Merge github.com:SimTk/openmm

plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h

@@ -172,6 +172,10 @@ private:
     std::vector<OutOfPlaneBendInfo> outOfPlaneBends;
 };
 
+/**
+ * This is an internal class used to record information about a bend.
+ * @private
+ */
 class AmoebaOutOfPlaneBendForce::OutOfPlaneBendInfo {
 public:
     int particle1, particle2, particle3, particle4;

plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h

@@ -121,6 +121,10 @@ private:
     std::vector<PiTorsionInfo> piTorsions;
 };
 
+/**
+ * This is an internal class used to record information about a torsion.
+ * @private
+ */
 class AmoebaPiTorsionForce::PiTorsionInfo {
 public:
     int particle1, particle2, particle3, particle4, particle5, particle6;

plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h

@@ -124,6 +124,10 @@ private:
     std::vector<StretchBendInfo> stretchBends;
 };
 
+/**
+ * This is an internal class used to record information about a stretch-bend.
+ * @private
+ */
 class AmoebaStretchBendForce::StretchBendInfo {
 public:
     int particle1, particle2, particle3;

plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h

@@ -145,6 +145,10 @@ private:
     std::vector<TorsionTorsionGridInfo> torsionTorsionGrids;
 };
 
+/**
+ * This is an internal class used to record information about a torsion-torsion term.
+ * @private
+ */
 class AmoebaTorsionTorsionForce::TorsionTorsionInfo {
 
 public:
@@ -163,6 +167,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a grid.
+ * @private
+ */
 class AmoebaTorsionTorsionForce::TorsionTorsionGridInfo {
 
 public:

plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -230,6 +230,10 @@ private:
     std::vector< std::vector< std::vector<double> > > sigEpsTable;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class AmoebaVdwForce::VdwInfo {
 public:
     int parentIndex;

plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h

@@ -137,6 +137,10 @@ private:
     std::vector<WcaDispersionInfo> parameters;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class AmoebaWcaDispersionForce::WcaDispersionInfo {
 public:
     double radius, epsilon;

plugins/amoeba/platforms/cuda/CMakeLists.txt

@@ -27,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMAMOEBACUDA_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)
@@ -109,7 +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_AMOEBA_TARGET} optimized ${SHARED_AMOEBA_TARGET})
-SET_TARGET_PROPERTIES(${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/amoeba/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_AMOEBA_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/amoeba/platforms/reference/CMakeLists.txt

