cmake/Platform/BluegeneQ*.cmake !filter
cmake/*.c !filter
cmake/*.c.cmakein !filter
-doxygen/Doxyfile-*.cmakein !filter
-doxygen/*.cpp !filter
-doxygen/examples/*.cpp filter=uncrustify_only
-doxygen/examples/*.c filter=uncrustify_only
-manual/UseLATEX.cmake !filter
+docs/doxygen/Doxyfile-*.cmakein !filter
+docs/doxygen/*.cpp !filter
+docs/doxygen/examples/*.cpp filter=uncrustify_only
+docs/doxygen/examples/*.c filter=uncrustify_only
+docs/manual/UseLATEX.cmake !filter
scripts/GMXRC.* !filter
scripts/make_gromos_rtp.py !filter
src/contrib/* !filter
# This variable is a list of pairs of names of source and destination
# directories. Most of these are used for content GROMACS generates as
# part of the configuration or build.
-set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/share/man/man1;share/man/man1;${CMAKE_BINARY_DIR}/share/man/man7;share/man/man7;${CMAKE_BINARY_DIR}/share/html/final;share/html/final;${CMAKE_BINARY_DIR}/install-guide/final;/")
+set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/docs/man/man1;docs/man/man1;${CMAKE_BINARY_DIR}/docs/man/man7;docs/man/man7;${CMAKE_BINARY_DIR}/docs/old-html/final;docs/old-html/final;${CMAKE_BINARY_DIR}/docs/install-guide/final;/")
set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
set(CPACK_GMX_BUILD_HELP "${GMX_BUILD_HELP}") #Works even though GMX_BUILD_HELP is defined later because it is off by default.
endif()
if (NOT GMX_BUILD_MDRUN_ONLY)
- add_subdirectory(doxygen)
- add_subdirectory(install-guide)
+ add_subdirectory(docs)
add_subdirectory(share)
add_subdirectory(scripts)
endif()
###########################
set_directory_properties(PROPERTIES
ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")
-
-########################################################################
-# Manual #
-########################################################################
-
-option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF)
-mark_as_advanced(GMX_BUILD_MANUAL)
-if(GMX_BUILD_MANUAL)
- # Make sure we only do detection of manual-building dependencies
- # when the user opted in for that.
- add_subdirectory(manual)
-endif()
#TODO: add check that source doesn't contain any untracked files
if(NOT CPACK_INSTALL_CMAKE_PROJECTS) #building source package
get_filename_component(CMAKE_BINARY_DIR ${CPACK_OUTPUT_CONFIG_FILE} PATH)
- if (NOT EXISTS "${CMAKE_BINARY_DIR}/share/man/man1/gmx-view.1" OR
- NOT EXISTS "${CMAKE_BINARY_DIR}/install-guide/final/INSTALL" OR
- NOT EXISTS "${CMAKE_BINARY_DIR}/share/html/final/online.html" OR
+ if (NOT EXISTS "${CMAKE_BINARY_DIR}/docs/man/man1/gmx-view.1" OR
+ NOT EXISTS "${CMAKE_BINARY_DIR}/docs/install-guide/final/INSTALL" OR
+ NOT EXISTS "${CMAKE_BINARY_DIR}/docs/old-html/final/online.html" OR
NOT EXISTS "${CMAKE_BINARY_DIR}/src/programs/completion/gmx-completion.bash" OR
- NOT EXISTS "${CMAKE_BINARY_DIR}/share/html/final/programs/gmx-view.html")
+ NOT EXISTS "${CMAKE_BINARY_DIR}/docs/old-html/final/programs/gmx-view.html")
message(FATAL_ERROR
"To create a complete source package, bash completions, "
"man and HTML pages, and INSTALL need to be generated. "
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# This directory provides a unified place for building all kinds of
+# GROMACS documentation. This includes some "static" content (Doxygen
+# code documentation, reference manual, install guide, old online HTML
+# pages), and content generated from the gmx program for the various
+# tools (man and HTML pages). It also provides the "webpage" target,
+# that combines all of the above (except man pages in man format) into
+# a form suitable for automated deployment to the GROMACS website.
+
+# Even if we aren't going to make the full webpage, set up to put all
+# the documentation output in the same place, for convenience
+set(HTML_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/html")
+file(MAKE_DIRECTORY ${HTML_OUTPUT_DIR})
+
+add_subdirectory(install-guide)
+add_subdirectory(man)
+add_subdirectory(old-html)
+add_subdirectory(doxygen)
+
+option(GMX_BUILD_WEBPAGE "Whether to try to configure to build the GROMACS static webpages" OFF)
+mark_as_advanced(GMX_BUILD_WEBPAGE)
+
+option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" ${GMX_BUILD_WEBPAGE})
+mark_as_advanced(GMX_BUILD_MANUAL)
+if(GMX_BUILD_MANUAL)
+ # Make sure we only do detection of manual-building dependencies
+ # when the user opted in for that.
+ add_subdirectory(manual)
+endif()
+
+find_package(Pandoc)
+
+set(HTML_BUILD_IS_POSSIBLE OFF)
+# We can only configure to build the webpage if the user asked for it,
+# the build is outside of the source dir, and all the components can
+# be built. There's no need to be talkative if we fail - most people
+# never need to know.
