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Commit 2e9c418a authored by peastman's avatar peastman
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Merge branch 'master' into gayberne

parents 8f532e31 a4d327f5
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.travis.yml
View file @ 2e9c418a
......@@ -17,6 +17,7 @@ env:
matrix:
include:
- sudo: required
dist: trusty
env: ==CPU_OPENCL==
OPENCL=true
CUDA=false
......@@ -33,7 +34,9 @@ matrix:
-DOPENMM_BUILD_AMOEBA_PLUGIN=OFF
-DOPENMM_BUILD_PYTHON_WRAPPERS=OFF
-DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=OFF
-DOPENMM_BUILD_EXAMPLES=OFF"
-DOPENMM_BUILD_EXAMPLES=OFF
-DOPENCL_INCLUDE_DIR=$HOME/AMDAPPSDK/include
-DOPENCL_LIBRARY=$HOME/AMDAPPSDK/lib/x86_64/libOpenCL.so"
addons: {apt: {packages: []}}
- sudo: required
......@@ -107,9 +110,16 @@ before_install:
sudo easy_install pytest;
fi
- if [[ "$OPENCL" == "true" ]]; then
sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu $(lsb_release -sc) main universe restricted multiverse";
sudo apt-get -yq update > /dev/null 2>&1 ;
sudo apt-get install -qq fglrx=2:8.960-0ubuntu1 opencl-headers;
wget https://jenkins.choderalab.org/userContent/AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2;
tar -xjf AMD-APP-SDK*.tar.bz2;
AMDAPPSDK=${HOME}/AMDAPPSDK;
export OPENCL_VENDOR_PATH=${AMDAPPSDK}/etc/OpenCL/vendors;
mkdir -p ${OPENCL_VENDOR_PATH};
sh AMD-APP-SDK*.sh --tar -xf -C ${AMDAPPSDK};
echo libamdocl64.so > ${OPENCL_VENDOR_PATH}/amdocl64.icd;
export LD_LIBRARY_PATH=${AMDAPPSDK}/lib/x86_64:${LD_LIBRARY_PATH};
chmod +x ${AMDAPPSDK}/bin/x86_64/clinfo;
${AMDAPPSDK}/bin/x86_64/clinfo;
fi
# Install swig for Python wrappers. However, testing CUDA and OpenCL, we
# skip the Python wrapper for speed. We're not using anaconda python,
......
README.md
View file @ 2e9c418a
......@@ -18,7 +18,7 @@ Need Help? Check out the [documentation](http://docs.openmm.org/) and [discussio
Badges
------
* Travis CI `linux` and `osx` integration tests:
* GitHub master [![Build Status](https://travis-ci.org/pandegroup/openmm.png?branch=master)](https://travis-ci.org/pandegroup/openmm)
* GitHub master [![Build Status](https://travis-ci.org/pandegroup/openmm.svg?branch=master)](https://travis-ci.org/pandegroup/openmm)
* `openmm-dev` recipe [![Build Status](https://travis-ci.org/omnia-md/conda-dev-recipes.svg?branch=master)](https://travis-ci.org/omnia-md/conda-dev-recipes)
* Anaconda Cloud `openmm` conda release: [![Binstar `openmm` conda release](https://anaconda.org/omnia/openmm/badges/version.svg)](https://anaconda.org/omnia/openmm)
* Anaconda Cloud `openmm-dev` conda package: [![Binstar `openmm-dev` conda package](https://anaconda.org/omnia/openmm-dev/badges/version.svg)](https://anaconda.org/omnia/openmm-dev)
devtools/packaging/scripts/linux/build.sh
View file @ 2e9c418a
......@@ -19,13 +19,14 @@ CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$INSTALL"
# setting the rpath so that libOpenMMPME.so finds the right libfftw3
#CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
CMAKE_FLAGS+=" -DCUDA_CUDART_LIBRARY=/usr/local/cuda-7.0/lib64/libcudart.so"
CMAKE_FLAGS+=" -DCUDA_NVCC_EXECUTABLE=/usr/local/cuda-7.0/bin/nvcc"
CMAKE_FLAGS+=" -DCUDA_SDK_ROOT_DIR=/usr/local/cuda-7.0/"
CMAKE_FLAGS+=" -DCUDA_TOOLKIT_INCLUDE=/usr/local/cuda-7.0/include"
CMAKE_FLAGS+=" -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0/"
CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=/opt/AMDAPPSDK-2.9-1/include/"
CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPPSDK-2.9-1/lib/x86_64/libOpenCL.so"
CMAKE_FLAGS+=" -DCUDA_CUDART_LIBRARY=/usr/local/cuda-7.5/lib64/libcudart.so"
CMAKE_FLAGS+=" -DCUDA_NVCC_EXECUTABLE=/usr/local/cuda-7.5/bin/nvcc"
CMAKE_FLAGS+=" -DCUDA_SDK_ROOT_DIR=/usr/local/cuda-7.5/"
CMAKE_FLAGS+=" -DCUDA_TOOLKIT_INCLUDE=/usr/local/cuda-7.5/include"
CMAKE_FLAGS+=" -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/"
CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=/opt/AMDAPPSDK-3.0/include/"
CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so"
CMAKE_FLAGS+=" -DOPENMM_GENERATE_API_DOCS=ON"
# Set location for FFTW3
PREFIX="$WORKSPACE/miniconda"
