-# get a list of all of the failed tests into this stupid ctest format
-python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
-if [ -s Testing/Temporary/LastTestsFailed.log ]; then
[OpenMM](https://simtk.org/home/openmm) is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
[OpenMM](http://openmm.org) is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
Getting Help
------------
Need Help? Check out the [documentation](https://simtk.org/docman/?group_id=161) and [discussion forums](https://simtk.org/forums/viewforum.php?f=161).
Need Help? Check out the [documentation](http://docs.openmm.org/) and [discussion forums](https://simtk.org/forums/viewforum.php?f=161).
[C++ API Reference](https://simtk.org/api_docs/openmm/api6_0/c++/)
[C++ API Reference](http://docs.openmm.org/6.3.0/api-c++/namespaceOpenMM.html)
[Python API Reference](https://simtk.org/api_docs/openmm/api6_0/python/)
[Python API Reference](http://docs.openmm.org/6.3.0/api-python/annotated.html)
Badges
------
* Travis CI `linux` integration tests: [](https://travis-ci.org/pandegroup/openmm)
-python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
-ps:>
If (Test-Path "Testing\\Temporary\\LastTestsFailed.log") {
# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
# generate Latex output.
GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
# put in front of it. If left blank `latex' will be used as the default path.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
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LATEX_CMD_NAME = latex
# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
# generate index for LaTeX. If left blank `makeindex' will be used as the
# default command name.
MAKEINDEX_CMD_NAME = makeindex
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EXTRA_PACKAGES =
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# the generated latex document. The header should contain everything until
# the first chapter. If it is left blank doxygen will generate a
# standard header. Notice: only use this tag if you know what you are doing!
LATEX_HEADER =
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# is prepared for conversion to pdf (using ps2pdf). The pdf file will
# contain links (just like the HTML output) instead of page references
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PDF_HYPERLINKS = YES
# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
# plain latex in the generated Makefile. Set this option to YES to get a
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# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
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# This option is also used when generating formulas in HTML.
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LATEX_HIDE_INDICES = NO
# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER.
The C++ API provides information about the classes and methods available in OpenMM for C++ developers. The public API is based on a small number of classes.
.. toctree::
:maxdepth: 2
library
:cpp:class:`System <OpenMM::System>`\ : A System specifies generic properties of the system to be
simulated: the number of particles it contains, the mass of each one, the size
of the periodic box, etc. The interactions between the particles are specified
through a set of Force objects (see below) that are added to the System. Force
field specific parameters, such as particle charges, are not direct properties
of the System. They are properties of the Force objects contained within the
System.
:cpp:class:`Force <OpenMM::Force>`\ : The Force objects added to a System define the behavior of the
particles. Force is an abstract class; subclasses implement specific behaviors.
The Force class is actually slightly more general than its name suggests. A
Force can, indeed, apply forces to particles, but it can also directly modify
particle positions and velocities in arbitrary ways. Some thermostats and
barostats, for example, can be implemented as Force classes. Examples of Force
subclasses include :cpp:class:`HarmonincBondForce <OpenMM::HarmonincBondForce>`, :cpp:class:`NonbondedForce <OpenMM::NonbondedForce>`, and :cpp:class:`MonteCarloBarostat <OpenMM::MonteCarloBarostat>`.
:cpp:class:`Context <OpenMM::Context>`\ : This stores all of the state information for a simulation:
particle positions and velocities, as well as arbitrary parameters defined by
the Forces in the System. It is possible to create multiple Contexts for a
single System, and thus have multiple simulations of that System in progress at
the same time.
:cpp:class:`Integrator <OpenMM::Integrator>`\ : This implements an algorithm for advancing the simulation
through time. It is an abstract class; subclasses implement specific
algorithms. Examples of Integrator subclasses include :cpp:class:`LangevinIntegrator <OpenMM::LangevinIntegrator>`,
:cpp:class:`VerletIntegrator <OpenMM::VerletIntegrator>`, and :cpp:class:`BrownianIntegrator <OpenMM::BrownianIntegrator>`.
:cpp:class:`State <OpenMM::State>`\ : A State stores a snapshot of the simulation at a particular point
in time. It is created by calling a method on a Context. This is the only way to query the
values of state variables, such as particle positions and velocities; Context
does not provide methods for accessing them directly.
