Merge github.com:SimTk/openmm

plugins/drude/serialization/include/openmm/serialization/DrudeLangevinIntegratorProxy.h

@@ -32,8 +32,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportDrudeSerialization.h"
 #include "openmm/serialization/SerializationProxy.h"
+#include "openmm/internal/windowsExportDrude.h"
 
 namespace OpenMM {
 
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing DrudeLangevinIntegrator objects.
  */
 
-class OPENMM_EXPORT_DRUDE_SERIALIZATION DrudeLangevinIntegratorProxy : public SerializationProxy {
+class OPENMM_EXPORT_DRUDE DrudeLangevinIntegratorProxy : public SerializationProxy {
 public:
     DrudeLangevinIntegratorProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/drude/serialization/include/openmm/serialization/internal/windowsExportDrudeSerialization.h

-#ifndef OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_H_
-#define OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_H_
-
-/*
- * Shared libraries are messy in Visual Studio. We have to distinguish three
- * cases:
- *   (1) this header is being used to build the OpenMM shared library
- *       (dllexport)
- *   (2) this header is being used by a *client* of the OpenMM shared
- *       library (dllimport)
- *   (3) we are building the OpenMM static library, or the client is
- *       being compiled with the expectation of linking with the
- *       OpenMM static library (nothing special needed)
- * In the CMake script for building this library, we define one of the symbols
- *     OPENMM_DRUDE_SERIALIZATION_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_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 OpenMM 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)
-    // Keep MS VC++ quiet about lack of dll export of private members.
-    #pragma warning(disable:4251)
-    #if defined(OPENMM_DRUDE_SERIALIZATION_BUILDING_SHARED_LIBRARY)
-        #define OPENMM_EXPORT_DRUDE_SERIALIZATION __declspec(dllexport)
-    #elif defined(OPENMM_DRUDE_SERIALIZATION_BUILDING_STATIC_LIBRARY) || defined(OPENMM_DRUDE_SERIALIZATION_USE_STATIC_LIBRARIES)
-        #define OPENMM_EXPORT_DRUDE_SERIALIZATION
-    #else
-        #define OPENMM_EXPORT_DRUDE_SERIALIZATION __declspec(dllimport)   // i.e., a client of a shared library
-    #endif
-#else
-    #define OPENMM_EXPORT_DRUDE_SERIALIZATION // Linux, Mac
-#endif
-
-#endif // OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_H_

plugins/drude/serialization/src/DrudeSerializationProxyRegistration.cpp

@@ -47,11 +47,10 @@
 
 #include "openmm/serialization/DrudeForceProxy.h"
 #include "openmm/serialization/DrudeLangevinIntegratorProxy.h"
-#include "openmm/serialization/internal/windowsExportDrudeSerialization.h"
 
 #if defined(WIN32)
     #include <windows.h>
-    extern "C" OPENMM_EXPORT_DRUDE_SERIALIZATION void registerDrudeSerializationProxies();
+    extern "C" OPENMM_EXPORT_DRUDE void registerDrudeSerializationProxies();
     BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
         if (ul_reason_for_call == DLL_PROCESS_ATTACH)
             registerDrudeSerializationProxies();
@@ -63,7 +62,7 @@
 
 using namespace OpenMM;
 
-extern "C" OPENMM_EXPORT_DRUDE_SERIALIZATION void registerDrudeSerializationProxies() {
+extern "C" OPENMM_EXPORT_DRUDE void registerDrudeSerializationProxies() {
     SerializationProxy::registerProxy(typeid(DrudeForce), new DrudeForceProxy());
     SerializationProxy::registerProxy(typeid(DrudeLangevinIntegrator), new DrudeLangevinIntegratorProxy());
 }

plugins/drude/serialization/tests/CMakeLists.txt

@@ -11,7 +11,8 @@ FOREACH(TEST_PROG ${TEST_PROGS})
 
     # All tests use shared libraries
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
-    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME} ${OPENMM_DRUDE_LIBRARY_NAME})
+    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_DRUDE_TARGET})
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/rpmd/CMakeLists.txt

