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

.travis.yml

@@ -131,16 +131,11 @@ script:
           make PythonInstall;
       fi;
       python -m simtk.testInstallation;
-      (cd python/tests && py.test -v *);
+      (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 --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
-  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then
-      ctest -I FailedTests.log;
-    fi
+  - python devtools/run-ctest.py -j2 --schedule-random --stop-time $CTEST_STOP_TIME
   - if [[ ! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true" ]]; then
       pip install sphinx sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen;
       make C++ApiDocs PythonApiDocs;

appveyor.yml

@@ -5,11 +5,10 @@ install:
 # Setup shell for VS2010, x64, release mode
   - >
     "%ProgramFiles%\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64 /release
-
 # Set path to python, git-bash tools.
   - "set PATH=C:\\Python34-x64;C:\\Python34-x64\\Scripts;%PATH%"
   - "set PATH=C:\\Program Files (x86)\\Git\\bin;%PATH%"
-  - pip install nose
+  - pip install pytest
 
 # Download FFTW3 for PME plugin
   - C:\MinGW\msys\1.0\bin\wget -q ftp://ftp.fftw.org/pub/fftw/fftw-3.3.4-dll64.zip
@@ -22,26 +21,40 @@ install:
 # Download and install some OpenMM build dependencies (doxygen, swig)
   - 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"'
+# Download OpenCL Headers and build the ICD loader
+  - ps: $opencl_registry = "https://www.khronos.org/registry/cl"
+  - ps: mkdir C:/opencl > $null
+  - ps: cd C:/opencl
+  - ps: wget $opencl_registry/specs/opencl-icd-1.2.11.0.tgz -OutFile opencl-icd-1.2.11.0.tgz
+  - ps: 7z x opencl-icd-1.2.11.0.tgz > $null
+  - ps: 7z x opencl-icd-1.2.11.0.tar > $null
+  - ps: mv .\icd\* .
+  - ps: mkdir inc/CL > $null
+  - ps: wget $opencl_registry/api/1.2/ | select -ExpandProperty links | where {$_.href -like "*.h*"} | select -ExpandProperty outerText | foreach{ wget $opencl_registry/api/1.2/$_ -OutFile inc/CL/$_ }
+  - ps: mkdir lib > $null
+  - ps: cd lib
+  - cmake -G "NMake Makefiles" ..
+  - nmake
+  - cd %APPVEYOR_BUILD_FOLDER%
+
+build_script:
+  - ps: $env:CMAKE_FLAGS =
+      "-DOPENMM_BUILD_PME_PLUGIN=ON
+       -DOPENCL_INCLUDE_DIR=C:/opencl/inc
+       -DOPENCL_LIBRARY=C:/opencl/lib/OpenCL.lib
+       -DFFTW_LIBRARY=C:/fftw/libfftw3f-3.lib
+       -DFFTW_INCLUDES=C:/fftw
+       -DOPENMM_BUILD_EXAMPLES=OFF
+       -DOPENMM_BUILD_OPENCL_TESTS=OFF
+       -DCMAKE_BUILD_TYPE=Release
+       -LA"
   - mkdir build
   - cd build
-  - cmake -G "NMake Makefiles" %CMAKE_FLAGS% -LA ..
-
-# Run the build
+  - cmake -G "NMake Makefiles" %CMAKE_FLAGS% -LA -DCMAKE_CXX_FLAGS_RELEASE="/MD /Od /Ob0 /D NDEBUG" ..
   - cmake --build . --target install
   - cmake --build . --target PythonInstall
 