......@@ -40,7 +41,8 @@ fi
mkdir build
cd build
cmake ../openmm $CMAKE_FLAGS
make -j4 all DoxygenApiDocs sphinxpdf
make -j4 all install
make -j4 PythonInstall C++ApiDocs PythonApiDocs sphinxpdf
# Install.
make install
devtools/packaging/scripts/linux/prepare.sh
View file @ 2e9c418a
#!/bin/tcsh
#!/bin/bash
# Prepare for build by ensuring necessary prerequisites are locally installed.
......@@ -6,16 +6,16 @@
export WORKSPACE=`pwd`
# Install miniconda
export VERSION="Latest"
export VERSION="latest"
export PLATFORM="Linux"
export ARCH="x86_64"
export MINICONDA="Miniconda-$VERSION-$PLATFORM-$ARCH.sh"
export MINICONDA="Miniconda2-$VERSION-$PLATFORM-$ARCH.sh"
if [ -f miniconda ];
then
echo "miniconda already exists"
else
echo "Downloading miniconda..."
rm -rf Miniconda-*
rm -rf Miniconda-* miniconda ~/.condarc
wget --quiet http://repo.continuum.io/miniconda/${MINICONDA}
bash ${MINICONDA} -b -p miniconda
PIP_ARGS="-U"
......@@ -25,6 +25,6 @@ fi
export PATH=$WORKSPACE/miniconda/bin:$PATH
# Ensure configuration is up to date.
conda config --add channels http://conda.binstar.org/omnia
conda install --yes --quiet swig fftw3f pip
pip install sphinxcontrib-bibtex
conda config --add channels omnia
conda install --yes --quiet swig fftw3f pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake
devtools/packaging/scripts/osx/build.sh
View file @ 2e9c418a
......@@ -22,6 +22,7 @@ CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$INSTALL"
CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
CMAKE_FLAGS+=" -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9"
CMAKE_FLAGS+=" -DCMAKE_OSX_SYSROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk"
CMAKE_FLAGS+=" -DOPENMM_GENERATE_API_DOCS=ON"
# Build in subdirectory.
# Set location for FFTW3
......@@ -37,7 +38,8 @@ fi
mkdir build
cd build
cmake ../openmm $CMAKE_FLAGS
make -j4 all DoxygenApiDocs sphinxpdf
make -j4 all install
make -j4 PythonInstall C++ApiDocs PythonApiDocs sphinxpdf
# Install.
make install
devtools/packaging/scripts/osx/prepare.sh
View file @ 2e9c418a
......@@ -27,4 +27,4 @@ export PATH=$WORKSPACE/miniconda/bin:$PATH
# Ensure configuration is up to date.
conda config --add channels http://conda.binstar.org/omnia
conda install --yes --quiet swig fftw3f pip
pip install sphinxcontrib-bibtex
pip install sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen
devtools/packaging/scripts/source/build.sh
View file @ 2e9c418a
......@@ -28,6 +28,7 @@ CMAKE_FLAGS+=" -DOPENMM_BUILD_DRUDE_OPENCL_LIB=OFF"
CMAKE_FLAGS+=" -DOPENMM_BUILD_OPENCL_LIB=OFF"
CMAKE_FLAGS+=" -DOPENMM_BUILD_RPMD_CUDA_LIB=OFF"
CMAKE_FLAGS+=" -DOPENMM_BUILD_RPMD_OPENCL_LIB=OFF"
CMAKE_FLAGS+=" -DOPENMM_GENERATE_API_DOCS=ON"
# Set location for FFTW3
#PREFIX="$WORKSPACE/miniconda"
......@@ -42,7 +43,8 @@ fi
mkdir build
cd build
cmake ../openmm $CMAKE_FLAGS
make -j4 all DoxygenApiDocs sphinxpdf
make -j4 all install
make -j4 PythonInstall C++ApiDocs PythonApiDocs sphinxpdf
# Install.
make install
devtools/packaging/scripts/source/prepare.sh
View file @ 2e9c418a
#!/bin/tcsh
#!/bin/bash
# Prepare for build by ensuring necessary prerequisites are locally installed.
# Set relative workspace path.
export WORKSPACE=`pwd`
# Install miniconda
export VERSION="Latest"
export VERSION="latest"
export PLATFORM="Linux"
export ARCH="x86_64"
export MINICONDA="Miniconda-$VERSION-$PLATFORM-$ARCH.sh"
export MINICONDA="Miniconda2-$VERSION-$PLATFORM-$ARCH.sh"
if [ -f miniconda ];
then
echo "miniconda already exists"
else
echo "Downloading miniconda..."
