ge.txt") & "Si.txt" \\ +alphax & & x component of normal (unit vector) to crystal planes. Vector is usually [0,0,1] for symmetric Laue. Crystal surface itself has normal [0,1,0]. & 0.0 \\ +alphay & & y component of normal (unit vector) to crystal planes. & 0.0 \\ +alphaz & & z component of normal (unit vector) to crystal planes. & 1.0 \\ +debye\_waller\_B & \AA{}$^{2}$ & Debye-Waller temperature factor, M=B*(sin(theta)/lambda)\textasciicircum{}2*(2/3), default=silicon at room temp, 0.4632 & 0.4632 \\ +crystal\_type & & 1 =\textgreater{} Mx\_crystal\_explicit: provide explicit real and imaginary form factor multipliers structure\_factor\_scale\_r, structure\_factor\_scale\_i, & 1 \\ +h & & 1st Miller index of reflection & 1 \\ +k & & 2nd Miller index of reflection & 1 \\ +l & & 3rd Miller index of reflection & 1 \\ +structure\_factor\_scale\_r & & real part of complex explicit override of structure factor multiplier for crystal structure if Bragg\_crystal\_explicit & 0.0 \\ +structure\_factor\_scale\_i & & imaginary part of complex explicit override of structure factor multiplier for crystal structure if Bragg\_crystal\_explicit & 0.0 \\ +transmission\_sampling & & enable sampling of transmission diffraction mode. & 1.0 \\ +forward\_diffraction\_sampling & & enable sampling of forward diffraftion mode. & 1.0 \\ +laue\_sampling & & enable sampling of Laue diffraction mode. & 1.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Laue\_crystal\_BC.comp}. + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{contrib/Laue_crystal_BC_static.tex}{\input{contrib/Laue_crystal_BC_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/Mirror_toroid_pothole.tex b/docs/manuals/mcxtrace/contrib/Mirror_toroid_pothole.tex new file mode 100644 index 0000000000..78bc198463 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/Mirror_toroid_pothole.tex @@ -0,0 +1,39 @@ +\section{The \texttt{Mirror\_toroid\_pothole} McXtrace Component} +Toroidal shape mirror (in XZ) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Jul 2016 +\end{itemize} + +\subsection*{Description} +This is an implementation of a toroidal mirror which may be curved in two dimensions. To avoid solving quartic equations, the intersection is computed as a combination of two intersections. First, the ray is intersected with a cylinder to catch (almost) the small radius curvature. Secondly, the ray is the intersected with an ellipsoid, with the curvatures matching that of the torus. + +The first incarnation (Mirror\_toroid.comp) the mirror curves outwards (a bump), but this incarnation (Mirror\_toroid\_pothole) curves inwards (a pothole). + +Example: Mirror\_toroid\_pothole( radius=0.1, radius\_o=1000, xwidth=5e-2, zdepth=2e-1,R0=1, coating="") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +zdepth & m & Length of mirror. & 0.1 \\ +xwidth & m & Width of mirror. & 0.01 \\ +\textbf{radius} & m & Curvature radius & \\ +\textbf{radius\_o} & m & Curvature radius, outwards & \\ +R0 & 1 & Reflectivity of mirror. & 0 \\ +coating & str & Datafile containing either mirror material constants or reflectivity numbers. & "" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Mirror\_toroid\_pothole.comp}. +\end{itemize} +\IfFileExists{contrib/Mirror_toroid_pothole_static.tex}{\input{contrib/Mirror_toroid_pothole_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/PSD_monitor_rad.tex b/docs/manuals/mcxtrace/contrib/PSD_monitor_rad.tex new file mode 100644 index 0000000000..c4c6e37560 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/PSD_monitor_rad.tex @@ -0,0 +1,35 @@ +\section{The \texttt{PSD\_monitor\_rad} McXtrace Component} +Position-sensitive monitor with radially averaging. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Henrich Frielinghaus + \item \textbf{Origin:} FZ-Juelich/FRJ-2/IFF/KWS-2 + \item \textbf{Date:} Sept 2004 +\end{itemize} + +\subsection*{Description} +Radial monitor that allows for radial averaging. Comment: The intensity is given as two files: 1) a radial sum 2) a radial average (i.e. intensity per area) + +Example: PSD\_monitor\_rad(rmax=0.2, nr=100, filename="Output.psd", filename\_av="Output\_av.psd") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nr & 1 & Number of concentric circles & 100 \\ +filename & text & Name of file in which to store the detector image & 0 \\ +filename\_av & text & Name of file in which to store the averaged detector image & 0 \\ +rmax & m & Outer radius of detector & 0.2 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{PSD\_monitor\_rad.comp}. +\end{itemize} +\IfFileExists{contrib/PSD_monitor_rad_static.tex}{\input{contrib/PSD_monitor_rad_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSCurve.tex b/docs/manuals/mcxtrace/contrib/SAXSCurve.tex new file mode 100644 index 0000000000..77b878ec1d --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSCurve.tex @@ -0,0 +1,40 @@ +\section{The \texttt{SAXSCurve} McXtrace Component} +A component mimicking the scattering from a given I(q)-curve by using +linear interpolation between the given points. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A box-shaped component simulating the scattering from any given I(q)-curve. The component uses linear interpolation to generate the points necessary to compute the scattering of any given photon. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +DeltaRho & cm/\AA{}$^{3}$ & Excess scattering length density of the particles. & 1.0e-14 \\ +Volume & \AA{}$^{3}$ & Volume of the particles. & 10000.0 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +FileWithCurve & str & Datafile with the given I(q). & "Curve.dat" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSCurve.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSCurve_static.tex}{\input{contrib/SAXSCurve_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSCylinders.tex b/docs/manuals/mcxtrace/contrib/SAXSCylinders.tex new file mode 100644 index 0000000000..5e7625319b --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSCylinders.tex @@ -0,0 +1,41 @@ +\section{The \texttt{SAXSCylinders} McXtrace Component} +A sample of monodisperse cylindrical particles in solution. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A component simulating the scattering from a box-shaped, thin solution of monodisperse, cylindrical particles. + +Example: SAXSCylinders( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, SampleToDetectorDistance = 0.48, DetectorRadius = 0.1 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +R & \AA{} & Semiaxis of the cross section of the cylinder. & 40.0 \\ +Height & \AA{} & Height of the cylinder. & 100.0 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +DeltaRho & cm/\AA{}$^{3}$ & Excess scattering length density of the particles. & 1.0e-14 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSCylinders.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSCylinders_static.tex}{\input{contrib/SAXSCylinders_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSEllipticCylinders.tex b/docs/manuals/mcxtrace/contrib/SAXSEllipticCylinders.tex new file mode 100644 index 0000000000..671720f420 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSEllipticCylinders.tex @@ -0,0 +1,43 @@ +\section{The \texttt{SAXSEllipticCylinders} McXtrace Component} +A sample of monodisperse cylindrical particles with elliptic cross section in +solution. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A component simulating the scattering from a box-shaped, thin solution of monodisperse, cylindrical particles with elliptic cross section. + +Example: SAXSEllipticCylinders( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, SampleToDetectorDistance = 0.48, DetectorRadius = 0.1 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +R1 & \AA{} & First semiaxis of the cross section of the elliptic cylinder. & 20.0 \\ +R2 & \AA{} & Second semiaxis of the cross section of the elliptic cylinder. & 40.0 \\ +Height & \AA{} & Height of the cylinder. & 100.0 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +DeltaRho & cm/\AA{}$^{3}$ & Excess scattering length density of the particles. & 1.0e-14 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSEllipticCylinders.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSEllipticCylinders_static.tex}{\input{contrib/SAXSEllipticCylinders_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSLiposomes.tex b/docs/manuals/mcxtrace/contrib/SAXSLiposomes.tex new file mode 100644 index 0000000000..8bb0c1e25f --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSLiposomes.tex @@ -0,0 +1,48 @@ +\section{The \texttt{SAXSLiposomes} McXtrace Component} +A sample of polydisperse liposomes in solution (water). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A component simulating the scattering from a box-shaped, thin solution (water) of liposomes described by a pentuple-shell model. + +Example: SAXSLiposomes( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, SampleToDetectorDistance = 0.48, DetectorRadius = 0.1 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +Radius & \AA{} & Average thickness of the liposomes. & 800.0 \\ +Thickness & \AA{} & Thickness of the bilayer. & 38.89 \\ +SigmaRadius & & Relative Gaussian deviation of the radius in the distribution of liposomes. & 0.20 \\ +nRadius & & Number of bins in Radius for polydisperse distribution. & 100 \\ +VolumeOfHeadgroup & \AA{}$^{3}$ & Volume of one lipid headgroup - default is POPC. & 319.0 \\ +VolumeOfCH2Tail & \AA{}$^{3}$ & Volume of the CH2-chains of one lipid - default is POPC. & 818.8 \\ +VolumeOfCH3Tail & \AA{}$^{3}$ & Volume of the CH3-tails of one lipid - default is POPC. & 108.6 \\ +ScatteringLengthOfHeadgroup & cm & Scattering length of one lipid headgroup - default is POPC. & 4.62E-11 \\ +ScatteringLengthOfCH2Tail & cm & Scattering length of the CH2-chains of one lipid - default is POPC. & 6.71E-11 \\ +ScatteringLengthOfCH3Tail & cm & Scattering length of the CH3-tails of one lipid - default is POPC. & 5.08E-12 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSLiposomes.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSLiposomes_static.tex}{\input{contrib/SAXSLiposomes_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSNanodiscs.tex b/docs/manuals/mcxtrace/contrib/SAXSNanodiscs.tex new file mode 100644 index 0000000000..d296573848 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSNanodiscs.tex @@ -0,0 +1,51 @@ +\section{The \texttt{SAXSNanodiscs} McXtrace Component} +A sample of monodisperse phospholipid bilayer nanodiscs in solution (water). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A component simulating the scattering from a box-shaped, thin solution (water) of monodisperse phospholipid bilayer nanodiscs. + +Example: SAXSNanodiscs( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, SampleToDetectorDistance = 0.48, DetectorRadius = 0.1 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +AxisRatio & & Axis ratio of the bilayer patch. & 1.4 \\ +NumberOfLipids & & Number of lipids per nanodisc. & 130.0 \\ +AreaPerLipidHeadgroup & \AA{}$^{2}$ & Area per lipid headgroup - default is POPC. & 65.0 \\ +HeightOfMSP & \AA{} & Height of the belt protein - default is MSP1D1. & 24.0 \\ +VolumeOfOneMSP & \AA{}$^{3}$ & Volume of one belt protein - default is MSP1D1. & 26296.5 \\ +VolumeOfHeadgroup & \AA{}$^{3}$ & Volume of one lipid headgroup - default is POPC. & 319.0 \\ +VolumeOfCH2Tail & \AA{}$^{3}$ & Volume of the CH2-chains of one lipid - default is POPC. & 818.8 \\ +VolumeOfCH3Tail & \AA{}$^{3}$ & Volume of the CH3-tails of one lipid - default is POPC. & 108.6 \\ +ScatteringLengthOfOneMSP & cm & Scattering length of one belt protein - default is MSP1D1. & 3.34E-9 \\ +ScatteringLengthOfHeadgroup & cm & Scattering length of one lipid headgroup - default is POPC. & 4.62E-11 \\ +ScatteringLengthOfCH2Tail & cm & Scattering length of the CH2-chains of one lipid - default is POPC. & 6.71E-11 \\ +ScatteringLengthOfCH3Tail & cm & Scattering length of the CH3-tails of one lipid - default is POPC. & 5.08E-12 \\ +Roughness & & Factor used to smear the interfaces of the nanodisc. & 3.5 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSNanodiscs.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSNanodiscs_static.tex}{\input{contrib/SAXSNanodiscs_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSNanodiscsFast.tex b/docs/manuals/mcxtrace/contrib/SAXSNanodiscsFast.tex new file mode 100644 index 0000000000..d6ae9dba5c --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSNanodiscsFast.tex @@ -0,0 +1,56 @@ +\section{The \texttt{SAXSNanodiscsFast} McXtrace Component} +Release: McXtrace 1.0 + +A sample of monodisperse phospholipid bilayer nanodiscs in solution (water). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A component very similar to SAXSNanodiscs.comp - however, the scattering profile is only computed once, and linear interpolation is then used to simulate the instrument. + +Example: SAXSNanodiscsFast( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, SampleToDetectorDistance = 0.48, DetectorRadius = 0.1 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +AxisRatio & & Axis ratio of the bilayer patch. & 1.4 \\ +NumberOfLipids & & Number of lipids per nanodisc. & 130.0 \\ +AreaPerLipidHeadgroup & \AA{}$^{2}$ & Area per lipid headgroup - default is POPC. & 65.0 \\ +HeightOfMSP & \AA{} & Height of the belt protein - default is MSP1D1. & 24.0 \\ +VolumeOfOneMSP & \AA{}$^{3}$ & Volume of one belt protein - default is MSP1D1. & 26296.5 \\ +VolumeOfHeadgroup & \AA{}$^{3}$ & Volume of one lipid headgroup - default is POPC. & 319.0 \\ +VolumeOfCH2Tail & \AA{}$^{3}$ & Volume of the CH2-chains of one lipid - default is POPC. & 818.8 \\ +VolumeOfCH3Tail & \AA{}$^{3}$ & Volume of the CH3-tails of one lipid - default is POPC. & 108.6 \\ +ScatteringLengthOfOneMSP & cm & Scattering length of one belt protein - default is MSP1D1. & 3.34E-9 \\ +ScatteringLengthOfHeadgroup & cm & Scattering length of one lipid headgroup - default is POPC. & 4.62E-11 \\ +ScatteringLengthOfCH2Tail & cm & Scattering length of the CH2-chains of one lipid - default is POPC. & 6.71E-11 \\ +ScatteringLengthOfCH3Tail & cm & Scattering length of the CH3-tails of one lipid - default is POPC. & 5.08E-12 \\ +Roughness & & Factor used to smear the interfaces of the nanodisc. & 3.5 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +qMin & \AA{}$^{-1}$ & Lowest q-value, for which a point is generated in the scattering profile & 0.001 \\ +qMax & \AA{}$^{-1}$ & Highest q-value, for which a point is generated in the scattering profile & 1.0 \\ +NumberOfQBins & & Number of points generated in inital scattering profile. & 200 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSNanodiscsFast.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSNanodiscsFast_static.tex}{\input{contrib/SAXSNanodiscsFast_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSNanodiscsWithTags.tex b/docs/manuals/mcxtrace/contrib/SAXSNanodiscsWithTags.tex new file mode 100644 index 0000000000..47c3f52c51 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSNanodiscsWithTags.tex @@ -0,0 +1,55 @@ +\section{The \texttt{SAXSNanodiscsWithTags} McXtrace Component} +A sample of monodisperse phospholipid bilayer nanodiscs in solution (water) - with +histidine tag still on the belt proteins. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A component simulating the scattering from a box-shaped, thin solution (water) of monodisperse phospholipid bilayer nanodiscs - with histidine tags still on the belt proteins. + +Example: SAXSNanodiscsWithTags( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, SampleToDetectorDistance = 0.48, DetectorRadius = 0.1 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +AxisRatio & & Axis ratio of the bilayer patch. & 1.4 \\ +NumberOfLipids & & Number of lipids per nanodisc. & 130.0 \\ +AreaPerLipidHeadgroup & \AA{}$^{2}$ & Area per lipid headgroup - default is POPC. & 65.0 \\ +HeightOfMSP & \AA{} & Height of the belt protein - default is MSP1D1. & 24.0 \\ +RadiusOfGyrationForHisTag & \AA{} & Radius of gyration for the his-tag. & 10.0 \\ +VolumeOfOneMSP & \AA{}$^{3}$ & Volume of one belt protein - default is MSP1D1. & 26296.5 \\ +VolumeOfHeadgroup & \AA{}$^{3}$ & Volume of one lipid headgroup - default is POPC. & 319.0 \\ +VolumeOfCH2Tail & \AA{}$^{3}$ & Volume of the CH2-chains of one lipid - default is POPC. & 818.8 \\ +VolumeOfCH3Tail & \AA{}$^{3}$ & Volume of the CH3-tails of one lipid - default is POPC. & 108.6 \\ +VolumeOfOneHisTag & \AA{}$^{3}$ & Volume of one his-tag. & 2987.3 \\ +ScatteringLengthOfOneMSP & cm & Scattering length of one belt protein - default is MSP1D1. & 3.34E-9 \\ +ScatteringLengthOfHeadgroup & cm & Scattering length of one lipid headgroup - default is POPC. & 4.62E-11 \\ +ScatteringLengthOfCH2Tail & cm & Scattering length of the CH2-chains of one lipid - default is POPC. & 6.71E-11 \\ +ScatteringLengthOfCH3Tail & cm & Scattering length of the CH3-tails of one lipid - default is POPC. & 5.08E-12 \\ +ScatteringLengthOfOneHisTag & & & 3.89E-10 \\ +Roughness & & Factor used to smear the interfaces of the nanodisc. & 3.5 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSNanodiscsWithTags.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSNanodiscsWithTags_static.tex}{\input{contrib/SAXSNanodiscsWithTags_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSNanodiscsWithTagsFast.tex b/docs/manuals/mcxtrace/contrib/SAXSNanodiscsWithTagsFast.tex new file mode 100644 index 0000000000..0b4a910117 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSNanodiscsWithTagsFast.tex @@ -0,0 +1,60 @@ +\section{The \texttt{SAXSNanodiscsWithTagsFast} McXtrace Component} +Release: McXtrace 1.0 + +A sample of monodisperse phospholipid bilayer nanodiscs in solution (water) - with +histidine tag still on the belt proteins. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A component very similar to SAXSNanodiscsWithTags.comp - however, the scattering profile is only computed once, and linear interpolation is then used to simulate the instrument. + +Example: SAXSNanodiscsWithTagsFast( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, SampleToDetectorDistance = 0.48, DetectorRadius = 0.1 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +AxisRatio & & Axis ratio of the bilayer patch. & 1.4 \\ +NumberOfLipids & & Number of lipids per nanodisc. & 130.0 \\ +AreaPerLipidHeadgroup & \AA{}$^{2}$ & Area per lipid headgroup - default is POPC. & 65.0 \\ +HeightOfMSP & \AA{} & Height of the belt protein - default is MSP1D1. & 24.0 \\ +RadiusOfGyrationForHisTag & \AA{} & Radius of gyration for the his-tag. & 12.7 \\ +VolumeOfOneMSP & \AA{}$^{3}$ & Volume of one belt protein - default is MSP1D1. & 26296.5 \\ +VolumeOfHeadgroup & \AA{}$^{3}$ & Volume of one lipid headgroup - default is POPC. & 319.0 \\ +VolumeOfCH2Tail & \AA{}$^{3}$ & Volume of the CH2-chains of one lipid - default is POPC. & 818.8 \\ +VolumeOfCH3Tail & \AA{}$^{3}$ & Volume of the CH3-tails of one lipid - default is POPC. & 108.6 \\ +VolumeOfOneHisTag & \AA{}$^{3}$ & Volume of one his-tag. & 2987.3 \\ +ScatteringLengthOfOneMSP & cm & Scattering length of one belt protein - default is MSP1D1. & 3.34E-9 \\ +ScatteringLengthOfHeadgroup & cm & Scattering length of one lipid headgroup - default is POPC. & 4.62E-11 \\ +ScatteringLengthOfCH2Tail & cm & Scattering length of the CH2-chains of one lipid - default is POPC. & 6.71E-11 \\ +ScatteringLengthOfCH3Tail & cm & Scattering length of the CH3-tails of one lipid - default is POPC. & 5.08E-12 \\ +ScatteringLengthOfOneHisTag & cm & Scattering length of one histidine tag. & 3.89E-10 \\ +Roughness & & Factor used to smear the interfaces of the nanodisc. & 3.5 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +qMin & \AA{}$^{-1}$ & Lowest q-value, for which a point is generated in the scattering profile & 0.001 \\ +qMax & \AA{}$^{-1}$ & Highest q-value, for which a point is generated in the scattering profile & 1.0 \\ +NumberOfQBins & & Number of points generated in inital scattering profile. & 200 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSNanodiscsWithTagsFast.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSNanodiscsWithTagsFast_static.tex}{\input{contrib/SAXSNanodiscsWithTagsFast_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSPDB.tex b/docs/manuals/mcxtrace/contrib/SAXSPDB.tex new file mode 100644 index 0000000000..17632264ee --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSPDB.tex @@ -0,0 +1,44 @@ +\section{The \texttt{SAXSPDB} McXtrace Component} +Release: McXtrace 1.0 + +A sample describing a thin solution of proteins. This components must be compiled +with the -lgsl and -lgslcblas flags (and possibly linked to the appropriate +libraries). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) and Søren Kynde (kynde@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +This components expands the formfactor amplitude of the protein on spherical harmonics and computes the scattering profile using these. The expansion is done on amino-acid level and does not take hydration layer into account. The component must have a valid .pdb-file as an argument. + +This component is very slow. You should rather use the SAXSPDBFast sample component. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +RhoSolvent & \AA{} & Scattering length density of the buffer. & 9.4e-14 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +PDBFilepath & & Path to the file describing the high resolution structure of the protein. & "PDBfile.pdb" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSPDB.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSPDB_static.tex}{\input{contrib/SAXSPDB_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSPDBFast.tex b/docs/manuals/mcxtrace/contrib/SAXSPDBFast.tex new file mode 100644 index 0000000000..b30f098ef3 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSPDBFast.tex @@ -0,0 +1,47 @@ +\section{The \texttt{SAXSPDBFast} McXtrace Component} +Release: McXtrace 1.0 + +A sample describing a thin solution of proteins using linear interpolation +to increase computational speed. This components must be compiled with the +-lgsl and -lgslcblas flags (and possibly linked to the appropriate libraries). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) and Søren Kynde (kynde@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +This components expands the formfactor amplitude of the protein on spherical harmonics and computes the scattering profile using these. The expansion is done on amino-acid level and does not take hydration layer into account. The component must have a valid .pdb-file as an argument. + +This is fast implementation of the SAXSPDB sample component. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +RhoSolvent & \AA{} & Scattering length density of the buffer. & 9.4e-14 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +qMin & \AA{}$^{-1}$ & Lowest q-value, for which a point is generated in the scattering profile & 0.001 \\ +qMax & \AA{}$^{-1}$ & Highest q-value, for which a point is generated in the scattering profile & 0.5 \\ +NumberOfQBins & & Number of points generated in inital scattering profile. & 200 \\ +PDBFilepath & & Path to the file describing the high resolution structure of the protein. & "PDBfile.pdb" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSPDBFast.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSPDBFast_static.tex}{\input{contrib/SAXSPDBFast_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSQMonitor.tex b/docs/manuals/mcxtrace/contrib/SAXSQMonitor.tex new file mode 100644 index 0000000000..77521cb68e --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSQMonitor.tex @@ -0,0 +1,43 @@ +\section{The \texttt{SAXSQMonitor} McXtrace Component} +Release: McXtrace 1.0 + +A circular detector measuring the radial average of intensity as a function +of the momentum transform in the sample. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A circular detector measuring the radial average of intensity as a function of the momentum transform in the sample. The q-range is set up to qMax = 4 * PI * sin(TwoThetaMax / 2.0) / LambdaMin; + +Example: SAXSQMonitor( RadiusDetector = 0.1, DistanceFromSample = 0.5, LambdaMin = 1, Lambda0 = 1.54, NumberOfBins = 2000 ) Example: SAXSQMonitor( RadiusDetector = 0.1, qMax = 5, Lambda0 = 1.54, NumberOfBins = 2000 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +RFilename & str & File used for storing I(r). & "RDetector" \\ +qFilename & str & File used for storing I(q). & "QDetector" \\ +NumberOfBins & 1 & Number of bins in the r (and q). & 100 \\ +restore\_xray & & If set to 1, the component restores the original x-ray. & 0 \\ +\textbf{RadiusDetector} & m & Radius of the detector (in the xy-plane). & \\ +\textbf{DistanceFromSample} & m & Distance from the sample to this component. & \\ +LambdaMin & \AA{} & Max sensitivity in lambda - used to compute the highest possible value of momentum transfer, q. & 1.0 \\ +Lambda0 & \AA{} & If given, the momentum transfers of all rays are computed from this value. Otherwise, instrumental effects are negated Lambda0=2PI/k. & 0.0 \\ +qMax & \AA{}-1 & Max momentum for the Q-monitor. use either qMax or LambdaMin. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSQMonitor.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSQMonitor_static.tex}{\input{contrib/SAXSQMonitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSShells.tex b/docs/manuals/mcxtrace/contrib/SAXSShells.tex new file mode 100644 index 0000000000..d3e2a265c8 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSShells.tex @@ -0,0 +1,43 @@ +\section{The \texttt{SAXSShells} McXtrace Component} +Release: McXtrace 1.0 + +A sample of monodisperse shell-like particles in solution. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 11, 2012 +\end{itemize} + +\subsection*{Description} +A simple component simulating the scattering from a box-shaped, thin solution of monodisperse, shell-like particles. + +Example: Sample1 = SAXSShells( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, SampleToDetectorDistance = 0.5, DetectorRadius = 0.1, R = 50.0, Thickness = 20.0 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +R & \AA{} & Average radius of the particles. & 100.0 \\ +Thickness & \AA{} & Thickness of the shell - so that the outer radius is R + Thickness and the inner is R - Thickness. & 5.0 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +DeltaRho & cm/\AA{}$^{3}$ & Excess scattering length density of the particles. & 1.0e-14 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSShells.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSShells_static.tex}{\input{contrib/SAXSShells_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/contrib/SAXSSpheres.tex b/docs/manuals/mcxtrace/contrib/SAXSSpheres.tex new file mode 100644 index 0000000000..3dcefcd632 --- /dev/null +++ b/docs/manuals/mcxtrace/contrib/SAXSSpheres.tex @@ -0,0 +1,40 @@ +\section{The \texttt{SAXSSpheres} McXtrace Component} +A sample of monodisperse spherical particles in solution. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} KU-Science + \item \textbf{Date:} May 2, 2012 +\end{itemize} + +\subsection*{Description} +A simple component simulating the scattering from a box-shaped, thin solution of monodisperse, spherical particles. + +Example: SAXSSpheres( xwidth = 0.01, yheight = 0.01, zdepth = 0.01, R = 50.0, SampleToDetectorDistance = 0.5, DetectorRadius = 0.1 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +R & \AA{} & Radius of the spherical particles. & 100.0 \\ +Concentration & mM & Concentration of sample. & 0.01 \\ +DeltaRho & cm/\AA{}$^{3}$ & Excess scattering length density of the particles. & 1.0e-14 \\ +AbsorptionCrosssection & 1/m & Absorption cross section of the sample. & 0.0 \\ +\textbf{xwidth} & m & Dimension of component in the x-direction. & \\ +\textbf{yheight} & m & Dimension of component in the y-direction. & \\ +\textbf{zdepth} & m & Dimension of component in the z-direction. & \\ +\textbf{SampleToDetectorDistance} & m & Distance from sample to detector (for focusing the scattered x-rays). & \\ +\textbf{DetectorRadius} & m & Radius of the detector (for focusing the scattered x-rays). & \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SAXSSpheres.comp}. +\end{itemize} +\IfFileExists{contrib/SAXSSpheres_static.tex}{\input{contrib/SAXSSpheres_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/generate-xbb-files.sh b/docs/manuals/mcxtrace/generate-xbb-files.sh new file mode 100644 index 0000000000..ddfde59d38 --- /dev/null +++ b/docs/manuals/mcxtrace/generate-xbb-files.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash +# Generate .xbb bounding-box files for every PDF/JPEG/PNG figure, needed by +# tex4ht's DVI-based image pipeline (unlike pdflatex, it can't read image +# geometry directly out of these formats). Run from the manual's build +# directory, before htlatex. +set -e +find figures -type f \( -iname '*.pdf' -o -iname '*.jpg' -o -iname '*.jpeg' -o -iname '*.png' \) -exec extractbb {} \; 2>/dev/null || true diff --git a/docs/manuals/mcxtrace/html-style-overrides.css b/docs/manuals/mcxtrace/html-style-overrides.css new file mode 100644 index 0000000000..4f67b81278 --- /dev/null +++ b/docs/manuals/mcxtrace/html-style-overrides.css @@ -0,0 +1,38 @@ +/* Custom style overrides for the McCode HTML manuals, appended to the + tex4ht-generated stylesheet on every build (see CMakeLists.txt). + Edit this file, not the generated <DOC>.css -- that one is regenerated + from scratch on every build and any direct edits will be lost. */ + +/* Base body font: change family/size here to affect all running text */ +body { + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 16px; + line-height: 1.5; +} + +/* Headings */ +h1, h2, h3, h4 { + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; +} + +/* Content figures: grow to ~80% of the document pane width (scales with + the actual available space, unlike a fixed pixel cap), centered. + Logos are excluded from this class by inject-toc-sidebar.py (matched + by filename), so they keep their small, natural size untouched. */ +.mccode-content-figure { + width: 80% !important; + height: auto !important; + display: block; + margin: 0 auto !important; +} + +/* Safe fallback for any image not tagged above (e.g. the logos): never + overflow its container, but don't force a size -- natural size wins. */ +img { + max-width: 100%; + height: auto; +} + +/* Code listings (from the listings package) usually want to stay monospace + and NOT be affected by the max-width rule above in the same way images + are -- no override needed here unless you want to change their font. */ diff --git a/docs/manuals/mcxtrace/inject-toc-sidebar.py b/docs/manuals/mcxtrace/inject-toc-sidebar.py new file mode 100644 index 0000000000..600f273afb --- /dev/null +++ b/docs/manuals/mcxtrace/inject-toc-sidebar.py @@ -0,0 +1,214 @@ +#!/usr/bin/env python3 +""" +inject-toc-sidebar.py + +Adds two persistent elements to every page of a tex4ht-generated HTML +manual, both by finding content tex4ht already generated on one "master" +page (the front page, where \maketitle and \tableofcontents land) and +re-embedding it into every other generated page: + + 1. A fixed-position table-of-contents sidebar on the left. + 2. A sticky header bar at the top showing the manual's title, linking + back to the master/front page. + +This is a pure build-time, static-HTML transformation -- no JavaScript, +no server features (SSI, fetch/AJAX) required, so it works identically +whether the resulting .tgz is served over HTTP or just extracted and +browsed locally via file://. + +Usage: + python3 inject-toc-sidebar.py <DOC> +where <DOC> is the manual's basename (e.g. "manual" or "Component_manual"), +run from the directory containing the generated <DOC>*.html files. +""" +import sys, re, glob, os, json + +SIDEBAR_CSS = """ +<style> + #mccode-toc-sidebar { + position: fixed; top: 0; left: 0; bottom: 0; width: 260px; + overflow-y: auto; box-sizing: border-box; padding: 12px; + border-right: 1px solid #ccc; background: #f7f7f7; + font-size: 13px; line-height: 1.4; + } + #mccode-toc-sidebar ul { list-style: none; margin: 0; padding-left: 1em; } + #mccode-toc-sidebar > ul { padding-left: 0; } + #mccode-toc-sidebar a { text-decoration: none; color: #06c; } + #mccode-toc-sidebar a:hover { text-decoration: underline; } + #mccode-page-content { margin-left: 280px; } + #mccode-page-header { + position: sticky; top: 0; z-index: 100; + background: #fff; border-bottom: 1px solid #ccc; + padding: 8px 14px; margin: 0 0 1em 0; + font-size: 15px; font-weight: bold; + } + #mccode-page-header a { text-decoration: none; color: #222; } + #mccode-page-header a:hover { text-decoration: underline; } + @media (max-width: 800px) { + /* Narrow viewports: drop the fixed sidebar, show TOC inline at the top + instead of clipping/overlapping the page content. */ + #mccode-toc-sidebar { position: static; width: auto; border-right: none; + border-bottom: 1px solid #ccc; max-height: 40vh; } + #mccode-page-content { margin-left: 0; } + } +</style> +""" + +def find_toc_source(doc): + """Return (filename, toc_html) for whichever generated page contains + the actual \\tableofcontents output -- tex4ht wraps it in + <div class="tableofcontents">...</div> (the literal word 'Contents' + inside it is just the first entry's link text, not a heading tag).""" + for fn in sorted(glob.glob(f"{doc}*.html")): + with open(fn, encoding="utf-8", errors="ignore") as f: + content = f.read() + m = re.search( + r'(<div class="tableofcontents">.*?</div>)', + content, re.IGNORECASE | re.DOTALL) + if m: + return fn, m.group(1) + return None, None + +def find_title(master_fn): + """Extract the manual's title as plain text from the master page. + Prefer the clean <h2 class="titleHead">...</h2> that \\maketitle + produces; fall back to the <title> tag (which may be duplicated due + to how tex4ht records TITLE metadata) if that class isn't found.""" + with open(master_fn, encoding="utf-8", errors="ignore") as f: + content = f.read() + m = re.search(r'<h2 class="titleHead">(.*?)</h2>', content, re.IGNORECASE | re.DOTALL) + if not m: + m = re.search(r'<title>(.*?)', content, re.IGNORECASE | re.DOTALL) + if not m: + return None + text = re.sub(r'<[^>]+>', ' ', m.group(1)) # strip any inline tags + text = re.sub(r'\s+', ' ', text).strip() + # crude de-duplication for the -tag fallback case, where the + # same title can appear twice separated by a comma-space + half = len(text) // 2 + if len(text) > 20 and text[:half].strip().rstrip(',') == text[half:].strip().lstrip(', '): + text = text[:half].strip().rstrip(',') + return text + +LOGO_FILENAMES = {"DTU_logo.png", "DTU_logo", "DTU_logo-.png", "DTU_logo-", + "mcstas_logo_reflection.png", "mcstas_logo_reflection", + "mcxtrace_logo", "mcxtrace_logo.png"} + +def mark_content_figures(content): + """Tag every <img> tag with class="mccode-content-figure", except the + known front-page logos (matched by filename, so this works regardless + of which page an image appears on) -- lets CSS grow content figures + without also blowing up the small, intentionally-sized logos.""" + def replacer(m): + img_tag = m.group(0) + src_match = re.search(r'src="([^"]+)"', img_tag) + if not src_match: + return img_tag + basename = src_match.group(1).rsplit('/', 1)[-1] + if basename in LOGO_FILENAMES: + return img_tag + if 'class="' in img_tag: + return re.sub(r'class="', 'class="mccode-content-figure ', img_tag, count=1) + return img_tag[:4] + ' class="mccode-content-figure"' + img_tag[4:] + return re.sub(r'<img\b[^>]*>', replacer, content, flags=re.IGNORECASE) + +# Every custom (non-standard) LaTeX macro found to be used inside math mode +# anywhere across the manuals (verified empirically against the actual +# generated output, not just recalled from memory) -- tex4ht's MathJax mode +# passes math source through un-expanded, so MathJax needs to be told about +# each of these directly; a few are flavour/chapter-specific but harmless to +# register everywhere (an unused macro registration is a no-op). +MATHJAX_MACROS = { + "PB": r"\mathbf{P}", "tP": r"\hat{\mathbf{P}}", "SB": r"\mathbf{S}", + "sB": r"\mathbf{s}", "BB": r"\mathbf{B}", "nB": r"\mathbf{n}", + "muB": r"\boldsymbol{\mu}", "muno": r"\hat{\boldsymbol{\mu}}", + "tauB": r"\boldsymbol{\sigma}", "dB": r"\mathbf{d}", "lB": r"\mathbf{l}", + "RB": r"\mathbf{R}", "Io": r"\hat{\mathbf{I}}", "so": r"\hat{\mathbf{s}}", + "sigmao": r"\boldsymbol{\hat\sigma}", "sigmaH": r"\hat\sigma", + "rhoo": r"\hat\rho", "alphao": r"\boldsymbol{\alpha}", + "betao": r"\boldsymbol{\beta}", "Q": r"\mathbf{Q}", + "tQ": r"\hat{\mathbf{Q}}", "tN": r"\hat{\mathbf{N}}", "FN": r"F_N", + "FM": r"F_M", "Ru": r"R_\uparrow", "Rd": r"R_\downarrow", + "nup": r"n^\uparrow", "nd": r"n^\downarrow", "Pu": r"P^\uparrow", + "Pd": r"P^\downarrow", "chiU": r"\chi_\uparrow", "chiD": r"\chi_\downarrow", + "madsq": r"\overline{|F_N(\mathbf{Q})|^2}", + "sqmad": r"\left|\overline{F_N(\mathbf{Q})}\right|^2", + "bd": r"\overline{|B_{ld}|^2}", "kappaB": r"\boldsymbol{\kappa}", + "etaB": r"\boldsymbol{\eta}", "alphaB": r"\boldsymbol{\alpha}", + "sigmaB": r"\boldsymbol{\sigma}", "Ombold": r"\boldsymbol{\Omega}", +} + +def inject_mathjax_macros(content): + """Replace tex4ht's default window.MathJax config (just tex.tags) with + an extended one that also registers MATHJAX_MACROS, so custom LaTeX + macros used in equations actually render instead of showing as raw + source text. No-op (returns content unchanged) if this page has no + MathJax config block at all (i.e. no math on the page).""" + new_config = ('<script>window.MathJax = { tex: { tags: "ams", macros: ' + + json.dumps(MATHJAX_MACROS) + ' } }; </script>') + content, n = re.subn(r'<script>window\.MathJax\s*=.*?</script>', + lambda m: new_config, content, count=1, flags=re.DOTALL) + return content + +def linkify_images(content): + """Wrap every <img> tag in <a href="SAME_SRC" target="_blank">, so + clicking any figure opens the raw image standalone in a new tab.""" + def replacer(m): + img_tag = m.group(0) + src_match = re.search(r'src="([^"]+)"', img_tag) + if not src_match: + return img_tag + return f'<a href="{src_match.group(1)}" target="_blank">{img_tag}</a>' + return re.sub(r'<img\b[^>]*>', replacer, content, flags=re.IGNORECASE) + +def inject(doc, toc_html, header_html): + sidebar = f'<nav id="mccode-toc-sidebar">{toc_html}</nav>' + files = sorted(glob.glob(f"{doc}*.html")) + changed = 0 + for fn in files: + with open(fn, encoding="utf-8", errors="ignore") as f: + content = f.read() + if 'id="mccode-toc-sidebar"' in content: + continue # already injected (re-run safety) + content = linkify_images(content) + content = mark_content_figures(content) + content = inject_mathjax_macros(content) + # Insert CSS + sidebar right after <body ...>, then the header bar, + # then open the content div; close it right before </body>. + content, n1 = re.subn( + r'(<body[^>]*>)', + r'\1' + SIDEBAR_CSS + sidebar + header_html + '<div id="mccode-page-content">', + content, count=1, flags=re.IGNORECASE) + content, n2 = re.subn( + r'(</body>)', + r'</div>\1', + content, count=1, flags=re.IGNORECASE) + if n1 and n2: + with open(fn, "w", encoding="utf-8") as f: + f.write(content) + changed += 1 + return changed + +if __name__ == "__main__": + if len(sys.argv) != 2: + sys.exit(f"Usage: {sys.argv[0]} <DOC>") + doc = sys.argv[1] + src_fn, toc_html = find_toc_source(doc) + if not toc_html: + print(f"[inject-toc-sidebar] WARNING: could not find a table of " + f"contents in any {doc}*.html file -- skipping sidebar/header " + f"injection (pages left unmodified).", file=sys.stderr) + sys.exit(0) # non-fatal: don't break the build over this + title = find_title(src_fn) + base_page = os.path.basename(src_fn) + if title: + header_html = (f'<div id="mccode-page-header">' + f'<a href="{base_page}">{title}</a></div>') + else: + print(f"[inject-toc-sidebar] WARNING: could not extract a title " + f"from {src_fn} -- injecting sidebar without a header bar.", + file=sys.stderr) + header_html = '' + n = inject(doc, toc_html, header_html) + print(f"[inject-toc-sidebar] TOC/title sourced from {src_fn}; " + f"sidebar{'+header' if title else ''} injected into {n} page(s).") diff --git a/docs/manuals/mcxtrace/kernel.tex b/docs/manuals/mcxtrace/kernel.tex index b4ae6e1371..d736dca480 100644 --- a/docs/manuals/mcxtrace/kernel.tex +++ b/docs/manuals/mcxtrace/kernel.tex @@ -83,9 +83,9 @@ \section{Notational conventions} In the instrument definitions, units of length (\textit{e.g}.\ component positions) are given in meters and units of angles (\textit{e.g}.\ rotations) are given in degrees. The state of the x-ray is given by -its position $(x,y,z)$ in \si{m}, its wavevector $(k_x, k_y, k_z)$ in -\si{\per\angstrom}, the time in \si{s},, the phase $\phi$ in \si{\radian}, and a polarisation vector -$\left( E_x, E_y, E_z \right)$, and finally the x-ray weight $p$ in photons~\si{\per s} as described in \cref{c:MCtechniques}. +its position $(x,y,z)$ in $\mathrm{m}$, its wavevector $(k_x, k_y, k_z)$ in +$\text{\AA}^{-1}$, the time in $\mathrm{s}$,, the phase $\phi$ in $\mathrm{rad}$, and a polarisation vector +$\left( E_x, E_y, E_z \right)$, and finally the x-ray weight $p$ in photons~$\mathrm{s}^{-1}$ as described in \cref{c:MCtechniques}. \section{Syntactical conventions} \label{s:syntax} diff --git a/docs/manuals/mcxtrace/misc/Air.tex b/docs/manuals/mcxtrace/misc/Air.tex new file mode 100644 index 0000000000..c24895c816 --- /dev/null +++ b/docs/manuals/mcxtrace/misc/Air.tex @@ -0,0 +1,57 @@ +\section{The \texttt{Air} McXtrace Component} +Release: McXtrace 1.4 + +Component simulating atmospheric air. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} M. B. Nielsen + \item \textbf{Origin:} DTU Fysik, NBI + \item \textbf{Date:} 05.02.2015 +\end{itemize} + +\subsection*{Description} +The component simulates air and can be inserted as if it was just some extra sample placed somewhere in the beam line. The air component is intended to be used in all kinds of setups where air may introduce background. Code structure in this component is based on the component Saxs\_spheres. The shape of the sample may be a filled box with dimensions xwidth, yheight, zdepth, a filled cylinder with dimensions radius and yheight, a filled sphere with radius R. (NB: As we assume air to be an ideal gas, the volume fractions of the elements in the gas are merely the mole fractional part of the given element. From this the number density of atoms/molecules is calculated) The air is dry and assumed to be made of nitrogen, oxygen and argon - all other constituents are neglected. + +So far the calculations of the scattering probability (and hence also the weight multiplier) assumes the x-ray source to be unpolarized. Further the component does not yet account for absorption of x-rays. I.e. absorption is simply omitted, but it may OR may NOT be negligible. I have not yet looked into this last question, so I can't say if the lack of absorption is a bad thing or if it is allowable. + +Example: COMPONENT air1 = Air( frac = 0.4, pressure = 50000, temperature = 270, xwidth = 0.5, yheight = 0.5, zdepth = 1.5, target\_index = 1, focus\_xw = 0.5, focus\_yh = 0.5) AT (0, 0, 15) RELATIVE Origin + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +frac & 0-1 & Fraction of rays to scatter from the air & 0.3 \\ +pressure & Pa & Total pressure of the air gas & 101325 \\ +temperature & K & Absolute temperature & 273.15+21.1 \\ +R\_gas & & & 8.3144621 \\ +bond\_N & & & 1.0976 \\ +bond\_O & & & 1.2074 \\ +Nitrogen\_part & & & 0.781 \\ +Oxygen\_part & & & 0.21 \\ +Argon\_part & & & 0.009 \\ +xwidth & m & Width of the air volume. & 0 \\ +yheight & m & Height of the air volume. & 0 \\ +zdepth & m & Depth of the air volume. & 0 \\ +radius & m & Radius of spherical or cylindrical air volume. & 0 \\ +target\_x & m & X-coordinate of sampling window. & 0 \\ +target\_y & m & Y-coordinate of sampling window. & 0 \\ +target\_z & m & Z-coordinate of sampling window. & 6 \\ +target\_index & & Index of target component putting sampling window on a subsequent component. & 0 \\ +focus\_xw & m & Width of the sampling window. & 0 \\ +focus\_yh & m & Height of the sampling window. & 0 \\ +focus\_aw & rad & Horizontal (width) opening angle of sampling window. & 0 \\ +focus\_ah & rad & Vertical (height) opening angle of sampling window. & 0 \\ +focus\_r & rad & Radius of circular sampling window. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Air.comp}. +\end{itemize} +\IfFileExists{misc/Air_static.tex}{\input{misc/Air_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/misc/File.tex b/docs/manuals/mcxtrace/misc/File.tex new file mode 100644 index 0000000000..2f7c39f621 --- /dev/null +++ b/docs/manuals/mcxtrace/misc/File.tex @@ -0,0 +1,33 @@ +\section{The \texttt{File} McXtrace Component} +File.comp - allows to generate instrument/component input-files +from METADATA blocks + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Greg Tucker + \item \textbf{Origin:} ESS + \item \textbf{Date:} 2024 +\end{itemize} + +\subsection*{Description} +File.comp - allows to generate instrument/component input-files from METADATA blocks - see test\_File.instr for an example. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +filename & string & Filename for output-file generated from metadata block & 0 \\ +\textbf{metadatakey} & string & METADATA-key for looking up file content (may belong to File instance or another comp) & \\ +keep & 1 & Flag to indicate if file should be kept post-simulation & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{File.comp}. +\end{itemize} +\IfFileExists{misc/File_static.tex}{\input{misc/File_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/misc/Focus.tex b/docs/manuals/mcxtrace/misc/Focus.tex new file mode 100644 index 0000000000..3808d9dcd9 --- /dev/null +++ b/docs/manuals/mcxtrace/misc/Focus.tex @@ -0,0 +1,37 @@ +\section{The \texttt{Focus} McXtrace Component} +Release: McXtrace 1.1 + +Turn a photon into a Huygens wavelet. To be used with the SPLIT keyword. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Carsten Detlefs, hacked from slit.comp + \item \textbf{Origin:} ESRF + \item \textbf{Date:} November 6, 2013 +\end{itemize} + +\subsection*{Description} +Changes direction of the photon to a random direction towards the specified target area. To be used in coherent simulations, preferably with the SPLIT keyword. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +dist & m & distance to target & 0.0 \\ +focus\_xw & m & x-width of target & 0.0 \\ +focus\_yh & m & y-height of target & 0.0 \\ +focus\_x0 & m & x-center of target & 0.0 \\ +focus\_y0 & m & y-center of target & 0.0 \\ +focus\_absolute & & Flag - if non-zero, focus\_x0 and focus\_y0 are in absolute (lab) coordinates. & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Focus.comp}. +\end{itemize} +\IfFileExists{misc/Focus_static.tex}{\input{misc/Focus_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/misc/MCPL_input.tex b/docs/manuals/mcxtrace/misc/MCPL_input.tex new file mode 100644 index 0000000000..dc8125b2db --- /dev/null +++ b/docs/manuals/mcxtrace/misc/MCPL_input.tex @@ -0,0 +1,45 @@ +\section{The \texttt{MCPL\_input} McXtrace Component} +Source-like component that reads photon state parameters from an mcpl-file. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Aug 2016 +\end{itemize} + +\subsection*{Description} +Source-like component that reads photon state parameters from a binary mcpl-file. + +MCPL is short for Monte Carlo Particle List, and is a new format for sharing events between e.g. MCNP(X), Geant4 and McXtrace . + +When used with MPI, the --ncount given on the commandline is overwritten by \#MPI nodes x \#events in the file. + +Example: MCPL\_input(filename=voutput,verbose=1,repeat\_count=1,E\_smear=0.1,pos\_smear=0.001,dir\_smear=0.01) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +filename & str & Name of photon mcpl file to read & 0 \\ +polarisationuse & & If !=0 read polarisation vectors from file & 1 \\ +verbose & & Print debugging information for first 10 particles read & 1 \\ +Emin & keV & Lower energy bound. Particles found in the MCPL-file below the limit are skipped & 0 \\ +Emax & keV & Upper energy bound. Particles found in the MCPL-file above the limit are skipped & FLT\_MAX \\ +repeat\_count & 1 & Repeat contents of the MCPL file this number of times. NB: When running MPI, repeating is implicit and is taken into account by integer division. MUST be combined sith the \_smear options! & 1 \\ +E\_smear & 1 & When repeating events, make a Gaussian MC choice within E\_smear*E around particle energy E & 0 \\ +pos\_smear & m & When repeating events, make a flat MC choice of position within pos\_smear around particle starting position & 0 \\ +dir\_smear & deg & When repeating events, make a Gaussian MC choice of direction within dir\_smear around particle direction & 0 \\ +preload & & Load particles during INITIALIZE. On GPU preload is forced & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{MCPL\_input.comp}. +\end{itemize} +\IfFileExists{misc/MCPL_input_static.tex}{\input{misc/MCPL_input_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/misc/MCPL_output.tex b/docs/manuals/mcxtrace/misc/MCPL_output.tex new file mode 100644 index 0000000000..d6796b9c2b --- /dev/null +++ b/docs/manuals/mcxtrace/misc/MCPL_output.tex @@ -0,0 +1,48 @@ +\section{The \texttt{MCPL\_output} McXtrace Component} +Detector-like component that writes photon state parameters into an mcpl-format +binary, virtual-source photon file. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Aug 2016 +\end{itemize} + +\subsection*{Description} +Detector-like component that writes photon state parameters into an mcpl-format binary, virtual-source photon file. + +MCPL is short for Monte Carlo Particle List, and is a new format for sharing events between e.g. MCNP(X), Geant4, and McXtrace. + +When used with MPI, the component will output \#MPI nodes individual MCPL files that can be merged using the mcpltool. + +MCPL\_output allows a few flags to tweak the output files: 1. If use\_polarisation is unset (default) the polarisation vector will not be stored (saving space) 2. If doubleprec is unset (default) data will be stored as 32 bit floating points, effectively cutting the output file size in half. 3. Extra information may be attached to each ray in the form of a userflag, a user-defined variable wich is packed into 32 bits. If the user variable does not fit in 32 bits the value will be truncated and likely garbage. If more than one variable is to be attached to each photon this must be packed into the 32 bits. + +These features are set this way to keep file sizes as manageable as possible. + +Example: MCPL\_output( filename="voutput", verbose=1, userflag="flag", userflagcomment="Photon Id" ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +filename & str & Name of photon file to write. If not given, the component name will be used. & 0 \\ +weight\_mode & 1 & weight\_mode=1: record initial ray count in MCPL stat:sum entry and rescale particle weights. weight\_mode=2: classical (deprecated) mode of outputting particle weights directly. & -1 \\ +verbose & 1 & If 1) Print summary information for created MCPL file. 2) Also print summary of first 10 particles information stored in the MCPL file. \textgreater{}2) Also print information for first 10 particles as they are being stored by McStas & 0 \\ +polarisationuse & 1 & Enable storing the polarisation state of the photon. & 0 \\ +doubleprec & 1 & Use double precision storage & 0 \\ +userflag & 1 & Extra variable to attach to each photon. The value of this variable will be packed into a 32 bit integer. & "" \\ +userflagcomment & str & String variable to describe the userflag. If this string is empty (the default) no userflags will be stored. & "" \\ +buffermax & 1 & Maximal number of events to save ( \textless{}= MAXINT), GPU/OpenACC only & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{MCPL\_output.comp}. +\end{itemize} +\IfFileExists{misc/MCPL_output_static.tex}{\input{misc/MCPL_output_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/misc/Progress_bar.tex b/docs/manuals/mcxtrace/misc/Progress_bar.tex new file mode 100644 index 0000000000..5af033911b --- /dev/null +++ b/docs/manuals/mcxtrace/misc/Progress_bar.tex @@ -0,0 +1,37 @@ +\section{The \texttt{Progress\_bar} McXtrace Component} +Release: McXtrace 1.0 + +A simulation progress bar + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Emmanuel Farhi + \item \textbf{Origin:} ILL + \item \textbf{Date:} 2009 +\end{itemize} + +\subsection*{Description} +An indicator of the progress of the simulation, monitoring the Init, Trace with the achieved percentage, and the Finally section. Intermediate savings (e.g. triggered by USR2 signal) are also shown. This component should be positioned at the very begining of the instrument The profile option will save the intensity and number of events for each component It may be used to evaluate the simulation efficiency. + +Example: Progress\_bar(percent=10,flag\_save=1) AT (0,0,0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +profile & str & file name to save the simulation profile in. If set to "", it is set to the name of the instrument. & "NULL" \\ +percent & 0-100 & percentage interval between updates. Default is 10\%. & 10 \\ +flag\_save & 0|1 & flag to enable intermediate saving for all monitors & 0 \\ +minutes & min & time in minutes between updates (Overrides percent flag). & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Progress\_bar.comp}. +\end{itemize} +\IfFileExists{misc/Progress_bar_static.tex}{\input{misc/Progress_bar_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/misc/Shadow_input.tex b/docs/manuals/mcxtrace/misc/Shadow_input.tex new file mode 100644 index 0000000000..7fb4285b11 --- /dev/null +++ b/docs/manuals/mcxtrace/misc/Shadow_input.tex @@ -0,0 +1,36 @@ +\section{The \texttt{Shadow\_input} McXtrace Component} +Release: McXtrace 0.1 + +Read x-ray state parameters from SHADOW x-ray event file. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Andrea Prodi + \item \textbf{Origin:} Risoe/ILL + \item \textbf{Date:} November 21, 2011 +\end{itemize} + +\subsection*{Description} +Source-like component reading x-ray state parameters from a SHADOW x-ray event file. Used to interface McXtrace components or simulations into SHADOW. + +Example: Shadow\_input(file="MySource.00", bufsize = 10000, repeat\_count = 2) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +file & string & Filename of x-ray file to read. Default (NULL) is standard input. Empty string "" unactivates component & "" \\ +bufsize & records & Size of x-ray input buffer & 10000 \\ +repeat\_count & 1 & Number of times to repeat each x-ray read & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Shadow\_input.comp}. +\end{itemize} +\IfFileExists{misc/Shadow_input_static.tex}{\input{misc/Shadow_input_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/misc/Shadow_output.tex b/docs/manuals/mcxtrace/misc/Shadow_output.tex new file mode 100644 index 0000000000..de125a2b20 --- /dev/null +++ b/docs/manuals/mcxtrace/misc/Shadow_output.tex @@ -0,0 +1,38 @@ +\section{The \texttt{Shadow\_output} McXtrace Component} +Release: McXtrace 0.1 + +Write x-ray state parameters to SHADOW x-ray event file. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Andrea Prodi + \item \textbf{Origin:} Risoe/ILL + \item \textbf{Date:} November 21, 2011 +\end{itemize} + +\subsection*{Description} +Detector-like component writing x-ray state parameters to a SHADOW x-ray file. Used to interface McXtrace components or simulations into SHADOW. Each photon is 104 bytes. + +Note that when standard output is used, as is the default, no monitors or other components that produce terminal output must be used, or the x-ray output from this component will become corrupted. + +Example: Shadow\_output(file="MySource.vit", bufsize = 10000, progress = 1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +file & string & Filename of x-ray file to write. Default is standard output & "" \\ +bufsize & records & Size of x-ray output buffer & 1000 \\ +progress & flag & If not zero, output dots as progress indicator & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Shadow\_output.comp}. +\end{itemize} +\IfFileExists{misc/Shadow_output_static.tex}{\input{misc/Shadow_output_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/misc/Shape.tex b/docs/manuals/mcxtrace/misc/Shape.tex new file mode 100644 index 0000000000..315b003491 --- /dev/null +++ b/docs/manuals/mcxtrace/misc/Shape.tex @@ -0,0 +1,60 @@ +\section{The \texttt{Shape} McXtrace Component} +A geometric shape without effect on X-raysX, for instrument display purpose. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} E. Farhi + \item \textbf{Origin:} ILL + \item \textbf{Date:} June 23rd 2009 +\end{itemize} + +\subsection*{Description} +An inactive geometrical shape, for drawing purposes only. It does not propagate X-rays, nor interact. \textbf{Shape:} Geometric shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth (thickness=0) +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} +cylinder: radius x yheight (thickness=0) +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} +sphere: radius (yheight=0 thickness=0) +hollow sphere: radius and thickness>0 (yheight=0) +any shape: geometry=OFF file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the X ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using qhull/powercrust, and viewed with geomview The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +Example: Shape(radius=0.05, yheight=0.1) Shape(geometry="socket.off") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +geometry & str & Name of an Object File Format (OFF) file for complex geometry. The OFF file may be generated from XYZ coordinates using qhull/powercrust & 0 \\ +radius & m & Outer radius of sample in (x,z) plane & 0 \\ +xwidth & m & Horiz. dimension of sample (bounding box if off file), as a width & 0 \\ +yheight & m & Vert. dimension of sample (bounding box if off file), as a height. A sphere shape is used when 0 and radius is set & 0 \\ +zdepth & m & Depth of sample (bounding box if off file) & 0 \\ +thickness & m & Thickness of hollow sample & 0 \\ +center & 1 & Flag to determine if OFF object is centered on its centre of mass. & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Shape.comp}. + \item Geomview and Object File Format (OFF) \textless{}http|://www.geomview.org\textgreater{} + \item Powercrust/qhull \textless{}http://www.cs.utexas.edu/users/amenta/powercrust\textgreater{} +\end{itemize} +\IfFileExists{misc/Shape_static.tex}{\input{misc/Shape_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/DivE_monitor.tex b/docs/manuals/mcxtrace/monitors/DivE_monitor.tex new file mode 100644 index 0000000000..f4f74d92c4 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/DivE_monitor.tex @@ -0,0 +1,44 @@ +\section{The \texttt{DivE\_monitor} McXtrace Component} +Divergence/Energy monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Jun. 2016 +\end{itemize} + +\subsection*{Description} +2D detector for intensity as a function of both horizontal divergence and Energy. + +Example: DivE\_monitor(nE=20, nh=20, filename="Output.div", xwidth=0.1, yheight=0.1, maxdiv\_h=2, Emin=2, Emax=10) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nE & 1 & Number of bins in energy & 20 \\ +nh & 1 & Number of bins in divergence & 20 \\ +filename & str & Name of file in which to store the detector image & 0 \\ +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +maxdiv\_h & deg & Maximal horizontal divergence detected & 2 \\ +\textbf{Emin} & keV & Minimum energy detected & \\ +\textbf{Emax} & keV & Maximum energy detected & \\ +restore\_xray & 1 & If set, the monitor does not influence the photon state & 0 \\ +nx & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane. & 0 \\ +ny & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane. & 0 \\ +nz & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane. & 1 \\ +nowritefile & 1 & If set, monitor will skip writing to disk. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{DivE\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/DivE_monitor_static.tex}{\input{monitors/DivE_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/DivPos_monitor.tex b/docs/manuals/mcxtrace/monitors/DivPos_monitor.tex new file mode 100644 index 0000000000..c2e34f3df5 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/DivPos_monitor.tex @@ -0,0 +1,44 @@ +\section{The \texttt{DivPos\_monitor} McXtrace Component} +Release: McXtrace 1.3 + +Divergence/position monitor (acceptance diagram). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Jun. 16 +\end{itemize} + +\subsection*{Description} +2D detector for intensity as a function of both horizontal position and wavelength. This gives information similar to an aceptance diagram used eg. to investigate beam profiles in neutron guides. + +Example: DivPos\_monitor(nh=20, ndiv=20, filename="Output.dip", xwidth=0.1, yheight=0.1, maxdiv\_h=2) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nh & 1 & Number of bins in position & 20 \\ +ndiv & 1 & Number of bins in divergence & 20 \\ +filename & str & Name of file in which to store the detector image & 0 \\ +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +maxdiv\_h & deg & Maximal horizontal divergence detected & 2 \\ +restore\_xray & 1 & If set, the monitor does not influence the photon state & 0 \\ +nx & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane & 0 \\ +ny & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane & 0 \\ +nz & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane & 1 \\ +nowritefile & 1 & If set, monitor will skip writing to disk. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{DivPos\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/DivPos_monitor_static.tex}{\input{monitors/DivPos_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/Divergence_monitor.tex b/docs/manuals/mcxtrace/monitors/Divergence_monitor.tex new file mode 100644 index 0000000000..f944efd57d --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/Divergence_monitor.tex @@ -0,0 +1,44 @@ +\section{The \texttt{Divergence\_monitor} McXtrace Component} +Horizontal+vertical divergence monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Jun. '16 +\end{itemize} + +\subsection*{Description} +A 2D divergence sensitive monitor. The counts are distributed in (n times m) pixels. + +Example: Divergence\_monitor(nh=20, nv=20, filename="Output.pos", xwidth=0.1, yheight=0.1, maxdiv\_h=2, maxdiv\_v=2) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nh & 1 & Number of pixel rows & 20 \\ +nv & 1 & Number of pixel columns & 20 \\ +rad & 1 & If set - divergence will be measured in radians. & 0 \\ +filename & str & Name of file in which to store the detector image text & 0 \\ +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +maxdiv\_h & degrees & Maximal horizontal divergence detected & 1 \\ +maxdiv\_v & degrees & Maximal vertical divergence detected & 1 \\ +restore\_xray & 1 & If set, the monitor does not influence the photon state & 0 \\ +nx & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane & 0 \\ +ny & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane & 0 \\ +nz & 1 & Vector definition of "forward" direction wrt. divergence, to be used e.g. when the monitor is rotated into the horizontal plane & 1 \\ +nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Divergence\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/Divergence_monitor_static.tex}{\input{monitors/Divergence_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/EPSD_monitor.tex b/docs/manuals/mcxtrace/monitors/EPSD_monitor.tex new file mode 100644 index 0000000000..36aeac9fd1 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/EPSD_monitor.tex @@ -0,0 +1,41 @@ +\section{The \texttt{EPSD\_monitor} McXtrace Component} +Position-energy-sensitive monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU + \item \textbf{Date:} June 22, 2009 +\end{itemize} + +\subsection*{Description} +An nx times ny pixel energy resolved PSD monitor, which only counts photons with energy in an interval given by Emin and Emax in nE energy bins. The default energy interval is (almost) infinite, with a single bin. If nE\textgreater{}1 the component will output nE detector files + one which is integrated over the full energy interval. + +Example: EPSD\_monitor(xwidth=0.1, yheight=0.1, nx=90, ny=90, filename="Output.psd") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nx & 1 & Number of pixel columns. & 90 \\ +ny & 1 & Number of pixel rows. & 90 \\ +filename & str & Name of file in which to store the detector image. & 0 \\ +restore\_xray & 1 & If set, the monitor does not influence the xray state. & 0 \\ +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +Emax & keV & Upper bound of energy interval. & 0 \\ +Emin & keV & Lower bound of energy interval. & 0 \\ +nE & 1 & Number of energy bins. & 1 \\ +nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{EPSD\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/EPSD_monitor_static.tex}{\input{monitors/EPSD_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/E_monitor.tex b/docs/manuals/mcxtrace/monitors/E_monitor.tex new file mode 100644 index 0000000000..ae94bb22e0 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/E_monitor.tex @@ -0,0 +1,40 @@ +\section{The \texttt{E\_monitor} McXtrace Component} +Release: McXtrace 0.1 + +Energy-sensitive monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 22, 2009 +\end{itemize} + +\subsection*{Description} +A square single monitor that measures the energy of the incoming x-rays. + +Example: E\_monitor(xwidth=0.1, yheight=0.1, Emin=1, Emax=50, nE=20, filename="Output.nrj") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nE & m & Number of energy channels. & 20 \\ +filename & str & Name of file in which to store the detector image. & 0 \\ +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +\textbf{Emin} & keV & Minimum energy to detect. & \\ +\textbf{Emax} & keV & Maximum energy to detect. & \\ +restore\_xray & 0/1 & If set, the monitor does not influence the x-ray state. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{E\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/E_monitor_static.tex}{\input{monitors/E_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/Event_monitor_simple.tex b/docs/manuals/mcxtrace/monitors/Event_monitor_simple.tex new file mode 100644 index 0000000000..9bcdb52704 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/Event_monitor_simple.tex @@ -0,0 +1,30 @@ +\section{The \texttt{Event\_monitor\_simple} McXtrace Component} +Low-key event-monitor for debugging purposes. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Peter Willendrup + \item \textbf{Origin:} DTU + \item \textbf{Date:} May 21st, 2025 +\end{itemize} + +\subsection*{Description} +Simple, low-key event-monitor for debugging purposes. No propagation, no MPI support. Simply prints the event list to a log file in the SAVE section. The filename is "comp-instance".log + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nevents & 1 & Number of events to store and print & 1e6 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Event\_monitor\_simple.comp}. +\end{itemize} +\IfFileExists{monitors/Event_monitor_simple_static.tex}{\input{monitors/Event_monitor_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/Flex_monitor_1D.tex b/docs/manuals/mcxtrace/monitors/Flex_monitor_1D.tex new file mode 100644 index 0000000000..bec5c3b0b7 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/Flex_monitor_1D.tex @@ -0,0 +1,39 @@ +\section{The \texttt{Flex\_monitor\_1D} McXtrace Component} +Flexible monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen \& Peter Willendrup + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Oct '20 +\end{itemize} + +\subsection*{Description} +Non-propagating monitor that measures intensity (or something else) as a function of some variable or parameter. + +Example: Flex\_monitor\_1D(nU=20, filename="Output", ustring="x", Umin=-.1, Umax=.1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nU & 1 & Number of U channels & 20 \\ +filename & string & Name of file in which to store the detector image & 0 \\ +\textbf{Umin} & & Minimum U to detect & \\ +\textbf{Umax} & & Maximum U to detect & \\ +uid & 1 & Integer index of uservar to be monitored. Overrides ustring. & -1 \\ +ustring & string & Name of variable (user or particle state parameter as a string) to be monitored. & "" \\ +signal & string & Name of variable to be used as an additive signal to be monitored. Default is intensity. & "p" \\ +nowritefile & 1 & Flag to indicate if monitor should not save any data. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Flex\_monitor\_1D.comp}. +\end{itemize} +\IfFileExists{monitors/Flex_monitor_1D_static.tex}{\input{monitors/Flex_monitor_1D_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/Flex_monitor_2D.tex b/docs/manuals/mcxtrace/monitors/Flex_monitor_2D.tex new file mode 100644 index 0000000000..d5d0fe8ab2 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/Flex_monitor_2D.tex @@ -0,0 +1,44 @@ +\section{The \texttt{Flex\_monitor\_2D} McXtrace Component} +Flexible monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen \& Peter Willendrup + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Oct '20 +\end{itemize} + +\subsection*{Description} +Non-propagating 2D monitor that measures intensity (or something else) as a function of two selectable variables or parameters. + +Example: Flex\_monitor\_2D(nU1=20, nU2=20, filename="Output", ustring1="x", ustring2="y", Umin1=-.1, Umax1=.1, Umin2=-.1, Umax2=.1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nU1 & 1 & Number of U1 channels & 20 \\ +nU2 & 1 & Number of U1 channels & 20 \\ +filename & string & Name of file in which to store the detector image & 0 \\ +\textbf{Umin1} & & Minimum U1 to detect & \\ +\textbf{Umax1} & & Maximum U1 to detect & \\ +uid1 & 1 & Integer index of uservar to be monitored. Overrides ustring1. & -1 \\ +ustring1 & string & Name of variable U1 (user or particle state parameter as a string) to be monitored. & "" \\ +\textbf{Umin2} & & Minimum U1 to detect & \\ +\textbf{Umax2} & & Maximum U1 to detect & \\ +uid2 & 1 & Integer index of uservar to be monitored. Overrides ustring2. & -1 \\ +ustring2 & string & Name of variable U2 (user or particle state parameter as a string) to be monitored. & "" \\ +signal & string & Name of variable to be used as an additive signal to be monitored. Default is intensity. & "p" \\ +nowritefile & 1 & Flag to indicate if monitor should not save any data. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Flex\_monitor\_2D.comp}. +\end{itemize} +\IfFileExists{monitors/Flex_monitor_2D_static.tex}{\input{monitors/Flex_monitor_2D_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/Flex_monitor_3D.tex b/docs/manuals/mcxtrace/monitors/Flex_monitor_3D.tex new file mode 100644 index 0000000000..8626f9da4f --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/Flex_monitor_3D.tex @@ -0,0 +1,49 @@ +\section{The \texttt{Flex\_monitor\_3D} McXtrace Component} +Flexible monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen \& Peter Willendrup + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Oct '20 +\end{itemize} + +\subsection*{Description} +Non-propagating 3D monitor that measures intensity (or something else) as a function of three selectable variables or parameters. The 3D data is saved as a series of 2D datasets, which names are filename\_index + +Example: Flex\_monitor\_3D(nU1=20, nU2=20, nU3=20, filename="Output", ustring1="x", ustring2="y", ustring1="z", Umin1=-.1, Umax1=.1, Umin2=-.1, Umax2=.1, Umin3=-.1, Umax3=.1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nU1 & 1 & Number of U1 channels & 20 \\ +nU2 & 1 & Number of U1 channels & 20 \\ +nU3 & 1 & Number of U3 channels & 20 \\ +filename & string & Name of file in which to store the detector image & 0 \\ +\textbf{Umin1} & & Minimum U1 to detect & \\ +\textbf{Umax1} & & Maximum U1 to detect & \\ +uid1 & 1 & Integer index of uservar to be monitored. Overrides ustring1. & -1 \\ +ustring1 & string & Name of variable U1 (user or particle state parameter as a string) to be monitored. & "" \\ +\textbf{Umin2} & & Minimum U1 to detect & \\ +\textbf{Umax2} & & Maximum U1 to detect & \\ +uid2 & 1 & Integer index of uservar to be monitored. Overrides ustring2. & -1 \\ +ustring2 & string & Name of variable U2 (user or particle state parameter as a string) to be monitored. & "" \\ +\textbf{Umin3} & & Minimum U3 to detect & \\ +\textbf{Umax3} & & Maximum U3 to detect & \\ +uid3 & 1 & Integer index of uservar to be monitored. Overrides ustring3. & -1 \\ +ustring3 & string & Name of variable U3 (user or particle state parameter as a string) to be monitored. & "" \\ +signal & string & Name of variable to be used as an additive signal to be monitored. Default is intensity. & "p" \\ +nowritefile & 1 & Flag to indicate if monitor should not save any data. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Flex\_monitor\_3D.comp}. +\end{itemize} +\IfFileExists{monitors/Flex_monitor_3D_static.tex}{\input{monitors/Flex_monitor_3D_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/Fluo_detector.tex b/docs/manuals/mcxtrace/monitors/Fluo_detector.tex new file mode 100644 index 0000000000..536f195a8b --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/Fluo_detector.tex @@ -0,0 +1,55 @@ +\section{The \texttt{Fluo\_detector} McXtrace Component} +Detector for fluorescence, e.g. Silicon Drift Detector (SDD) or High Purity Germanium (HPGe). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} E. Farhi + \item \textbf{Origin:} Synchrotron SOLEIL + \item \textbf{Date:} May 2025 +\end{itemize} + +\subsection*{Description} +A detector that records energy spectrum from e.g. fluorescence. This component handles: - fluorescence detector escape (energy shift from detector K-alpha) - fluorescence detector pile-up (sum aka time-coincidence aka pile-up within detector dead-time) - energy resolution (above Fano level) + +The detector geometry can be a rectangle xwidth*yheight, or a disk of given 'radius'. When the radius is given negative, a 4PI detector sphere of given radius is assumed. + +The detector escape corresponds with a fluorescence excitation within the detector itself that subtracts the K-alpha detector level from the sample scattered energy. The level of escape peaks in set as 'escape\_ratio', e.g. 1-2 \%. + +The detector pile-up is related to the detector dead-time, within which time coincidence between two fluorescence photons are summed-up. The level of pile-up is set as 'pileup\_ratio', e.g. 1-2 \% which can increase for high count rates that saturate the detector. + +Last, the fluorescence peak shape is broadened using an electronic noise (at E=0) and a nominal resolution at E=resolution\_energy (in keV). You may set the electronic\_noise to zero for a perfect detector (Fano limit). To use a constant resolution, set the resolution\_energy=0. + +Example: Fluo\_detector(xwidth=0.1, yheight=0.1, Emin=1, Emax=50, nE=20, filename="Output.nrj") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & m & Radius of disk detector (in XY plane). When given as negative, a 4PI sphere is assumed. & 0 \\ +xwidth & m & Width of rectangle detector. & 0 \\ +yheight & m & Height of rectangle detector. & 0 \\ +Emin & keV & Minimum energy to detect. & 1 \\ +Emax & keV & Maximum energy to detect. & 39 \\ +nE & m & Number of energy channels. & 2000 \\ +filename & str & Name of file in which to store the detector image. & 0 \\ +restore\_xray & 0/1 & If set, the monitor does not influence the x-ray state. & 0 \\ +escape\_ratio & 1 & Detector escape peak ratio, e.g. 0.01-0.02. Zero inactivates. & 0.01 \\ +escape\_energy & keV & Detector escape peak energy, e.g. 1.739 for Si, 9.886 for Ge. & 1.739 \\ +pileup\_ratio & 1 & Sum aka time coincidence aka pile-up detector peak ratio, e.g. 0.01-0.02. This is e.g. the dead-time ratio. Zero inactivates. & 0.01 \\ +electronic\_noise & keV & Electronic noise at E=0, FWHM in keV. Use electronic\_noise=0 for Fano limit. & 0.1 \\ +resolution\_energy & keV & Energy at which resolution is given, e.g. 5.9 keV Mn K-alpha. & 6 \\ +resolution & keV & Resolution FWHM in keV at resolution\_energy. & 0.2 \\ +flag\_lorentzian & 1 & When 1, the line shapes are assumed to be Lorentzian, else Gaussian. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Fluo\_detector.comp}. + \item Fluorescence https://en.wikipedia.org/wiki/Fluorescence +\end{itemize} +\IfFileExists{monitors/Fluo_detector_static.tex}{\input{monitors/Fluo_detector_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/L_monitor.tex b/docs/manuals/mcxtrace/monitors/L_monitor.tex new file mode 100644 index 0000000000..c615164240 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/L_monitor.tex @@ -0,0 +1,40 @@ +\section{The \texttt{L\_monitor} McXtrace Component} +Release: McXtrace 0.1 + +Wavelength-sensitive monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Kristian Nielsen and Kim Lefmann + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 22, 2009 +\end{itemize} + +\subsection*{Description} +A square single monitor that measures the wavelength of the incoming xray. + +Example: L\_monitor(xmin=-0.1, xwidth=0.1, yheight=0.1, nL=20, filename="Output.L", Lmin=0.1, Lmax=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nL & m & Number of wavelength channels. & 20 \\ +filename & str & Name of file in which to store the detector image. & 0 \\ +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +\textbf{Lmin} & \AA{} & Minimum wavelength to detect. & \\ +\textbf{Lmax} & \AA{} & Maximum wavelength to detect. & \\ +restore\_xray & & If set, the monitor does not influence the x-ray state. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{L\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/L_monitor_static.tex}{\input{monitors/L_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/Monitor.tex b/docs/manuals/mcxtrace/monitors/Monitor.tex new file mode 100644 index 0000000000..173347a50d --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/Monitor.tex @@ -0,0 +1,36 @@ +\section{The \texttt{Monitor} McXtrace Component} +Release: McXtrace 0.1 + +Simple monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 22, 2009 +\end{itemize} + +\subsection*{Description} +A square single monitor that measures the intergated intensity of the incoming x-rays. + +Example: Monitor(xwidth=0.1, yheight=0.1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +restore\_xray & m & If set, the monitor does not influence the xray state & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Monitor.comp}. +\end{itemize} +\IfFileExists{monitors/Monitor_static.tex}{\input{monitors/Monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/Monitor_nD.tex b/docs/manuals/mcxtrace/monitors/Monitor_nD.tex new file mode 100644 index 0000000000..be6d274f87 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/Monitor_nD.tex @@ -0,0 +1,206 @@ +\section{The \texttt{Monitor\_nD} McXtrace Component} +Release: McXtrace 1.2 + +This component is a general Monitor that can output 0/1/2D signals +(Intensity or signal vs. [something] and vs. [something] ...) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} \textless{}a href="mailto:farhi@ill.fr"\textgreater{}Emmanuel Farhi\textless{}/a\textgreater{} + \item \textbf{Origin:} \textless{}a href="http://www.ill.fr"\textgreater{}ILL\textless{}/a\textgreater{} + \item \textbf{Date:} 14th Feb 2000. +\end{itemize} + +\subsection*{Description} +This component is a general Monitor that can output 0/1/2D signals It can produce many 1D signals (one for any variable specified in option list), or a single 2D output (two variables correlation). Also, an additional 'list' of photon events can be produced. By default, monitor is square (in x/y plane). A disk shape is also possible The 'cylinder' and 'banana' option will change that for a banana shape The 'sphere' option simulates spherical detector. The 'box' is a box. The cylinder, sphere and banana should be centered on the scattering point. In normal configuration, the Monitor\_nD measures the current parameters of the photon that is beeing detected. USERVARS may be used in order to study correlations between a neutron being detected in a Monitor\_nD place, and given parameters that are monitored elsewhere (at the point of initialisation of the USERVARS). The monitor can also act as a 3He gas detector, taking into account the detection efficiency. + +The 'bins' and 'limits' modifiers are to be used after each variable, and 'auto','log' and 'abs' come before it. (eg: auto abs log hdiv bins=10 limits=[-5 5]) When placed after all variables, these two latter modifiers apply to the signal (e.g. intensity). Unknown keywords are ignored. If no limits are specified for a given observable, reasonable defaults will be applied. Note that these implicit limits are \textbf{even} applied in list mode. + +\textbf{Implicit limits for typical variables:} (consult monitor\_nd-lib.c if you don't find your variable here) x, y, z: Derived from detection-object geometry + +\begin{verbatim} +k: [0 10] Angs-1 +v: [0 1e6] m/s +t: [0 1] s +\end{verbatim} + +p: [0 FLT\_MAX] in intensity-units + +\begin{verbatim} +vx, vy: [-1000 1000] m/s +vz: [0 10000] m/s +kx, ky: [-1 1] Angs-1 +kz: [-10 10] Angs-1 +\end{verbatim} + +energy, omega: [0 100] meV lambda,wavelength: [0 100] \AA{} sx, sy, sz: [-1 1] in polarisation-units angle: [-50 50] deg divergence, vdiv, hdiv, xdiv, ydiv: [-5 5] deg longitude, lattitude: [-180 180] deg photon: [0 simulaton\_ncount] id, pixel id: [0 FLT\_MAX] + +\begin{verbatim} +uservars u0,u1,u2,u3,u4,u5,u6,u7,u8,u9: [-1e10 1e10] +\end{verbatim} + +In the case of multiple components at the same position, the 'parallel' keyword must be used in each instance instead of defining a GROUP. + +\textbf{Possible options are} Variables to record: kx ky kz k wavevector [\AA{}-1] Wavevector on x,y,z and norm + +\begin{verbatim} +vx vy vz v [m/s] Velocity on x,y,z and norm +x y z radius [m] Distance, Position and norm +xy, yz, xz [m] Radial position in xy, yz and xz plane +kxy kyz kxz [Angs-1] Radial wavevector in xy, yz and xz plane +vxy vyz vxz [m/s] Radial velocity in xy, yz and xz plane +t time [s] Time of Flight +energy omega [keV] energy of photon +lambda wavelength [Angs] wavelength of photon +sx sy sz [1] Spin +vdiv ydiv dy [deg] vertical divergence (y) +hdiv divergence xdiv [deg] horizontal divergence (x) +angle [deg] divergence from <z> direction +theta longitude [deg] longitude (x/z) for sphere and cylinder +phi lattitude [deg] lattitude (y/z) for sphere and cylinder +\end{verbatim} + +\begin{verbatim} +user0 user1 will monitor the [Mon_Name]_Vars.UserVariable{0|1|2|3|4|5} +user2 user3 to be assigned in an other component (see below) +\end{verbatim} + +user4 user5 user6 user7 user8 user9 + +\begin{verbatim} +Premonitoring: Please use uservars in place of the former PreMonitor_nD. +\end{verbatim} + +\begin{verbatim} +p intensity flux [phts/s or phts/cm^2/s] +ncounts n photon [1] photon ID, i.e current event index +pixel id [1] pixelID in histogram made of preceeding vars, e.g. 'theta y'. To set an offset PixelID use the 'min=value' keyword. Sets event mode. +\end{verbatim} + +\textbf{Other options keywords are:} + +\begin{verbatim} +abs Will monitor the abs of the following variable or of the signal (if used after all variables) +auto Automatically set detector limits for one/all +all {limits|bins|auto} To set all limits or bins values or auto mode +binary {float|double} with 'source' option, saves in compact files +bins=[bins=20] Number of bins in the detector along dimension +borders To also count off-limits photons (X < min or X > max) +capture weight by capture flux (not validated) +exclusive absorb photon out of monitor limits +file=string Detector image file name. default is component name, plus date and variable extension. +incoming Monitor incoming beam in non flat det +limits=[min max] Lower/Upper limits for axes (see up for the variable unit) +\end{verbatim} + +list=[counts=1000] or all For a long file of photon characteristics with [counts] or all events + +\begin{verbatim} +log Will monitor the log of the following variable or of the signal (if used after all variables) +min=[min_value] Same as limits, but only sets the min or max +\end{verbatim} + +max=[max\_value] + +\begin{verbatim} +multiple Create multiple independant 1D monitors files +no or not Revert next option +outgoing Monitor outgoing beam (default) +parallel Use this option when the next component is at the same position (parallel components) +per cm2 Intensity will be per cm^2 (detector area). Displays beam section. +per steradian Intensity will be per steradian (requires auto) +signal=[var] Will monitor [var] instead of usual intensity +slit or absorb Absorb photons that are out detector +source The monitor will save photon states +inactivate To inactivate detector (0D detector) +verbose To display additional informations +\end{verbatim} + +Detector shape options (specified as xwidth,yheight,zdepth or x/y/z/min/max) + +\begin{verbatim} +box Box of size xwidth, yheight, zdepth. +cylinder To get a cylindrical monitor (diameter is xwidth or set radius, height is yheight). +banana Same as cylinder, without top/bottom, on restricted angular area; use theta variable with limits to define arc. (diameter is xwidth or set radius, height is yheight). +disk Disk flat xy monitor. diameter is xwidth. +sphere To get a spherical monitor (e.g. a 4PI) (diameter is xwidth or set radius). +square Square flat xy monitor (xwidth, yheight). +previous The monitor uses PREVIOUS component as detector surface. +\end{verbatim} + +\textbf{EXAMPLES:} MyMon = Monitor\_nD( xwidth = 0.1, yheight = 0.1, zdepth = 0, options = "intensity per cm2 angle,limits=[-5 5] bins=10,with borders, file = mon1"); will monitor photon angle from [z] axis, between -5 and 5 degrees, in 10 bins, into "mon1.A" output 1D file options = "sphere theta phi outgoing" for a sphere PSD detector (out beam) and saves into file "MyMon\_[Date\_ID].th\_ph" options = "banana, theta limits=[10,130], bins=120, y" a theta/height banana detector + +\begin{verbatim} +options = "angle radius all auto" is a 2D monitor with automatic limits +\end{verbatim} + +options = "list=1000 kx ky kz energy" records 1000 photon event in a file options = "multiple kx ky kz, auto abs log t, and list all photons" makes 4 output 1D files and produces a complete list for all photons and monitor log(abs(tof)) within automatic limits (for t) options = "theta y, sphere, pixel min=100" a 4pi detector which outputs an event list with pixelID from the actual detector surface, starting from index 100. + +To dynamically define a number of bins, or limits: + +\begin{verbatim} +Use in DECLARE: char op[256]; +\end{verbatim} + +Use in INITIALIZE: sprintf(op, "lambda limits=[\%g \%g], bins=\%i", lmin, lmax, lbin); + +\begin{verbatim} +Use in TRACE: Monitor_nD(... options=op ...) +\end{verbatim} + +\textbf{How to monitor any instrument/component variable into a Monitor\_nD} Suppose you want to monitor a variable 'age' which you assign somwhere in the instrument: COMPONENT MyMonitor = Monitor\_nD( xwidth = 0.1, yheight = 0.1, user1="age", username1="Age of the Captain [years]", options="user1, auto") + +\begin{verbatim} +AT ... +\end{verbatim} + +\%BUGS The 'auto' option for guessing optimal variable bounds should NOT be used with MPI as each process may use different limits. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +user0 & str & Variable name of USERVAR to be monitored by user0. & "" \\ +user1 & str & Variable name of USERVAR to be monitored by user1. & "" \\ +user2 & str & Variable name of USERVAR to be monitored by user2. & "" \\ +user3 & str & Variable name of USERVAR to be monitored by user3. & "" \\ +user4 & str & Variable name of USERVAR to be monitored by user4. & "" \\ +user5 & str & Variable name of USERVAR to be monitored by user5. & "" \\ +user6 & str & Variable name of USERVAR to be monitored by user6. & "" \\ +user7 & str & Variable name of USERVAR to be monitored by user7. & "" \\ +user8 & str & Variable name of USERVAR to be monitored by user8. & "" \\ +user9 & str & Variable name of USERVAR to be monitored by user9. & "" \\ +xwidth & m & Width of detector. & 0 \\ +yheight & m & Height of detector. & 0 \\ +zdepth & m & Thickness of detector (z). & 0 \\ +bins & 1 & Number of bins to force for all variables. Use 'bins' keyword in 'options' for heterogeneous bins & 0 \\ +min & u & Minimum range value to force for all variables. Use 'min' or 'limits' keyword in 'options' for other limits & -1e40 \\ +max & u & Maximum range value to force for all variables. Use 'max' or 'limits' keyword in 'options' for other limits & 1e40 \\ +restore\_xray & 0|1 & If set, the monitor does not influence the photon state. Equivalent to setting the 'parallel' option. & 0 \\ +radius & m & Radius of sphere/banana shape monitor & 0 \\ +options & str & String that specifies the configuration of the monitor. The general syntax is "[x] options..." (see \textless{}b\textgreater{}Descr.\textless{}/b\textgreater{}). & "NULL" \\ +filename & str & Output file name (overrides file=XX option). & "NULL" \\ +geometry & str & Name of an OFF file to specify a complex geometry detector & "NULL" \\ +nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ +username0 & str & Name assigned to User0 & "NULL" \\ +username1 & str & Name assigned to User1 & "NULL" \\ +username2 & str & Name assigned to User2 & "NULL" \\ +username3 & str & Name assigned to User3 & "NULL" \\ +username4 & str & Name assigned to User4 & "NULL" \\ +username5 & str & Name assigned to User5 & "NULL" \\ +username6 & str & Name assigned to User6 & "NULL" \\ +username7 & str & Name assigned to User7 & "NULL" \\ +username8 & str & Name assigned to User8 & "NULL" \\ +username9 & str & Name assigned to User9 & "NULL" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Monitor\_nD.comp}. +\end{itemize} +\IfFileExists{monitors/Monitor_nD_static.tex}{\input{monitors/Monitor_nD_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/PSD_monitor.tex b/docs/manuals/mcxtrace/monitors/PSD_monitor.tex new file mode 100644 index 0000000000..213e3005f3 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/PSD_monitor.tex @@ -0,0 +1,40 @@ +\section{The \texttt{PSD\_monitor} McXtrace Component} +Position-sensitive monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 22, 2009 +\end{itemize} + +\subsection*{Description} +Based on neutron component written by Kim Lefmann An (nx times ny) pixel PSD monitor. This component may also be used as a beam detector. If instead of xwidth, yheight a radius is given, the component has a circular footprint and integrates circularly (caking). + +Example: PSD\_monitor(xwidth=0.1, yheight=0.1, nx=90, ny=90, filename="Output.psd") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +filename & str & Name of file in which to store the detector image. & 0 \\ +xwidth & m & Width of detector. & 0.05 \\ +yheight & m & Height of detector. & 0.05 \\ +radius & m & Radius of circular detetor. & 0 \\ +restore\_xray & 1 & If set, the monitor does not influence the xray state. & 1 \\ +nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ +nx & 1 & Number of pixel columns. & 90 \\ +ny & 1 & Number of pixel rows. & 90 \\ +nr & 1 & Number of radial pixels. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{PSD\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/PSD_monitor_static.tex}{\input{monitors/PSD_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/PSD_monitor_4PI.tex b/docs/manuals/mcxtrace/monitors/PSD_monitor_4PI.tex new file mode 100644 index 0000000000..25fa181c9b --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/PSD_monitor_4PI.tex @@ -0,0 +1,38 @@ +\section{The \texttt{PSD\_monitor\_4PI} McXtrace Component} +Release: McXtrace 0.1 + +Spherical position-sensitive detector. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 23rd, 2009 +\end{itemize} + +\subsection*{Description} +Based on neutron component by Kim Lefmann and Kristian Nielsen An (n times m) pixel spherical PSD monitor using a cylindrical projection. Mostly for test and debugging purposes. + +Example: PSD\_monitor\_4PI(radius=0.1, nx=90, ny=90, filename="Output.psd") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & m & Radius of detector & 1 \\ +restore\_xray & 1 & If set, the monitor does not influence the xray state & 0 \\ +nx & 1 & Number of pixel columns & 90 \\ +ny & 1 & Number of pixel rows & 90 \\ +filename & str & Name of file in which to store the detector image & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{PSD\_monitor\_4PI.comp}. +\end{itemize} +\IfFileExists{monitors/PSD_monitor_4PI_static.tex}{\input{monitors/PSD_monitor_4PI_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/PSD_monitor_coh.tex b/docs/manuals/mcxtrace/monitors/PSD_monitor_coh.tex new file mode 100644 index 0000000000..3befd1ed7d --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/PSD_monitor_coh.tex @@ -0,0 +1,42 @@ +\section{The \texttt{PSD\_monitor\_coh} McXtrace Component} +Position-sensitive monitor with phase integration. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} March 13, 2010 +\end{itemize} + +\subsection*{Description} +An (n times m) pixel PSD monitor taking phase into account. As the i:th ray hits a pixel (j,k) in the monitor the intensity in that pixel will be updated as a complex sum, i.e. \textless{}math\textgreater{}P\_i = P\_\{i-1\} + p\_i exp\{-\textbackslash{}phi\_i\}\textless{}/math\textgreater{}. + +By setting ratio\textless{}1 the effective pixel area becomes a fraction of the ideal (which is to divide the xwidth and yheight intervals into nx and ny abutting subintervals). This reduces the monitor effective area by ratio\textasciicircum{}2. If the centering flag is set - the monitor will treat all rays as if they hit a pixel center. This behaves as if ratio -\textgreater{} 0, but at no cost in statistics. + +Example: PSD\_monitor\_coh(xwidth=0.1, yheight=0.1, nx=90, ny=90, filename="Output.psd") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nx & & Number of pixel columns. & 90 \\ +ny & & Number of pixel rows. & 90 \\ +filename & m & Name of file in which to store the detector images - the suffixes .abs and .arg will be added. & 0 \\ +restore\_xray & & If set, the monitor does not influence the xray state. & 0 \\ +xwidth & m & Width of detector. & 0.05 \\ +yheight & m & Height of detector. & 0.05 \\ +ratio & & ratio between pixel area and effective pixel area. & 1 \\ +centering & & Treat all rays as if they hit the center of the pixel. & 1 \\ +nowritefile & 1 & If set, monitor will skip writing to disk & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{PSD\_monitor\_coh.comp}. +\end{itemize} +\IfFileExists{monitors/PSD_monitor_coh_static.tex}{\input{monitors/PSD_monitor_coh_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/TOF_monitor.tex b/docs/manuals/mcxtrace/monitors/TOF_monitor.tex new file mode 100644 index 0000000000..667cfd2fea --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/TOF_monitor.tex @@ -0,0 +1,39 @@ +\section{The \texttt{TOF\_monitor} McXtrace Component} +Release: 1.2 + +Rectangular Time-of-flight monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} British Airways + \item \textbf{Date:} Aug. 2014 +\end{itemize} + +\subsection*{Description} +Rectangular Time-of-flight monitor. You may either give the time-step or the time range. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nt & 1 & Number of time bins & 20 \\ +filename & str & Name of file in which to store the detector image & 0 \\ +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +tmin & mu-s & Lower time limit & 0 \\ +tmax & mu-s & Upper time limit. When left as 0, use dt to compute tmax. & 0 \\ +dt & mu-s & Length of each time bin & 1.0 \\ +restore\_xray & 1 & If set, the monitor does not influence the xray state & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{TOF\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/TOF_monitor_static.tex}{\input{monitors/TOF_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/monitors/W_psd_monitor.tex b/docs/manuals/mcxtrace/monitors/W_psd_monitor.tex new file mode 100644 index 0000000000..cb29e5f916 --- /dev/null +++ b/docs/manuals/mcxtrace/monitors/W_psd_monitor.tex @@ -0,0 +1,39 @@ +\section{The \texttt{W\_psd\_monitor} McXtrace Component} +Release: McXtrace 0.1 + +Position-sensitive wattage monitor. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 22, 2009 +\end{itemize} + +\subsection*{Description} +Based on neutron PSD component written by Kim Lefmann An n times m pixel PSD wattage monitor. This component may also be used as a beam detector. + +Example: W\_psd\_monitor(xwidth=0.1, yheight=0.1, nx=90, ny=90, filename="Output.psd") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +nx & 1 & Number of pixel columns & 90 \\ +ny & 1 & Number of pixel rows & 90 \\ +filename & str & Name of file in which to store the detector image & 0 \\ +restore\_xray & 1 & If set, the monitor does not influence the xray state & 0 \\ +xwidth & m & Width of detector. & 0.1 \\ +yheight & m & Height of detector. & 0.1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{W\_psd\_monitor.comp}. +\end{itemize} +\IfFileExists{monitors/W_psd_monitor_static.tex}{\input{monitors/W_psd_monitor_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/obsolete/Lens_Kinoform.tex b/docs/manuals/mcxtrace/obsolete/Lens_Kinoform.tex new file mode 100644 index 0000000000..466e855edb --- /dev/null +++ b/docs/manuals/mcxtrace/obsolete/Lens_Kinoform.tex @@ -0,0 +1,44 @@ +\section{The \texttt{Lens\_Kinoform} McXtrace Component} +A model of a specific kinoform used by the BNL + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser and Erik Knudsen + \item \textbf{Origin:} NBI + \item \textbf{Date:} January 2012 +\end{itemize} + +\subsection*{Description} +KINOFORM. A model of a specific kinoform used by the BNL team during the APS beamtime. + +\begin{verbatim} +z: [0 0.002033m] +xmin=-0.0002634 +xmax=0.0002634 +\end{verbatim} + +the principles of the kinoform's operation are described here: http://neutrons.ornl.gov/workshops/nni\_05/presentations/min050616\_xray\_evans-lutterodt\_ken\_nni05.pdf + +You may as well use a kinoform with: Lens\_parab\_Cyl(r=.5e-3,yheight=1.3e-3,xwidth=1.3e-3,d=.1e-3,N=21, material\_datafile="Be.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +datafile & & & "kinoform.txt" \\ +material\_datafile & & & "Si.txt" \\ +yheight & m & height of the lens. & 1e-2 \\ +xwidth & m & width of the lens & 5.268e-4 \\ +deltaN & & & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Lens\_Kinoform.comp}. +\end{itemize} +\IfFileExists{obsolete/Lens_Kinoform_static.tex}{\input{obsolete/Lens_Kinoform_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/obsolete/Lens_parab_Cyl_rough.tex b/docs/manuals/mcxtrace/obsolete/Lens_parab_Cyl_rough.tex new file mode 100644 index 0000000000..06d0bb2138 --- /dev/null +++ b/docs/manuals/mcxtrace/obsolete/Lens_parab_Cyl_rough.tex @@ -0,0 +1,38 @@ +\section{The \texttt{Lens\_parab\_Cyl\_rough} McXtrace Component} +Lens\_parab\_Cyl\_rough component + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser and Erik Knudsen + \item \textbf{Origin:} + \item \textbf{Date:} April 2011 +\end{itemize} + +\subsection*{Description} +A simple X-ray compound refractive lens (CRL) with a parabolic cylinder profile, it focuses in 1D. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_datafile & & & "Be.txt" \\ +r & m & radius of curvature (circular approximation at the tip of the profile) & .5e-3 \\ +yheight & m & the CRL's dimensions along Y, aka aperture & 1.2e-3 \\ +xwidth & & & 1.2e-3 \\ +d & & & .1e-3 \\ +T & & & .99 \\ +N & & & 1 \\ +rough\_z & & & 0 \\ +rough\_xy & & & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Lens\_parab\_Cyl\_rough.comp}. +\end{itemize} +\IfFileExists{obsolete/Lens_parab_Cyl_rough_static.tex}{\input{obsolete/Lens_parab_Cyl_rough_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/obsolete/Lens_parab_rough.tex b/docs/manuals/mcxtrace/obsolete/Lens_parab_rough.tex new file mode 100644 index 0000000000..02bf401e39 --- /dev/null +++ b/docs/manuals/mcxtrace/obsolete/Lens_parab_rough.tex @@ -0,0 +1,39 @@ +\section{The \texttt{Lens\_parab\_rough} McXtrace Component} +Lens\_parab\_rough component + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser and Erik Knudsen + \item \textbf{Origin:} + \item \textbf{Date:} August 2010, modified July 2011 +\end{itemize} + +\subsection*{Description} +A simple X-ray compound refractive lens (CRL) with a profile of the parabola in rotation simulates the photons' movement on passing through it. The CRL focuses in 2D. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_datafile & Be.txt & File where the material parameters for the filter may be found. Format is similar to what may be found off the NIST website. & "Be.txt" \\ +r & m & radius of curvature (circular approximation at the tip of the profile) & 0.5e-3 \\ +yheight & m & the CRL's dimensions along Y, aka aperture & 1.4e-3 \\ +xwidth & m & the CRL's dimensions along X & 1.4e-3 \\ +d & m & distance between two surfaces of the lens along the propagation axis; & .1e-3 \\ +T & 1 & transmission of the lens & .99 \\ +N & 1 & amount of single lenses in a stack. & 1 \\ +rough\_z & rms & waviness along z & 0 \\ +rough\_xy & rms & waviness along x and y & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Lens\_parab\_rough.comp}. + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{obsolete/Lens_parab_rough_static.tex}{\input{obsolete/Lens_parab_rough_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/obsolete/Perfect_crystal.tex b/docs/manuals/mcxtrace/obsolete/Perfect_crystal.tex new file mode 100644 index 0000000000..7210e5f7fd --- /dev/null +++ b/docs/manuals/mcxtrace/obsolete/Perfect_crystal.tex @@ -0,0 +1,43 @@ +\section{The \texttt{Perfect\_crystal} McXtrace Component} +Perfect crystal with diamond or zincblende structure + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Anette Vickery, Andrea Prodi, Erik Knudsen + \item \textbf{Origin:} NBI + \item \textbf{Date:} April 2011 +\end{itemize} + +\subsection*{Description} +Reads atomic formfactors from a data input file. The PerfectCrystal code reflects ray in an ideal geometry, does not include surface imperfections or mosaicity + +The crystal is positioned such that the long axis of the crystal surface coincides with z-axis. The angle between the Bragg planes and the crystal surface is alpha + +The algorithm: Incoming photon's coordinates and direction (k-vector) are transformed into an elliptical reference frame (elliptical parameters are calculated according to the mirror's position and its focusing distances and the * incident angle), the intersection point is then defined. A new, reflected photon is then starting at the point of intersection. Notation follows Tadashi Matsushita and Hiro-O Hashizume, X-RAY MONOCHROMATORS. Handbook on Synchrotron Radiation,North-Holland Publishing Company, 1:263–274, 1983. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +form\_factors & & & "FormFactors.txt" \\ +material & & & "Si.txt" \\ +R0 & & Reflectivity. Overrides the computed Darwin reflectivity. Probably only useful for debugging. & 0 \\ +length & m & length of the crystal (along z-axis) & 0.05 \\ +width & m & width of the crystal (along x-axis) & 0.02 \\ +V & \AA{}$^{3}$ & unit cell volum & 160.1826 \\ +h & & Miller index of reflection & 1 \\ +k & & Miller index of reflection & 1 \\ +l & & Miller index of reflection & 1 \\ +alpha & rad & asymmetry angle (alpha=0 for symmetric reflection, ie the Bragg planes are parallel to the crystal surface) & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Perfect\_crystal.comp}. +\end{itemize} +\IfFileExists{obsolete/Perfect_crystal_static.tex}{\input{obsolete/Perfect_crystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Arm.tex b/docs/manuals/mcxtrace/optics/Arm.tex new file mode 100644 index 0000000000..0c53926037 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Arm.tex @@ -0,0 +1,31 @@ +\section{The \texttt{Arm} McXtrace Component} +Arm/optical bench + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Kim Lefmann and Kristian Nielsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} September 2009 +\end{itemize} + +\subsection*{Description} +An arm does not actually do anything, it is just there to set up a new coordinate system. + +Example: Arm() + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Arm.comp}. +\end{itemize} +\IfFileExists{optics/Arm_static.tex}{\input{optics/Arm_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Beamstop.tex b/docs/manuals/mcxtrace/optics/Beamstop.tex new file mode 100644 index 0000000000..e111f37690 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Beamstop.tex @@ -0,0 +1,38 @@ +\section{The \texttt{Beamstop} McXtrace Component} +Rectangular/circular beam stop. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Kristian Nielsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} March 2011 +\end{itemize} + +\subsection*{Description} +A simple rectangular or circular beam stop. Infinitely thin and infinitely absorbing. The beam stop is by default rectangular. You may either specify the radius (circular shape), or the rectangular bounds. + +Example: Beamstop(xmin=-0.05, xmax=0.05, ymin=-0.05, ymax=0.05) Beamstop(radius=0.1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +xmin & m & Lower x bound & -0.05 \\ +xmax & m & Upper x bound & 0.05 \\ +ymin & m & Lower y bound & -0.05 \\ +ymax & m & Upper y bound & 0.05 \\ +xwidth & m & Width of beamstop (x). Overrides xmin,xmax. & 0 \\ +yheight & m & Height of beamstop (y). Overrides ymin,ymax. & 0 \\ +radius & m & Radius of the beam stop in the z=0 plane, centered at Origo & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Beamstop.comp}. +\end{itemize} +\IfFileExists{optics/Beamstop_static.tex}{\input{optics/Beamstop_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Bragg_crystal.tex b/docs/manuals/mcxtrace/optics/Bragg_crystal.tex new file mode 100644 index 0000000000..c1603a7a69 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Bragg_crystal.tex @@ -0,0 +1,65 @@ +\section{The \texttt{Bragg\_crystal} McXtrace Component} +Perfect, reflecting crystal with common cubic structures (diamond, fcc, or bcc, and others if symmetry form factor multipliers provided explicitly) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Marcus H Mendenhall, NIST \textless{}marcus.mendenhall@nist.gov\textgreater{} + \item \textbf{Origin:} NIST, Gaithersburg, MD, USA + \item \textbf{Date:} December 1, 2016 +\end{itemize} + +\subsection*{Description} +Bragg\_crystal.comp supercedes Perfect\_Crystal.comp with major edits and corrections. + +For details see: The optics of focusing bent-crystal monochromators on X-ray powder diffractometers with application to lattice parameter determination and microstructure analysis, Marcus H. Mendenhall,* David Black and James P. Cline, J. Appl. Cryst. (2019). 52, https://doi.org/10.1107/S1600576719010951 + +Reads atomic formfactors from a data input file. + +The crystal code reflects ray in an ideal geometry, i.e. does not include surface imperfections or mosaicity. The crystal planes from which the reflection is made lies in the X-Z plane on the unbent crystal rotated by an angle alpha about the Y axis with respect to the crystal surface. + +The crystal itself is set in the X-Z plane positioned such that the long axis of the crystal surface coincides with the Z-axis, with its normam pointing in the positve Y-direction. The angle between the Bragg planes and the crystal surface is alpha + +This code has been validated against both experimental data (2 channel-cut 3-bounce Si 440 crystals together in non-dispersive mode, at Cu kalpha) and against theoretical rocking rocking curves from XOP for Si220 at Sc kalpha and Si440 at Cu kalpha. + +Changelog: - Off-axis rays fixed June 2015 so axial divergence corrections are right - Inclusion of polarization and temperature dependence (via Debye-Waller factor), June-September 2015 - Errors in complex arithmetic in DarwinReflectivity2 corrected, September 2015, MHM - Symmetries for form factors corrected 20150924 - Rotation code updated to use exact DarwinReflectivity Theta0, Thetah so answer is right even if alpha != 0. 20151009 MHM - Results for (1,1,1) etc. with complex form factor made to agree with XOP. December 1st, 2016 + +Notation follows Tadashi Matsushita and Hiro-O Hashizume, X-RAY MONOCHROMATORS. Handbook on Synchrotron Radiation,North-Holland Publishing Company, 1:263–274, 1983. + +Non-copyright notice: Contributed by the National Institute of Standards and Technology; not subject to copyright in the United States. This is not an official contribution, in that the results are in no way certified by NIST. + +Example: Bragg\_crystal( + +\begin{verbatim} +length=0.05, width=0.02, V=160.1826, h=1, k=1, l=1, alpha=0) +\end{verbatim} + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +length & m & z depth (length) of the crystal. & 0.05 \\ +width & m & x width of the crystal. & 0.02 \\ +V & \AA{}$^{3}$ & Unit cell volume & 160.1826 \\ +form\_factors & str & File for X-ray form factors & "FormFactors.txt" \\ +material & str & Si, Ge (maybe also GaAs?) & "Si.txt" \\ +alpha & rad & Asymmetry angle (alpha=0 for symmetric reflection, ie the Bragg planes are parallel to the crystal surface). alpha is defined so that positive alpha reduces the Bragg angle to the plane i.e. alpha=Thetain grazes the planes. if alpha!=0, one should restrict to rays which have small kx values, since otherwise the alpha rotation is not around the diffraction axis. & 0.0 \\ +R0 & 0-1 & Reflectivity. Overrides the computed Darwin reflectivity. Probably only useful for debugging. & 0 \\ +debye\_waller\_B & \AA{}$^{2}$ & Debye-Waller temperature factor, M=B*(sin(theta)/lambda)\textasciicircum{}2*(2/3), default=silicon at room temp. & 0.4632 \\ +crystal\_type & 1 & 1 =\textgreater{} Mx\_crystal\_explicit: provide explicit real and imaginary form factor multipliers structure\_factor\_scale\_r, structure\_factor\_scale\_i; 2 =\textgreater{} Mx\_crystal\_diamond: diamond; 3 =\textgreater{} Mx\_crystal\_fcc: fcc; 4 =\textgreater{} Mx\_crystal\_fcc: bcc & 1 \\ +h & 1 & Miller index of reflection & 1 \\ +k & 1 & Miller index of reflection & 1 \\ +l & 1 & Miller index of reflection & 1 \\ +structure\_factor\_scale\_r & 1 & real form factor multiplier & 0.0 \\ +structure\_factor\_scale\_i & 1 & imaginary form factor multiplier & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Bragg\_crystal.comp}. +\end{itemize} +\IfFileExists{optics/Bragg_crystal_static.tex}{\input{optics/Bragg_crystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Bragg_crystal_bent.tex b/docs/manuals/mcxtrace/optics/Bragg_crystal_bent.tex new file mode 100644 index 0000000000..11c418d445 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Bragg_crystal_bent.tex @@ -0,0 +1,66 @@ +\section{The \texttt{Bragg\_crystal\_bent} McXtrace Component} +Bent, perfect, reflecting crystal with common cubic structures (diamond, fcc, or bcc, and others if symmetry form factor multipliers provided explicitly) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Marcus H Mendenhall, NIST \textless{}marcus.mendenhall@nist.gov\textgreater{} + \item \textbf{Origin:} Marcus H. Mendenhall, NIST, Gaithersburg, MD, USA + \item \textbf{Date:} December 1, 2016 +\end{itemize} + +\subsection*{Description} +Bragg\_crystal\_bent.comp supercedes Perfect\_Crystal\_bent.comp with major edits and corrections. + +Reads atomic formfactors from a data input file. + +The crystal code reflects ray in an ideal geometry, does not include surface imperfections or mosaicity The crystal planes from which the reflection is made must lie in the X-Z plane on the unbent crystal rotated by an angle alpha about the x axis with respect to the crystal surface. + +The external geometry of the crystal follows that of Elliptic\_mirror.comp. I.e. the crystal is positioned such that the a-axis of the ellipsoid is on the z-axis, the b-axis is along the y-axis and the c is along the x-axis. The reference point of the crystal is the ellipsoid centre, offset by one half-axis along the y-axis. (See the component manual for Elliptic\_mirror for a drawing). + +N.B. The component does not work for negative curvature, nor for rays hitting the back of the monochromator. + +Notation follows Tadashi Matsushita and Hiro-O Hashizume, X-RAY MONOCHROMATORS. Handbook on Synchrotron Radiation,North-Holland Publishing Company, 1:263–274, 1983. + +Non-copyright notice: Contributed by the National Institute of Standards and Technology; not subject to copyright in the United States. This is not an official contribution, in that the results are in no way certified by NIST. + +NOTE: elliptical coordinate code and documentation taken from Mirror\_elliptic.comp distributed in McXtrace v1.2 However, the coordinates are rotated to be consistent with Bragg\_crystal\_flat.comp and Perfect\_Crystal.comp. Idealized elliptic mirror with surface ellipse and lattice ellipses independent, to allow construction of Johansson optics, for example. + +Example: Bragg\_crystal\_bent( length=0.05, width=0.02, V=160.1826, h=1, k=1, l=1, alpha=0,y\_b=1, lattice\_y\_b=1, z\_c=1, lattice\_z\_c=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +x\_a & m & 1st short half axis (along x). Commonly set to zero, which really implies infinite value, so crystal is an elliptic cylinder. & 0 \\ +y\_b & m & 2nd short half axis (along y), which is also the presumed near-normal direction, reflection near the y-z plane. & 1.0 \\ +z\_c & m & Long half axis (along z). Commonly a=0. b=c, which creates a circular cylindrical surface. & 1.0 \\ +lattice\_x\_a & m & Curvature matrix for underlying lattice, for bent/ground/rebent crystals THERE HAS BEEN NO TESTING for the case in which lattice\_x\_a != x\_a. & 0 \\ +lattice\_y\_b & m & Curvature matrix for underlying lattice, for bent/ground/rebent crystals & 1.0 \\ +lattice\_z\_c & m & Curvature matrix for underlying lattice, for bent/ground/rebent crystals & 1.0 \\ +length & m & z depth (length) of the crystal. & 0.05 \\ +width & m & x width of the crystal. & 0.02 \\ +V & \AA{}$^{3}$ & Unit cell volume & 160.1826 \\ +form\_factors & str & File for X-ray form factors & "FormFactors.txt" \\ +material & str & Si, Ge (maybe also GaAs?) & "Si.txt" \\ +alpha & rad & Asymmetry angle (alpha=0 for symmetric reflection, ie the Bragg planes are parallel to the crystal surface); alpha is defined so that positive alpha reduces the Bragg angle to the plane i.e. alpha=Thetain grazes the planes; if alpha!=0, one should restrict to rays which have small kx values, since otherwise the alpha rotation is not around the diffraction axis. & 0.0 \\ +R0 & 0-1 & Reflectivity. Overrides the computed Darwin reflectivity. Probably only useful for debugging. & 0 \\ +debye\_waller\_B & \AA{}$^{2}$ & Debye-Waller temperature factor, M=B*(sin(theta)/lambda)\textasciicircum{}2*(2/3), default=silicon at room temp. & 0.4632 \\ +crystal\_type & 1 & 1 =\textgreater{} Bragg\_crystal\_explicit: provide explicit real and imaginary form factor multipliers structure\_factor\_scale\_r, structure\_factor\_scale\_i; 2 =\textgreater{} Bragg\_crystal\_diamond: diamond; 3 =\textgreater{} Bragg\_crystal\_fcc: fcc; 4 =\textgreater{} Bragg\_crystal\_fcc: bcc & 1 \\ +h & 1 & Miller index of reflection & 1 \\ +k & 1 & Miller index of reflection & 1 \\ +l & 1 & Miller index of reflection & 1 \\ +structure\_factor\_scale\_r & 1 & real form factor multiplier & 0.0 \\ +structure\_factor\_scale\_i & 1 & imaginary form factor multiplier & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Bragg\_crystal\_bent.comp}. + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{optics/Bragg_crystal_bent_static.tex}{\input{optics/Bragg_crystal_bent_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Capillary.tex b/docs/manuals/mcxtrace/optics/Capillary.tex new file mode 100644 index 0000000000..f208a0697e --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Capillary.tex @@ -0,0 +1,40 @@ +\section{The \texttt{Capillary} McXtrace Component} +Release: McXtrace 1.2 + +A capillary tube + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} July 2015 +\end{itemize} + +\subsection*{Description} +A Capillary tube allowing for reflections along the tube. A material coating can be applied. Multilayer coatings may be handled by generating a reflectivity file (e.g. by IMD) and setting rtable=1. Waviness is implemented using the model described in Wang et.al., J. Appl. Phys., 1996 where the grazing incidence angle \textless{}span class="latex"\textgreater{}\$\textbackslash{}theta\$\textless{}/span\textgreater{} is altered as \\ \textless{}div class="latex"\textgreater{} \$\textbackslash{}theta' = \textbackslash{}theta + \textbackslash{}delta \textbackslash{}theta \textbackslash{}in [-min(theta,\textbackslash{}Delta\textbackslash{}theta,\textbackslash{}Delta\textbackslash{}theta]\$ \textless{}/div\textgreater{} This ensures that reflected rays will never be scattered into the capillary. \textless{}span class="latex"\textgreater{}\$\textbackslash{}Delta\textbackslash{}theta\$\textless{}/span\textgreater{} is the value specified by the parameter waviness. + +Example: Capillary( radius=1e-4,length=0.1, R0=0, coating="Rh.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +coating & str & Name of file containing the material data (i.e. f1 and f2) for the coating & "Be.txt" \\ +longw & 0/1 & If non-zero, waviness is purely longitudinal in its nature. & 1 \\ +radius & m & Radius of curvature. & 1 \\ +length & m & Length of the unbent mirror. & 0.2 \\ +R0 & 0-1 & Fixed constant reflectivity & 0 \\ +rtable & 0/1 & If nonzero, the coating file contains an E,theta parameterized matrix of raw reflectivities. & 0 \\ +waviness & rad & The momentaneous waviness is uniformly distributed in the range [-waviness,waviness]. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Capillary.comp}. +\end{itemize} +\IfFileExists{optics/Capillary_static.tex}{\input{optics/Capillary_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Chopper_simple.tex b/docs/manuals/mcxtrace/optics/Chopper_simple.tex new file mode 100644 index 0000000000..82dcb5cade --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Chopper_simple.tex @@ -0,0 +1,45 @@ +\section{The \texttt{Chopper\_simple} McXtrace Component} +Ideal chopper + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} + \item \textbf{Origin:} Risoe + \item \textbf{Date:} August 2011 +\end{itemize} + +\subsection*{Description} +Ideal model of a chopper situated at Z=0. If a photon arrives at the chopper plane at a time of t = [t0 +-n*T: t0 +-n*T +tau], where T is the period of the chopper, t0 the initial delay and tau the opening time of the chopper, it is left untouched - otherwise it is ABSORBed. If on a continous source the isfirst parameter may be used. In this case the photon time is \_defined\_ by the chopper. In other words no photons are absorbed, the photon time is merely sampled within the chopper window. t\_rise is the rise-time of the chopper opening giving a trapezoidal shape. Limitations: this component does not take chopper geometry into account. If isfirst only samples in the first chopper opening window. + +Example: Chopper\_simple( + +\begin{verbatim} +t0 = -0.5/M_C, T = 20e-6, tau = 100e-12, xwidth = 1e-4, +\end{verbatim} + +yheight = 1e-4, isfirst = 1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +t0 & s & Initial delay of the opening time & 0 \\ +T & s & Period of the chopper & 1 \\ +tau & s & Opening time of the chopper & 0.1 \\ +xwidth & m & Height of the chopper opening & 0.1 \\ +yheight & m & Width of the chopeper opening & 0.1 \\ +isfirst & 0/1 & Is the chopper the first chopper on a continous source. & 0 \\ +t\_rise & s & Rise time of the chopper pulse. & 0 \\ +tjit & 1 & Timing jitter in terms of the opening time tau. For each ray the opening window will be shifted by a random amount within t=[-tjit*.5*tau,tjit*.5*tau] & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Chopper\_simple.comp}. +\end{itemize} +\IfFileExists{optics/Chopper_simple_static.tex}{\input{optics/Chopper_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Collimator_linear.tex b/docs/manuals/mcxtrace/optics/Collimator_linear.tex new file mode 100644 index 0000000000..1ec8a8b465 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Collimator_linear.tex @@ -0,0 +1,41 @@ +\section{The \texttt{Collimator\_linear} McXtrace Component} +A simple analytical Soller collimator (with triangular transmission). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Peter Willendrup + \item \textbf{Origin:} DTU + \item \textbf{Date:} October 2024 +\end{itemize} + +\subsection*{Description} +Soller collimator with rectangular opening and specified length. The transmission function is an average and does not utilize knowledge of the actual neutron trajectory. A zero divergence disables collimation (then the component works as a double slit). + +Example: Collimator\_linear(xmin=-0.1, xmax=0.1, ymin=-0.1, ymax=0.1, length=0.25, divergence=40,transmission=0.7) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +xmin & m & Lower x bound on slits & -0.01 \\ +xmax & m & Upper x bound on slits & 0.01 \\ +ymin & m & Lower y bound on slits & -0.025 \\ +ymax & m & Upper y bound on slits & 0.025 \\ +xwidth & m & Width of slits & 0 \\ +yheight & m & Height of slits & 0 \\ +length & m & Distance between input and output slits & 0.1 \\ +divergence & minutes of arc & Divergence horizontal angle (calculated as atan(d/length), where d is the blade spacing) & 10 \\ +transmission & 1 & Transmission of Soller (0\textless{}=t\textless{}=1) & 1 \\ +divergenceV & minutes of arc & Divergence vertical angle & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Collimator\_linear.comp}. +\end{itemize} +\IfFileExists{optics/Collimator_linear_static.tex}{\input{optics/Collimator_linear_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Diaphragm.tex b/docs/manuals/mcxtrace/optics/Diaphragm.tex new file mode 100644 index 0000000000..e79e7f87f4 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Diaphragm.tex @@ -0,0 +1,33 @@ +\section{The \texttt{Diaphragm} McXtrace Component} +Rectangular/circular diaphragm (alias of the Slit component) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Peter Willendrup + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} February 2025 +\end{itemize} + +\subsection*{Description} +A simple rectangular or circular diaphragm. You may either specify the radius (circular shape), or the rectangular bounds. No transmission around the diaphragm is allowed. + +Example: Diaphragm(xmin=-0.01, xmax=0.01, ymin=-0.01, ymax=0.01) Diaphragm(radius=0.01) + +For \textbf{INPUT PARAMETERS} - please consult \htmladdnormallink{Slit.comp}{Slit.html} as Diaphragm is a copy of that component. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Diaphragm.comp}. +\end{itemize} +\IfFileExists{optics/Diaphragm_static.tex}{\input{optics/Diaphragm_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Filter.tex b/docs/manuals/mcxtrace/optics/Filter.tex new file mode 100644 index 0000000000..39deabbbb3 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Filter.tex @@ -0,0 +1,57 @@ +\section{The \texttt{Filter} McXtrace Component} +Release: McXtrace 1.1 + +Block of an attenuating material + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Jan 24, 2011 +\end{itemize} + +\subsection*{Description} +A chunk of attenuating material. Attenuation is computed through the effective length travelled within the material. No scattering is modelled at present. + +Filter shape may be a cylinder, a sphere, a box or any other shape. + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth +cylinder: radius x yheight (along Y axis) +sphere: radius +any shape: geometry=OFF/PLY_file +\end{verbatim} + +Example: Filter(material\_datafile="Ge.txt", geometry="wire.ply",xwidth=0.02,yheight=0,zdepth=0) Example: Filter(material\_datafile="Ge.txt",xwidth=0.02,yheight=0.02, zdepth=1e-4) Example: Filter(material\_datafile="Ge.txt",radius=1e-4,yheight=0.02) Example: Filter(material\_datafile="Ge.txt",radius=1e-3, refraction=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +refraction & 0/1 & If nonzero, refraction is enabled. (Only functional for basic geometries, does not yet work for OFF) & 0 \\ +fixed\_delta & 0/1 & Use a fixed delta to compute refraction - useful for debugging. & 0 \\ +material\_datafile & str & File where the material parameters for the filter may be found. Format is similar to what may be found off the NIST website. [Be.txt] & "Be.txt" \\ +geometry & str & File containing the polygon definition of a general shape object. When xwidth is also given, the object is rescaled accordingly (OFF/PLY) & 0 \\ +xwidth & m & Width of block. & 0 \\ +yheight & m & Height of block. & 0 \\ +zdepth & m & Thickness of block. & 0 \\ +radius & m & Radius of cylinder or sphere. & 0 \\ +mu\_col & idx & Column index to pick up absorption length mu, counted from 0. Use with non-standard input file, e.g. 2-3 column files. -1 means attempt autodetect. & -1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Filter.comp}. + \item \htmladdnormallink{Meshlab}{https://www.meshlab.net/} - viewer for OFF files + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} - OFF file definition and examples + \item \htmladdnormallink{jroff.jar - Java version of Geomview (display only)}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{Qhull}{http://qhull.org} - for calculating a convex hull from points. + \item \htmladdnormallink{Powercrust}{https://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} - for reconstructing a solid geometry from a point cloud. + \item Most material datafile inpus may obtained from \htmladdnormallink{NIST FFast}{https://physics.nist.gov/PhysRefData/FFast/form.html} +\end{itemize} +\IfFileExists{optics/Filter_static.tex}{\input{optics/Filter_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Grating_reflect.tex b/docs/manuals/mcxtrace/optics/Grating_reflect.tex new file mode 100644 index 0000000000..d9a0393d21 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Grating_reflect.tex @@ -0,0 +1,41 @@ +\section{The \texttt{Grating\_reflect} McXtrace Component} +A reflective grating. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen (erkn@fysik.dtu.dk), Kristian Sorensen and Philip Smith + \item \textbf{Origin:} DTU + \item \textbf{Date:} June 2021 +\end{itemize} + +\subsection*{Description} +A reflective grating that diffracts incident photons. The grating is in the XZ-plane. It then reflects the incoming photon using a MC picked angle, where the angle is picked from a uniform distribution of width d\_phi, i.e. U[-d\_phi/2,d\_phi/2] The Monte Carlo wight of the ray is then adjusted wrt. to the grating interference pattern, and the diffraction pattern associated with each grating line. All lines are considered equal. For more efficient sampling of a particular direction the centre of the d\_phi may be shifted using the parameters order or phi0. In the latter case a set angle is chosen as the centre of the sampled interval, in the former the centre angle is computed from the specified grating order. + +In an upcoming release this grating model will also include a blazed grating. + +Example: Grating\_reflect( d\_phi=1,order=0,rho\_l=100,zdepth=102e-3,xwidth=102e-3) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +d\_phi & deg & Range of diffraction angle that is to be simulated -d\_phi/2 ; d\_phi/2. & 1 \\ +R0 & 0-1 & Constant reflecticity of the grating [0;1]. & 1 \\ +rho\_l & l/mm & Number of lines pr mm of the grating. & 800 \\ +order & 1 & The target order of the grating. If non-zero d\_phi will be centered around this scattering line. & 0 \\ +phi0 & deg & Target angle to center d\_phi. If this is set to 0 the 0th (or any other chosen by the parameter order) order line will be used. & 0 \\ +zdepth & m & The length of the grating. & 0.015 \\ +xwidth & m & The width of the grating. & 0.136 \\ +verbose & 0/1 & If non-zero, more information will be displayed. Nb. generates much output. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Grating\_reflect.comp}. +\end{itemize} +\IfFileExists{optics/Grating_reflect_static.tex}{\input{optics/Grating_reflect_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Grating_trans.tex b/docs/manuals/mcxtrace/optics/Grating_trans.tex new file mode 100644 index 0000000000..9f92f6f21f --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Grating_trans.tex @@ -0,0 +1,43 @@ +\section{The \texttt{Grating\_trans} McXtrace Component} +Transmission grating + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen (erkn@fysik.dtu.dk) + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} December 2016 +\end{itemize} + +\subsection*{Description} +Model of a 1D rectangular transmission grating based on the theory developed in Schnopper et. al., Applied Optics, 1977. The grating lines are assumed to be vertical. Within each period a fraction gamma is the "open" fraction. (I.e. 1 is completely open). At present only absorption in the substrate (modelled by the thickness sdepth) is included. + +This component is currently undergoing validation. + +Example: Grating\_trans( xwidth=25e-3, yheight=25e-3, gamma=0.4, period=2000e-10, zdepth=5100e-10, max\_order=3, material="Au.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +xwidth & m & Width of the grating. Defines how many lines there are in total. & 1e-3 \\ +yheight & m & Height of the grating. & 1e-3 \\ +period & m & Distance between grating grooves. & 1e-6 \\ +gamma & 0-1 & Ratio between groove and period aka duty cycle. 1 means fully open. & 0.5 \\ +zdepth & m & Depth of grooves. & 1e-6 \\ +sdepth & m & Thickness of substrate. The default is to have no substrate - i.e. rods. & 0 \\ +material & str & Data file containing the material from which the grating is made. & "Au.txt" \\ +substrate & str & Data file containing material data for the substrate. & "" \\ +max\_order & 1 & Maximum order to diffract & 2 \\ +fixed\_delta & 0/1 & Set delta to the given constant. Useful for debugging. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Grating\_trans.comp}. +\end{itemize} +\IfFileExists{optics/Grating_trans_static.tex}{\input{optics/Grating_trans_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Lens_CRL_RTM.tex b/docs/manuals/mcxtrace/optics/Lens_CRL_RTM.tex new file mode 100644 index 0000000000..620348cc56 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Lens_CRL_RTM.tex @@ -0,0 +1,45 @@ +\section{The \texttt{Lens\_CRL\_RTM} McXtrace Component} +1D CRL stack based on RTM formalism + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Jan '21 +\end{itemize} + +\subsection*{Description} +A CRL stack component based on the formalism presented by Simons et.al. J. Synch. Rad. + +\begin{verbatim} +2017, vol. 24. +\end{verbatim} + +We model a 1D lens stack focusing in the y-direction. I.e. invariant along x. + +Example: Lens\_CRL\_RTM( r=0.5e-3, N=10, fast=1, yheight=0, d=0.1e-3,xwidth=1e-4, zdepth=4e-4) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +r & m & Radius of curavature at the lens apex. & 0.5e-3 \\ +d & m & Thickness of a single lens & 0.1e-3 \\ +material & str & Datafile containing f1 constants & "Be.txt" \\ +N & m & Number of lenslets in the stack. & 1 \\ +zdepth & m & Thickness of a single lenslet. & 2e-3 \\ +yheight & m & Height of lens opening. If zero this is set by the lens thickness. & 1e-3 \\ +xwidth & m & Width of the lenslets. & 1.2e-3 \\ +fast & m & Use fast calculation - should be off for better display with mxdisplay & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Lens\_CRL\_RTM.comp}. +\end{itemize} +\IfFileExists{optics/Lens_CRL_RTM_static.tex}{\input{optics/Lens_CRL_RTM_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Lens_elliptical.tex b/docs/manuals/mcxtrace/optics/Lens_elliptical.tex new file mode 100644 index 0000000000..bea9d16447 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Lens_elliptical.tex @@ -0,0 +1,37 @@ +\section{The \texttt{Lens\_elliptical} McXtrace Component} +X-ray compound refractive lens (CRL) with an elliptic profile + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser and Erik Knudsen + \item \textbf{Origin:} NBI + \item \textbf{Date:} August 2010 +\end{itemize} + +\subsection*{Description} +A simple X-ray compound refractive lens (CRL) with an elliptic profile simulates the photons' movement on passing through it. Attenuation coefficient mu is taken from the NIST database and Be.txt + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_datafile & Be.txt & File where the material parameters for the filter may be found. Format is similar to what may be found off the NIST website. & "Be.txt" \\ +r1 & m & Radius of the profile along the X axis & 0.42e-3 \\ +r2 & m & Radius of the profile along the Y axis & 0.8e-3 \\ +w & m & Parabola parameter, constraining it along the propagation axis & 0.46e-3 \\ +d & m & Distance between two surfaces of the lens along the propagation axis & 0.2e-4 \\ +Transmission & & & 1 \\ +N & 1 & Amount of single lenses in a stack & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Lens\_elliptical.comp}. + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{optics/Lens_elliptical_static.tex}{\input{optics/Lens_elliptical_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Lens_parab.tex b/docs/manuals/mcxtrace/optics/Lens_parab.tex new file mode 100644 index 0000000000..a59df12e2e --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Lens_parab.tex @@ -0,0 +1,38 @@ +\section{The \texttt{Lens\_parab} McXtrace Component} +X-ray compound refractive lens (CRL) with a profile of the parabola + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser and Erik Knudsen + \item \textbf{Origin:} NBI + \item \textbf{Date:} August 2010, modified July 2011 +\end{itemize} + +\subsection*{Description} +A simple X-ray compound refractive lens (CRL) with a profile of the parabola in rotation simulates the photons' movement on passing through it. The CRL focuses in 2D + +Example: Lens\_parab(material\_datafile = "Be.txt", r=200e-6, r\_ap=0.5e-3, d=50e-6, N=16) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_datafile & str & Datafile containing f1 constants & "Be.txt" \\ +r & m & Radius of curvature (circular approximation at the tip of the profile). & 0.5e-3 \\ +r\_ap & m & Radius of circular aperture, which also defines the depth of the lens profile. & 1.4e-3 \\ +d & m & Distance between two surfaces of the lens along the propagation axis. & .1e-3 \\ +N & m & Number of single lenses in a stack. & 1 \\ +rough\_z & rad & RMS value of random slope error along z. & 0 \\ +rough\_xy & rad & RMS value of random slope error along x and y. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Lens\_parab.comp}. +\end{itemize} +\IfFileExists{optics/Lens_parab_static.tex}{\input{optics/Lens_parab_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Lens_parab_Cyl.tex b/docs/manuals/mcxtrace/optics/Lens_parab_Cyl.tex new file mode 100644 index 0000000000..91c03ec8cd --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Lens_parab_Cyl.tex @@ -0,0 +1,41 @@ +\section{The \texttt{Lens\_parab\_Cyl} McXtrace Component} +X-ray compound refractive lens (CRL) with a parabolic cylinder shape + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser and Erik Knudsen + \item \textbf{Origin:} NBI + \item \textbf{Date:} April 2011 +\end{itemize} + +\subsection*{Description} +An X-ray compound refractive lens (CRL) with a parabolic cylinder profile focusing in 1D, i.e. onto a line + +The lens is invariant along the x-axis and has a parabolic profile along the y-axis defined as z/c = y\textasciicircum{}2/b\textasciicircum{}2. Thus, i.e. it focuses onto a line along the x-axis. N\textgreater{}1 means that a stack of lenses is to be simulated. Each lens consists of a pair of two opposing parabolic surfaces with a distance d between them. The reference point of the component is at the bottom of the first parabolic surface. + +Example: Lens\_parab\_Cyl(r=.5e-3,yheight=1.3e-3,xwidth=1.3e-3,d=.1e-3,N=21, material\_datafile="Be.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_datafile & str & Datafile containing f1 constants & "Be.txt" \\ +r & m & Radius of curvature (circular approximation at the tip of the profile). & .5e-3 \\ +yheight & m & The CRL's aperture along Y. & 1.2e-3 \\ +xwidth & m & The width of the CRL in the invariant direction x. & 1.2e-3 \\ +d & m & Distance between two surfaces of the lens along the propagation axis. & .1e-3 \\ +N & 1 & Number of single lenses in a stack. & 1 \\ +rough\_z & rad & RMS value of random slope along z. & 0 \\ +rough\_xy & rad & RMS value of random slope along x and y. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Lens\_parab\_Cyl.comp}. +\end{itemize} +\IfFileExists{optics/Lens_parab_Cyl_static.tex}{\input{optics/Lens_parab_Cyl_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Lens_simple.tex b/docs/manuals/mcxtrace/optics/Lens_simple.tex new file mode 100644 index 0000000000..5b026b9c37 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Lens_simple.tex @@ -0,0 +1,41 @@ +\section{The \texttt{Lens\_simple} McXtrace Component} +Simple refractive x-ray lens + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 16, 2009 +\end{itemize} + +\subsection*{Description} +Models a stack of N refractive lenses, with a radius of curvature, r, at the apex. The model is a thin-lens approximation where photons are refracted in a the XY plane at Z=0. Absorption is generally disregarded may be handled through the use of the optional transmission parameter T, where 0\textless{}=T\textless{}=1. Thus, the lens has the focal length of f=R/(2*N*\&delta) where the x-ray refractive index is written: n = 1 - \&delta + i \&beta. + +Example: Lens\_simple(xwidth=1e-5, yheight=1e-5, material\_datafile="Be.txt",N=100,r=0.3e-3) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +xwidth & m & Width of lens aperture. & 0 \\ +yheight & m & Height of lens aperture. & 0 \\ +radius & m & Radius of lens aperture (overrides xwidth \& yheight). & 1e-3 \\ +T & 0-1 & Transmission efficiency of the lens. & 1 \\ +r & m & The radius of curvature of the lens. & 3e-4 \\ +N & 1 & The number of successive lenses in the stack. & 1 \\ +verbose & 0/1 & Extra information for debugging. & 0 \\ +f & m & Focal length - overrides the material\_datafile - and diregards chromatic aberration. & 0 \\ +material\_datafile & & File where the material parameters for the lens may be found. Format is similar to what may be found off the NIST website. & "Be.txt" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Lens\_simple.comp}. + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{optics/Lens_simple_static.tex}{\input{optics/Lens_simple_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Mask.tex b/docs/manuals/mcxtrace/optics/Mask.tex new file mode 100644 index 0000000000..b7606104da --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Mask.tex @@ -0,0 +1,52 @@ +\section{The \texttt{Mask} McXtrace Component} +A masking image object + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} March 2014 +\end{itemize} + +\subsection*{Description} +The Mask component takes an image as input either as an standard image file in png or pnm format, or as an ascii file (see below for format), and uses the image as a mask. For instance as a manner of measuring resolution for imaging applications. If the image is supplied as a png or pnm file, they interpretation of the pixels varies depending on the file. If the image is grayscale the pixel values are directly mapped to opacity (or transparency if invert is set) values in the range [0..1]. If the image has RGB channels the R channel is considered most significant, the B channel least significant. The resulting number, e.g. R*255\textasciicircum{}2 + G*255 + B, is then mapped to a real valued opacity. Additionally png images may have an alpha channel - which is then considered the least significant channel. Palette mapped pngs are as of yet \_not\_ supported. A regular ascii file may be supplied - in which case the file is like the one below \#any initial line starting with a hash is silently ignored + +\begin{verbatim} +0.0 1.0 0.0 1.0 0.0 +0.5 0.0 0.5 0.0 0.5 +0.0 0.25 0.0 0.25 0.0 +0.75 0.0 0.75 0.0 0.75 +1.0 0.0 1.0 0.0 1.0 +\end{verbatim} + +...which defines a 5x5 mask with a kind of checkerboard pattern. + +By default the values from the masking image are interepreted as opacity (1 is fully blocking). If invert is nonzero this is inverted and the values are considered as transparency (1 is fully transmissive) + +N.b. If you want to use the png-option of the component you must have libpng installed \_and\_ link your compiled instrument to it. Assuming libpng is installed you may do this by adding "-DUSE\_PNG=1 -lpng" to 1) the MCXTRACE\_CFLAGS environment variable or 2) to the compiler flags textbox in the GUI. Open File-\textgreater{}Configuration and edit the textbox. + +The virtual option of the Mask, is intended as a help to use a png-image as a grayscale distribution. If the virtual flag is set, rays are propagated to the mask plane and the pixel value at the intersection point is read, but the rays remain unaffected. The pixel value is stored in the variable named in the string maskvar. This should be a USERVAR set from the instrument file. + +Example: Mask(xwidth=0.1, yheight=0.1, mask=Test\_Mask\_input\_file.mask) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +xwidth & m & Width of the masking object & 0.1 \\ +yheight & m & Height of the masking object & 0.1 \\ +mask & str & Name of file containing the masking image & "Test\_Mask\_input\_file.mask" \\ +invert & 0/1 & When 0 =\textgreater{} masked values are opaque, when 1 =\textgreater{} masked values are transparent. & 0 \\ +virtual & 0/1 & Mask does not affect the x-ray, but does still read the pixel value of the pixel hit and stores it in masking. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Mask.comp}. +\end{itemize} +\IfFileExists{optics/Mask_static.tex}{\input{optics/Mask_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Mirror_curved.tex b/docs/manuals/mcxtrace/optics/Mirror_curved.tex new file mode 100644 index 0000000000..b2e9c614b4 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Mirror_curved.tex @@ -0,0 +1,38 @@ +\section{The \texttt{Mirror\_curved} McXtrace Component} +A cylindrically curved mirror (in YZ) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} September 25th, 2009 +\end{itemize} + +\subsection*{Description} +mirror is in the YZ-plane curved towards positive X if radius is positive + +Example: Mirror\_curved( radius=2, length=20e-3, width=40e-3, coating="AlMgF2\_disco.dat") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & m & Radius of curvature, along Z. & 1 \\ +R0 & 1 & Constant reflectivity value (mostly relevant for debugging, when coating=""). & 1 \\ +coating & str & Name of file containing the material data (i.e. f1 and f2) for the coating & "Be.txt" \\ +zdepth & m & Length of the unbent mirror along Z. & 0.2 \\ +yheight & m & Width of the mirror along Y. & 0.2 \\ +length & m & Length of the unbent mirror along Z = zdepth & 0 \\ +width & m & Width of the mirror along Y = yheight & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Mirror\_curved.comp}. +\end{itemize} +\IfFileExists{optics/Mirror_curved_static.tex}{\input{optics/Mirror_curved_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Mirror_elliptic.tex b/docs/manuals/mcxtrace/optics/Mirror_elliptic.tex new file mode 100644 index 0000000000..0f1963448c --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Mirror_elliptic.tex @@ -0,0 +1,41 @@ +\section{The \texttt{Mirror\_elliptic} McXtrace Component} +Idealized elliptic mirror. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} Feb 11, 2010 +\end{itemize} + +\subsection*{Description} +Takes a reflectivity as input and reflects rays in a ideal geometry elliptic mirror. The mirror is positioned such that the a-axis of the mirror ellipsoid is on the x-axis, the b-axis is along the y-axis and the c is along the z-axis. The reference point of the mirror is the ellipsoid centre, offset by one half-axis along the y-axis (See the component manual for a drawing). This means that to position the mirror correctly, the user positions the ellipsoid governing the mirror shape, not the mirror itself. + +Example: Mirror\_elliptic( length=150e-3, width=150e-3, x\_a=1.025, y\_b=1.025, z\_c=1.025) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +x\_a & m & 1st short half axis (along x). Commonly set to zero, which really implies infinite value, so crystal is an elliptic cylinder. & 0 \\ +y\_b & m & 2nd short half axis (along y), which is also the presumed near-normal direction, reflection near the y-z plane. & 1.0 \\ +z\_c & m & long half axis (along z). Commonly a=0. b=c, which creates a circular cylindrical surface. & 1.0 \\ +zdepth & m & Depth (length) of the mirror along Z. & 0.2 \\ +xwidth & m & Width of the mirror along X. & 0.2 \\ +R0 & 1 & Reflectivity of mirror (mostly relevant for debugging, when coating="") & 1 \\ +coating & str & Datafile containing either mirror material constants or reflectivity numbers. & "Be.txt" \\ +length & m & alternate name for zdepth (obsolete) & 0 \\ +width & m & alternate name for xwidth (obsolete) & 0 \\ +radius & m & Spherical radius, Sets x\_a=y\_b=z\_c=radius & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Mirror\_elliptic.comp}. +\end{itemize} +\IfFileExists{optics/Mirror_elliptic_static.tex}{\input{optics/Mirror_elliptic_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Mirror_parabolic.tex b/docs/manuals/mcxtrace/optics/Mirror_parabolic.tex new file mode 100644 index 0000000000..f6980466b9 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Mirror_parabolic.tex @@ -0,0 +1,40 @@ +\section{The \texttt{Mirror\_parabolic} McXtrace Component} +Idealized parabolic mirror (in XZ) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} Feb 11, 2010 +\end{itemize} + +\subsection*{Description} +Takes a reflectivity as input and reflects rays in a ideal geometry parabolic mirror. The mirror is positioned in the zx-plane curving towards positive y. I.e. the focal point is (0,0,f(a,b)) The geometry of the paraboloid is governed by the equation: y = x\textasciicircum{}2 / a\textasciicircum{}2 + z\textasciicircum{}2 / b\textasciicircum{}2 Hence, the focal length for the 'x' curve is f=a\textasciicircum{}2 / 4, and analogous for z. + +Example: Mirror\_parabolic(R0=1, a=1, b=0, xwidth=0.02, yheight=0, zdepth=0.05) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +R0 & 1 & Reflectivity of mirror. & 1 \\ +a & sqrt(m) & Transverse curvature scale, if zero - the mirror is flat along x. & 1 \\ +b & sqrt(m) & Longitudinal curvature scale, if zero, flat along z. & 1 \\ +xwidth & m & Width of mirror. & 0.1 \\ +zdepth & m & Length of mirror. & 0.1 \\ +yheight & m & Thickness of mirror. If 0 (the default) the mirror is mathemticlly thin. Only has an effect for hitting the mirror from the side. & 0 \\ +focusx & m & Transverse focal length along X. Sets a. & 0 \\ +focusz & m & Longitudinal focal length along Z. Sets b. & 0 \\ +radius & m & Focal length. Sets focusx and focusz. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Mirror\_parabolic.comp}. +\end{itemize} +\IfFileExists{optics/Mirror_parabolic_static.tex}{\input{optics/Mirror_parabolic_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Mirror_toroid.tex b/docs/manuals/mcxtrace/optics/Mirror_toroid.tex new file mode 100644 index 0000000000..7ce5e02a2b --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Mirror_toroid.tex @@ -0,0 +1,39 @@ +\section{The \texttt{Mirror\_toroid} McXtrace Component} +Toroidal shape mirror (in XZ) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Jul 2016 +\end{itemize} + +\subsection*{Description} +This is an implementation of a toroidal mirror which may be curved in two dimensions. To avoid solving quartic equations, the intersection is compited as a combination of two intersections. First, the ray is intersected with a cylinder to catch (almost) the small radius curvature. Secondly, the ray is the intersected with an ellipsoid, with the curvatures matching that of the torus. + +In the first incarnation we assume the mirror to be curving outwards (a bump). + +Example: Mirror\_toroid(zdepth=0.340,xwidth=0.020,radius=246.9254,radius\_o=246.9254,R0=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +coating & str & Datafile containing either mirror material constants or reflectivity numbers. & "" \\ +zdepth & m & Length of mirror. & 0.1 \\ +xwidth & m & Width of mirror. & 0.01 \\ +\textbf{radius} & m & Curvature radius & \\ +\textbf{radius\_o} & m & Curvature radius, outwards & \\ +R0 & 1 & Reflectivity of mirror. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Mirror\_toroid.comp}. +\end{itemize} +\IfFileExists{optics/Mirror_toroid_static.tex}{\input{optics/Mirror_toroid_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Multilayer_elliptic.tex b/docs/manuals/mcxtrace/optics/Multilayer_elliptic.tex new file mode 100644 index 0000000000..1cbbde9f76 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Multilayer_elliptic.tex @@ -0,0 +1,57 @@ +\section{The \texttt{Multilayer\_elliptic} McXtrace Component} +Elliptic multilayer mirror (in XZ) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser, Peter Willendrup, Anette Vickery, Andrea Prodi, Erik Knudsen + \item \textbf{Origin:} NBI + \item \textbf{Date:} February 2011 +\end{itemize} + +\subsection*{Description} +Reads reflectivity values from a data input file (Ref.dat) for a Si/W multilayer. The multilayer code reflects ray in an ideal geometry, does not include surface imperfections + +The mirror is positioned such that the long axis of the mirror elliptical surface coincides with z-axis + +The algorithm: Incoming photon's coordinates and direction (k-vector) are transformed into an elliptical reference frame (elliptical parameters are calculated according to the mirror's position and its focusing distances and the incident angle), the intersection point is then defined. A new, reflected photon is then starting at the point of intersection. + +Example: Multilayer\_elliptic( coating = "Ref\_W\_B4C.txt", theta = 1.2, + +\begin{verbatim} +s1 = 1, s2 = 2, length = 0.1, width = 0.1, R0 = 1, +\end{verbatim} + +Emin=7, Emax=10, Estep=0.05) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +coating & str & Datafile containing reflectivity values as a function of q and E. & "Ref\_W\_B4C.txt" \\ +theta & deg & Design angle of incidence. & 1.2 \\ +s1 & m & Design distance from the source to the multilayer. & 0 \\ +s2 & m & Design focusing distance of the multilayer. & 0 \\ +length & m & alternate name for zdepth (obsolete) & 0.5 \\ +width & m & alternate name for xwidth (obsolete) & 0.2 \\ +R0 & 1 & Maximal reflectivity & 1 \\ +Emin & keV & Lower limit of energy interval in datafile. Overrides what's written in the datafile header. & -1 \\ +Emax & keV & Upper limit of energy interval in datafile. Overrides what's written in the datafile header. & -1 \\ +Estep & keV & Step between energy sample points in datafile. Overrides what's written in the datafile header. & -1 \\ +Gamma & & High electron density fraction of bilayer (in kinematical appr.). & 0 \\ +Lambda & m & Thickness of bilayer (in kinematical appr.). & 0 \\ +rho\_AB & & Number electron density constrast in bilayer (in kinematical appr.). & 0 \\ +N & 1 & Number of bilayers (in kinematical appr.). & 0 \\ +xwidth & m & Width of the mirror along X-axis. & 0 \\ +zdepth & m & Length of the mirror along Z. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Multilayer\_elliptic.comp}. +\end{itemize} +\IfFileExists{optics/Multilayer_elliptic_static.tex}{\input{optics/Multilayer_elliptic_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Place.tex b/docs/manuals/mcxtrace/optics/Place.tex new file mode 100644 index 0000000000..60b6feeff8 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Place.tex @@ -0,0 +1,31 @@ +\section{The \texttt{Place} McXtrace Component} +A place in space - alias of Arm + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Peter Willendrup + \item \textbf{Origin:} DTU + \item \textbf{Date:} June 2025 +\end{itemize} + +\subsection*{Description} +Just like Arm, Place does not actually do anything, it is just there to set up a new coordinate system. + +Example: Place() + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Place.comp}. +\end{itemize} +\IfFileExists{optics/Place_static.tex}{\input{optics/Place_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Slit.tex b/docs/manuals/mcxtrace/optics/Slit.tex new file mode 100644 index 0000000000..23c2724519 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Slit.tex @@ -0,0 +1,43 @@ +\section{The \texttt{Slit} McXtrace Component} +Rectangular/circular slit + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} June 16, 2009 +\end{itemize} + +\subsection*{Description} +Based on Slit-comp by Kim Lefmann and Henrik Roennow A simple rectangular or circular slit. You may either specify the radius (circular shape), which takes precedence, or rectangular bounds. No transmission around the slit is allowed. + +Example: Slit(xmin=-0.01, xmax=0.01, ymin=-0.01, ymax=0.01) Slit(radius=0.01) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +xmin & m & Lower x bound. & 0 \\ +xmax & m & Upper x bound. & 0 \\ +ymin & m & Lower y bound. & 0 \\ +ymax & m & Upper y bound. & 0 \\ +radius & m & Radius of slit in the z=0 plane, centered at Origin. & 0 \\ +xwidth & m & Width of slit. Overrides xmin,xmax. & 0.001 \\ +yheight & m & Height of slit. Overrides ymin,ymax. & 0.001 \\ +dist & m & Distance from slit plane to plane containing resampling target. & 0 \\ +focus\_xw & m & Width of resampling window. & 0 \\ +focus\_yh & m & Height of resampling window. & 0 \\ +focus\_x0 & m & Centre (x) of resampling window. & 0 \\ +focus\_y0 & m & Centre (y) of resampling window. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Slit.comp}. +\end{itemize} +\IfFileExists{optics/Slit_static.tex}{\input{optics/Slit_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/Slit_N.tex b/docs/manuals/mcxtrace/optics/Slit_N.tex new file mode 100644 index 0000000000..82ff31b84b --- /dev/null +++ b/docs/manuals/mcxtrace/optics/Slit_N.tex @@ -0,0 +1,39 @@ +\section{The \texttt{Slit\_N} McXtrace Component} +Release: McXtrace 0.1 + +Rectangular/circular slit, duplicated + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 16, 2009 +\end{itemize} + +\subsection*{Description} +Based on Slit-comp by Kim Lefmann and Henrik Roennow A simple rectangular or circular slit. You may either specify the radius (circular shape), which takes precedence, or the rectangular bounds. The slits are separated with 'd', and arranged along X. No transmission around the slit is allowed. If cutting option is used, low-weight x-rays are ABSORBED + +Example: Slit\_N(xwidth=0.01, yheight=0.01, d=0.02) Slit\_N(radius=0.01, cut=1e-10, d=0.03) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & m & Radius of slit in the z=0 plane, centered at Origo & 0 \\ +cut & & Lower limit for allowed weight (1) & 0 \\ +xwidth & m & Width of slit. Overrides xmin,xmax. & 0 \\ +yheight & m & Height of slit. Overrides ymin,ymax. & 0 \\ +N & 1 & Number of slit openings along X & 2 \\ +d & m & Separation of slits & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Slit\_N.comp}. +\end{itemize} +\IfFileExists{optics/Slit_N_static.tex}{\input{optics/Slit_N_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/TwinKB_ML.tex b/docs/manuals/mcxtrace/optics/TwinKB_ML.tex new file mode 100644 index 0000000000..cd1c9e5e0e --- /dev/null +++ b/docs/manuals/mcxtrace/optics/TwinKB_ML.tex @@ -0,0 +1,44 @@ +\section{The \texttt{TwinKB\_ML} McXtrace Component} +Montel optic model (aka side-by-side Kirkpatrick Baez) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser, Peter Willendrup, Anette Vickery, Andrea Prodi, Erik Knudsen, Jesper Buch Jensen + \item \textbf{Origin:} NBI + \item \textbf{Date:} May 2012 +\end{itemize} + +\subsection*{Description} +Models a Montel optic, or Twin Kirkpatrick Baez mirror optic (hence the component name). The mirror are fully abutting, i.e. there's is no gap between them, and perfectly elliptic. + +Reads reflectivity values from a data input file for a W/B4C multilayer. The multilayer code reflects ray in an ideal geometry, the reflectivity datafile accounts for surface roughness, sigma. + +The mirror is positioned such that the long axis of the mirror elliptical surface coincides with the z-axis. + +The algorithm: Incoming photon's coordinates and direction (k-vector) are transformed into an elliptical reference frame (elliptical parameters are calculated according to the mirror's position and its focusing distances and the * incident angle), the intersection point is then defined. A new, reflected photon is then starting at the point of intersection. + +Example: TwinKB\_ML( theta=1.2, s1=.045 , s2=.9 , length=0.06 , width=0.2 , R0=0 , reflectivity\_datafile="Ref\_W\_B4C.txt") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +reflectivity\_datafile & str & File which contains reflectivities as a function of q. & "Ref.txt" \\ +theta & deg & Incident angle & 1.2 \\ +\textbf{s1} & m & Distance from the source to the multilayer & \\ +\textbf{s2} & m & Focusing distance of the multilayer & \\ +length & m & Length of the mirrors & 0.6 \\ +width & m & Width of the mirror along x-axis & 0.2 \\ +R0 & 0-1 & Constant reflectivity, R0=1 for an ideal situation. If R0=0, the code reads the reflectivity from the datafile & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{TwinKB\_ML.comp}. +\end{itemize} +\IfFileExists{optics/TwinKB_ML_static.tex}{\input{optics/TwinKB_ML_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/ZonePlate.tex b/docs/manuals/mcxtrace/optics/ZonePlate.tex new file mode 100644 index 0000000000..8f238fa840 --- /dev/null +++ b/docs/manuals/mcxtrace/optics/ZonePlate.tex @@ -0,0 +1,47 @@ +\section{The \texttt{ZonePlate} McXtrace Component} +Release: McXtrace 1.4 + +Zone plate based on Monte Carlo sampling of the Fresnel-Kirchhoff integral + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} June 16, 2009 +\end{itemize} + +\subsection*{Description} +A component which models a zone plate by consierding the plate a secondary source and then by means of Monte Carlo sampling, evaluating the Fresnel-Kirchhoff integral implicitly by resampling the beam in a window defined by the focus\_xw,focus\_yh parameters. + +Caveat emptor I: this is a computationally heavy component to run. Caveat emptor II: for correct modelling of phase-interference phenomena, detectors used after the ZonePlate should be of the \textbf{"PSD\_monitor\_coh"} type. + +The zone plate can be either circular or linear. In the linear case, the "slits" are along the x-axis. + +Example: ZonePlate(radius=0.00015, L=0.15, lambda0=1, focus\_xw=300e-9, focus\_yh = 300e-9, focus\_x0 = 0.0, focus\_y0 = 0.0, dist=1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & m & The outer radius of the zone plate. Triggers a circular zone plate. Takes precedence over xwidth,yheight. & 0 \\ +xwidth & m & Width of linear zone plate. & 0 \\ +yheight & m & Height of linear zone plate & 0 \\ +\textbf{L} & m & Focal length. & \\ +\textbf{lambda0} & \AA{} & The nominal wavelength that the zone plate is designed to focus. & \\ +focus\_x0 & m & Offset of resampling window along the x-axis. & 0 \\ +focus\_y0 & m & Offset of resampling window along the y-axis. & 0 \\ +\textbf{focus\_xw} & m & Width of the resampling window. & \\ +\textbf{focus\_yh} & m & Height of the resampling window. & \\ +\textbf{dist} & m & Distance along the z-axis from zone plate to the resampling window. & \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{ZonePlate.comp}. +\end{itemize} +\IfFileExists{optics/ZonePlate_static.tex}{\input{optics/ZonePlate_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/optics/mirror.tex b/docs/manuals/mcxtrace/optics/mirror.tex index 406a4390cc..c2bde2e46e 100644 --- a/docs/manuals/mcxtrace/optics/mirror.tex +++ b/docs/manuals/mcxtrace/optics/mirror.tex @@ -1,9 +1,39 @@ -\section{Mirrors etc.} -\label{s:mirrors} -\index{Optics|textbf} - -This section describes advanced X-ray optics -components such as mirrors and analyzer crystals. -A description of the reflectivity of a mirror is found -in section~\ref{ss:mirrorreflect}. - +\section{The \texttt{Mirror} McXtrace Component} +Perfectly flat mirror (in XZ or YZ), or polygonal + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} July 2016 +\end{itemize} + +\subsection*{Description} +This is a simple implementation of a perfectly flat mirror. The mirror plane is in the XZ-plane. It can be oriented in the YZ plane by setting 'yheight'. It may also be a complex polygonal geometry (OFF/PLY) by setting 'geometry'. + +Reflectivity may be specified either as a number (R0) or by means of a material datafile. The material datafile may be specified as a coating or as relfectivity - either parameterized by q or E,theta. If the datafile is identified as a coating recipe, an ab-initio reflectivity calculation is triggered. + +Example: Mirror(xwidth=5e-2, zdepth=2e-1, R0=1, coating="B4C.dat") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +zdepth & m & The length of the mirror & 0.1 \\ +xwidth & m & The width of the mirror & 0.01 \\ +yheight & m & The height of the mirror. This overrides xwidth and puts the mirror in the yz-plane. & 0 \\ +coating & str & Filename containing reflectivities (or coating). & "" \\ +R0 & 0-1 & Constant reflectivity & 0 \\ +geometry & str & Filename of an OFF/PLY geometry providing a polygonal surface. When xwidth/yheight/zdepth are also given, the object is rescaled accordingly. & "" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Mirror.comp}. +\end{itemize} +\IfFileExists{optics/Mirror_static.tex}{\input{optics/Mirror_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/preamble.tex b/docs/manuals/mcxtrace/preamble.tex.in similarity index 96% rename from docs/manuals/mcxtrace/preamble.tex rename to docs/manuals/mcxtrace/preamble.tex.in index a687deae3c..d9db077dc9 100644 --- a/docs/manuals/mcxtrace/preamble.tex +++ b/docs/manuals/mcxtrace/preamble.tex.in @@ -40,9 +40,9 @@ \newcommand{\MCX}{McXtrace\xspace} \newcommand{\MCS}{McStas\xspace} -\newcommand{\version}{3.8.5\xspace} +\newcommand{\version}{@MCCODE_VERSION@\xspace} \newcommand{\reldate}{September, 2026\xspace} -\newcommand{\Ombold}{\mbox{\boldmath $\Omega$}} +\newcommand{\Ombold}{\boldsymbol{\Omega}} \newcommand{\NBIlong}{Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.\xspace} \newcommand{\Lifelong}{Faculty for Life Sciences, University of Copenhagen, Copenhagen, Denmark.\xspace} @@ -91,3 +91,4 @@ \makeindex % enable index generation +\providecommand{\hyperindexformat}[2]{#1{#2}} diff --git a/docs/manuals/mcxtrace/preamble_comp.tex b/docs/manuals/mcxtrace/preamble_comp.tex.in similarity index 96% rename from docs/manuals/mcxtrace/preamble_comp.tex rename to docs/manuals/mcxtrace/preamble_comp.tex.in index 5ba250bfe3..c7ef7e1cea 100644 --- a/docs/manuals/mcxtrace/preamble_comp.tex +++ b/docs/manuals/mcxtrace/preamble_comp.tex.in @@ -39,9 +39,9 @@ \newcommand{\MCX}{McXtrace\xspace} \newcommand{\MCS}{McStas\xspace} -\newcommand{\version}{3.8.5\xspace} +\newcommand{\version}{@MCCODE_VERSION@\xspace} \newcommand{\reldate}{September, 2026\xspace} -\newcommand{\Ombold}{\mbox{\boldmath $\Omega$}} +\newcommand{\Ombold}{\boldsymbol{\Omega}} \newcommand{\NBIlong}{Niels Bohr Institute, Univeristy of Copenhagen, Copenhagen, Denmark.\xspace} \newcommand{\Lifelong}{Faculty for Life Sciences, University of Copenhagen, Copenhagen, Denmark.\xspace} @@ -91,3 +91,4 @@ } \makeindex % enable index generation +\providecommand{\hyperindexformat}[2]{#1{#2}} diff --git a/docs/manuals/mcxtrace/samples/Abs_objects.tex b/docs/manuals/mcxtrace/samples/Abs_objects.tex new file mode 100644 index 0000000000..ff303b815d --- /dev/null +++ b/docs/manuals/mcxtrace/samples/Abs_objects.tex @@ -0,0 +1,44 @@ +\section{The \texttt{Abs\_objects} McXtrace Component} +Release: McXtrace 1.1 + +Blocks of attenuating material in off format + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Jan 24, 2011 +\end{itemize} + +\subsection*{Description} +This component is a model of 1 or more off-shaped blocks attenuating the x-ray beam. Which shapes are present and their relative positions are described in a file of the follwing format: \#objects Material-filename OFF-filename x y z xwidth yheight zdepth ... + +An example is; 2 + +\begin{verbatim} +Be.txt cube.off 0 0.01 0 0 0 0 +Rh.txt chess.off 0 -0.01 0 0 0 0 +\end{verbatim} + +A xwidth etc of zero means use whatever dimensions are in the off/ply file. If xwidth (or yheight or zdepth) is nonzero, the component scales the object to fill that dimension. The xyz coordinates indicate the object shift. + +Example: Abs\_objects(objects="input\_abs\_objects\_template.dat") + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +refraction & str & Flag to enable refraction at interfaces. & 1 \\ +objects & str & Input file where the off-shapes are defined. & "input\_abs\_objects\_template.dat" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Abs\_objects.comp}. +\end{itemize} +\IfFileExists{samples/Abs_objects_static.tex}{\input{samples/Abs_objects_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/Absorption_sample.tex b/docs/manuals/mcxtrace/samples/Absorption_sample.tex new file mode 100644 index 0000000000..bd5c8e292f --- /dev/null +++ b/docs/manuals/mcxtrace/samples/Absorption_sample.tex @@ -0,0 +1,62 @@ +\section{The \texttt{Absorption\_sample} McXtrace Component} +Sample component with absorbing materials. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} March 2011 +\end{itemize} + +\subsection*{Description} +A sample component consisting of a volume of one material and volume of another material inside. This is useful as a phantom for simulating tomography experiments. The inner material can be left unset (all 0), to only have one volume. + +Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth +cylinder: radius x yheight +sphere: radius (yheight=0) +any shape: geometry=OFF/PLY file +\end{verbatim} + +Example: Absorption\_sample( material\_datafile\_o="Mn.txt", xwidth\_o = 0.5, yheight\_o = 0.5, zdepth\_o = 0.0001, rho\_o=7.15 ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_datafile\_i & str & Name of file containing material data for inclusion. & "" \\ +material\_datafile\_o & str & Name of file containing material data for outer volume. & "" \\ +radius\_o & m & Radius of "outer" enclosing material cylinder (0) & 0 \\ +xwidth\_o & m & Width of "outer" enclosing material box (yheight) & 0 \\ +yheight\_o & m & Height of "outer enclosing material box (1) & 1 \\ +zdepth\_o & m & Thickness of outer enclosing material box (yheight) & 0 \\ +radius\_i & m & Radius of "inner" enclosed material cylinder (0) & 0 \\ +xwidth\_i & m & Width of "inner" enclosed material box (yheight) & 0 \\ +yheight\_i & m & Height of "inner enclosed material (1) & 0.0 \\ +zdepth\_i & m & Thickness of inner enclosed material box (yheight) & 0 \\ +x\_i & m & Center x-coordinate of "inner" object & 0 \\ +y\_i & m & Center y-coordinate of "inner" object & 0 \\ +z\_i & m & Center z-coordinate of "inner" object & 0 \\ +rho\_i & g/cm$^{3}$ & density of the enclosed material & 0 \\ +rho\_o & g/cm$^{3}$ & density of the enclosing material & 0 \\ +geometry\_i & str & Name of an inner Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust [str] & "" \\ +geometry\_o & str & Name of the outer Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust & "" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Absorption\_sample.comp}. + \item Meshlab https://www.meshlab.net/ + \item Geomview and Object File Format (OFF) \textless{}http://www.geomview.org\textgreater{} + \item Java version of Geomview (display only) jroff.jar \textless{}http://www.holmes3d.net/graphics/roffview/\textgreater{} + \item qhull \textless{}http://qhull.org\textgreater{} + \item Powercrust https://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html +\end{itemize} +\IfFileExists{samples/Absorption_sample_static.tex}{\input{samples/Absorption_sample_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/FluoCrystal.tex b/docs/manuals/mcxtrace/samples/FluoCrystal.tex new file mode 100644 index 0000000000..89b7dc4dd1 --- /dev/null +++ b/docs/manuals/mcxtrace/samples/FluoCrystal.tex @@ -0,0 +1,145 @@ +\section{The \texttt{FluoCrystal} McXtrace Component} +Release: McXtrace 3.5 + +Sample model handling absorption, fluorescence, Compton, Rayleigh scattering and single crystal diffraction. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Emmanuel Farhi (emmanuel.farhi.synchrotron-soleil.fr) + \item \textbf{Origin:} Synchrotron SOLEIL + \item \textbf{Date:} April 2025 +\end{itemize} + +\subsection*{Description} +Sample that models multiple photon-matter interactions: + +\begin{verbatim} +- absorption (photon excites an electron and creates a hole) +- fluorescence (excited electrons emit light while falling into lower states) +\end{verbatim} + +- Compton scattering (inelastic, incoherent) + +\begin{verbatim} +- Rayleigh scattering (elastic, coherent) +- crystal diffraction (elastic, coherent) +\end{verbatim} + +The 'material' specification is given as a chemical formulae, e.g. "LaB6". It may also be given as a file name (CIF/LAU/LAZ/FullProf format) in which case the formulae is guessed (but may be approximative), and the crystal diffraction is computed, following same options as the \textbf{PowderN} sample component. The fluorescence is handled for atoms from Z=5 to Z=90. + +By setting the 'order' to 1, the absorption along the scattered path is handled. A higher 'order' will handle multiple scattering events, and final absorption. For instance, a value order\textgreater{}=2 handles e.g. fluorescence iterative cascades in the material. Leaving 'order=0' handles the single scattering only. + +The single crystal diffraction model is simplified wrt the \textbf{Single\_crystal} component. Use that latter with a Fluorescence in a GROUP for more complex features. + +Example: FluoCrystal(material="LaB6.cif", xwidth=0.001,yheight=0.001,zdepth=0.0001, p\_interact=0.99, mosaic=3) + +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth (thickness=0) +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} +cylinder: radius x yheight (thickness=0) +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} +sphere: radius (yheight=0 thickness=0) +hollow sphere: radius and thickness>0 (yheight=0) +any shape: geometry=OFF file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the photon ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF, PLY and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +\textbf{Concentric components:} This component has the ability to contain other components when used in hollow cylinder geometry (namely sample environment, e.g. cryostat and furnace structure). Such component 'shells' should be split into input and output side surrounding the 'inside' components. First part must then use 'concentric=1' flag to enter the inside part. The component itself must be repeated to mark the end of the concentric zone. The number of concentric shells and number of components inside is not limited. + +COMPONENT F\_in = FluoCrystal(material="Al", concentric=1, ...) AT (0,0,0) RELATIVE sample\_position + +COMPONENT something\_inside ... // e.g. the sample itself or other materials + +COMPONENT F\_out = COPY(F\_in)(concentric=0) AT (0,0,0) RELATIVE sample\_position + +\textbf{Enhancing computation efficiency:} An important option to enhance statistics is to set 'p\_interact' to, say, 30 percent (0.3) in order to force a fraction of the beam to scatter. This will result on a larger number of scattered events, retaining intensity. + +In addition, it may be desirable to define a 'target' for the fluorescence processes via e.g. the 'target\_index' and the 'focus\_xw / focus\_yh' options. This target should e.g. be the SDD area. + +The SPLIT feature is currently BROKEN with this component. Do not use it. + +If you get strange results, check the crystal mosaicity and delta(d)/d parameters, as this component is not suited for ideal/perfect mosaic crystals. + +The fluorescence is computed via the XRayLib (apt install libxrl-dev) https://github.com/tschoonj/xraylib. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +geometry & str & Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust. & 0 \\ +radius & m & Outer radius of sample in (x,z) plane. cylinder/sphere. & 0 \\ +thickness & m & Thickness of hollow sample Negative value extends the hollow volume outside of the box/cylinder. & 0 \\ +xwidth & m & Width for a box sample shape. & 0 \\ +yheight & m & Height of sample in vertical direction for box/cylinder shapes. & 0 \\ +zdepth & m & Depth for a box sample shape. & 0 \\ +concentric & 1 & Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere). & 0 \\ +material & str & A CIF/LAZ/LAU file e.g. "LaB6.cif" to handle diffraction or chemical formulae, e.g. "Pb2SnO4" (no diffraction). & "LaB6.cif" \\ +packing\_factor & 1 & How dense is the material compared to bulk 0-1. & 0 \\ +density & g/cm$^{3}$ & Density of material. V\_rho=density/weight/1e24*N\_A at/\AA{}\textasciicircum{}3. & 0 \\ +weight & g/mol & Atomic/molecular weight of material. & 0 \\ +p\_interact & 1 & Force a given fraction of the beam to scatter, keeping intensity right, to enhance small signals (-1 inactivate). & 0 \\ +target\_x & m & Position of target to focus at, along X (for fluorescence). & 0 \\ +target\_y & m & Position of target to focus at, along Y (for fluorescence). & 0 \\ +target\_z & m & Position of target to focus at, along Z (for fluorescence). & 0 \\ +focus\_r & m & Radius of disk containing target. Use 0 for full space (for fluorescence). & 0 \\ +focus\_xw & m & Horiz. dimension of a rectangular area (for fluorescence). & 0 \\ +focus\_yh & m & Vert. dimension of a rectangular area (for fluorescence). & 0 \\ +focus\_aw & deg & Horiz. angular dimension of a rectangular area (for fluorescence). & 0 \\ +focus\_ah & deg & Vert. angular dimension of a rectangular area (for fluorescence). & 0 \\ +target\_index & 1 & Relative index of component to focus at, e.g. next is +1 (for fluorescence). & 0 \\ +flag\_compton & 1 & When 0, the Compton scattering is ignored. & 1 \\ +flag\_rayleigh & 1 & When 0, the Rayleigh scattering is ignored. & 1 \\ +flag\_lorentzian & 1 & When 1, the fluorescence line shapes are assumed to be Lorentzian, else Gaussian. & 0 \\ +flag\_kissel & 1 & When 1 (slower), handle M-lines XRF from Kissel for Z\textgreater{}=52 Te (else only K and L-lines). & 0 \\ +sx\_refl & str & A CIF/LAZ/LAU reflection file as for PowderN. When not given, 'material' is used. Specify it when 'material' is a chemical formula. & "" \\ +int flag\_sx & & & 1 \\ +delta\_d\_d & 1 & Lattice spacing variance, gaussian RMS (longitudinal mosaic) e.g. 1e-4 to 1e-3. & 1e-3 \\ +int barns & & & 1 \\ +recip\_cell & 1 & Choice of direct/reciprocal (0/1) unit cell definition & 0 \\ +ax & \AA{} or \AA{}$^{-1}$ & Coordinates of first (direct/recip) unit cell vector & 0 \\ +ay & \AA{} or \AA{}$^{-1}$ & a on y axis & 0 \\ +az & \AA{} or \AA{}$^{-1}$ & a on z axis & 0 \\ +bx & \AA{} or \AA{}$^{-1}$ & Coordinates of second (direct/recip) unit cell vector & 0 \\ +by & \AA{} or \AA{}$^{-1}$ & b on y axis & 0 \\ +bz & \AA{} or \AA{}$^{-1}$ & b on z axis & 0 \\ +cx & \AA{} or \AA{}$^{-1}$ & Coordinates of third (direct/recip) unit cell vector & 0 \\ +cy & \AA{} or \AA{}$^{-1}$ & c on y axis & 0 \\ +cz & \AA{} or \AA{}$^{-1}$ & c on z axis & 0 \\ +aa & & & 0 \\ +bb & & & 0 \\ +cc & & & 0 \\ +mosaic\_AB & arc\_minutes, arc\_minutes,1, 1, 1, 1, 1, 1 & In Plane mosaic rotation and plane vectors (anisotropic), mosaic\_A, mosaic\_B, A\_h,A\_k,A\_l, B\_h,B\_k,B\_l. Puts the crystal in the in-plane mosaic state. Vectors A and B define plane in which the crystal roation is defined, and mosaic\_A, mosaic\_B, denotes the resp. mosaicities (gaussian RMS) with respect to the two reflections chosen by A and B (Miller indices). & \{0,0, 0,0,0, 0,0,0\} \\ +mosaic & arc min & Crystal mosaic (isotropic), gaussian RMS. Puts the crystal in the isotropic mosaic model state, thus disregarding other mosaicity parameters, e.g. 1-10. & 3 \\ +mosaic\_a & arc min & Horizontal (rotation around lattice vector a) mosaic (anisotropic), gaussian RMS. Put the crystal in the anisotropic crystal vector state. I.e. model mosaicity through rotation around the crystal lattice vectors. Has precedence over in-plane mosaic model. & -1 \\ +mosaic\_b & arc min & Vertical (rotation around lattice vector b) mosaic (anisotropic), gaussian RMS. & -1 \\ +mosaic\_c & arc min & Out-of-plane (Rotation around lattice vector c) mosaic (anisotropic), gaussian RMS & -1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{FluoCrystal.comp}. + \item The XRayLib https://github.com/tschoonj/xraylib http://dx.doi.org/10.1016/j.sab.2011.09.011 + \item Fluorescence https://en.wikipedia.org/wiki/Fluorescence + \item Rayleigh https://en.wikipedia.org/wiki/Rayleigh\_scattering + \item Compton https://en.wikipedia.org/wiki/Compton\_scattering + \item X-ray absorption edges http://skuld.bmsc.washington.edu/scatter/AS\_periodic.html + \item X-ray fluorescence spectra http://www.xrfresearch.com/xrf-spectra/ + \item X-ray edges and fluo lines https://physics.nist.gov/PhysRefData/XrayTrans/Html/search.html +\end{itemize} +\IfFileExists{samples/FluoCrystal_static.tex}{\input{samples/FluoCrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/FluoPowder.tex b/docs/manuals/mcxtrace/samples/FluoPowder.tex new file mode 100644 index 0000000000..6711b26608 --- /dev/null +++ b/docs/manuals/mcxtrace/samples/FluoPowder.tex @@ -0,0 +1,129 @@ +\section{The \texttt{FluoPowder} McXtrace Component} +Release: McXtrace 3.5 + +Sample model handling absorption, fluorescence, Compton, Rayleigh scattering and powder diffraction. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Emmanuel Farhi (emmanuel.farhi.synchrotron-soleil.fr) + \item \textbf{Origin:} Synchrotron SOLEIL + \item \textbf{Date:} April 2025 +\end{itemize} + +\subsection*{Description} +Sample that models multiple photon-matter interactions: + +\begin{verbatim} +- absorption (photon excites an electron and creates a hole) +- fluorescence (excited electrons emit light while falling into lower states) +\end{verbatim} + +- Compton scattering (inelastic, incoherent) + +\begin{verbatim} +- Rayleigh scattering (elastic, coherent) +- powder diffraction (elastic, coherent) +\end{verbatim} + +The 'material' specification is given as a chemical formulae, e.g. "LaB6". It may also be given as a file name (CIF/LAU/LAZ/FullProf format) in which case the formulae is guessed (but may be approximative), and the powder diffraction is computed, following same options as the \textbf{PowderN} sample component. The fluorescence is handled for atoms from Z=5 to Z=90. + +By setting the 'order' to 1, the absorption along the scattered path is handled. A higher 'order' will handle multiple scattering events, and final absorption. For instance, a value order\textgreater{}=2 handles e.g. fluorescence iterative cascades in the material. Leaving 'order=0' handles the single scattering only. + +Example: FluoPowder(material="LaB6.cif", xwidth=0.001,yheight=0.001,zdepth=0.0001, p\_interact=0.99, target\_index=1, focus\_xw=0.0005, focus\_yh=0.0005) + +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth (thickness=0) +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} +cylinder: radius x yheight (thickness=0) +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} +sphere: radius (yheight=0 thickness=0) +hollow sphere: radius and thickness>0 (yheight=0) +any shape: geometry=OFF file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the photon ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF, PLY and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +\textbf{Concentric components:} This component has the ability to contain other components when used in hollow cylinder geometry (namely sample environment, e.g. cryostat and furnace structure). Such component 'shells' should be split into input and output side surrounding the 'inside' components. First part must then use 'concentric=1' flag to enter the inside part. The component itself must be repeated to mark the end of the concentric zone. The number of concentric shells and number of components inside is not limited. + +COMPONENT F\_in = FluoPowder(material="Al", concentric=1, ...) AT (0,0,0) RELATIVE sample\_position + +COMPONENT something\_inside ... // e.g. the sample itself or other materials + +COMPONENT F\_out = COPY(F\_in)(concentric=0) AT (0,0,0) RELATIVE sample\_position + +\textbf{Enhancing computation efficiency:} An important option to enhance statistics is to set 'p\_interact' to, say, 30 percent (0.3) in order to force a fraction of the beam to scatter. This will result on a larger number of scattered events, retaining intensity. + +In addition, it may be desirable to define a 'target' for the fluorescence processes via e.g. the 'target\_index' and the 'focus\_xw / focus\_yh' options. This target should e.g. be the SDD area. The powder scattering can be focused along an horizontal tore via the 'd\_phi' and 'tth\_sign' options. To get a vertical tore, rotate the sample by 90 deg around Z. + +This sample component can advantageously benefit from the SPLIT feature, e.g. SPLIT COMPONENT sample = FluoPowder(...) + +The fluorescence is computed via the XRayLib (apt install libxrl-dev) https://github.com/tschoonj/xraylib. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +geometry & str & Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust. & 0 \\ +radius & m & Outer radius of sample in (x,z) plane. cylinder/sphere. & 0 \\ +thickness & m & Thickness of hollow sample Negative value extends the hollow volume outside of the box/cylinder. & 0 \\ +xwidth & m & Width for a box sample shape. & 0 \\ +yheight & m & Height of sample in vertical direction for box/cylinder shapes. & 0 \\ +zdepth & m & Depth for a box sample shape. & 0 \\ +concentric & 1 & Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere). & 0 \\ +material & str & A CIF/LAZ/LAU file e.g. "LaB6.cif" to handle diffraction or chemical formulae, e.g. "Pb2SnO4" (no diffraction). & "LaB6.cif" \\ +packing\_factor & 1 & How dense is the material compared to bulk 0-1. & 0 \\ +density & g/cm$^{3}$ & Density of material. V\_rho=density/weight/1e24*N\_A at/\AA{}\textasciicircum{}3. & 0 \\ +weight & g/mol & Atomic/molecular weight of material. & 0 \\ +p\_interact & 1 & Force a given fraction of the beam to scatter, keeping intensity right, to enhance small signals (-1 inactivate). & 0 \\ +target\_x & m & Position of target to focus at, along X (for fluorescence). & 0 \\ +target\_y & m & Position of target to focus at, along Y (for fluorescence). & 0 \\ +target\_z & m & Position of target to focus at, along Z (for fluorescence). & 0 \\ +focus\_r & m & Radius of disk containing target. Use 0 for full space (for fluorescence). & 0 \\ +focus\_xw & m & Horiz. dimension of a rectangular area (for fluorescence). & 0 \\ +focus\_yh & m & Vert. dimension of a rectangular area (for fluorescence). & 0 \\ +focus\_aw & deg & Horiz. angular dimension of a rectangular area (for fluorescence). & 0 \\ +focus\_ah & deg & Vert. angular dimension of a rectangular area (for fluorescence). & 0 \\ +target\_index & 1 & Relative index of component to focus at, e.g. next is +1 (for fluorescence). & 0 \\ +flag\_compton & 1 & When 0, the Compton scattering is ignored. & 1 \\ +flag\_rayleigh & 1 & When 0, the Rayleigh scattering is ignored. & 1 \\ +flag\_lorentzian & 1 & When 1, the fluorescence line shapes are assumed to be Lorentzian, else Gaussian. & 0 \\ +flag\_powder & 1 & When 0, the powder diffraction is ignored. & 1 \\ +flag\_kissel & 1 & When 1 (slower), handle M-lines XRF from Kissel for Z\textgreater{}=52 Te (else only K and L-lines). & 0 \\ +powder\_refl & str & A CIF/LAZ/LAU reflection file as for PowderN. When not given, 'material' is used. Specify it when 'material' is a chemical formula. & "" \\ +powder\_format & \{\} & List of structure file column indexes. See the PowderN component. & \{0,0,0,0,0,0,0,0\} \\ +Vc & \AA{}$^{3}$ & Volume of unit cell=nb atoms per cell/density of atoms. & 0 \\ +delta\_d\_d & \AA{} & Global relative difraction Delta\_d/d spreading when the 'w' column is not available, e.g. 1e-4 to 1e-3. Use 0 if ideal. & 0 \\ +DW & 1 & Global difraction Debye-Waller factor when the 'DW' column is not available. Use 1 if included in F2. & 0 \\ +d\_phi & deg & Angle corresponding to the difraction vertical angular range to focus to, e.g. detector height. 0 for no focusing. You may as well define focus\_ah or focus\_yh and target. & 0 \\ +nb\_atoms & 1 & Number of sub-unit per unit cell, that is ratio of sigma for chemical formula to sigma per unit cell. & 1 \\ +barns & 1 & Flag to indicate if |F|\textasciicircum{}2 from 'material' is in barns or fm\textasciicircum{}2, (barns=1 for laz/cif, barns=0 for lau type files). & 1 \\ +tth\_sign & 1 & Sign of the diffraction angle. If 0, the sign is chosen randomly (left and right). & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{FluoPowder.comp}. + \item The XRayLib https://github.com/tschoonj/xraylib http://dx.doi.org/10.1016/j.sab.2011.09.011 + \item Fluorescence https://en.wikipedia.org/wiki/Fluorescence + \item Rayleigh https://en.wikipedia.org/wiki/Rayleigh\_scattering + \item Compton https://en.wikipedia.org/wiki/Compton\_scattering + \item X-ray absorption edges http://skuld.bmsc.washington.edu/scatter/AS\_periodic.html + \item X-ray fluorescence spectra http://www.xrfresearch.com/xrf-spectra/ + \item X-ray edges and fluo lines https://physics.nist.gov/PhysRefData/XrayTrans/Html/search.html +\end{itemize} +\IfFileExists{samples/FluoPowder_static.tex}{\input{samples/FluoPowder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/Fluorescence.tex b/docs/manuals/mcxtrace/samples/Fluorescence.tex new file mode 100644 index 0000000000..fd1515add2 --- /dev/null +++ b/docs/manuals/mcxtrace/samples/Fluorescence.tex @@ -0,0 +1,117 @@ +\section{The \texttt{Fluorescence} McXtrace Component} +Sample model handling absorption, fluorescence, Compton and Rayleigh scattering. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} E. Farhi + \item \textbf{Origin:} Synchrotron SOLEIL + \item \textbf{Date:} March 2022 +\end{itemize} + +\subsection*{Description} +Sample that models many photon-matter interactions: + +\begin{verbatim} +- absorption (photon excites an electron and creates a hole) +- fluorescence (excited electrons emit light while falling into lower states) +- Compton scattering (inelastic, transfer some energy to an electron, incoherent) +- Rayleigh scattering (elastic, dipolar radiation of excitated electrons, coherent) +\end{verbatim} + +Use the \textbf{FluoPowder} sample component to properly handle powder diffraction with fluorescence. + +The 'material' specification is given as a chemical formulae, e.g. "LaB6". It may also be given as a file name (CIF/LAU/LAZ/FullProf format) in which case the formulae is guessed (but may be approximative). Atoms from Z=5 to Z=90 are handled. + +By setting the 'order' to 1, the absorption along the scattered path is handled. A higher 'order' will handle multiple scattering events, and final absorption. For instance, a value order\textgreater{}=2 handles e.g. fluorescence iterative cascades in the material. Leaving 'order=0' handles the single scattering only. + +Example: Fluorescence(material="LaB6", xwidth=0.001,yheight=0.001,zdepth=0.0001, p\_interact=0.99, target\_index=1, focus\_xw=0.0005, focus\_yh=0.0005) + +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth (thickness=0) +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} +cylinder: radius x yheight (thickness=0) +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} +sphere: radius (yheight=0 thickness=0) +hollow sphere: radius and thickness>0 (yheight=0) +any shape: geometry=OFF file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the photon ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF, PLY and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +\textbf{Concentric components:} This component has the ability to contain other components when used in hollow cylinder geometry (namely sample environment, e.g. cryostat and furnace structure). Such component 'shells' should be split into input and output side surrounding the 'inside' components. First part must then use 'concentric=1' flag to enter the inside part. The component itself must be repeated to mark the end of the concentric zone. The number of concentric shells and number of components inside is not limited. + +COMPONENT F\_in = Fluorescence(material="Al", concentric=1, ...) AT (0,0,0) RELATIVE sample\_position + +COMPONENT something\_inside ... // e.g. the sample itself or other materials + +COMPONENT F\_out = COPY(F\_in)(concentric=0) AT (0,0,0) RELATIVE sample\_position + +\textbf{Enhancing computation efficiency:} * An important option to enhance statistics is to set 'p\_interact' to, say, 30 percent (0.3) in order to force a fraction of the beam to scatter. This will result on a larger number of scattered events, retaining intensity. + +In addition, it may be desirable to define a 'target' for the fluorescence processes via e.g. the 'target\_index' and the 'focus\_xw / focus\_yh' options. This target should e.g. be the SDD area. + +This sample component can advantageously benefit from the SPLIT feature, e.g. SPLIT COMPONENT sample = Fluorescence(...) + +The computation is made via the XRayLib (apt install libxrl-dev) https://github.com/tschoonj/xraylib. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +geometry & str & Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust. & 0 \\ +radius & m & Outer radius of sample in (x,z) plane. cylinder/sphere. & 0 \\ +thickness & m & Thickness of hollow sample Negative value extends the hollow volume outside of the box/cylinder. & 0 \\ +xwidth & m & Width for a box sample shape. & 0 \\ +yheight & m & Height of sample in vertical direction for box/cylinder shapes. & 0 \\ +zdepth & m & Depth for a box sample shape. & 0 \\ +concentric & 1 & Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere). & 0 \\ +material & str & Chemical formulae, e.g. "LaB6", "Pb2SnO4". If may also be a CIF/LAZ/LAU file. & "LaB6" \\ +packing\_factor & 1 & How dense is the material compared to bulk 0-1. & 0 \\ +rho & \AA{}-3 & Density of scattering elements (nb atoms/unit cell V\_0). & 0 \\ +density & g/cm$^{3}$ & Density of material. V\_rho=density/weight/1e24*N\_A. & 0 \\ +weight & g/mol & Atomic/molecular weight of material. & 0 \\ +p\_interact & 1 & Force a given fraction of the beam to scatter, keeping intensity right, to enhance small signals (-1 inactivate). & 0 \\ +target\_x & m & Position of target to focus at, along X. & 0 \\ +target\_y & m & Position of target to focus at, along Y. & 0 \\ +target\_z & m & Position of target to focus at, along Z. & 0 \\ +focus\_r & m & Radius of disk containing target. Use 0 for full space. & 0 \\ +focus\_xw & m & Horiz. dimension of a rectangular area. & 0 \\ +focus\_yh & m & Vert. dimension of a rectangular area. & 0 \\ +focus\_aw & deg & Horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & Vert. angular dimension of a rectangular area. & 0 \\ +target\_index & 1 & Relative index of component to focus at, e.g. next is +1. & 0 \\ +flag\_compton & 1 & When 0, the Compton scattering is ignored. & 1 \\ +flag\_rayleigh & 1 & When 0, the Rayleigh scattering is ignored. & 1 \\ +flag\_lorentzian & 1 & When 1, the line shapes are assumed to be Lorentzian, else Gaussian. & 0 \\ +flag\_kissel & 1 & When 1 (slower), handle M-lines XRF from Kissel for Z\textgreater{}=52 Te (else only K and L-lines). & 0 \\ +flag\_low\_z & 1 & When 1, enhances low concentration atoms, else uses cross-sections weighting. & 0 \\ +order & 1 & Limit multiple fluorescence up to given order. Last iteration is absorption only. & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Fluorescence.comp}. + \item The XRayLib https://github.com/tschoonj/xraylib http://dx.doi.org/10.1016/j.sab.2011.09.011 + \item Fluorescence https://en.wikipedia.org/wiki/Fluorescence + \item Rayleigh https://en.wikipedia.org/wiki/Rayleigh\_scattering + \item Compton https://en.wikipedia.org/wiki/Compton\_scattering + \item X-ray absorption edges http://skuld.bmsc.washington.edu/scatter/AS\_periodic.html + \item X-ray fluorescence spectra http://www.xrfresearch.com/xrf-spectra/ + \item X-ray edges and fluo lines https://physics.nist.gov/PhysRefData/XrayTrans/Html/search.html +\end{itemize} +\IfFileExists{samples/Fluorescence_static.tex}{\input{samples/Fluorescence_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/Isotropic_Sqw.tex b/docs/manuals/mcxtrace/samples/Isotropic_Sqw.tex new file mode 100644 index 0000000000..1b74ae48bd --- /dev/null +++ b/docs/manuals/mcxtrace/samples/Isotropic_Sqw.tex @@ -0,0 +1,167 @@ +\section{The \texttt{Isotropic\_Sqw} McXtrace Component} +Isotropic sample handling multiple scattering and absorption for a general +S(q,w) (coherent) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} E. Farhi, V. Hugouvieux + \item \textbf{Origin:} Synchrotron SOLEIL + \item \textbf{Date:} March 2022 +\end{itemize} + +\subsection*{Description} +An isotropic sample handling multiple scattering and including as input the dynamic structure factor of the chosen sample (e.g. from Molecular Dynamics). Handles elastic/inelastic, coherent scattering - depending on the input S(q,w) - with multiple scattering and absorption. Only the norm of q is handled (not the vector), and thus suitable for liquids, gazes, amorphous and powder samples. + +The implementation will automatically nornalise S(q,w) so that S(q) -\textgreater{} 1 at large q (parameter norm=-1). Alternatively, the S(q,w) data will be multiplied by 'norm' for positive values. Use norm=0 or 1 to use the raw data as input. + +The material temperature can be defined in the S(q,w) data files (see below) or set manually as parameter T. Setting T=-1 disables detailed balance. Setting T=-2 attempts to guess the temperature from the input S(q,w) data which must then be non-classical and extend on both energy sides (+/-). To use the S(q,w) data as is, without temperature effect, set T=-1 and norm=1. + +Both non symmetric (quantum) and classical S(q,w) data sets can be given by mean of the 'classical' parameter (see below). + +Additionally, for single order scattering (order=1), you may restrict the vertical spreading of the scattering area using d\_phi parameter. + +An important option to enhance statistics is to set 'p\_interact' to, say, 30 percent (0.3) in order to force a fraction of the beam to scatter. This will result on a larger number of scattered events, retaining intensity. + +If you use this component and produce valuable scientific results, please cite authors with references bellow (in \htmladdnormallink{Links}{\#links}). E. Farhi et al, J Comp Phys 228 (2009) 5251 + +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth (thickness=0) +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} +cylinder: radius x yheight (thickness=0) +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} +sphere: radius (yheight=0 thickness=0) +hollow sphere: radius and thickness>0 (yheight=0) +any shape: geometry=OFF file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the photon ray with the object transparently, so that it can be used like a regular sample object. It supports the OFF, PLY and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +\textbf{Concentric components:} This component has the ability to contain other components when used in hollow cylinder geometry (namely sample environment, e.g. cryostat and furnace structure). Such component 'shells' should be split into input and output side surrounding the 'inside' components. First part must then use 'concentric=1' flag to enter the inside part. The component itself must be repeated to mark the end of the concentric zone. The number of concentric shells and number of components inside is not limited. + +COMPONENT S\_in = Isotropic\_Sqw(Sqw\_coh="Al.laz", concentric=1, ...) AT (0,0,0) RELATIVE sample\_position + +COMPONENT something\_inside ... // e.g. the sample itself or other materials + +COMPONENT S\_out = COPY(S\_in)(concentric=0) AT (0,0,0) RELATIVE sample\_position + +\textbf{Sqw file format:} File format for S(Q,w) (coherent) should contain 3 numerical blocks, defining q axis values (vector), then energy axis values (vector), then a matrix with one line per q axis value, containing Sqw values for each energy axis value. Comments (starting with '\#') and non numerical lines are ignored and used to separate blocks. Sampling must be regular. Some parameters can be specified in comment lines, namely (00 is a numerical value): + +\begin{verbatim} +# sigma_coh 00 coherent scattering cross section in [barn], e.g. 0.66524*f +\end{verbatim} + +\# Temperature 00 in [K] + +\begin{verbatim} +# V_rho 00 atom density per Angs^3 +# density 00 in [g/cm^3] +# weight 00 in [g/mol] +# classical 00 [0=contains Bose factor (measurement) ; 1=classical symmetric] +\end{verbatim} + +Example: \# q axis values \# vector of m values in Angstroem-1 + +\begin{verbatim} +0.001000 .... 3.591000 +\end{verbatim} + +\# w axis values \# vector of n values in meV + +\begin{verbatim} +0.001391 ... 1.681391 +\end{verbatim} + +\# sqw values (one line per q axis value) \# matrix of S(q,w) values (m rows x n values), one line per q value, + +\begin{verbatim} +9.721422 10.599145 ... 0.000000 +10.054191 11.025244 ... 0.000000 +\end{verbatim} + +... + +\begin{verbatim} +0.000000 ... 3.860253 +\end{verbatim} + +See for instance file He4\_liq\_coh.sqw. Such files may be obtained from e.g. INX, Nathan, Lamp and IDA softwares, as well as Molecular Dynamics (nMoldyn). When the provided S(q,w) data is obtained from the classical correlation function G(r,t), which is real and symmetric in time, the 'classical=1' parameter should be set in order to multiply the file data with exp(hw/2kT). Otherwise, the S(q,w) is NOT symmetrised (classical). If the S(q,w) data set includes both negative and positive energy values, setting 'classical=-1' will attempt to guess what type of S(q,w) it is. The temperature can also be determined this way. In case you do not know if the data is classical or quantum, assume it is usually classical at high temperatures, and quantum otherwise (T \textless{} typical mode excitations). The positive energy values correspond to Stokes processes, i.e. material gains energy, and photons loose energy. The energy range is symmetrized to allow up and down scattering, taking into account detailed balance exp(-hw/2kT). + +You may also generate such S(q,w) 2D files using \htmladdnormallink{iFit}{http://ifit.mccode.org/McStas.html\#mozTocId297488} + +\textbf{Powder file format:} Files for coherent elastic powder scattering may also be used. Format specification follows the same principle as in the PowderN component, with parameters: + +powder\_format= Crystallographica: \{ 4,5,7,0,0,0,0, 0,0 \} + +\begin{verbatim} +Fullprof: { 4,0,8,0,0,5,0, 0,0 } +Undefined: { 0,0,0,0,0,0,0, 0,0 } +Lazy: {17,6,0,0,0,0,0,13,0 } +qSq: {-1,0,0,0,0,0,1, 0,0 } // special case for [q,Sq] table +or: {j,d,F2,DW,Delta_d/d,1/2d,q,F,strain} +\end{verbatim} + +or column indexes (starting from 1) given as comments in the file header (e.g. '\#column\_j 4'). Refer to the PowderN component for more details. Delta\_d/d and Debye-Waller factor may be specified for all lines with the 'powder\_Dd' and 'powder\_DW' parameters. The reflection list should be ordered by decreasing d-spacing values. + +Additionally a special [q,Sq] format is also defined with: powder\_format=qSq for which column 1 is 'q' and column 2 is 'S(q)'. + +\textbf{Examples:} Isotropic\_Sqw(radius=0.0005, yheight=0.001, Sqw\_coh="Rb\_liq\_coh.sqw",verbose=3, p\_interact=0.95) + +2- powder sample Isotropic\_Sqw(..., Sqw\_coh="Al.laz") + +\%BUGS: When used in concentric mode, multiple bouncing scattering (traversing the hollow part) is not taken into account. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +powder\_format & no quotes & name or definition of column indexes in file & \{0,0,0,0,0,0,0,0,0\} \\ +Sqw\_coh & str & Name of the file containing the values of Q, w and S(Q,w) Coherent part; Q in \AA{}-1, E in meV, S(q,w) in meV-1. Use 0, NULL or "" to disable. & 0 \\ +geometry & str & Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust & 0 \\ +material & str & Absorption file. & "NULL" \\ +radius & m & Outer radius of sample in (x,z) plane. cylinder/sphere. & 0 \\ +thickness & m & Thickness of hollow sample Negative value extends the hollow volume outside of the box/cylinder. & 0 \\ +xwidth & m & width for a box sample shape & 0 \\ +yheight & m & Height of sample in vertical direction for box/cylinder shapes & 0 \\ +zdepth & m & depth for a box sample shape & 0 \\ +threshold & 1 & Value under which S(Q,w) is not accounted for. to set according to the S(Q,w) values, i.e. not too low. & 1e-20 \\ +order & 1 & Limit multiple scattering up to given order 0:all (default), 1:single, 2:double, ... & 0 \\ +T & K & Temperature of sample, detailed balance. Use T=-1 to disable it, and T=-2 to guess it from non-classical S(q,w) input. & 0 \\ +verbose & 1 & Verbosity level (0:silent, 1:normal, 2:verbose, 3:debug). A verbosity\textgreater{}1 also computes dispersions and S(q,w) analysis. & 1 \\ +d\_phi & deg & scattering vertical angular spreading (usually the height of the next component/detector). Use 0 for full space. This is only relevant for single scattering (order=1). & 0 \\ +concentric & 1 & Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere) [1] & 0 \\ +rho & \AA{}-3 & Density of scattering elements (nb atoms/unit cell V\_0). & 0 \\ +sigma\_coh & barns & Thomson cross-section of the material. For an atom, this is f*0.665 barns, where f is the number of free electrons, f -\textgreater{} atomic number Z. & 0.66524 \\ +classical & 1 & Assumes the S(q,w) data from the files is a classical S(q,w), and multiply that data by exp(hw/2kT) on up/down energy sides. Use 0 when obtained from raw experiments, 1 from molecular dynamics. Use -1 to guess from a data set including both energy sides. & -1 \\ +powder\_Dd & 1 & global Delta\_d/d spreading, or 0 if ideal. & 0 \\ +powder\_DW & 1 & global Debey-Waller factor, if not in |F2| or 1. & 0 \\ +powder\_Vc & \AA{}$^{3}$ & volume of the unit cell & 0 \\ +density & g/cm$^{3}$ & density of material. V\_rho=density/weight/1e24*N\_A & 0 \\ +weight & g/mol & atomic/molecular weight of material & 0 \\ +p\_interact & 1 & Force a given fraction of the beam to scatter, keeping intensity right, to enhance small signals (-1 inactivate). & -1 \\ +norm & 1 & Normalize S(q,w) when -1 (default). Use raw data when 1, multiplier for S(q,w) when norm\textgreater{}0. & -1 \\ +powder\_barns & 1 & 0 when |F2| data in powder file are fm\textasciicircum{}2, 1 when in barns (barns=1 for laz, barns=0 for lau type files). & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Isotropic\_Sqw.comp}. + \item Atomic form factors f http://lampx.tugraz.at/\textasciitilde{}hadley/ss1/crystaldiffraction/atomicformfactors/formfactors.php + \item E. Farhi, V. Hugouvieux, M.R. Johnson, and W. Kob, Journal of Computational Physics 228 (2009) 5251-5261 "Virtual experiments: Combining realistic neutron scattering instrument and sample simulations" + \item H. Schober, Collection SFN 10 (2010) 159-336 +\end{itemize} +\IfFileExists{samples/Isotropic_Sqw_static.tex}{\input{samples/Isotropic_Sqw_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/Molecule_2state.tex b/docs/manuals/mcxtrace/samples/Molecule_2state.tex new file mode 100644 index 0000000000..d561b6005c --- /dev/null +++ b/docs/manuals/mcxtrace/samples/Molecule_2state.tex @@ -0,0 +1,52 @@ +\section{The \texttt{Molecule\_2state} McXtrace Component} +Disordered optical-excitable molecule sample. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} October 2012 +\end{itemize} + +\subsection*{Description} +A sample model for pump probe experiments which models disordered molecules in a volume (rectangular, cylindrical, or spherical). Molecules can be in one of two states (0 and 1). Scattering is either specified through F vs. q scattering curves or as a set of atom positions from which F vs. q is computed. At t=-delta\_t, a fraction of the molecules are put in state 1, from which they decay exponentially, with time constant t\_relax, into state 0. For t\textless{}-delta\_t all of the molecules are in the state specified by \textit{initial\_state}. To improve statistics, scattering may be limited to a "forward" cone with opening angle in [psimin, psimax]. Furthermore, scattering may be restricted to the azimuthal segment between [etamin,etamax]. + +Example: Molecule\_2state( nq=512,state\_0\_file="Fe\_bpy\_GS\_DFT.txt",state\_1\_file="Fe\_bpy\_ES\_DFT.txt",radius=0.01, psimin=0, psimax=15*DEG2RAD, etamin=-1*DEG2RAD,etamax=1*DEG2RAD, t\_relax=600e-12, delta\_t=100e-9, excitation\_yield=0.2) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +delta\_t & s & Delay between the exciting event t=0. delay is negative, i.e. delta\_t\textgreater{}0 means the exciting event happens before t=0. & 100e-9 \\ +excitation\_yield & 1 & Mean fraction of molecules that get excited. & 0.2 \\ +t\_relax & s & Mean relaxation time (into state 0) of excited molecules. & 100e-9 \\ +initial\_state & 0/1 & Which state is Molecule\_2state in for t\textless{}delta\_t? Useful for modelling something that changes state slowly. & 0 \\ +psimin & rad & Minimum scattering angle off the optical axis. & 0 \\ +psimax & rad & Maximum scattering angle off the optical axis. & M\_PI\_2 \\ +etamin & rad & Minimum scattering angle around the optical axis. & -M\_PI \\ +etamax & rad & Maximum scattering angle around the optical axis. & M\_PI \\ +radius & m & Radius of cylindrical of spherical sample. & 0 \\ +yheight & m & Height of rectangular or cylindrical sample. & 0 \\ +xwidth & m & Width of rectangular sample. & 0 \\ +zdepth & m & Depth (thickness) of rectangular sample. & 0 \\ +concentration & m & Concentration or packing factor of sample. & 1 \\ +p\_transmit & m & Fraction of statistics devoted to sample direct (unscattered) beam. & 0.1 \\ +form\_factors & str & File from which to read atomic form factors. Defualt amounts to use the one shipped with McXtrace. & "FormFactors.txt" \\ +state\_0\_file & str & Isotropic scattering factors (parameterized by q), or atom positions are specified for state 0. & NULL \\ +state\_1\_file & str & Isotropic scattering factors (parameterized by q), or atom positions are specified for state 1. & NULL \\ +nq & 1 & Number of q-bins if F is to be computed from atom positions (Debye formalism). & 512 \\ +material\_datafile & str & Where to read f1 and f2 factors from in order to handle absorption. & "Be.txt" \\ +q\_parametric & 0/1 & When 0: Assume that datafiles contains atom positions. 