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tsoc
openmm
Commits
18a837c0
Commit
18a837c0
authored
Jun 01, 2011
by
Peter Eastman
Browse files
Initial implementation of RPMD plugin
parent
839ab51e
Changes
8
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8 changed files
with
1403 additions
and
539 deletions
+1403
-539
CMakeLists.txt
CMakeLists.txt
+544
-535
platforms/reference/src/SimTKReference/fftpack.h
platforms/reference/src/SimTKReference/fftpack.h
+28
-4
plugins/rpmd/CMakeLists.txt
plugins/rpmd/CMakeLists.txt
+207
-0
plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h
plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h
+164
-0
plugins/rpmd/openmmapi/include/openmm/RpmdKernels.h
plugins/rpmd/openmmapi/include/openmm/RpmdKernels.h
+85
-0
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
+86
-0
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
...ins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
+201
-0
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.h
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.h
+88
-0
No files found.
CMakeLists.txt
View file @
18a837c0
#---------------------------------------------------
# OpenMM
#
# Creates OpenMM library, base name=OpenMM.
# Default libraries are shared & optimized. Variants
# are created for static (_static) and debug (_d).
#
# Windows:
# OpenMM[_d].dll
# OpenMM[_d].lib
# OpenMM_static[_d].lib
# Unix:
# libOpenMM[_d].so
# libOpenMM_static[_d].a
#----------------------------------------------------
# Don't create a new project name if this is part of a mega-build from the
# parent directory
IF
(
NOT PROJECT_NAME
)
PROJECT
(
OpenMM
)
ENDIF
(
NOT PROJECT_NAME
)
CMAKE_MINIMUM_REQUIRED
(
VERSION 2.8
)
#SET(CMAKE_VERBOSE_MAKEFILE 1)
# CMake 2.4 on dart server only needs to know about Dart
INCLUDE
(
Dart
)
MARK_AS_ADVANCED
(
DART_ROOT
)
# Avoid dart server problem with cmake 2.4 --cmb
set
(
cmv
"
${
CMAKE_MAJOR_VERSION
}
.
${
CMAKE_MINOR_VERSION
}
"
)
IF
(
NOT cmv EQUAL
"2.4"
)
# This whole file...
# We have custom cmake modules for FindOpenMM and running python tests
SET
(
CMAKE_MODULE_PATH
${
CMAKE_MODULE_PATH
}
"
${
CMAKE_SOURCE_DIR
}
/cmake_modules"
)
# Older cmake versions do not have cmake_policy command
# Cmake 2.4.5, the default cmake on red hat linux, has the
# cmake_policy command, but it does not work
# "if(POLICY ..." does not work with cmake 2.4.[56] on red hat
# (cmake 2.4.7 is OK)
if
(
COMMAND cmake_policy
)
if
(
CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5
)
cmake_policy
(
SET CMP0003 NEW
)
cmake_policy
(
SET CMP0005 NEW
)
endif
(
CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5
)
if
(
CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2
)
cmake_policy
(
SET CMP0011 NEW
)
endif
(
CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2
)
endif
(
COMMAND cmake_policy
)
# Where to install
IF
(
${
CMAKE_C_COMPILER
}
MATCHES
"gcc"
)
IF
(
NOT OPENMM_INSTALL_PREFIX
)
SET
(
OPENMM_INSTALL_PREFIX
"/usr/local/openmm"
CACHE PATH
"Where to install OpenMM"
)
ENDIF
(
NOT OPENMM_INSTALL_PREFIX
)
ELSE
(
${
CMAKE_C_COMPILER
}
MATCHES
"gcc"
)
IF
(
NOT OPENMM_INSTALL_PREFIX
)
SET
(
OPENMM_INSTALL_PREFIX
"$ENV{ProgramFiles}/OpenMM"
CACHE PATH
"Where to install OpenMM"
)
ENDIF
(
NOT OPENMM_INSTALL_PREFIX
)
ENDIF
(
${
CMAKE_C_COMPILER
}
MATCHES
"gcc"
)
MARK_AS_ADVANCED
(
OPENMM_INSTALL_PREFIX
)
