endforeach()
gmx_add_custom_output_target(sphinx-input OUTPUT STAMP
DEPENDS ${SPHINX_INPUT_FILES})
+ gmx_add_custom_output_target(sphinx-programs OUTPUT STAMP
+ COMMAND ${CMAKE_COMMAND} -E make_directory programs
+ COMMAND gmx -quiet help -export rst
+ DEPENDS gmx
+ WORKING_DIRECTORY ${SPHINX_INPUT_DIR}
+ COMMENT "Generating reStructuredText help")
+ # This dependency ensures that the directories exist before the
+ # executable tries to write things there.
+ add_dependencies(sphinx-programs sphinx-input)
# Make the INSTALL file for CPack for the tarball. This gets put
# into the tarball via the CPack rules below, which requires that
COMMENT "Building HTML documentation with Sphinx"
VERBATIM
)
- add_dependencies(webpage-sphinx sphinx-input)
+ add_dependencies(webpage-sphinx sphinx-input sphinx-programs)
endif()
set(HTML_BUILD_IS_POSSIBLE OFF)
.. _sample mdp file: ../online/mdp.html
.. _download: ../download.html
-.. TODO Consider generating these (e.g. with the commandline module that also generates the link targets). For now,
- the Jenkins link checker will keep things working.
-
-.. _gmx bar: ../programs/gmx-bar.html
-.. _gmx energy: ../programs/gmx-energy.html
-.. _gmx convert-tpr: ../programs/gmx-convert-tpr.html
-.. _gmx dipoles: ../programs/gmx-dipoles.html
-.. _gmx tune_pme: ../programs/gmx-tune_pme.html
-.. _gmx do_dssp: ../programs/gmx-do_dssp.html
-.. _gmx view: ../programs/gmx-view.html
-.. _gmx eneconv: ../programs/gmx-eneconv.html
-.. _gmx wham: ../programs/gmx-wham.html
-.. _gmx grompp: ../programs/gmx-grompp.html
-.. _gmx solvate: ../programs/gmx-solvate.html
-.. _gmx editconf: ../programs/gmx-editconf.html
-.. _gmx pdb2gmx: ../programs/gmx-pdb2gmx.html
-.. _gmx trjconv: ../programs/gmx-trjconv.html
-.. _gmx trjcat: ../programs/gmx-trjcat.html
-.. _gmx eneconv: ../programs/gmx-eneconv.html
-.. _gmx mdrun: ../programs/gmx-mdrun.html
-.. _mdrun: ../programs/gmx-mdrun.html
-.. _mdrun_mpi: ../programs/gmx-mdrun.html
-
.. _pdb: ../online/pdb.html
.. _gro: ../online/gro.html
.. _top: ../online/top.html
* ``-DCMAKE_CXX_COMPILER=xxx`` equal to the name of the C++98 `compiler`_ you wish to use (or the environment variable ``CXX``)
* ``-DGMX_MPI=on`` to build using `MPI support`_
* ``-DGMX_GPU=on`` to build using nvcc to run with an NVIDIA `native GPU acceleration`_
-* ``-DGMX_SIMD=xxx`` to specify the level of `SIMD support`_ of the node on which mdrun_ will run
+* ``-DGMX_SIMD=xxx`` to specify the level of `SIMD support`_ of the node on which :ref:`gmx mdrun` will run
* ``-DGMX_BUILD_MDRUN_ONLY=on`` for `building only mdrun`_, e.g. for compute cluster back-end nodes
* ``-DGMX_DOUBLE=on`` to run |Gromacs| in double precision (slower, and not normally useful)
* ``-DCMAKE_PREFIX_PATH=xxx`` to add a non-standard location for CMake to `search for libraries, headers or programs`_
simulations you want to run. You will still get *good*,
performance with the default build and runtime options, but if you
truly want to push your hardware to the performance limit, the days of
-just blindly starting programs with mdrun_ are gone.
+just blindly starting programs with :ref:`gmx mdrun` are gone.
CMake
-----
matrix manipulation, but they do not provide any benefits for normal
simulations. Configuring these are discussed at
`linear algebra libraries`_.
-* The built-in |Gromacs| trajectory viewer `gmx view`_ requires X11 and
+* The built-in |Gromacs| trajectory viewer :ref:`gmx view` requires X11 and
Motif/Lesstif libraries and header files. You may prefer to use
third-party software for visualization, such as VMD_ or PyMol_.