-#---------------------------------------------------
-# OpenMMAmoeba REFERENCE Platform
-#
-# Creates OpenMM library, base name=OpenMMAmoebaReference.
-# Default libraries are shared & optimized. Variants
-# are created for static (_static) and debug (_d).
-#
-# Windows:
-#   OpenMMAmoebaReference[_d].dll
-#   OpenMMAmoebaReference[_d].lib
-#   OpenMMAmoebaReference_static[_d].lib
-# Unix:
-#   libOpenMMAmoebaReference[_d].so
-#   libOpenMMAmoebaReference_static[_d].a
-#----------------------------------------------------
-
-# ----------------------------------------------------------------------------
-# logging
-
-SET(LOG TRUE)
-   
-IF(LOG)
-   SET(LOG_FILE "CMakeLog.txt" )
-   FILE( WRITE ${LOG_FILE} "In plugins/amoeba/platforms/reference\n")
-ENDIF(LOG)
-
-IF(LOG)
-   MACRO(LOG_DIR LOG_FILE DIR_LIST )
-   
-      FILE( APPEND ${LOG_FILE} "\n${DIR_LIST}\n")
-      FOREACH(currentFile ${ARGN})
-         FILE( APPEND ${LOG_FILE} "   ${currentFile}\n" )
-      ENDFOREACH(currentFile)
-   
-   ENDMACRO(LOG_DIR) 
-ENDIF(LOG)
-
-MESSAGE( "YYY Reference tests")
-# ----------------------------------------------------------------------------
-
-SET(DO_TESTS TRUE)
-
-# 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_AMOEBA_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_REFERENCE_LIBRARY_NAME OpenMMAmoebaReference)
-
-SET(SHARED_TARGET ${OPENMM_REFERENCE_LIBRARY_NAME})
-SET(STATIC_TARGET ${OPENMM_REFERENCE_LIBRARY_NAME}_static)
-
-# Ensure that debug libraries have "_d" appended to their names.
-# CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
-    SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
-
-# But on Unix or Cygwin we have to add the suffix manually
-IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-    SET(SHARED_TARGET ${SHARED_TARGET}_d)
-    SET(STATIC_TARGET ${STATIC_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_AMOEBA_INCLUDE_DIRS) # start empty
-FOREACH(subdir ${OPENMM_AMOEBA_SOURCE_SUBDIRS})
-    # append
-    SET(API_AMOEBA_INCLUDE_DIRS ${API_AMOEBA_INCLUDE_DIRS}
-                                ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
-ENDFOREACH(subdir)
-
-## ----------------------------------------------------------------------------
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "OPENMM_SOURCE_SUBDIRS"              ${OPENMM_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "OPENMM_AMOEBA_SOURCE_SUBDIRS"       ${OPENMM_AMOEBA_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "API_AMOEBA_INCLUDE_DIRS"            ${API_AMOEBA_INCLUDE_DIRS} )
-   LOG_DIR( ${LOG_FILE} "CMAKE_CURRENT_SOURCE_DIR"           ${CMAKE_CURRENT_SOURCE_DIR} )
-ENDIF(LOG)
-## ----------------------------------------------------------------------------
-
-# We'll need both *relative* path names, starting with their API_AMOEBA_INCLUDE_DIRS,
-# and absolute pathnames.
-SET(API_AMOEBA_REL_INCLUDE_FILES)   # start these out empty
-SET(API_AMOEBA_ABS_INCLUDE_FILES)
-
-FOREACH(dir ${API_AMOEBA_INCLUDE_DIRS})
-    FILE(GLOB fullpaths ${dir}/*.h)	# returns full pathnames
-    SET(API_AMOEBA_ABS_INCLUDE_FILES ${API_AMOEBA_ABS_INCLUDE_FILES} ${fullpaths})
-
-    FOREACH(pathname ${fullpaths})
-        GET_FILENAME_COMPONENT(filename ${pathname} NAME)
-        SET(API_AMOEBA_REL_INCLUDE_FILES ${API_AMOEBA_REL_INCLUDE_FILES} ${dir}/${filename})
-    ENDFOREACH(pathname)
-ENDFOREACH(dir)
-
-## ----------------------------------------------------------------------------
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "API_AMOEBA_REL_INCLUDE_FILES" ${API_AMOEBA_REL_INCLUDE_FILES} )
-   LOG_DIR( ${LOG_FILE} "OPENMM_DIR" ${OPENMM_DIR} )
-ENDIF(LOG)
-## ----------------------------------------------------------------------------
-
-# collect up source files
-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)
-    SET(SOURCE_FILES         ${SOURCE_FILES}         ${src_files})   #append
-    SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
-    IF(LOG)
-        LOG_DIR( ${LOG_FILE} "Adding include dir: " ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include )
-    ENDIF(LOG)
-    INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
-ENDFOREACH(subdir)
-INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/include)
-INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/src)
-INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/src/SimTKReference)
-
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "CMAKE_CURRENT_SOURCE_DIR" ${CMAKE_CURRENT_SOURCE_DIR} )
-   FILE( APPEND ${LOG_FILE} "CMAKE_CURRENT_SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}\n" )
-   LOG_DIR( ${LOG_FILE} "SOURCE_FILES" ${SOURCE_FILES} )
-   LOG_DIR( ${LOG_FILE} "SOURCE_INCLUDE_FILES" ${SOURCE_INCLUDE_FILES} )
-ENDIF(LOG)
-
-INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/src)
-
-MESSAGE( "YYY Reference tests")
-# SUBDIRS (sharedTarget staticTarget)
-SUBDIRS (sharedTarget)
-SUBDIRS (tests)
-
+#---------------------------------------------------
+# OpenMM Reference Amoeba Implementation
+#
+# Creates OpenMM library, base name=OpenMMAmoebaReference.
+# Default libraries are shared & optimized. Variants
+# are created for debug (_d).
+#
+# Windows:
+#   OpenMMAmoebaReference[_d].dll
+#   OpenMMAmoebaReference[_d].lib
+# Unix:
+#   libOpenMMAmoebaReference[_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 .)
+
+# 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(OPENMMAMOEBAREFERENCE_LIBRARY_NAME OpenMMAmoebaReference)
+
+SET(SHARED_TARGET ${OPENMMAMOEBAREFERENCE_LIBRARY_NAME})
+
+# Ensure that debug libraries have "_d" appended to their names.
+# CMake gets this right on Windows automatically with this definition.
+IF (MSVC)
+    SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
+ENDIF (MSVC)
+
+# But on Unix or Cygwin we have to add the suffix manually
+IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    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
+FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
+    # append
+    SET(API_INCLUDE_DIRS ${API_INCLUDE_DIRS}
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
+ENDFOREACH(subdir)
+
+# We'll need both *relative* path names, starting with their API_INCLUDE_DIRS,
+# and absolute pathnames.
+SET(API_REL_INCLUDE_FILES)   # start these out empty
+SET(API_ABS_INCLUDE_FILES)
+
+FOREACH(dir ${API_INCLUDE_DIRS})
+    FILE(GLOB fullpaths ${dir}/*.h)	# returns full pathnames
+    SET(API_ABS_INCLUDE_FILES ${API_ABS_INCLUDE_FILES} ${fullpaths})
+
+    FOREACH(pathname ${fullpaths})
+        GET_FILENAME_COMPONENT(filename ${pathname} NAME)
+        SET(API_REL_INCLUDE_FILES ${API_REL_INCLUDE_FILES} ${dir}/${filename})
+    ENDFOREACH(pathname)
+ENDFOREACH(dir)
+
+# collect up source files
+SET(SOURCE_FILES) # empty
+SET(SOURCE_INCLUDE_FILES)
+
+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)
+ENDFOREACH(subdir)
+
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src/SimTKReference)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/include)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/src/SimTKReference)
+
+# Create the library
+
+ADD_LIBRARY(${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_AMOEBA_TARGET} optimized ${SHARED_AMOEBA_TARGET})
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+
+INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
+SUBDIRS (tests)