@@ -22,7 +22,7 @@ SET(CREATE_SERIALIZABLE_OPENMM_RPMD FALSE )
 
 # 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_RPMD_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
+SET(OPENMM_RPMD_PLUGIN_SOURCE_SUBDIRS . openmmapi)
 
 SET(OPENMM_RPMD_LIBRARY_NAME OpenMMRPMD)
 SET(SHARED_RPMD_TARGET ${OPENMM_RPMD_LIBRARY_NAME})
@@ -80,46 +80,18 @@ FOREACH(subdir ${OPENMM_RPMD_PLUGIN_SOURCE_SUBDIRS})
     INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
 ENDFOREACH(subdir)
 
-INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src)
-INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src)
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/SimTKReference)
-
 # ----------------------------------------------------------------------------
 
-# If API_RPMD wrappers are being generated, and add them to the build.
-#IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
-#    ADD_SUBDIRECTORY(wrappers)
-#    SET(SOURCE_RPMD_FILES ${SOURCE_RPMD_FILES} wrappers/RPMDOpenMMCWrapper.cpp  wrappers/RPMDOpenMMFortranWrapper.cpp)
-#    SET_SOURCE_FILES_PROPERTIES(wrappers/RPMDOpenMMCWrapper.cpp wrappers/RPMDOpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE)
-#ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
-
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 ADD_LIBRARY(${SHARED_RPMD_TARGET} SHARED ${SOURCE_RPMD_FILES} ${SOURCE_RPMD_INCLUDE_FILES} ${API_RPMD_ABS_INCLUDE_FILES})
-SET_TARGET_PROPERTIES(${SHARED_RPMD_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_RPMD_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
-
-#IF( CREATE_SERIALIZABLE_OPENMM_RPMD )
-#    ADD_LIBRARY(${SHARED_RPMD_SERIALIZABLE_TARGET} SHARED ${SOURCE_RPMD_FILES} ${SOURCE_RPMD_INCLUDE_FILES} ${API_RPMD_ABS_INCLUDE_FILES})
-#    SET_TARGET_PROPERTIES(${SHARED_RPMD_SERIALIZABLE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_RPMD_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_SERIALIZE")
-#    INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../serialization/include)
-#ENDIF( CREATE_SERIALIZABLE_OPENMM_RPMD )
+SET_TARGET_PROPERTIES(${SHARED_RPMD_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_RPMD_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
 
 IF(OPENMM_BUILD_STATIC_LIB)
   ADD_LIBRARY(${STATIC_RPMD_TARGET} STATIC ${SOURCE_RPMD_FILES} ${SOURCE_RPMD_INCLUDE_FILES} ${API_RPMD_ABS_INCLUDE_FILES})
-  SET_TARGET_PROPERTIES(${STATIC_RPMD_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
+  SET_TARGET_PROPERTIES(${STATIC_RPMD_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
 ENDIF(OPENMM_BUILD_STATIC_LIB)
 
-#IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
-#    ADD_DEPENDENCIES(${SHARED_RPMD_TARGET} RPMDApiWrappers)
-#    IF( CREATE_SERIALIZABLE_OPENMM_RPMD )
-#        ADD_DEPENDENCIES(${SHARED_RPMD_SERIALIZABLE_TARGET} RPMDApiWrappers)
-#    ENDIF( CREATE_SERIALIZABLE_OPENMM_RPMD )
-#    IF(OPENMM_BUILD_STATIC_LIB)
-#        ADD_DEPENDENCIES(${STATIC_RPMD_TARGET} RPMDApiWrappers)
-#    ENDIF(OPENMM_BUILD_STATIC_LIB)
-#ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
-
 # ----------------------------------------------------------------------------
 
 # On Linux need to link to libdl
@@ -148,18 +120,9 @@ IF(OPENMM_BUILD_STATIC_LIB)
     TARGET_LINK_LIBRARIES( ${STATIC_RPMD_TARGET} ${STATIC_TARGET} )
 ENDIF(OPENMM_BUILD_STATIC_LIB)
 