* An external TNG library for trajectory-file handling can be used,
8. ``Sparc64_HPC_ACE`` Fujitsu machines like the K computer have this.
The CMake configure system will check that the compiler you have
-chosen can target the architecture you have chosen. mdrun_ will check
+chosen can target the architecture you have chosen. :ref:`gmx mdrun` will check
further at runtime, so if in doubt, choose the lowest setting you
-think might work, and see what mdrun_ says. The configure system also
+think might work, and see what :ref:`gmx mdrun` says. The configure system also
works around many known issues in many versions of common HPC
compilers. However, since the options also enable general compiler
flags for the platform in question, you can end up in situations
where e.g. an ``AVX_128_FMA`` binary will just crash on any
Intel machine, since the code will try to execute general illegal
-instructions (inserted by the compiler) before mdrun_ gets to the
+instructions (inserted by the compiler) before :ref:`gmx mdrun` gets to the
architecture detection routines.
A further ``GMX_SIMD=Reference`` option exists, which is a special
discourage attempts to use a single |Gromacs| installation when the
execution environment is heterogeneous, such as a mix of AVX and
earlier hardware, because this will lead to programs (especially
-mdrun_) that run slowly on the new hardware. Building two full
+:ref:`gmx mdrun`) that run slowly on the new hardware. Building two full
installations and locally managing how to call the correct one
(e.g. using the module system) is the recommended
approach. Alternatively, as at the moment the |Gromacs| tools do not
make strong use of SIMD acceleration, it can be convenient to create
an installation with tools portable across different x86 machines, but
-with separate mdrun_ binaries for each architecture. To achieve this,
+with separate :ref:`gmx mdrun` binaries for each architecture. To achieve this,
one can first build a full installation with the
least-common-denominator SIMD instruction set, e.g. ``-DGMX_SIMD=SSE2``,
-then build separate mdrun_ binaries for each architecture present in
+then build separate :ref:`gmx mdrun` binaries for each architecture present in
the heterogeneous environment. By using custom binary and library
suffixes for the mdrun-only builds, these can be installed to the
same location as the "generic" tools installation.
It is sometimes convenient to have different versions of the same
|Gromacs| programs installed. The most common use cases have been single
and double precision, and with and without MPI. This mechanism can
-also be used to install side-by-side multiple versions of mdrun_
+also be used to install side-by-side multiple versions of :ref:`gmx mdrun`
optimized for different CPU architectures, as mentioned previously.
By default, |Gromacs| will suffix programs and libraries for such builds
Past versions of the build system offered "mdrun" and "install-mdrun"
targets (similarly for other programs too) to build and install only
the mdrun program, respectively. Such a build is useful when the
-configuration is only relevant for mdrun_ (such as with
+configuration is only relevant for :ref:`gmx mdrun` (such as with
parallelization options for MPI, SIMD, GPUs, or on BlueGene or Cray),
or the length of time for the compile-link-install cycle is relevant
when developing.
This is now supported with the ``cmake`` option
``-DGMX_BUILD_MDRUN_ONLY=ON``, which will build a cut-down version of
-``libgromacs`` and/or the mdrun_ program (according to whether shared
+``libgromacs`` and/or the :ref:`gmx mdrun` program (according to whether shared
or static). Naturally, now ``make install`` installs only those
products. By default, mdrun-only builds will default to static linking
against |Gromacs| libraries, because this is generally a good idea for
source /your/installation/prefix/here/bin/GMXRC
./gmxtest.pl all -np 2
-If your mdrun_ program has been suffixed in a non-standard way, then
+If your :ref:`gmx mdrun` program has been suffixed in a non-standard way, then
the ``./gmxtest.pl -mdrun`` option will let you specify that name to the
test machinery. You can use ``./gmxtest.pl -double`` to test the
double-precision version. You can use ``./gmxtest.pl -crosscompiling``
We are still working on a set of benchmark systems for testing
the performance of |Gromacs|. Until that is ready, we recommend that
you try a few different parallelization options, and experiment with
-tools such as `gmx tune_pme`_.
+tools such as :ref:`gmx tune_pme`.
Having difficulty?