plugins/amoeba/platforms/reference/sharedTarget/CMakeLists.txt

-#
-# Include REFERENCE related files.
-#
-# ----------------------------------------------------------------------------
-# logging
-
-SET(LOG FALSE)
-   
-IF(LOG)
-   SET(LOG_FILE "CMakeLog.txt" )
-   FILE( WRITE ${LOG_FILE} "In amoeba/platforms/reference/sharedTarget Cmake\n")
-#  FILE( APPEND ${LOG_FILE} "BROOK_LIB_PATH=${BROOK_LIB_PATH}\n")
-ENDIF(LOG)
-
-IF(LOG)
-   MACRO(LOG_DIR LOG_FILE DIR_LIST )
-   
-      FILE( APPEND ${LOG_FILE} "\n${DIR_LIST}\n")
-      FOREACH(currentFile ${ARGN})
-         FILE( APPEND ${LOG_FILE} "   ${currentFile}\n" )
-      ENDFOREACH(currentFile)
-   
-   ENDMACRO(LOG_DIR) 
-ENDIF(LOG)
-
-# ----------------------------------------------------------------------------
-
-SET(OPENMM_BUILD_AMOEBA_PATH ${CMAKE_SOURCE_DIR}/plugins/amoeba) 
-
-# ----------------------------------------------------------------------------
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "Pre OPENMM_SOURCE_SUBDIRS" ${OPENMM_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "Pre OPENMM_AMOEBA_SOURCE_SUBDIRS " ${OPENMM_AMOEBA_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "Pre SOURCE_FILES" ${SOURCE_FILES} )
-ENDIF(LOG)
-## ----------------------------------------------------------------------------
-
-INCLUDE_DIRECTORIES(${REFERENCE_INCLUDE})
-LINK_DIRECTORIES(${REFERENCE_TARGET_LINK})
-FOREACH(subdir ${OPENMM_AMOEBA_SOURCE_SUBDIRS})
-    FILE(GLOB src_files ${OPENMM_BUILD_AMOEBA_PATH}/platforms/reference/${subdir}/src/*.cu ${OPENMM_BUILD_AMOEBA_PATH}/platforms/reference/src/*/*.cu)
-    SET(SOURCE_FILES ${SOURCE_FILES} ${src_files})
-    INCLUDE_DIRECTORIES(BEFORE ${OPENMM_BUILD_AMOEBA_PATH}/platforms/reference/../${subdir}/include)
-ENDFOREACH(subdir)
-
-# ----------------------------------------------------------------------------
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "OPENMM_BUILD_AMOEBA_PATH" ${OPENMM_BUILD_AMOEBA_PATH} )
-   FILE( APPEND ${LOG_FILE} "OPENMM_BUILD_AMOEBA_PATH=${OPENMM_BUILD_AMOEBA_PATH}\n")
-   LOG_DIR( ${LOG_FILE} "OPENMM_SOURCE_SUBDIRS" ${OPENMM_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "CMAKE_SOURCE_DIR" ${CMAKE_SOURCE_DIR} )
-   LOG_DIR( ${LOG_FILE} "REFERENCE_INCLUDE" ${REFERENCE_INCLUDE} )
-   LOG_DIR( ${LOG_FILE} "REFERENCE_TARGET_LINK" ${REFERENCE_TARGET_LINK} )
-   LOG_DIR( ${LOG_FILE} "SHARED_TARGET" ${SHARED_TARGET} )
-   LOG_DIR( ${LOG_FILE} "OPENMM_DIR" ${OPENMM_DIR} )
-   LOG_DIR( ${LOG_FILE} "SOURCE_FILES" ${SOURCE_FILES} )
-ENDIF(LOG)
-## ----------------------------------------------------------------------------
-
-# REFERENCE_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/jama/include)
-
-INCLUDE_DIRECTORIES(${OPENMM_BUILD_AMOEBA_PATH}/platforms/reference/../src
-                         ${OPENMM_BUILD_AMOEBA_PATH}/platforms/reference/include
-                         ${OPENMM_DIR}/platforms/reference/src
-                         ${OPENMM_DIR}/platforms/reference/include
-                         ${OPENMM_DIR}/platforms/reference/src/kernels
-                         ${OPENMM_DIR}/openmmapi/include ) 
-
-ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME} )
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}Cuda_d optimized ${OPENMM_LIBRARY_NAME}Cuda )
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_AMOEBA_LIBRARY_NAME}_d optimized ${OPENMM_AMOEBA_LIBRARY_NAME} )
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMMREFERENCE_BUILDING_SHARED_LIBRARY -DOPENMMREFERENCEAMOEBA_BUILDING_SHARED_LIBRARY")
-
-INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernelFactory.cpp