1: datafiles contains F vs. q data. & 0 \\ +Emax & keV & Maximal energy for which scattering factors are computed. Must be larger than the maximal impinging energy. & 80 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Molecule\_2state.comp}. +\end{itemize} +\IfFileExists{samples/Molecule_2state_static.tex}{\input{samples/Molecule_2state_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/Polycrystal.tex b/docs/manuals/mcxtrace/samples/Polycrystal.tex new file mode 100644 index 0000000000..54c5b4d448 --- /dev/null +++ b/docs/manuals/mcxtrace/samples/Polycrystal.tex @@ -0,0 +1,65 @@ +\section{The \texttt{Polycrystal} McXtrace Component} +Release: McXtrace 1.0 + +Polycrystal made from single crystal-like voxels + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Martin Cramer Pedersen (mcpe@nbi.dk) + \item \textbf{Origin:} University of Copenhagen + \item \textbf{Date:} January 2015 +\end{itemize} + +\subsection*{Description} +The component creates a threedimensional grid of cubic instances of the Single\_crystal-component,through which the rays are propagated. The component relies on a list of possible orientations and stretches of the initial unit cell and a list correlating each voxel of the polycrystal to an entry in the list of rotations and stretches. + +Example: Polycrystal( MapFile= "polycrystal\_1layer\_2orts.map", OrientationsFile= "stretch\_2orts.orts", ReflectionsDatafile= "GeReduced.lau", xwidth= 200e-6, yheight= 200e-6, zdepth = 50e-6, DeltadOverd = 0.001, Mosaicity = 1, SigmaAbsorbtion = 0.0, SigmaIncoherent = 0.0, + +\begin{verbatim} +MaxNumberOfReflections = 1, ProbabilityOfTransmission = 0.5, +ax = 5.6579, ay = 0.0000, az = 0.0000, bx = 0.0000, by = 5.6579, bz = 0.0000, cx = 0.0000, cy = 0.0000, cz = 5.6579 ) +\end{verbatim} + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +MapFile & str & File describing, which orientation is found in which voxel & "" \\ +OrientationsFile & str & File describing the different orientations & "" \\ +ReflectionsDatafile & str & File describing the reflections in the relevant lattice (usually in .lau-format) & "Si.lau" \\ +MaterialDatafile & str & File describing the scattering and absorbtion properties of the material & "Si.txt" \\ +xwidth & m & Width of the sample & 0.0 \\ +yheight & m & Height of the sample & 0.0 \\ +zdepth & m & Depth of the sample & 0.0 \\ +ax & \AA{} & x-coordinate of the first internal unit cell vector in the sample & 5.43 \\ +ay & \AA{} & y-coordinate of the first internal unit cell vector in the sample & 0.00 \\ +az & \AA{} & z-coordinate of the first internal unit cell vector in the sample & 0.00 \\ +bx & \AA{} & x-coordinate of the second internal unit cell vector in the sample & 0.00 \\ +by & \AA{} & y-coordinate of the second internal unit cell vector in the sample & 5.43 \\ +bz & \AA{} & z-coordinate of the second internal unit cell vector in the sample & 0.00 \\ +cx & \AA{} & x-coordinate of the third internal unit cell vector in the sample & 0.00 \\ +cy & \AA{} & y-coordinate of the third internal unit cell vector in the sample & 0.00 \\ +cz & \AA{} & z-coordinate of the third internal unit cell vector in the sample & 5.43 \\ +Mosaicity & moa & Gaussian mosaicity & 3.0 \\ +MosaicityA & moa & Anisotropic mosaicity around the first unit cell vector & 0.0 \\ +MosaicityB & moa & Anisotropic mosaicity around the second unit cell vector & 0.0 \\ +MosaicityC & moa & Anisotropic mosaicity around the third unit cell vector & 0.0 \\ +DeltadOverd & 1 & Statistical description of the lattice spacing & 0.01 \\ +ProbabilityOfTransmission & 0-1 & Probability that a ray will not interact with the sample & 0.01 \\ +SigmaAbsorbtion & fm$^{2}$ & Absorbtion crosssection of the sample & 0.0 \\ +SigmaIncoherent & fm$^{2}$ & Incoherent crosssection of the sample & 0.0 \\ +MaxNumberOfReflections & 1 & Highest number of allowed scattering events in the entire crystal - to prevent computationally expensive high-order multiple scattering. If this parameter is set to 0, all possible orders of scattering are considered. & 1 \\ +Reciprocal & 0/1 & If this parameter is set to 0, then the lattice vectors should be given in real space. Anything else implies that the vectors are given in reciprocal space. & 0 \\ +verbose & 0/1 & If nonzero - output more info to the console. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Polycrystal.comp}. +\end{itemize} +\IfFileExists{samples/Polycrystal_static.tex}{\input{samples/Polycrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/PowderN.tex b/docs/manuals/mcxtrace/samples/PowderN.tex new file mode 100644 index 0000000000..4ff7e2b495 --- /dev/null +++ b/docs/manuals/mcxtrace/samples/PowderN.tex @@ -0,0 +1,158 @@ +\section{The \texttt{PowderN} McXtrace Component} +General powder sample (N lines, single scattering, incoherent scattering) + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} P. Willendrup, L. Chapon, K. Lefmann, A.B.Abrahamsen, N.B.Christensen, E.M.Lauridsen. + \item \textbf{Origin:} McXtrace release 1.2 + \item \textbf{Date:} 4.2.98 +\end{itemize} + +\subsection*{Description} +General powder sample with many scattering vectors possibility for intrinsic line broadening incoherent background ratio is computed from material datafile. No multiple scattering. No secondary extinction. + +Based on Powder1/Powder2/Single\_crystal. Geometry is a powder filled cylinder, sphere, box or any shape from an OFF file. Incoherent scattering is only provided here to account for a background. The efficient is highly improved when restricting the vertical scattering range on the Debye-Scherrer cone (with 'd\_phi' and 'focus\_flip'). The unit cell volume Vc may also be computed when giving the density, the atomic/molecular weight and the number of atoms per unit cell. + +\textbf{Sample shape:} Sample shape may be a cylinder, a sphere, a box or any other shape. + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth (thickness=0) +\end{verbatim} + +hollow box/plate:xwidth x yheight x zdepth and thickness\textgreater{}0 + +\begin{verbatim} +cylinder: radius x yheight (thickness=0) +\end{verbatim} + +hollow cylinder: radius x yheight and thickness\textgreater{}0 + +\begin{verbatim} +sphere: radius (yheight=0 thickness=0) +hollow sphere: radius and thickness>0 (yheight=0) +any shape: geometry=OFF_file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the xray with the object transparently, so that it can be used like a regular sample object. It supports the PLY, OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends of the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +If you use this component and produce valuable scientific results, please cite authors with references bellow (in \htmladdnormallink{Links}{\#links}). + +Example: PowderN(reflections = "c60.lau", d\_phi = 15 , radius = 0.01, + +\begin{verbatim} +yheight = 0.05, Vc = 1076.89, delta_d_d=0, DW=1) +\end{verbatim} + +\textbf{Powder definition file format} Powder structure is specified with an ascii data file 'reflections'. The powder data are free-text column based files. The reflection list should be ordered by decreasing d-spacing values. + +\begin{verbatim} +... d ... F2 +\end{verbatim} + +Lines begining by '\#' are read as comments (ignored) but they may contain the following keywords (in the header): + +\begin{verbatim} +#Vc <value of unit cell volume Vc [Angs^3]> +\end{verbatim} + +\#Debye\_Waller \textless{}value of Debye-Waller factor DW\textgreater{} + +\begin{verbatim} +#delta_d_d/d <value of delta_d_d/d width for all lines> +\end{verbatim} + +These values are not read if entered as component parameters (Vc=...) + +The signification of the columns in the numerical block may be set using the 'format' parameter, by defining signification of the columns as a vector of indexes in the order format=\{j,d,F2,DW,delta\_d\_d/d,1/2d,q,F\} Signification of the symbols is given below. Indices start at 1. Indices with zero means that the column are not present, so that: Crystallographica=\{ 4,5,7,0,0,0,0,0 \} + +\begin{verbatim} +Fullprof ={ 4,0,8,0,0,5,0,0 } +Lazy ={17,6,0,0,0,0,0,13} +\end{verbatim} + +At last, the format may be overridden by direct definition of the column indexes in the file itself by using the following keywords in the header (e.g. '\#column\_j 4'): + +\begin{verbatim} +#column_j <index of the multiplicity 'j' column> +#column_d <index of the d-spacing 'd' column [Angs]> +#column_F2 <index of the squared str. factor '|F|^2' column [b]> +#column_F <index of the structure factor norm '|F|' column> +#column_DW <index of the Debye-Waller factor 'DW' column> +#column_Dd <index of the relative line width delta_d_d/d broadening 'Dd' column> +\end{verbatim} + +\#column\_inv2d \textless{}index of the 1/2d=sin(theta)/lambda 'inv2d' column\textgreater{} + +\begin{verbatim} +#column_q <index of the scattering wavevector 'q' column [Angs-1]> +\end{verbatim} + +Last, CIF, FullProf and ShelX files can be read, and converted to F2(hkl) lists if 'cif2hkl' is installed. The CIF2HKL env variable can be used to point to a proper executable, else the McCode, then the system installed versions are used. + +\textbf{Concentricity} + +PowderN assumes 'concentric' shape, i.e. can contain other components inside its optional inner hollow. Example, Sample in Al cryostat: + +COMPONENT Cryo = PowderN(reflections="Al.laz", radius = 0.01, thickness = 0.001, concentric = 1, p\_interact=0.1) AT (0,0,0) RELATIVE Somewhere + +COMPONENT Sample = some\_other\_component(with geometry FULLY enclosed in the hollow) AT (0,0,0) RELATIVE Somewhere + +COMPONENT Cryo2 = COPY(Cryo)(concentric = 0) AT (0,0,0) RELATIVE Somewhere + +(The second instance of the cryostat component can also be written out completely using PowderN(...). In both cases, this second instance needs concentric = 0.) The concentric arrangment can not be used with OFF geometry specification. + +This sample component can advantageously benefit from the SPLIT feature, e.g. SPLIT COMPONENT pow = PowderN(...) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +reflections & str & Input file for reflections (LAZ LAU CIF, FullProf, ShelX). Use only incoherent scattering if NULL or "". & "NULL" \\ +material & Be.txt & File where the material parameters for the absorption may be found. Format is similar to what may be found off the NIST website. & "NULL" \\ +geometry & str & Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust. & "NULL" \\ +format & \{\} & Name of the format, or list of column indexes (see Description). N.b. no quotes! & \{0,0,0,0,0,0,0,0\} \\ +mat\_format & \{\} & Format of the asorption parameter file. & \{0,0,0,0,0\} \\ +radius & m & Outer radius of sample in (x,z) plane. & 0 \\ +yheight & m & Height of sample y direction. & 0 \\ +xwidth & m & Horiz. dimension of sample, as a width. & 0 \\ +zdepth & m & Depth of box sample. & 0 \\ +thickness & m & Thickness of hollow sample. Negative value extends the hollow volume outside of the box/cylinder. & 0 \\ +pack & 1 & Packing factor & 1 \\ +Vc & \AA{}$^{3}$ & Volume of unit cell=nb atoms per cell/density of atoms. & 0 \\ +delta\_d\_d & 1 & Global relative Delta\_d/d spreading when the 'w' column is not available. Use 0 if ideal. & 0 \\ +p\_inc & 1 & Fraction of incoherently scattered rays. & 0.1 \\ +p\_transmit & 1 & Fraction of transmitted (only attenuated) rays. & 0.1 \\ +DW & 1 & Global Debye-Waller factor when the 'DW' column is not available. Use 1 if included in F2. & 0 \\ +nb\_atoms & 1 & Number of sub-unit per unit cell, that is ratio of sigma for chemical formula to sigma per unit cell. & 1 \\ +d\_omega & deg & Horizontal focus range (only for incoherent scattering), 0 for no focusing. & 0 \\ +d\_phi & deg & Angle corresponding to the vertical angular range to focus to, e.g. detector height. 0 for no focusing. & 0 \\ +tth\_sign & 1 & Sign of the scattering angle. If 0, the sign is chosen randomly (left and right). ONLY functional in combination with d\_phi and ONLY applies to bragg lines. & 0 \\ +p\_interact & 1 & Fraction of events interacting with sample, e.g. 1-p\_transmit-p\_inc. & 0 \\ +concentric & 1 & Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere). & 0 \\ +density & g/cm$^{3}$ & Density of material. rho=density/weight/1e24*N\_A. & 0 \\ +weight & g/mol & Atomic/molecular weight of material. & 0 \\ +barns & 1 & Flag to indicate if |F|\textasciicircum{}2 from 'reflections' is in barns or fm\textasciicircum{}2, (barns=1 for laz/cif, barns=0 for lau type files). & 1 \\ +focus\_flip & 1 & Controls the sense of d\_phi. If 0 d\_phi is measured against the xz-plane. If !=0 d\_phi is measured against zy-plane. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{PowderN.comp}. + \item See also: Single\_crystal + \item See \htmladdnormallink{ICSD}{http://icsd.ill.fr} Inorganic Crystal Structure Database + \item \htmladdnormallink{Web Elements}{http://www.webelements.com/} + \item \htmladdnormallink{Fullprof}{http://www.ill.eu/sites/fullprof/index.html} powder refinement + \item \htmladdnormallink{Crystallographica}{http://www.crystallographica.com/} software (free license) + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} + \item Java version of Geomview (display only) \htmladdnormallink{jroff.jar}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{qhull}{http://qhull.org} + \item \htmladdnormallink{powercrust}{http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} + \item cif2hkl https://gitlab.com/soleil-data-treatment/soleil-software-projects/cif2hkl + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl +\end{itemize} +\IfFileExists{samples/PowderN_static.tex}{\input{samples/PowderN_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/Saxs_spheres.tex b/docs/manuals/mcxtrace/samples/Saxs_spheres.tex new file mode 100644 index 0000000000..29454c8588 --- /dev/null +++ b/docs/manuals/mcxtrace/samples/Saxs_spheres.tex @@ -0,0 +1,51 @@ +\section{The \texttt{Saxs\_spheres} McXtrace Component} +Release: McXtrace 1.1 + +Sample for Small Angle X-ray Scattering - hard spheres in thin solution, mono disperse. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} E. B. Knudsen, P. Willendrup, K. Lefmann, L. Arleth + \item \textbf{Origin:} DTU Fysik + \item \textbf{Date:} 28.10.2010 +\end{itemize} + +\subsection*{Description} +Sample for use in a SAXS instrument, models hard, monodisperse spheres in thin solution. The shape of the sample may be a filled box with dimensions xwidth, yheight, zdepth, a cylinder with dimensions radius and yheight, a filled sphere with radius R. + +Example: Saxs\_spheres(R = 20, Phi = 1e-3, Delta\_rho = 0.6, sigma\_abs = 50, xwidth=0.01, yheight=0.01, zdepth=0.005) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sphere\_mtrl & str & Material datafile from which to find absorption. If none is given absorption is neglected. & "" \\ +R & \AA{} & Radius of scattering hard spheres & 100 \\ +Phi & 1 & Particle volume fraction & 1e-3 \\ +Delta\_rho & fm/\AA{}$^{3}$ & Excess scattering length density & 0.6 \\ +xwidth & m & Horiz. dimension of sample, as a width & 0 \\ +yheight & m & Vert . dimension of sample, as a height for cylinder/box & 0 \\ +zdepth & m & Depth of sample & 0 \\ +radius & m & Outer radius of sample in (x,z) plane for cylinder/sphere & 0 \\ +target\_x & m & Position of target to focus at, along X & 0 \\ +target\_y & m & Position of target to focus at, along Y & 0 \\ +target\_z & m & Position of target to focus at, along Z & 6 \\ +target\_index & 1 & Relative index of component to focus at, e.g. next is +1 & 0 \\ +focus\_xw & m & Horiz. dimension of a rectangular area & 0 \\ +focus\_yh & m & Vert. dimension of a rectangular area & 0 \\ +focus\_aw & deg & Horiz. angular dimension of a rectangular area & 0 \\ +focus\_ah & deg & Vert. angular dimension of a rectangular area & 0 \\ +focus\_r & m & Detector (disk-shaped) radius & 0 \\ +mu\_c & 5 & Column of the datafile which contains absorption coefficients. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Saxs\_spheres.comp}. +\end{itemize} +\IfFileExists{samples/Saxs_spheres_static.tex}{\input{samples/Saxs_spheres_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/Single_crystal.tex b/docs/manuals/mcxtrace/samples/Single_crystal.tex new file mode 100644 index 0000000000..673044b010 --- /dev/null +++ b/docs/manuals/mcxtrace/samples/Single_crystal.tex @@ -0,0 +1,135 @@ +\section{The \texttt{Single\_crystal} McXtrace Component} +Mosaic single crystal with multiple scattering vectors, optimised for speed +with large crystals and many reflections. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Kristian Nielsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} December 1999 +\end{itemize} + +\subsection*{Description} +Single crystal with mosaic. Delta-D/D option for finite-size effects. Rectangular geometry. Multiple scattering and secondary extinction included. The mosaic may EITHER be specified isotropic by setting the mosaic input parameter, OR anisotropic by setting the mosaic\_a, mosaic\_b, and mosaic\_c parameters. If you get strange results, check the mosaicity and delta(d)/d parameters, as this component is not suited for ideal/perfect mosaic crystals. The crystal lattice can be bent locally, keeping the external geometry unchanged. Curvature is spherical along vertical and horizontal axes. + +\textbf{Speed/stat optimisation using SPLIT} In order to dramatically improve the simulation efficiency, we recommend to use a SPLIT keyword on this component (or prior to it), as well as to disable the multiple scattering handling by setting order=1. This is especially powerful for large reflection lists such as with macromolecular proteins. When an incoming particle is identical to the preceeding, reciprocal space initialisation is skipped, and a Monte Carlo choice is done on available reflections from the last repciprocal space calculation! To assist the user in choosing a "relevant" value of the SPLIT, a rolling average of the number of available reflections is calculated and presented in the component output. + +\textbf{Mosacitiy modes} The component features three independent ways of parametrising mosaicity: a) The original algorithm where mosaicity is implemented by extending each reflection by a Gaussian "cigar" in reciprocal space, characterised by the parameters mosaic and delta\_d\_d. (Also known as "isotropic mosaicity"). b) A similar mode where mosaicities can be non-isotropic and given as the parameters mosaic\_a, mosaic\_b and mosaic\_c, around the unit cell axes. (Also known as "anisotropic mosaicity"). c) Given two "macroscopically"/experimentally measured width/mosaicities of two independent reflections, parametrised by the list mosaic\_AB = \{mos\_a, mos\_b, a\_h, a\_k, a\_l, b\_h, b\_k, b\_l\}, a set of microscopic mosaicities as in b) are estimated (internally) and applied. (Also known as "phenomenological mosaicity"). + +\textbf{Powder-mode} When the powder mode is used (powder=0-1), a randomised transformation of the particle direction is made before and after scattering, thereby letting the single crystal behave as a crystallite of either a powder (crystallite orientation fully randomised). + +\textbf{Curved crystal mode} The component features a method to curve the lattice planes slightly with respect to the outer geometry of the crystal. The method is implemented as a transformation on the particle direction vector, and should be used only in cases where: a) The reflection lattice vector is \textasciitilde{} orthogonal to the crystal surface. b) The modelled curvarture is "small" with respect to the crystal surface. + +\textbf{Sample shape} Sample shape may be a cylinder, a sphere, a box or any other shape: + +\begin{verbatim} +box/plate: xwidth x yheight x zdepth +cylinder: radius x yheight +sphere: radius (yheight=0) +any shape: geometry=OFF/PLY file +\end{verbatim} + +The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the photon ray with the object transparently, so that it can be used like a regular sample object. It supports the PLY, OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull \textless{} coordinates.xyz Qx Qv Tv o \textgreater{} geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends on the OFF/PLY file data, but its bounding box may be resized using xwidth,yheight and zdepth. + +\textbf{Crystal definition file format} Crystal structure is specified with an ascii data file. Each line contains 4 or more numbers, separated by white spaces: + +\begin{verbatim} +h k l ... F2 +\end{verbatim} + +The first three numbers are the (h,k,l) indices of the reciprocal lattice point, and the 7-th number is the value of the structure factor |F|**2, in barns. The rest of the numbers are not used; the file is in the format output by the Crystallographica program. The reflection list should be ordered by decreasing d-spacing values. Lines begining by '\#' are read as comments (ignored). Most sample parameters may be defined from the data file header, following the same mechanism as PowderN. + +Current data file header keywords include, for data format specification: \#column\_h \textless{}index of the Bragg Qh column\textgreater{} \#column\_k \textless{}index of the Bragg Qk column\textgreater{} \#column\_l \textless{}index of the Bragg Ql column\textgreater{} \#column\_F2 \textless{}index of the squared str. factor '|F|\textasciicircum{}2' column [b]\textgreater{} \#column\_F \textless{}index of the structure factor norm '|F|' column\textgreater{} and for material specification: \#sigma\_inc \textless{}value of incoherent cross section [barns]\textgreater{} \#Delta\_d/d \textless{}value of Delta\_d/d width for all lines\textgreater{} \#lattice\_a \textless{}value of the a lattice parameter [\AA{}]\textgreater{} \#lattice\_b \textless{}value of the b lattice parameter [\AA{}]\textgreater{} \#lattice\_c \textless{}value of the c lattice parameter [\AA{}]\textgreater{} \#lattice\_aa \textless{}value of the alpha lattice angle [deg]\textgreater{} \#lattice\_bb \textless{}value of the beta lattice angle [deg]\textgreater{} \#lattice\_cc \textless{}value of the gamma lattice angle [deg]\textgreater{} + +Last, CIF, FullProf and ShelX files can be read, and converted to F2(hkl) lists when 'cif2hkl' is installed. The CIF2HKL env variable can be used to point to a proper executable, else the McCode or the system installed versions are used. + +\textbf{Satellite Bragg peaks - surface crystal truncation rods (CTR)} It is known that scattering from a finite crystal introduces a broadening of Bragg peaks, seen in surface diffraction at grazing angle [Robinson and Tweet, Rep. Prog. Phys. 55 (1992) 599)]. The CTR is specified as two vectors, which hold the squared Fourier transform of the crystal geometry, for instance: + +\begin{verbatim} +bulk: Dirac peak (FT of infinity) +half-bulk: Dirac+1/k^2 (FT of half plane, k in rlu) +layer: sinc(PI*k*d)^2 (FT of a top-hat, thickness 'd') +\end{verbatim} + +These vectors are given as 'surf\_k' [in 1/\AA{}] and 'surf\_FT2', both of length 'surf\_size'. The CTR is to be applied along vector 'surf\_dir' which indicates the surface normal \{nx,ny,nz\} in real space. When surf\_size=-1, the component sets the proper truncation function (only for thin box and disk shapes). This feature is an approximation of the real surface scattering, and does not handle complex geometries (clusters, wetting, multi-layers, ...). It may be used as well to describe over-structure satellite peaks. + +Example: Single\_crystal(xwidth=0.01, yheight=0.01, zdepth=0.01, mosaic = 5, reflections="Si.lau") + +A diamond crystal plate, cut for (002) reflections Single\_crystal(xwidth = 0.002, yheight = 0.1, zdepth = 0.1, mosaic = 5, delta\_d\_d=3e-4, reflections = "C-diamond.lau", + +\begin{verbatim} +ax=0, ay=2.14, az=-1.24, +bx = 0, by = 0, bz = 2.47, +cx = 6.71, cy = 0, cz = 0) +\end{verbatim} + +A adrenaline protein Single\_crystal(xwidth=0.005, yheight=0.005, zdepth=0.005, mosaic = 5, reflections="adrenaline.lau") + +Also, always use a non-zero value of delta\_d\_d. + +This sample component can advantageously benefit from the SPLIT feature, e.g. SPLIT COMPONENT sx = Single\_crystal(...) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +reflections & string & File name containing structure factors of reflections (LAZ LAU CIF, FullProf, ShelX). Use empty ("") or NULL for incoherent scattering only & 0 \\ +geometry & str & Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust & 0 \\ +mosaic\_AB & arc\_minutes, arc\_minutes,1, 1, 1, 1, 1, 1 & In-plane mosaic rotation and plane vectors (anisotropic), mosaic\_A, mosaic\_B, A\_h,A\_k,A\_l, B\_h,B\_k,B\_l. Puts the crystal in the in-plane mosaic state. Vectors A and B define plane in which the crystal roation is defined, and mosaic\_A, mosaic\_B, denotes the resp. mosaicities (gaussian RMS) with respect to the two reflections chosen by A and B (Miller indices). & \{0,0, 0,0,0, 0,0,0\} \\ +xwidth & m & Width of crystal & 0 \\ +yheight & m & Height of crystal & 0 \\ +zdepth & m & Depth of crystal (no extinction simulated) & 0 \\ +radius & m & Outer radius of sample in (x,z) plane & 0 \\ +delta\_d\_d & 1 & Lattice spacing variance, gaussian RMS (longitudinal mosaic) e.g. 1e-4 to 1e-3. & 1e-3 \\ +mosaic & arc minutes & Crystal mosaic (isotropic), gaussian RMS. Puts the crystal in the isotropic mosaic model state, thus disregarding other mosaicity parameters, e.g. 1-10. & -1 \\ +mosaic\_a & arc minutes & Horizontal (rotation around lattice vector a) mosaic (anisotropic), gaussian RMS. Put the crystal in the anisotropic crystal vector state. i.e. model mosaicity through rotation around the crystal lattice vectors. Has precedence over in-plane mosaic model. & -1 \\ +mosaic\_b & arc minutes & Vertical (rotation around lattice vector b) mosaic (anisotropic), gaussian RMS. & -1 \\ +mosaic\_c & arc minutes & Out-of-plane (Rotation around lattice vector c) mosaic (anisotropic), gaussian RMS & -1 \\ +recip\_cell & 1 & Choice of direct/reciprocal (0/1) unit cell definition & 0 \\ +barns & 1 & Flag to indicate if |F|\textasciicircum{}2 from 'reflections' is in barns or fm\textasciicircum{}2. barns=1 for laz/cif and isotropic constant elastic scattering (reflections=NULL), barns=0 for lau type files & 0 \\ +ax & \AA{} or \AA{}$^{-1}$ & Coordinates of first (direct/recip) unit cell vector & 0 \\ +ay & \AA{} or \AA{}$^{-1}$ & a on y axis & 0 \\ +az & \AA{} or \AA{}$^{-1}$ & a on z axis & 0 \\ +bx & \AA{} or \AA{}$^{-1}$ & Coordinates of second (direct/recip) unit cell vector & 0 \\ +by & \AA{} or \AA{}$^{-1}$ & b on y axis & 0 \\ +bz & \AA{} or \AA{}$^{-1}$ & b on z axis & 0 \\ +cx & \AA{} or \AA{}$^{-1}$ & Coordinates of third (direct/recip) unit cell vector & 0 \\ +cy & \AA{} or \AA{}$^{-1}$ & c on y axis & 0 \\ +cz & \AA{} or \AA{}$^{-1}$ & c on z axis & 0 \\ +p\_transmit & 1 & Monte Carlo probability for photons to be transmitted without any scattering. Used to improve statistics from weak reflections & 0.001 \\ +sigma\_inc & barns & Incoherent scattering cross-section per unit cell (uniform). Fully isotropic and constant. Use -1 to inactivate & 0 \\ +aa & deg & Unit cell angles alpha, beta and gamma. Then uses norms of vectors a,b and c as lattice parameters & 0 \\ +bb & deg & Beta angle & 0 \\ +cc & deg & Gamma angle & 0 \\ +order & 1 & Limit multiple scattering up to given order (0: all, 1: first, 2: second, ...) & 1 \\ +extra\_order & 1 & When using order, allow additional multiple scattering without coherent scattering, sensible with very large unit cells (0: disable, 1: one extra, 2: two extra, ...) & 0 \\ +RX & m & Radius of horizontal along X lattice curvature. flat for 0 & 0 \\ +RY & m & Radius of vertical along Y lattice curvature. flat for 0 & 0 \\ +powder & 1 & Flag to indicate powder mode, for simulation of Debye-Scherrer cones via random crystallite orientation. A powder texture can be approximated with powder within 0-1 & 0 \\ +deltak & \AA{}-1 & Equality-threshold for use in SPLIT settings. If difference between all ki\_\{x,y,z\} are less than deltak from previous particle, the two are considered alike enough to jump directly to the MC choice between 'active' reflections & 1e-6 \\ +material\_datafile & Be.txt & File where the material parameters for the absorption may be found. Format is similar to what may be found off the NIST website. & "Si.txt" \\ +surf\_size & 1 & Length of the surf\_k and surf\_FT vectors. When set as -1, CTR is automatically set for the box/thin disk geometry. & 0 \\ +surf\_k & 1/\AA{} & Momentum 'k' distribution around 0 for the CTR, length 'surf\_size'. & NULL \\ +surf\_FT2 & 1 & Intensity |FT(real space)|\textasciicircum{}2 distribution as CTR of a single Bragg peak, length 'surf\_size'. & NULL \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Single\_crystal.comp}. + \item See \htmladdnormallink{ICSD}{http://icsd.ill.fr} Inorganic Crystal Structure Database + \item \htmladdnormallink{Web Elements}{http://www.webelements.com/} + \item \htmladdnormallink{Fullprof}{http://www.ill.eu/sites/fullprof/index.html} powder refinement + \item \htmladdnormallink{Crystallographica}{http://www.crystallographica.com/} software + \item \htmladdnormallink{Geomview and Object File Format (OFF)}{http://www.geomview.org} + \item Java version of Geomview (display only) \htmladdnormallink{jroff.jar}{http://www.holmes3d.net/graphics/roffview/} + \item \htmladdnormallink{qhull}{http://qhull.org} + \item \htmladdnormallink{powercrust}{http://www.cs.ucdavis.edu/\textasciitilde{}amenta/powercrust.html} + \item material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl + \item cif2hkl https://gitlab.com/soleil-data-treatment/soleil-software-projects/cif2hkl +\end{itemize} +\IfFileExists{samples/Single_crystal_static.tex}{\input{samples/Single_crystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/samples/Single_crystal_static.tex b/docs/manuals/mcxtrace/samples/Single_crystal_static.tex index 9be9bbfda9..9661f54259 100644 --- a/docs/manuals/mcxtrace/samples/Single_crystal_static.tex +++ b/docs/manuals/mcxtrace/samples/Single_crystal_static.tex @@ -32,7 +32,7 @@ \subsection*{The single crystal component} %$(\textit{ax}, \textit{ay}, \textit{az})$, $(\textit{bx}, \textit{by}, %\textit{bz})$, and $(\textit{cx}, \textit{cy}, \textit{cz})$ to define %the axes of the direct lattice of the crystal (the sides of the unit -%cell) in units of {\AA}ngstr{\o}m; and \textit{reflections}, a string +%cell) in units of Ångström; and \textit{reflections}, a string %giving the name of the file with the list of structure factors to %consider. %The mosaic is specified \emph{either} isotropically as diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_adsorbed_layer.tex b/docs/manuals/mcxtrace/sasmodels/SasView_adsorbed_layer.tex new file mode 100644 index 0000000000..58f69f7a32 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_adsorbed_layer.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_adsorbed\_layer} McXtrace Component} +SasView adsorbed\_layer model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_adsorbed\_layer component, generated from adsorbed\_layer.c in sasmodels. + +Example: SasView\_adsorbed\_layer(second\_moment, adsorbed\_amount, density\_shell, radius, volfraction, sld\_shell, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +second\_moment & \AA{} & ([0.0, inf]) Second moment of polymer distribution. & 23.0 \\ +adsorbed\_amount & mg/m$^{2}$ & ([0.0, inf]) Adsorbed amount of polymer. & 1.9 \\ +density\_shell & g/cm$^{3}$ & ([0.0, inf]) Bulk density of polymer in the shell. & 0.7 \\ +radius & \AA{} & ([0.0, inf]) Core particle radius. & 500.0 \\ +volfraction & None & ([0.0, inf]) Core particle volume fraction. & 0.14 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Polymer shell SLD. & 1.5 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent SLD. & 6.3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_adsorbed\_layer.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_adsorbed_layer_static.tex}{\input{sasmodels/SasView_adsorbed_layer_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_barbell.tex b/docs/manuals/mcxtrace/sasmodels/SasView_barbell.tex new file mode 100644 index 0000000000..7ff72903ff --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_barbell.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_barbell} McXtrace Component} +SasView barbell model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_barbell component, generated from barbell.c in sasmodels. + +Example: SasView\_barbell(sld, sld\_solvent, radius\_bell, radius, length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_bell=0.0, pd\_radius=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Barbell scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_bell & \AA{} & ([0, inf]) Spherical bell radius. & 40 \\ +radius & \AA{} & ([0, inf]) Cylindrical bar radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder bar length. & 400 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_bell & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_barbell.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_barbell_static.tex}{\input{sasmodels/SasView_barbell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_barbell_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_barbell_aniso.tex new file mode 100644 index 0000000000..11a9fa667a --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_barbell_aniso.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_barbell\_aniso} McXtrace Component} +SasView barbell model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_barbell component, generated from barbell.c in sasmodels. + +Example: SasView\_barbell\_aniso(sld, sld\_solvent, radius\_bell, radius, length, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_bell=0.0, pd\_radius=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Barbell scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_bell & \AA{} & ([0, inf]) Spherical bell radius. & 40 \\ +radius & \AA{} & ([0, inf]) Cylindrical bar radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder bar length. & 400 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_bell & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_barbell\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_barbell_aniso_static.tex}{\input{sasmodels/SasView_barbell_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_bcc_paracrystal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_bcc_paracrystal.tex new file mode 100644 index 0000000000..30d1ca3df5 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_bcc_paracrystal.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_bcc\_paracrystal} McXtrace Component} +SasView bcc\_paracrystal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_bcc\_paracrystal component, generated from bcc\_paracrystal.c in sasmodels. + +Example: SasView\_bcc\_paracrystal(dnn, d\_factor, radius, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +dnn & \AA{} & ([-inf, inf]) Nearest neighbour distance. & 220 \\ +d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 40 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_bcc\_paracrystal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_bcc_paracrystal_static.tex}{\input{sasmodels/SasView_bcc_paracrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_bcc_paracrystal_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_bcc_paracrystal_aniso.tex new file mode 100644 index 0000000000..752393deaf --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_bcc_paracrystal_aniso.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_bcc\_paracrystal\_aniso} McXtrace Component} +SasView bcc\_paracrystal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_bcc\_paracrystal component, generated from bcc\_paracrystal.c in sasmodels. + +Example: SasView\_bcc\_paracrystal\_aniso(dnn, d\_factor, radius, sld, sld\_solvent, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +dnn & \AA{} & ([-inf, inf]) Nearest neighbour distance. & 220 \\ +d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 40 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +Psi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_bcc\_paracrystal\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_bcc_paracrystal_aniso_static.tex}{\input{sasmodels/SasView_bcc_paracrystal_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_binary_hard_sphere.tex b/docs/manuals/mcxtrace/sasmodels/SasView_binary_hard_sphere.tex new file mode 100644 index 0000000000..9e5ff40643 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_binary_hard_sphere.tex @@ -0,0 +1,55 @@ +\section{The \texttt{SasView\_binary\_hard\_sphere} McXtrace Component} +SasView binary\_hard\_sphere model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_binary\_hard\_sphere component, generated from binary\_hard\_sphere.c in sasmodels. + +Example: SasView\_binary\_hard\_sphere(radius\_lg, radius\_sm, volfraction\_lg, volfraction\_sm, sld\_lg, sld\_sm, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_lg=0.0, pd\_radius\_sm=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_lg & \AA{} & ([0, inf]) radius of large particle. & 100 \\ +radius\_sm & \AA{} & ([0, inf]) radius of small particle. & 25 \\ +volfraction\_lg & & ([0, 1]) volume fraction of large particle. & 0.1 \\ +volfraction\_sm & & ([0, 1]) volume fraction of small particle. & 0.2 \\ +sld\_lg & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) scattering length density of large particle. & 3.5 \\ +sld\_sm & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) scattering length density of small particle. & 0.5 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.36 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_lg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_sm & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_binary\_hard\_sphere.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_binary_hard_sphere_static.tex}{\input{sasmodels/SasView_binary_hard_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_broad_peak.tex b/docs/manuals/mcxtrace/sasmodels/SasView_broad_peak.tex new file mode 100644 index 0000000000..e1493534fb --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_broad_peak.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_broad\_peak} McXtrace Component} +SasView broad\_peak model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_broad\_peak component, generated from broad\_peak.c in sasmodels. + +Example: SasView\_broad\_peak(porod\_scale, porod\_exp, peak\_scale, correlation\_length, peak\_pos, width\_exp, shape\_exp, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_correlation\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +porod\_scale & & ([-inf, inf]) Power law scale factor. & 1e-05 \\ +porod\_exp & & ([-inf, inf]) Exponent of power law. & 3.0 \\ +peak\_scale & & ([-inf, inf]) Scale factor for broad peak. & 10.0 \\ +correlation\_length & \AA{} & ([-inf, inf]) screening length. & 50.0 \\ +peak\_pos & 1/\AA{} & ([-inf, inf]) Peak position in q. & 0.1 \\ +width\_exp & & ([-inf, inf]) Exponent of peak width. & 2.0 \\ +shape\_exp & & ([-inf, inf]) Exponent of peak shape. & 1.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_correlation\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_broad\_peak.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_broad_peak_static.tex}{\input{sasmodels/SasView_broad_peak_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_capped_cylinder.tex b/docs/manuals/mcxtrace/sasmodels/SasView_capped_cylinder.tex new file mode 100644 index 0000000000..3bdea3928c --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_capped_cylinder.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_capped\_cylinder} McXtrace Component} +SasView capped\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_capped\_cylinder component, generated from capped\_cylinder.c in sasmodels. + +Example: SasView\_capped\_cylinder(sld, sld\_solvent, radius, radius\_cap, length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_radius\_cap=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder radius. & 20 \\ +radius\_cap & \AA{} & ([0, inf]) Cap radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_cap & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_capped\_cylinder.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_capped_cylinder_static.tex}{\input{sasmodels/SasView_capped_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_capped_cylinder_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_capped_cylinder_aniso.tex new file mode 100644 index 0000000000..6fab875abc --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_capped_cylinder_aniso.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_capped\_cylinder\_aniso} McXtrace Component} +SasView capped\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_capped\_cylinder component, generated from capped\_cylinder.c in sasmodels. + +Example: SasView\_capped\_cylinder\_aniso(sld, sld\_solvent, radius, radius\_cap, length, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_radius\_cap=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder radius. & 20 \\ +radius\_cap & \AA{} & ([0, inf]) Cap radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_cap & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_capped\_cylinder\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_capped_cylinder_aniso_static.tex}{\input{sasmodels/SasView_capped_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_multi_shell.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_multi_shell.tex new file mode 100644 index 0000000000..f76b8cb4e3 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_multi_shell.tex @@ -0,0 +1,31 @@ +\section{The \texttt{SasView\_core\_multi\_shell} McXtrace Component} +SasView core\_multi\_shell model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_multi\_shell component, generated from core\_multi\_shell.c in sasmodels. + +Example: SasView\_core\_multi\_shell(sld\_core, radius, sld\_solvent, n, sld[n], thickness[n], model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness[n]=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_multi\_shell.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_multi_shell_static.tex}{\input{sasmodels/SasView_core_multi_shell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle.tex new file mode 100644 index 0000000000..160dd5e426 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_core\_shell\_bicelle} McXtrace Component} +SasView core\_shell\_bicelle model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_bicelle component, generated from core\_shell\_bicelle.c in sasmodels. + +Example: SasView\_core\_shell\_bicelle(radius, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Cylinder core radius. & 80 \\ +thick\_rim & \AA{} & ([0, inf]) Rim shell thickness. & 10 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 10 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 1 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 4 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_face & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_bicelle_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_aniso.tex new file mode 100644 index 0000000000..2f04e55d5a --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_aniso.tex @@ -0,0 +1,62 @@ +\section{The \texttt{SasView\_core\_shell\_bicelle\_aniso} McXtrace Component} +SasView core\_shell\_bicelle model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_bicelle component, generated from core\_shell\_bicelle.c in sasmodels. + +Example: SasView\_core\_shell\_bicelle\_aniso(radius, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Cylinder core radius. & 80 \\ +thick\_rim & \AA{} & ([0, inf]) Rim shell thickness. & 10 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 10 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 1 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 4 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +theta & & & 90 \\ +Phi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_face & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_bicelle_aniso_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical.tex new file mode 100644 index 0000000000..1135105af7 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical.tex @@ -0,0 +1,59 @@ +\section{The \texttt{SasView\_core\_shell\_bicelle\_elliptical} McXtrace Component} +SasView core\_shell\_bicelle\_elliptical model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_bicelle\_elliptical component, generated from core\_shell\_bicelle\_elliptical.c in sasmodels. + +Example: SasView\_core\_shell\_bicelle\_elliptical(radius, x\_core, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ +x\_core & None & ([0, inf]) Axial ratio of core, X = r\_major/r\_minor. & 3 \\ +thick\_rim & \AA{} & ([0, inf]) Rim shell thickness. & 8 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 14 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_face & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_elliptical.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_bicelle_elliptical_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_elliptical_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_aniso.tex new file mode 100644 index 0000000000..2c9400db77 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_aniso.tex @@ -0,0 +1,65 @@ +\section{The \texttt{SasView\_core\_shell\_bicelle\_elliptical\_aniso} McXtrace Component} +SasView core\_shell\_bicelle\_elliptical model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_bicelle\_elliptical component, generated from core\_shell\_bicelle\_elliptical.c in sasmodels. + +Example: SasView\_core\_shell\_bicelle\_elliptical\_aniso(radius, x\_core, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ +x\_core & None & ([0, inf]) Axial ratio of core, X = r\_major/r\_minor. & 3 \\ +thick\_rim & \AA{} & ([0, inf]) Rim shell thickness. & 8 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 14 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +theta & & & 90.0 \\ +Phi & & & 0 \\ +Psi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_face & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_elliptical\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_bicelle_elliptical_aniso_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_elliptical_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough.tex new file mode 100644 index 0000000000..94fab5ac99 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough.tex @@ -0,0 +1,60 @@ +\section{The \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough} McXtrace Component} +SasView core\_shell\_bicelle\_elliptical\_belt\_rough model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough component, generated from core\_shell\_bicelle\_elliptical\_belt\_rough.c in sasmodels. + +Example: SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough(radius, x\_core, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, sigma, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ +x\_core & None & ([0, inf]) Axial ratio of core, X = r\_major/r\_minor. & 3 \\ +thick\_rim & \AA{} & ([0, inf]) Rim or belt shell thickness. & 8 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 14 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +sigma & \AA{} & ([0, inf]) Interfacial roughness. & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_face & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso.tex new file mode 100644 index 0000000000..c45fb2f9f4 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso.tex @@ -0,0 +1,66 @@ +\section{The \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough\_aniso} McXtrace Component} +SasView core\_shell\_bicelle\_elliptical\_belt\_rough model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough component, generated from core\_shell\_bicelle\_elliptical\_belt\_rough.c in sasmodels. + +Example: SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough\_aniso(radius, x\_core, thick\_rim, thick\_face, length, sld\_core, sld\_face, sld\_rim, sld\_solvent, sigma, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_rim=0.0, pd\_thick\_face=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Cylinder core radius r\_minor. & 30 \\ +x\_core & None & ([0, inf]) Axial ratio of core, X = r\_major/r\_minor. & 3 \\ +thick\_rim & \AA{} & ([0, inf]) Rim or belt shell thickness. & 8 \\ +thick\_face & \AA{} & ([0, inf]) Cylinder face thickness. & 14 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 50 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_face & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder face scattering length density. & 7 \\ +sld\_rim & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder rim scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +sigma & \AA{} & ([0, inf]) Interfacial roughness. & 0 \\ +theta & & & 90.0 \\ +Phi & & & 0 \\ +Psi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_face & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_bicelle\_elliptical\_belt\_rough\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso_static.tex}{\input{sasmodels/SasView_core_shell_bicelle_elliptical_belt_rough_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_cylinder.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_cylinder.tex new file mode 100644 index 0000000000..860c984c04 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_cylinder.tex @@ -0,0 +1,55 @@ +\section{The \texttt{SasView\_core\_shell\_cylinder} McXtrace Component} +SasView core\_shell\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_cylinder component, generated from core\_shell\_cylinder.c in sasmodels. + +Example: SasView\_core\_shell\_cylinder(sld\_core, sld\_shell, sld\_solvent, radius, thickness, length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder shell scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius. & 20 \\ +thickness & \AA{} & ([0, inf]) Cylinder shell thickness. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_cylinder.