------------------
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015, 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.
set(OUTPUT_DIR final)
-set(HTML_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/${OUTPUT_DIR})
if (GMX_BUILD_HELP)
# Unlike the man and completion targets, this target is not built
# automatically with GMX_BUILD_HELP=AUTO, since most people will not
endif()
set_directory_properties(PROPERTIES
ADDITIONAL_MAKE_CLEAN_FILES "${OUTPUT_DIR};header.html")
- set(HTML_PAGE_DIR ${CMAKE_CURRENT_BINARY_DIR}/${OUTPUT_DIR})
endif()
-
-if (SOURCE_IS_SOURCE_DISTRIBUTION OR GMX_BUILD_HELP_FORCE)
- install(DIRECTORY ${HTML_PAGE_DIR}/
- DESTINATION ${DATA_INSTALL_DIR}/html
- COMPONENT html)
-endif()
-gmx_cpack_add_generated_source_directory(${OUTPUT_DIR})
Molecular Topology file (``.top``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-The molecular topology file is generated by the program `gmx
-pdb2gmx`_. `gmx pdb2gmx`_ translates a PDB_ structure file of any
+The molecular topology file is generated by the program :ref:`gmx pdb2gmx`.
+:ref:`gmx pdb2gmx` translates a PDB_ structure file of any
peptide or protein to a molecular topology file. This topology file
contains a complete description of all the interactions in your
peptide or protein.
Molecular Structure file (``.gro``, ``.pdb``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-When `gmx pdb2gmx`_ is executed to generate a molecular topology, it
+When :ref:`gmx pdb2gmx` is executed to generate a molecular topology, it
also translates the structure file (pdb_ file) to a GROMOS structure
file (gro_ file). The main difference between a pdb_ file and a gromos
file is their format and that a gro_ file can also hold
velocities. However, if you do not need the velocities, you can also
use a PDB_ file in all programs. To generate a box of solvent
-molecules around the peptide, the program `gmx solvate`_ is
-used. First the program `gmx editconf`_ should be used to define a box
-of appropriate size around the molecule. `gmx solvate`_ solvates a
+molecules around the peptide, the program :ref:`gmx solvate` is
+used. First the program :ref:`gmx editconf` should be used to define a box
+of appropriate size around the molecule. :ref:`gmx solvate` solvates a
solute molecule (the peptide) into any solvent (in this case,
-water). The output of `gmx solvate`_ is a gromos structure file of the
-peptide solvated in water. `gmx solvate`_ also changes the molecular
-topology file (generated by `gmx pdb2gmx`_) to add solvent to the
+water). The output of :ref:`gmx solvate` is a gromos structure file of the
+peptide solvated in water. :ref:`gmx solvate` also changes the molecular
+topology file (generated by :ref:`gmx pdb2gmx`) to add solvent to the
topology.
Molecular Dynamics parameter file (``.mdp``)
topology (top_ file) MD-parameters (mdp_ file) and (optionally) the
index file (ndx_) to generate a run input file (tpr_ extension). This
file contains all information needed to start a simulation with
-|Gromacs|. The `gmx grompp`_ program processes all input files and
+|Gromacs|. The :ref:`gmx grompp` program processes all input files and
generates the run input tpr_ file.
Trajectory file (``.trr``, ``.tng``, or ``.xtc``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Once the run input file is available, we can start the simulation. The
-program which starts the simulation is called `gmx mdrun`_ (or
-sometimes just mdrun, or mdrun_mpi). The only input file of `gmx
-mdrun`_ that you usually need in order to start a run is the run input
-file (tpr_ file). The typical output files of `gmx mdrun`_ are the
+program which starts the simulation is called :ref:`gmx mdrun` (or
+sometimes just mdrun, or mdrun_mpi). The only input file of :ref:`gmx mdrun`
+that you usually need in order to start a run is the run input
+file (tpr_ file). The typical output files of :ref:`gmx mdrun` are the
trajectory file (trr_ file), a logfile (log_ file), and perhaps a
checkpoint file (cpt_ file).
|Gromacs| includes many tools for preparing, running and analysing
molecular dynamics simulations. These are all structured as part of the
-gmx wrapper binary, and invoked with commands like `gmx grompp`_. mdrun_
-is the only other binary that
+gmx wrapper binary, and invoked with commands like :ref:`gmx grompp`.
+:ref:`mdrun <gmx mdrun>` is the only other binary that
:ref:`can be built <building just the mdrun binary>`; in the normal
build it can be run with ``gmx mdrun``. Documentation for these can
-be found at the links below.
+be found at the links below:
-- Tools documentation `by name <../programs/byname.html>`_
-- Tools documentation `by topic <../programs/bytopic.html>`_
+.. toctree::
+
+ /programs/byname
+ /programs/bytopic
+
+.. toctree::
+ :hidden:
+ :glob:
+
+ /programs/gmx-*
Common options and behaviour
----------------------------
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, 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.