@@ -6,8 +6,8 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
- * Authors:                                                                   *
+ * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * This program is free software: you can redistribute it and/or modify       *
@@ -32,40 +32,33 @@
 
 using namespace OpenMM;
 
-#if defined(WIN32)
-    #include <windows.h>
-    extern "C" void initAmoebaReferenceKernels();
-    BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
-        if (ul_reason_for_call == DLL_PROCESS_ATTACH)
-            initAmoebaReferenceKernels();
-        return TRUE;
-    }
-#else
-    extern "C" void __attribute__((constructor)) initAmoebaReferenceKernels();
-#endif
-
-extern "C" void initAmoebaReferenceKernels() {
-    for( int ii = 0; ii < Platform::getNumPlatforms(); ii++ ){
-        Platform& platform = Platform::getPlatform(ii);
-        if( platform.getName() == "Reference" ){
+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) {
              AmoebaReferenceKernelFactory* factory = new AmoebaReferenceKernelFactory();
-
-             platform.registerKernelFactory(CalcAmoebaBondForceKernel::Name(),          factory);
-             platform.registerKernelFactory(CalcAmoebaAngleForceKernel::Name(),         factory);
-             platform.registerKernelFactory(CalcAmoebaInPlaneAngleForceKernel::Name(),  factory);
-             platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(),             factory);
-             platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(),           factory);
-             platform.registerKernelFactory(CalcAmoebaOutOfPlaneBendForceKernel::Name(),        factory);
-             platform.registerKernelFactory(CalcAmoebaTorsionTorsionForceKernel::Name(),        factory);
-             platform.registerKernelFactory(CalcAmoebaVdwForceKernel::Name(),                   factory);
-             platform.registerKernelFactory(CalcAmoebaMultipoleForceKernel::Name(),             factory);
+             platform.registerKernelFactory(CalcAmoebaBondForceKernel::Name(), factory);
+             platform.registerKernelFactory(CalcAmoebaAngleForceKernel::Name(), factory);
+             platform.registerKernelFactory(CalcAmoebaInPlaneAngleForceKernel::Name(), factory);
+             platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(), factory);
+             platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(), factory);
+             platform.registerKernelFactory(CalcAmoebaOutOfPlaneBendForceKernel::Name(), factory);
+             platform.registerKernelFactory(CalcAmoebaTorsionTorsionForceKernel::Name(), factory);
+             platform.registerKernelFactory(CalcAmoebaVdwForceKernel::Name(), factory);
+             platform.registerKernelFactory(CalcAmoebaMultipoleForceKernel::Name(), factory);
              platform.registerKernelFactory(CalcAmoebaGeneralizedKirkwoodForceKernel::Name(), factory);
              platform.registerKernelFactory(CalcAmoebaWcaDispersionForceKernel::Name(), factory);
         }
     }
 }
 
