Merge branch 'master' of https://github.com/SimTk/openmm

platforms/cuda/CMakeLists.txt

@@ -14,10 +14,6 @@
 #   libOpenMMCUDA_static[_d].a
 #----------------------------------------------------
 
-IF (APPLE)
-    SET (CMAKE_OSX_DEPLOYMENT_TARGET "10.6")
-ENDIF (APPLE)
-
 set(OPENMM_BUILD_CUDA_TESTS TRUE CACHE BOOL "Whether to build CUDA test cases")
 if(OPENMM_BUILD_CUDA_TESTS)
     SUBDIRS (tests)

platforms/cuda/include/CudaContext.h

@@ -623,6 +623,8 @@ public:
  */
 class CudaContext::ForcePreComputation {
 public:
+    virtual ~ForcePreComputation() {
+    }
     /**
      * @param includeForce  true if forces should be computed
      * @param includeEnergy true if potential energy should be computed
@@ -639,6 +641,8 @@ public:
  */
 class CudaContext::ForcePostComputation {
 public:
+    virtual ~ForcePostComputation() {
+    }
     /**
      * @param includeForce  true if forces should be computed
      * @param includeEnergy true if potential energy should be computed

platforms/cuda/sharedTarget/CMakeLists.txt

@@ -20,5 +20,8 @@ ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB} ${CUDA_CUDA_LIBRARY} ${CUDA_cufft_LIBRARY} ${PTHREADS_LIB})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_CUDA_BUILDING_SHARED_LIBRARY")
+IF (APPLE)
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+ENDIF (APPLE)
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

platforms/cuda/tests/CMakeLists.txt

@@ -25,6 +25,9 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # Link with shared library
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
+    IF (APPLE)
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+    ENDIF (APPLE)
 
     IF( ${TEST_ROOT} STREQUAL "TestCUDAGBSAOBCForce2" )
 

platforms/cuda/tests/TestCudaGBSAOBCForce.cpp

@@ -71,7 +71,7 @@ void testSingleParticle() {
     double bornRadius = 0.15-0.009; // dielectric offset
     double eps0 = EPSILON0;
     double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/gbsa->getSoluteDielectric()-1.0/gbsa->getSolventDielectric())/bornRadius;
-    double extendedRadius = bornRadius+0.14; // probe radius
+    double extendedRadius = 0.15+0.14; // probe radius
     double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from?  Just copied it from CpuImplicitSolvent.cpp
     ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
     

platforms/opencl/CMakeLists.txt

@@ -14,10 +14,6 @@
 #   libOpenMMOpenCL_static[_d].a
 #----------------------------------------------------
 
-IF (APPLE)
-    SET (CMAKE_OSX_DEPLOYMENT_TARGET "10.6")
-ENDIF (APPLE)
-
 set(OPENMM_BUILD_OPENCL_TESTS TRUE CACHE BOOL "Whether to build OpenCL test cases")
 if(OPENMM_BUILD_OPENCL_TESTS)
     SUBDIRS (tests)

platforms/opencl/include/OpenCLContext.h

@@ -736,6 +736,8 @@ public:
  */
 class OpenCLContext::ForcePreComputation {
 public:
+    virtual ~ForcePreComputation() {
+    }
     /**
      * @param includeForce  true if forces should be computed
      * @param includeEnergy true if potential energy should be computed
@@ -752,6 +754,8 @@ public:
  */
 class OpenCLContext::ForcePostComputation {
 public:
+    virtual ~ForcePostComputation() {
+    }
     /**
      * @param includeForce  true if forces should be computed
      * @param includeEnergy true if potential energy should be computed

platforms/opencl/tests/TestOpenCLGBSAOBCForce.cpp

@@ -71,7 +71,7 @@ void testSingleParticle() {
     double bornRadius = 0.15-0.009; // dielectric offset
     double eps0 = EPSILON0;
     double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/gbsa->getSoluteDielectric()-1.0/gbsa->getSolventDielectric())/bornRadius;
-    double extendedRadius = bornRadius+0.14; // probe radius
+    double extendedRadius = 0.15+0.14; // probe radius
     double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from?  Just copied it from CpuImplicitSolvent.cpp
     ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
     

platforms/reference/tests/TestReferenceGBSAOBCForce.cpp

@@ -66,7 +66,7 @@ void testSingleParticle() {
     double bornRadius = 0.15-0.009; // dielectric offset
     double eps0 = EPSILON0;
     double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
-    double extendedRadius = bornRadius+0.14; // probe radius
+    double extendedRadius = 0.15+0.14; // probe radius
     double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from?  Just copied it from CpuImplicitSolvent.cpp
     ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
     
@@ -171,7 +171,7 @@ void testForce() {
         norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
     }
     norm = std::sqrt(norm);
-    const double delta = 1e-3;
+    const double delta = 1e-2;
     double step = 0.5*delta/norm;
     vector<Vec3> positions2(numParticles), positions3(numParticles);
     for (int i = 0; i < numParticles; ++i) {

plugins/amoeba/platforms/cuda/CMakeLists.txt

@@ -110,6 +110,9 @@ TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${CUDA_LIBRARIES} ${P
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}CUDA_d optimized ${OPENMM_LIBRARY_NAME}CUDA)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_AMOEBA_TARGET} optimized ${SHARED_AMOEBA_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
+IF (APPLE)
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+ENDIF (APPLE)
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 # Ensure that links to the main CUDA library will be resolved.

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

@@ -14,6 +14,9 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # Link with shared library
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET})
+    IF (APPLE)
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+    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/cpupme/CMakeLists.txt

@@ -11,10 +11,6 @@
 #   libOpenMMPME[_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 .)

plugins/drude/platforms/cuda/CMakeLists.txt

@@ -12,10 +12,6 @@
 #   libOpenMMDrudeCUDA[_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 .)
@@ -114,6 +110,9 @@ TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${CUDA_LIBRARIES} ${P
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}CUDA_d optimized ${OPENMM_LIBRARY_NAME}CUDA)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_DRUDE_TARGET} optimized ${SHARED_DRUDE_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
+IF (APPLE)
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+ENDIF (APPLE)
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 # Ensure that links to the main CUDA library will be resolved.

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

@@ -14,6 +14,9 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # Link with shared library
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_DRUDE_TARGET} ${SHARED_TARGET})
+    IF (APPLE)
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+    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/drude/platforms/opencl/CMakeLists.txt

@@ -12,10 +12,6 @@
 #   libOpenMMDrudeOpenCL[_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 .)

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 .)
@@ -114,6 +110,9 @@ TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${CUDA_LIBRARIES} ${P
 TARGET_LINK_LIBRARIES(${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")
+IF (APPLE)
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
+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/tests/CMakeLists.txt

@@ -14,6 +14,9 @@ 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 "-F/Library/Frameworks -framework CUDA")
+    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/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 .)

wrappers/python/simtk/openmm/app/modeller.py

@@ -776,22 +776,35 @@ class Modeller(object):
             system.addForce(nonbonded)
             system.addForce(bonds)
             system.addForce(angles)
+            bondedTo = []
             for atom in newTopology.atoms():
                 nonbonded.addParticle([])
                 if atom.element != elem.hydrogen:
                     system.addParticle(0.0)
                 else:
                     system.addParticle(1.0)
+                bondedTo.append([])
             for atom1, atom2 in newTopology.bonds():
                 if atom1.element == elem.hydrogen or atom2.element == elem.hydrogen:
                     bonds.addBond(atom1.index, atom2.index, 0.1, 100000.0)
+                bondedTo[atom1.index].append(atom2)
+                bondedTo[atom2.index].append(atom1)
             for residue in newTopology.residues():
                 if residue.name == 'HOH':
+                    # Add an angle term to make the water geometry correct.
+                    
                     atoms = list(residue.atoms())
                     oindex = [i for i in range(len(atoms)) if atoms[i].element == elem.oxygen]
                     if len(atoms) == 3 and len(oindex) == 1:
                         hindex = list(set([0,1,2])-set(oindex))
                         angles.addAngle(atoms[hindex[0]].index, atoms[oindex[0]].index, atoms[hindex[1]].index, 1.824, 836.8)
+                else:
+                    # Add angle terms for any hydroxyls.
+                    
+                    for atom in residue.atoms():
+                        index = atom.index
+                        if atom.element == elem.oxygen and len(bondedTo[index]) == 2 and elem.hydrogen in (a.element for a in bondedTo[index]):
+                            angles.addAngle(bondedTo[index][0].index, index, bondedTo[index][1].index, 1.894, 460.24)
             
         if platform is None:
             context = Context(system, VerletIntegrator(0.0))