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Commit ef830210 authored by peastman's avatar peastman
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Plugins work with CPU platform. This involved separating the reference... 

Plugins work with CPU platform.  This involved separating the reference implementations of plugins into their own libraries.
parent b4150b1b
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Showing with 218 additions and 290 deletions
plugins/amoeba/CMakeLists.txt
View file @ ef830210
......@@ -24,7 +24,7 @@ SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA 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_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi)
# 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.
......@@ -94,11 +94,6 @@ FOREACH(subdir ${OPENMM_AMOEBA_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_AMOEBA wrappers are being generated, and add them to the build.
......@@ -162,9 +157,10 @@ IF(OPENMM_BUILD_STATIC_LIB)
TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} )
ENDIF(OPENMM_BUILD_STATIC_LIB)
ADD_SUBDIRECTORY(platforms/reference/tests)
# Which hardware platforms to build
ADD_SUBDIRECTORY(platforms/reference)
IF(CUDA_FOUND)
SET(OPENMM_BUILD_AMOEBA_CUDA_LIB ON CACHE BOOL "Build OpenMMAmoebaCuda library for Nvidia GPUs")
ELSE(CUDA_FOUND)
......@@ -175,16 +171,10 @@ SET(OPENMM_BUILD_AMOEBA_PATH)
SET(OPENMM_BUILD_AMOEBA_CUDA_PATH)
IF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
ADD_SUBDIRECTORY(platforms/cuda)
SET(OPENMM_BUILD_AMOEBA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
SET(OPENMM_BUILD_AMOEBA_CUDA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
SET(OPENMM_AMOEBA_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda)
ENDIF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
#SET(OPENMM_BUILD_OPENCL_LIB OFF CACHE BOOL "Build OpenMMOpenCL library for Nvidia GPUs")
#IF(OPENMM_BUILD_OPENCL_LIB)
# ADD_SUBDIRECTORY(platforms/opencl)
#ENDIF(OPENMM_BUILD_OPENCL_LIB)
INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_AMOEBA_TARGET})
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_AMOEBA_SERIALIZABLE_TARGET})
......@@ -199,18 +189,6 @@ INSTALL_FILES(/include FILES ${CORE_HEADERS})
INSTALL_FILES(/include/openmm FILES ${TOP_HEADERS})
INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS})
#
# Allow automated build and dashboard.
#
#INCLUDE (Dart)
#IF (UNIX AND NOT CYGWIN AND NOT APPLE)
# IF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
# ADD_DEFINITIONS(-fprofile-arcs -ftest-coverage)
# LINK_LIBRARIES(gcov)
# ENDIF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
#ENDIF (UNIX AND NOT CYGWIN AND NOT APPLE)
#
# Testing
#
......@@ -226,8 +204,3 @@ ENDIF (EXECUTABLE_OUTPUT_PATH)
IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
ADD_SUBDIRECTORY(serialization)
ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
#INCLUDE(ApiDoxygen.cmake)
#ADD_SUBDIRECTORY(tests)
#ADD_SUBDIRECTORY(examples)
plugins/amoeba/platforms/reference/CMakeLists.txt
View file @ ef830210
#---------------------------------------------------
# OpenMMAmoeba REFERENCE Platform
# OpenMM Reference Amoeba Implementation
#
# Creates OpenMM library, base name=OpenMMAmoebaReference.
# Default libraries are shared & optimized. Variants
# are created for static (_static) and debug (_d).
# are created for 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 .)
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_REFERENCE_LIBRARY_NAME OpenMMAmoebaReference)
SET(OPENMMAMOEBAREFERENCE_LIBRARY_NAME OpenMMAmoebaReference)
SET(SHARED_TARGET ${OPENMM_REFERENCE_LIBRARY_NAME})
SET(STATIC_TARGET ${OPENMM_REFERENCE_LIBRARY_NAME}_static)
SET(SHARED_TARGET ${OPENMMAMOEBAREFERENCE_LIBRARY_NAME})
# Ensure that debug libraries have "_d" appended to their names.
# CMake gets this right on Windows automatically with this definition.
......@@ -61,78 +32,64 @@ ENDIF (${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})
SET(API_INCLUDE_DIRS) # start empty
FOREACH(subdir ${OPENMM_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)
SET(API_INCLUDE_DIRS ${API_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,