* HelpExportHtml
*/
-/*! \internal \brief
+/*! \internal
+ * \brief
* Implements export for HTML help.
*
+ * This whole class can go once docs/old-html/ no longer requires header.html
+ * that it generates.
+ *
* \ingroup module_commandline
*/
class HelpExportHtml : public HelpExportInterface
{
public:
//! Initializes HTML exporter.
- explicit HelpExportHtml(const CommandLineHelpModuleImpl &helpModule);
+ HelpExportHtml();
+
+ virtual void startModuleExport() {}
+ virtual void exportModuleHelp(
+ const CommandLineModuleInterface & /*module*/,
+ const std::string & /*tag*/,
+ const std::string & /*displayName*/) {}
+ virtual void finishModuleExport() {}
+
+ virtual void startModuleGroupExport() {}
+ virtual void exportModuleGroup(const char * /*title*/,
+ const ModuleGroupContents & /*modules*/) {}
+ virtual void finishModuleGroupExport() {}
+};
+
+HelpExportHtml::HelpExportHtml()
+{
+ std::string header = gmx::File::readToString("header.html.in");
+ header = replaceAll(header, "@VERSION@", gmx_version());
+ gmx::File::writeFileFromString("header.html", header);
+}
+
+/********************************************************************
+ * HelpExportReStructuredText
+ */
+
+/*! \internal \brief
+ * Implements export for web pages as reStructuredText.
+ *
+ * \ingroup module_commandline
+ */
+class HelpExportReStructuredText : public HelpExportInterface
+{
+ public:
+ //! Initializes reST exporter.
+ explicit HelpExportReStructuredText(
+ const CommandLineHelpModuleImpl &helpModule);
virtual void startModuleExport();
virtual void exportModuleHelp(
virtual void finishModuleGroupExport();
private:
- void setupHeaderAndFooter();
-
- void writeHtmlHeader(File *file, const std::string &title) const;
- void writeHtmlFooter(File *file) const;
-
HelpLinks links_;
boost::scoped_ptr<File> indexFile_;
- std::string header_;
- std::string footer_;
};
-HelpExportHtml::HelpExportHtml(const CommandLineHelpModuleImpl &helpModule)
- : links_(eHelpOutputFormat_Html)
+HelpExportReStructuredText::HelpExportReStructuredText(
+ const CommandLineHelpModuleImpl &helpModule)
+ : links_(eHelpOutputFormat_Rst)
{
+#if 0 // TODO: Investigate how these links can be made to work again.
File linksFile("links.dat", "r");
std::string line;
while (linksFile.readLine(&line))
links_.addLink(line, "../online/" + line, line);
}
linksFile.close();
+#endif
initProgramLinks(&links_, helpModule);
- setupHeaderAndFooter();
}
-void HelpExportHtml::setupHeaderAndFooter()
+void HelpExportReStructuredText::startModuleExport()
{
- header_ = gmx::File::readToString("header.html.in");
- header_ = replaceAll(header_, "@VERSION@", gmx_version());
- gmx::File::writeFileFromString("header.html", header_);
- header_ = replaceAll(header_, "@ROOTPATH@", "../");
- footer_ = gmx::File::readToString("footer.html");
+ indexFile_.reset(new File("programs/byname.rst", "w"));
+ indexFile_->writeLine("Tools by Name");
+ indexFile_->writeLine("=============");
}
-void HelpExportHtml::startModuleExport()
-{
- indexFile_.reset(new File("final/programs/byname.html", "w"));
- writeHtmlHeader(indexFile_.get(), "GROMACS Programs by Name");
- indexFile_->writeLine("<H3>GROMACS Programs Alphabetically</H3>");
-}
-
-void HelpExportHtml::exportModuleHelp(
+void HelpExportReStructuredText::exportModuleHelp(
const CommandLineModuleInterface &module,
const std::string &tag,
const std::string &displayName)
{
- File file("final/programs/" + tag + ".html", "w");
- writeHtmlHeader(&file, displayName);
-
- CommandLineHelpContext context(&file, eHelpOutputFormat_Html, &links_);
+ // TODO: Ideally, the file would only be touched if it really changes.
+ // This would make Sphinx reruns much faster.