# It seems that on linux and mac, everything is trying to be installed in /usr/local/openmm
# But if every install target is prefixed with /openmm/, on Windows the install files
# end up in C:/Program Files/OpenMM/openmm/ which is ugly.
# Better to set CMAKE_INSTALL_PREFIX to /usr/local/openmm and leave /openmm/ off the
# install target names. Plus, the user now has the opportunity to install into /usr/local/
# if she so chooses. --cmb
IF
(
${
CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT
}
)
SET
(
CMAKE_INSTALL_PREFIX
${
OPENMM_INSTALL_PREFIX
}
CACHE PATH
"Where to install OpenMM"
FORCE
)
ENDIF
(
${
CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT
}
)
# 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 . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs platforms/reference libraries/validate
)
IF
(
WIN32
)
SET
(
OPENMM_SOURCE_SUBDIRS
${
OPENMM_SOURCE_SUBDIRS
}
libraries/pthreads
)
ADD_CUSTOM_TARGET
(
PthreadsLibraries ALL
)
FILE
(
GLOB PTHREADS_LIBRARIES libraries/pthreads/lib/*.dll libraries/pthreads/lib/*.lib
)
FOREACH
(
lib
${
PTHREADS_LIBRARIES
}
)
ADD_CUSTOM_COMMAND
(
TARGET PthreadsLibraries COMMAND
${
CMAKE_COMMAND
}
ARGS -E copy
${
lib
}
"
${
CMAKE_CURRENT_BINARY_DIR
}
/
${
CMAKE_CFG_INTDIR
}
"
)
INSTALL
(
FILES
${
lib
}
DESTINATION
"lib/"
)
ENDFOREACH
(
lib
)
LINK_DIRECTORIES
(
"
${
CMAKE_CURRENT_BINARY_DIR
}
/
${
CMAKE_CFG_INTDIR
}
"
)
SET
(
PTHREADS_LIB pthreadVC2
)
ELSE
(
WIN32
)
SET
(
PTHREADS_LIB pthread
)
ENDIF
(
WIN32
)
# The build system will set ARCH64 for 64 bit builds, which require
# use of the lib64/ library directories rather than lib/.
#SET( ARCH64 OFF CACHE BOOL "ON for 64bit builds, OFF for 32bit builds")
#MARK_AS_ADVANCED( ARCH64 )
#IF (ARCH64)
# SET(LIB64 64)
#ELSE (ARCH64)
# SET(LIB64) # nothing
#ENDIF (ARCH64)
IF
(
CMAKE_SIZEOF_VOID_P EQUAL 8
)
SET
(
LIB64 64
)
ELSE
(
CMAKE_SIZEOF_VOID_P EQUAL 8
)
SET
(
LIB64
)
ENDIF
(
CMAKE_SIZEOF_VOID_P EQUAL 8
)
# Build universal binaries compatible with OS X 10.5
IF
(
APPLE AND NOT CMAKE_OSX_DEPLOYMENT_TARGET
)
SET
(
CMAKE_OSX_ARCHITECTURES
"i386;x86_64"
CACHE STRING
"The processor architectures to build for"
FORCE
)
SET
(
CMAKE_OSX_DEPLOYMENT_TARGET
"10.5"
CACHE STRING
"The minimum version of OS X to support"
FORCE
)
SET
(
CMAKE_OSX_SYSROOT
"/Developer/SDKs/MacOSX10.5.sdk"
CACHE STRING
"The SDK to build against"
FORCE
)
ENDIF
(
APPLE AND NOT CMAKE_OSX_DEPLOYMENT_TARGET
)
IF
(
UNIX AND NOT CMAKE_BUILD_TYPE
)
SET
(
CMAKE_BUILD_TYPE Release CACHE STRING
"Debug or Release build"
FORCE
)
ENDIF
(
UNIX AND NOT CMAKE_BUILD_TYPE
)
IF
(
NOT CMAKE_CXX_FLAGS_DEBUG
)
SET
(
CMAKE_CXX_FLAGS_DEBUG
"-g"
CACHE STRING
"To use when CMAKE_BUILD_TYPE=Debug"
FORCE
)
ENDIF
(
NOT CMAKE_CXX_FLAGS_DEBUG
)
IF
(
NOT CMAKE_CXX_FLAGS_RELEASE
)
SET
(
CMAKE_CXX_FLAGS_RELEASE
"-O3 -DNDEBUG"
CACHE STRING
"To use when CMAKE_BUILD_TYPE=Release"
FORCE
)
ENDIF
(
NOT CMAKE_CXX_FLAGS_RELEASE
)
# 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_LIBRARY_NAME OpenMM
)
SET
(
OPENMM_MAJOR_VERSION 1
)
SET
(
OPENMM_MINOR_VERSION 0
)
SET
(
OPENMM_BUILD_VERSION 0
)
SET
(
OPENMM_COPYRIGHT_YEARS
"2008"
)
# underbar separated list of dotted authors, no spaces or commas
SET
(
OPENMM_AUTHORS
"Peter.Eastman"
)