+if(GMX_BUILD_WEBPAGE AND
+ GMX_BUILD_HELP AND
+ NOT ${CMAKE_BINARY_DIR} STREQUAL ${CMAKE_SOURCE_DIR} AND
+ INSTALL_GUIDE_BUILD_IS_POSSIBLE AND
+ MANUAL_BUILD_IS_POSSIBLE AND
+ PANDOC_EXECUTABLE AND
+ DOXYGEN_EXECUTABLE AND
+ DOXYGEN_MSCGEN_EXECUTABLE)
+ set(HTML_BUILD_IS_POSSIBLE ON)
+endif()
+
+if(HTML_BUILD_IS_POSSIBLE)
+ # For a real build of the webpage, the md5sum of the tarballs must
+ # already be known, and so we may as well require that the real
+ # build of the webpage take place from cmake run from the unpacked
+ # tarball. Then, the *_MD5SUM and *_TARBALL variables will be able
+ # to be set on the cmake command line (e.g. by a Jenkins job
+ # configuration), and we can require that they are set. For local
+ # building of the webpages (e.g. for debugging), the *_MD5SUM
+ # variables need a fallback.
+ if(NOT SOURCE_IS_SOURCE_DISTRIBUTION)
+ if (SOURCE_TARBALL AND SOURCE_MD5SUM AND
+ REGRESSIONTESTS_TARBALL AND REGRESSIONTESTS_MD5SUM)
+ set(BUILD_DOWNLOAD_SECTION on)
+ else()
+ set(BUILD_DOWNLOAD_SECTION off)
+ endif()
+ else()
+ foreach(VAR SOURCE_MD5SUM REGRESSIONTESTS_MD5SUM SOURCE_TARBALL REGRESSIONTESTS_TARBALL)
+ if(NOT DEFINED ${VAR})
+ message(FATAL_ERROR "The build of the webpage requires that ${VAR} is set in the cmake cache, e.g. on the CMake command line")
+ endif()
+ endforeach()
+ set(BUILD_DOWNLOAD_SECTION on)
+ endif()
+
+ # If building from the repo, then tarballs may not exist, and if
+ # so, it would not make sense to build that part of the front
+ # page.
+ if(BUILD_DOWNLOAD_SECTION)
+ set(DOWNLOAD_SECTION
+"# Downloads
+
+* Source code - [gromacs-${PROJECT_VERSION}.tar.gz](gromacs-${PROJECT_VERSION}.tar.gz)
+ (md5sum ${SOURCE_MD5SUM})
+ Other source code versions may be found at <ftp://ftp.gromacs.org/pub/gromacs/>
+
+* Regression tests - [regressiontests-${PROJECT_VERSION}.tar.gz](regressiontests-${PROJECT_VERSION}.tar.gz)
+ (md5sum ${REGRESSIONTESTS_MD5SUM})
+")
+
+ # Copy the source tarball to the webpage output
+ add_custom_command(
+ OUTPUT ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz
+ COMMAND ${CMAKE_COMMAND}
+ -E copy ${SOURCE_TARBALL} ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz
+ VERBATIM
+ )
+
+ # Copy the regressiontests tarball to the webpage output
+ add_custom_command(
+ OUTPUT ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz
+ COMMAND ${CMAKE_COMMAND}
+ -E copy ${REGRESSIONTESTS_TARBALL} ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz
+ VERBATIM
+ )
+ else()
+ set(DOWNLOAD_SECTION "")
+ endif()
+
+ # Do replacement of CMake variables for version strings, etc.
+ configure_file(configure-html.cmake.in
+ ${CMAKE_CURRENT_BINARY_DIR}/configure-html.cmake
+ @ONLY)
+
+ # This defers until build time the configuration of
+ # index.md, which could be faster
+ add_custom_command(
+ OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/index.md
+ COMMAND ${CMAKE_COMMAND}
+ -P ${CMAKE_CURRENT_BINARY_DIR}/configure-html.cmake
+ DEPENDS
+ ${CMAKE_CURRENT_BINARY_DIR}/configure-html.cmake
+ ${CMAKE_CURRENT_SOURCE_DIR}/index.md
+ COMMENT "Configuring index.md"
+ VERBATIM
+ )
+
+ # Put the CSS in the HTML output directory
+ add_custom_command(
+ OUTPUT ${HTML_OUTPUT_DIR}/buttondown.css
+ COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/buttondown.css ${HTML_OUTPUT_DIR}/buttondown.css
+ DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/buttondown.css
+ VERBATIM
+ )
+ list(APPEND extra_webpage_dependencies ${HTML_OUTPUT_DIR}/buttondown.css)
+
+ # Make the top-level index.html
+ add_custom_command(
+ OUTPUT ${HTML_OUTPUT_DIR}/index.html
+ COMMAND ${PANDOC_EXECUTABLE} -o ${HTML_OUTPUT_DIR}/index.html index.md -s --css buttondown.css
+ DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/index.md ${HTML_OUTPUT_DIR}/buttondown.css
+ VERBATIM
+ )
+
+ # Make the PDF reference guide
+ # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR}
+ add_custom_command(
+ OUTPUT ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf
+ COMMAND ${CMAKE_COMMAND}
+ -E remove -f ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf
+ COMMAND ${CMAKE_COMMAND}
+ -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf
+ # UseLATEX.cmake makes a target called pdf, not ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf
+ DEPENDS pdf
+ VERBATIM
+ )
+
+ # TODO Move content from the "old" html output into the new user
+ # guide, or delete, as appropriate.