-build: false
 test_script:
-  - ctest || exit 0
-  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
-  - ps: >
-     If (Test-Path "Testing\\Temporary\\LastTestsFailed.log") {
-         cat Testing\\Temporary\\LastTestsFailed.log
-         cat FailedTests.log
-         ctest -I FailedTests.log
-     }
+  - python %APPVEYOR_BUILD_FOLDER%\devtools\run-ctest.py
   - cd python\tests
-  - nosetests -vv --processes=-1 --process-timeout=200
-  - cd %APPVEYOR_BUILD_FOLDER%
+  - py.test -v

devtools/run-ctest.py

+from __future__ import print_function
+import sys
+from os.path import join, exists
+from subprocess import call
+
+def main():
+    # pass any extra arguments to the first ctest invocation
+    if call(['ctest', '--output-on-failure'] + sys.argv[1:], shell=True) == 0:
+        return 0
+
+    # load the log file containing the failed tests and reformat
+    # it in a way so that ctest can take it as input to rerun
+    # the failing tests
+    log = join('Testing', 'Temporary', 'LastTestsFailed.log')
+    assert exists(log)
+
+    failed = []
+    for line in open(log):
+        failed.append(line.split(':')[0])
+
+    with open('FailedTests.log', 'w') as f:
+        print(','.join(x + ',' + x for x in failed), file=f)
+
+    return call(['ctest', '--output-on-failure', '-I', 'FailedTests.log'])
+
+
+if __name__ == '__main__':
+    sys.exit(main())
+

olla/include/openmm/Kernel.h

@@ -62,7 +62,7 @@ public:
     /**
      * Create a Kernel that wraps a KernelImpl.
      *
-     * @param name the name of the kernel to create
+     * @param KernelImpl the KernelImpl to wrap
      */
     Kernel(KernelImpl* impl);
     ~Kernel();

olla/include/openmm/Platform.h

@@ -53,7 +53,7 @@ class KernelFactory;
  * To get a Platform object, call
  *
  * <pre>
- * Platform& platform Platform::findPlatform(kernelNames);
+ * Platform& platform = Platform::findPlatform(kernelNames);
  * </pre>
  *
  * passing in the names of all kernels that will be required for the calculation you plan to perform.  It
@@ -78,6 +78,9 @@ public:
     /**
      * Get whether this Platform supports double precision arithmetic.  If this returns false, the platform
      * is permitted to represent double precision values internally as single precision.
+     *
+     * @deprecated This method is not well defined, and is too simplistic to describe the actual behavior of
+     * some Platforms, such as ones that offer multiple precision modes.  It will be removed in a future release.
      */
     virtual bool supportsDoublePrecision() const = 0;
     /**

openmmapi/include/openmm/CustomHbondForce.h

@@ -369,8 +369,8 @@ public:
      * Get the donor and acceptor in a pair whose interaction should be excluded.
      *
      * @param index           the index of the exclusion for which to get donor and acceptor indices
-     * @param[out] particle1  the index of the donor
-     * @param[out] particle2  the index of the acceptor
+     * @param[out] donor      the index of the donor
+     * @param[out] acceptor   the index of the acceptor
      */
     void getExclusionParticles(int index, int& donor, int& acceptor) const;
     /**