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_cylinder_static.tex}{\input{sasmodels/SasView_core_shell_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_cylinder_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_cylinder_aniso.tex new file mode 100644 index 0000000000..7e1cffe9fb --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_cylinder_aniso.tex @@ -0,0 +1,59 @@ +\section{The \texttt{SasView\_core\_shell\_cylinder\_aniso} McXtrace Component} +SasView core\_shell\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_cylinder component, generated from core\_shell\_cylinder.c in sasmodels. + +Example: SasView\_core\_shell\_cylinder\_aniso(sld\_core, sld\_shell, sld\_solvent, radius, thickness, length, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder core scattering length density. & 4 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder shell scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder core radius. & 20 \\ +thickness & \AA{} & ([0, inf]) Cylinder shell thickness. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_cylinder\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_cylinder_aniso_static.tex}{\input{sasmodels/SasView_core_shell_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_ellipsoid.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_ellipsoid.tex new file mode 100644 index 0000000000..827527da0d --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_ellipsoid.tex @@ -0,0 +1,55 @@ +\section{The \texttt{SasView\_core\_shell\_ellipsoid} McXtrace Component} +SasView core\_shell\_ellipsoid model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_ellipsoid component, generated from core\_shell\_ellipsoid.c in sasmodels. + +Example: SasView\_core\_shell\_ellipsoid(radius\_equat\_core, x\_core, thick\_shell, x\_polar\_shell, sld\_core, sld\_shell, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_equat\_core=0.0, pd\_thick\_shell=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_equat\_core & \AA{} & ([0, inf]) Equatorial radius of core. & 20 \\ +x\_core & None & ([0, inf]) axial ratio of core, X = r\_polar/r\_equatorial. & 3 \\ +thick\_shell & \AA{} & ([0, inf]) thickness of shell at equator. & 30 \\ +x\_polar\_shell & & ([0, inf]) ratio of thickness of shell at pole to that at equator. & 1 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Core scattering length density. & 2 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Shell scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_equat\_core & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_shell & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_ellipsoid.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_ellipsoid_static.tex}{\input{sasmodels/SasView_core_shell_ellipsoid_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_ellipsoid_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_ellipsoid_aniso.tex new file mode 100644 index 0000000000..66ddfc0f76 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_ellipsoid_aniso.tex @@ -0,0 +1,59 @@ +\section{The \texttt{SasView\_core\_shell\_ellipsoid\_aniso} McXtrace Component} +SasView core\_shell\_ellipsoid model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_ellipsoid component, generated from core\_shell\_ellipsoid.c in sasmodels. + +Example: SasView\_core\_shell\_ellipsoid\_aniso(radius\_equat\_core, x\_core, thick\_shell, x\_polar\_shell, sld\_core, sld\_shell, sld\_solvent, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_equat\_core=0.0, pd\_thick\_shell=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_equat\_core & \AA{} & ([0, inf]) Equatorial radius of core. & 20 \\ +x\_core & None & ([0, inf]) axial ratio of core, X = r\_polar/r\_equatorial. & 3 \\ +thick\_shell & \AA{} & ([0, inf]) thickness of shell at equator. & 30 \\ +x\_polar\_shell & & ([0, inf]) ratio of thickness of shell at pole to that at equator. & 1 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Core scattering length density. & 2 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Shell scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ +theta & & & 0 \\ +Phi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_equat\_core & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_shell & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_ellipsoid\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_ellipsoid_aniso_static.tex}{\input{sasmodels/SasView_core_shell_ellipsoid_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_parallelepiped.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_parallelepiped.tex new file mode 100644 index 0000000000..c227655fb0 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_parallelepiped.tex @@ -0,0 +1,63 @@ +\section{The \texttt{SasView\_core\_shell\_parallelepiped} McXtrace Component} +SasView core\_shell\_parallelepiped model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_parallelepiped component, generated from core\_shell\_parallelepiped.c in sasmodels. + +Example: SasView\_core\_shell\_parallelepiped(sld\_core, sld\_a, sld\_b, sld\_c, sld\_solvent, length\_a, length\_b, length\_c, thick\_rim\_a, thick\_rim\_b, thick\_rim\_c, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_length\_b=0.0, pd\_length\_c=0.0, pd\_thick\_rim\_a=0.0, pd\_thick\_rim\_b=0.0, pd\_thick\_rim\_c=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped core scattering length density. & 1 \\ +sld\_a & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped A rim scattering length density. & 2 \\ +sld\_b & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped B rim scattering length density. & 4 \\ +sld\_c & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped C rim scattering length density. & 2 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +length\_b & \AA{} & ([0, inf]) Second side of the parallelepiped. & 75 \\ +length\_c & \AA{} & ([0, inf]) Larger side of the parallelepiped. & 400 \\ +thick\_rim\_a & \AA{} & ([0, inf]) Thickness of A rim. & 10 \\ +thick\_rim\_b & \AA{} & ([0, inf]) Thickness of B rim. & 10 \\ +thick\_rim\_c & \AA{} & ([0, inf]) Thickness of C rim. & 10 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_b & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_c & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim\_b & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim\_c & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_parallelepiped.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_parallelepiped_static.tex}{\input{sasmodels/SasView_core_shell_parallelepiped_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_parallelepiped_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_parallelepiped_aniso.tex new file mode 100644 index 0000000000..cf991f6945 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_parallelepiped_aniso.tex @@ -0,0 +1,69 @@ +\section{The \texttt{SasView\_core\_shell\_parallelepiped\_aniso} McXtrace Component} +SasView core\_shell\_parallelepiped model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_parallelepiped component, generated from core\_shell\_parallelepiped.c in sasmodels. + +Example: SasView\_core\_shell\_parallelepiped\_aniso(sld\_core, sld\_a, sld\_b, sld\_c, sld\_solvent, length\_a, length\_b, length\_c, thick\_rim\_a, thick\_rim\_b, thick\_rim\_c, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_length\_b=0.0, pd\_length\_c=0.0, pd\_thick\_rim\_a=0.0, pd\_thick\_rim\_b=0.0, pd\_thick\_rim\_c=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped core scattering length density. & 1 \\ +sld\_a & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped A rim scattering length density. & 2 \\ +sld\_b & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped B rim scattering length density. & 4 \\ +sld\_c & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped C rim scattering length density. & 2 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +length\_b & \AA{} & ([0, inf]) Second side of the parallelepiped. & 75 \\ +length\_c & \AA{} & ([0, inf]) Larger side of the parallelepiped. & 400 \\ +thick\_rim\_a & \AA{} & ([0, inf]) Thickness of A rim. & 10 \\ +thick\_rim\_b & \AA{} & ([0, inf]) Thickness of B rim. & 10 \\ +thick\_rim\_c & \AA{} & ([0, inf]) Thickness of C rim. & 10 \\ +theta & & & 0 \\ +Phi & & & 0 \\ +Psi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_b & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_c & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim\_b & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_rim\_c & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_parallelepiped\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_parallelepiped_aniso_static.tex}{\input{sasmodels/SasView_core_shell_parallelepiped_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_sphere.tex b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_sphere.tex new file mode 100644 index 0000000000..056334b949 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_core_shell_sphere.tex @@ -0,0 +1,53 @@ +\section{The \texttt{SasView\_core\_shell\_sphere} McXtrace Component} +SasView core\_shell\_sphere model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_core\_shell\_sphere component, generated from core\_shell\_sphere.c in sasmodels. + +Example: SasView\_core\_shell\_sphere(radius, thickness, sld\_core, sld\_shell, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Sphere core radius. & 60.0 \\ +thickness & \AA{} & ([0, inf]) Sphere shell thickness. & 10.0 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) core scattering length density. & 1.0 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) shell scattering length density. & 2.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 3.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_core\_shell\_sphere.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_core_shell_sphere_static.tex}{\input{sasmodels/SasView_core_shell_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_correlation_length.tex b/docs/manuals/mcxtrace/sasmodels/SasView_correlation_length.tex new file mode 100644 index 0000000000..f19a8adefc --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_correlation_length.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_correlation\_length} McXtrace Component} +SasView correlation\_length model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_correlation\_length component, generated from correlation\_length.c in sasmodels. + +Example: SasView\_correlation\_length(lorentz\_scale, porod\_scale, cor\_length, porod\_exp, lorentz\_exp, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_cor\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +lorentz\_scale & & ([0, inf]) Lorentzian Scaling Factor. & 10.0 \\ +porod\_scale & & ([0, inf]) Porod Scaling Factor. & 1e-06 \\ +cor\_length & \AA{} & ([0, inf]) Correlation length, xi, in Lorentzian. & 50.0 \\ +porod\_exp & & ([0, inf]) Porod Exponent, n, in q\textasciicircum{}-n. & 3.0 \\ +lorentz\_exp & & ([0, inf]) Lorentzian Exponent, m, in 1/( 1 + (q.xi)\textasciicircum{}m). & 2.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_cor\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_correlation\_length.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_correlation_length_static.tex}{\input{sasmodels/SasView_correlation_length_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_cylinder.tex b/docs/manuals/mcxtrace/sasmodels/SasView_cylinder.tex new file mode 100644 index 0000000000..f1525f22fc --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_cylinder.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_cylinder} McXtrace Component} +SasView cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_cylinder component, generated from cylinder.c in sasmodels. + +Example: SasView\_cylinder(sld, sld\_solvent, radius, length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_cylinder.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_cylinder_static.tex}{\input{sasmodels/SasView_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_cylinder_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_cylinder_aniso.tex new file mode 100644 index 0000000000..94a40c5980 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_cylinder_aniso.tex @@ -0,0 +1,56 @@ +\section{The \texttt{SasView\_cylinder\_aniso} McXtrace Component} +SasView cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_cylinder component, generated from cylinder.c in sasmodels. + +Example: SasView\_cylinder\_aniso(sld, sld\_solvent, radius, length, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius & \AA{} & ([0, inf]) Cylinder radius. & 20 \\ +length & \AA{} & ([0, inf]) Cylinder length. & 400 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_cylinder\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_cylinder_aniso_static.tex}{\input{sasmodels/SasView_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_dab.tex b/docs/manuals/mcxtrace/sasmodels/SasView_dab.tex new file mode 100644 index 0000000000..6d04c9f6e2 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_dab.tex @@ -0,0 +1,48 @@ +\section{The \texttt{SasView\_dab} McXtrace Component} +SasView dab model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_dab component, generated from dab.c in sasmodels. + +Example: SasView\_dab(cor\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_cor\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +cor\_length & \AA{} & ([0, inf]) correlation length. & 50.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_cor\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_dab.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_dab_static.tex}{\input{sasmodels/SasView_dab_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_ellipsoid.tex b/docs/manuals/mcxtrace/sasmodels/SasView_ellipsoid.tex new file mode 100644 index 0000000000..a3dcee9e3c --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_ellipsoid.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_ellipsoid} McXtrace Component} +SasView ellipsoid model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_ellipsoid component, generated from ellipsoid.c in sasmodels. + +Example: SasView\_ellipsoid(sld, sld\_solvent, radius\_polar, radius\_equatorial, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_polar=0.0, pd\_radius\_equatorial=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_polar & \AA{} & ([0, inf]) Polar radius. & 20 \\ +radius\_equatorial & \AA{} & ([0, inf]) Equatorial radius. & 400 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_polar & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_equatorial & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_ellipsoid.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_ellipsoid_static.tex}{\input{sasmodels/SasView_ellipsoid_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_ellipsoid_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_ellipsoid_aniso.tex new file mode 100644 index 0000000000..808a89d1cf --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_ellipsoid_aniso.tex @@ -0,0 +1,56 @@ +\section{The \texttt{SasView\_ellipsoid\_aniso} McXtrace Component} +SasView ellipsoid model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_ellipsoid component, generated from ellipsoid.c in sasmodels. + +Example: SasView\_ellipsoid\_aniso(sld, sld\_solvent, radius\_polar, radius\_equatorial, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_polar=0.0, pd\_radius\_equatorial=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_polar & \AA{} & ([0, inf]) Polar radius. & 20 \\ +radius\_equatorial & \AA{} & ([0, inf]) Equatorial radius. & 400 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_polar & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_equatorial & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_ellipsoid\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_ellipsoid_aniso_static.tex}{\input{sasmodels/SasView_ellipsoid_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_elliptical_cylinder.tex b/docs/manuals/mcxtrace/sasmodels/SasView_elliptical_cylinder.tex new file mode 100644 index 0000000000..9cad19e1aa --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_elliptical_cylinder.tex @@ -0,0 +1,53 @@ +\section{The \texttt{SasView\_elliptical\_cylinder} McXtrace Component} +SasView elliptical\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_elliptical\_cylinder component, generated from elliptical\_cylinder.c in sasmodels. + +Example: SasView\_elliptical\_cylinder(radius\_minor, r\_ratio, length, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_minor=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_minor & \AA{} & ([0, inf]) Ellipse minor radius. & 20.0 \\ +r\_ratio & & ([1, inf]) Ratio of major radius over minor radius. & 1.5 \\ +length & \AA{} & ([1, inf]) Length of the cylinder. & 400.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_minor & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_elliptical\_cylinder.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_elliptical_cylinder_static.tex}{\input{sasmodels/SasView_elliptical_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_elliptical_cylinder_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_elliptical_cylinder_aniso.tex new file mode 100644 index 0000000000..fb74514cdc --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_elliptical_cylinder_aniso.tex @@ -0,0 +1,59 @@ +\section{The \texttt{SasView\_elliptical\_cylinder\_aniso} McXtrace Component} +SasView elliptical\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_elliptical\_cylinder component, generated from elliptical\_cylinder.c in sasmodels. + +Example: SasView\_elliptical\_cylinder\_aniso(radius\_minor, r\_ratio, length, sld, sld\_solvent, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_minor=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_minor & \AA{} & ([0, inf]) Ellipse minor radius. & 20.0 \\ +r\_ratio & & ([1, inf]) Ratio of major radius over minor radius. & 1.5 \\ +length & \AA{} & ([1, inf]) Length of the cylinder. & 400.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 4.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ +theta & & & 90.0 \\ +Phi & & & 0 \\ +Psi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_minor & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_elliptical\_cylinder\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_elliptical_cylinder_aniso_static.tex}{\input{sasmodels/SasView_elliptical_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_fcc_paracrystal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_fcc_paracrystal.tex new file mode 100644 index 0000000000..e26f22dbf3 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_fcc_paracrystal.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_fcc\_paracrystal} McXtrace Component} +SasView fcc\_paracrystal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_fcc\_paracrystal component, generated from fcc\_paracrystal.c in sasmodels. + +Example: SasView\_fcc\_paracrystal(dnn, d\_factor, radius, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +dnn & \AA{} & ([-inf, inf]) Nearest neighbour distance. & 220 \\ +d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 40 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_fcc\_paracrystal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_fcc_paracrystal_static.tex}{\input{sasmodels/SasView_fcc_paracrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_fcc_paracrystal_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_fcc_paracrystal_aniso.tex new file mode 100644 index 0000000000..bf64f966d9 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_fcc_paracrystal_aniso.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_fcc\_paracrystal\_aniso} McXtrace Component} +SasView fcc\_paracrystal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_fcc\_paracrystal component, generated from fcc\_paracrystal.c in sasmodels. + +Example: SasView\_fcc\_paracrystal\_aniso(dnn, d\_factor, radius, sld, sld\_solvent, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +dnn & \AA{} & ([-inf, inf]) Nearest neighbour distance. & 220 \\ +d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ +radius & \AA{} & ([0, inf]) Particle radius. & 40 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +Psi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_fcc\_paracrystal\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_fcc_paracrystal_aniso_static.tex}{\input{sasmodels/SasView_fcc_paracrystal_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_flexible_cylinder.tex b/docs/manuals/mcxtrace/sasmodels/SasView_flexible_cylinder.tex new file mode 100644 index 0000000000..c9fd80b5b9 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_flexible_cylinder.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_flexible\_cylinder} McXtrace Component} +SasView flexible\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_flexible\_cylinder component, generated from flexible\_cylinder.c in sasmodels. + +Example: SasView\_flexible\_cylinder(length, kuhn\_length, radius, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length=0.0, pd\_kuhn\_length=0.0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +length & \AA{} & ([0, inf]) Length of the flexible cylinder. & 1000.0 \\ +kuhn\_length & \AA{} & ([0, inf]) Kuhn length of the flexible cylinder. & 100.0 \\ +radius & \AA{} & ([0, inf]) Radius of the flexible cylinder. & 20.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_kuhn\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_flexible\_cylinder.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_flexible_cylinder_static.tex}{\input{sasmodels/SasView_flexible_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_flexible_cylinder_elliptical.tex b/docs/manuals/mcxtrace/sasmodels/SasView_flexible_cylinder_elliptical.tex new file mode 100644 index 0000000000..5c2f02aca3 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_flexible_cylinder_elliptical.tex @@ -0,0 +1,55 @@ +\section{The \texttt{SasView\_flexible\_cylinder\_elliptical} McXtrace Component} +SasView flexible\_cylinder\_elliptical model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_flexible\_cylinder\_elliptical component, generated from flexible\_cylinder\_elliptical.c in sasmodels. + +Example: SasView\_flexible\_cylinder\_elliptical(length, kuhn\_length, radius, axis\_ratio, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length=0.0, pd\_kuhn\_length=0.0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +length & \AA{} & ([0, inf]) Length of the flexible cylinder. & 1000.0 \\ +kuhn\_length & \AA{} & ([0, inf]) Kuhn length of the flexible cylinder. & 100.0 \\ +radius & \AA{} & ([1, inf]) Radius of the flexible cylinder. & 20.0 \\ +axis\_ratio & & ([0, inf]) Axis\_ratio (major\_radius/minor\_radius. & 1.5 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder scattering length density. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_kuhn\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_flexible\_cylinder\_elliptical.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_flexible_cylinder_elliptical_static.tex}{\input{sasmodels/SasView_flexible_cylinder_elliptical_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_fractal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_fractal.tex new file mode 100644 index 0000000000..f91491fc1a --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_fractal.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_fractal} McXtrace Component} +SasView fractal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_fractal component, generated from fractal.c in sasmodels. + +Example: SasView\_fractal(volfraction, radius, fractal\_dim, cor\_length, sld\_block, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_cor\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +volfraction & & ([0.0, 1]) volume fraction of blocks. & 0.05 \\ +radius & \AA{} & ([0.0, inf]) radius of particles. & 5.0 \\ +fractal\_dim & & ([0.0, 6.0]) fractal dimension. & 2.0 \\ +cor\_length & \AA{} & ([0.0, inf]) cluster correlation length. & 100.0 \\ +sld\_block & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) scattering length density of particles. & 2.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) scattering length density of solvent. & 6.4 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_cor\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_fractal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_fractal_static.tex}{\input{sasmodels/SasView_fractal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_fractal_core_shell.tex b/docs/manuals/mcxtrace/sasmodels/SasView_fractal_core_shell.tex new file mode 100644 index 0000000000..e6d66e2432 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_fractal_core_shell.tex @@ -0,0 +1,57 @@ +\section{The \texttt{SasView\_fractal\_core\_shell} McXtrace Component} +SasView fractal\_core\_shell model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_fractal\_core\_shell component, generated from fractal\_core\_shell.c in sasmodels. + +Example: SasView\_fractal\_core\_shell(radius, thickness, sld\_core, sld\_shell, sld\_solvent, volfraction, fractal\_dim, cor\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_cor\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0.0, inf]) Sphere core radius. & 60.0 \\ +thickness & \AA{} & ([0.0, inf]) Sphere shell thickness. & 10.0 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Sphere core scattering length density. & 1.0 \\ +sld\_shell & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Sphere shell scattering length density. & 2.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 3.0 \\ +volfraction & & ([0.0, inf]) Volume fraction of building block spheres. & 0.05 \\ +fractal\_dim & & ([0.0, 6.0]) Fractal dimension. & 2.0 \\ +cor\_length & \AA{} & ([0.0, inf]) Correlation length of fractal-like aggregates. & 100.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_cor\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_fractal\_core\_shell.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_fractal_core_shell_static.tex}{\input{sasmodels/SasView_fractal_core_shell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_fuzzy_sphere.tex b/docs/manuals/mcxtrace/sasmodels/SasView_fuzzy_sphere.tex new file mode 100644 index 0000000000..6c79f2cd92 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_fuzzy_sphere.tex @@ -0,0 +1,51 @@ +\section{The \texttt{SasView\_fuzzy\_sphere} McXtrace Component} +SasView fuzzy\_sphere model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_fuzzy\_sphere component, generated from fuzzy\_sphere.c in sasmodels. + +Example: SasView\_fuzzy\_sphere(sld, sld\_solvent, radius, fuzziness, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Particle scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 3 \\ +radius & \AA{} & ([0, inf]) Sphere radius. & 60 \\ +fuzziness & \AA{} & ([0, inf]) std deviation of Gaussian convolution for interface (must be \textless{}\textless{} radius). & 10 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_fuzzy\_sphere.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_fuzzy_sphere_static.tex}{\input{sasmodels/SasView_fuzzy_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_gauss_lorentz_gel.tex b/docs/manuals/mcxtrace/sasmodels/SasView_gauss_lorentz_gel.tex new file mode 100644 index 0000000000..6baa96cb6b --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_gauss_lorentz_gel.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_gauss\_lorentz\_gel} McXtrace Component} +SasView gauss\_lorentz\_gel model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_gauss\_lorentz\_gel component, generated from gauss\_lorentz\_gel.c in sasmodels. + +Example: SasView\_gauss\_lorentz\_gel(gauss\_scale, cor\_length\_static, lorentz\_scale, cor\_length\_dynamic, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_cor\_length\_static=0.0, pd\_cor\_length\_dynamic=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +gauss\_scale & & ([-inf, inf]) Gauss scale factor. & 100.0 \\ +cor\_length\_static & \AA{} & ([0, inf]) Static correlation length. & 100.0 \\ +lorentz\_scale & & ([-inf, inf]) Lorentzian scale factor. & 50.0 \\ +cor\_length\_dynamic & \AA{} & ([0, inf]) Dynamic correlation length. & 20.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_cor\_length\_static & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_cor\_length\_dynamic & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_gauss\_lorentz\_gel.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_gauss_lorentz_gel_static.tex}{\input{sasmodels/SasView_gauss_lorentz_gel_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_gaussian_peak.tex b/docs/manuals/mcxtrace/sasmodels/SasView_gaussian_peak.tex new file mode 100644 index 0000000000..9cd1de3bc9 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_gaussian_peak.tex @@ -0,0 +1,48 @@ +\section{The \texttt{SasView\_gaussian\_peak} McXtrace Component} +SasView gaussian\_peak model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_gaussian\_peak component, generated from gaussian\_peak.c in sasmodels. + +Example: SasView\_gaussian\_peak(peak\_pos, sigma, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +peak\_pos & 1/\AA{} & ([-inf, inf]) Peak position. & 0.05 \\ +sigma & 1/\AA{} & ([0, inf]) Peak width (standard deviation). & 0.005 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_gaussian\_peak.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_gaussian_peak_static.tex}{\input{sasmodels/SasView_gaussian_peak_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_gel_fit.tex b/docs/manuals/mcxtrace/sasmodels/SasView_gel_fit.tex new file mode 100644 index 0000000000..25a5f2dc9b --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_gel_fit.tex @@ -0,0 +1,53 @@ +\section{The \texttt{SasView\_gel\_fit} McXtrace Component} +SasView gel\_fit model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_gel\_fit component, generated from gel\_fit.c in sasmodels. + +Example: SasView\_gel\_fit(guinier\_scale, lorentz\_scale, rg, fractal\_dim, cor\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0, pd\_cor\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +guinier\_scale & cm$^{-1}$ & ([-inf, inf]) Guinier term scale. & 1.7 \\ +lorentz\_scale & cm$^{-1}$ & ([-inf, inf]) Lorentz term scale. & 3.5 \\ +rg & \AA{} & ([2, inf]) Radius of gyration. & 104.0 \\ +fractal\_dim & & ([0, inf]) Fractal exponent. & 2.0 \\ +cor\_length & \AA{} & ([0, inf]) Correlation length. & 16.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_rg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_cor\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_gel\_fit.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_gel_fit_static.tex}{\input{sasmodels/SasView_gel_fit_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_guinier.tex b/docs/manuals/mcxtrace/sasmodels/SasView_guinier.tex new file mode 100644 index 0000000000..2f52c97d39 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_guinier.tex @@ -0,0 +1,48 @@ +\section{The \texttt{SasView\_guinier} McXtrace Component} +SasView guinier model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_guinier component, generated from guinier.c in sasmodels. + +Example: SasView\_guinier(rg, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +rg & \AA{} & ([-inf, inf]) Radius of Gyration. & 60.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_rg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_guinier.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_guinier_static.tex}{\input{sasmodels/SasView_guinier_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_guinier_porod.tex b/docs/manuals/mcxtrace/sasmodels/SasView_guinier_porod.tex new file mode 100644 index 0000000000..ef0afd39ab --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_guinier_porod.tex @@ -0,0 +1,50 @@ +\section{The \texttt{SasView\_guinier\_porod} McXtrace Component} +SasView guinier\_porod model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_guinier\_porod component, generated from guinier\_porod.c in sasmodels. + +Example: SasView\_guinier\_porod(rg, s, porod\_exp, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +rg & \AA{} & ([0, inf]) Radius of gyration. & 60.0 \\ +s & & ([0, inf]) Dimension variable. & 1.0 \\ +porod\_exp & & ([0, inf]) Porod exponent. & 3.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_rg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_guinier\_porod.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_guinier_porod_static.tex}{\input{sasmodels/SasView_guinier_porod_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_hardsphere.tex b/docs/manuals/mcxtrace/sasmodels/SasView_hardsphere.tex new file mode 100644 index 0000000000..b88a91ddf6 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_hardsphere.tex @@ -0,0 +1,49 @@ +\section{The \texttt{SasView\_hardsphere} McXtrace Component} +SasView hardsphere model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_hardsphere component, generated from hardsphere.c in sasmodels. + +Example: SasView\_hardsphere(radius\_effective, volfraction, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_effective=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_effective & \AA{} & ([0, inf]) effective radius of hard sphere. & 50.0 \\ +volfraction & & ([0, 0.74]) volume fraction of hard spheres. & 0.2 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_effective & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_hardsphere.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_hardsphere_static.tex}{\input{sasmodels/SasView_hardsphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_hayter_msa.tex b/docs/manuals/mcxtrace/sasmodels/SasView_hayter_msa.tex new file mode 100644 index 0000000000..95dc089b3b --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_hayter_msa.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_hayter\_msa} McXtrace Component} +SasView hayter\_msa model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_hayter\_msa component, generated from hayter\_msa.c in sasmodels. + +Example: SasView\_hayter\_msa(radius\_effective, volfraction, charge, temperature, concentration\_salt, dielectconst, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_effective=0.0, pd\_charge=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_effective & \AA{} & ([0, inf]) effective radius of charged sphere. & 20.75 \\ +volfraction & None & ([0, 0.74]) volume fraction of spheres. & 0.0192 \\ +charge & e & ([1e-06, 200]) charge on sphere (in electrons). & 19.0 \\ +temperature & K & ([0, 450]) temperature, in Kelvin, for Debye length calculation. & 318.16 \\ +concentration\_salt & M & ([0, inf]) conc of salt, moles/litre, 1:1 electolyte, for Debye length. & 0.0 \\ +dielectconst & None & ([-inf, inf]) dielectric constant (relative permittivity) of solvent, kappa, default water, for Debye length. & 71.08 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_effective & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_charge & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_hayter\_msa.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_hayter_msa_static.tex}{\input{sasmodels/SasView_hayter_msa_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_hollow_cylinder.tex b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_cylinder.tex new file mode 100644 index 0000000000..4aecb6e985 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_cylinder.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_hollow\_cylinder} McXtrace Component} +SasView hollow\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_hollow\_cylinder component, generated from hollow\_cylinder.c in sasmodels. + +Example: SasView\_hollow\_cylinder(radius, thickness, length, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Cylinder core radius. & 20.0 \\ +thickness & \AA{} & ([0, inf]) Cylinder wall thickness. & 10.0 \\ +length & \AA{} & ([0, inf]) Cylinder total length. & 400.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder sld. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent sld. & 1 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_hollow\_cylinder.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_hollow_cylinder_static.tex}{\input{sasmodels/SasView_hollow_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_hollow_cylinder_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_cylinder_aniso.tex new file mode 100644 index 0000000000..3f65709ada --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_cylinder_aniso.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_hollow\_cylinder\_aniso} McXtrace Component} +SasView hollow\_cylinder model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_hollow\_cylinder component, generated from hollow\_cylinder.c in sasmodels. + +Example: SasView\_hollow\_cylinder\_aniso(radius, thickness, length, sld, sld\_solvent, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0, pd\_length=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Cylinder core radius. & 20.0 \\ +thickness & \AA{} & ([0, inf]) Cylinder wall thickness. & 10.0 \\ +length & \AA{} & ([0, inf]) Cylinder total length. & 400.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Cylinder sld. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent sld. & 1 \\ +theta & & & 90 \\ +Phi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_hollow\_cylinder\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_hollow_cylinder_aniso_static.tex}{\input{sasmodels/SasView_hollow_cylinder_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism.tex b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism.tex new file mode 100644 index 0000000000..d741814d87 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_hollow\_rectangular\_prism} McXtrace Component} +SasView hollow\_rectangular\_prism model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_hollow\_rectangular\_prism component, generated from hollow\_rectangular\_prism.c in sasmodels. + +Example: SasView\_hollow\_rectangular\_prism(sld, sld\_solvent, length\_a, b2a\_ratio, c2a\_ratio, thickness, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_thickness=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shortest, external, size of the parallelepiped. & 35 \\ +b2a\_ratio & \AA{} & ([0, inf]) Ratio sides b/a. & 1 \\ +c2a\_ratio & \AA{} & ([0, inf]) Ratio sides c/a. & 1 \\ +thickness & \AA{} & ([0, inf]) Thickness of parallelepiped. & 1 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_hollow\_rectangular\_prism.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_hollow_rectangular_prism_static.tex}{\input{sasmodels/SasView_hollow_rectangular_prism_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism_aniso.tex new file mode 100644 index 0000000000..7cdb71e3ba --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism_aniso.tex @@ -0,0 +1,60 @@ +\section{The \texttt{SasView\_hollow\_rectangular\_prism\_aniso} McXtrace Component} +SasView hollow\_rectangular\_prism model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_hollow\_rectangular\_prism component, generated from hollow\_rectangular\_prism.c in sasmodels. + +Example: SasView\_hollow\_rectangular\_prism\_aniso(sld, sld\_solvent, length\_a, b2a\_ratio, c2a\_ratio, thickness, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_thickness=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shortest, external, size of the parallelepiped. & 35 \\ +b2a\_ratio & \AA{} & ([0, inf]) Ratio sides b/a. & 1 \\ +c2a\_ratio & \AA{} & ([0, inf]) Ratio sides c/a. & 1 \\ +thickness & \AA{} & ([0, inf]) Thickness of parallelepiped. & 1 \\ +theta & & & 0 \\ +Phi & & & 0 \\ +Psi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_hollow\_rectangular\_prism\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_hollow_rectangular_prism_aniso_static.tex}{\input{sasmodels/SasView_hollow_rectangular_prism_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism_thin_walls.tex b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism_thin_walls.tex new file mode 100644 index 0000000000..6b2f3d7309 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_hollow_rectangular_prism_thin_walls.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_hollow\_rectangular\_prism\_thin\_walls} McXtrace Component} +SasView hollow\_rectangular\_prism\_thin\_walls model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_hollow\_rectangular\_prism\_thin\_walls component, generated from hollow\_rectangular\_prism\_thin\_walls.c in sasmodels. + +Example: SasView\_hollow\_rectangular\_prism\_thin\_walls(sld, sld\_solvent, length\_a, b2a\_ratio, c2a\_ratio, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +b2a\_ratio & \AA{} & ([0, inf]) Ratio sides b/a. & 1 \\ +c2a\_ratio & \AA{} & ([0, inf]) Ratio sides c/a. & 1 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_hollow\_rectangular\_prism\_thin\_walls.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_hollow_rectangular_prism_thin_walls_static.tex}{\input{sasmodels/SasView_hollow_rectangular_prism_thin_walls_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_hg.tex b/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_hg.tex new file mode 100644 index 0000000000..b89abc7785 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_hg.tex @@ -0,0 +1,53 @@ +\section{The \texttt{SasView\_lamellar\_hg} McXtrace Component} +SasView lamellar\_hg model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_lamellar\_hg component, generated from lamellar\_hg.c in sasmodels. + +Example: SasView\_lamellar\_hg(length\_tail, length\_head, sld, sld\_head, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_tail=0.0, pd\_length\_head=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +length\_tail & \AA{} & ([0, inf]) Tail thickness ( total = H+T+T+H). & 15 \\ +length\_head & \AA{} & ([0, inf]) Head thickness. & 10 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Tail scattering length density. & 0.4 \\ +sld\_head & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Head scattering length density. & 3.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_tail & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_head & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_lamellar\_hg.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_lamellar_hg_static.tex}{\input{sasmodels/SasView_lamellar_hg_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_hg_stack_caille.tex b/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_hg_stack_caille.tex new file mode 100644 index 0000000000..b5d9947754 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_hg_stack_caille.tex @@ -0,0 +1,56 @@ +\section{The \texttt{SasView\_lamellar\_hg\_stack\_caille} McXtrace Component} +SasView lamellar\_hg\_stack\_caille model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_lamellar\_hg\_stack\_caille component, generated from lamellar\_hg\_stack\_caille.c in sasmodels. + +Example: SasView\_lamellar\_hg\_stack\_caille(length\_tail, length\_head, Nlayers, d\_spacing, Caille\_parameter, sld, sld\_head, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_tail=0.0, pd\_length\_head=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +length\_tail & \AA{} & ([0, inf]) Tail thickness. & 10 \\ +length\_head & \AA{} & ([0, inf]) head thickness. & 2 \\ +Nlayers & & ([1, inf]) Number of layers. & 30 \\ +d\_spacing & \AA{} & ([0.0, inf]) lamellar d-spacing of Caille S(Q). & 40.0 \\ +Caille\_parameter & & ([0.0, 0.8]) Caille parameter. & 0.001 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Tail scattering length density. & 0.4 \\ +sld\_head & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Head scattering length density. & 2.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_tail & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_head & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_lamellar\_hg\_stack\_caille.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_lamellar_hg_stack_caille_static.tex}{\input{sasmodels/SasView_lamellar_hg_stack_caille_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_stack_caille.tex b/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_stack_caille.tex new file mode 100644 index 0000000000..07fa52d278 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_stack_caille.tex @@ -0,0 +1,53 @@ +\section{The \texttt{SasView\_lamellar\_stack\_caille} McXtrace Component} +SasView lamellar\_stack\_caille model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_lamellar\_stack\_caille component, generated from lamellar\_stack\_caille.c in sasmodels. + +Example: SasView\_lamellar\_stack\_caille(thickness, Nlayers, d\_spacing, Caille\_parameter, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_thickness=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +thickness & \AA{} & ([0, inf]) sheet thickness. & 30.0 \\ +Nlayers & & ([1, inf]) Number of layers. & 20 \\ +d\_spacing & \AA{} & ([0.0, inf]) lamellar d-spacing of Caille S(Q). & 400.0 \\ +Caille\_parameter & 1/\AA{}$^{2}$ & ([0.0, 0.8]) Caille parameter. & 0.1 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) layer scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_lamellar\_stack\_caille.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_lamellar_stack_caille_static.tex}{\input{sasmodels/SasView_lamellar_stack_caille_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_stack_paracrystal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_stack_paracrystal.tex new file mode 100644 index 0000000000..0ad278c372 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_lamellar_stack_paracrystal.tex @@ -0,0 +1,53 @@ +\section{The \texttt{SasView\_lamellar\_stack\_paracrystal} McXtrace Component} +SasView lamellar\_stack\_paracrystal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_lamellar\_stack\_paracrystal component, generated from lamellar\_stack\_paracrystal.c in sasmodels. + +Example: SasView\_lamellar\_stack\_paracrystal(thickness, Nlayers, d\_spacing, sigma\_d, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_thickness=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +thickness & \AA{} & ([0, inf]) sheet thickness. & 33.0 \\ +Nlayers & & ([1, inf]) Number of layers. & 20 \\ +d\_spacing & \AA{} & ([0.0, inf]) lamellar spacing of paracrystal stack. & 250.0 \\ +sigma\_d & \AA{} & ([0.0, inf]) Sigma (polydispersity) of the lamellar spacing. & 0.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) layer scattering length density. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6.34 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_lamellar\_stack\_paracrystal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_lamellar_stack_paracrystal_static.tex}{\input{sasmodels/SasView_lamellar_stack_paracrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_line.tex b/docs/manuals/mcxtrace/sasmodels/SasView_line.tex new file mode 100644 index 0000000000..48504f972f --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_line.tex @@ -0,0 +1,48 @@ +\section{The \texttt{SasView\_line} McXtrace Component} +SasView line model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_line component, generated from line.c in sasmodels. + +Example: SasView\_line(intercept, slope, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +intercept & 1/cm & ([-inf, inf]) intercept in linear model. & 1.0 \\ +slope & \AA{}/cm & ([-inf, inf]) slope in linear model. & 1.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_line.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_line_static.tex}{\input{sasmodels/SasView_line_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_linear_pearls.tex b/docs/manuals/mcxtrace/sasmodels/SasView_linear_pearls.tex new file mode 100644 index 0000000000..7d0b314bc6 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_linear_pearls.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_linear\_pearls} McXtrace Component} +SasView linear\_pearls model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_linear\_pearls component, generated from linear\_pearls.c in sasmodels. + +Example: SasView\_linear\_pearls(radius, edge\_sep, num\_pearls, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Radius of the pearls. & 80.0 \\ +edge\_sep & \AA{} & ([0, inf]) Length of the string segment - surface to surface. & 350.0 \\ +num\_pearls & & ([1, inf]) Number of the pearls. & 3.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) SLD of the pearl spheres. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) SLD of the solvent. & 6.3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_linear\_pearls.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_linear_pearls_static.tex}{\input{sasmodels/SasView_linear_pearls_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_lorentz.tex b/docs/manuals/mcxtrace/sasmodels/SasView_lorentz.tex new file mode 100644 index 0000000000..462c8290a7 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_lorentz.tex @@ -0,0 +1,48 @@ +\section{The \texttt{SasView\_lorentz} McXtrace Component} +SasView lorentz model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_lorentz component, generated from lorentz.c in sasmodels. + +Example: SasView\_lorentz(cor\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_cor\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +cor\_length & \AA{} & ([0, inf]) Screening length. & 50.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_cor\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_lorentz.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_lorentz_static.tex}{\input{sasmodels/SasView_lorentz_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_mass_fractal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_mass_fractal.tex new file mode 100644 index 0000000000..c5d8718875 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_mass_fractal.tex @@ -0,0 +1,51 @@ +\section{The \texttt{SasView\_mass\_fractal} McXtrace Component} +SasView mass\_fractal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_mass\_fractal component, generated from mass\_fractal.c in sasmodels. + +Example: SasView\_mass\_fractal(radius, fractal\_dim\_mass, cutoff\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_cutoff\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0.0, inf]) Particle radius. & 10.0 \\ +fractal\_dim\_mass & & ([1.0, 6.0]) Mass fractal dimension. & 1.9 \\ +cutoff\_length & \AA{} & ([0.0, inf]) Cut-off length. & 100.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_cutoff\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_mass\_fractal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_mass_fractal_static.tex}{\input{sasmodels/SasView_mass_fractal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_mass_surface_fractal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_mass_surface_fractal.tex new file mode 100644 index 0000000000..ba6d746adb --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_mass_surface_fractal.