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Commit d56c21b0 authored by peastman's avatar peastman
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Merged latest changes from main branch

parents 1049add2 8d062ebb
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Showing with 211 additions and 337 deletions
CMakeLists.txt
View file @ d56c21b0
......@@ -116,9 +116,13 @@ IF (APPLE)
# Improve the linking behavior of Mac libraries
SET (CMAKE_INSTALL_NAME_DIR "@rpath")
SET(EXTRA_COMPILE_FLAGS "-stdlib=libc++")
SET(EXTRA_COMPILE_FLAGS "-msse2 -stdlib=libc++")
ELSE (APPLE)
IF (WIN32)
SET(EXTRA_COMPILE_FLAGS)
ELSE (WIN32)
SET(EXTRA_COMPILE_FLAGS "-msse2")
ENDIF (WIN32)
ENDIF (APPLE)
IF(UNIX AND NOT CMAKE_BUILD_TYPE)
......@@ -257,7 +261,7 @@ FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
## OpenMM was previously installed there.
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
ENDFOREACH(subdir)
SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-msse2 -DHAVE_SSE2=1")
SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-DHAVE_SSE2=1")
# If API wrappers are being generated, and add them to the build.
SET(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS ON CACHE BOOL "Build wrappers for C and Fortran")
......
libraries/lepton/include/lepton/Operation.h
View file @ d56c21b0
......@@ -40,6 +40,7 @@
#include <string>
#include <vector>
#include <sstream>
#include <algorithm>
namespace Lepton {
......
libraries/lepton/src/MSVC_erfc.h
View file @ d56c21b0
......@@ -2,16 +2,16 @@
#define LEPTON_MSVC_ERFC_H_
/*
* At least up to version 8 (VC++ 2005), Microsoft does not support the
* standard C99 erf() and erfc() functions. For now we're including these
* definitions for an MSVC compilation; if these are added later then
* the #ifdef below should change to compare _MSC_VER with a particular
* version level.
* Up to version 11 (VC++ 2012), Microsoft does not support the
* standard C99 erf() and erfc() functions so we have to fake them here.
* These were added in version 12 (VC++ 2013), which sets _MSC_VER=1800
* (VC11 has _MSC_VER=1700).
*/
#ifdef _MSC_VER
#if defined(_MSC_VER)
#define M_PI 3.14159265358979323846264338327950288
#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12
/***************************
* erf.cpp
* author: Steve Strand
......@@ -20,8 +20,6 @@
#include <cmath>
#define M_PI 3.14159265358979323846264338327950288
static const double rel_error= 1E-12; //calculate 12 significant figures
//you can adjust rel_error to trade off between accuracy and speed
//but don't ask for > 15 figures (assuming usual 52 bit mantissa in a double)
......@@ -83,6 +81,7 @@ static double erfc(double x)
return one_sqrtpi*exp(-x*x)*q2;
}
#endif // _MSC_VER <= 1700
#endif // _MSC_VER
#endif // LEPTON_MSVC_ERFC_H_
openmmapi/include/openmm/internal/MSVC_erfc.h
View file @ d56c21b0
......@@ -2,16 +2,16 @@
#define OPENMM_MSVC_ERFC_H_
/*
* At least up to version 8 (VC++ 2005), Microsoft does not support the
* standard C99 erf() and erfc() functions. For now we're including these
* definitions for an MSVC compilation; if these are added later then
* the #ifdef below should change to compare _MSC_VER with a particular
* version level.
* Up to version 11 (VC++ 2012), Microsoft does not support the
* standard C99 erf() and erfc() functions so we have to fake them here.
* These were added in version 12 (VC++ 2013), which sets _MSC_VER=1800
* (VC11 has _MSC_VER=1700).
*/
#ifdef _MSC_VER
#if defined(_MSC_VER)
#define M_PI 3.14159265358979323846264338327950288
#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12
/***************************
* erf.cpp
* author: Steve Strand
......@@ -81,6 +81,7 @@ static double erfc(double x)
return one_sqrtpi*exp(-x*x)*q2;
}
#endif // _MSC_VER <= 1700
#endif // _MSC_VER
#endif // OPENMM_MSVC_ERFC_H_
platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp
View file @ d56c21b0
......@@ -72,6 +72,7 @@ using OpenMM::RealVec;
for (int j = 0; j < (int) atomGroups[i].size(); j++) {
int atom = atomGroups[i][j];
if (atomMasses[atom] != 0) {
const RealOpenMM velocityScale = static_cast<RealOpenMM>(sqrt(BOLTZ*temperature/atomMasses[atom]));
atomVelocities[atom][0] = velocityScale*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
atomVelocities[atom][1] = velocityScale*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
......@@ -79,6 +80,7 @@ using OpenMM::RealVec;
}
}
}
}
}
plugins/amoeba/CMakeLists.txt
View file @ d56c21b0
......@@ -18,7 +18,7 @@
# 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 serialization)
SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi serialization)
# 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.
......@@ -82,11 +82,6 @@ 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.
......@@ -138,9 +133,10 @@ 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)
......@@ -151,16 +147,10 @@ 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(OPENMM_BUILD_STATIC_LIB)
INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_AMOEBA_TARGET})
......@@ -172,18 +162,6 @@ 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
#
......@@ -197,8 +175,3 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
ENDIF (EXECUTABLE_OUTPUT_PATH)
ADD_SUBDIRECTORY(serialization/tests)
#INCLUDE(ApiDoxygen.cmake)
#ADD_SUBDIRECTORY(tests)
#ADD_SUBDIRECTORY(examples)
plugins/amoeba/platforms/reference/CMakeLists.txt
View file @ d56c21b0
#---------------------------------------------------
# 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 @ 1049add2
#
# 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 @ d56c21b0
......@@ -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 @ d56c21b0
#
# 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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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 @ d56c21b0
......@@ -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;
......
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