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories() {
+    registerKernelFactories();
+}
+
 KernelImpl* AmoebaReferenceKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
     ReferencePlatform::PlatformData& referencePlatformData = *static_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
 

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

 #
 # 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(${OPENMM_DIR}/platforms/reference/src/kernels)
-
-#SET(SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET   "AmoebaTinkerParameterFile" )
-#SET(AMOEBA_TINKER_PARAMETER_FILE_SOURCE_FILES    "AmoebaTinkerParameterFile.cpp" )
-#SET(AMOEBA_TINKER_PARAMETER_FILE_INCLUDE_FILES   "AmoebaTinkerParameterFile.h" )
-
-Set( SHARED_OPENMM__AMOEBA_TARGET OpenMMAmoeba)
-Set( STATIC_OPENMM_TARGET OpenMMAmoeba_static)
-Set( SHARED_CUDA_TARGET OpenMMAmoebaCuda )
-Set( STATIC_CUDA_TARGET OpenMMCuda_static OpenMMAmoebaCuda_static)
-
-#ADD_LIBRARY(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} SHARED ${AMOEBA_TINKER_PARAMETER_FILE_SOURCE_FILES} ${AMOEBA_TINKER_PARAMETER_FILE_INCLUDE_FILES} )
-#SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY")
-#TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME})
-#TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${SHARED_OPENMM__AMOEBA_TARGET}_d optimized ${SHARED_OPENMM__AMOEBA_TARGET})
-#TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${SHARED_CUDA_TARGET}_d optimized ${SHARED_CUDA_TARGET})
-
-
-IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-    SET(SHARED_CUDA_TARGET   ${SHARED_CUDA_TARGET}_d)
-    SET(SHARED_OPENMM__AMOEBA_TARGET ${SHARED_OPENMM__AMOEBA_TARGET}_d)
-    #SET(STATIC_CUDA_TARGET ${STATIC_CUDA_TARGET}_d)
-    #Set(STATIC_OPENMM_TARGET ${STATIC_OPENMM_TARGET}_d)
-ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 
-#LINK_DIRECTORIES
+ENABLE_TESTING()
 
 # Automatically create tests using files named "Test*.cpp"
 FILE(GLOB TEST_PROGS "*Test*.cpp")
@@ -39,43 +10,9 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
 
     # Link with shared library
-
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
-    #TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET} ${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET})
-    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM__AMOEBA_TARGET} )
+    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET})
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 
-    # Link with static library
-#     SET(TEST_STATIC ${TEST_ROOT}Static)
-#     CUDA_ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
-#     SET_TARGET_PROPERTIES(${TEST_STATIC}
-#                 PROPERTIES
-#                 COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
-#                 )
-#     TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_OPENMM_TARGET} ${STATIC_CUDA_TARGET})
-#     ADD_TEST(${TEST_STATIC} ${EXECUTABLE_OUTPUT_PATH}/${TEST_STATIC})
-
 ENDFOREACH(TEST_PROG ${TEST_PROGS})
-
-# TestCudaUsingParameterFile customized w/ command-line argument (input file name used in test) 
-
-#ADD_EXECUTABLE(TestAmoebaCudaUsingParameterFile TstAmoebaCudaUsingParameterFile.cpp)
-#TARGET_LINK_LIBRARIES(TestAmoebaCudaUsingParameterFile ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET})
-#ADD_TEST(TestCudaUsingParameterFile "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFile" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/lambdaSdObcParameters.txt")
-#ADD_TEST(TestCudaUsingParameterFile "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFile" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfNoPbcParameters.txt")
-#
-#SET(TEST_ROOT TestCudaUsingParameterFile)
-#SET(TEST_PROG TstCudaUsingParameterFile.cpp)
-#SET(TEST_STATIC ${TEST_ROOT}Static)
-#SET(INCLUDE_CUDA_STATIC 1)
-#IF(INCLUDE_CUDA_STATIC)
-#   ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
-#   SET_TARGET_PROPERTIES(${TEST_STATIC}
-#                         PROPERTIES
-#                         COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
-#                        )
-#   TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_BROOK_TARGET})
-#   ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/lambdaSdObcParameters.txt")
-#   ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfNoPbcParameters.txt")
-#  ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfPbcParameters.txt" " +checkEnergyForceConsistent -checkForces" )
-#ENDIF(INCLUDE_CUDA_STATIC)