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_mass\_surface\_fractal} McXtrace Component} +SasView mass\_surface\_fractal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_mass\_surface\_fractal component, generated from mass\_surface\_fractal.c in sasmodels. + +Example: SasView\_mass\_surface\_fractal(fractal\_dim\_mass, fractal\_dim\_surf, rg\_cluster, rg\_primary, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg\_cluster=0.0, pd\_rg\_primary=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +fractal\_dim\_mass & & ([0.0, 6.0]) Mass fractal dimension. & 1.8 \\ +fractal\_dim\_surf & & ([0.0, 6.0]) Surface fractal dimension. & 2.3 \\ +rg\_cluster & \AA{} & ([0.0, inf]) Cluster radius of gyration. & 4000.0 \\ +rg\_primary & \AA{} & ([0.0, inf]) Primary particle radius of gyration. & 86.7 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_rg\_cluster & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_rg\_primary & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_mass\_surface\_fractal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_mass_surface_fractal_static.tex}{\input{sasmodels/SasView_mass_surface_fractal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_mono_gauss_coil.tex b/docs/manuals/mcxtrace/sasmodels/SasView_mono_gauss_coil.tex new file mode 100644 index 0000000000..f4e6a5d16b --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_mono_gauss_coil.tex @@ -0,0 +1,49 @@ +\section{The \texttt{SasView\_mono\_gauss\_coil} McXtrace Component} +SasView mono\_gauss\_coil model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_mono\_gauss\_coil component, generated from mono\_gauss\_coil.c in sasmodels. + +Example: SasView\_mono\_gauss\_coil(i\_zero, rg, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +i\_zero & 1/cm & ([0.0, inf]) Intensity at q=0. & 70.0 \\ +rg & \AA{} & ([0.0, inf]) Radius of gyration. & 75.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_rg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_mono\_gauss\_coil.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_mono_gauss_coil_static.tex}{\input{sasmodels/SasView_mono_gauss_coil_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_multilayer_vesicle.tex b/docs/manuals/mcxtrace/sasmodels/SasView_multilayer_vesicle.tex new file mode 100644 index 0000000000..6d26967a25 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_multilayer_vesicle.tex @@ -0,0 +1,56 @@ +\section{The \texttt{SasView\_multilayer\_vesicle} McXtrace Component} +SasView multilayer\_vesicle model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_multilayer\_vesicle component, generated from multilayer\_vesicle.c in sasmodels. + +Example: SasView\_multilayer\_vesicle(volfraction, radius, thick\_shell, thick\_solvent, sld\_solvent, sld, n\_shells, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_shell=0.0, pd\_thick\_solvent=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +volfraction & & ([0.0, 1]) volume fraction of vesicles. & 0.05 \\ +radius & \AA{} & ([0.0, inf]) radius of solvent filled core. & 60.0 \\ +thick\_shell & \AA{} & ([0.0, inf]) thickness of one shell. & 10.0 \\ +thick\_solvent & \AA{} & ([0.0, inf]) solvent thickness between shells. & 10.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) solvent scattering length density. & 6.4 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Shell scattering length density. & 0.4 \\ +n\_shells & & ([1.0, inf]) Number of shell plus solvent layer pairs (must be integer). & 2.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_shell & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_solvent & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_multilayer\_vesicle.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_multilayer_vesicle_static.tex}{\input{sasmodels/SasView_multilayer_vesicle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_onion.tex b/docs/manuals/mcxtrace/sasmodels/SasView_onion.tex new file mode 100644 index 0000000000..c19bd15741 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_onion.tex @@ -0,0 +1,31 @@ +\section{The \texttt{SasView\_onion} McXtrace Component} +SasView onion model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_onion component, generated from onion.c in sasmodels. + +Example: SasView\_onion(sld\_core, radius\_core, sld\_solvent, n\_shells, sld\_in[n\_shells], sld\_out[n\_shells], thickness[n\_shells], A[n\_shells], model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_core=0.0, pd\_thickness[n\_shells]=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_onion.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_onion_static.tex}{\input{sasmodels/SasView_onion_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_parallelepiped.tex b/docs/manuals/mcxtrace/sasmodels/SasView_parallelepiped.tex new file mode 100644 index 0000000000..36fb292c97 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_parallelepiped.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_parallelepiped} McXtrace Component} +SasView parallelepiped model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_parallelepiped component, generated from parallelepiped.c in sasmodels. + +Example: SasView\_parallelepiped(sld, sld\_solvent, length\_a, length\_b, length\_c, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_length\_b=0.0, pd\_length\_c=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +length\_b & \AA{} & ([0, inf]) Second side of the parallelepiped. & 75 \\ +length\_c & \AA{} & ([0, inf]) Larger side of the parallelepiped. & 400 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_b & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_c & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_parallelepiped.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_parallelepiped_static.tex}{\input{sasmodels/SasView_parallelepiped_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_parallelepiped_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_parallelepiped_aniso.tex new file mode 100644 index 0000000000..55a9cdc13f --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_parallelepiped_aniso.tex @@ -0,0 +1,60 @@ +\section{The \texttt{SasView\_parallelepiped\_aniso} McXtrace Component} +SasView parallelepiped model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_parallelepiped component, generated from parallelepiped.c in sasmodels. + +Example: SasView\_parallelepiped\_aniso(sld, sld\_solvent, length\_a, length\_b, length\_c, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_length\_b=0.0, pd\_length\_c=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +length\_b & \AA{} & ([0, inf]) Second side of the parallelepiped. & 75 \\ +length\_c & \AA{} & ([0, inf]) Larger side of the parallelepiped. & 400 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +Psi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_b & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_length\_c & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_parallelepiped\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_parallelepiped_aniso_static.tex}{\input{sasmodels/SasView_parallelepiped_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_peak_lorentz.tex b/docs/manuals/mcxtrace/sasmodels/SasView_peak_lorentz.tex new file mode 100644 index 0000000000..def0cedaeb --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_peak_lorentz.tex @@ -0,0 +1,48 @@ +\section{The \texttt{SasView\_peak\_lorentz} McXtrace Component} +SasView peak\_lorentz model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_peak\_lorentz component, generated from peak\_lorentz.c in sasmodels. + +Example: SasView\_peak\_lorentz(peak\_pos, peak\_hwhm, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +peak\_pos & 1/\AA{} & ([-inf, inf]) Peak postion in q. & 0.05 \\ +peak\_hwhm & 1/\AA{} & ([-inf, inf]) HWHM of peak. & 0.005 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_peak\_lorentz.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_peak_lorentz_static.tex}{\input{sasmodels/SasView_peak_lorentz_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_pearl_necklace.tex b/docs/manuals/mcxtrace/sasmodels/SasView_pearl_necklace.tex new file mode 100644 index 0000000000..6450d156f1 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_pearl_necklace.tex @@ -0,0 +1,55 @@ +\section{The \texttt{SasView\_pearl\_necklace} McXtrace Component} +SasView pearl\_necklace model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_pearl\_necklace component, generated from pearl\_necklace.c in sasmodels. + +Example: SasView\_pearl\_necklace(radius, edge\_sep, thick\_string, num\_pearls, sld, sld\_string, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thick\_string=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Mean radius of the chained spheres. & 80.0 \\ +edge\_sep & \AA{} & ([0, inf]) Mean separation of chained particles. & 350.0 \\ +thick\_string & \AA{} & ([0, inf]) Thickness of the chain linkage. & 2.5 \\ +num\_pearls & none & ([1, inf]) Number of pearls in the necklace (must be integer). & 3 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Scattering length density of the chained spheres. & 1.0 \\ +sld\_string & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Scattering length density of the chain linkage. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Scattering length density of the solvent. & 6.3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_string & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_pearl\_necklace.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_pearl_necklace_static.tex}{\input{sasmodels/SasView_pearl_necklace_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_poly_gauss_coil.tex b/docs/manuals/mcxtrace/sasmodels/SasView_poly_gauss_coil.tex new file mode 100644 index 0000000000..7198980926 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_poly_gauss_coil.tex @@ -0,0 +1,50 @@ +\section{The \texttt{SasView\_poly\_gauss\_coil} McXtrace Component} +SasView poly\_gauss\_coil model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_poly\_gauss\_coil component, generated from poly\_gauss\_coil.c in sasmodels. + +Example: SasView\_poly\_gauss\_coil(i\_zero, rg, polydispersity, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +i\_zero & 1/cm & ([0.0, inf]) Intensity at q=0. & 70.0 \\ +rg & \AA{} & ([0.0, inf]) Radius of gyration. & 75.0 \\ +polydispersity & None & ([1.0, inf]) Polymer Mw/Mn. & 2.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_rg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_poly\_gauss\_coil.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_poly_gauss_coil_static.tex}{\input{sasmodels/SasView_poly_gauss_coil_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_polymer_excl_volume.tex b/docs/manuals/mcxtrace/sasmodels/SasView_polymer_excl_volume.tex new file mode 100644 index 0000000000..39655903de --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_polymer_excl_volume.tex @@ -0,0 +1,49 @@ +\section{The \texttt{SasView\_polymer\_excl\_volume} McXtrace Component} +SasView polymer\_excl\_volume model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_polymer\_excl\_volume component, generated from polymer\_excl\_volume.c in sasmodels. + +Example: SasView\_polymer\_excl\_volume(rg, porod\_exp, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +rg & \AA{} & ([0, inf]) Radius of Gyration. & 60.0 \\ +porod\_exp & & ([0, inf]) Porod exponent. & 3.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_rg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_polymer\_excl\_volume.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_polymer_excl_volume_static.tex}{\input{sasmodels/SasView_polymer_excl_volume_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_polymer_micelle.tex b/docs/manuals/mcxtrace/sasmodels/SasView_polymer_micelle.tex new file mode 100644 index 0000000000..f3017b2f16 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_polymer_micelle.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_polymer\_micelle} McXtrace Component} +SasView polymer\_micelle model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_polymer\_micelle component, generated from polymer\_micelle.c in sasmodels. + +Example: SasView\_polymer\_micelle(ndensity, v\_core, v\_corona, sld\_solvent, sld\_core, sld\_corona, radius\_core, rg, d\_penetration, n\_aggreg, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_core=0.0, pd\_rg=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +ndensity & 1e15/cm$^{3}$ & ([0.0, inf]) Number density of micelles. & 8.94 \\ +v\_core & \AA{}$^{3}$ & ([0.0, inf]) Core volume . & 62624.0 \\ +v\_corona & \AA{}$^{3}$ & ([0.0, inf]) Corona volume. & 61940.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Solvent scattering length density. & 6.4 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Core scattering length density. & 0.34 \\ +sld\_corona & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Corona scattering length density. & 0.8 \\ +radius\_core & \AA{} & ([0.0, inf]) Radius of core ( must be \textgreater{}\textgreater{} rg ). & 45.0 \\ +rg & \AA{} & ([0.0, inf]) Radius of gyration of chains in corona. & 20.0 \\ +d\_penetration & & ([-inf, inf]) Factor to mimic non-penetration of Gaussian chains. & 1.0 \\ +n\_aggreg & & ([-inf, inf]) Aggregation number of the micelle. & 6.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_core & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_rg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_polymer\_micelle.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_polymer_micelle_static.tex}{\input{sasmodels/SasView_polymer_micelle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_porod.tex b/docs/manuals/mcxtrace/sasmodels/SasView_porod.tex new file mode 100644 index 0000000000..35ed6d280a --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_porod.tex @@ -0,0 +1,46 @@ +\section{The \texttt{SasView\_porod} McXtrace Component} +SasView porod model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_porod component, generated from porod.c in sasmodels. + +Example: SasView\_porod(, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_porod.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_porod_static.tex}{\input{sasmodels/SasView_porod_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_power_law.tex b/docs/manuals/mcxtrace/sasmodels/SasView_power_law.tex new file mode 100644 index 0000000000..6e994b7544 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_power_law.tex @@ -0,0 +1,47 @@ +\section{The \texttt{SasView\_power\_law} McXtrace Component} +SasView power\_law model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_power\_law component, generated from power\_law.c in sasmodels. + +Example: SasView\_power\_law(power, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +power & & ([-inf, inf]) Power law exponent. & 4.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_power\_law.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_power_law_static.tex}{\input{sasmodels/SasView_power_law_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_pringle.tex b/docs/manuals/mcxtrace/sasmodels/SasView_pringle.tex new file mode 100644 index 0000000000..b3f9dd63d7 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_pringle.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_pringle} McXtrace Component} +SasView pringle model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_pringle component, generated from pringle.c in sasmodels. + +Example: SasView\_pringle(radius, thickness, alpha, beta, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Pringle radius. & 60.0 \\ +thickness & \AA{} & ([0, inf]) Thickness of pringle. & 10.0 \\ +alpha & & ([-inf, inf]) Curvature parameter alpha. & 0.001 \\ +beta & & ([-inf, inf]) Curvature paramter beta. & 0.02 \\ +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Pringle sld. & 1.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent sld. & 6.3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_pringle.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_pringle_static.tex}{\input{sasmodels/SasView_pringle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_raspberry.tex b/docs/manuals/mcxtrace/sasmodels/SasView_raspberry.tex new file mode 100644 index 0000000000..3bba8336ff --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_raspberry.tex @@ -0,0 +1,57 @@ +\section{The \texttt{SasView\_raspberry} McXtrace Component} +SasView raspberry model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_raspberry component, generated from raspberry.c in sasmodels. + +Example: SasView\_raspberry(sld\_lg, sld\_sm, sld\_solvent, volfraction\_lg, volfraction\_sm, surface\_fraction, radius\_lg, radius\_sm, penetration, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_lg=0.0, pd\_radius\_sm=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld\_lg & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) large particle scattering length density. & -0.4 \\ +sld\_sm & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) small particle scattering length density. & 3.5 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) solvent scattering length density. & 6.36 \\ +volfraction\_lg & & ([-inf, inf]) volume fraction of large spheres. & 0.05 \\ +volfraction\_sm & & ([-inf, inf]) volume fraction of small spheres. & 0.005 \\ +surface\_fraction & & ([-inf, inf]) fraction of small spheres at surface. & 0.4 \\ +radius\_lg & \AA{} & ([0, inf]) radius of large spheres. & 5000 \\ +radius\_sm & \AA{} & ([0, inf]) radius of small spheres. & 100 \\ +penetration & \AA{} & ([-1, 1]) fractional penetration depth of small spheres into large sphere. & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_lg & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_sm & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_raspberry.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_raspberry_static.tex}{\input{sasmodels/SasView_raspberry_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_rectangular_prism.tex b/docs/manuals/mcxtrace/sasmodels/SasView_rectangular_prism.tex new file mode 100644 index 0000000000..a0877df4c2 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_rectangular_prism.tex @@ -0,0 +1,50 @@ +\section{The \texttt{SasView\_rectangular\_prism} McXtrace Component} +SasView rectangular\_prism model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} + + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & & & 6.3 \\ +sld\_solvent & & & 1 \\ +length\_a & & & 35 \\ +b2a\_ratio & & & 1 \\ +c2a\_ratio & & & 1 \\ +model\_scale & & & 1.0 \\ +model\_abs & & & 0.0 \\ +xwidth & & & 0.01 \\ +yheight & & & 0.01 \\ +zdepth & & & 0.005 \\ +R & & & 0 \\ +target\_x & & & 0 \\ +target\_y & & & 0 \\ +target\_z & & & 1 \\ +target\_index & & & 1 \\ +focus\_xw & & & 0.5 \\ +focus\_yh & & & 0.5 \\ +focus\_aw & & & 0 \\ +focus\_ah & & & 0 \\ +focus\_r & & & 0 \\ +pd\_length\_a & & & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_rectangular\_prism.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_rectangular_prism_static.tex}{\input{sasmodels/SasView_rectangular_prism_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_rectangular_prism_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_rectangular_prism_aniso.tex new file mode 100644 index 0000000000..038fb0cfd5 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_rectangular_prism_aniso.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_rectangular\_prism\_aniso} McXtrace Component} +SasView rectangular\_prism model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_rectangular\_prism component, generated from rectangular\_prism.c in sasmodels. + +Example: SasView\_rectangular\_prism\_aniso(sld, sld\_solvent, length\_a, b2a\_ratio, c2a\_ratio, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Parallelepiped scattering length density. & 6.3 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Shorter side of the parallelepiped. & 35 \\ +b2a\_ratio & & ([0, inf]) Ratio sides b/a. & 1 \\ +c2a\_ratio & & ([0, inf]) Ratio sides c/a. & 1 \\ +theta & & & 0 \\ +Phi & & & 0 \\ +Psi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_rectangular\_prism\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_rectangular_prism_aniso_static.tex}{\input{sasmodels/SasView_rectangular_prism_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_rpa.tex b/docs/manuals/mcxtrace/sasmodels/SasView_rpa.tex new file mode 100644 index 0000000000..9f57e979f4 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_rpa.tex @@ -0,0 +1,37 @@ +\section{The \texttt{SasView\_rpa} McXtrace Component} +SasView rpa model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_rpa component, generated from rpa.c in sasmodels. + +Example: + +\begin{verbatim} +SasView_rpa(case_num, N[4], Phi[4], v[4], L[4], b[4], K12, K13, K14, K23, K24, K34, +\end{verbatim} + +model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_rpa.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_rpa_static.tex}{\input{sasmodels/SasView_rpa_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_sc_paracrystal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_sc_paracrystal.tex new file mode 100644 index 0000000000..c11468f0e1 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_sc_paracrystal.tex @@ -0,0 +1,52 @@ +\section{The \texttt{SasView\_sc\_paracrystal} McXtrace Component} +SasView sc\_paracrystal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_sc\_paracrystal component, generated from sc\_paracrystal.c in sasmodels. + +Example: SasView\_sc\_paracrystal(dnn, d\_factor, radius, sld, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +dnn & \AA{} & ([0.0, inf]) Nearest neighbor distance. & 220.0 \\ +d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ +radius & \AA{} & ([0.0, inf]) Radius of sphere. & 40.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Sphere scattering length density. & 3.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Solvent scattering length density. & 6.3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_sc\_paracrystal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_sc_paracrystal_static.tex}{\input{sasmodels/SasView_sc_paracrystal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_sc_paracrystal_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_sc_paracrystal_aniso.tex new file mode 100644 index 0000000000..f0ad4a1477 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_sc_paracrystal_aniso.tex @@ -0,0 +1,58 @@ +\section{The \texttt{SasView\_sc\_paracrystal\_aniso} McXtrace Component} +SasView sc\_paracrystal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_sc\_paracrystal component, generated from sc\_paracrystal.c in sasmodels. + +Example: SasView\_sc\_paracrystal\_aniso(dnn, d\_factor, radius, sld, sld\_solvent, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +dnn & \AA{} & ([0.0, inf]) Nearest neighbor distance. & 220.0 \\ +d\_factor & & ([-inf, inf]) Paracrystal distortion factor. & 0.06 \\ +radius & \AA{} & ([0.0, inf]) Radius of sphere. & 40.0 \\ +sld & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Sphere scattering length density. & 3.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([0.0, inf]) Solvent scattering length density. & 6.3 \\ +theta & & & 0 \\ +Phi & & & 0 \\ +Psi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_sc\_paracrystal\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_sc_paracrystal_aniso_static.tex}{\input{sasmodels/SasView_sc_paracrystal_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_sphere.tex b/docs/manuals/mcxtrace/sasmodels/SasView_sphere.tex new file mode 100644 index 0000000000..9007a6267d --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_sphere.tex @@ -0,0 +1,50 @@ +\section{The \texttt{SasView\_sphere} McXtrace Component} +SasView sphere model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_sphere component, generated from sphere.c in sasmodels. + +Example: SasView\_sphere(sld, sld\_solvent, radius, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Layer scattering length density. & 1 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 6 \\ +radius & \AA{} & ([0, inf]) Sphere radius. & 50 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_sphere.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_sphere_static.tex}{\input{sasmodels/SasView_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_spinodal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_spinodal.tex new file mode 100644 index 0000000000..073122811d --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_spinodal.tex @@ -0,0 +1,48 @@ +\section{The \texttt{SasView\_spinodal} McXtrace Component} +SasView spinodal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_spinodal component, generated from spinodal.c in sasmodels. + +Example: SasView\_spinodal(gamma, q\_0, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +gamma & & ([-inf, inf]) Exponent. & 3.0 \\ +q\_0 & 1/\AA{} & ([-inf, inf]) Correlation peak position. & 0.1 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_spinodal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_spinodal_static.tex}{\input{sasmodels/SasView_spinodal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_squarewell.tex b/docs/manuals/mcxtrace/sasmodels/SasView_squarewell.tex new file mode 100644 index 0000000000..cbcd693c8c --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_squarewell.tex @@ -0,0 +1,51 @@ +\section{The \texttt{SasView\_squarewell} McXtrace Component} +SasView squarewell model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_squarewell component, generated from squarewell.c in sasmodels. + +Example: SasView\_squarewell(radius\_effective, volfraction, welldepth, wellwidth, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_effective=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_effective & \AA{} & ([0, inf]) effective radius of hard sphere. & 50.0 \\ +volfraction & & ([0, 0.08]) volume fraction of spheres. & 0.04 \\ +welldepth & kT & ([0.0, 1.5]) depth of well, epsilon. & 1.5 \\ +wellwidth & diameters & ([1.0, inf]) width of well in diameters (=2R) units, must be \textgreater{} 1. & 1.2 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_effective & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_squarewell.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_squarewell_static.tex}{\input{sasmodels/SasView_squarewell_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_stacked_disks.tex b/docs/manuals/mcxtrace/sasmodels/SasView_stacked_disks.tex new file mode 100644 index 0000000000..614d907a90 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_stacked_disks.tex @@ -0,0 +1,57 @@ +\section{The \texttt{SasView\_stacked\_disks} McXtrace Component} +SasView stacked\_disks model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_stacked\_disks component, generated from stacked\_disks.c in sasmodels. + +Example: SasView\_stacked\_disks(thick\_core, thick\_layer, radius, n\_stacking, sigma\_d, sld\_core, sld\_layer, sld\_solvent, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_thick\_core=0.0, pd\_thick\_layer=0.0, pd\_radius=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +thick\_core & \AA{} & ([0, inf]) Thickness of the core disk. & 10.0 \\ +thick\_layer & \AA{} & ([0, inf]) Thickness of layer each side of core. & 10.0 \\ +radius & \AA{} & ([0, inf]) Radius of the stacked disk. & 15.0 \\ +n\_stacking & & ([1, inf]) Number of stacked layer/core/layer disks. & 1.0 \\ +sigma\_d & \AA{} & ([0, inf]) Sigma of nearest neighbor spacing. & 0 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Core scattering length density. & 4 \\ +sld\_layer & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Layer scattering length density. & 0.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 5.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_thick\_core & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_layer & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_stacked\_disks.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_stacked_disks_static.tex}{\input{sasmodels/SasView_stacked_disks_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_stacked_disks_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_stacked_disks_aniso.tex new file mode 100644 index 0000000000..cfc8fa0ac6 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_stacked_disks_aniso.tex @@ -0,0 +1,61 @@ +\section{The \texttt{SasView\_stacked\_disks\_aniso} McXtrace Component} +SasView stacked\_disks model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_stacked\_disks component, generated from stacked\_disks.c in sasmodels. + +Example: SasView\_stacked\_disks\_aniso(thick\_core, thick\_layer, radius, n\_stacking, sigma\_d, sld\_core, sld\_layer, sld\_solvent, theta, Phi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_thick\_core=0.0, pd\_thick\_layer=0.0, pd\_radius=0.0, pd\_theta=0.0, pd\_Phi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +thick\_core & \AA{} & ([0, inf]) Thickness of the core disk. & 10.0 \\ +thick\_layer & \AA{} & ([0, inf]) Thickness of layer each side of core. & 10.0 \\ +radius & \AA{} & ([0, inf]) Radius of the stacked disk. & 15.0 \\ +n\_stacking & & ([1, inf]) Number of stacked layer/core/layer disks. & 1.0 \\ +sigma\_d & \AA{} & ([0, inf]) Sigma of nearest neighbor spacing. & 0 \\ +sld\_core & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Core scattering length density. & 4 \\ +sld\_layer & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Layer scattering length density. & 0.0 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 5.0 \\ +theta & & & 0 \\ +Phi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_thick\_core & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thick\_layer & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_stacked\_disks\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_stacked_disks_aniso_static.tex}{\input{sasmodels/SasView_stacked_disks_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_star_polymer.tex b/docs/manuals/mcxtrace/sasmodels/SasView_star_polymer.tex new file mode 100644 index 0000000000..e799731be9 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_star_polymer.tex @@ -0,0 +1,49 @@ +\section{The \texttt{SasView\_star\_polymer} McXtrace Component} +SasView star\_polymer model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_star\_polymer component, generated from star\_polymer.c in sasmodels. + +Example: SasView\_star\_polymer(rg\_squared, arms, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_rg\_squared=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +rg\_squared & \AA{}$^{2}$ & ([0.0, inf]) Ensemble radius of gyration SQUARED of the full polymer. & 100.0 \\ +arms & & ([1.0, 6.0]) Number of arms in the model. & 3 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_rg\_squared & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_star\_polymer.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_star_polymer_static.tex}{\input{sasmodels/SasView_star_polymer_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_stickyhardsphere.tex b/docs/manuals/mcxtrace/sasmodels/SasView_stickyhardsphere.tex new file mode 100644 index 0000000000..f0c66f6a88 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_stickyhardsphere.tex @@ -0,0 +1,51 @@ +\section{The \texttt{SasView\_stickyhardsphere} McXtrace Component} +SasView stickyhardsphere model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_stickyhardsphere component, generated from stickyhardsphere.c in sasmodels. + +Example: SasView\_stickyhardsphere(radius\_effective, volfraction, perturb, stickiness, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_effective=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius\_effective & \AA{} & ([0, inf]) effective radius of hard sphere. & 50.0 \\ +volfraction & & ([0, 0.74]) volume fraction of hard spheres. & 0.2 \\ +perturb & & ([0.01, 0.1]) perturbation parameter, tau. & 0.05 \\ +stickiness & & ([-inf, inf]) stickiness, epsilon. & 0.2 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_effective & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_stickyhardsphere.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_stickyhardsphere_static.tex}{\input{sasmodels/SasView_stickyhardsphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_superball.tex b/docs/manuals/mcxtrace/sasmodels/SasView_superball.tex new file mode 100644 index 0000000000..2265b4eb83 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_superball.tex @@ -0,0 +1,51 @@ +\section{The \texttt{SasView\_superball} McXtrace Component} +SasView superball model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_superball component, generated from superball.c in sasmodels. + +Example: SasView\_superball(sld, sld\_solvent, length\_a, exponent\_p, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Superball scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Cube edge length of the superball. & 50 \\ +exponent\_p & & ([0, inf]) Exponent describing the roundness of the superball. & 2.5 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_superball.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_superball_static.tex}{\input{sasmodels/SasView_superball_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_superball_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_superball_aniso.tex new file mode 100644 index 0000000000..b9855b7b52 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_superball_aniso.tex @@ -0,0 +1,57 @@ +\section{The \texttt{SasView\_superball\_aniso} McXtrace Component} +SasView superball model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_superball component, generated from superball.c in sasmodels. + +Example: SasView\_superball\_aniso(sld, sld\_solvent, length\_a, exponent\_p, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_length\_a=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Superball scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +length\_a & \AA{} & ([0, inf]) Cube edge length of the superball. & 50 \\ +exponent\_p & & ([0, inf]) Exponent describing the roundness of the superball. & 2.5 \\ +theta & & & 0 \\ +Phi & & & 0 \\ +Psi & & & 0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_length\_a & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_superball\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_superball_aniso_static.tex}{\input{sasmodels/SasView_superball_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_surface_fractal.tex b/docs/manuals/mcxtrace/sasmodels/SasView_surface_fractal.tex new file mode 100644 index 0000000000..54d7d81f9c --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_surface_fractal.tex @@ -0,0 +1,51 @@ +\section{The \texttt{SasView\_surface\_fractal} McXtrace Component} +SasView surface\_fractal model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_surface\_fractal component, generated from surface\_fractal.c in sasmodels. + +Example: SasView\_surface\_fractal(radius, fractal\_dim\_surf, cutoff\_length, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_cutoff\_length=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & \AA{} & ([0, inf]) Particle radius. & 10.0 \\ +fractal\_dim\_surf & & ([1, 3]) Surface fractal dimension. & 2.0 \\ +cutoff\_length & \AA{} & ([0.0, inf]) Cut-off Length. & 500.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_cutoff\_length & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_surface\_fractal.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_surface_fractal_static.tex}{\input{sasmodels/SasView_surface_fractal_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_teubner_strey.tex b/docs/manuals/mcxtrace/sasmodels/SasView_teubner_strey.tex new file mode 100644 index 0000000000..143eea4687 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_teubner_strey.tex @@ -0,0 +1,51 @@ +\section{The \texttt{SasView\_teubner\_strey} McXtrace Component} +SasView teubner\_strey model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_teubner\_strey component, generated from teubner\_strey.c in sasmodels. + +Example: SasView\_teubner\_strey(volfraction\_a, sld\_a, sld\_b, d, xi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +volfraction\_a & & ([0, 1.0]) Volume fraction of phase a. & 0.5 \\ +sld\_a & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) SLD of phase a. & 0.3 \\ +sld\_b & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) SLD of phase b. & 6.3 \\ +d & \AA{} & ([0, inf]) Domain size (periodicity). & 100.0 \\ +xi & \AA{} & ([0, inf]) Correlation length. & 30.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_teubner\_strey.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_teubner_strey_static.tex}{\input{sasmodels/SasView_teubner_strey_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_triaxial_ellipsoid.tex b/docs/manuals/mcxtrace/sasmodels/SasView_triaxial_ellipsoid.tex new file mode 100644 index 0000000000..5e11947bf4 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_triaxial_ellipsoid.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_triaxial\_ellipsoid} McXtrace Component} +SasView triaxial\_ellipsoid model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_triaxial\_ellipsoid component, generated from triaxial\_ellipsoid.c in sasmodels. + +Example: SasView\_triaxial\_ellipsoid(sld, sld\_solvent, radius\_equat\_minor, radius\_equat\_major, radius\_polar, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_equat\_minor=0.0, pd\_radius\_equat\_major=0.0, pd\_radius\_polar=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_equat\_minor & \AA{} & ([0, inf]) Minor equatorial radius, Ra. & 20 \\ +radius\_equat\_major & \AA{} & ([0, inf]) Major equatorial radius, Rb. & 400 \\ +radius\_polar & \AA{} & ([0, inf]) Polar radius, Rc. & 10 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_equat\_minor & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_equat\_major & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_polar & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_triaxial\_ellipsoid.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_triaxial_ellipsoid_static.tex}{\input{sasmodels/SasView_triaxial_ellipsoid_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_triaxial_ellipsoid_aniso.tex b/docs/manuals/mcxtrace/sasmodels/SasView_triaxial_ellipsoid_aniso.tex new file mode 100644 index 0000000000..b0c4c571fd --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_triaxial_ellipsoid_aniso.tex @@ -0,0 +1,60 @@ +\section{The \texttt{SasView\_triaxial\_ellipsoid\_aniso} McXtrace Component} +SasView triaxial\_ellipsoid model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_triaxial\_ellipsoid component, generated from triaxial\_ellipsoid.c in sasmodels. + +Example: SasView\_triaxial\_ellipsoid\_aniso(sld, sld\_solvent, radius\_equat\_minor, radius\_equat\_major, radius\_polar, theta, Phi, Psi, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius\_equat\_minor=0.0, pd\_radius\_equat\_major=0.0, pd\_radius\_polar=0.0, pd\_theta=0.0, pd\_Phi=0.0, pd\_Psi=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Ellipsoid scattering length density. & 4 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) Solvent scattering length density. & 1 \\ +radius\_equat\_minor & \AA{} & ([0, inf]) Minor equatorial radius, Ra. & 20 \\ +radius\_equat\_major & \AA{} & ([0, inf]) Major equatorial radius, Rb. & 400 \\ +radius\_polar & \AA{} & ([0, inf]) Polar radius, Rc. & 10 \\ +theta & & & 60 \\ +Phi & & & 60 \\ +Psi & & & 60 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius\_equat\_minor & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_equat\_major & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_radius\_polar & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_theta & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Phi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_Psi & & (0,360) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_triaxial\_ellipsoid\_aniso.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_triaxial_ellipsoid_aniso_static.tex}{\input{sasmodels/SasView_triaxial_ellipsoid_aniso_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_two_lorentzian.tex b/docs/manuals/mcxtrace/sasmodels/SasView_two_lorentzian.tex new file mode 100644 index 0000000000..79feed1aea --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_two_lorentzian.tex @@ -0,0 +1,54 @@ +\section{The \texttt{SasView\_two\_lorentzian} McXtrace Component} +SasView two\_lorentzian model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_two\_lorentzian component, generated from two\_lorentzian.c in sasmodels. + +Example: SasView\_two\_lorentzian(lorentz\_scale\_1, lorentz\_length\_1, lorentz\_exp\_1, lorentz\_scale\_2, lorentz\_length\_2, lorentz\_exp\_2, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_lorentz\_length\_1=0.0, pd\_lorentz\_length\_2=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +lorentz\_scale\_1 & & ([-inf, inf]) First power law scale factor. & 10.0 \\ +lorentz\_length\_1 & \AA{} & ([-inf, inf]) First Lorentzian screening length. & 100.0 \\ +lorentz\_exp\_1 & & ([-inf, inf]) First exponent of power law. & 3.0 \\ +lorentz\_scale\_2 & & ([-inf, inf]) Second scale factor for broad Lorentzian peak. & 1.0 \\ +lorentz\_length\_2 & \AA{} & ([-inf, inf]) Second Lorentzian screening length. & 10.0 \\ +lorentz\_exp\_2 & & ([-inf, inf]) Second exponent of power law. & 2.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_lorentz\_length\_1 & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_lorentz\_length\_2 & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_two\_lorentzian.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_two_lorentzian_static.tex}{\input{sasmodels/SasView_two_lorentzian_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_two_power_law.tex b/docs/manuals/mcxtrace/sasmodels/SasView_two_power_law.tex new file mode 100644 index 0000000000..2594d0308d --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_two_power_law.tex @@ -0,0 +1,50 @@ +\section{The \texttt{SasView\_two\_power\_law} McXtrace Component} +SasView two\_power\_law model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_two\_power\_law component, generated from two\_power\_law.c in sasmodels. + +Example: SasView\_two\_power\_law(coefficent\_1, crossover, power\_1, power\_2, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, ) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +coefficent\_1 & & ([-inf, inf]) coefficent A in low Q region. & 1.0 \\ +crossover & 1/\AA{} & ([0, inf]) crossover location. & 0.04 \\ +power\_1 & & ([0, inf]) power law exponent at low Q. & 1.0 \\ +power\_2 & & ([0, inf]) power law exponent at high Q. & 4.0 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_two\_power\_law.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_two_power_law_static.tex}{\input{sasmodels/SasView_two_power_law_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sasmodels/SasView_vesicle.tex b/docs/manuals/mcxtrace/sasmodels/SasView_vesicle.tex new file mode 100644 index 0000000000..16d0da2630 --- /dev/null +++ b/docs/manuals/mcxtrace/sasmodels/SasView_vesicle.tex @@ -0,0 +1,53 @@ +\section{The \texttt{SasView\_vesicle} McXtrace Component} +SasView vesicle model component as sample description. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jose Robledo + \item \textbf{Origin:} FZJ / DTU / ESS DMSC + \item \textbf{Date:} +\end{itemize} + +\subsection*{Description} +SasView\_vesicle component, generated from vesicle.c in sasmodels. + +Example: SasView\_vesicle(sld, sld\_solvent, volfraction, radius, thickness, model\_scale=1.0, model\_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, int target\_index=1, target\_x=0, target\_y=0, target\_z=1, focus\_xw=0.5, focus\_yh=0.5, focus\_aw=0, focus\_ah=0, focus\_r=0, pd\_radius=0.0, pd\_thickness=0.0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sld & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) vesicle shell scattering length density. & 0.5 \\ +sld\_solvent & 1e-6/\AA{}$^{2}$ & ([-inf, inf]) solvent scattering length density. & 6.36 \\ +volfraction & & ([0, 1.0]) volume fraction of shell. & 0.05 \\ +radius & \AA{} & ([0, inf]) vesicle core radius. & 100 \\ +thickness & \AA{} & ([0, inf]) vesicle shell thickness. & 30 \\ +model\_scale & & Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. & 1.0 \\ +model\_abs & & Absorption cross section density at 2200 m/s. & 0.0 \\ +xwidth & m & ([-inf, inf]) Horiz. dimension of sample, as a width. & 0.01 \\ +yheight & m & ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box & 0.01 \\ +zdepth & m & ([-inf, inf]) depth of sample & 0.005 \\ +R & m & Outer radius of sample in (x,z) plane for cylinder/sphere. & 0 \\ +target\_x & m & relative focus target position. & 0 \\ +target\_y & m & relative focus target position. & 0 \\ +target\_z & m & relative focus target position. & 1 \\ +target\_index & & Relative index of component to focus at, e.g. next is +1. & 1 \\ +focus\_xw & m & horiz. dimension of a rectangular area. & 0.5 \\ +focus\_yh & m & , vert. dimension of a rectangular area. & 0.5 \\ +focus\_aw & deg & , horiz. angular dimension of a rectangular area. & 0 \\ +focus\_ah & deg & , vert. angular dimension of a rectangular area. & 0 \\ +focus\_r & m & case of circular focusing, focusing radius. & 0 \\ +pd\_radius & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. & 0.0 \\ +pd\_thickness & & (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable & 0.0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{SasView\_vesicle.comp}. +\end{itemize} +\IfFileExists{sasmodels/SasView_vesicle_static.tex}{\input{sasmodels/SasView_vesicle_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Bending_magnet.tex b/docs/manuals/mcxtrace/sources/Bending_magnet.tex new file mode 100644 index 0000000000..358b8fd10b --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Bending_magnet.tex @@ -0,0 +1,51 @@ +\section{The \texttt{Bending\_magnet} McXtrace Component} +Model of a bending magnet source + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B. Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} May, 2013. +\end{itemize} + +\subsection*{Description} +A source model based on the derivation from B.D. Patterson, Am. J. Phys. 79, 1046 (2011); doi: 10.1119/1.3614033 + +Example: Bending\_magnet( + +\begin{verbatim} +E0 = 14, dE = 7, Ee = 2.75, +Ie = 0.5, B = 1.72, sigey=9.3e-6, sigex=215.7e-6) +\end{verbatim} + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +E0 & keV & Center of emitted energy spectrum (overrides lambda0) & 0 \\ +dE & keV & Half-width of emitted energy spectrum & 0 \\ +lambda0 & \AA{} & Center of emitted wavelength spectrum & 0 \\ +dlambda & \AA{} & Half-width of emitted wavelength spectrum & 0 \\ +phase & rad & Initial phase of radiation. & 0 \\ +randomphase & 0/1 & If !=0 phase will be random (I.e. the emitted radiation is completely incoherent) & 1 \\ +Ee & GeV & Storage ring electron energy (typically a few GeV) & 2.4 \\ +Ie & A & Ring current & 0.4 \\ +B & T & Magnet field strength & 1.6 \\ +sigey & m & Electron ring beam size in vertical plane (rms) & 0 \\ +sigex & m & Electron ring beam size in horizontal plane (rms) & 0 \\ +focus\_xw & m & Width of target window & 0 \\ +focus\_yh & m & Height of traget window & 0 \\ +dist & m & Distance from source plane to target window along the optical axis & 1 \\ +gauss\_t & 0/1 & If 0 the target window will be sampled uniformly and the weight adjusted accordingly, otherwise we will use a gaussian sampling scheme & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Bending\_magnet.comp}. +\end{itemize} +\IfFileExists{sources/Bending_magnet_static.tex}{\input{sources/Bending_magnet_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_div.tex b/docs/manuals/mcxtrace/sources/Source_div.tex new file mode 100644 index 0000000000..dbb5052947 --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_div.tex @@ -0,0 +1,53 @@ +\section{The \texttt{Source\_div} McXtrace Component} +Release: McXtrace 0.1 + +X-ray source with Gaussian or uniform divergence + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} November 11, 2009 +\end{itemize} + +\subsection*{Description} +A flat rectangular surface source with uniform or Gaussian divergence profile and focussing. If the parametere gauss is not set (the default) the divergence profile is flat in the range [-focus\_ax,focus\_ay]. If gauss is set, the focux\_ax,focus\_ay is considered the standard deviation of the gaussian profile. Currently focussing is only active for flat profile. The "focus window" is defined by focus\_xw,focus\_yh and dist. The spectral intensity profile is uniformly distributed in the energy interval defined by e0+-dE/2 or by wavelength lambda0+-dlambda/2 + +Example: Source\_div(xwidth=0.1, yheight=0.1, focus\_aw=2, focus\_ah=2, E0=14, dE=2, gauss=0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +spectrum\_file & string & File from which to read the spectral intensity profile & "NULL" \\ +xwidth & m & Width of source. & 0 \\ +yheight & m & Height of source. & 0 \\ +dist & m & Downstream distance to place sampling target window & 0 \\ +focus\_xw & m & Width of sampling window & 0 \\ +focus\_yh & m & Height of sampling window & 0 \\ +focus\_aw & rad & Standard deviation (Gaussian) or maximal (uniform) horz. width divergence. & 0 \\ +focus\_ah & rad & Standard deviation (Gaussian) or maximal (uniform) vert. height divergence. & 0 \\ +focus\_ar & rad & Standard deviation (Gaussian) or maximal (uniform) radial divergence. & 0 \\ +radius & m & Radius of circular source & 0 \\ +E0 & keV & Mean energy of X-rays. & 0 \\ +dE & keV & Energy half spread of X-rays. If gauss==0 dE is the half-spread, i.e. E\textbackslash{}in[E0-dE,E0+dE], if gauss!=0 it's interpreted as the standard dev. & 0 \\ +lambda0 & \AA{} & Mean wavelength of X-rays (only relevant for E0=0). & 0 \\ +dlambda & \AA{} & Wavelength half spread of X-rays. & 0 \\ +flux & 1/(s * mm**2 *mrad**2 * energy unit) & flux per energy unit, \AA{} or keV. & 0 \\ +gauss & 1 & Criterion: 0: uniform, 1: Gaussian distribution of energy/wavelength. & 0 \\ +gauss\_a & 1 & Criterion: 0: uniform, 1: Gaussian divergence distribution. & 0 \\ +randomphase & 1 & If !