rm -rf Miniconda-*
rm -rf Miniconda-* miniconda ~/.condarc
wget --quiet http://repo.continuum.io/miniconda/${MINICONDA}
bash ${MINICONDA} -b -p miniconda
PIP_ARGS="-U"
......@@ -25,6 +26,6 @@ fi
export PATH=$WORKSPACE/miniconda/bin:$PATH
# Ensure configuration is up to date.
conda config --add channels http://conda.binstar.org/omnia
conda install --yes --quiet swig fftw3f pip
pip install sphinxcontrib-bibtex
conda config --add channels omnia
conda install --yes --quiet swig fftw3f pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake
docs-source/CMakeLists.txt
View file @ 2e9c418a
......@@ -27,16 +27,23 @@ FILE(MAKE_DIRECTORY "${SPHINX_BUILD_DIR}")
FILE(GLOB_RECURSE USER_GUIDE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/usersguide/*)
FILE(GLOB_RECURSE DEVELOPER_GUIDE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/developerguide/*)
IF(WIN32)
SET(SPHINX_MAKE_USERGUIDE_COMMAND "${CMAKE_COMMAND}" -E env "OPENMM_VERSION=${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" "BUILDDIR=${SPHINX_BUILD_DIR}/userguide" make.bat)
SET(SPHINX_MAKE_DEVELOPERGUIDE_COMMAND "${CMAKE_COMMAND}" -E env "OPENMM_VERSION=${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" "BUILDDIR=${SPHINX_BUILD_DIR}/developerguide" make.bat)
ELSE(WIN32)
SET(SPHINX_MAKE_USERGUIDE_COMMAND "${CMAKE_MAKE_PROGRAM}" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide")
SET(SPHINX_MAKE_DEVELOPERGUIDE_COMMAND "${CMAKE_MAKE_PROGRAM}" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide")
ENDIF(WIN32)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
COMMAND ${SPHINX_MAKE_USERGUIDE_COMMAND} latexpdf
DEPENDS ${USER_GUIDE_FILES}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
COMMENT "Generating PDF user guide"
)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/developerguide/latex/OpenMMDeveloperGuide.pdf"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
COMMAND ${SPHINX_MAKE_DEVELOPERGUIDE_COMMAND} latexpdf
DEPENDS ${DEVELOPER_GUIDE_FILES}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
COMMENT "Generating PDF developer guide"
......@@ -47,14 +54,14 @@ ADD_CUSTOM_TARGET(sphinxpdf
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/userguide/html/index.html"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
COMMAND ${SPHINX_MAKE_USERGUIDE_COMMAND} html
DEPENDS ${USER_GUIDE_FILES}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
COMMENT "Generating HTML user guide"
)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/developerguide/html/index.html"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
COMMAND ${SPHINX_MAKE_DEVELOPERGUIDE_COMMAND} html
DEPENDS ${DEVELOPER_GUIDE_FILES}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
COMMENT "Generating HTML developer guide"
......
docs-source/developerguide/license.rst
View file @ 2e9c418a
Portions copyright (c) 2011-2015 Stanford University and the Authors
Portions copyright (c) 2011-2016 Stanford University and the Authors
Contributors: Peter Eastman
......
docs-source/developerguide/make.bat 0 → 100644
View file @ 2e9c418a
@ECHO OFF
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
REM set BUILDDIR=_build
set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
set I18NSPHINXOPTS=%SPHINXOPTS% .
if NOT "%PAPER%" == "" (
set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
)
if "%1" == "" goto help
if "%1" == "help" (
:help
echo.Please use `make ^<target^>` where ^<target^> is one of
echo. html to make standalone HTML files
echo. dirhtml to make HTML files named index.html in directories
echo. singlehtml to make a single large HTML file
echo. pickle to make pickle files
echo. json to make JSON files
echo. htmlhelp to make HTML files and a HTML help project
echo. qthelp to make HTML files and a qthelp project
echo. devhelp to make HTML files and a Devhelp project
echo. epub to make an epub
echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
echo. text to make text files
echo. man to make manual pages
echo. texinfo to make Texinfo files
echo. gettext to make PO message catalogs
echo. changes to make an overview over all changed/added/deprecated items
echo. xml to make Docutils-native XML files
echo. pseudoxml to make pseudoxml-XML files for display purposes
echo. linkcheck to check all external links for integrity
echo. doctest to run all doctests embedded in the documentation if enabled
echo. coverage to run coverage check of the documentation if enabled
goto end
)
if "%1" == "clean" (
for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
del /q /s %BUILDDIR%\*
goto end
)
REM Check if sphinx-build is available and fallback to Python version if any
%SPHINXBUILD% 2> nul
if errorlevel 9009 goto sphinx_python
goto sphinx_ok
:sphinx_python
set SPHINXBUILD=python -m sphinx.__init__
%SPHINXBUILD% 2> nul
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
:sphinx_ok
if "%1" == "html" (
%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/html.
goto end
)
if "%1" == "dirhtml" (
%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
goto end
)
if "%1" == "singlehtml" (
%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
goto end
)
if "%1" == "pickle" (
%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the pickle files.
goto end
)
if "%1" == "json" (
%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the JSON files.
goto end
)
if "%1" == "htmlhelp" (
%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run HTML Help Workshop with the ^
.hhp project file in %BUILDDIR%/htmlhelp.