+ if(NOT SOURCE_IS_SOURCE_DISTRIBUTION)
+ # TODO If content remains here once the user guide is in
+ # decent shape, try to make the generated HTML arrive directly
+ # in ${HTML_OUTPUT_DIR}
+ add_custom_target(webpage-html
+ ${CMAKE_COMMAND} -E copy_directory old-html/final ${HTML_OUTPUT_DIR}
+ )
+ add_dependencies(webpage-html html)
+ else()
+ # In the source distribution, the html pages are already
+ # built, so we can avoid making gmx via the html target
+ add_custom_target(webpage-html
+ ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/old-html/final ${HTML_OUTPUT_DIR}
+ )
+ endif()
+
+ # The Doxygen configuration in doxygen/Doxyfile-common.cmakein
+ # makes all the Doxygen output directly in
+ # ${HTML_OUTPUT_DIR}/doxygen (and makes the directory if it needs
+ # to).
+
+ # Add other dependencies for doing the webpage build from the real
+ # tarball
+ if(BUILD_DOWNLOAD_SECTION)
+ list(APPEND extra_webpage_dependencies
+ ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz
+ ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz
+ )
+ endif()
+
+ # Add a top-level target for the others to hook onto
+ add_custom_target(webpage
+ DEPENDS
+ ${HTML_OUTPUT_DIR}/index.html
+ install-guide
+ ${HTML_OUTPUT_DIR}/install-guide.html
+ ${HTML_OUTPUT_DIR}/install-guide.pdf
+ ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf
+ ${extra_webpage_dependencies}
+ VERBATIM
+ )
+ add_dependencies(webpage webpage-html doc-all)
+endif()
--- /dev/null
+/* CSS sourced for GROMACS from https://gist.github.com/ryangray/1882525
+ No usage restrictions are asserted there.
+*/
+/*
+ Buttondown
+ A Markdown/MultiMarkdown/Pandoc HTML output CSS stylesheet
+ Author: Ryan Gray
+ Date: 15 Feb 2011
+ Revised: 21 Feb 2012
+
+ General style is clean, with minimal re-definition of the defaults or
+ overrides of user font settings. The body text and header styles are
+ left alone except title, author and date classes are centered. A Pandoc TOC
+ is not printed, URLs are printed after hyperlinks in parentheses.
+ Block quotes are italicized. Tables are lightly styled with lines above
+ and below the table and below the header with a boldface header. Code
+ blocks are line wrapped.
+
+ All elements that Pandoc and MultiMarkdown use should be listed here, even
+ if the style is empty so you can easily add styling to anything.
+
+ There are some elements in here for HTML5 output of Pandoc, but I have not
+ gotten around to testing that yet.
+*/
+
+/* NOTES:
+
+ Stuff tried and failed:
+
+ It seems that specifying font-family:serif in Safari will always use
+ Times New Roman rather than the user's preferences setting.
+
+ Making the font size different or a fixed value for print in case the screen
+ font size is making the print font too big: Making font-size different for
+ print than for screen causes horizontal lines to disappear in math when using
+ MathJax under Safari.
+*/
+
+/* ---- Front Matter ---- */
+
+/* Pandoc header DIV. Contains .title, .author and .date. Comes before div#TOC.
+ Only appears if one of those three are in the document.
+*/
+
+div#header, header
+ {
+ /* Put border on bottom. Separates it from TOC or body that comes after it. */
+ border-bottom: 1px solid #aaa;
+ margin-bottom: 0.5em;
+ }
+
+.title /* Pandoc title header (h1.title) */
+ {
+ text-align: center;
+ }
+
+.author, .date /* Pandoc author(s) and date headers (h2.author and h3.date) */
+ {
+ text-align: center;
+ }
+
+/* Pandoc table of contents DIV when using the --toc option.
+ NOTE: this doesn't support Pandoc's --id-prefix option for #TOC and #header.
+ Probably would need to use div[id$='TOC'] and div[id$='header'] as selectors.
+*/
+
+div#TOC, nav#TOC
+ {
+ /* Put border on bottom to separate it from body. */
+ border-bottom: 1px solid #aaa;
+ margin-bottom: 0.5em;
+ }
+
+@media print
+ {
+ div#TOC, nav#TOC
+ {
+ /* Don't display TOC in print */
+ display: none;
+ }
+ }
+
+/* ---- Headers and sections ---- */
+
+h1, h2, h3, h4, h5, h6
+{
+ font-family: "Helvetica Neue", Helvetica, "Liberation Sans", Calibri, Arial, sans-serif; /* Sans-serif headers */
+
+ /* font-family: "Liberation Serif", "Georgia", "Times New Roman", serif; /* Serif headers */
+
+ page-break-after: avoid; /* Firefox, Chrome, and Safari do not support the property value "avoid" */
+}
+
+/* Pandoc with --section-divs option */
+
+div div, section section /* Nested sections */
+ {
+ margin-left: 2em; /* This will increasingly indent nested header sections */
+ }
+
+p {}
+
+blockquote
+ {
+ font-style: italic;
+ }
+
+li /* All list items */
+ {
+ }
+
+li > p /* Loosely spaced list item */
+ {
+ margin-top: 1em; /* IE: lack of space above a <li> when the item is inside a <p> */
+ }
+
+ul /* Whole unordered list */
+ {
+ }
+
+ul li /* Unordered list item */
+ {
+ }
+
+ol /* Whole ordered list */
+ {
+ }
+
+ol li /* Ordered list item */
+ {
+ }
+
+hr {}
+
+/* ---- Some span elements --- */
+
+sub /* Subscripts. Pandoc: H~2~O */
+ {
+ }
+
+sup /* Superscripts. Pandoc: The 2^nd^ try. */
+ {
+ }
+
+em /* Emphasis. Markdown: *emphasis* or _emphasis_ */
+ {
+ }
+
+em > em /* Emphasis within emphasis: *This is all *emphasized* except that* */
+ {
+ font-style: normal;
+ }
+
+strong /* Markdown **strong** or __strong__ */
+ {
+ }
+
+/* ---- Links (anchors) ---- */
+
+a /* All links */
+ {
+ /* Keep links clean. On screen, they are colored; in print, they do nothing anyway. */
+ text-decoration: none;
+ }
+
+@media screen
+ {
+ a:hover
+ {
+ /* On hover, we indicate a bit more that it is a link. */
+ text-decoration: underline;
+ }
+ }
+
+@media print
+ {
+ a {
+ /* In print, a colored link is useless, so un-style it. */
+ color: black;
+ background: transparent;
+ }
+
+ a[href^="http://"]:after, a[href^="https://"]:after
+ {
+ /* However, links that go somewhere else, might be useful to the reader,
+ so for http and https links, print the URL after what was the link
+ text in parens
+ */
+ content: " (" attr(href) ") ";
+ font-size: 90%;
+ }
+ }
+
+/* ---- Images ---- */
+
+img
+ {
+ /* Let it be inline left/right where it wants to be, but verticality make
+ it in the middle to look nicer, but opinions differ, and if in a multi-line
+ paragraph, it might not be so great.