# We'll need both *relative* path names, starting with their API_INCLUDE_DIRS,
# and absolute pathnames.
SET(API_AMOEBA_REL_INCLUDE_FILES) # start these out empty
SET(API_AMOEBA_ABS_INCLUDE_FILES)
SET(API_REL_INCLUDE_FILES) # start these out empty
SET(API_ABS_INCLUDE_FILES)
FOREACH(dir ${API_AMOEBA_INCLUDE_DIRS})
FOREACH(dir ${API_INCLUDE_DIRS})
FILE(GLOB fullpaths ${dir}/*.h) # returns full pathnames
SET(API_AMOEBA_ABS_INCLUDE_FILES ${API_AMOEBA_ABS_INCLUDE_FILES} ${fullpaths})
SET(API_ABS_INCLUDE_FILES ${API_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})
SET(API_REL_INCLUDE_FILES ${API_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})
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})
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)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${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)
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 deleted 100644 → 0
View file @ b4150b1b
#
# 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
View file @ ef830210
......@@ -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 *
......@@ -32,25 +32,14 @@
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);
......@@ -66,6 +55,10 @@ extern "C" void initAmoebaReferenceKernels() {
}
}
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
View file @ ef830210
#
# Testing
#
ENABLE_TESTING()
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__AMOEBA_TARGET OpenMMAmoeba)
Set( STATIC_OPENMM_TARGET OpenMMAmoeba_static)
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_OPENMM__AMOEBA_TARGET ${SHARED_OPENMM__AMOEBA_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")
......@@ -22,9 +10,8 @@ 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} ${SHARED_OPENMM__AMOEBA_TARGET} )
TARGET_LINK_LIBRARIES(${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})
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp
View file @ ef830210
......@@ -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
View file @ ef830210
......@@ -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
View file @ ef830210
......@@ -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
View file @ ef830210
......@@ -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
View file @ ef830210
......@@ -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
View file @ ef830210
......@@ -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
View file @ ef830210
......@@ -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
View file @ ef830210
......@@ -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;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp
View file @ ef830210
......@@ -44,6 +44,9 @@
#include <vector>
using namespace OpenMM;
extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-4;
TorsionTorsionGrid& getTorsionGrid( int gridIndex ) {
......@@ -2683,6 +2686,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestReferenceAmoebaTorsionTorsionForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
//registerAmoebaCudaKernelFactories();
FILE* log = NULL;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp
View file @ ef830210
......@@ -51,6 +51,8 @@
using namespace OpenMM;
extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-4;
void testVdw( FILE* log ) {
......@@ -1983,6 +1985,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestReferenceAmoebaVdwForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
FILE* log = NULL;
......
plugins/amoeba/platforms/reference/tests/TestReferenceWcaDispersionForce.cpp
View file @ ef830210
......@@ -50,6 +50,9 @@
using namespace OpenMM;
extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-4;
void compareForcesEnergy( std::string& testName, double expectedEnergy, double energy,
......@@ -171,6 +174,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaWcaDispersionForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
FILE* log = NULL;
......
plugins/drude/CMakeLists.txt
View file @ ef830210
......@@ -22,7 +22,7 @@ SET(CREATE_SERIALIZABLE_OPENMM_DRUDE 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_DRUDE_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
SET(OPENMM_DRUDE_PLUGIN_SOURCE_SUBDIRS . openmmapi)
SET(OPENMM_DRUDE_LIBRARY_NAME OpenMMDrude)
SET(SHARED_DRUDE_TARGET ${OPENMM_DRUDE_LIBRARY_NAME})
......@@ -80,46 +80,18 @@ FOREACH(subdir ${OPENMM_DRUDE_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_DRUDE wrappers are being generated, and add them to the build.
#IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
# ADD_SUBDIRECTORY(wrappers)
# SET(SOURCE_DRUDE_FILES ${SOURCE_DRUDE_FILES} wrappers/DrudeOpenMMCWrapper.cpp wrappers/DrudeOpenMMFortranWrapper.cpp)
# SET_SOURCE_FILES_PROPERTIES(wrappers/DrudeOpenMMCWrapper.cpp wrappers/DrudeOpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE)
#ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