-ADD_SUBDIRECTORY(platforms/reference/tests)
-
 # Which hardware platforms to build
 
-#SET(OPENMM_BUILD_RPMD_PATH)
-#SET(OPENMM_BUILD_RPMD_CUDA_PATH)
-#IF(OPENMM_BUILD_RPMD_CUDA_LIB)
-#    ADD_SUBDIRECTORY(platforms/cuda)
-#    SET(OPENMM_BUILD_RPMD_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
-#    SET(OPENMM_BUILD_RPMD_CUDA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
-#    SET(OPENMM_RPMD_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda)
-#ENDIF(OPENMM_BUILD_RPMD_CUDA_LIB)
+ADD_SUBDIRECTORY(platforms/reference)
 
 IF(OPENCL_FOUND)
     SET(OPENMM_BUILD_RPMD_OPENCL_LIB ON CACHE BOOL "Build RPMD implementation for OpenCL")
@@ -208,7 +171,3 @@ ENDIF (EXECUTABLE_OUTPUT_PATH)
 #IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
 #    ADD_SUBDIRECTORY(serialization)
 #ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
-
-#INCLUDE(ApiDoxygen.cmake)
-
-#ADD_SUBDIRECTORY(tests)

plugins/rpmd/platforms/cuda/CMakeLists.txt

@@ -12,10 +12,6 @@
 #   libOpenMMRPMDCUDA[_d].so
 #----------------------------------------------------
 
-IF (APPLE)
-    SET (CMAKE_OSX_DEPLOYMENT_TARGET "10.6")
-ENDIF (APPLE)
-
 # 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 .)
@@ -31,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMRPMDCUDA_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
@@ -113,7 +109,12 @@ ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${CUDA_LIBRARIES} ${PTHREADS_LIB})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}CUDA_d optimized ${OPENMM_LIBRARY_NAME}CUDA)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_RPMD_TARGET} optimized ${SHARED_RPMD_TARGET})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
+IF (APPLE)
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
+ELSE (APPLE)
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+ENDIF (APPLE)
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 # Ensure that links to the main CUDA library will be resolved.

plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp

@@ -252,7 +252,18 @@ void CudaIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
                 &cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
         cu.executeKernel(copyToContextKernel, copyToContextArgs, cu.getNumAtoms());
         context.computeVirtualSites();
+        Vec3 initialBox[3];
+        context.getPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
         context.updateContextState();
+        Vec3 finalBox[3];
+        context.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
+        if (initialBox[0] != finalBox[0] || initialBox[1] != finalBox[1] || initialBox[2] != finalBox[2]) {
+            // A barostat was applied during updateContextState().  Adjust the particle positions in all the
+            // other copies to match this one.
+            
+            void* args[] = {&positions->getDevicePointer(), &cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
+            cu.executeKernel(translateKernel, args, cu.getNumAtoms());
+        }
         context.calcForcesAndEnergy(true, false, groupsNotContracted);
         void* copyFromContextArgs[] = {&cu.getForce().getDevicePointer(), &forces->getDevicePointer(), &cu.getVelm().getDevicePointer(),
                 &velocities->getDevicePointer(), &cu.getPosq().getDevicePointer(), &positions->getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};

plugins/rpmd/platforms/cuda/src/kernels/rpmd.cu

@@ -217,7 +217,7 @@ extern "C" __global__ void copyDataFromContext(long long* srcForce, long long* d
 }
 
 /**
- * Update atom positions so all copies are offset by the same number of periodic box widths.
+ * Atom positions in one copy have been modified.  Apply the same offsets to all the other copies.
  */
 extern "C" __global__ void applyCellTranslations(mixed4* posq, real4* movedPos, int* order, int movedCopy) {
     for (int particle = blockIdx.x*blockDim.x+threadIdx.x; particle < NUM_ATOMS; particle += blockDim.x*gridDim.x) {

plugins/rpmd/platforms/cuda/tests/CMakeLists.txt

@@ -14,6 +14,11 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # Link with shared library
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_RPMD_TARGET} ${SHARED_TARGET})
+    IF (APPLE)
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    ELSE (APPLE)
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    ENDIF (APPLE)
     ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
     IF (OPENMM_BUILD_CUDA_DOUBLE_PRECISION_TESTS)
         ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed)

plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp

@@ -38,6 +38,7 @@
 #include "openmm/Context.h"
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/HarmonicBondForce.h"
+#include "openmm/MonteCarloBarostat.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/Platform.h"
 #include "openmm/System.h"
@@ -496,6 +497,80 @@ void testWithoutThermostat() {
     }
 }
 
+void testWithBarostat() {
+    const int gridSize = 3;
+    const int numMolecules = gridSize*gridSize*gridSize;
+    const int numParticles = numMolecules*2;
+    const int numCopies = 10;
+    const double spacing = 2.0;
+    const double cutoff = 3.0;
+    const double boxSize = spacing*(gridSize+1);
+    const double temperature = 300.0;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    system.addForce(bonds);
+    NonbondedForce* nonbonded = new NonbondedForce();
+    nonbonded->setCutoffDistance(cutoff);
+    nonbonded->setNonbondedMethod(NonbondedForce::PME);
+    nonbonded->setForceGroup(1);
+    nonbonded->setReciprocalSpaceForceGroup(2);
+    system.addForce(nonbonded);
+    system.addForce(new MonteCarloBarostat(0.5, temperature));
+
+    // Create a cloud of molecules.
+
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numMolecules; i++) {
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        nonbonded->addParticle(-0.2, 0.2, 0.2);
+        nonbonded->addParticle(0.2, 0.2, 0.2);
+        nonbonded->addException(2*i, 2*i+1, 0, 1, 0);
+        bonds->addBond(2*i, 2*i+1, 1.0, 10000.0);
+    }
+    RPMDIntegrator integ(numCopies, temperature, 50.0, 0.001);
+    Platform& platform = Platform::getPlatformByName("CUDA");
+    Context context(system, integ, platform);
+    for (int copy = 0; copy < numCopies; copy++) {
+        for (int i = 0; i < gridSize; i++)
+            for (int j = 0; j < gridSize; j++)
+                for (int k = 0; k < gridSize; k++) {
+                    Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
+                    int index = k+gridSize*(j+gridSize*i);
+                    positions[2*index] = pos;
+                    positions[2*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
+                }
+        integ.setPositions(copy, positions);
+    }
+
+    // Check the temperature.
+    
+    const int numSteps = 500;
+    integ.step(100);
+    vector<double> ke(numCopies, 0.0);
+    for (int i = 0; i < numSteps; i++) {
+        integ.step(1);
+        vector<State> state(numCopies);
+        for (int j = 0; j < numCopies; j++)
+            state[j] = integ.getState(j, State::Velocities, true);
+        for (int j = 0; j < numParticles; j++) {
+            for (int k = 0; k < numCopies; k++) {
+                Vec3 v = state[k].getVelocities()[j];
+                ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
+            }
+        }
+    }
+    double meanKE = 0.0;
+    for (int i = 0; i < numCopies; i++)
+        meanKE += ke[i];
+    meanKE /= numSteps*numCopies;
+    double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
+    ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
+}
+
 int main(int argc, char* argv[]) {
     try {
         registerRPMDCudaKernelFactories();
@@ -507,6 +582,7 @@ int main(int argc, char* argv[]) {
         testVirtualSites();
         testContractions();
         testWithoutThermostat();
+        testWithBarostat();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/rpmd/platforms/opencl/CMakeLists.txt

@@ -12,10 +12,6 @@
 #   libOpenMMRPMDOpenCL[_d].so
 #----------------------------------------------------
 
-IF (APPLE)
-    SET (CMAKE_OSX_DEPLOYMENT_TARGET "10.6")
-ENDIF (APPLE)
-
 # 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 .)
@@ -31,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMRPMDOPENCL_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
@@ -112,7 +108,7 @@ ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}OpenCL_d optimized ${OPENMM_LIBRARY_NAME}OpenCL)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_RPMD_TARGET} optimized ${SHARED_RPMD_TARGET})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-msse2 -DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 # Ensure that links to the main OpenCL library will be resolved.

plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp

@@ -268,7 +268,18 @@ void OpenCLIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
         copyToContextKernel.setArg<cl_int>(5, i);
         cl.executeKernel(copyToContextKernel, cl.getNumAtoms());
         context.computeVirtualSites();
+        Vec3 initialBox[3];
+        context.getPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
         context.updateContextState();
+        Vec3 finalBox[3];
+        context.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
+        if (initialBox[0] != finalBox[0] || initialBox[1] != finalBox[1] || initialBox[2] != finalBox[2]) {
+            // A barostat was applied during updateContextState().  Adjust the particle positions in all the
+            // other copies to match this one.
+            
+            translateKernel.setArg<cl_int>(3, i);
+            cl.executeKernel(translateKernel, cl.getNumAtoms());
+        }
         context.calcForcesAndEnergy(true, false, groupsNotContracted);
         copyFromContextKernel.setArg<cl_int>(7, i);
         cl.executeKernel(copyFromContextKernel, cl.getNumAtoms());

plugins/rpmd/platforms/opencl/src/kernels/rpmd.cl

@@ -204,7 +204,7 @@ __kernel void copyDataFromContext(__global real4* srcForce, __global real4* dstF
 }
 
 /**
- * Update atom positions so all copies are offset by the same number of periodic box widths.
+ * Atom positions in one copy have been modified.  Apply the same offsets to all the other copies.
  */
 __kernel void applyCellTranslations(__global mixed4* posq, __global real4* movedPos, __global int* order, int movedCopy) {
     for (int particle = get_global_id(0); particle < NUM_ATOMS; particle += get_global_size(0)) {

plugins/rpmd/platforms/opencl/tests/CMakeLists.txt

@@ -14,6 +14,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # Link with shared library
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_RPMD_TARGET} ${SHARED_TARGET})
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
     IF (OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
         ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed)

plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp

@@ -38,6 +38,7 @@
 #include "openmm/Context.h"
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/HarmonicBondForce.h"
+#include "openmm/MonteCarloBarostat.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/Platform.h"
 #include "openmm/System.h"
@@ -497,6 +498,80 @@ void testWithoutThermostat() {
     }
 }
 
+void testWithBarostat() {
+    const int gridSize = 3;
+    const int numMolecules = gridSize*gridSize*gridSize;
+    const int numParticles = numMolecules*2;
+    const int numCopies = 10;
+    const double spacing = 2.0;
+    const double cutoff = 3.0;
+    const double boxSize = spacing*(gridSize+1);
+    const double temperature = 300.0;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    system.addForce(bonds);
+    NonbondedForce* nonbonded = new NonbondedForce();
+    nonbonded->setCutoffDistance(cutoff);
+    nonbonded->setNonbondedMethod(NonbondedForce::PME);
+    nonbonded->setForceGroup(1);
+    nonbonded->setReciprocalSpaceForceGroup(2);
+    system.addForce(nonbonded);
+    system.addForce(new MonteCarloBarostat(0.5, temperature));
+
+    // Create a cloud of molecules.
+
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numMolecules; i++) {
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        nonbonded->addParticle(-0.2, 0.2, 0.2);
+        nonbonded->addParticle(0.2, 0.2, 0.2);
+        nonbonded->addException(2*i, 2*i+1, 0, 1, 0);
+        bonds->addBond(2*i, 2*i+1, 1.0, 10000.0);
+    }
+    RPMDIntegrator integ(numCopies, temperature, 50.0, 0.001);
+    Platform& platform = Platform::getPlatformByName("OpenCL");
+    Context context(system, integ, platform);
+    for (int copy = 0; copy < numCopies; copy++) {
+        for (int i = 0; i < gridSize; i++)
+            for (int j = 0; j < gridSize; j++)
+                for (int k = 0; k < gridSize; k++) {
+                    Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
+                    int index = k+gridSize*(j+gridSize*i);
+                    positions[2*index] = pos;
+                    positions[2*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
+                }
+        integ.setPositions(copy, positions);
+    }
+
+    // Check the temperature.
+    
+    const int numSteps = 500;
+    integ.step(100);
+    vector<double> ke(numCopies, 0.0);
+    for (int i = 0; i < numSteps; i++) {
+        integ.step(1);
+        vector<State> state(numCopies);
+        for (int j = 0; j < numCopies; j++)
+            state[j] = integ.getState(j, State::Velocities, true);
+        for (int j = 0; j < numParticles; j++) {
+            for (int k = 0; k < numCopies; k++) {
+                Vec3 v = state[k].getVelocities()[j];
+                ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
+            }
+        }
+    }
+    double meanKE = 0.0;
+    for (int i = 0; i < numCopies; i++)
+        meanKE += ke[i];
+    meanKE /= numSteps*numCopies;
+    double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
+    ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
+}
+
 int main(int argc, char* argv[]) {
     try {
         registerRPMDOpenCLKernelFactories();
@@ -508,6 +583,7 @@ int main(int argc, char* argv[]) {
         testVirtualSites();
         testContractions();
         testWithoutThermostat();
+        testWithBarostat();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/serialization/CMakeLists.txt → plugins/rpmd/platforms/reference/CMakeLists.txt

 #---------------------------------------------------
-# OpenMMAmoeba Serialization Library
+# OpenMM Reference RPMD Integrator
 #
-# Creates OpenMMAmoeba serializatin library, base name=OpenMMAmoebaSerialization.
+# Creates OpenMM library, base name=OpenMMRPMDReference.
 # Default libraries are shared & optimized. Variants
-# are created for static (_static) and debug (_d).
+# are created for debug (_d).
 #
 # Windows:
-#   OpenMMAmoebaSerialization[_d].dll
-#   OpenMMAmoebaSerialization[_d].lib
+#   OpenMMRPMDReference[_d].dll
+#   OpenMMRPMDReference[_d].lib
 # Unix:
-#   libOpenMMAmoebaSerialization[_d].so
+#   libOpenMMRPMDReference[_d].so
 #----------------------------------------------------
 
 # 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 . ../../../serialization)
-SET(OPENMM_AMOEBA_SOURCE_SUBDIRS . )
+SET(OPENMM_SOURCE_SUBDIRS .)
+
 
 # Collect up information about the version of the OpenMM library we're building
 # and make it available to the code so it can be built into the binaries.
 
-SET(OPENMM_AMOEBA_LIBRARY_NAME OpenMMAmoeba)
-SET(OPENMM_SERIALIZATION_LIBRARY_NAME OpenMMSerialization)
-SET(OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME OpenMMAmoebaSerialization)
+SET(OPENMMRPMDREFERENCE_LIBRARY_NAME OpenMMRPMDReference)
+
+SET(SHARED_TARGET ${OPENMMRPMDREFERENCE_LIBRARY_NAME})
+
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-    SET(OPENMM_AMOEBA_LIBRARY_NAME ${OPENMM_AMOEBA_LIBRARY_NAME}_d)
-    SET(OPENMM_SERIALIZATION_LIBRARY_NAME ${OPENMM_SERIALIZATION_LIBRARY_NAME}_d)
-    SET(OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME}_d)
+    SET(SHARED_TARGET ${SHARED_TARGET}_d)
 ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 
+
 # These are all the places to search for header files which are
 # to be part of the API.
 SET(API_INCLUDE_DIRS) # start empty
@@ -66,22 +66,32 @@ ENDFOREACH(dir)
 SET(SOURCE_FILES) # empty
 SET(SOURCE_INCLUDE_FILES)
 