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp

@@ -43,6 +43,8 @@
 
 using namespace OpenMM;
 
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
+
 const double TOL = 1e-5;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308
@@ -315,6 +317,7 @@ int main( int numberOfArguments, char* argv[] ) {
 
     try {
         std::cout << "TestCudaAmoebaAngleForce running test..." << std::endl;
+        registerAmoebaReferenceKernelFactories();
         //FILE* log = fopen( "AmoebaAngleForce.log", "w" );;
         FILE* log = NULL;
         //FILE* log = stderr;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaBondForce.cpp

@@ -44,6 +44,8 @@
 
 using namespace OpenMM;
 
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
+
 const double TOL = 1e-5;
 
 static void computeAmoebaBondForce(int bondIndex,  std::vector<Vec3>& positions, AmoebaBondForce& AmoebaBondForce,
@@ -222,6 +224,7 @@ int main( int numberOfArguments, char* argv[] ) {
 
     try {
         std::cout << "TestReferenceAmoebaBondForce running test..." << std::endl;
+        registerAmoebaReferenceKernelFactories();
         FILE* log = NULL;
         //FILE* log = stderr;
 

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp

@@ -50,6 +50,9 @@
 using namespace OpenMM;
+
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
+
 const double TOL = 1e-4;
 // setup for 2 ammonia molecules
@@ -8470,6 +8473,7 @@ int main( int numberOfArguments, char* argv[] ) {
     try {
         std::cout << "TestReferenceAmoebaGeneralizedKirkwoodForce running test..." << std::endl;
+        registerAmoebaReferenceKernelFactories();
         FILE* log = NULL;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.cpp

@@ -44,6 +44,8 @@
 
 using namespace OpenMM;
 
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
+
 const double TOL = 1e-5;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308
@@ -391,6 +393,7 @@ int main( int numberOfArguments, char* argv[] ) {
 
     try {
         std::cout << "TestReferenceAmoebaInPlaneAngleForce running test..." << std::endl;
+        registerAmoebaReferenceKernelFactories();
         FILE* log = NULL;
         //FILE* log = stderr;
         //FILE* log = fopen( "AmoebaInPlaneAngleForce.log", "w" );;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp

@@ -50,6 +50,9 @@
 
 
 using namespace OpenMM;
+
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
+
 const double TOL = 1e-4;
 
 // setup for 2 ammonia molecules
@@ -2803,6 +2806,7 @@ int main( int numberOfArguments, char* argv[] ) {
 
     try {
         std::cout << "TestReferenceAmoebaMultipoleForce running test..." << std::endl;
+        registerAmoebaReferenceKernelFactories();
 
         FILE* log = NULL;
 

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.cpp

@@ -44,6 +44,8 @@
 
 using namespace OpenMM;
 
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
+
 const double TOL = 1e-3;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308
@@ -521,6 +523,7 @@ int main( int numberOfArguments, char* argv[] ) {
 
     try {
         std::cout << "TestReferenceAmoebaOutOfPlaneBendForce running test..." << std::endl;
+        registerAmoebaReferenceKernelFactories();
 
         //FILE* log = stderr;
         FILE* log = NULL;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPiTorsionForce.cpp

@@ -43,6 +43,8 @@
 
 using namespace OpenMM;
 
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
+
 const double TOL = 1e-5;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308
@@ -318,6 +320,7 @@ int main( int numberOfArguments, char* argv[] ) {
 
     try {
         std::cout << "TestReferenceAmoebaPiTorsionForce running test..." << std::endl;
+        registerAmoebaReferenceKernelFactories();
         FILE* log = NULL;
         //FILE* log = stderr;
         //FILE* log = fopen( "AmoebaPiTorsionForce1.log", "w" );;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaStretchBendForce.cpp

@@ -45,6 +45,8 @@ const double DegreesToRadians = 3.14159265/180.0;
 
 using namespace OpenMM;
 
+extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
+
 const double TOL = 1e-4;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308
@@ -304,6 +306,7 @@ int main( int numberOfArguments, char* argv[] ) {
 
     try {
         std::cout << "TestReferenceAmoebaStretchBendForce running test..." << std::endl;
+        registerAmoebaReferenceKernelFactories();
 
         FILE* log = NULL;
         //FILE* log = stderr;