=0 the photon phase is chosen randomly. & 1 \\ +phase & 1 & Value of the photon phase (if randomphase==0). & 0 \\ +verbose & 0/1 & Show more information & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_div.comp}. +\end{itemize} +\IfFileExists{sources/Source_div_static.tex}{\input{sources/Source_div_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_div_quasi.tex b/docs/manuals/mcxtrace/sources/Source_div_quasi.tex new file mode 100644 index 0000000000..19f1ab68f5 --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_div_quasi.tex @@ -0,0 +1,53 @@ +\section{The \texttt{Source\_div\_quasi} McXtrace Component} +Release: McXtrace 1.6 + +Quasi-stochastic X-ray source with Gaussian or uniform divergence + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Carlsen and Erik B Knudsen (erkn@fysik.dtu.dk) + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} Apr 21 +\end{itemize} + +\subsection*{Description} +A flat rectangular surface source with uniform or Gaussian divergence profile and focussing. If the parametere gauss is not set (the default) the divergence profile is flat in the range [-focus\_ax,focus\_ay]. If gauss is set, the focux\_ax,focus\_ay is considered the standard deviation of the gaussian profile. Currently focussing is only active for flat profile. The "focus window" is defined by focus\_xw,focus\_yh and dist. The spectral intensity profile is uniformly distributed in the energy interval defined by e0+-dE/2 or by wavelength lambda0+-dlambda/2 + +The phase space sapnned by the generated X-rays is sampled by means of Halton-sequences, instead of regular pseudo random numbers. This ensures that samples are evenly distributed within the phase space region of interest. + +Example: Source\_div\_quasi(xwidth=0.1, yheight=0.1, focus\_aw=2, focus\_ah=2, E0=14, dE=2, gauss=0) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +spectrum\_file & string & File from which to read the spectral intensity profile & "" \\ +xwidth & m & Width of source & 0 \\ +yheight & m & Height of source & 0 \\ +focus\_xw & m & Width of sampling window & 0 \\ +focus\_yh & m & Height of sampling window & 0 \\ +dist & m & Downstream distance to place sampling target window & 0 \\ +focus\_aw & rad & Std. dev. (Gaussian) or maximal (uniform) horz. width divergence. focus\_xw overrrides if it is more restrictive. & 0 \\ +focus\_ah & rad & Std. dev. (Gaussian) or maximal (uniform) vert. height divergence. focus\_yh overrrides if it is more restrictive. & 0 \\ +E0 & keV & Mean energy of X-rays. & 0 \\ +dE & keV & Energy spread of X-rays. & 0 \\ +lambda0 & \AA{} & Mean wavelength of X-rays (only relevant for E0=0) & 0 \\ +dlambda & \AA{} & Wavelength half spread of X-rays. & 0 \\ +flux & 1/(s*cm**2*st*energy unit) & Flux per energy unit, \AA{} or meV & 0 \\ +gauss & 1 & Criterion: 0: uniform, 1: Gaussian distribution of energy/wavelength & 0 \\ +gauss\_a & 1 & Criterion: 0: uniform, 1: Gaussian divergence distribution & 0 \\ +randomphase & 0/1 & When=1, the X-ray phase is randomised & 1 \\ +phase & rad & Set to finite value to define X-ray phase (0:2 pi) & 0 \\ +verbose & 0/1 & Generate more output on the console. & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_div\_quasi.comp}. +\end{itemize} +\IfFileExists{sources/Source_div_quasi_static.tex}{\input{sources/Source_div_quasi_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_flat.tex b/docs/manuals/mcxtrace/sources/Source_flat.tex new file mode 100644 index 0000000000..490fca9bad --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_flat.tex @@ -0,0 +1,50 @@ +\section{The \texttt{Source\_flat} McXtrace Component} +Release: McXtrace 0.1\_alpha + +A flat rectangular or circular surface emitting x-rays + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} September 25, 2009 +\end{itemize} + +\subsection*{Description} +A circular or rectangular xray source. Spectrum may be either gaussian or uniform around a central wavelength/energy or read from a datafile. Xrays are considered emitted uniformly into 4pi, but a square target retricts the beam to that window and scales the beam intensity accordingly. If an input spectrum datafile (spectrum\_file) is not specified, the beam is restricted to emit photons between E0+-dE keV, or lambda0+-dlambda \AA{}, whichever is given. The input spectrum file should be formatted such that x-ray energy/wavelength is in the first column and the intensity in the second. Any preceding lines starting with \# are considered part of the file header. If a datafile is given, a nonzero E0 value indicates that is is parametrized by energy (in keV) as opposed to wavelength (in \AA{}). Wavelength is the default. Flux is set in the unit photons/s + +Example: Source\_flat(xwidth=1e-3,yheight=1e-3, focus\_xw=0.5e-2, focus\_yh=0.45e-2,dist=1, E0=E0, dE=DE) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +radius & m & Radius of circle in (x,y,0) plane where x-rays are generated. & 0 \\ +yheight & m & Height of rectangle in (x,y,0) plane where x-rays are generated. & 0 \\ +xwidth & m & Width of rectangle in (x,y,0) plane where x-rays are generated. Overrides xmin and xmax. & 0 \\ +xmin & m & Lower bound of x-interval where photons are generated. & 0 \\ +xmax & m & Upper bound of x-interval where photons are generated. & 0 \\ +dist & m & Distance to target along z axis. & 0 \\ +focus\_xw & m & Width of target & .045 \\ +focus\_yh & m & Height of target & .12 \\ +E0 & keV & Mean energy of xrays. & 0 \\ +dE & keV & Energy half spread of x-rays (flat or gaussian sigma). & 0 \\ +lambda0 & \AA{} & Mean wavelength of x-rays. & 0 \\ +dlambda & \AA{} & Wavelength half spread of x-rays. & 0 \\ +flux & pht/s & Total flux radiated from the source & 0 \\ +gauss & 1 & Gaussian (1) or Flat (0) energy/wavelength distribution & 0 \\ +randomphase & & If nonzero, the phase of the emotted photon is random, i.e. source is fully incoherent. otherwise the value of phase is used. & 1 \\ +phase & rad & Set phase to something given. & 0 \\ +spectrum\_file & string & Filename for optional spectrum-file & "" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_flat.comp}. +\end{itemize} +\IfFileExists{sources/Source_flat_static.tex}{\input{sources/Source_flat_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_gaussian.tex b/docs/manuals/mcxtrace/sources/Source_gaussian.tex new file mode 100644 index 0000000000..0c2d4362db --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_gaussian.tex @@ -0,0 +1,48 @@ +\section{The \texttt{Source\_gaussian} McXtrace Component} +Gaussian cross-section source + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Jana Baltser \& Erik Knudsen + \item \textbf{Origin:} NBI + \item \textbf{Date:} April, 2011. +\end{itemize} + +\subsection*{Description} +A simple source model emitting photons from a gaussian distribution in the X-Y plane with the specified standard deviations and divergence. A square target centered on the beam (Z-axis) may be used to restrict the beam to that aperture. If no target aperture is given the full gaussian cross-section is used. Further, the beam is restricted to emit photons between E0+-dE keV, or lambda0+-dlambda, whichever is given, if a spectrum\_file is not specified, in which case the contents of the file dictates the emitted spectrum. + +Example: Source\_gaussian(sig\_x=10e-6,sig\_y=10e-6,dist=15,sigPr\_x=9e-6, sigPr\_y=9e-6,E0=12.5, dE=0.1) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +spectrum\_file & & File from which to read the spectral intensity profile & "NULL" \\ +sig\_x & m & Horizontal standard deviation of source (rms source size). & 1 \\ +sig\_y & m & Vertical standard deviation of source (rms source size). & 0 \\ +sigPr\_x & rad & Angular horizontal divergence & 0 \\ +sigPr\_y & rad & Angular vertical divergence & 0 \\ +flux & & Scaling factor to set the total emitted unrestricted flux. & 1 \\ +brilliance & & Unit in spectrum\_file is Brilliance - apply corrections to get to raw flux. & 0 \\ +dist & m & Distance from source plane to sampling window. & 1 \\ +gauss & 0/1 & Gaussian (1) or uniform (0) spectrum profile. & 0 \\ +focus\_xw & m & Width of sampling window dist m downstream from source to allow focused sampling. & 0 \\ +focus\_yh & m & Height of sampling window dist m downstream from source to allow focused sampling. & 0 \\ +E0 & keV & Centre of emitted energy spectrum (overrides spectrum\_file) & 0 \\ +dE & kev & Half-width (or std. dev.) of emitted energy spectrum. & 0 \\ +lambda0 & \AA{} & Centre of emitted wavelength spectrum. & 0 \\ +dlambda & \AA{} & Half-width (or std. dev.) of emitted wavelength spectrum. & -1 \\ +phase & rad & The initial phase of the photons. & 0 \\ +randomphase & rad & If nonzero phase is random (incoherent radiation), otherwise it is set to the value of phase & 1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_gaussian.comp}. +\end{itemize} +\IfFileExists{sources/Source_gaussian_static.tex}{\input{sources/Source_gaussian_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_genesis13.tex b/docs/manuals/mcxtrace/sources/Source_genesis13.tex new file mode 100644 index 0000000000..890d6e8e11 --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_genesis13.tex @@ -0,0 +1,46 @@ +\section{The \texttt{Source\_genesis13} McXtrace Component} +Release: McXtrace 1.2 + +Interface source for importing GENESIS 1.3 generated X-ray pulses into McXtrace + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} Aug. 10th, 2014 +\end{itemize} + +\subsection*{Description} +This source model reads the dumped radiation field output from GENESIS 1.3 and samples it to be used in McXtrace. + +Example: Source\_pt(dist=1,focus\_xw=0.1,focus\_yh=0.1, lamda=0.231, dlambda=0.002) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +gridpoints & int & Number of mesh points along 1 axis. & 101 \\ +fname & string & Filename of main output file of GENESIS 1.3. & "template.out" \\ +focus\_xw & m & Width of target. & 0 \\ +focus\_yh & m & Height of target. & 0 \\ +dist & m & Distance to target along z axis. & 1 \\ +E0 & keV & Mean energy of xrays. & 0 \\ +dE & kev & Half-width (or std. dev.) of emitted energy spectrum. & 0 \\ +meshsize & m & Spacing between mesh points (equal in x and y). & 1e-5 \\ +nslices & int & Number of slices simulated & 102 \\ +s0 & m & Back end of pulse time sampling windows scaled by c\textasciicircum{}-1. & -2e-3 \\ +s1 & m & Front end of pulse time sampling window scaled by c\textasciicircum{}-1. & 2e-3 \\ +flux & 1 & Flux-multiplier & 1.0 \\ +focus\_a & rad & Mean divergence angle. & 0.1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_genesis13.comp}. +\end{itemize} +\IfFileExists{sources/Source_genesis13_static.tex}{\input{sources/Source_genesis13_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_lab.tex b/docs/manuals/mcxtrace/sources/Source_lab.tex new file mode 100644 index 0000000000..9f0f7b123c --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_lab.tex @@ -0,0 +1,50 @@ +\section{The \texttt{Source\_lab} McXtrace Component} +Laboratory x-ray source. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B. Knudsen + \item \textbf{Origin:} Kgs. Lyngby + \item \textbf{Date:} May 2012 +\end{itemize} + +\subsection*{Description} +Model of a laboratory x-ray tube, generating x-rays by bombarding a target by electrons. Given a input energy E0 of the electron beam, x-rays are emitted from the accessible emission lines The geometry of the tube is assumed to be: \# The electron beam hits a slab of surface material surface at a right angle illuminating an area of width by height, \# where width is measured along the component X-axis. \# The centre of the electron beam at the anode surface is the origin of the component. \# The Z-axis of the component points at the centre of the exit window (focus\_xw by focus yh) placed at a distance dist from the origin. \# The angle between the Z-axis and the anode surface is the take\_off angle. For a detailed sketch of the geometry see the componnent manual. + +The Bremsstrahlung emitted is modelled using the model of Kramer (1923) as restated in International Tables of Crystallography C 4.1 Characteristic radiation is modelled by Lorentzian (default) or Gaussian energy profiles with line-energies from Bearden (1967), widths from Krause (1979) and intensity from Honkimäki (1990) and x-ray data booklet. Absoprtion of emitted x-rays while travelling through the target anode is included. + +Example: Source\_lab(material\_datafile="Cu.txt",Emin=1, E0=80) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_datafile & string & Name of datafile which describes the target material. & "Cu.txt" \\ +width & m & Width of electron beam impinging on the anode. & 1e-3 \\ +height & m & Height of electron beam impinging on the anode. & 1e-3 \\ +thickness & m & Thickness of the anode material slab. & 100e-6 \\ +E0 & kV & Acceleration voltage of xray tube. & 20 \\ +Emax & keV & Maximum energy to sample. Default (Emax=0) is to set it to E0. & 0 \\ +Emin & keV & Minimum energy to sample. & 1 \\ +focus\_xw & m & Width of exit window. & 5e-3 \\ +focus\_yh & m & Height of exit window. & 5e-3 \\ +take\_off & deg & Take off angle of beam centre. & 6 \\ +dist & m & Distance between centre of illuminated target and exit window. & 1 \\ +tube\_current & A & Electron beam current. & 1e-3 \\ +frac & 0-1 & Fraction of statistic to use for Bremsstrahlung. & 0.1 \\ +lorentzian & 0/1 & If nonzero Lorentzian (more correct) line profiles are used. & 1 \\ +xwidth & m & Width of the anode material slab. & 0 \\ +yheight & m & Height of the anode material slab. & 0 \\ +exit\_window\_refpt & m & If set, the AT position and exit window will coincide (legacy behaviour). & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_lab.comp}. +\end{itemize} +\IfFileExists{sources/Source_lab_static.tex}{\input{sources/Source_lab_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_pt.tex b/docs/manuals/mcxtrace/sources/Source_pt.tex new file mode 100644 index 0000000000..c47a478e93 --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_pt.tex @@ -0,0 +1,48 @@ +\section{The \texttt{Source\_pt} McXtrace Component} +Release: McXtrace 0.1 + +An x-ray point source + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} June 29th, 2009 +\end{itemize} + +\subsection*{Description} +A simple source model emitting photons from a point source uniformly into 4pi. A square target centered on the Z-axis restricts the beam to that aperture. If an input spectrum datafile (spectrum\_file) is not specified, the beam is restricted to emit photons between E0+-dE keV, or lambda0+-dlambda \AA{}, whichever is given. The input spectrum file should be formatted such that x-ray energy/wavelength is in the first column and the intensity in the second. Any preceding lines starting with \# are considered part of the file header. If a datafile is given, a nonzero E¤0 value indicates that is is parametrized by energy ( in keV) as opposed to wavelength (in \AA{}). Wavelength is the default. Flux is given in the unit photons/s + +Example: Source\_pt(dist=1,focus\_xw=0.1,focus\_yh=0.1, lamda=0.231, dlambda=0.002) + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +focus\_xw & m & Width of target & 0 \\ +focus\_yh & m & Height of target & 0 \\ +focus\_x0 & m & x-cocordinate of target centre. & 0 \\ +focus\_y0 & m & y-coordinate of target centre. & 0 \\ +flux & ph/s & Total flux radiated from the source. & 0 \\ +dist & m & Distance from source plane to sampling window. & 1 \\ +E0 & keV & Mean energy of xrays. & 0 \\ +dE & keV & Energy half spread of x-rays. & 0 \\ +lambda0 & \AA{} & Mean wavelength of x-rays. & 0 \\ +dlambda & \AA{} & Wavelength half spread of x-rays (flat or gaussian sigma). & 0 \\ +phase & rad & Set phase to something given. & 0 \\ +randomphase & 0/1 & If nonzero, the phase of the emotted photon is random, i.e. source is fully incoherent. otherwise the value of phase is used. & 1 \\ +gauss & 1 & Gaussian (1) or Flat (0) energy/wavelength distribution & 0 \\ +spectrum\_file & string & File from which to read an input spectrum. & "" \\ +verbose & 1 & Output more information runtime. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_pt.comp}. +\end{itemize} +\IfFileExists{sources/Source_pt_static.tex}{\input{sources/Source_pt_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_simplex.tex b/docs/manuals/mcxtrace/sources/Source_simplex.tex new file mode 100644 index 0000000000..cdb9356c6d --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_simplex.tex @@ -0,0 +1,46 @@ +\section{The \texttt{Source\_simplex} McXtrace Component} +Release: McXtrace 1.2 + +Interface source for importing Simplex generated X-ray pulses into McXtrace + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} Aug. 10th, 2014 +\end{itemize} + +\subsection*{Description} +This source model reads the dumped radiation field output from Simplex and samples it to be used in McXtrace. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +gridpoints & int & Number of mesh points along 1 axis. & 101 \\ +fname & string & Filename of main output file of GENESIS 1.3. & "template.fld" \\ +focus\_xw & m & Width of target. & 0 \\ +focus\_yh & m & Height of target. & 0 \\ +dist & m & Distance to target along z axis. & 1 \\ +E0 & keV & Mean energy of xrays. & 0 \\ +dE & keV & Energy half spread of x-rays. & 0 \\ +meshsize & m & Spacing between mesh points (equal in x and y). & 1e-5 \\ +nslices & 1 & Number of slices simulated. & 102 \\ +s0 & m & Back end of pulse time sampling windows scaled by c\textasciicircum{}-1. & -2e-3 \\ +s1 & m & Front end of pulse time sampling window scaled by c\textasciicircum{}-1. & 2e-3 \\ +flux & 1 & Flux-multiplier. & 1.0 \\ +focus\_a & rad & Mean divergence angle. & 0.1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_simplex.comp}. + \item Tanaka, Journal of Synchrotron Radiation 22, 1319 (2015) http://journals.iucr.org/s/issues/2015/05/00/gb5029/ + \item http://radiant.harima.riken.go.jp/simplex/ +\end{itemize} +\IfFileExists{sources/Source_simplex_static.tex}{\input{sources/Source_simplex_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Source_spectra.tex b/docs/manuals/mcxtrace/sources/Source_spectra.tex new file mode 100644 index 0000000000..a000b5c27a --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Source_spectra.tex @@ -0,0 +1,60 @@ +\section{The \texttt{Source\_spectra} McXtrace Component} +Release: McXtrace 1.5 + +Specialized X-ray source for reading in SPECTRA 10 source definitions + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik Knudsen + \item \textbf{Origin:} Risoe + \item \textbf{Date:} November 11, 2019 +\end{itemize} + +\subsection*{Description} +This is a source component for connecting SPECTRA 10-output files with McXtrace. json-style SPECTRA 11 output files are not yet supported. + +SPECTRA is an application software to calculate optical properties of synchrotron radiation (SR) emitted from bending magnets, wigglers (conventional and elliptical) and undulators (conventional, helical, elliptical and figure-8). Calculations of radiation from an arbitrary magnetic field distribution are also available. Parameters on the electron beam and the source can be edited completely on graphical user interfaces (GUIs) and it is possible to show the calculation result graphically. The energy spectrum and radiation power after transmitting various filters and convolution of detector's resolution are also available. See \htmladdnormallink{SPECTRA}{http://spectrax.org/spectra/}. + +If the source is symmetric in x and/or y it is possible to speed up the spectra calculations by only including one half-plane or quadrant. The other side/quadrants will then be mirrored by McXtrace. + +\%BUGS Absolute intensity of 4D (x,y,x',y') is nor correctly normalized. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +spectra\_stem\_x & str & Filename stem of x-projection of source distribution. -n.xxx will be added where n is a serial number and xxx spectra\_suffix. & "" \\ +spectra\_stem\_y & str & Filename stem of y-projection of source distribution. -n.xxx will be added where n is a serial number and xxx spectra\_suffix. & "" \\ +spectra\_stem & str & Filename stem of x,x',y,y'-source distribution distribution. -n.xxx will be added where n is a serial number and xxx spectra\_suffix. & "" \\ +spectra\_suffix & str & Suffix of spectra output files. & "dsc" \\ +E0 & keV & Mean energy of X-rays. & 0 \\ +dE & keV & Energy spread of X-rays. & 0 \\ +\textbf{Emin} & keV & Energy of low end of the Spectra-calculated data. & \\ +\textbf{Emax} & keV & Energy of high end of the Spectra-calculated data. & \\ +\textbf{nE} & int & Number of steps in the spectra-calculations. & \\ +randomphase & 0/1 & If !=0 the photon phase is chosen randomly. & 1 \\ +phase & rad & Value of the photon phase (only used if randomphase==0). & 0 \\ +nx & int & Number of grid points along x in datafiles. If zero this is computed from the files. & 0 \\ +ny & int & Number of grid points along y in datafiles. If zero this is computed from the files. & 0 \\ +npx & int & Number of grid points along x' in datafiles. If zero this is computed from the files. & 0 \\ +npy & int & Number of grid points along y' in datafiles. If zero this is computed from the files. & 0 \\ +initial\_serial & int & First serial number of the series of spectra files. & 1 \\ +symmetricx & 0/1 & If nonzero the source is mirrored in the x-axis. This to allow smaller spectra-calculations. & 0 \\ +symmetricy & 0/1 & If nonzero the source is mirrored in the y-axis. This to allow smaller spectra-calculations. & 0 \\ +verbose & 0/1 & If non-zero output more warning messages. & 0 \\ +flag4d & 0/1 & Use either (0) x,y-projections or (1) full 4D x,y,x',y' datafiles. & 0 \\ +noinit & 0/1 & Do no initialize the component. Can be usefiul in conjunction with a deactivating WHEN-clause. & 0 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Source\_spectra.comp}. + \item Tanaka, J. Synchrotron Rad. (2001). 8, 1221-1228. https://doi.org/10.1107/S090904950101425X + \item http://spectrax.org/spectra/ +\end{itemize} +\IfFileExists{sources/Source_spectra_static.tex}{\input{sources/Source_spectra_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Undulator.tex b/docs/manuals/mcxtrace/sources/Undulator.tex new file mode 100644 index 0000000000..ce479fe185 --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Undulator.tex @@ -0,0 +1,63 @@ +\section{The \texttt{Undulator} McXtrace Component} +Model of an undulator source + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B. Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} May, 2013. +\end{itemize} + +\subsection*{Description} +A undulator source model based on the derivation by K.J. Kim, AIP, conf. proc., 184, 1989. doi:10.1063/1.38046. + +SOLEIL\_PX2a U24 + +\begin{verbatim} +Example: Undulator( E0=12.65, dE=1, Ee=2.75, dEe=0.001, Ie=0.5, K=1.788, Nper=80, +\end{verbatim} + +lu=24e-3, sigey=9.3e-6, sigex=215.7e-6, sigepx=29.3e-6, sigepy=4.2e-6, + +\begin{verbatim} +dist=29.5, E1st=12.400 ) +\end{verbatim} + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +E0 & keV & Center of emitted energy spectrum. & 0 \\ +dE & keV & Half-width of emitted energy spectrum. & 0 \\ +phase & rad & Initial phase of radiation. & 0 \\ +randomphase & 0/1 & If !=0 phase will be random (I.e. the emitted radiation is completely incoherent). & 1 \\ +Ee & GeV & Storage ring electron energy [typically a few GeV). & 2.4 \\ +dEe & percent & Relative electron energy beam spread (sigma/Ee). & 0 \\ +Ie & A & Ring current. & 0.4 \\ +B & T & Peak magnet field strength. Overrides K. & 0 \\ +K & 1 & Dimensionless deflection undulator parameter. When K \textgreater{}\textgreater{} 1 (ie B*lu is large) you get a wiggler. & 0 \\ +Nper & int & Number of magnetic periods in the undulator. & 1 \\ +lu & m & Magnetic period length of the undulator aka lambda\_u. & 16e-3 \\ +sigey & m & Electron ring beam size in vertical plane (rms). & 0 \\ +sigex & m & Electron ring beam size in horizontal plane (rms). & 0 \\ +sigepx & rad & Electron ring beam horizontal divergence (rms). & 0 \\ +sigepy & rad & Electron ring beam vertical divergence (rms). & 0 \\ +focus\_xw & m & Width of target window. & 0 \\ +focus\_yh & m & Height of target window. & 0 \\ +dist & m & Distance from source plane to target window along the optical axis. & 1 \\ +quick\_integ & 0/1 & If nonzero, use faster (but less accurate) integration scheme. & 0 \\ +E1st & keV & Energy of the fundmental (1st) undulator harmonic. & 0 \\ +verbose & 0/1 & If nonzero, output extra information. & 0 \\ +Br & T & Remanent field (1.35T for Nd2Fe14B) for gap estimate & 1.35 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Undulator.comp}. +\end{itemize} +\IfFileExists{sources/Undulator_static.tex}{\input{sources/Undulator_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/sources/Wiggler.tex b/docs/manuals/mcxtrace/sources/Wiggler.tex new file mode 100644 index 0000000000..a598b6194b --- /dev/null +++ b/docs/manuals/mcxtrace/sources/Wiggler.tex @@ -0,0 +1,56 @@ +\section{The \texttt{Wiggler} McXtrace Component} +Model of a wiggler source + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Erik B. Knudsen + \item \textbf{Origin:} DTU Physics + \item \textbf{Date:} May, 2013. +\end{itemize} + +\subsection*{Description} +A source model based on the derivation from B.D. Patterson, Am. J. Phys. 79, 1046 (2011); doi: 10.1119/1.3614033 + +Example: Wiggler( + +\begin{verbatim} +E0 = 14, dE = 12, +Ee = 2.75, Ie = 0.5, B = 2.1, K=10, Nper=41, sigey=9.3e-6, sigex=215.7e-6) +\end{verbatim} + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +E0 & keV & Center of emitted energy spectrum (overrides lambda0) & 0 \\ +dE & keV & Half-width of emitted energy spectrum & 0 \\ +lambda0 & \AA{} & Center of emitted wavelength spectrum & 0 \\ +dlambda & \AA{} & Half-width of emitted wavelength spectrum & 0 \\ +phase & rad & Initial phase of radiation. & 0 \\ +randomphase & 0/1 & If !=0 phase will be random (I.e. the emitted radiation is completely incoherent) & 1 \\ +Ee & GeV & Storage ring electron energy (typically a few GeV) & 2.4 \\ +Ie & A & Ring current & 0.4 \\ +B & & TT] Peak magnet field strength & 1.6 \\ +K & 1 & Dimensionless undulator parameter, e.g. K \textgreater{}\textgreater{} 1. overrides B. & 3 \\ +Nper & int & Number of magnetic periods in the wiggler & 1 \\ +length & m & Length of the Wiggler. & 1 \\ +sigey & m & Electron ring beam size in vertical plane (rms) & 0 \\ +sigex & m & Electron ring beam size in horizontal plane (rms) & 0 \\ +focus\_xw & m & Width of target window & 0 \\ +focus\_yh & m & Height of target window & 0 \\ +dist & m & Distance from source plane to target window along the optical axis & 1 \\ +gauss\_t & 0/1 & If 0 the target window will be sampled uniformly and the weight adjusted accordingly, otherwise we will use a gaussian sampling scheme. & 0 \\ +verbose & 0/1 & If nonzero, output extra information & 0 \\ +Br & & & 1.35 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Wiggler.comp}. +\end{itemize} +\IfFileExists{sources/Wiggler_static.tex}{\input{sources/Wiggler_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/title.tex b/docs/manuals/mcxtrace/title.tex.in similarity index 68% rename from docs/manuals/mcxtrace/title.tex rename to docs/manuals/mcxtrace/title.tex.in index 617ff628ee..fa0edb5fe7 100644 --- a/docs/manuals/mcxtrace/title.tex +++ b/docs/manuals/mcxtrace/title.tex.in @@ -1,14 +1,10 @@ -\title{User and Programmers' Guide to the X Ray-Tracing Package \MCX ,\\ version \version\\[15mm] - \begin{center} - %\includegraphics[width=50mm]{figures/mcstas_logo_reflection}\\[4mm] - \end{center} - } +\title{User and Programmers' Guide to the X Ray-Tracing Package McXtrace, version @MCCODE_VERSION@} \author{E. B. Knudsen, P. Willendrup, E. Farhi, K. Lefmann, S. Schmidt} \date{\reldate} \titlehead{ \begin{minipage}{12mm} -\includegraphics[width=9mm]{figures/DTU_logo}% +\includegraphics[width=9mm]{figures/DTU_logo.pdf}% \end{minipage} \begin{minipage}[top]{80mm} Physics Physics Department,\\ % diff --git a/docs/manuals/mcxtrace/title_comp.tex b/docs/manuals/mcxtrace/title_comp.tex.in similarity index 62% rename from docs/manuals/mcxtrace/title_comp.tex rename to docs/manuals/mcxtrace/title_comp.tex.in index f6c475b5bd..dab0b023e0 100644 --- a/docs/manuals/mcxtrace/title_comp.tex +++ b/docs/manuals/mcxtrace/title_comp.tex.in @@ -1,15 +1,11 @@ -\title{Component Manual for the Xray-Tracing Package \MCX ,\\ version \version\\[15mm] - \begin{center} - %\includegraphics[width=50mm]{figures/mcxtrace_logo}\\[4mm] - \end{center} - } +\title{Component Manual for the Xray-Tracing Package McXtrace, version @MCCODE_VERSION@} \author{E. B. Knudsen, A. Prodi, J. Baltser, P. Willendrup,\\ A. Vickery, E. Farhi, K. Lefmann, S. Schmidt} \date{\reldate} \titlehead{ \begin{minipage}{12mm} -\includegraphics[width=9mm]{figures/DTU_logo}% +\includegraphics[width=9mm]{figures/DTU_logo.pdf}% \end{minipage} \begin{minipage}[top]{80mm} Physics Department,\\ % diff --git a/docs/manuals/mcxtrace/union/Compton_xrl_process.tex b/docs/manuals/mcxtrace/union/Compton_xrl_process.tex new file mode 100644 index 0000000000..c75a48d3d9 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Compton_xrl_process.tex @@ -0,0 +1,44 @@ +\section{The \texttt{Compton\_xrl\_process} McXtrace Component} +Component that implements a Compton scattering process + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics \& United Neux + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +This Union\_process is based on the Incoherent.comp component originally written by Kim Lefmann and Kristian Nielsen + +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +density & g/cm$^{3}$ & Nominal density of material. & 0 \\ +atomno & 1 & Atomic number. & 14 \\ +element & str & The element (symbol) of the material. Overrides atomno. & "" \\ +init & str & Name of Union inititaliser component & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Compton\_xrl\_process.comp}. + \item The test/example instrument \htmladdnormallink{Test\_Phonon.instr}{../examples/Test\_Phonon.instr}. +\end{itemize} +\IfFileExists{union/Compton_xrl_process_static.tex}{\input{union/Compton_xrl_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Incoherent_process.tex b/docs/manuals/mcxtrace/union/Incoherent_process.tex new file mode 100644 index 0000000000..30a705415b --- /dev/null +++ b/docs/manuals/mcxtrace/union/Incoherent_process.tex @@ -0,0 +1,47 @@ +\section{The \texttt{Incoherent\_process} McXtrace Component} +Component implementing a true incoherent scattering process + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +This Union\_process is based on the Incoherent.comp component originally written by Kim Lefmann and Kristian Nielsen. + +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: This component is an approximation. It scatters completely isotropically. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sigma & barns & Incoherent scattering cross section & 5.08 \\ +f\_QE & 1 & Fraction of quasielastic scattering (rest is elastic) & 0 \\ +gamma & 1 & Lorentzian width of quasielastic broadening (HWHM) & 0 \\ +packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ +unit\_cell\_volume & \AA{}$^{3}$ & Unit\_cell\_volume & 13.8 \\ +interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ +init & string & name of Union\_init component (typically "init", default) & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Incoherent\_process.comp}. + \item The test/example instrument \htmladdnormallink{Test\_Phonon.instr}{../examples/Test\_Phonon.instr}. +\end{itemize} +\IfFileExists{union/Incoherent_process_static.tex}{\input{union/Incoherent_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/KN_xrl_process.tex b/docs/manuals/mcxtrace/union/KN_xrl_process.tex new file mode 100644 index 0000000000..5f1661fe72 --- /dev/null +++ b/docs/manuals/mcxtrace/union/KN_xrl_process.tex @@ -0,0 +1,42 @@ +\section{The \texttt{KN\_xrl\_process} McXtrace Component} +A component implementing the Klein-Nishina cross section as a Union physics process + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics \& United Neux + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +This Union\_process is based on the Incoherent.comp component originally written by Kim Lefmann and Kristian Nielsen + +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +density & g/cm$^{3}$ & Nominal density of material. & 0 \\ +init & str & Name of Union inititaliser component & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{KN\_xrl\_process.comp}. + \item The test/example instrument \htmladdnormallink{Test\_Phonon.instr}{../examples/Test\_Phonon.instr}. +\end{itemize} +\IfFileExists{union/KN_xrl_process_static.tex}{\input{union/KN_xrl_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Powder_process.tex b/docs/manuals/mcxtrace/union/Powder_process.tex new file mode 100644 index 0000000000..8302504f04 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Powder_process.tex @@ -0,0 +1,53 @@ +\section{The \texttt{Powder\_process} McXtrace Component} +A sample component implementing a powder scattering process + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics \& United Neux + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +This Union\_process is based on the PowerN.comp component. + +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +reflections & string & Input file for reflections. No scattering if NULL or "" [string] & "NULL" \\ +material & str & Reflection list for power & "NULL" \\ +packing\_factor & 1 & How dense is the material compared to optimal 0-1 & 1 \\ +Vc & \AA{}$^{3}$ & Volume of unit cell=nb atoms per cell/density of atoms. & 0 \\ +delta\_d\_d & 0/1 & Global relative delta\_d\_d/d broadening when the 'w' column is not available. Use 0 if ideal. & 0 \\ +DW & 1 & Global Debye-Waller factor when the 'DW' column is not available. Use 1 if included in F2 & 0 \\ +nb\_atoms & 1 & Number of sub-unit per unit cell, that is ratio of sigma for chemical formula to sigma per unit cell & 1 \\ +density & g/cm$^{3}$ & Density of material. rho=density/weight/1e24*N\_A. & 0 \\ +weight & g/mol & Atomic/molecular weight of material. & 0 \\ +barns & 1 & Flag to indicate if |F|\textasciicircum{}2 from 'reflections' is in barns or fm\textasciicircum{}2 (barns=1 for laz, barns=0 for lau type files). & 1 \\ +Strain & ppm & Global relative delta\_d\_d/d shift when the 'Strain' column is not available. Use 0 if ideal. & 0 \\ +interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ +format & no quotes & Name of the format, or list of column indexes (see Description). & \{0, 0, 0, 0, 0, 0, 0, 0, 0\} \\ +mat\_format & vector & List order in reflection list file & \{0,0,0,0,0\} \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Powder\_process.comp}. +\end{itemize} +\IfFileExists{union/Powder_process_static.tex}{\input{union/Powder_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Rayleigh_xrl_process.tex b/docs/manuals/mcxtrace/union/Rayleigh_xrl_process.tex new file mode 100644 index 0000000000..5875942013 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Rayleigh_xrl_process.tex @@ -0,0 +1,44 @@ +\section{The \texttt{Rayleigh\_xrl\_process} McXtrace Component} +Component that implements a Rayleigh scattering process + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics \& United Neux + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +This Union\_process is based on the Incoherent.comp component originally written by Kim Lefmann and Kristian Nielsen + +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +density & g/cm$^{3}$ & Nominal density of material. & 0 \\ +atomno & 1 & Atomic number. & 14 \\ +element & str & The element (symbol) of the material. Overrides atomno. & "" \\ +init & str & Name of Union inititaliser component & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Rayleigh\_xrl\_process.comp}. + \item The test/example instrument \htmladdnormallink{Test\_Phonon.instr}{../examples/Test\_Phonon.instr}. +\end{itemize} +\IfFileExists{union/Rayleigh_xrl_process_static.tex}{\input{union/Rayleigh_xrl_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Template_process.tex b/docs/manuals/mcxtrace/union/Template_process.tex new file mode 100644 index 0000000000..3f4fc7b477 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Template_process.tex @@ -0,0 +1,43 @@ +\section{The \texttt{Template\_process} McXtrace Component} +Template for a new contributor to create their own physical process. + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +This is a template for a new contributor to create their own physical process. The comments in this file are meant to teach the user about creating their own process file, rather than explaining this one. For comments on how this code works, look in the Incoherent\_process.comp. + +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components like this one 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box / Union\_cylinder, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +sigma & barns & Scattering cross section & 5.08 \\ +packing\_factor & 1 & Material packing factor & 1 \\ +unit\_cell\_volume & \AA{}$^{3}$ & Unit cell volume & 13.8 \\ +interact\_fraction & 1 & How large a part of the scattering events should use this process 0-1 (sum of all processes in material = 1) & -1 \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Template\_process.comp}. +\end{itemize} +\IfFileExists{union/Template_process_static.tex}{\input{union/Template_process_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Union_box.tex b/docs/manuals/mcxtrace/union/Union_box.tex new file mode 100644 index 0000000000..6c12f987ef --- /dev/null +++ b/docs/manuals/mcxtrace/union/Union_box.tex @@ -0,0 +1,63 @@ +\section{The \texttt{Union\_box} McXtrace Component} +Implementation of a box geometry - to be filled with a material + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union components + +The position of this component is the center of the box, extending xwidth/2, yheight/2, and zdepth/2 in each direction respectively. + +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincide. This will crash the code on run time. + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_string & str & material name of this volume, defined using Union\_make\_material & 0 \\ +\textbf{priority} & 1 & priotiry of the volume (can not be the same as another volume) A high priority is on top of low. & \\ +\textbf{xwidth} & m & width of the box volume & \\ +\textbf{yheight} & m & height of the box volume & \\ +\textbf{zdepth} & m & depth of the box volume & \\ +xwidth2 & m & optional different width at the +z box face & -1 \\ +yheight2 & m & optional different height at the +z box face & -1 \\ +visualize & 1 & set to 0 if you wish to hide this geometry in mcdisplay & 1 \\ +target\_index & 1 & Focuses on component a component this many steps further in the component sequence & 0 \\ +target\_x & m & \textbackslash{} & 0 \\ +target\_y & m & - Position of target to focus at & 0 \\ +target\_z & m & / & 0 \\ +focus\_aw & deg & horiz. angular dimension of a rectangular area & 0 \\ +focus\_ah & deg & vert. angular dimension of a rectangular area & 0 \\ +focus\_xw & m & horiz. dimension of a rectangular area & 0 \\ +focus\_xh & m & vert. dimension of a rectangular area & 0 \\ +focus\_r & m & focusing on circle with this radius & 0 \\ +p\_interact & 1 & probability to interact with this geometry [0-1] & 0 \\ +mask\_string & str & Comma separated list of geometry names which this geometry should mask & 0 \\ +mask\_setting & str & "All" or "Any", should the masked volume be simulated when the ray is in just one mask, or all. & 0 \\ +number\_of\_activations & 1 & Number of subsequent Union\_master components that will simulate this geometry & 1 \\ +init & str & Name of Union inititaliser component & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Union\_box.comp}. +\end{itemize} +\IfFileExists{union/Union_box_static.tex}{\input{union/Union_box_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Union_cone.tex b/docs/manuals/mcxtrace/union/Union_cone.tex new file mode 100644 index 0000000000..dfc624ac25 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Union_cone.tex @@ -0,0 +1,60 @@ +\section{The \texttt{Union\_cone} McXtrace Component} +Cone geometry component for Union components + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union components + +The position of this component is the center of the cone, and it thus extends yheight/2 up and down along y axis. + +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincide. This will crash the code on run time. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_string & string & Material name of this volume, defined using Union\_make\_material & 0 \\ +\textbf{priority} & 1 & Priotiry of the volume (can not be the same as another volume) A high priority is on top of low. & \\ +radius & m & Radius volume in (x,z) plane & 0 \\ +radius\_top & m & Top radius volume in (x,z) plane & 0 \\ +radius\_bottom & m & Bottom radius volume in (x,z) plane & 0 \\ +\textbf{yheight} & m & Cone height in (y) direction & \\ +visualize & 1 & Set to 0 if you wish to hide this geometry in mcdisplay & 1 \\ +target\_index & 1 & Focuses on component a component this many steps further in the component sequence & 0 \\ +target\_x & m & \textbackslash{} & 0 \\ +target\_y & m & - Position of target to focus at & 0 \\ +target\_z & m & / & 0 \\ +focus\_aw & deg & Horiz. angular dimension of a rectangular area & 0 \\ +focus\_ah & deg & Vert. angular dimension of a rectangular area & 0 \\ +focus\_xw & m & Horiz. dimension of a rectangular area & 0 \\ +focus\_xh & m & Vert. dimension of a rectangular area & 0 \\ +focus\_r & m & Focusing on circle with this radius & 0 \\ +p\_interact & 1 & Probability to interact with this geometry [0-1] & 0 \\ +mask\_string & string & Comma seperated list of geometry names which this geometry should mask & 0 \\ +mask\_setting & string & "All" or "Any", should the masked volume be simulated when the ray is in just one mask, or all. & 0 \\ +number\_of\_activations & 1 & Number of subsequent Union\_master components that will simulate this geometry & 1 \\ +init & string & Name of Union\_init component (typically "init", default) & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Union\_cone.comp}. +\end{itemize} +\IfFileExists{union/Union_cone_static.tex}{\input{union/Union_cone_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Union_cylinder.tex b/docs/manuals/mcxtrace/union/Union_cylinder.tex new file mode 100644 index 0000000000..eb12ec38b9 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Union_cylinder.tex @@ -0,0 +1,58 @@ +\section{The \texttt{Union\_cylinder} McXtrace Component} +Implementation of a cylinder geometry - to be filled with a material + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union components + +The position of this component is the center of the cylinder, and it thus extends yheight/2 up and down along y axis. + +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincide. This will crash the code on run time. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_string & str & material name of this volume, defined using Union\_make\_material & 0 \\ +\textbf{priority} & 1 & priority of the volume (can not be the same as another volume) A high priority is on top of low. & \\ +\textbf{radius} & m & Outer radius volume in (x,z) plane & \\ +\textbf{yheight} & m & Cylinder height in (y) direction & \\ +visualize & 1 & set to 0 if you wish to hide this geometry in mcdisplay & 1 \\ +target\_index & 1 & Focus on a component this many steps further in the component sequence. & 0 \\ +target\_x & m & \textbackslash{} & 0 \\ +target\_y & m & - Position of target to focus at & 0 \\ +target\_z & m & / & 0 \\ +focus\_aw & deg & horiz. angular dimension of a rectangular area & 0 \\ +focus\_ah & deg & vert. angular dimension of a rectangular area & 0 \\ +focus\_xw & m & horiz. dimension of a rectangular area & 0 \\ +focus\_xh & m & vert. dimension of a rectangular area & 0 \\ +focus\_r & m & focusing on circle with this radius & 0 \\ +p\_interact & 1 & probability to interact with this geometry [0-1] & 0 \\ +mask\_string & str & Comma seperated list of geometry names which this geometry should mask & 0 \\ +mask\_setting & str & "All" or "Any", should the masked volume be simulated when the ray is in just one mask, or all. & 0 \\ +number\_of\_activations & 1 & Number of subsequent Union\_master components that will simulate this geometry & 1 \\ +init & string & Name of Union\_init component (typically "init", default) & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Union\_cylinder.comp}. +\end{itemize} +\IfFileExists{union/Union_cylinder_static.tex}{\input{union/Union_cylinder_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Union_init.tex b/docs/manuals/mcxtrace/union/Union_init.tex new file mode 100644 index 0000000000..41f91436c3 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Union_init.tex @@ -0,0 +1,37 @@ +\section{The \texttt{Union\_init} McXtrace Component} +Initialize component that needs to be place before any Union component + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen + \item \textbf{Origin:} ESS DMSC + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McStas. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components 2) These are gathered into material definitions using this component 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Union\_init.comp}. +\end{itemize} +\IfFileExists{union/Union_init_static.tex}{\input{union/Union_init_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Union_make_material.tex b/docs/manuals/mcxtrace/union/Union_make_material.tex new file mode 100644 index 0000000000..84507a090e --- /dev/null +++ b/docs/manuals/mcxtrace/union/Union_make_material.tex @@ -0,0 +1,42 @@ +\section{The \texttt{Union\_make\_material} McXtrace Component} +Component that takes a number of Union processes and constructs a Union material + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components 2) These are gathered into material definitions using this component 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before the master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +process\_string & string & Comma seperated names of physical processes & "NULL" \\ +\textbf{my\_absorption} & 1/m & Inverse penetration depth from absorption at standard energy & \\ +absorber & 0/1 & Control parameter, if set to 1 the material will have no scattering processes & 0 \\ +material\_string & string & List of elements present in the material. Triggers a search for materials constants files. & "NULL" \\ +init & string & Name of Union\_init component (typically "init", default) & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Union\_make\_material.comp}. +\end{itemize} +\IfFileExists{union/Union_make_material_static.tex}{\input{union/Union_make_material_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Union_master.tex b/docs/manuals/mcxtrace/union/Union_master.tex new file mode 100644 index 0000000000..dd8fcef19d --- /dev/null +++ b/docs/manuals/mcxtrace/union/Union_master.tex @@ -0,0 +1,46 @@ +\section{The \texttt{Union\_master} McXtrace Component} +The Master Union assembles specifications (e.g. processes, materials, geometries). + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +Part of the Union components, a set of components that work together and thus sperates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) This master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union\_components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +verbal & 0/1 & Toogles terminal output describing the defined simulation & 1 \\ +list\_verbal & 0/1 & Toogles information of all internal lists in intersection network & 0 \\ +finally\_verbal & 0/1 & Toogles information about cleanup performed in finally section & 0 \\ +allow\_inside\_start & 0/1 & Set to 1 if rays are expected to start inside a volume in this master & 0 \\ +enable\_tagging & 0/1 & Enable tagging of ray history (geometry, scattering process) & 0 \\ +history\_limit & 1 & Limit the number of unique histories that are saved & 300000 \\ +enable\_conditionals & 0/1 & Use conditionals with this master & 1 \\ +inherit\_number\_of\_scattering\_events & 0/1 & Inherit the number of scattering events from last master & 0 \\ +init & string & Name of Union\_init component (typically "init", default) & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Union\_master.comp}. +\end{itemize} +\IfFileExists{union/Union_master_static.tex}{\input{union/Union_master_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Union_sphere.tex b/docs/manuals/mcxtrace/union/Union_sphere.tex new file mode 100644 index 0000000000..45c6c892d7 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Union_sphere.tex @@ -0,0 +1,57 @@ +\section{The \texttt{Union\_sphere} McXtrace Component} +Implementation of a sphere geometry - to be filled with a material + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union components + +The position of this component is the center of the sphere. + +It is allowed to overlap components, but it is not allowed to have two parallel planes that coincide. This will crash the code on run time. + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +material\_string & str & material name of this volume, defined using Union\_make\_material & 0 \\ +\textbf{priority} & 1 & priority of the volume (can not be the same as another volume) A high priority is on top of low. & \\ +\textbf{radius} & m & Radius of sphere & \\ +visualize & 1 & set to 0 if you wish to hide this geometry in mcdisplay & 1 \\ +target\_index & 1 & Focus on a component this many steps further in the component sequence. & 0 \\ +target\_x & m & \textbackslash{} & 0 \\ +target\_y & m & - Position of target to focus at & 0 \\ +target\_z & m & / & 0 \\ +focus\_aw & deg & horiz. angular dimension of a rectangular area & 0 \\ +focus\_ah & deg & vert. angular dimension of a rectangular area & 0 \\ +focus\_xw & m & horiz. dimension of a rectangular area & 0 \\ +focus\_xh & m & vert. dimension of a rectangular area & 0 \\ +focus\_r & m & focusing on circle with this radius & 0 \\ +p\_interact & 1 & probability to interact with this geometry [0-1] & 0 \\ +mask\_string & & Comma separated list of geometry names which this geometry should mask & 0 \\ +mask\_setting & & "All" or "Any", should the masked volume be simulated when the ray is in just one mask, or all. & 0 \\ +number\_of\_activations & 1 & Number of subsequent Union\_master components that will simulate this geometry & 1 \\ +init & str & Name of Union inititaliser component & "init" \\ +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Union\_sphere.comp}. +\end{itemize} +\IfFileExists{union/Union_sphere_static.tex}{\input{union/Union_sphere_static.tex}}{} \ No newline at end of file diff --git a/docs/manuals/mcxtrace/union/Union_stop.tex b/docs/manuals/mcxtrace/union/Union_stop.tex new file mode 100644 index 0000000000..ce71a77b61 --- /dev/null +++ b/docs/manuals/mcxtrace/union/Union_stop.tex @@ -0,0 +1,37 @@ +\section{The \texttt{Union\_stop} McXtrace Component} +Stop component that must be placed after all Union components for instrument to compile correctly + +\subsection*{Identification} +\begin{itemize} + \item \textbf{Author:} Mads Bertelsen and Erik B Knudsen + \item \textbf{Origin:} ESS DMSC \& DTU Physics + \item \textbf{Date:} 20.08.15 +\end{itemize} + +\subsection*{Description} +Part of the Union components, a set of components that work together and thus separates geometry and physics within McXtrace. The use of this component requires other components to be used. + +1) One specifies a number of processes using process components 2) These are gathered into material definitions using Union\_make\_material 3) Geometries are placed using Union\_box/cylinder/sphere, assigned a material 4) A Union\_master component placed after all of the above + +Only in step 4 will any simulation happen, and per default all geometries defined before this master, but after the previous will be simulated here. + +There is a dedicated manual available for the Union components + +Algorithm: Described elsewhere + +\subsection*{Input parameters} +Parameters in \textbf{boldface} are required; the others are optional. + +\begin{longtable}{p{0.22\textwidth}p{0.12\textwidth}p{0.46\textwidth}p{0.14\textwidth}} +\toprule +\textbf{Name} & \textbf{Unit} & \textbf{Description} & \textbf{Default} \\ +\midrule +\endhead +\bottomrule +\end{longtable} + +\subsection*{Links} +\begin{itemize} + \item Component source code found in file \texttt{Union\_stop.comp}. +\end{itemize} +\IfFileExists{union/Union_stop_static.tex}{\input{union/Union_stop_static.tex}}{} \ No newline at end of file diff --git a/tools/Python/mcdoc/mcdoc.py b/tools/Python/mcdoc/mcdoc.py index b03d799964..1ad1876cd7 100644 --- a/tools/Python/mcdoc/mcdoc.py +++ b/tools/Python/mcdoc/mcdoc.py @@ -608,10 +608,14 @@ def create(self): [ <a href="README.html">Tool docs</a> | <a href="Instrument/INSTRUMENT_Grammar.html">Instrument Grammar</a> | <a href="Component/COMPONENT_Grammar.html">Component Grammar</a> -| <a href="file://%MCCODE_DOCDIR%/mcstas-manual.pdf">User Manual</a> -| <a href="file://%MCCODE_DOCDIR%/mcstas-components.pdf">Component Manual</a> ] | <a href="file://%MCCODE_LIBDIR%/">McCode lib dir</a> ] </P> +<P ALIGN=CENTER> +[ <a href="file://%MCCODE_DOCDIR%/mcstas-manual/manual.html">User Manual (html)</a> +| <a href="file://%MCCODE_DOCDIR%/mcstas-manual.pdf">User Manual (PDF)</a> +| <a href="file://%MCCODE_DOCDIR%/mcstas-components/Component_manual.html">Component Manual (html)</a> +| <a href="file://%MCCODE_DOCDIR%/mcstas-components.pdf">Component Manual (PDF)</a> ] +</P> <CENTER><H1>Components and Instruments from the Library for <i>McStas</i></H1></CENTER>