-FOREACH(subdir ${OPENMM_AMOEBA_SOURCE_SUBDIRS})
-    FILE(GLOB_RECURSE src_files   ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.c)
-    FILE(GLOB incl_files  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.hpp)
+FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
+    FILE(GLOB_RECURSE src_files  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.c)
+    FILE(GLOB incl_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h)
     SET(SOURCE_FILES         ${SOURCE_FILES}         ${src_files})   #append
     SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
-    INCLUDE_DIRECTORIES(BEFORE  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
-    INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../../serialization/${subdir}/include)
+    INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
 ENDFOREACH(subdir)
-#Message( "API_REL_INCLUDE_FILES=${API_REL_INCLUDE_FILES}\n" )
 
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src )
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/include)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/src)
 
 # Create the library
-ADD_LIBRARY(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-TARGET_LINK_LIBRARIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} ${OPENMM_AMOEBA_LIBRARY_NAME} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${SHARED_TARGET})
-SET_TARGET_PROPERTIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_SERIALIZATION_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
-INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME})
 
-ADD_SUBDIRECTORY(tests)
+INCLUDE_DIRECTORIES(${REFERENCE_INCLUDE_DIR})
+
+ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+
+IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME}_d)
+ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
+ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_RPMD_TARGET} optimized ${SHARED_RPMD_TARGET})
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
+
+INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
+SUBDIRS (tests)

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernelFactory.cpp

@@ -32,22 +32,21 @@
 
 using namespace OpenMM;
 
-#if defined(WIN32)
-    #include <windows.h>
-    extern "C" void initRpmdReferenceKernels();
-    BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
-        if (ul_reason_for_call == DLL_PROCESS_ATTACH)
-            initRpmdReferenceKernels();
-        return TRUE;
+extern "C" OPENMM_EXPORT void registerPlatforms() {
+}
+
+extern "C" OPENMM_EXPORT void registerKernelFactories() {
+    for (int i = 0; i < Platform::getNumPlatforms(); i++) {
+        Platform& platform = Platform::getPlatform(i);
+        if (dynamic_cast<ReferencePlatform*>(&platform) != NULL) {
+            ReferenceRpmdKernelFactory* factory = new ReferenceRpmdKernelFactory();
+            platform.registerKernelFactory(IntegrateRPMDStepKernel::Name(), factory);
+        }
     }
-#else
-    extern "C" void __attribute__((constructor)) initRpmdReferenceKernels();
-#endif
+}
 
-extern "C" void initRpmdReferenceKernels() {
-    Platform& platform = Platform::getPlatformByName("Reference");
-    ReferenceRpmdKernelFactory* factory = new ReferenceRpmdKernelFactory();
-    platform.registerKernelFactory(IntegrateRPMDStepKernel::Name(), factory);
+extern "C" OPENMM_EXPORT void registerRpmdReferenceKernelFactories() {
+    registerKernelFactories();
 }
 
 KernelImpl* ReferenceRpmdKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp

@@ -275,7 +275,22 @@ void ReferenceIntegrateRPMDStepKernel::computeForces(ContextImpl& context, const
         pos = positions[i];
         vel = velocities[i];
         context.computeVirtualSites();
+        Vec3 initialBox[3];
+        context.getPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
         context.updateContextState();
+        Vec3 finalBox[3];
+        context.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
+        if (initialBox[0] != finalBox[0] || initialBox[1] != finalBox[1] || initialBox[2] != finalBox[2]) {
+            // A barostat was applied during updateContextState().  Adjust the particle positions in all the
+            // other copies to match this one.
+            
+            for (int j = 0; j < numParticles; j++) {
+                Vec3 delta = pos[j]-positions[i][j];
+                for (int k = 0; k < totalCopies; k++)
+                    if (k != i)
+                        positions[k][j] += delta;
+            }
+        }
         positions[i] = pos;
         velocities[i] = vel;
         context.calcForcesAndEnergy(true, false, groupsNotContracted);

plugins/rpmd/platforms/reference/tests/CMakeLists.txt

@@ -2,11 +2,9 @@
 # Testing
 #
 ENABLE_TESTING()
-#INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/include)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/openmmapi/include/openmm)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/src)
-#INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/src/kernels)
 
 SET(SHARED_OPENMM_RPMD_TARGET OpenMMRPMD)
 
@@ -26,5 +24,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
 
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM_RPMD_TARGET})
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp

@@ -37,6 +37,7 @@
 #include "openmm/CMMotionRemover.h"
 #include "openmm/Context.h"
 #include "openmm/HarmonicBondForce.h"
+#include "openmm/MonteCarloBarostat.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/Platform.h"
 #include "openmm/System.h"
@@ -50,6 +51,8 @@
 using namespace OpenMM;
 using namespace std;
 
+extern "C" OPENMM_EXPORT void registerRpmdReferenceKernelFactories();
+
 void testFreeParticles() {
     const int numParticles = 100;
     const int numCopies = 30;
@@ -378,13 +381,89 @@ void testWithoutThermostat() {
     }
 }
 
+void testWithBarostat() {
+    const int gridSize = 3;
+    const int numMolecules = gridSize*gridSize*gridSize;
+    const int numParticles = numMolecules*2;
+    const int numCopies = 5;
+    const double spacing = 2.0;
+    const double cutoff = 3.0;
+    const double boxSize = spacing*(gridSize+1);
+    const double temperature = 300.0;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    system.addForce(bonds);
+    NonbondedForce* nonbonded = new NonbondedForce();
+    nonbonded->setCutoffDistance(cutoff);
+    nonbonded->setNonbondedMethod(NonbondedForce::PME);
+    nonbonded->setForceGroup(1);
+    nonbonded->setReciprocalSpaceForceGroup(2);
+    system.addForce(nonbonded);
+    system.addForce(new MonteCarloBarostat(0.5, temperature));
+
+    // Create a cloud of molecules.
+
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numMolecules; i++) {
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        nonbonded->addParticle(-0.2, 0.2, 0.2);
+        nonbonded->addParticle(0.2, 0.2, 0.2);
+        nonbonded->addException(2*i, 2*i+1, 0, 1, 0);
+        bonds->addBond(2*i, 2*i+1, 1.0, 10000.0);
+    }
+    RPMDIntegrator integ(numCopies, temperature, 50.0, 0.001);
+    Platform& platform = Platform::getPlatformByName("Reference");
+    Context context(system, integ, platform);
+    for (int copy = 0; copy < numCopies; copy++) {
+        for (int i = 0; i < gridSize; i++)
+            for (int j = 0; j < gridSize; j++)
+                for (int k = 0; k < gridSize; k++) {
+                    Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
+                    int index = k+gridSize*(j+gridSize*i);
+                    positions[2*index] = pos;
+                    positions[2*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
+                }
+        integ.setPositions(copy, positions);
+    }
+
+    // Check the temperature.
+    
+    const int numSteps = 500;
+    integ.step(100);
+    vector<double> ke(numCopies, 0.0);
+    for (int i = 0; i < numSteps; i++) {
+        integ.step(1);
+        vector<State> state(numCopies);
+        for (int j = 0; j < numCopies; j++)
+            state[j] = integ.getState(j, State::Velocities, true);
+        for (int j = 0; j < numParticles; j++) {
+            for (int k = 0; k < numCopies; k++) {
+                Vec3 v = state[k].getVelocities()[j];
+                ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
+            }
+        }
+    }
+    double meanKE = 0.0;
+    for (int i = 0; i < numCopies; i++)
+        meanKE += ke[i];
+    meanKE /= numSteps*numCopies;
+    double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
+    ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
+}
+
 int main() {
     try {
+        registerRpmdReferenceKernelFactories();
         testFreeParticles();
         testCMMotionRemoval();
         testVirtualSites();
         testContractions();
         testWithoutThermostat();
+        testWithBarostat();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;