+ */
+ vertical-align: middle;
+ }
+
+div.figure /* Pandoc figure-style image */
+ {
+ /* Center the image and caption */
+ margin-left: auto;
+ margin-right: auto;
+ text-align: center;
+ font-style: italic;
+ }
+
+p.caption /* Pandoc figure-style caption within div.figure */
+ {
+ /* Inherits div.figure props by default */
+ }
+
+/* ---- Code blocks and spans ---- */
+
+pre, code
+ {
+ background-color: #fdf7ee;
+ /* BEGIN word wrap */
+ /* Need all the following to word wrap instead of scroll box */
+ /* This will override the overflow:auto if present */
+ white-space: pre-wrap; /* css-3 */
+ white-space: -moz-pre-wrap !important; /* Mozilla, since 1999 */
+ white-space: -pre-wrap; /* Opera 4-6 */
+ white-space: -o-pre-wrap; /* Opera 7 */
+ word-wrap: break-word; /* Internet Explorer 5.5+ */
+ /* END word wrap */
+ }
+
+pre /* Code blocks */
+ {
+ /* Distinguish pre blocks from other text by more than the font with a background tint. */
+ padding: 0.5em; /* Since we have a background color */
+ border-radius: 5px; /* Softens it */
+ /* Give it a some definition */
+ border: 1px solid #aaa;
+ /* Set it off left and right, seems to look a bit nicer when we have a background */
+ margin-left: 0.5em;
+ margin-right: 0.5em;
+ }
+
+@media screen
+ {
+ pre
+ {
+ /* On screen, use an auto scroll box for long lines, unless word-wrap is enabled */
+ white-space: pre;
+ overflow: auto;
+ /* Dotted looks better on screen and solid seems to print better. */
+ border: 1px dotted #777;
+ }
+ }
+
+code /* All inline code spans */
+ {
+ }
+
+p > code, li > code /* Code spans in paragraphs and tight lists */
+ {
+ /* Pad a little from adjacent text */
+ padding-left: 2px;
+ padding-right: 2px;
+ }
+
+li > p code /* Code span in a loose list */
+ {
+ /* We have room for some more background color above and below */
+ padding: 2px;
+ }
+
+/* ---- Math ---- */
+
+span.math /* Pandoc inline math default and --jsmath inline math */
+ {
+ /* Tried font-style:italic here, and it messed up MathJax rendering in some browsers. Maybe don't mess with at all. */
+ }
+
+div.math /* Pandoc --jsmath display math */
+ {
+ }
+
+span.LaTeX /* Pandoc --latexmathml math */
+ {
+ }
+
+eq /* Pandoc --gladtex math */
+ {
+ }
+
+/* ---- Tables ---- */
+
+/* A clean textbook-like style with horizontal lines above and below and under
+ the header. Rows highlight on hover to help scanning the table on screen.
+*/
+
+table
+ {
+ border-collapse: collapse;
+ border-spacing: 0; /* IE 6 */
+
+ border-bottom: 2pt solid #000;
+ border-top: 2pt solid #000; /* The caption on top will not have a bottom-border */
+
+ /* Center */
+ margin-left: auto;
+ margin-right: auto;
+ }
+
+thead /* Entire table header */
+ {
+ border-bottom: 1pt solid #000;
+ background-color: #eee; /* Does this BG print well? */
+ }
+
+tr.header /* Each header row */
+ {
+ }
+
+tbody /* Entire table body */
+ {
+ }
+
+/* Table body rows */
+
+tr {
+ }
+tr.odd:hover, tr.even:hover /* Use .odd and .even classes to avoid styling rows in other tables */
+ {
+ background-color: #eee;
+ }
+
+/* Odd and even rows */
+tr.odd {}
+tr.even {}
+
+td, th /* Table cells and table header cells */
+ {
+ vertical-align: top; /* Word */
+ vertical-align: baseline; /* Others */
+ padding-left: 0.5em;
+ padding-right: 0.5em;
+ padding-top: 0.2em;
+ padding-bottom: 0.2em;
+ }
+
+/* Removes padding on left and right of table for a tight look. Good if thead has no background color*/
+/*
+tr td:last-child, tr th:last-child
+ {
+ padding-right: 0;
+ }
+tr td:first-child, tr th:first-child
+ {
+ padding-left: 0;
+ }
+*/
+
+th /* Table header cells */
+ {
+ font-weight: bold;
+ }
+
+tfoot /* Table footer (what appears here if caption is on top?) */
+ {
+ }
+
+caption /* This is for a table caption tag, not the p.caption Pandoc uses in a div.figure */
+ {
+ caption-side: top;
+ border: none;
+ font-size: 0.9em;
+ font-style: italic;
+ text-align: center;
+ margin-bottom: 0.3em; /* Good for when on top */
+ padding-bottom: 0.2em;
+ }
+
+/* ---- Definition lists ---- */
+
+dl /* The whole list */
+ {
+ border-top: 2pt solid black;
+ padding-top: 0.5em;
+ border-bottom: 2pt solid black;
+ }
+
+dt /* Definition term */
+ {
+ font-weight: bold;
+ }
+
+dd+dt /* 2nd or greater term in the list */
+ {
+ border-top: 1pt solid black;
+ padding-top: 0.5em;
+ }
+
+dd /* A definition */
+ {
+ margin-bottom: 0.5em;
+ }
+
+dd+dd /* 2nd or greater definition of a term */
+ {
+ border-top: 1px solid black; /* To separate multiple definitions */
+ }
+
+/* ---- Footnotes ---- */
+
+a.footnote, a.footnoteRef { /* Pandoc, MultiMarkdown footnote links */
+ font-size: small;
+ vertical-align: text-top;
+}
+
+a[href^="#fnref"], a.reversefootnote /* Pandoc, MultiMarkdown, ?? footnote back links */
+ {
+ }
+
+@media print
+ {
+ a[href^="#fnref"], a.reversefootnote /* Pandoc, MultiMarkdown */
+ {
+ /* Don't display these at all in print since the arrow is only something to click on */
+ display: none;
+ }
+ }
+
+div.footnotes /* Pandoc footnotes div at end of the document */
+ {
+ }
+
+div.footnotes li[id^="fn"] /* A footnote item within that div */
+ {
+ }
+
+/* You can class stuff as "noprint" to not print.
+ Useful since you can't set this media conditional inside an HTML element's
+ style attribute (I think), and you don't want to make another stylesheet that
+ imports this one and adds a class just to do this.
+*/
+
+@media print
+ {
+ .noprint
+ {
+ display:none;
+ }
+ }
--- /dev/null
+# Helper script that defers configure_file until build time, so that
+# changes to the files configured for the html files don't trigger a
+# global reconfigure
+
+set(SRC_DIR "@CMAKE_CURRENT_SOURCE_DIR@")
+set(BIN_DIR "@CMAKE_CURRENT_BINARY_DIR@")
+
+set(PROJECT_VERSION "@PROJECT_VERSION@")
+set(DOWNLOAD_SECTION "@DOWNLOAD_SECTION@")
+
+configure_file(${SRC_DIR}/index.md
+ ${BIN_DIR}/index.md @ONLY)
"@INCLUDE = ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-compact\n")
endif()
- FILE(COPY index.html DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
configure_file(RunDoxygen.cmake.cmakein RunDoxygen.cmake @ONLY)
add_custom_target(doc-full
${CMAKE_COMMAND} -DDOCTYPE=full -P RunDoxygen.cmake
# FILE_PATTERNS += *.cu *.cuh
EXAMPLE_PATH = @CMAKE_SOURCE_DIR@
RECURSIVE = YES
-EXCLUDE = @CMAKE_SOURCE_DIR@/doxygen/examples \
+EXCLUDE = @CMAKE_CURRENT_SOURCE_DIR@/examples \
@CMAKE_SOURCE_DIR@/src/contrib \
@CMAKE_SOURCE_DIR@/src/external \
@CMAKE_SOURCE_DIR@/src/gromacs/selection/parser.cpp \
DOT_MULTI_TARGETS = YES
# According to Doxygen docs, this is required for svg support on IE
HTML_FILE_EXTENSION = .xhtml
+
+OUTPUT_DIRECTORY = @HTML_OUTPUT_DIR@/doxygen
# These pages include documentation that does not belong to the public API
# documentation; exclude them from the generated documentation
-EXCLUDE += @CMAKE_SOURCE_DIR@/doxygen/doxygen.md
-EXCLUDE += @CMAKE_SOURCE_DIR@/doxygen/unittesting.md
-EXCLUDE += @CMAKE_SOURCE_DIR@/doxygen/wrapperbinary.md
-EXCLUDE += @CMAKE_SOURCE_DIR@/doxygen/simd.md
+EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/doxygen.md
+EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/unittesting.md
+EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/wrapperbinary.md
+EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/simd.md
INTERNAL_DOCS = NO
HIDE_UNDOC_CLASSES = YES
if (result)
message(FATAL_ERROR "Doxygen failed. "
"Please run '${DOXYGEN_EXECUTABLE} Doxyfile-${DOCTYPE}' "
- "in the doxygen/ subdirectory in the build tree to see the details.")
+ "in the docs/doxygen/ subdirectory in the build tree to see the details.")
endif()
file(READ doxygen-${DOCTYPE}.log DOXYGEN_WARNINGS)
==========================
If you simply want to see up-to-date documentation, you can go to
-http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-lib/index.xhtml
+http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml
to see the documentation for the current development version.
-Jenkins also runs Doxygen for all changes pushed to Gerrit for master, and the
+Jenkins also runs Doxygen for all changes pushed to Gerrit for
+release-5-0 and master branches, and the
resulting documentation can be viewed from the link posted by Jenkins. The
Doxygen build is marked as unstable if it introduces any Doxygen warnings.
CMake option, which removes some large generated graphs from the documentation
and speeds up the process significantly.
-All files related to Doxygen reside in the `doxygen/` subdirectory in the source
+All files related to Doxygen reside in the `docs/doxygen/` subdirectory in the source
and build trees. In a freshly checked out source tree, this directory contains
various `Doxyfile-*.cmakein` files. When you run CMake, corresponding files
`Doxyfile-user`, `Doxyfile-lib`, and `Doxyfile-full` are generated at the
be produced under the current working directory), or build one of the
`doc-user`, `doc-lib`, and `doc-full` targets. The targets run Doxygen in a
quieter mode and only show the warnings if there were any, and put the output
-under `doxygen/` in the build tree. The `doc-all` target builds all three
+under `docs/html/doxygen/` in the build tree, so that the Doxygen build
+cooperates with the broader `webpage` target. The `doc-all` target builds all three
targets with less typing.
The generated documentation is put under `html-user/`, `html-lib/`, and/or
-`html-full/` in the output directory. Open `index.xhtml` file from one of
+`html-full/`. Open `index.xhtml` file from one of
these subdirectories to start browsing (for \Gromacs developers, the
`html-lib/` is a reasonable starting point). Log files with all Doxygen
-warnings are also produced as `doxygen-*.log`, so you can inspect them after
+warnings are also produced as `docs/doxygen/doxygen-*.log`, so you can inspect them after
the run.
You will need Doxygen 1.8.5 to build the current documentation. Other versions
Empty lines and lines starting with `#` are ignored.
To add suppression for an issue, the line that reports the issue can be copied
-into `suppressios.txt`, and the line number (if any) removed. If the
+into `suppressions.txt`, and the line number (if any) removed. If the
issue does not have a file name (or a pseudo-file) associated, a leading `:`
must be added. To cover many similar issues, parts of the line can then be
replaced with wildcards.
As a side effect, the XML extraction makes Doxygen parse all comments in the
code, even if they do not appear in the documentation. This can reveal latent
issues in the comments, like invalid Doxygen syntax. The messages from the XML
-parsing are stored in `doxygen/doxygen-xml.log` in the build tree, similar to
+parsing are stored in `docs/doxygen/doxygen-xml.log` in the build tree, similar to
other Doxygen runs.
The `doc-check` target requires Python 2.7 (other versions may work, but have
-------------
The pages that are accessible through navigation from the front page are
-written using Markdown and are located under `doxygen/`. Each page should be
+written using Markdown and are located under `docs/doxygen/`. Each page should be
placed in the page hierarchy by making it a subpage of another page, i.e., it
should be referenced once using \c \\subpage. `mainpage.md` is the root of the
hierarchy.
module. The name of the group should be `module_`<em>name</em>, where _name_
is the name of the subdirectory that hosts the module.
-The module should be added to an appropriate group (see `doxygen/misc.cpp` for
+The module should be added to an appropriate group (see `docs/doxygen/misc.cpp` for
definitions) using \c \\ingroup to organize the "Modules" tab in the generated
documentation.
provide a high-level overview of the source tree on the generated "Files" page.
A reference to the module is typically sufficient as a brief description for a
directory. All directories are currently documented in
-`doxygen/directories.cpp`.
+`docs/doxygen/directories.cpp`.
Examples
If only_files is True, XML data is not loaded for code constructs, but
only for files, directories, and their potential parents.
"""
- xmldir = os.path.join(self._build_root, 'doxygen', 'xml')
+ xmldir = os.path.join(self._build_root, 'docs', 'html', 'doxygen', 'xml')
self._docset = xml.DocumentationSet(xmldir, self._reporter)
if only_files:
self._docset.load_file_details()
--- /dev/null
+% GROMACS @PROJECT_VERSION@
+
+@DOWNLOAD_SECTION@
+
+[/a/]: # (TODO in release-5-0 branch: consolidate at least some of the material in the Documentation links below into the new user guide, along with all of http://www.gromacs.org/Documentation/Cut-off_schemes, http://www.gromacs.org/Documentation/Acceleration_and_parallelization and http://www.gromacs.org/Documentation/Performance_checklist)
+
+# Documentation
+
+* [Installation Guide](install-guide.html)
+ As [PDF](install-guide.pdf)
+
+* User Guide - coming soon!
+
+* [Online Reference](online.html)
+
+* [Reference manual](manual-@PROJECT_VERSION@.pdf) (PDF format)
+
+* Answers to [Frequently Asked Questions](http://www.gromacs.org/Documentation/FAQs)
+
+* Coping with [GROMACS errors](http://www.gromacs.org/Documentation/Errors)
+
+* Links to [tutorial material](http://www.gromacs.org/Documentation/Tutorials)
+
+# Documentation for developers
+
+* [Doxygen code documentation](doxygen/html-lib/index.xhtml)
+
+* Developer Guide - coming soon (in master branch)!
+
+[/b/]: # (TODO in master branch: consolidate much of the wiki material into a proper developer guide, and link to it here)
if(INSTALL_GUIDE_BUILD_IS_POSSIBLE)
# Do replacement of CMake variables for version strings, etc.
+ # This defers until build time the configuration of
+ # install-guide.md, which could be faster for all the
+ # configurations that don't make the install guide even though it
+ # was possible.
configure_file(configure-install-guide.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/configure-install-guide.cmake
@ONLY)
- # This defers until build time the configuration of
- # install-guide.md, which could be faster
+ # Configure the install-guide.md at build time
add_custom_command(
- OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/install-guide.md
+ OUTPUT ${CMAKE_BINARY_DIR}/install-guide.md
COMMAND ${CMAKE_COMMAND}
-P ${CMAKE_CURRENT_BINARY_DIR}/configure-install-guide.cmake
DEPENDS
VERBATIM
)
- # Make the HTML install guide
- add_custom_command(
- OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/install-guide.html
- COMMAND pandoc -t html -o ${CMAKE_CURRENT_BINARY_DIR}/install-guide.html install-guide.md -s --toc
- DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/install-guide.md
- VERBATIM
- )
-
# Make the INSTALL file for CPack for the tarball. This gets put
# into the tarball via the CPack rules in the top-level
# CMakeLists.txt
add_custom_command(
OUTPUT final/INSTALL
COMMAND ${CMAKE_COMMAND} -E make_directory final
- COMMAND pandoc -t plain -o final/INSTALL install-guide.md
- DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/install-guide.md
+ COMMAND ${PANDOC_EXECUTABLE} -t plain -o final/INSTALL install-guide.md
+ DEPENDS
+ ${CMAKE_BINARY_DIR}/install-guide.md
VERBATIM
)
- # Add a top-level target for the others to hook onto
+ # Make the single-page HTML install guide
+ add_custom_command(
+ OUTPUT ${HTML_OUTPUT_DIR}/install-guide.html
+ COMMAND
+ ${PANDOC_EXECUTABLE} install-guide.md -o ${HTML_OUTPUT_DIR}/install-guide.html -s --toc --css buttondown.css
+ DEPENDS
+ ${CMAKE_BINARY_DIR}/install-guide.md
+ VERBATIM
+ )
+
+ # Make the PDF install guide
+ add_custom_command(
+ OUTPUT ${HTML_OUTPUT_DIR}/install-guide.pdf
+ COMMAND
+ ${PANDOC_EXECUTABLE} install-guide.md -o ${HTML_OUTPUT_DIR}/install-guide.pdf -s --toc
+ DEPENDS
+ ${CMAKE_BINARY_DIR}/install-guide.md
+ VERBATIM
+ )
+
+ # Make the multi-page HTML install guide
+ #
+ # TODO This is currently disabled, because the pandoc-specific
+ # buttondown.css doesn't work with the different kind of output
+ # makeinfo produces. When we understand better how we want to
+ # do generation, decide whether we want multi-page HTML output
+ # and how to make it work well.
+ #
+ # add_custom_command(
+ # OUTPUT ${HTML_OUTPUT_DIR}/index.html
+ # COMMAND
+ # ${PANDOC_EXECUTABLE} install-guide.md -o install-guide.texi -s
+ # COMMAND
+ # ${MAKEINFO_EXECUTABLE} install-guide.texi --html -o ${HTML_OUTPUT_DIR}/install-guide --css-ref buttondown.css
+ # DEPENDS
+ # ${CMAKE_BINARY_DIR}/install-guide.md
+ # VERBATIM
+ # )
+
+ # Add a top-level target for the webpage build to hook onto
add_custom_target(install-guide
DEPENDS
- ${CMAKE_CURRENT_BINARY_DIR}/install-guide.html
- final/INSTALL
+ final/INSTALL
+ ${HTML_OUTPUT_DIR}/install-guide.html
+ ${HTML_OUTPUT_DIR}/install-guide.pdf
VERBATIM
)
endif()
+
+set(INSTALL_GUIDE_BUILD_IS_POSSIBLE ${INSTALL_GUIDE_BUILD_IS_POSSIBLE} PARENT_SCOPE)
% Installation guide for GROMACS @PROJECT_VERSION@
-# Building GROMACS #
+# Introduction to building GROMACS #
These instructions pertain to building GROMACS
@PROJECT_VERSION@. Up-to-date installation instructions may be found
at <http://www.gromacs.org/Documentation/Installation_Instructions>.
-# Quick and dirty installation #
+## Quick and dirty installation ##
1. Get the latest version of your C and C++ compilers.
2. Check that you have CMake version @GMX_CMAKE_MINIMUM_REQUIRED_VERSION@ or later.
hardware, libraries, and compilers are only going to continue to get
more complex.
-# Typical GROMACS installation #
+## Typical GROMACS installation ##
As above, and with further details below, but you should consider
using the following [CMake options](#using-cmake-command-line-options) with the
* `-DGMX_FFT_LIBRARY=xxx` to select whether to use `fftw`, `mkl` or `fftpack` libraries for [FFT support](#fast-fourier-transform-library)
* `-DCMAKE_BUILD_TYPE=Debug` to build GROMACS in debug mode
-# Building older GROMACS versions #
+## Building older GROMACS versions ##
For installation instructions for old GROMACS versions, see the
documentation at
transforms, and a software library to perform these is always
required. We recommend [FFTW](http://www.fftw.org) (version 3 or
higher only) or
-[Intel MKL](http://software.intel.com/en-us/intel-mkl). The choice of
+[Intel MKL](https://software.intel.com/en-us/intel-mkl). The choice of
library can be set with `cmake -DGMX_FFT_LIBRARY=<name>`, where
`<name>` is one of `fftw`, `mkl`, or `fftpack`. FFTPACK is bundled
with GROMACS as a fallback, and is acceptable if mdrun performance is
`share/man/`
: Installed man pages go here.