+ File file("programs/" + tag + ".rst", "w");
+ file.writeLine(formatString(".. _%s:", displayName.c_str()));
+ file.writeLine();
+ file.writeLine(displayName);
+ file.writeLine(std::string(displayName.length(), '='));
+ CommandLineHelpContext context(&file, eHelpOutputFormat_Rst, &links_);
context.setModuleDisplayName(displayName);
module.writeHelp(context);
-
- writeHtmlFooter(&file);
file.close();
- indexFile_->writeLine(formatString("<a href=\"%s.html\">%s</a> - %s<br>",
- tag.c_str(), displayName.c_str(),
+ indexFile_->writeLine(formatString("* :doc:`%s <%s>` - %s",
+ displayName.c_str(), tag.c_str(),
module.shortDescription()));
}
-void HelpExportHtml::finishModuleExport()
+void HelpExportReStructuredText::finishModuleExport()
{
- writeHtmlFooter(indexFile_.get());
indexFile_->close();
+ indexFile_.reset();
}
-void HelpExportHtml::startModuleGroupExport()
+void HelpExportReStructuredText::startModuleGroupExport()
{
- indexFile_.reset(new File("final/programs/bytopic.html", "w"));
- writeHtmlHeader(indexFile_.get(), "GROMACS Programs by Topic");
- indexFile_->writeLine("<H3>GROMACS Programs by Topic</H3>");
+ indexFile_.reset(new File("programs/bytopic.rst", "w"));
+ indexFile_->writeLine("Tools by Topic");
+ indexFile_->writeLine("==============");
}
-void HelpExportHtml::exportModuleGroup(const char *title,
- const ModuleGroupContents &modules)
+void HelpExportReStructuredText::exportModuleGroup(
+ const char *title,
+ const ModuleGroupContents &modules)
{
- indexFile_->writeLine(formatString("<H4>%s</H4>", title));
+ indexFile_->writeLine(title);
+ indexFile_->writeLine(std::string(std::strlen(title), '-'));
ModuleGroupContents::const_iterator module;
for (module = modules.begin(); module != modules.end(); ++module)
std::string displayName(tag);
// TODO: This does not work if the binary name would contain a dash,
// but that is not currently the case.
- size_t dashPos = displayName.find('-');
+ const size_t dashPos = displayName.find('-');
GMX_RELEASE_ASSERT(dashPos != std::string::npos,
"There should always be at least one dash in the tag");
displayName[dashPos] = ' ';
- indexFile_->writeLine(formatString("<a href=\"%s.html\">%s</a> - %s<br>",
- tag.c_str(), displayName.c_str(),
+ indexFile_->writeLine(formatString("| :doc:`%s <%s>` - %s",
+ displayName.c_str(), tag.c_str(),
module->second));
}
+ indexFile_->writeLine();
}
-void HelpExportHtml::finishModuleGroupExport()
+void HelpExportReStructuredText::finishModuleGroupExport()
{
- writeHtmlFooter(indexFile_.get());
indexFile_->close();
-}
-
-void HelpExportHtml::writeHtmlHeader(File *file, const std::string &title) const
-{
- file->writeLine(replaceAll(header_, "@TITLE@", title));
-}
-
-void HelpExportHtml::writeHtmlFooter(File *file) const
-{
- file->writeLine(footer_);
+ indexFile_.reset();
}
/********************************************************************
// Add internal topics lazily here.
addTopic(HelpTopicPointer(new CommandsHelpTopic(*impl_)));
- const char *const exportFormats[] = { "man", "html", "completion" };
+ const char *const exportFormats[] = { "man", "html", "rst", "completion" };
std::string exportFormat;
Options options(NULL, NULL);
options.addOption(StringOption("export").store(&exportFormat)
}
else if (exportFormat == "html")
{
- exporter.reset(new HelpExportHtml(*impl_));
+ exporter.reset(new HelpExportHtml());
+ }
+ else if (exportFormat == "rst")
+ {
+ exporter.reset(new HelpExportReStructuredText(*impl_));
}
else if (exportFormat == "completion")
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, 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.