openmmapi/include/openmm/TabulatedFunction.h

@@ -80,11 +80,11 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min
+     * @param[out] values         the tabulated values of the function f(x) at uniformly spaced values of x between min
      *                            and max.  A natural cubic spline is used to interpolate between the tabulated values.
      *                            The function is assumed to be zero for x < min or x > max.
-     * @param min            the value of x corresponding to the first element of values
-     * @param max            the value of x corresponding to the last element of values
+     * @param[out] min            the value of x corresponding to the first element of values
+     * @param[out] max            the value of x corresponding to the last element of values
      */
     void getFunctionParameters(std::vector<double>& values, double& min, double& max) const;
     /**
@@ -129,16 +129,16 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values     the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
+     * @param[out] values     the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
      *                        and xmax, and ysize values of y between ymin and ymax.  A natural cubic spline is used to interpolate between the tabulated values.
      *                        The function is assumed to be zero when x or y is outside its specified range.  The values should be ordered so that
      *                        values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x.  This must be of length xsize*ysize.
-     * @param xsize      the number of table elements along the x direction
-     * @param ysize      the number of table elements along the y direction
-     * @param xmin       the value of x corresponding to the first element of values
-     * @param xmax       the value of x corresponding to the last element of values
-     * @param ymin       the value of y corresponding to the first element of values
-     * @param ymax       the value of y corresponding to the last element of values
+     * @param[out] xsize      the number of table elements along the x direction
+     * @param[out] ysize      the number of table elements along the y direction
+     * @param[out] xmin       the value of x corresponding to the first element of values
+     * @param[out] xmax       the value of x corresponding to the last element of values
+     * @param[out] ymin       the value of y corresponding to the first element of values
+     * @param[out] ymax       the value of y corresponding to the last element of values
      */
     void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const;
     /**
@@ -194,21 +194,21 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values     the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
+     * @param[out] values     the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
      *                        and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
      *                        A natural cubic spline is used to interpolate between the tabulated values.  The function is
      *                        assumed to be zero when x, y, or z is outside its specified range.  The values should be ordered so
      *                        that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
      *                        This must be of length xsize*ysize*zsize.
-     * @param xsize      the number of table elements along the x direction
-     * @param ysize      the number of table elements along the y direction
-     * @param ysize      the number of table elements along the z direction
-     * @param xmin       the value of x corresponding to the first element of values
-     * @param xmax       the value of x corresponding to the last element of values
-     * @param ymin       the value of y corresponding to the first element of values
-     * @param ymax       the value of y corresponding to the last element of values
-     * @param zmin       the value of z corresponding to the first element of values
-     * @param zmax       the value of z corresponding to the last element of values
+     * @param[out] xsize      the number of table elements along the x direction
+     * @param[out] ysize      the number of table elements along the y direction
+     * @param[out] zsize      the number of table elements along the z direction
+     * @param[out] xmin       the value of x corresponding to the first element of values
+     * @param[out] xmax       the value of x corresponding to the last element of values
+     * @param[out] ymin       the value of y corresponding to the first element of values
+     * @param[out] ymax       the value of y corresponding to the last element of values
+     * @param[out] zmin       the value of z corresponding to the first element of values
+     * @param[out] zmax       the value of z corresponding to the last element of values
      */
     void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax, double& zmin, double& zmax) const;
     /**
@@ -222,7 +222,7 @@ public:
      *                   This must be of length xsize*ysize*zsize.
      * @param xsize      the number of table elements along the x direction
      * @param ysize      the number of table elements along the y direction
-     * @param ysize      the number of table elements along the z direction
+     * @param zsize      the number of table elements along the z direction
      * @param xmin       the value of x corresponding to the first element of values
      * @param xmax       the value of x corresponding to the last element of values
      * @param ymin       the value of y corresponding to the first element of values
@@ -257,7 +257,7 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values         the tabulated values of the function f(x)
+     * @param[out] values    the tabulated values of the function f(x)
      */
     void getFunctionParameters(std::vector<double>& values) const;
     /**
@@ -293,9 +293,9 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param xsize     the number of table elements along the x direction
-     * @param ysize     the number of table elements along the y direction
-     * @param values    the tabulated values of the function f(x,y), ordered so that
+     * @param[out] xsize     the number of table elements along the x direction
+     * @param[out] ysize     the number of table elements along the y direction
+     * @param[out] values    the tabulated values of the function f(x,y), ordered so that
      *                       values[i+xsize*j] = f(i,j).  This must be of length xsize*ysize.
      */
     void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values) const;
@@ -337,10 +337,10 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param xsize     the number of table elements along the x direction
-     * @param ysize     the number of table elements along the y direction
-     * @param zsize     the number of table elements along the z direction
-     * @param values    the tabulated values of the function f(x,y,z), ordered so that
+     * @param[out] xsize     the number of table elements along the x direction
+     * @param[out] ysize     the number of table elements along the y direction
+     * @param[out] zsize     the number of table elements along the z direction
+     * @param[out] values    the tabulated values of the function f(x,y,z), ordered so that
      *                       values[i+xsize*j+xsize*ysize*k] = f(i,j,k).  This must be of length xsize*ysize*zsize.
      */
     void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values) const;

platforms/cuda/src/CudaContext.cpp

@@ -76,7 +76,7 @@ bool CudaContext::hasInitializedCuda = false;
 CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const string& precision, const string& compiler,
         const string& tempDir, const std::string& hostCompiler, CudaPlatform::PlatformData& platformData) : system(system), currentStream(0),
         time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), contextIsValid(false), atomsWereReordered(false), hasCompilerKernel(false),
-        pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
+        pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), atomIndexDevice(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
     this->compiler = "\""+compiler+"\"";
     if (platformData.context != NULL) {
         try {
@@ -339,6 +339,8 @@ CudaContext::~CudaContext() {
         delete force;
     if (energyBuffer != NULL)
         delete energyBuffer;
+    if (atomIndexDevice != NULL)
+        delete atomIndexDevice;
     if (integration != NULL)
         delete integration;
     if (expression != NULL)

platforms/cuda/src/CudaKernels.cpp

@@ -1643,6 +1643,9 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         defines["USE_EWALD"] = "1";
         if (cu.getContextIndex() == 0) {
             ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
+            char deviceName[100];
+            cuDeviceGetName(deviceName, 100, cu.getDevice());
+            usePmeStream = (string(deviceName) != "GeForce GTX 980"); // Using a separate stream is slower on GTX 980
             pmeDefines["PME_ORDER"] = cu.intToString(PmeOrder);
             pmeDefines["NUM_ATOMS"] = cu.intToString(numParticles);
             pmeDefines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
@@ -1654,6 +1657,8 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
             pmeDefines["M_PI"] = cu.doubleToString(M_PI);
             if (cu.getUseDoublePrecision())
                 pmeDefines["USE_DOUBLE_PRECISION"] = "1";
+            if (usePmeStream)
+                pmeDefines["USE_PME_STREAM"] = "1";
             CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaKernelSources::pme, pmeDefines);
             if (cu.getPlatformData().useCpuPme) {
                 // Create the CPU PME kernel.
@@ -1713,9 +1718,6 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
                 
                 // Prepare for doing PME on its own stream.
                 
-                char deviceName[100];
-                cuDeviceGetName(deviceName, 100, cu.getDevice());
-                usePmeStream = (string(deviceName) != "GeForce GTX 980"); // Using a separate stream is slower on GTX 980
                 if (usePmeStream) {
                     cuStreamCreate(&pmeStream, CU_STREAM_NON_BLOCKING);
                     if (useCudaFFT) {

platforms/cuda/src/kernels/pme.cu

@@ -188,7 +188,11 @@ gridEvaluateEnergy(real2* __restrict__ halfcomplex_pmeGrid, mixed* __restrict__
             energy += eterm*(grid.x*grid.x + grid.y*grid.y);
         }
     }
+#ifdef USE_PME_STREAM
     energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] = 0.5f*energy;
+#else
+    energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += 0.5f*energy;
+#endif
 }
 
 extern "C" __global__

platforms/opencl/src/OpenCLKernels.cpp

@@ -1687,6 +1687,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
                     pmeDefines["USE_ALTERNATE_MEMORY_ACCESS_PATTERN"] = "1";
                 usePmeQueue = isNvidia;
                 if (usePmeQueue) {
+                    pmeDefines["USE_PME_STREAM"] = "1";
                     pmeQueue = cl::CommandQueue(cl.getContext(), cl.getDevice());
                     int recipForceGroup = force.getReciprocalSpaceForceGroup();
                     if (recipForceGroup < 0)

platforms/opencl/src/kernels/pme.cl

@@ -84,7 +84,7 @@ __kernel void recordZIndex(__global int2* restrict pmeAtomGridIndex, __global co
 
 __kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
         __global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
-    const real4 scale = 1/(real) (PME_ORDER-1);
+    const real scale = 1/(real) (PME_ORDER-1);
     real4 data[PME_ORDER];
     
     // Process the atoms in spatially sorted order.  This improves efficiency when writing
@@ -118,7 +118,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
             data[j-1] = div*dr*data[j-2];
             for (int k = 1; k < (j-1); k++)
                 data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]);
-            data[0] = div*(- dr+1.0f)*data[0];
+            data[0] = div*(-dr+1.0f)*data[0];
         }
         data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
         for (int j = 1; j < (PME_ORDER-1); j++)
@@ -362,12 +362,16 @@ __kernel void gridEvaluateEnergy(__global real2* restrict pmeGrid, __global mixe
             energy += eterm*(grid.x*grid.x + grid.y*grid.y);
         }
     }
+#ifdef USE_PME_STREAM
     energyBuffer[get_global_id(0)] = 0.5f*energy;
+#else
+    energyBuffer[get_global_id(0)] += 0.5f*energy;
+#endif
 }
 
 __kernel void gridInterpolateForce(__global const real4* restrict posq, __global real4* restrict forceBuffers, __global const real* restrict pmeGrid,
         real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
-    const real4 scale = 1/(real) (PME_ORDER-1);
+    const real scale = 1/(real) (PME_ORDER-1);
     real4 data[PME_ORDER];
     real4 ddata[PME_ORDER];
     
@@ -403,7 +407,7 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
             data[j-1] = div*dr*data[j-2];
             for (int k = 1; k < (j-1); k++)
                 data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]);
-            data[0] = div*(- dr+1.0f)*data[0];
+            data[0] = div*(-dr+1.0f)*data[0];
         }
         ddata[0] = -data[0];
         for (int j = 1; j < PME_ORDER; j++)

serialization/include/openmm/serialization/CustomCentroidBondForceProxy.h

+#ifndef OPENMM_CUSTOMCENTROIDBONDFORCE_PROXY_H_
+#define OPENMM_CUSTOMCENTROIDBONDFORCE_PROXY_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) 2015 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing CustomCentroidBondForce objects.
+ */
+
+class OPENMM_EXPORT CustomCentroidBondForceProxy : public SerializationProxy {
+public:
+    CustomCentroidBondForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMCENTROIDBONDFORCE_PROXY_H_*/

serialization/src/CustomCentroidBondForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2010-2015 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/CustomCentroidBondForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/CustomCentroidBondForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+CustomCentroidBondForceProxy::CustomCentroidBondForceProxy() : SerializationProxy("CustomCentroidBondForce") {
+}
+
+void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const CustomCentroidBondForce& force = *reinterpret_cast<const CustomCentroidBondForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setIntProperty("groups", force.getNumGroupsPerBond());
+    node.setStringProperty("energy", force.getEnergyFunction());
+    SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
+    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
+        perBondParams.createChildNode("Parameter").setStringProperty("name", force.getPerBondParameterName(i));
+    }
+    SerializationNode& globalParams = node.createChildNode("GlobalParameters");
+    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
+        globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
+    }
+    SerializationNode& groups = node.createChildNode("Groups");
+    for (int i = 0; i < force.getNumGroups(); i++) {
+        vector<int> particles;
+        vector<double> weights;
+        force.getGroupParameters(i, particles, weights);
+        SerializationNode& group = groups.createChildNode("Group");
+        for (int j = 0; j < (int) particles.size(); j++) {
+            SerializationNode& node = group.createChildNode("Particle");
+            node.setIntProperty("p", particles[j]);
+            node.setDoubleProperty("weight", weights[j]);
+        }
+    }
+    SerializationNode& bonds = node.createChildNode("Bonds");
+    for (int i = 0; i < force.getNumBonds(); i++) {
+        vector<int> groups;
+        vector<double> params;
+        force.getBondParameters(i, groups, params);
+        SerializationNode& node = bonds.createChildNode("Bond");
+        for (int j = 0; j < (int) groups.size(); j++) {
+            stringstream key;
+            key << "g";
+            key << j+1;
+            node.setIntProperty(key.str(), groups[j]);
+        }
+        for (int j = 0; j < (int) params.size(); j++) {
+            stringstream key;
+            key << "param";
+            key << j+1;
+            node.setDoubleProperty(key.str(), params[j]);
+        }
+    }
+    SerializationNode& functions = node.createChildNode("Functions");
+    for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
+        functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
+}
+
+void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    CustomCentroidBondForce* force = NULL;
+    try {
+        CustomCentroidBondForce* force = new CustomCentroidBondForce(node.getIntProperty("groups"), node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
+        for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
+            const SerializationNode& parameter = perBondParams.getChildren()[i];
+            force->addPerBondParameter(parameter.getStringProperty("name"));
+        }
+        const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
+        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
+            const SerializationNode& parameter = globalParams.getChildren()[i];
+            force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
+        }
+        const SerializationNode& groups = node.getChildNode("Groups");
+        for (int i = 0; i < (int) groups.getChildren().size(); i++) {
+            const SerializationNode& group = groups.getChildren()[i];
+            vector<int> particles;
+            vector<double> weights;
+            for (int j = 0; j < (int) group.getChildren().size(); j++) {
+                particles.push_back(group.getChildren()[j].getIntProperty("p"));
+                weights.push_back(group.getChildren()[j].getDoubleProperty("weight"));
+            }
+            force->addGroup(particles, weights);
+        }
+        const SerializationNode& bonds = node.getChildNode("Bonds");
+        vector<int> bondGroups(force->getNumGroupsPerBond());
+        vector<double> params(force->getNumPerBondParameters());
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            for (int j = 0; j < (int) bondGroups.size(); j++) {
+                stringstream key;
+                key << "g";
+                key << j+1;
+                bondGroups[j] = bond.getIntProperty(key.str());
+            }
+            for (int j = 0; j < (int) params.size(); j++) {
+                stringstream key;
+                key << "param";
+                key << j+1;
+                params[j] = bond.getDoubleProperty(key.str());
+            }
+            force->addBond(bondGroups, params);
+        }
+        const SerializationNode& functions = node.getChildNode("Functions");
+        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
+            const SerializationNode& function = functions.getChildren()[i];
+            if (function.hasProperty("type")) {
+                force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
+            }
+            else {
+                // This is an old file created before TabulatedFunction existed.
+
+                const SerializationNode& valuesNode = function.getChildNode("Values");
+                vector<double> values;
+                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
+                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
+            }
+        }
+        return force;
+    }
+    catch (...) {
+        if (force != NULL)
+            delete force;
+        throw;
+    }
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -36,6 +36,7 @@
 #include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomAngleForce.h"
 #include "openmm/CustomBondForce.h"
+#include "openmm/CustomCentroidBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
 #include "openmm/CustomExternalForce.h"
 #include "openmm/CustomGBForce.h"
@@ -68,6 +69,7 @@
 #include "openmm/serialization/CompoundIntegratorProxy.h"
 #include "openmm/serialization/CustomAngleForceProxy.h"
 #include "openmm/serialization/CustomBondForceProxy.h"
+#include "openmm/serialization/CustomCentroidBondForceProxy.h"
 #include "openmm/serialization/CustomCompoundBondForceProxy.h"
 #include "openmm/serialization/CustomExternalForceProxy.h"
 #include "openmm/serialization/CustomGBForceProxy.h"
@@ -118,6 +120,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(Continuous3DFunction), new Continuous3DFunctionProxy());
     SerializationProxy::registerProxy(typeid(CustomAngleForce), new CustomAngleForceProxy());
     SerializationProxy::registerProxy(typeid(CustomBondForce), new CustomBondForceProxy());
+    SerializationProxy::registerProxy(typeid(CustomCentroidBondForce), new CustomCentroidBondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomCompoundBondForce), new CustomCompoundBondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomExternalForce), new CustomExternalForceProxy());
     SerializationProxy::registerProxy(typeid(CustomGBForce), new CustomGBForceProxy());

serialization/tests/TestSerializeCustomCentroidBondForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2010-2015 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/CustomCentroidBondForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    CustomCentroidBondForce force(3, "5*sin(distance(g1,g2))^2+y*z");
+    force.setForceGroup(3);
+    force.addGlobalParameter("x", 1.3);
+    force.addGlobalParameter("y", 2.221);
+    force.addPerBondParameter("z");
+    for (int i = 0; i < 3; i++) {
+        vector<int> particles;
+        vector<double> weights;
+        for (int j = 0; j < i+1; j++) {
+            particles.push_back(i+j);
+            weights.push_back(1.0/(i+1));
+        }
+        force.addGroup(particles, weights);
+    }
+    vector<int> groups(3);
+    vector<double> params(1);
+    groups[0] = 0;
+    groups[1] = 1;
+    groups[2] = 2;
+    params[0] = 1.0;
+    force.addBond(groups, params);
+    groups[0] = 2;
+    groups[1] = 3;
+    groups[2] = 4;
+    params[0] = -3.3;
+    force.addBond(groups, params);
+    groups[0] = 3;
+    groups[1] = 5;
+    groups[2] = 1;
+    params[0] = 2.1;
+    force.addBond(groups, params);
+    vector<double> values(10);
+    for (int i = 0; i < 10; i++)
+        values[i] = sin((double) i);
+    force.addTabulatedFunction("f", new Continuous1DFunction(values, 0.5, 1.5));
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<CustomCentroidBondForce>(&force, "Force", buffer);
+    CustomCentroidBondForce* copy = XmlSerializer::deserialize<CustomCentroidBondForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    CustomCentroidBondForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.getNumGroupsPerBond(), force2.getNumGroupsPerBond());
+    ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
+    ASSERT_EQUAL(force.getNumPerBondParameters(), force2.getNumPerBondParameters());
+    for (int i = 0; i < force.getNumPerBondParameters(); i++)
+        ASSERT_EQUAL(force.getPerBondParameterName(i), force2.getPerBondParameterName(i));
+    ASSERT_EQUAL(force.getNumGlobalParameters(), force2.getNumGlobalParameters());
+    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
+        ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
+        ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
+    }
+    ASSERT_EQUAL(force.getNumGroups(), force2.getNumGroups());
+    for (int i = 0; i < force.getNumGroups(); i++) {
+        vector<int> particles1, particles2;
+        vector<double> weights1, weights2;
+        force.getGroupParameters(i, particles1, weights1);
+        force2.getGroupParameters(i, particles2, weights2);
+        ASSERT_EQUAL(weights1.size(), weights2.size());
+        for (int j = 0; j < (int) weights1.size(); j++)
+            ASSERT_EQUAL(weights1[j], weights2[j]);
+        ASSERT_EQUAL(particles1.size(), particles2.size());
+        for (int j = 0; j < (int) particles1.size(); j++)
+            ASSERT_EQUAL(particles1[j], particles2[j]);
+    }
+    ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
+    for (int i = 0; i < force.getNumBonds(); i++) {
+        vector<int> groups1, groups2;
+        vector<double> params1, params2;
+        force.getBondParameters(i, groups1, params1);
+        force2.getBondParameters(i, groups2, params2);
+        ASSERT_EQUAL(params1.size(), params2.size());
+        for (int j = 0; j < (int) params1.size(); j++)
+            ASSERT_EQUAL(params1[j], params2[j]);
+        ASSERT_EQUAL(groups1.size(), groups2.size());
+        for (int j = 0; j < (int) groups1.size(); j++)
+            ASSERT_EQUAL(groups1[j], groups2[j]);
+    }
+    ASSERT_EQUAL(force.getNumTabulatedFunctions(), force2.getNumTabulatedFunctions());
+    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
+        double min1, min2, max1, max2;
+        vector<double> val1, val2;
+        dynamic_cast<Continuous1DFunction&>(force.getTabulatedFunction(i)).getFunctionParameters(val1, min1, max1);
+        dynamic_cast<Continuous1DFunction&>(force2.getTabulatedFunction(i)).getFunctionParameters(val2, min2, max2);
+        ASSERT_EQUAL(force.getTabulatedFunctionName(i), force2.getTabulatedFunctionName(i));
+        ASSERT_EQUAL(min1, min2);
+        ASSERT_EQUAL(max1, max2);
+        ASSERT_EQUAL(val1.size(), val2.size());
+        for (int j = 0; j < (int) val1.size(); j++)
+            ASSERT_EQUAL(val1[j], val2[j]);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

wrappers/python/CMakeLists.txt

@@ -50,6 +50,7 @@ foreach(SUBDIR ${SUBDIRS})
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*README.txt"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.py"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.i"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.ini"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.sh"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"

wrappers/python/tests/pytest.ini

+[pytest]
+python_files=Test*.py
\ No newline at end of file