-## Building GROMACS ##
+## Compiling and linking ##
-Once you have configured with `cmake`, you can build GROMACS. It is
-expected that the `make` procedure will always complete successfully,
-and give few or no warnings. The tests GROMACS makes on the settings
+Once you have configured with `cmake`, you can build GROMACS with `make`.
+It is expected that this will always complete successfully, and
+give few or no warnings. The CMake-time tests GROMACS makes on the settings
you choose are pretty extensive, but there are probably a few cases we
have not thought of yet. Search the web first for solutions to
problems, but if you need help, ask on gmx-users, being sure to
If you have a multi-core or multi-CPU machine with `N`
processors, then using
+
$ make -j N
+
will generally speed things up by quite a bit. Other build generator systems
supported by `cmake` (e.g. `ninja`) also work well.
--- /dev/null
+# .ini-style config file for linkchecker. Recommended use
+# for testing the GROMACS webpage is
+#
+# linkchecker index.html --ignore-url html-full --ignore-url html-user --ignore-url html-lib -f linkcheckerrc
+[filtering]
+# This site gives warnings about changed URLs, and suggests
+# using... the same URLs. Well done, someone.
+ignore=www.ks.uiuc.edu
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# updates in that HTML file without copying files by hand.
ADD_CUSTOM_COMMAND(OUTPUT ${output_dir}/mdp_opt.tex
- COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/mkmdp ARGS ${CMAKE_SOURCE_DIR}/share/html
- DEPENDS mkmdp ${CMAKE_SOURCE_DIR}/share/html/online/mdp_opt.html
+ COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/mkmdp ARGS ${CMAKE_CURRENT_SOURCE_DIR}/../old-html
+ DEPENDS mkmdp ${CMAKE_CURRENT_SOURCE_DIR}/../old-html/online/mdp_opt.html
)
# Finally, the command to build the manual.
# TODO Arrange for the "make manual" target to explain that this can't
# be done
endif()
+
+set(MANUAL_BUILD_IS_POSSIBLE ${MANUAL_BUILD_IS_POSSIBLE} PARENT_SCOPE)
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013, by the GROMACS development team, led by
+% Copyright (c) 2013,2014, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013, by the GROMACS development team, led by
+% Copyright (c) 2013,2014, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013, by the GROMACS development team, led by
+% Copyright (c) 2013,2014, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013, by the GROMACS development team, led by
+% Copyright (c) 2013,2014, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013, by the GROMACS development team, led by
+% Copyright (c) 2013,2014, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013, by the GROMACS development team, led by
+% Copyright (c) 2013,2014, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
Files with the edi file extension contain information for
<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
to run Molecular Dynamics with Essential Dynamics constraints.
-These files can be generated by the program <tt>WEDSAM</tt> which uses
+<!-- WEDSAM and ESSDYN seem to have vanished from WhatIf and the web-->
+<!--These files can be generated by the program <tt>WEDSAM</tt> which uses
output from the programs in the <tt>ESSDYN</tt> menu of the
-<A HREF="http://www.sander.embl-heidelberg.de/whatif/">WHAT IF</A> program.
+<A HREF="http://www.sander.embl-heidelberg.de/whatif/">WHAT IF</A> program.-->
<a href="../programs/gmx-grompp.html">gmx grompp</a> and
<a href="../programs/gmx-convert-tpr.html">gmx convert-tpr</a>
<dt><a href="m2p.html">m2p</a>
-<dd>input for <a href="../programs/xpm2ps.html">gmx xpm2ps</a>
+<dd>input for <a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</a>
</dl>
<br><dt><h3>Structure files</h3>
--- /dev/null
+<title>hdb file format</title>
+<H3>Description</H3>
+The hdb file extension stands for hydrogen database
+Such a file is needed by <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
+when building hydrogen atoms that were either originally missing, or that
+were removed with <tt>-ignh</tt>.
+</PRE>
<hr>
<p>
-With this input <a href="grompp.html"><tt>grompp</tt></a> will produce
+With this input <a href="../programs/gmx-grompp.html"><tt>grompp</tt></a> will produce
an <tt>mdout.mdp</tt> with all the options and descriptions:
</p>
performed, for instance making use of the fact that atoms close
in sequence are usually close in space too (e.g. a water molecule).
To this end, the <i>xdr</i> library is extended with a special routine
-to write 3-D float coordinates. This routine was written by Frans van Hoesel
-as part of an Europort project, and can be obtained through <a href="http://hpcv100.rc.rug.nl/xdrf.html">this link</a>.
+to write 3-D float coordinates. <!-- link is broken--><!-- This routine was written by Frans van Hoesel
+as part of an Europort project, and can be obtained through <a href="http://hpcv100.rc.rug.nl/xdrf.html">this link</a>.-->
<p>
All the data is stored using calls to <i>xdr</i> routines.
+++ /dev/null
-<html>
-<body>
- <h1>Doxygen documentation for Gromacs</h1>
- <p>
- Each set of documentation below includes all the information from
- the sets above it.
- </p>
- <ul>
- <li><a href="html-user/index.xhtml">Public API documentation</a></li>
- <li><a href="html-lib/index.xhtml">Library documentation, excluding intramodule documentation</a></li>
- <li><a href="html-full/index.xhtml">Full documentation including internal functions</a></li>
- </ul>
-</body>
-</html>
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-add_subdirectory(html)
-add_subdirectory(man)
add_subdirectory(template)
install(FILES README.tutor README_FreeEnergyModifications.txt
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff
