Merge branch 'master' of github.com:pandegroup/openmm into genpt

.travis.yml

 language: python
-python:
-  - "2.7_with_system_site_packages"
-  - "3.4"
 
-sudo: false
 addons:
   apt:
-    sources:
-      - ubuntu-toolchain-r-test
     packages:
-      - libpcre3
-      - libpcre3-dev
       - gromacs
       - doxygen
       - python-numpy
       - python-scipy
+      - libfftw3-dev
 
+matrix:
+  include:
+    - sudo: required
+      env: ==CPU_OPENCL==
+           OPENCL=true
+           CUDA=false
+           CC=gcc
+           CXX=g++
+           CMAKE_FLAGS="
+           -OPENMM_BUILD_OPENCL_LIB=ON
+           -DOPENMM_BUILD_OPENCL_TESTS=ON
+           -DOPENMM_BUILD_STATIC_LIB=OFF
+           -DOPENMM_BUILD_CPU_LIB=OFF
+           -DOPENMM_BUILD_REFERENCE_TESTS=OFF
+           -DOPENMM_BUILD_SERIALIZATION_TESTS=OFF
+           -DOPENMM_BUILD_PME_PLUGIN=OFF
+           -DOPENMM_BUILD_AMOEBA_PLUGIN=OFF
+           -DOPENMM_BUILD_PYTHON_WRAPPERS=OFF
+           -DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=OFF
+           -DOPENMM_BUILD_EXAMPLES=OFF"
+      addons: {apt: {packages: []}}
 
-env:
-  matrix:
-    - OPENMM_BUILD_STATIC_LIB="OFF"
-    - OPENMM_BUILD_STATIC_LIB="ON"
+    - sudo: required
+      env: ==CUDA_COMPILE==
+           CUDA=true
+           OPENCL=false
+           CUDA_VERSION="7.0-28"
+           CMAKE_FLAGS="
+             -DOPENMM_BUILD_CUDA_TESTS=OFF
+             -DOPENMM_BUILD_OPENCL_TESTS=OFF
+             -DOPENMM_BUILD_PYTHON_WRAPPERS=OFF
+             -DOPENMM_BUILD_REFERENCE_TESTS=OFF
+             -DOPENMM_BUILD_SERIALIZATION_TESTS=OFF
+             -DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=OFF
+             -DOPENMM_BUILD_EXAMPLES=OFF
+             -DOPENCL_LIBRARY=/usr/local/cuda-7.0/lib64/libOpenCL.so"
+      addons: {apt: {packages: []}}
+
+    - language: objective-c
+      os: osx
+      env: ==OSX==
+           OPENCL=false
+           CUDA=false
+           CMAKE_FLAGS="
+             -DOPENMM_BUILD_OPENCL_TESTS=OFF
+             -DSWIG_EXECUTABLE=/usr/local/Cellar/swig/3.0.2/bin/swig"
+      addons: {apt: {packages: []}}
+
+    - sudo: false
+      python: 2.7_with_system_site_packages
+      env: ==STATIC_LIB==
+           OPENCL=false
+           CUDA=false
+           CC=clang
+           CXX=clang++
+           CMAKE_FLAGS="-DOPENMM_BUILD_STATIC_LIB=ON"
+
+    - sudo: false
+      python: 2.7_with_system_site_packages
+      env: ==PYTNON_2==
+           OPENCL=false
+           CUDA=false
+           CC=clang
+           CXX=clang++
+           DOCS_DEPLOY=true
+           CMAKE_FLAGS=""
+
+    - sudo: false
+      python: 3.4
+      env: ==PYTHON_3==
+           OPENCL=false
+           CUDA=false
+           CC=gcc
+           CXX=g++
+           CMAKE_FLAGS=""
 
 before_install:
-  - export CC=clang
-  - export CXX=clang++
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+      brew install doxygen swig fftw;
+      sudo easy_install pytest;
+    fi
+  - if [[ "$OPENCL" == "true" ]]; then
+      sudo apt-get -yq update > /dev/null 2>&1 ;
+      sudo apt-get install -qq fglrx=2:8.960-0ubuntu1 opencl-headers;
+    fi
+  # Install swig for Python wrappers. However, testing CUDA and OpenCL, we
+  # skip the Python wrapper for speed. We're not using anaconda python,
+  # but this is a fast way to get an apparently functional precompiled
+  # build of swig that's more modern than what's in apt.
+  - if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "linux" ]]; then
+      wget https://anaconda.org/omnia/swig/3.0.7/download/linux-64/swig-3.0.7-0.tar.bz2;
+      mkdir $HOME/swig;
+      tar -xjvf swig-3.0.7-0.tar.bz2 -C $HOME/swig;
+      export PATH=$HOME/swig/bin:$PATH;
+      export SWIG_LIB=$HOME/swig/share/swig/3.0.7;
+    fi
 
-  - wget https://anaconda.org/anaconda/swig/3.0.2/download/linux-64/swig-3.0.2-0.tar.bz2
-  - mkdir $HOME/swig
-  - tar -xjvf swig-3.0.2-0.tar.bz2 -C $HOME/swig
-  - export PATH=$HOME/swig/bin:$PATH
-  - export SWIG_LIB=$HOME/swig/share/swig/3.0.2
+  - if [[ "$CUDA" == "true" ]]; then
+      wget "http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1204/x86_64/cuda-repo-ubuntu1204_${CUDA_VERSION}_amd64.deb";
+      sudo dpkg -i cuda-repo-ubuntu1204_${CUDA_VERSION}_amd64.deb;
+      sudo apt-get update -qq;
+      export CUDA_APT=${CUDA_VERSION%-*};
+      export CUDA_APT=${CUDA_APT/./-};
+      sudo apt-get install -y cuda-drivers cuda-core-${CUDA_APT} cuda-cudart-dev-${CUDA_APT} cuda-cufft-dev-${CUDA_APT};
+      sudo apt-get clean;
+      export CUDA_HOME=/usr/local/cuda-${CUDA_VERSION%%-*};
+      export LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH};
+      export PATH=${CUDA_HOME}/bin:${PATH};
+    fi
 
 script:
-  - cmake -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM -DOPENMM_BUILD_STATIC_LIB=$OPENMM_BUILD_STATIC_LIB .
-  - make -j2
+  - CTEST_STOP_TIME=$(python -c "from datetime import datetime, timedelta; import sys; sys.stdout.write((datetime.now() + timedelta(minutes=25)).strftime('%H:%M:%S'))")
+  - cmake . $CMAKE_FLAGS -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM
   - make -j2 install
-  - make PythonInstall
-  - # Run the testInstallation script
-  - python -m simtk.testInstallation
+  - if [[ "$OPENCL" == "true" ]]; then ./TestOpenCLDeviceQuery; fi
+  - if [[ "$OPENCL" == "false" && "$CUDA" == "false" ]]; then
+      if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+          sudo make PythonInstall;
+      else
+          make PythonInstall;
+      fi;
+      python -m simtk.testInstallation;
+      (cd python/tests && py.test -v *);
+    fi
+
   - # run all of the tests, making sure failures at this stage don't cause travis failures
-  - ctest -j2 || true
+  - ctest -j2 --output-on-failure --schedule-random --stop-time $CTEST_STOP_TIME || true
   - # get a list of all of the failed tests into this stupid ctest format
   - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
-  - # rerun all of the failed tests
-  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then ctest -I FailedTests.log; fi;
-  - # run the python tests too
-  - cd python/tests  
-  - # nosetests -vv --processes=-1 --process-timeout=200
-  - # nosetests -vv
-  - py.test -v *
-  - cd -
+  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then
+      ctest -I FailedTests.log;
+    fi
+  - if [[ ! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true" ]]; then
+      pip install sphinx numpydoc;
+      make DoxygenApiDocs PythonApiDocs;
+      mkdir -p api-docs;
+      mv api-python api-docs;
+      mv api-c++ api-docs;
+    fi
+
+deploy:
+  - provider: s3
+    access_key_id:
+      secure: "AjE3nuj6kVuf21mOf0aZydW/3S/uCWsaoXC/huRxkxrmsNlnHBNGHZ9N48san1IxZAQM5pyaf7Yo9gkHur9obgq+e3lNgGvPp2mfkNXtLYcLJ46JF4kYliAtutjLWskrLg25Gu3xzF4EQkqSe0Le/oWldWWbTgvvH+KRq/vTHzI="
+    secret_access_key:
+      secure: "ISDQNSG2t0666PULtffo4wsKLFdu622EzuZxmiTxvLkjQGQlqm5+qn1Gd5UMLk7Ts2E0psdnmSrf6LVVCfrrQO/hcZHiJw3ZslMPDBBlRr8Epwdldn98ULhVoyQKtjXjCPzroa2UZCl1RFs4Nwb/VdDlI490XV0Lp4Woj1AT8tY="
+    bucket: "docs.openmm.org"
+    skip_cleanup: true
+    region: us-west-1
+    local_dir: api-docs/
+    upload_dir: development
+    on:
+      branch: master
+      condition: '! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true"'

CMakeLists.txt

@@ -65,6 +65,11 @@ ELSE(WIN32)
     ENDIF(NOT OPENMM_INSTALL_PREFIX)
 ENDIF(WIN32)
 
+IF(WIN32)
+    ADD_DEFINITIONS(-DWIN32)
+ENDIF(WIN32)
+
+
 # Include CPU-Features for Android
 IF (ANDROID)
     INCLUDE_DIRECTORIES(${ANDROID_NDK}/sources/cpufeatures)
@@ -82,7 +87,7 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
-SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/validate libraries/irrxml)
+SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/irrxml libraries/vecmath)
 IF(WIN32)
     SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/pthreads)
 ELSE(WIN32)
@@ -109,6 +114,7 @@ ELSE( CMAKE_SIZEOF_VOID_P EQUAL 8 )
   SET( LIB64  )
 ENDIF( CMAKE_SIZEOF_VOID_P EQUAL 8 )
 
+
 IF (APPLE AND (NOT PNACL))
     # Build 64 bit binaries compatible with OS X 10.7
     IF (NOT CMAKE_OSX_DEPLOYMENT_TARGET)
@@ -117,6 +123,14 @@ IF (APPLE AND (NOT PNACL))
     IF (NOT CMAKE_OSX_ARCHITECTURES)
         SET (CMAKE_OSX_ARCHITECTURES "x86_64" CACHE STRING "The processor architectures to build for" FORCE)
     ENDIF (NOT CMAKE_OSX_ARCHITECTURES)
+    IF (NOT CMAKE_OSX_SYSROOT)
+        EXECUTE_PROCESS(COMMAND "xcrun" "--show-sdk-path" OUTPUT_VARIABLE XCRUN_OSX_SYSROOT RESULT_VARIABLE XCRUN_OSX_SYSROOT_STATUS OUTPUT_STRIP_TRAILING_WHITESPACE)
+        IF (XCRUN_OSX_SYSROOT_STATUS EQUAL 0)
+            SET (CMAKE_OSX_SYSROOT "${XCRUN_OSX_SYSROOT}" CACHE STRING "SDK Path" FORCE)
+        ENDIF (XCRUN_OSX_SYSROOT_STATUS EQUAL 0)
+        UNSET(XCRUN_OSX_SYSROOT)
+        UNSET(XCRUN_OSX_SYSROOT_STATUS)
+    ENDIF (NOT CMAKE_OSX_SYSROOT)
 
     # Improve the linking behavior of Mac libraries
     SET (CMAKE_INSTALL_NAME_DIR "@rpath")
@@ -302,14 +316,14 @@ ENDIF (MSVC)
 
 IF(OPENMM_BUILD_SHARED_LIB)
     ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY -DPTHREAD_BUILDING_SHARED_LIBRARY")
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DPTHREAD_BUILDING_SHARED_LIBRARY")
 ENDIF(OPENMM_BUILD_SHARED_LIB)
 
 SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
 IF(OPENMM_BUILD_STATIC_LIB)
     ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
     SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB")
-    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY -DPTHREAD_BUILDING_STATIC_LIBRARY")
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_BUILDING_STATIC_LIBRARY -DPTHREAD_BUILDING_STATIC_LIBRARY")
 ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
@@ -341,9 +355,14 @@ ENDIF(DL_LIBRARY)
 
 IF(BUILD_TESTING)
     INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/tests)
-    ADD_SUBDIRECTORY(platforms/reference/tests)
 ENDIF(BUILD_TESTING)
 
+set(OPENMM_BUILD_REFERENCE_TESTS TRUE CACHE BOOL "Whether to build Reference platform test cases")
+MARK_AS_ADVANCED(OPENMM_BUILD_REFERENCE_TESTS)
+IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
+    ADD_SUBDIRECTORY(platforms/reference/tests)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
+
 # Which hardware platforms to build
 
 # A bit of tedium because we are using custom FindCUDA files that happen to work...

appveyor.yml

@@ -20,13 +20,13 @@ install:
   - "set PATH=C:\\fftw;%PATH%"
 
 # Download and install some OpenMM build dependencies (doxygen, swig)
-  - choco install -y doxygen.portable swig jom
+  - choco install -y doxygen.portable swig > null
 
 # Set CMake options
   - ps: $env:CMAKE_FLAGS='-DOPENMM_BUILD_PME_PLUGIN=ON -DFFTW_LIBRARY=C:/fftw/libfftw3f-3.lib -DFFTW_INCLUDES=C:/fftw -DCMAKE_BUILD_TYPE=Release -DOPENMM_BUILD_EXAMPLES=OFF -DCMAKE_CXX_FLAGS_RELEASE="/MD /Od /Ob0 /D NDEBUG"'
   - mkdir build
   - cd build
-  - cmake -G "NMake Makefiles JOM" %CMAKE_FLAGS% -LA ..
+  - cmake -G "NMake Makefiles" %CMAKE_FLAGS% -LA ..
 
 # Run the build
   - cmake --build . --target install

docs-source/usersguide/application.rst

@@ -1125,6 +1125,13 @@ perform integration on a modified potential energy surface to allow much faster
 sampling of conformations.  For details on how to use them, consult the API
 documentation.
 
+Compound Integrator
+-------------------
+
+The :class:`CompoundIntegrator` class is useful for cases where you want to use
+multiple integration algorithms within a single simulation.  It allows you to
+create multiple integrators, then switch back and forth between them.  For
+details on how to use it, consult the API documentation.
 
 Temperature Coupling
 ====================
@@ -1843,7 +1850,7 @@ The :code:`<ForceField>` tag contains the following children:
 * Zero or more tags defining specific forces
 
 
-The order of these tags does not matter.  They are described in details below.
+The order of these tags does not matter.  They are described in detail below.
 
 <AtomTypes>
 ===========
@@ -1882,12 +1889,12 @@ The residue template definitions look like this:
       <Atom name="HH33" type="710"/>
       <Atom name="C" type="712"/>
       <Atom name="O" type="713"/>
-      <Bond from="0" to="1"/>
-      <Bond from="1" to="2"/>
-      <Bond from="1" to="3"/>
-      <Bond from="1" to="4"/>
-      <Bond from="4" to="5"/>
-      <ExternalBond from="4"/>
+      <Bond atomName1="HH31" atomName2="CH3"/>
+      <Bond atomName1="CH3" atomName2="HH32"/>
+      <Bond atomName1="CH3" atomName2="HH33"/>
+      <Bond atomName1="CH3" atomName2="C"/>
+      <Bond atomName1="C" atomName2="O"/>
+      <ExternalBond atomName="C"/>
      </Residue>
      <Residue name="ALA">
       ...
@@ -1901,12 +1908,16 @@ contains the following tags:
 * An :code:`<Atom>` tag for each atom in the residue.  This specifies the
   name of the atom and its atom type.
 * A :code:`<Bond>` tag for each pair of atoms that are bonded to each
-  other.  The :code:`to` and :code:`from` attributes are the indices of
-  the two bonded atoms (starting from 0) in the order they were listed.  For
-  example, :code:`<Bond from="1" to="3"/>` describes a bond between atom CH3
-  and atom HH33.
+  other.  The :code:`atomName1` and :code:`atomName2` attributes are the names
+  of the two bonded atoms.  (Some older force fields use the alternate tags
+  :code:`to` and :code:`from` to specify the atoms by index instead of name.
+  This is still supported for backward compatibility, but specifying atoms by
+  name is recommended, since it makes the residue definition much easier to
+  understand.)
 * An :code:`<ExternalBond>` tag for each atom that will be bonded to an
-  atom of a different residue.
+  atom of a different residue.  :code:`atomName` is the name of the atom.
+  (Alternatively, the deprecated :code:`from` tag may indicate the atom by
+  index instead of name.)
 
 
 The :code:`<Residue>` tag may also contain :code:`<VirtualSite>` tags,
@@ -1919,26 +1930,32 @@ as in the following example:
      <Atom name="H1" type="tip4pew-H"/>
      <Atom name="H2" type="tip4pew-H"/>
      <Atom name="M" type="tip4pew-M"/>
-     <VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2"
+     <VirtualSite type="average3" siteName="M" atomName1="O" atomName2="H1" atomName3="H2"
          weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
-     <Bond from="0" to="1"/>
-     <Bond from="0" to="2"/>
+     <Bond atomName1="O" atomName2="H1"/>
+     <Bond atomName1="O" atomName2="H2"/>
     </Residue>
 
 Each :code:`<VirtualSite>` tag indicates an atom in the residue that should
 be represented with a virtual site.  The :code:`type` attribute may equal
-:code:`"average2"`\ , :code:`"average3"`\ , or :code:`"outOfPlane"`\ , which
-correspond to the TwoParticleAverageSite, ThreeParticleAverageSite, and
-OutOfPlaneSite classes respectively.  The :code:`index` attribute gives the
-index (starting from 0) of the atom to represent with a virtual site.  The atoms
-it is calculated based on are specified by :code:`atom1`\ , :code:`atom2`\ ,
-and (for virtual site classes that involve three atoms) :code:`atom3`\ .  The
-remaining attributes are specific to the virtual site class, and specify the
+:code:`"average2"`\ , :code:`"average3"`\ , :code:`"outOfPlane"`\ , or
+:code:`"localCoords"`\ , which correspond to the TwoParticleAverageSite, ThreeParticleAverageSite,
+OutOfPlaneSite, and LocalCoordinatesSite classes respectively.  The :code:`siteName`
+attribute gives the name of the atom to represent with a virtual site.  The atoms
+it is calculated based on are specified by :code:`atomName1`\ , :code:`atomName2`\ ,
+and (for virtual site classes that involve three atoms) :code:`atomName3`\ .
+(Some old force fields use the deprecated tags :code:`index`, :code:`atom1`,
+:code:`atom2`, and :code:`atom3` to refer to them by index instead of name.)
+
+The remaining attributes are specific to the virtual site class, and specify the
 parameters for calculating the site position.  For a TwoParticleAverageSite,
 they are :code:`weight1` and :code:`weight2`\ .  For a
 ThreeParticleAverageSite, they are :code:`weight1`\ , :code:`weight2`\ , and
 \ :code:`weight3`\ . For an OutOfPlaneSite, they are :code:`weight12`\ ,
-:code:`weight13`\ , and :code:`weightCross`\ .
+:code:`weight13`\ , and :code:`weightCross`\ . For a LocalCoordinatesSite, they
+are :code:`wo1`\ , :code:`wo2`\ , :code:`wo3`\ , :code:`wx1`\ , :code:`wx2`\ ,
+:code:`wx3`\ , :code:`wy1`\ , :code:`wy2`\ , :code:`wy3`\ , :code:`p1`\ ,
+:code:`p2`\ , and :code:`p3`\ .
 
 
 <HarmonicBondForce>
@@ -2496,8 +2513,9 @@ The following operators are supported: + (add), - (subtract), * (multiply), /
 
 The following standard functions are supported: sqrt, exp, log, sin, cos, sec,
 csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs,
-step. step(x) = 0 if x < 0, 1 otherwise.  Some custom forces allow additional
-functions to be defined from tabulated values.
+floor, ceil, step, delta, select. step(x) = 0 if x < 0, 1 otherwise.
+delta(x) = 1 if x is 0, 0 otherwise.  select(x,y,z) = z if x = 0, y otherwise.
+Some custom forces allow additional functions to be defined from tabulated values.
 
 Numbers may be given in either decimal or exponential form.  All of the
 following are valid numbers: 5, -3.1, 1e6, and 3.12e-2.
@@ -2521,8 +2539,8 @@ values.  All uses of a value must appear *before* that value’s definition.
 
 .. _tabulated-functions:
 
-TabulatedFunctions
-==================
+Tabulated Functions
+===================
 
 Some forces, such as CustomNonbondedForce and CustomGBForce, allow you to define
 tabulated functions.  To define a function, include a :code:`<Function>` tag inside the
@@ -2569,6 +2587,47 @@ successive values separated by white space.  See the API documentation for more
 details.
 
 
+Residue Template Parameters
+===========================
+
+In forces that use an :code:`<Atom>` tag to define parameters for atom types or
+classes, there is an alternate mechanism you can also use: defining those
+parameter values in the residue template.  This is useful for situations that
+come up in certain force fields.  For example, :code:`NonbondedForce` and
+:code:`GBSAOBCForce` each have a :code:`charge` attribute.  If you only have to
+define the charge of each atom type once, that is more convenient and avoids
+potential bugs.  Also, many force fields have a different charge for each atom
+type, but Lennard-Jones parameters that are the same for all types in a class.
+It would be preferable not to have to repeat those parameter values many times
+over.
+
+When writing a residue template, you can add arbitrary additional attributes
+to each :code:`<Atom>` tag.  For example, you might include a :code:`charge`
+attribute as follows:
+
+.. code-block:: xml
+
+   <Atom name="CA" type="53" charge="0.0381"/>
+
+When writing the tag for a force, you can then include a
+:code:`<UseAttributeFromResidue>` tag inside it.  This indicates that a
+specified attribute should be taken from the residue template.  Finally, you
+simply omit that attribute in the force's own :code:`<Atom>` tags.  For example:
+
+.. code-block:: xml
+
+    <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+     <UseAttributeFromResidue name="charge"/>
+     <Atom class="CX" sigma="0.339966950842" epsilon="0.4577296"/>
+     ...
+    </NonbondedForce>
+
+Notice that the :code:`charge` attribute is missing, and that the parameters
+are specified by class, not by type.  This means that sigma and epsilon only
+need to be specified once for each class.  The atom charges, which are different
+for each type, are taken from the residue template instead.
+
+
 Using Multiple Files
 ********************
 

examples/simulateGromacs.py

@@ -4,7 +4,7 @@ from simtk.unit import *
 from sys import stdout
 
 gro = GromacsGroFile('input.gro')
-top = GromacsTopFile('input.top', periodicBoxVectors=gro.getPeriodicBoxVectors(), includeDir='/usr/local/gromacs/share/gromacs/top')
+top = GromacsTopFile('input.top', periodicBoxVectors=gro.getPeriodicBoxVectors())
 system = top.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
 integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
 simulation = Simulation(top.topology, system, integrator)

libraries/pthreads/include/pthread.h

@@ -121,6 +121,9 @@
 #endif
 
 
+#if _MSC_VER >= 1900
+#include <ctime>
+#else
 /* Windows doesn't have this, so declare it ourselves. */
 struct timespec
 {
@@ -128,6 +131,7 @@ struct timespec
 	long long tv_sec;
 	long long tv_nsec;
 };
+#endif
 
 typedef struct _pthread_cleanup _pthread_cleanup;
 struct _pthread_cleanup

libraries/validate/include/ValidateOpenMM.h

-#ifndef VALIDATE_OPENMM_H_
-#define VALIDATE_OPENMM_H_
-
-/* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from   *
- * Simbios, the NIH National Center for Physics-Based Simulation of           *
- * Biological Structures at Stanford, funded under the NIH Roadmap for        *
- * Medical Research, grant U54 GM072970. See https://simtk.org.               *
- *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
- * Authors: Mark Friedrichs                                                   *
- * Contributors:                                                              *
- *                                                                            *
- * This program 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 3 of the License, or       *
- * (at your option) any later version.                                        *
- *                                                                            *
- * This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.      *
- * -------------------------------------------------------------------------- */
-
-#include "OpenMM.h"
-#include "../../../platforms/reference/include/ReferencePlatform.h"
-#include "openmm/Context.h"
-#include "openmm/System.h"
-#include "ValidateWindowsIncludes.h"
-
-// free-energy plugin includes
-
-//#define	INCLUDE_FREE_ENERGY_PLUGIN
-#ifdef INCLUDE_FREE_ENERGY_PLUGIN
-#include "../../../plugins/freeEnergy/openmmapi/include/OpenMMFreeEnergy.h"
-#include "../../../plugins/freeEnergy/openmmapi/include/openmm/freeEnergyKernels.h"
-//#include "../../../plugins/freeEnergy/platforms/reference/include/ReferenceFreeEnergyPlatform.h"
-#include "../../../plugins/freeEnergy/platforms/reference/include/ReferenceFreeEnergyKernelFactory.h"
-#endif
-
-#include <sstream>
-#include <typeinfo>
-
-#include <limits>
-#include <cstdlib>
-#include <cstring>
-#include <cstdio>
-
-namespace OpenMM {
-
-typedef std::map< std::string, int > StringIntMap;
-typedef StringIntMap::iterator StringIntMapI;
-typedef StringIntMap::const_iterator StringIntMapCI;
-
-typedef std::map< std::string, double > StringDoubleMap;
-typedef StringDoubleMap::iterator StringDoubleMapI;
-typedef StringDoubleMap::const_iterator StringDoubleMapCI;
-
-typedef std::map< std::string, unsigned int > StringUIntMap;
-typedef StringUIntMap::iterator StringUIntMapI;
-typedef StringUIntMap::const_iterator StringUIntMapCI;
-
-typedef std::vector< std::string > StringVector;
-typedef StringVector::iterator StringVectorI;
-typedef StringVector::const_iterator StringVectorCI;
-
-typedef std::vector< int > IntVector;
-typedef IntVector::iterator IntVectorI;
-typedef IntVector::const_iterator IntVectorCI;
-
-typedef std::map< std::string, std::vector<std::string> > StringStringVectorMap;
-typedef StringStringVectorMap::iterator StringStringVectorMapI;
-typedef StringStringVectorMap::const_iterator StringStringVectorMapCI;
-
-/**
- * Base class w/ common functionality 
- */
-class ValidateOpenMM {
-public:
-
-    ValidateOpenMM();
-    ~ValidateOpenMM();
-
-    // force names
-    
-    static const std::string HARMONIC_BOND_FORCE;
-    static const std::string HARMONIC_ANGLE_FORCE;
-    static const std::string PERIODIC_TORSION_FORCE;
-    static const std::string RB_TORSION_FORCE;
-    
-    static const std::string NB_FORCE;
-    static const std::string NB_SOFTCORE_FORCE;
-    
-    static const std::string NB_EXCEPTION_FORCE;
-    static const std::string NB_EXCEPTION_SOFTCORE_FORCE;
-    
-    static const std::string GBSA_OBC_FORCE;
-    static const std::string GBSA_OBC_SOFTCORE_FORCE;
-    
-    static const std::string GBVI_FORCE;
-    static const std::string GBVI_SOFTCORE_FORCE;
-
-    static const std::string CM_MOTION_REMOVER;
-    static const std::string ANDERSEN_THERMOSTAT;
-    static const std::string CUSTOM_BOND_FORCE;
-    static const std::string CUSTOM_EXTERNAL_FORCE;
-    static const std::string CUSTOM_NONBONDED_FORCE;
-
-    /**
-     * Return true if input number is nan or infinity
-     *
-     * @param number   number to test
-     *
-     * @return true if number is nan or infinity
-     */
-    
-    static int isNanOrInfinity( double number );
-    
-    /**
-     * Get force name
-     * 
-     * @param force      OpenMM system force 
-     *
-     * @return force name or "NA" if force is not recognized
-     */
-    std::string getForceName(const Force& force ) const;
-
-    /**
-     * Copy force 
-     * 
-     * @param force      OpenMM system force to copy 
-     *
-     * @return force or NULL if not recognized
-     */
-    Force* copyForce(const Force& force) const;
-
-    /**
-     * Get copy of input system, but omit forces
-     * 
-     * @param systemToCopy   system to copy
-     *
-     * @return copy of system but w/o forces
-     */
-    System* copySystemExcludingForces( const System& systemToCopy ) const;
-
-    /**
-     *
-     * Set the velocities/positions of context2 to those of context1
-     * 
-     * @param context1                 context1 
-     * @param context2                 context2 
-     *
-     * @return 0
-     */
-    void synchContexts( const Context& context1, Context& context2 ) const;
-    
-    /**
-     *
-     * Get log FILE* reference
-     * 
-     * @return log
-     *
-     */
-    FILE* getLog() const;
-    
-    /**
-     *
-     * Set log FILE* reference
-     * 
-     * @param log  log
-     *
-     */
-    void OPENMM_VALIDATE_EXPORT setLog( FILE* log );
-    
-    /**---------------------------------------------------------------------------------------
-    
-       Copy constraints
-    
-       @param systemToCopy         system whose constraints are to be copied
-       @param system               system to add constraints to
-       @param log                  log file pointer -- may be NULL
-    
-       --------------------------------------------------------------------------------------- */
-    
-    void copyConstraints( const System& systemToCopy, System* system, FILE* log = NULL ) const;
-    
-    /**---------------------------------------------------------------------------------------
-    
-       Get force dependencies
-    
-       @param forceName            force to check if there exist any dependencies
-       @param returnVector         vector of forces the input force is dependent on (example: GBSAOBC force requires Nonbonded force since
-                                   on Cuda platofrm they are computed in same loop and hence are inseparable)
-    
-       --------------------------------------------------------------------------------------- */
-    
-    void getForceDependencies( std::string forceName, StringVector& returnVector ) const;
-    
-    /**
-     * Write masses to parameter file
-     *
-     * @param filePtr    file to write masses to
-     * @param system     write masses in system
-     */
-    
-    void writeMasses( FILE* filePtr, const System& system ) const;
-    
-    /**
-     * Write constraints to parameter file
-     *
-     * @param filePtr    file to write constraints to
-     * @param system     write constraints in system
-     *
-     */
-    
-    void writeConstraints( FILE* filePtr, const System& system ) const;
-    
-    /**
-     * Write harmonicBondForce parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param harmonicBondForce     write harmonicBondForce parameters
-     *
-     */
-    
-    void writeHarmonicBondForce( FILE* filePtr, const HarmonicBondForce& harmonicBondForce ) const;
-
-    /**
-     * Write harmonicAngleForce parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param harmonicAngleForce     write harmonicAngleForce parameters
-     *
-     */
-    
-    void writeHarmonicAngleForce( FILE* filePtr, const HarmonicAngleForce& harmonicAngleForce ) const;
-    
-    /**
-     * Write rbTorsionForce parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param rbTorsionForce         write rbTorsionForce parameters
-     *
-     */
-    
-    void writeRbTorsionForce( FILE* filePtr, const RBTorsionForce& rbTorsionForce ) const;
-    
-    /**
-     * Write periodicTorsionForce parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param periodicTorsionForce   write periodicTorsionForce parameters
-     *
-     */
-    
-    void writePeriodicTorsionForce( FILE* filePtr, const PeriodicTorsionForce& periodicTorsionForce ) const;
-    
-    /**
-     * Write nonbonded parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param nonbondedForce         write nonbondedForce parameters
-     *
-     */
-    
-    void writeNonbondedForce( FILE* filePtr, const NonbondedForce & nonbondedForce ) const;
-    
-    /**
-     * Write GBSAOBCForce parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param gbsaObcForce           write gbsaObcForce parameters
-     *
-     */
-    
-    void writeGbsaObcForce( FILE* filePtr, const GBSAOBCForce& gbsaObcForce ) const;
-    
-    /**
-     * Write GBSA GB/VI Force parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param gbviObcForce           write gbviObcForce parameters
-     *
-     */
-    
-    void writeGBVIForce( FILE* filePtr, const GBVIForce& gbviForce ) const;
-    
-#ifdef INCLUDE_FREE_ENERGY_PLUGIN
-    
-    /**
-     * Write nonbonded softcore parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param nonbondedForce         write nonbondedForce parameters
-     */
-    
-    void writeNonbondedSoftcoreForce( FILE* filePtr, const NonbondedSoftcoreForce & nonbondedSoftcoreForce ) const;
-
-    /**
-     * Write GBSAOBCSoftcoreForce parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param gbsaObcForce           write gbsaObcForce parameters
-     *
-     */
-    
-    void writeGbsaObcSoftcoreForce( FILE* filePtr, const GBSAOBCSoftcoreForce& gbsaObcForce ) const;
-    
-    /**
-     * Write GBSA GB/VI softcore force parameters to file
-     *
-     * @param filePtr                file to write forces to
-     * @param gbviObcForce           write gbviObcForce parameters
-     *
-     */
-    
-    void writeGBVISoftcoreForce( FILE* filePtr, const GBVISoftcoreForce& gbviSoftcoreForce ) const;
-    
-#endif
-    
-    /**
-     * Write coordinates, velocities, ... to file
-     *
-     * @param filePtr                file to write Vec3 entries to
-     * @param vect3Array             write array of Vec3
-     *
-     */
-    
-    void writeVec3( FILE* filePtr, const std::vector<Vec3>& vect3Array ) const;
-    
-    /**
-     * Write context info to file (positions, velocities, forces, energies)
-     *
-     * @param filePtr                file to write entries to
-     * @param context                write context positions, velocities, forces, energies to file
-     *
-     */
-    
-    void writeContext( FILE* filePtr, const Context& context ) const;
-    
-    /**
-     * Write integrator
-     *
-     * @param filePtr                file to write integrator info to
-     * @param integrator             write integrator info (time step, seed, ... as applicable)
-     *
-     */
-    
-    void writeIntegrator( FILE* filePtr, const Integrator& integrator ) const;
-    
-    /**
-     * Write parameter file
-     * @param context                context whose entries are to be written to file
-     * @param parameterFileName      file name
-     *
-     */
-    
-    void writeParameterFile( const Context& context, const std::string& parameterFileName ) const;
-    
-private:
-
-    FILE* _log;
-
-    // map of force dependencies (e.g., GBSAObc requires NB force on CudaPlatform)
-
-    StringStringVectorMap _forceDependencies;
-};
-
-
-} // namespace OpenMM
-
-#endif /*VALIDATE_OPENMM_H_*/

libraries/validate/include/ValidateOpenMMForces.h

-#ifndef VALIDATE_OPENMM_FORCES_H_
-#define VALIDATE_OPENMM_FORCES_H_
-
-/* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from   *
- * Simbios, the NIH National Center for Physics-Based Simulation of           *
- * Biological Structures at Stanford, funded under the NIH Roadmap for        *
- * Medical Research, grant U54 GM072970. See https://simtk.org.               *
- *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
- * Authors: Mark Friedrichs                                                   *
- * Contributors:                                                              *
- *                                                                            *
- * This program 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 3 of the License, or       *
- * (at your option) any later version.                                        *
- *                                                                            *
- * This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.      *
- * -------------------------------------------------------------------------- */
-
-#include "ValidateOpenMM.h"
-
-namespace OpenMM {
-
-typedef std::map< int, int > MapIntInt;
-typedef MapIntInt::iterator MapIntIntI;
-typedef MapIntInt::const_iterator MapIntIntCI;
-
-// Helper class for ValidateOpenMMForces class used to store force results and facitilitate comparisons of
-// resulting forces
-
-class ForceValidationResult {
-public:
-
-    ForceValidationResult(const Context& context1, const Context& context2, StringUIntMap& forceNamesMap);
-    ~ForceValidationResult();
-
-    /**
-     * Get potential energy at specified platform index (0 || 1)
-     * 
-     * @return  potential energy for spercifed platform
-     *
-     * @throws OpenMMException if energyIndex is not 0 or 1
-     */
-    double getPotentialEnergy(int energyIndex) const;
-
-    /**
-     * Get array of forces at specified platform index (0 || 1)
-     * 
-     * @return array of force norms
-     *
-     * @throws OpenMMException if forceIndex is not 0 or 1
-     */
-    std::vector<double> getForceNorms(int forceIndex) const;
-
-    /**
-     * Get array of forces at platform index (0 || 1)
-     * 
-     * @return force array
-     *
-     * @throws OpenMMException if forceIndex is not 0 or 1
-     */
-    std::vector<Vec3> getForces(int forceIndex) const;
-
-    /**
-     * Get maximum delta in force norm
-     * 
-     * @param maxIndex  return atom index of entry with maximum delta norm (optional)
-     *
-     * @return max delta in norm of forces
-     */
-    double getMaxDeltaForceNorm(int* maxIndex = NULL) const;
-
-    /**
-     * Get maximum relative delta in force norm
-     * 
-     * @param maxIndex  return atom index of entry w/ maximum relative delta norm (optional)
-     *
-     * @return max relative delta in norm of forces
-     */
-    double getMaxRelativeDeltaForceNorm(int* maxIndex = NULL) const;
-
-    /**
-     * Get maximum dot product between forces
-     * 
-     * @param maxIndex  return atom index of entry w/ maximum dot product between forces (optional)
-     *
-     * @return max dot product between forces
-     */
-    double getMaxDotProduct(int* maxIndex = NULL) const;
-
-    /**
-     * Get name of force associated w/ computed results
-     * 
-     * @return force name(s); if more than one force active in computation, 
-     * then names are concatenated and separated by '::' (e.g., 'NB_FORCE::GBSA_OBC_FORCE')
-     */
-    std::string getForceName() const;
-
-    /**
-     * Get platform name
-     * 
-     * @param index index of platform (0 or 1)
-     *
-     * @return platform name
-     *
-     * @throws OpenMMException if index is not 0 or 1
-     */
-    std::string getPlatformName(int index) const;
-
-    /**
-     * Register index of two entries that differ by a specified tolerance
-     * 
-     * @param index inconsistent index
-     *
-     */
-    void registerInconsistentForceIndex(int index, int value = 1);
-
-    /**
-     * Clear list of entries that differ by a specified tolerance
-     * 
-     */
-    void clearInconsistentForceIndexList();
-
-    /**
-     * Get list of entries that differ by a specified tolerance
-     * 
-     */
-    void getInconsistentForceIndexList(std::vector<int>& inconsistentIndices) const;
-
-    /**
-     * Get number of entries in inconsistent index list
-     * 
-     */
-    int getNumberOfInconsistentForceEntries() const;
-
-    /**
-     * Return true if nans were detected
-     * 
-     * @return true if nans were detected
-     */
-    int nansDetected() const;
-
-    /**
-     * Determine if force norms are valid
-     * 
-     * @param tolerance              tolerance
-     */
-    void compareForceNorms(double tolerance);
-
-    /**
-     * Determine if forces are valid
-     * 
-     * @param tolerance   tolerance
-     */
-    void compareForces(double tolerance);
-
-private:
-
-    // computed potential energies and forces fror two platforms
-
-    double _potentialEnergies[2];
-    std::vector<Vec3> _forces[2];
-
-    // platform and force names
-
-    std::string _platforms[2];
-    std::vector<std::string> _forceNames;
-
-    // force norms and stat entries
-
-    std::vector<double> _norms[2];
-    std::vector<double> _normStatVectors[2];
-
-    // map of indicies w/ inconsistent force entries
-
-    std::map<int, int> _inconsistentForceIndicies;
-
-    // if set, then nans detected
-
-    int _nansDetected;
-
-    /**
-     * Calculate norms of vectors
-     * 
-     */
-    void _calculateNorms();
-
-    /**
-     * Calculate norms of specified vector
-     * 
-     */
-    void _calculateNormOfForceVector(int forceIndex);
-
-    // stat indices
-
-    static const int STAT_AVG = 0;
-    static const int STAT_STD = 1;
-    static const int STAT_MIN = 2;
-    static const int STAT_ID1 = 3;
-    static const int STAT_MAX = 4;
-    static const int STAT_ID2 = 5;
-    static const int STAT_CNT = 6;
-    static const int STAT_END = 7;
-
-    /**
-     * Find vector stats
-     * 
-     */
-    void _findStatsForDouble(const std::vector<double>& array, std::vector<double>& statVector) const;
-};
-
-// Class used to compare forces/potential energies on two platforms
-
-class ValidateOpenMMForces : public ValidateOpenMM {
-public:
-
-    OPENMM_VALIDATE_EXPORT ValidateOpenMMForces();
-    OPENMM_VALIDATE_EXPORT ~ValidateOpenMMForces();
-
-    /**
-     * Validate force/energy by comparing the results between the forces/energies computed on user-provided context platform
-     * with Reference platform
-     * 
-     * @param context          context reference
-     * @param summaryString    output summary string of results of comparison (optional)
-     *
-     * @return number of inconsistent entries
-     */
-     int OPENMM_VALIDATE_EXPORT compareWithReferencePlatform(Context& context, std::string* summaryString = NULL);
-
-    /**
-     * Validate force/energy by comparing the results between the forces/energies computed on two different platforms
-     * 
-     * @param context          context reference
-     * @param compareForces    indices of force to be tested
-     * @param platform1        first platform to compute forces
-     * @param platform2        second platform to compute forces
-     *
-     * @return ForceValidationResult reference containing results of force/energy computations
-     *         on the two input platforms
-     */
-     ForceValidationResult* compareForce(Context& context, std::vector<int>& compareForces,
-                                         Platform& platform1, Platform& platform2) const;
-
-    /**
-     * Compare individual forces by comparing calculations across two platforms (platform associated w/ input context and
-     * comparisonPlatform)
-     * 
-     * @param context                 context reference
-     * @param platform                comparsion platform reference 
-     * @param forceValidationResults  output vector of ForceValidationResult ptrs (user is responsible for deleting
-     *                                individual ForceValidationResult objects)
-     */
-    void compareOpenMMForces(Context& context, Platform& comparisonPlatform, std::vector<ForceValidationResult*>& forceValidationResults) const;
-
-    /**
-     * Determine if results are consistent
-     * 
-     * @param forceValidationResults  vector of ForceValidationResult ptrs to check if forces are consistent
-     */
-    void checkForInconsistentForceEntries(std::vector<ForceValidationResult*>& forceValidationResults) const;
-
-    /**
-     * Get total number of force entries that are inconsistent
-     * 
-     * @param forceValidationResults  vector of ForceValidationResult ptrs to check if forces are consistent
-     */
-    int getTotalNumberOfInconsistentForceEntries(std::vector<ForceValidationResult*>& forceValidationResults) const;
-
-    /**
-     * Get summary string of results
-     * 
-     * @param forceValidationResults  vector of ForceValidationResult ptrs
-     */
-    std::string getSummary(std::vector<ForceValidationResult*>& forceValidationResults) const;
-
-    /**
-     * Set force tolerance
-     * 
-     * @param tolerance     force tolerance
-     */
-    void setForceTolerance(double tolerance);
-
-    /**
-     * Get force tolerance
-     * 
-     * @return force tolerance
-     */
-    double getForceTolerance() const;
-
-    /* 
-     * Get force tolerance for specified force
-     *
-     * @param forceName   name of force
-     *
-     * @return force tolerance
-     *
-     * */
-      
-    double getForceTolerance(const std::string& forceName) const;
-       
-    /* 
-     * Get max errors to print in summary string
-     *
-     * @return max errors to print
-     *
-     * */
-      
-    int getMaxErrorsToPrint() const;
-       
-    /* 
-     * Set max errors to print in summary string
-     *
-     * @param maxErrorsToPrint max errors to print
-     *
-     * */
-      
-    void setMaxErrorsToPrint(int maxErrorsToPrint);
-       
-    /* 
-     * Return true if force is not to be validated (Andersen thermostat, CM motion remover, ...)
-     *
-     * @param forceName   force name
-     *
-     * @return true if force is not currently validated
-     **/
-      
-    int isExcludedForce(std::string forceName) const;
-       
-private:
-
-     // initialize class entries
-
-     void _initialize();
-
-      /* 
-       * Format output line
-       *
-       * @param tab         tab
-       * @param description description
-       * @param value       value
-       *
-       * @return string containing contents
-       *
-       * */
-      
-      std::string _getLine(const std::string& tab,
-                           const std::string& description,
-                           const std::string& value) const;
-      
-     std::vector<ForceValidationResult*> _forceValidationResults;
-
-     // max errors to print
-
-     int _maxErrorsToPrint;
-
-     // tolerence
-
-     double _forceTolerance;
-
-     // map of force tolerances to type (name)
-
-     StringDoubleMap _forceTolerances;
-     
-     // forces to be excluded from validation
-
-     StringIntMap _forcesToBeExcluded;
-};
-
-} // namespace OpenMM
-
-#endif /*VALIDATE_OPENMM_FORCES_H_*/

libraries/validate/include/ValidateWindowsIncludes.h

-#ifndef OPENMM_VALIDATE_WINDOW_INCLUDE_H_
-#define OPENMM_VALIDATE_WINDOW_INCLUDE_H_
-
-/*
- * Shared libraries are messy in Visual Studio. We have to distinguish three
- * cases:
- *   (1) this header is being used to build the OpenMMValidate shared library
- *       (dllexport)
- *   (2) this header is being used by a *client* of the OpenMMValidate shared
- *       library (dllimport)
- *   (3) we are building the OpenMMValidate static library, or the client is
- *       being compiled with the expectation of linking with the
- *       OpenMMValidate static library (nothing special needed)
- * In the CMake script for building this library, we define one of the symbols
- *     OpenMMValidate_BUILDING_{SHARED|STATIC}_LIBRARY
- * Client code normally has no special symbol defined, in which case we'll
- * assume it wants to use the shared library. However, if the client defines
- * the symbol OPENMM_VALIDATE_USE_STATIC_LIBRARIES we'll suppress the dllimport so
- * that the client code can be linked with static libraries. Note that
- * the client symbol is not library dependent, while the library symbols
- * affect only the OpenMMValidate library, meaning that other libraries can
- * be clients of this one. However, we are assuming all-static or all-shared.
- */
-
-#ifdef _MSC_VER
-    // We don't want to hear about how sprintf is "unsafe".
-    #pragma warning(disable:4996)
-    #if defined(OPENMM_VALIDATE_BUILDING_SHARED_LIBRARY)
-        #define OPENMM_VALIDATE_EXPORT __declspec(dllexport)
-        // Keep MS VC++ quiet about lack of dll export of private members.
-        #pragma warning(disable:4251)
-    #elif defined(OPENMM_VALIDATE_BUILDING_STATIC_LIBRARY) || defined(OPENMM_VALIDATE_USE_STATIC_LIBRARIES)
-		#define OPENMM_VALIDATE_EXPORT
-    #else
-		#define OPENMM_VALIDATE_EXPORT __declspec(dllimport)   // i.e., a client of a shared library
-    #endif
-#else
-    #define OPENMM_VALIDATE_EXPORT // Linux, Mac
-#endif
-
-#endif // OPENMM_VALIDATE_WINDOW_INCLUDE_H_

libraries/vecmath/src/vecmath.cpp

+#if defined(__ANDROID__)
+    #include "neon_mathfun.h"
+#else
+    #if !defined(__PNACL__)
+        #define USE_SSE2
+        #include "sse_mathfun.h"
+    #endif
+#endif

olla/include/openmm/kernels.h

@@ -48,7 +48,6 @@
 #include "openmm/CustomManyParticleForce.h"
 #include "openmm/CustomTorsionForce.h"
 #include "openmm/GBSAOBCForce.h"
-#include "openmm/GBVIForce.h"
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/KernelImpl.h"
@@ -667,35 +666,6 @@ public:
     virtual void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force) = 0;
 };
 
-/**
- * This kernel is invoked by GBVIForce to calculate the forces acting on the system and the energy of the system.
- */
-class CalcGBVIForceKernel : public KernelImpl {
-public:
-    static std::string Name() {
-        return "CalcGBVIForce";
-    }
-    CalcGBVIForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
-    }
-    /**
-     * Initialize the kernel.
-     * 
-     * @param system      the System this kernel will be applied to
-     * @param force       the GBVIForce this kernel will be used for
-     * @param scaledRadii scaled radii
-     */
-    virtual void initialize(const System& system, const GBVIForce& force, const std::vector<double>& scaledRadii) = 0;
-    /**
-     * Execute the kernel to calculate the forces and/or energy.
-     *
-     * @param context        the context in which to execute this kernel
-     * @param includeForces  true if forces should be calculated
-     * @param includeEnergy  true if the energy should be calculated
-     * @return the potential energy due to the force
-     */
-    virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
-};
-
 /**
  * This kernel is invoked by CustomGBForce to calculate the forces acting on the system and the energy of the system.
  */

openmmapi/include/OpenMM.h

@@ -36,6 +36,7 @@
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomBondForce.h"
 #include "openmm/CustomCentroidBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
@@ -49,7 +50,6 @@
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/Force.h"
 #include "openmm/GBSAOBCForce.h"
-#include "openmm/GBVIForce.h"
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/Integrator.h"