goto end
)
if "%1" == "qthelp" (
%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run "qcollectiongenerator" with the ^
.qhcp project file in %BUILDDIR%/qthelp, like this:
echo.^> qcollectiongenerator %BUILDDIR%\qthelp\OpenMM.qhcp
echo.To view the help file:
echo.^> assistant -collectionFile %BUILDDIR%\qthelp\OpenMM.ghc
goto end
)
if "%1" == "devhelp" (
%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished.
goto end
)
if "%1" == "epub" (
%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The epub file is in %BUILDDIR%/epub.
goto end
)
if "%1" == "latex" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
if errorlevel 1 exit /b 1
echo.
echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdf" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf
cd %~dp0
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdfja" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf-ja
cd %~dp0
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "text" (
%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The text files are in %BUILDDIR%/text.
goto end
)
if "%1" == "man" (
%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The manual pages are in %BUILDDIR%/man.
goto end
)
if "%1" == "texinfo" (
%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
goto end
)
if "%1" == "gettext" (
%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
goto end
)
if "%1" == "changes" (
%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
if errorlevel 1 exit /b 1
echo.
echo.The overview file is in %BUILDDIR%/changes.
goto end
)
if "%1" == "linkcheck" (
%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
if errorlevel 1 exit /b 1
echo.
echo.Link check complete; look for any errors in the above output ^
or in %BUILDDIR%/linkcheck/output.txt.
goto end
)
if "%1" == "doctest" (
%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
if errorlevel 1 exit /b 1
echo.
echo.Testing of doctests in the sources finished, look at the ^
results in %BUILDDIR%/doctest/output.txt.
goto end
)
if "%1" == "coverage" (
%SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
if errorlevel 1 exit /b 1
echo.
echo.Testing of coverage in the sources finished, look at the ^
results in %BUILDDIR%/coverage/python.txt.
goto end
)
if "%1" == "xml" (
%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The XML files are in %BUILDDIR%/xml.
goto end
)
if "%1" == "pseudoxml" (
%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
goto end
)
:end
docs-source/usersguide/application.rst
View file @ 2e9c418a
......@@ -395,7 +395,7 @@ files in the newer PDBx/mmCIF format: just change :class:`PDBFile` to :class:`PD
This line specifies the force field to use for the simulation. Force fields are
defined by XML files. OpenMM includes XML files defining lots of standard force fields (see Section :ref:`force-fields`).
If you find you need to extend the repertoire of force fields available,
you can find more information on how to create these XML files in Section :ref:`creating-force-fields`.
you can find more information on how to create these XML files in Chapter :ref:`creating-force-fields`.
In this case we load two of those files: :file:`amber99sb.xml`, which contains the
Amber99SB force field, and :file:`tip3p.xml`, which contains the TIP3P water model. The
:class:`ForceField` object is assigned to a variable called :code:`forcefield`\ .
......@@ -417,10 +417,8 @@ Note the way we specified the cutoff distance 1 nm using :code:`1*nanometer`:
This is an example of the powerful units tracking and automatic conversion facility
built into the OpenMM Python API that makes specifying unit-bearing quantities
convenient and less error-prone. We could have equivalently specified
:code:`10*angstrom` instead of :code:`1*nanometer` and achieved the same result,
but had we specified the wrong dimensions, such as :code:`1*(nanometer**2)` or
:code:`1*picoseconds`, OpenMM would have thrown an exception. The units system
will be described in more detail later, in Section :ref:`units-and-dimensional-analysis`.
:code:`10*angstrom` instead of :code:`1*nanometer` and achieved the same result.
The units system will be described in more detail later, in Section :ref:`units-and-dimensional-analysis`.
::
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
......@@ -748,7 +746,7 @@ double precision:
::
platform = Platform.getPlatformByName('CUDA')
properties = {'CudaDeviceIndex': '0,1', 'CudaPrecision': 'double'}
properties = {'DeviceIndex': '0,1', 'Precision': 'double'}
simulation = Simulation(prmtop.topology, system, integrator, platform, properties)
.. _force-fields:
......@@ -1322,11 +1320,12 @@ Writing Trajectories
====================
OpenMM can save simulation trajectories to disk in two formats: PDB_ and DCD_.
Both of these are widely supported formats, so you should be able to read them
into most analysis and visualization programs.
OpenMM can save simulation trajectories to disk in three formats: PDB_,
`PDBx/mmCIF`_, and DCD_. All of these are widely supported formats, so you
should be able to read them into most analysis and visualization programs.
.. _PDB: http://www.wwpdb.org/documentation/format33/v3.3.html
.. _PDBx/mmCIF: http://mmcif.wwpdb.org
.. _DCD: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html
To save a trajectory, just add a “reporter” to the simulation, as shown in the
......@@ -1336,9 +1335,9 @@ example scripts above:
simulation.reporters.append(PDBReporter('output.pdb', 1000))
The two parameters of the :class:`PDBReporter` are the output filename and how often (in
number of time steps) output structures should be written. To use DCD format,
just replace :class:`PDBReporter` with :class:`DCDReporter`. The parameters represent the
same values:
number of time steps) output structures should be written. To use PDBx/mmCIF or
DCD format, just replace :class:`PDBReporter` with :class:`PDBxReporter` or
:class:`DCDReporter`. The parameters represent the same values:
::
simulation.reporters.append(DCDReporter('output.dcd', 1000))
......@@ -1771,8 +1770,8 @@ not an arbitrary choice.
Extracting and Reporting Forces (and other data)
************************************************
OpenMM provides reporters for two output formats: PDB_ and DCD_. Both of those
formats store only positions, not velocities, forces, or other data. In this
OpenMM provides reporters for three output formats: PDB_, `PDBx/mmCIF`_ and DCD_.
All of those formats store only positions, not velocities, forces, or other data. In this
section, we create a new reporter that outputs forces. This illustrates two
important things: how to write a reporter, and how to query the simulation for
forces or other data.
......@@ -1862,7 +1861,7 @@ the potential energy of each one. Assume we have already created our :class:`Sy
pdb = PDBFile(os.path.join('structures', file))
simulation.context.setPositions(pdb.positions)
state = simulation.context.getState(getEnergy=True)
print file, state.getPotentialEnergy()
print(file, state.getPotentialEnergy())
.. caption::
......@@ -2068,9 +2067,9 @@ Missing residue templates
=========================
.. CAUTION::
These features are experimental, and its API is subject to change.
These features are experimental, and their API is subject to change.
You can use the :method:`getUnmatchedResidues()` method to get a list of residues
You can use the :meth:`getUnmatchedResidues()` method to get a list of residues
in the provided :code:`topology` object that do not currently have a matching
residue template defined in the :class:`ForceField`.
::
......@@ -2084,7 +2083,7 @@ with residue template definitions, or identifying which additional residues need
to be parameterized.
As a convenience for parameterizing new residues, you can also get a list of
residues and empty residue templates using :method:`generateTemplatesForUnmatchedResidues`
residues and empty residue templates using :meth:`generateTemplatesForUnmatchedResidues`
::
pdb = PDBFile('input.pdb')
......@@ -2098,7 +2097,7 @@ residues and empty residue templates using :method:`generateTemplatesForUnmatche
forcefield.registerResidueTemplate(template)
If you find that templates seem to be incorrectly matched, another useful
function :method:`getMatchingTemplates()` can help you identify which templates
function :meth:`getMatchingTemplates()` can help you identify which templates
are being matched:
::
......@@ -2106,7 +2105,7 @@ are being matched:
forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
templates = forcefield.getMatchingTemplates(topology)
for (residue, template) in zip(pdb.topology.residues(), templates):
print "Residue %d %s matched template %s" % (residue.id, residue.name, template.name)
print("Residue %d %s matched template %s" % (residue.id, residue.name, template.name))
<HarmonicBondForce>
===================
......@@ -2916,17 +2915,19 @@ This :code:`generator` function must conform to the following API:
-------
success : bool
If the generator is able to successfully parameterize the residue, `True` is returned.
If the generator cannot parameterize the residue, it should return `False` and not modify `forcefield`.
If the generator cannot parameterize the residue, it should return `False` and not
modify `forcefield`.
The generator should either register a residue template directly with `forcefield.registerResidueTemplate(template)`
or it should call `forcefield.loadFile(file)` to load residue definitions from an ffxml file.
The generator should either register a residue template directly with
`forcefield.registerResidueTemplate(template)` or it should call `forcefield.loadFile(file)`
to load residue definitions from an ffxml file.
It can also use the `ForceField` programmatic API to add additional atom types (via `forcefield.registerAtomType(parameters)`)
or additional parameters.
It can also use the `ForceField` programmatic API to add additional atom types (via
`forcefield.registerAtomType(parameters)`) or additional parameters.
"""
The :code:`ForceField` object will be modified by the residue template generator as residues without previously
defined templates are encountered. Because these templates are added to `ForceField` as new residue
The :class:`ForceField` object will be modified by the residue template generator as residues without previously
defined templates are encountered. Because these templates are added to the :class:`ForceField` as new residue
types are encountered, subsequent residues will be parameterized using the same residue templates without
calling the :code:`generator` again.
docs-source/usersguide/library.rst
View file @ 2e9c418a
......@@ -347,11 +347,6 @@ The choice of which platform to use for a simulation depends on various factors:
OpenCL platform running on the CPU.
#. The CUDA platform can only be used with NVIDIA GPUs. For using an AMD or
Intel GPU, use the OpenCL platform.
#. When running on recent NVIDIA GPUs (Fermi and Kepler generations), the CUDA
platform is usually faster and should be used. On older GPUs, the OpenCL
platform is likely to be faster. Also, some very old GPUs (GeForce 8000 and
9000 series) are only supported by the OpenCL platform, not by the CUDA
platform.
#. The AMOEBA force field only works with the CUDA platform, not with the OpenCL
platform. It also works with the Reference and CPU platforms, but the performance
is usually too slow to be useful on those platforms.
......@@ -393,14 +388,9 @@ Mac and Linux: clang or gcc
Use clang or gcc on Mac/Linux. OpenMM should compile correctly with all recent
versions of these compilers. We recommend clang since it produces faster code,
especially when using the CPU platform.
If you do not already have a compiler installed, you will need to download and
install it. On Mac OS X, this means downloading the Xcode Tools from the App
Store. (With Xcode 4.3, you must then launch Xcode, open the Preferences window,
go to the Downloads tab, and tell it to install the command line tools. With
Xcode 4.2 and earlier, the command line tools are automatically installed when
you install Xcode.)
especially when using the CPU platform. If you do not already have a compiler
installed, you will need to download and install it. On Mac OS X, this means
downloading the Xcode Tools from the App Store.
Windows: Visual Studio
----------------------
......@@ -545,6 +535,8 @@ There are several variables that can be adjusted in the CMake interface:
and documentation.
* Set the variable CMAKE_INSTALL_PREFIX to the location where you want to
install OpenMM.
* Set the variable PYTHON_EXECUTABLE to the Python interpreter you plan to use
OpenMM with.
Configure (press “c”) again. Adjust any variables that cause an
......@@ -1844,7 +1836,7 @@ Context constructor:
Platform& platform = Platform::getPlatformByName("OpenCL");
map<string, string> properties;
properties["OpenCLDeviceIndex"] = "1";
properties["DeviceIndex"] = "1";
Context context(system, integrator, platform, properties);
After a Context is created, you can use the Platform’s \
......@@ -1855,7 +1847,7 @@ OpenCL Platform
The OpenCL Platform recognizes the following Platform-specific properties:
* OpenCLPrecision: This selects what numeric precision to use for calculations.
* Precision: This selects what numeric precision to use for calculations.
The allowed values are “single”, “mixed”, and “double”. If it is set to
“single”, nearly all calculations are done in single precision. This is the
fastest option but also the least accurate. If it is set to “mixed”, forces are
......@@ -1863,7 +1855,7 @@ The OpenCL Platform recognizes the following Platform-specific properties:
gives much better energy conservation with only a slight decrease in speed.
If it is set to “double”, all calculations are done in double precision. This
is the most accurate option, but is usually much slower than the others.
* OpenCLUseCpuPme: This selects whether to use the CPU-based PME
* UseCpuPme: This selects whether to use the CPU-based PME
implementation. The allowed values are “true” or “false”. Depending on your
hardware, this might (or might not) improve performance. To use this option,
you must have FFTW (single precision, multithreaded) installed, and your CPU
......@@ -1873,19 +1865,19 @@ The OpenCL Platform recognizes the following Platform-specific properties:
zero-based index of the platform (in the OpenCL sense, not the OpenMM sense) to use,
in the order they are returned by the OpenCL platform API. This is useful, for
example, in selecting whether to use a GPU or CPU based OpenCL implementation.
* OpenCLDeviceIndex: When multiple OpenCL devices are available on your
* DeviceIndex: When multiple OpenCL devices are available on your
computer, this is used to select which one to use. The value is the zero-based
index of the device to use, in the order they are returned by the OpenCL device
API.
The OpenCL Platform also supports parallelizing a simulation across multiple
GPUs. To do that, set the OpenCLDeviceIndex property to a comma separated list
GPUs. To do that, set the DeviceIndex property to a comma separated list
of values. For example,
.. code-block:: c
properties["OpenCLDeviceIndex"] = "0,1";
properties["DeviceIndex"] = "0,1";
This tells it to use both devices 0 and 1, splitting the work between them.
......@@ -1894,7 +1886,7 @@ CUDA Platform
The CUDA Platform recognizes the following Platform-specific properties:
* CudaPrecision: This selects what numeric precision to use for calculations.
* Precision: This selects what numeric precision to use for calculations.
The allowed values are “single”, “mixed”, and “double”. If it is set to
“single”, nearly all calculations are done in single precision. This is the
fastest option but also the least accurate. If it is set to “mixed”, forces are
......@@ -1902,7 +1894,7 @@ The CUDA Platform recognizes the following Platform-specific properties:
gives much better energy conservation with only a slight decrease in speed.
If it is set to “double”, all calculations are done in double precision. This
is the most accurate option, but is usually much slower than the others.
* CudaUseCpuPme: This selects whether to use the CPU-based PME implementation.
* UseCpuPme: This selects whether to use the CPU-based PME implementation.
The allowed values are “true” or “false”. Depending on your hardware, this
might (or might not) improve performance. To use this option, you must have
FFTW (single precision, multithreaded) installed, and your CPU must support SSE
......@@ -1920,28 +1912,36 @@ The CUDA Platform recognizes the following Platform-specific properties:
appends \nvcc.exe to it. That environment variable is set by the CUDA
installer, so it usually is present.
* CudaTempDirectory: This specifies a directory where temporary files can be
* TempDirectory: This specifies a directory where temporary files can be
written while compiling kernels. OpenMM usually can locate your operating
system’s temp directory automatically (for example, by looking for the TEMP
environment variable), so you rarely need to specify this.
* CudaDeviceIndex: When multiple CUDA devices are available on your computer,
* DeviceIndex: When multiple CUDA devices are available on your computer,
this is used to select which one to use. The value is the zero-based index of
the device to use, in the order they are returned by the CUDA API.
* CudaUseBlockingSync: This is used to control how the CUDA runtime
* UseBlockingSync: This is used to control how the CUDA runtime
synchronizes between the CPU and GPU. If this is set to “true” (the default),
CUDA will allow the calling thread to sleep while the GPU is performing a
computation, allowing the CPU to do other work. If it is set to “false”, CUDA
will spin-lock while the GPU is working. Setting it to "false" can improve performance slightly,
but also prevents the CPU from doing anything else while the GPU is working.
* DeterministicForces: In some cases, the CUDA platform may compute forces
in ways that are not fully deterministic (typically differing in what order a
set of numbers get added together). This means that if you compute the forces
twice for the same particle positions, there may be tiny differences in the
results. In most cases this is not a problem, but certain algorithms depend
on forces being exactly reproducible to the last bit. If you set this
property to "true", it will instead do these calculations in a way that
produces fully deterministic results, at the cost of a small decrease in
performance.
The CUDA Platform also supports parallelizing a simulation across multiple GPUs.
To do that, set the CudaDeviceIndex property to a comma separated list of
To do that, set the DeviceIndex property to a comma separated list of
values. For example,
.. code-block:: c
properties["CudaDeviceIndex"] = "0,1";
properties["DeviceIndex"] = "0,1";
This tells it to use both devices 0 and 1, splitting the work between them.
......@@ -1950,7 +1950,7 @@ CPU Platform
The CPU Platform recognizes the following Platform-specific properties:
* CpuThreads: This specifies the number of CPU threads to use. If you do not
* Threads: This specifies the number of CPU threads to use. If you do not
specify this, OpenMM will select a default number of threads as follows:
* If an environment variable called OPENMM_CPU_THREADS is set, its value is
......
docs-source/usersguide/license.rst
View file @ 2e9c418a
Portions copyright (c) 2008-2015 Stanford University and the Authors
Portions copyright (c) 2008-2016 Stanford University and the Authors
Contributors: Kyle Beauchamp, Christopher Bruns, John Chodera, Peter Eastman, Mark
Friedrichs, Joy P. Ku, Tom Markland, Vijay Pande, Randy Radmer, Michael Sherman,
......
docs-source/usersguide/make.bat 0 → 100644
View file @ 2e9c418a
@ECHO OFF
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
REM set BUILDDIR=_build
set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
set I18NSPHINXOPTS=%SPHINXOPTS% .
if NOT "%PAPER%" == "" (
set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
)
if "%1" == "" goto help
if "%1" == "help" (
:help
echo.Please use `make ^<target^>` where ^<target^> is one of
echo. html to make standalone HTML files
echo. dirhtml to make HTML files named index.html in directories
echo. singlehtml to make a single large HTML file
echo. pickle to make pickle files
echo. json to make JSON files
echo. htmlhelp to make HTML files and a HTML help project
echo. qthelp to make HTML files and a qthelp project
echo. devhelp to make HTML files and a Devhelp project
echo. epub to make an epub
echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
echo. text to make text files
echo. man to make manual pages
echo. texinfo to make Texinfo files
echo. gettext to make PO message catalogs
echo. changes to make an overview over all changed/added/deprecated items
echo. xml to make Docutils-native XML files
echo. pseudoxml to make pseudoxml-XML files for display purposes
echo. linkcheck to check all external links for integrity
echo. doctest to run all doctests embedded in the documentation if enabled
echo. coverage to run coverage check of the documentation if enabled
goto end
)
if "%1" == "clean" (
for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
del /q /s %BUILDDIR%\*
goto end
)
REM Check if sphinx-build is available and fallback to Python version if any
%SPHINXBUILD% 2> nul
if errorlevel 9009 goto sphinx_python
goto sphinx_ok
:sphinx_python
set SPHINXBUILD=python -m sphinx.__init__
%SPHINXBUILD% 2> nul
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
:sphinx_ok
if "%1" == "html" (
%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/html.
goto end
)
if "%1" == "dirhtml" (
%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
goto end
)
if "%1" == "singlehtml" (
%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
goto end
)
if "%1" == "pickle" (
%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the pickle files.
goto end
)
if "%1" == "json" (
%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the JSON files.
goto end
)
if "%1" == "htmlhelp" (
%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run HTML Help Workshop with the ^
.hhp project file in %BUILDDIR%/htmlhelp.
goto end
)
if "%1" == "qthelp" (
%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run "qcollectiongenerator" with the ^
.qhcp project file in %BUILDDIR%/qthelp, like this:
echo.^> qcollectiongenerator %BUILDDIR%\qthelp\OpenMM.qhcp
echo.To view the help file:
echo.^> assistant -collectionFile %BUILDDIR%\qthelp\OpenMM.ghc
goto end
)
if "%1" == "devhelp" (
%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished.
goto end
)
if "%1" == "epub" (
%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The epub file is in %BUILDDIR%/epub.
goto end
)
if "%1" == "latex" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
if errorlevel 1 exit /b 1
echo.
echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdf" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf
cd %~dp0
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdfja" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf-ja
cd %~dp0
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "text" (
%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The text files are in %BUILDDIR%/text.
goto end
)
if "%1" == "man" (
%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The manual pages are in %BUILDDIR%/man.
goto end
)
if "%1" == "texinfo" (
%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
goto end
)
if "%1" == "gettext" (
%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
goto end
)
if "%1" == "changes" (
%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
if errorlevel 1 exit /b 1
echo.
echo.The overview file is in %BUILDDIR%/changes.
goto end
)
if "%1" == "linkcheck" (
%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
if errorlevel 1 exit /b 1
echo.
echo.Link check complete; look for any errors in the above output ^
or in %BUILDDIR%/linkcheck/output.txt.
goto end
)
if "%1" == "doctest" (
%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
if errorlevel 1 exit /b 1
echo.
echo.Testing of doctests in the sources finished, look at the ^
results in %BUILDDIR%/doctest/output.txt.
goto end
)
if "%1" == "coverage" (
%SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
if errorlevel 1 exit /b 1
echo.
echo.Testing of coverage in the sources finished, look at the ^
results in %BUILDDIR%/coverage/python.txt.
goto end
)
if "%1" == "xml" (
%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The XML files are in %BUILDDIR%/xml.
goto end
)
if "%1" == "pseudoxml" (
%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
goto end
)
:end
examples/benchmark.py
View file @ 2e9c418a
......@@ -81,18 +81,12 @@ def runOneTest(testName, options):
print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
properties = {}
initialSteps = 5
if options.device is not None:
if platform.getName() == 'CUDA':
properties['CudaDeviceIndex'] = options.device
elif platform.getName() == 'OpenCL':
properties['OpenCLDeviceIndex'] = options.device
if options.device is not None and platform.getName() in ('CUDA', 'OpenCL'):
properties['DeviceIndex'] = options.device
if ',' in options.device or ' ' in options.device:
initialSteps = 250
if options.precision is not None:
if platform.getName() == 'CUDA':
properties['CudaPrecision'] = options.precision
elif platform.getName() == 'OpenCL':
properties['OpenCLPrecision'] = options.precision
if options.precision is not None and platform.getName() in ('CUDA', 'OpenCL'):
properties['Precision'] = options.precision
# Run the simulation.
......
libraries/irrxml/include/CXMLReaderImpl.h
View file @ 2e9c418a
......@@ -2,6 +2,8 @@
// This file is part of the "Irrlicht Engine" and the "irrXML" project.
// For conditions of distribution and use, see copyright notice in irrlicht.h and/or irrXML.h
// MODIFIED by Peter Eastman, Feb. 4, 2016, to support numeric escape sequences
#ifndef __ICXML_READER_IMPL_H_INCLUDED__
#define __ICXML_READER_IMPL_H_INCLUDED__
......@@ -529,10 +531,37 @@ private:
pos += SpecialCharacters[specialChar].size();
}
else
{
int semicolonPos = origstr.findNext(L';', pos);
if (semicolonPos != -1 && origstr.c_str()[pos+1] == L'#')
{
// it is a numeric character reference
int number;
core::string<char> numberString;
if (origstr.c_str()[pos+2] == L'x')
{
// hex value
for (int i=pos+3; i<semicolonPos; ++i)
numberString.append((char) origstr[i]);
sscanf(numberString.c_str(), "%x", &number);
}
else
{
// decimal value
for (int i=pos+2; i<semicolonPos; ++i)
numberString.append((char) origstr[i]);
sscanf(numberString.c_str(), "%d", &number);
}
newstr.append(origstr.subString(oldPos, pos - oldPos));
newstr.append((char_type) number);
pos = semicolonPos+1;
}
else
{
newstr.append(origstr.subString(oldPos, pos - oldPos + 1));
pos += 1;
}
}
// find next &
oldPos = pos;
......
libraries/lepton/src/CompiledExpression.cpp
View file @ 2e9c418a
......@@ -78,6 +78,7 @@ CompiledExpression& CompiledExpression::operator=(const CompiledExpression& expr
for (int i = 0; i < (int) operation.size(); i++)
operation[i] = expression.operation[i]->clone();
#ifdef LEPTON_USE_JIT
if (workspace.size() > 0)
generateJitCode();
#endif
return *this;
......
olla/include/openmm/Platform.h
View file @ 2e9c418a
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -236,7 +236,9 @@ protected:
*/
const ContextImpl& getContextImpl(const Context& context) const;
std::vector<std::string> platformProperties;
std::map<std::string, std::string> deprecatedPropertyReplacements;
private:
friend class ContextImpl;
std::map<std::string, KernelFactory*> kernelFactories;
std::map<std::string, std::string> defaultProperties;
static std::vector<Platform*>& getPlatforms();
......
olla/include/openmm/kernels.h
View file @ 2e9c418a
......@@ -188,7 +188,7 @@ public:
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
*/
virtual void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const = 0;
virtual void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) = 0;
/**
* Create a checkpoint recording the current state of the Context.
*
......
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