lineLength_ = 70;
file.writeString(name);
break;
- case eHelpOutputFormat_Html:
- lineLength_ = 78;
- file.writeLine("<pre>");
+ case eHelpOutputFormat_Rst:
+ lineLength_ = 74;
+ indent_ += 4;
+ file.writeLine("::");
+ file.writeLine();
+ file.writeString(" ");
file.writeString(name);
break;
default:
{
File &file = context_.outputFile();
file.writeLine();
- if (context_.outputFormat() == eHelpOutputFormat_Html)
- {
- file.writeLine("</pre>");
- }
file.writeLine();
}
fullOptionText.append("]");
const int totalLength = fullOptionText.size();
- if (context_.outputFormat() == eHelpOutputFormat_Html)
- {
- value = replaceAll(value, "<", "<");
- value = replaceAll(value, ">", ">");
- }
-
- File &file = context_.outputFile();
+ File &file = context_.outputFile();
currentLength_ += totalLength;
if (currentLength_ >= lineLength_)
{
return;
}
context.writeTitle("Known Issues");
- if (context.outputFormat() != eHelpOutputFormat_Console)
- {
- context.writeTextBlock("[UL]");
- }
ConstArrayRef<const char *>::const_iterator i;
for (i = bugs_.begin(); i != bugs_.end(); ++i)
{
const char *const bug = *i;
// TODO: The context should be able to do this also for console output, but
// that requires a lot more elaborate parser for the markup.
- if (context.outputFormat() == eHelpOutputFormat_Console)
+ if (context.outputFormat() != eHelpOutputFormat_Man)
{
TextLineWrapperSettings settings;
settings.setIndent(2);
}
else
{
- context.writeTextBlock(formatString("[LI]%s", bug));
+ context.writeTextBlock(formatString("\n- %s", bug));
}
}
- if (context.outputFormat() != eHelpOutputFormat_Console)
- {
- context.writeTextBlock("[ul]");
- }
}
{ "-binwidth", FALSE, etINT, {&ndeg},
"bin width for histograms (degrees)" },
{ "-core_rotamer", FALSE, etREAL, {&core_frac},
- "only the central [TT]-core_rotamer[tt]*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
+ "only the central [TT]-core_rotamer[tt]\\*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
{ "-maxchi", FALSE, etENUM, {maxchistr},
"calculate first ndih [GRK]chi[grk] dihedrals" },
{ "-normhisto", FALSE, etBOOL, {&bNormHisto},
"Option [TT]-temp[tt] sets the temperature required for the computation of the static dielectric constant.",
"[PAR]",
"Option [TT]-eps[tt] controls the dielectric constant of the surrounding medium for simulations using",
- "a Reaction Field or dipole corrections of the Ewald summation ([TT]-eps[tt]=0 corresponds to",
+ "a Reaction Field or dipole corrections of the Ewald summation ([TT]-eps[tt]\\=0 corresponds to",
"tin-foil boundary conditions).",
"[PAR]",
"[TT]-[no]nojump[tt] unfolds the coordinates to allow free diffusion. This is required to get a continuous",
/* "It is also possible to analyse specific hydrogen bonds with",
"[TT]-sel[tt]. This index file must contain a group of atom triplets",
"Donor Hydrogen Acceptor, in the following way:[PAR]",
+ "[TT]",
+ "[ selected ][BR]",
+ " 20 21 24[BR]",
+ " 25 26 29[BR]",
+ " 1 3 6[BR]",
+ "[tt][BR]",
+ "Note that the triplets need not be on separate lines.",
+ "Each atom triplet specifies a hydrogen bond to be analyzed,",
+ "note also that no check is made for the types of atoms.[PAR]",
*/
- "[TT]",
- "[ selected ][BR]",
- " 20 21 24[BR]",
- " 25 26 29[BR]",
- " 1 3 6[BR]",
- "[tt][BR]",
- "Note that the triplets need not be on separate lines.",
- "Each atom triplet specifies a hydrogen bond to be analyzed,",
- "note also that no check is made for the types of atoms.[PAR]",
"[BB]Output:[bb][BR]",
"[TT]-num[tt]: number of hydrogen bonds as a function of time.[BR]",
"of atom pairs with 1/r^3 and 1/r^6 averaged distance below the",
"maximum distance ([TT]-max[tt], which will default to 0.6 in this case)",
"can be generated, by default averaging over equivalent hydrogens",
- "(all triplets of hydrogens named *[123]). Additionally a list of",
+ "(all triplets of hydrogens named \\*[123]). Additionally a list of",
"equivalent atoms can be supplied ([TT]-equiv[tt]), each line containing",
"a set of equivalent atoms specified as residue number and name and",
"atom name; e.g.:[PAR]",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
"If the [TT]-demux[tt] option is given, the N trajectories that are",
"read, are written in another order as specified in the [TT].xvg[tt] file.",
"The [TT].xvg[tt] file should contain something like:[PAR]",
- "[TT]0 0 1 2 3 4 5[BR]",
- "2 1 0 2 3 5 4[tt][BR]",
+ "[TT]0 0 1 2 3 4 5[tt][BR]",
+ "[TT]2 1 0 2 3 5 4[tt][BR]",
"Where the first number is the time, and subsequent numbers point to",
"trajectory indices.",
"The frames corresponding to the numbers present at the first line",
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, 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.
"After calling [gmx-mdrun] several times, detailed performance information",
"is available in the output file [TT]perf.out[tt].",
"[BB]Note[bb] that during the benchmarks, a couple of temporary files are written",
- "(options [TT]-b[tt]*), these will be automatically deleted after each test.[PAR]",
+ "(options [TT]-b*[tt]), these will be automatically deleted after each test.[PAR]",
"If you want the simulation to be started automatically with the",
"optimized parameters, use the command line option [TT]-launch[tt].[PAR]",
"Basic support for GPU-enabled [TT]mdrun[tt] exists. Give a string containing the IDs",
" reaction coordinate you may also generate your own [TT].pdo[tt] files and",
" feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [TT].pdo[tt] file header",
" must be similar to the following:[PAR]",
- "[TT]# UMBRELLA 3.0[BR]",
+ "# UMBRELLA 3.0[BR]",
"# Component selection: 0 0 1[BR]",
"# nSkip 1[BR]",
"# Ref. Group 'TestAtom'[BR]",
"# Nr. of pull groups 2[BR]",
"# Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0[BR]",
"# Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0[BR]",
- "#####[tt][PAR]",
+ "#####[PAR]",
"The number of pull groups, umbrella positions, force constants, and names ",
"may (of course) differ. Following the header, a time column and ",
"a data column for each pull group follows (i.e. the displacement",
"#include <filename>[PAR]",
"The functioning of these statements in your topology may be modulated by",
"using the following two flags in your [TT].mdp[tt] file:[PAR]",
- "[TT]define = -DVARIABLE1 -DVARIABLE2[BR]",
- "include = -I/home/john/doe[tt][BR]",
+ "[TT]define = -DVARIABLE1 -DVARIABLE2[tt][BR]",
+ "[TT]include = -I/home/john/doe[tt][BR]",
"For further information a C-programming textbook may help you out.",
"Specifying the [TT]-pp[tt] flag will get the pre-processed",
"topology file written out so that you can verify its contents.[PAR]",
- /* cpp has been unnecessary for some time, hasn't it?
- "If your system does not have a C-preprocessor, you can still",
- "use [TT]grompp[tt], but you do not have access to the features ",
- "from the cpp. Command line options to the C-preprocessor can be given",
- "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
- */
-
"When using position restraints a file with restraint coordinates",
"can be supplied with [TT]-r[tt], otherwise restraining will be done",
"with respect to the conformation from the [TT]-c[tt] option.",
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, 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.
//! List of replacements for console output.
const t_sandr sandrTty[] = {
+ { "\\*", "*" },
+ { "\\=", "=" },
{ "[TT]", "" },
{ "[tt]", "" },
{ "[BB]", "" },
//! List of replacements for man page output.
const t_sandr sandrMan[] = {
+ { "\\*", "*" },
+ { "\\=", "=" },
{ "[TT]", "\\fB" },
{ "[tt]", "\\fR" },
{ "[BB]", "\\fB" },
{ "[grk]", "" }
};
-//! List of replacements for HTML output.
-const t_sandr sandrHtml[] = {
- { "<", "<" },
- { ">", ">" },
- { "[TT]", "<tt>" },
- { "[tt]", "</tt>" },
- { "[BB]", "<b>" },
- { "[bb]", "</b>" },
- { "[IT]", "<it>" },
- { "[it]", "</it>" },
+//! List of replacements for reStructuredText output.
+const t_sandr sandrRst[] = {
+ { "[TT]", "``" },
+ { "[tt]", "``" },
+ { "[BB]", "**" },
+ { "[bb]", "**" },
+ { "[IT]", "*" },
+ { "[it]", "*" },
{ "[MATH]", "" },
{ "[math]", "" },
- { "[CHEVRON]", "<" },
- { "[chevron]", ">" },
- { "[MAG]", "|" },
- { "[mag]", "|" },
+ { "[CHEVRON]", "<" },
+ { "[chevron]", ">" },
+ { "[MAG]", "\\|" },
+ { "[mag]", "\\|" },
{ "[INT]", "integral" },
{ "[FROM]", " from " },
{ "[from]", "" },
{ "[SUB]", "_" },
{ "[sub]", "" },
{ "[SQRT]", "sqrt(" },
- { "[sqrt]", ")", },
+ { "[sqrt]", ")" },
{ "[EXP]", "exp(" },
{ "[exp]", ")" },
{ "[LN]", "ln(" },
{ "[sinh]", ")" },
{ "[TANH]", "tanh(" },
{ "[tanh]", ")" },
- { "[PAR]", "<p>" },
- { "[BR]", "<br>" },
- { "[UL]", "<ul>" },
- { "[LI]", "<li>" },
- { "[ul]", "</ul>" },
- { "[GRK]", "&" },
- { "[grk]", ";" }
+ { "[PAR]", "\n\n" },
+ // [BR] is fundamentally incompatible with rst
+ { "[BR]", "\n\n"},
+ { "[GRK]", "" },
+ { "[grk]", "" }
};
/*! \brief
case eHelpOutputFormat_Man:
replacement = repall(displayName, sandrMan);
break;
- case eHelpOutputFormat_Html:
+ case eHelpOutputFormat_Rst:
replacement = formatString(
- "<a href=\"%s.html\">%s</a>", targetName.c_str(),
- repall(displayName, sandrHtml).c_str());
+ ":doc:`%s <%s>`", repall(displayName, sandrTty).c_str(),
+ targetName.c_str());
break;
default:
GMX_RELEASE_ASSERT(false, "Output format not implemented for links");
result = repall(result, sandrMan);
return wrapper->wrap(result);
}
- case eHelpOutputFormat_Html:
+ case eHelpOutputFormat_Rst:
{
- result = repall(result, sandrHtml);
+ result = repall(result, sandrRst);
result = replaceLinks(result);
return wrapper->wrap(result);
}
case eHelpOutputFormat_Man:
file.writeLine(formatString(".SH %s", toUpperCase(title).c_str()));
break;
- case eHelpOutputFormat_Html:
- file.writeLine(formatString("<H3>%s</H3>", title.c_str()));
+ case eHelpOutputFormat_Rst:
+ file.writeLine(title);
+ file.writeLine(std::string(title.length(), '-'));
break;
default:
GMX_THROW(NotImplementedError(
void HelpWriterContext::writeOptionListStart() const
{
- if (outputFormat() == eHelpOutputFormat_Html)
- {
- outputFile().writeLine("<dl>");
- }
}
void HelpWriterContext::writeOptionItem(const std::string &name,
writeTextBlock(description);
file.writeLine();
break;
- case eHelpOutputFormat_Html:
+ case eHelpOutputFormat_Rst:
{
- std::string substArgs =
- substituteMarkupAndWrapToString(TextLineWrapperSettings(), args);
- file.writeLine(formatString("<dt><b><tt>%s</tt></b> %s</dt>", name.c_str(),
- substArgs.c_str()));
- file.writeLine("<dd>");
- writeTextBlock(description);
- file.writeLine("</dd>");
+ file.writeLine(formatString("``%s`` %s", name.c_str(), args.c_str()));
+ TextLineWrapperSettings settings;
+ settings.setIndent(4);
+ file.writeLine(substituteMarkupAndWrapToString(settings, description));
break;
}
default:
void HelpWriterContext::writeOptionListEnd() const
{
- if (outputFormat() == eHelpOutputFormat_Html)
- {
- outputFile().writeLine("</dl>");
- }
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, 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.
{
eHelpOutputFormat_Console, //!< Plain text directly on the console.
eHelpOutputFormat_Man, //!< Man page.
- eHelpOutputFormat_Html, //!< Html output for online manual.
+ eHelpOutputFormat_Rst, //!< reStructuredText for online manual.
eHelpOutputFormat_Other, //!< Used for extensions in other modules.
eHelpOutputFormat_NR //!< Used for the number of output formats.
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
// Add option for selecting a subset of atoms
options->addOption(SelectionOption("select")
.store(&sel_).defaultSelectionText("all")
- .onlyAtoms());
+ .onlyAtoms()
+ .description("Atoms that are considered as part of the excluded volume"));
// Add option for the probe radius and initialize it
options->addOption(DoubleOption("radius").store(&probeRadius_)
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
- "exceeds [TT]-maxh[tt]*0.99 hours. This option is particularly useful in",
+ "exceeds [TT]-maxh[tt]\\*0.99 hours. This option is particularly useful in",
"combination with setting [TT]nsteps[tt] to -1 either in the mdp or using the",
"similarly named command line option. This results in an infinite run,",
"terminated only when the time limit set by [TT]-maxh[tt] is reached (if any)"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff