Merged changes from main branch

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

@@ -15,7 +15,9 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_DRUDE_TARGET} ${SHARED_TARGET})
     IF (APPLE)
-        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+        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)

plugins/drude/platforms/opencl/CMakeLists.txt

@@ -109,7 +109,7 @@ 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_DRUDE_TARGET} optimized ${SHARED_DRUDE_TARGET})
-SET_TARGET_PROPERTIES(${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} -msse2 -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/drude/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_DRUDE_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/drude/platforms/reference/src/ReferenceDrudeKernels.cpp

@@ -56,7 +56,12 @@ static vector<RealVec>& extractForces(ContextImpl& context) {
     return *((vector<RealVec>*) data->forces);
 }
 
-static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& inverseMasses, double timeShift, ReferenceConstraintAlgorithm* constraints) {
+static ReferenceConstraints& extractConstraints(ContextImpl& context) {
+    ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
+    return *(ReferenceConstraints*) data->constraints;
+}
+
+static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& inverseMasses, double timeShift) {
     const System& system = context.getSystem();
     int numParticles = system.getNumParticles();
     vector<RealVec>& posData = extractPositions(context);
@@ -75,10 +80,7 @@ static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>&
     
     // Apply constraints to them.
     
-    if (constraints != NULL) {
-        constraints->setTolerance(1e-4);
-        constraints->applyToVelocities(posData, shiftedVel, inverseMasses);
-    }
+    extractConstraints(context).applyToVelocities(posData, shiftedVel, inverseMasses, 1e-4);
     
     // Compute the kinetic energy.
     
@@ -224,8 +226,6 @@ void ReferenceCalcDrudeForceKernel::copyParametersToContext(ContextImpl& context
 }
 
 ReferenceIntegrateDrudeLangevinStepKernel::~ReferenceIntegrateDrudeLangevinStepKernel() {
-    if (constraints != NULL)
-        delete constraints;
 }
 
 void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system, const DrudeLangevinIntegrator& integrator, const DrudeForce& force) {
@@ -254,23 +254,6 @@ void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system,
         pairInvReducedMass.push_back((m1+m2)/(m1*m2));
     }
     normalParticles.insert(normalParticles.begin(), particles.begin(), particles.end());
-    
-    // Prepare constraints.
-    
-    if (system.getNumConstraints() > 0) {
-        vector<pair<int, int> > constraintIndices;
-        vector<RealOpenMM> constraintDistances;
-        for (int i = 0; i < system.getNumConstraints(); ++i) {
-            int particle1, particle2;
-            double distance;
-            system.getConstraintParameters(i, particle1, particle2, distance);
-            if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
-                constraintIndices.push_back(make_pair(particle1, particle2));
-                constraintDistances.push_back(distance);
-            }
-        }
-        constraints = new ReferenceConstraints(system, (RealOpenMM) integrator.getConstraintTolerance());
-    }
 }
 
 void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
@@ -330,8 +313,7 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
     
     // Apply constraints.
     
-    if (constraints != NULL)
-        constraints->apply(pos, xPrime, particleInvMass);
+    extractConstraints(context).apply(pos, xPrime, particleInvMass, integrator.getConstraintTolerance());
     
     // Record the constrained positions and velocities.
     
@@ -348,12 +330,10 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
 }
 
 double ReferenceIntegrateDrudeLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
-    return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize(), constraints);
+    return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize());
 }
 
 ReferenceIntegrateDrudeSCFStepKernel::~ReferenceIntegrateDrudeSCFStepKernel() {
-    if (constraints != NULL)
-        delete constraints;
     if (minimizerPos != NULL)
         lbfgs_free(minimizerPos);
 }
@@ -377,23 +357,6 @@ void ReferenceIntegrateDrudeSCFStepKernel::initialize(const System& system, cons
         particleInvMass.push_back(mass == 0.0 ? 0.0 : 1.0/mass);
     }
     
-    // Prepare constraints.
-    
-    if (system.getNumConstraints() > 0) {
-        vector<pair<int, int> > constraintIndices;
-        vector<RealOpenMM> constraintDistances;
-        for (int i = 0; i < system.getNumConstraints(); ++i) {
-            int particle1, particle2;
-            double distance;
-            system.getConstraintParameters(i, particle1, particle2, distance);
-            if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
-                constraintIndices.push_back(make_pair(particle1, particle2));
-                constraintDistances.push_back(distance);
-            }
-        }
-        constraints = new ReferenceConstraints(system, (RealOpenMM) integrator.getConstraintTolerance());
-    }
-    
     // Initialize the energy minimizer.
     
     minimizerPos = lbfgs_malloc(drudeParticles.size()*3);
@@ -424,8 +387,7 @@ void ReferenceIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const D
         
     // Apply constraints.
     
-    if (constraints != NULL)
-        constraints->apply(pos, xPrime, particleInvMass);
+    extractConstraints(context).apply(pos, xPrime, particleInvMass, integrator.getConstraintTolerance());
     
     // Record the constrained positions and velocities.
     
@@ -446,7 +408,7 @@ void ReferenceIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const D
 }
 
 double ReferenceIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
-    return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize(), constraints);
+    return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize());
 }
 
 struct MinimizerData {

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.h

@@ -86,7 +86,7 @@ private:
 class ReferenceIntegrateDrudeLangevinStepKernel : public IntegrateDrudeLangevinStepKernel {
 public:
     ReferenceIntegrateDrudeLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
-        IntegrateDrudeLangevinStepKernel(name, platform), data(data), constraints(NULL) {
+        IntegrateDrudeLangevinStepKernel(name, platform), data(data) {
     }
     ~ReferenceIntegrateDrudeLangevinStepKernel();
     /**
@@ -118,7 +118,6 @@ private:
     std::vector<double> particleInvMass;
     std::vector<double> pairInvTotalMass;
     std::vector<double> pairInvReducedMass;
-    ReferenceConstraintAlgorithm* constraints;
 };
 
 /**
@@ -127,7 +126,7 @@ private:
 class ReferenceIntegrateDrudeSCFStepKernel : public IntegrateDrudeSCFStepKernel {
 public:
     ReferenceIntegrateDrudeSCFStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
-        IntegrateDrudeSCFStepKernel(name, platform), data(data), constraints(NULL), minimizerPos(NULL) {
+        IntegrateDrudeSCFStepKernel(name, platform), data(data), minimizerPos(NULL) {
     }
     ~ReferenceIntegrateDrudeSCFStepKernel();
     /**
@@ -157,7 +156,6 @@ private:
     ReferencePlatform::PlatformData& data;
     std::vector<int> drudeParticles;
     std::vector<double> particleInvMass;
-    ReferenceConstraintAlgorithm* constraints;
     lbfgsfloatval_t *minimizerPos;
     lbfgs_parameter_t minimizerParams;
 };

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

@@ -26,5 +26,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
 
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM_DRUDE_TARGET})
+    SET_TARGET_PROPERTIES(${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/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} ${OPENMM_DRUDE_LIBRARY_NAME})
+    SET_TARGET_PROPERTIES(${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

@@ -97,7 +97,7 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/S
 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")
+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( CREATE_SERIALIZABLE_OPENMM_RPMD )
 #    ADD_LIBRARY(${SHARED_RPMD_SERIALIZABLE_TARGET} SHARED ${SOURCE_RPMD_FILES} ${SOURCE_RPMD_INCLUDE_FILES} ${API_RPMD_ABS_INCLUDE_FILES})
@@ -107,7 +107,7 @@ SET_TARGET_PROPERTIES(${SHARED_RPMD_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_R
 
 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)

plugins/rpmd/platforms/cuda/CMakeLists.txt

@@ -109,9 +109,11 @@ 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(${SHARED_TARGET} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+    SET_TARGET_PROPERTIES(${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)

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

@@ -15,7 +15,9 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_RPMD_TARGET} ${SHARED_TARGET})
     IF (APPLE)
-        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+        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)

plugins/rpmd/platforms/opencl/CMakeLists.txt

@@ -108,7 +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} -msse2 -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/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/reference/tests/CMakeLists.txt

@@ -26,5 +26,6 @@ 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})

serialization/tests/CMakeLists.txt

@@ -12,6 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # All tests use shared libraries
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
+    SET_TARGET_PROPERTIES(${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})

tests/CMakeLists.txt

@@ -11,6 +11,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # All tests use shared library only
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
+    SET_TARGET_PROPERTIES(${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})
 

wrappers/python/setup.py

@@ -195,11 +195,8 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         extra_compile_args.append('/EHsc')
     else:
         if platform.system() == 'Darwin':
-            macVersion = [int(x) for x in platform.mac_ver()[0].split('.')]
-            if tuple(macVersion) < (10, 6):
-                os.environ['MACOSX_DEPLOYMENT_TARGET']='10.5'
-            extra_link_args.append('-Wl,-rpath,'+openmm_lib_path)
-
+            extra_compile_args += ['-stdlib=libc++', '-mmacosx-version-min=10.7']                                                                                                                                       
+            extra_link_args += ['-stdlib=libc++', '-mmacosx-version-min=10.7', '-Wl', '-rpath', openmm_lib_path]                                                                                                          
 
     library_dirs=[openmm_lib_path]
     include_dirs=openmm_include_path.split(';')

wrappers/python/simtk/unit/basedimension.py

@@ -90,6 +90,16 @@ class BaseDimension(object):
     def __repr__(self):
         return 'BaseDimension("%s")' % self.name
     
+    def __eq__(self, other):
+        if isinstance(other, BaseDimension):
+            return self._index == other._index
+        return False
+    
+    def __ne__(self, other):
+        if isinstance(other, BaseDimension):
+            return self._index != other._index
+        return False
+
 
 # run module directly for testing
 if __name__=='__main__':