ADD_LIBRARY(${SHARED_DRUDE_TARGET} SHARED ${SOURCE_DRUDE_FILES} ${SOURCE_DRUDE_INCLUDE_FILES} ${API_DRUDE_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${SHARED_DRUDE_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_DRUDE_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
#IF( CREATE_SERIALIZABLE_OPENMM_DRUDE )
# ADD_LIBRARY(${SHARED_DRUDE_SERIALIZABLE_TARGET} SHARED ${SOURCE_DRUDE_FILES} ${SOURCE_DRUDE_INCLUDE_FILES} ${API_DRUDE_ABS_INCLUDE_FILES})
# SET_TARGET_PROPERTIES(${SHARED_DRUDE_SERIALIZABLE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_DRUDE_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_SERIALIZE")
# INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../serialization/include)
#ENDIF( CREATE_SERIALIZABLE_OPENMM_DRUDE )
IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_DRUDE_TARGET} STATIC ${SOURCE_DRUDE_FILES} ${SOURCE_DRUDE_INCLUDE_FILES} ${API_DRUDE_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${STATIC_DRUDE_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(${SHARED_DRUDE_TARGET} DrudeApiWrappers)
# IF( CREATE_SERIALIZABLE_OPENMM_DRUDE )
# ADD_DEPENDENCIES(${SHARED_DRUDE_SERIALIZABLE_TARGET} DrudeApiWrappers)
# ENDIF( CREATE_SERIALIZABLE_OPENMM_DRUDE )
# IF(OPENMM_BUILD_STATIC_LIB)
# ADD_DEPENDENCIES(${STATIC_DRUDE_TARGET} DrudeApiWrappers)
# 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_DRUDE_TARGET} ${STATIC_TARGET} )
ENDIF(OPENMM_BUILD_STATIC_LIB)
ADD_SUBDIRECTORY(platforms/reference/tests)
# Which hardware platforms to build
#SET(OPENMM_BUILD_DRUDE_PATH)
#SET(OPENMM_BUILD_DRUDE_CUDA_PATH)
#IF(OPENMM_BUILD_DRUDE_CUDA_LIB)
# ADD_SUBDIRECTORY(platforms/cuda)
# SET(OPENMM_BUILD_DRUDE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
# SET(OPENMM_BUILD_DRUDE_CUDA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
# SET(OPENMM_DRUDE_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda)
#ENDIF(OPENMM_BUILD_DRUDE_CUDA_LIB)
ADD_SUBDIRECTORY(platforms/reference)
IF(OPENCL_FOUND)
SET(OPENMM_BUILD_DRUDE_OPENCL_LIB ON CACHE BOOL "Build Drude implementation for OpenCL")
......
plugins/drude/platforms/reference/CMakeLists.txt 0 → 100644
View file @ ef830210
#---------------------------------------------------
# OpenMM Reference Drude Integrator
#
# Creates OpenMM library, base name=OpenMMDrudeReference.
# Default libraries are shared & optimized. Variants
# are created for debug (_d).
#
# Windows:
# OpenMMDrudeReference[_d].dll
# OpenMMDrudeReference[_d].lib
# Unix:
# libOpenMMDrudeReference[_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(OPENMMDRUDEREFERENCE_LIBRARY_NAME OpenMMDrudeReference)
SET(SHARED_TARGET ${OPENMMDRUDEREFERENCE_LIBRARY_NAME})
# Ensure that debug libraries have "_d" appended to their names.
# CMake gets this right on Windows automatically with this definition.
IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
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)
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_SOURCE_DIR}/platforms/reference/include)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/src)
# Create the library
INCLUDE_DIRECTORIES(${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_DRUDE_TARGET} optimized ${SHARED_DRUDE_TARGET})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse2 -DOPENMM_BUILDING_SHARED_LIBRARY")
INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
SUBDIRS (tests)
plugins/drude/platforms/reference/src/ReferenceDrudeKernelFactory.cpp
View file @ ef830210
......@@ -32,24 +32,23 @@
using namespace OpenMM;
#if defined(WIN32)
#include <windows.h>
extern "C" void initDrudeReferenceKernels();
BOOL WINAPI DllMain(HANDLE hModule, DWORD ul_reason_for_call, LPVOID lpReserved) {
if (ul_reason_for_call == DLL_PROCESS_ATTACH)
initDrudeReferenceKernels();
return TRUE;
}
#else
extern "C" void __attribute__((constructor)) initDrudeReferenceKernels();
#endif
extern "C" OPENMM_EXPORT void registerPlatforms() {
}
extern "C" void initDrudeReferenceKernels() {
Platform& platform = Platform::getPlatformByName("Reference");
extern "C" OPENMM_EXPORT void registerKernelFactories() {
for (int i = 0; i < Platform::getNumPlatforms(); i++) {
Platform& platform = Platform::getPlatform(i);
if (dynamic_cast<ReferencePlatform*>(&platform) != NULL) {
ReferenceDrudeKernelFactory* factory = new ReferenceDrudeKernelFactory();
platform.registerKernelFactory(CalcDrudeForceKernel::Name(), factory);
platform.registerKernelFactory(IntegrateDrudeLangevinStepKernel::Name(), factory);
platform.registerKernelFactory(IntegrateDrudeSCFStepKernel::Name(), factory);
}
}
}
extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories() {
registerKernelFactories();
}
KernelImpl* ReferenceDrudeKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
......
plugins/drude/platforms/reference/tests/CMakeLists.txt
View file @ ef830210
......@@ -2,11 +2,9 @@
# Testing
#
ENABLE_TESTING()
#INCLUDE_DIRECTORIES(${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_DRUDE_TARGET OpenMMDrude)
......
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