# Get the subversion revision number if we can
# It's possible that WIN32 installs use svnversion through cygwin
# so we'll try for both svnversion.exe and svnversion. Note that
# this will result in warnings if all you have is Tortoise without
# Cygwin, and your "about" string will say "unknown" rather than
# providing the SVN version of the source.
FIND_PROGRAM
(
SVNVERSION_PROGRAM svnversion
PATHS
"C:/cygwin/bin"
)
IF
(
SVNVERSION_PROGRAM
)
EXEC_PROGRAM
(
${
SVNVERSION_PROGRAM
}
ARGS \"
${
CMAKE_CURRENT_SOURCE_DIR
}
\"
OUTPUT_VARIABLE OPENMM_SVN_REVISION
)
ELSE
(
SVNVERSION_PROGRAM
)
MESSAGE
(
STATUS
"Could not find 'svnversion' executable; 'about' will be wrong. (Cygwin provides one on Windows.)"
)
SET
(
OPENMM_SVN_REVISION unknown
)
ENDIF
(
SVNVERSION_PROGRAM
)
# Remove colon from build version, for easier placement in directory names
STRING
(
REPLACE
":"
"_"
OPENMM_SVN_REVISION
${
OPENMM_SVN_REVISION
}
)
SET
(
OPENMM_SVN_REVISION
"
${
OPENMM_SVN_REVISION
}
"
CACHE STRING
"subversion repository revision of OpenMM"
FORCE
)
ADD_DEFINITIONS
(
-DOPENMM_LIBRARY_NAME=
${
OPENMM_LIBRARY_NAME
}
-DOPENMM_MAJOR_VERSION=
${
OPENMM_MAJOR_VERSION
}
-DOPENMM_MINOR_VERSION=
${
OPENMM_MINOR_VERSION
}
-DOPENMM_BUILD_VERSION=
${
OPENMM_BUILD_VERSION
}
)
# CMake quotes automatically when building Visual Studio projects but we need
# to add them ourselves for Linux or Cygwin. Two cases to avoid duplicate quotes
# in Visual Studio which end up in the binary.
IF
(
${
CMAKE_GENERATOR
}
MATCHES
"Visual Studio"
)
SET
(
NEED_QUOTES FALSE
)
ELSE
(
${
CMAKE_GENERATOR
}
MATCHES
"Visual Studio"
)
SET
(
NEED_QUOTES TRUE
)
ENDIF
(
${
CMAKE_GENERATOR
}
MATCHES
"Visual Studio"
)
##TODO: doesn't work without quotes in nightly build
SET
(
NEED_QUOTES TRUE
)
IF
(
NEED_QUOTES
)
ADD_DEFINITIONS
(
-DOPENMM_SVN_REVISION=
"
${
OPENMM_SVN_REVISION
}
"
-DOPENMM_COPYRIGHT_YEARS=
"
${
OPENMM_COPYRIGHT_YEARS
}
"
-DOPENMM_AUTHORS=
"
${
OPENMM_AUTHORS
}
"
)
ELSE
(
NEED_QUOTES
)
ADD_DEFINITIONS
(
-DOPENMM_SVN_REVISION=
${
OPENMM_SVN_REVISION
}
-DOPENMM_COPYRIGHT_YEARS=
${
OPENMM_COPYRIGHT_YEARS
}
-DOPENMM_AUTHORS=
${
OPENMM_AUTHORS
}
)
ENDIF
(
NEED_QUOTES
)
# -DOPENMM_TYPE has to be defined in the target subdirectories.
# -Dsimbody_EXPORTS defined automatically when Windows DLL build is being done.
# Report the version number to the CMake UI
SET
(
OPENMM_VERSION
"
${
OPENMM_MAJOR_VERSION
}
.
${
OPENMM_MINOR_VERSION
}
.
${
OPENMM_BUILD_VERSION
}
"
CACHE STRING
"This is the version of OpenMM which will be built."
FORCE
)
# We don't actually use this version for anything yet
MARK_AS_ADVANCED
(
OPENMM_VERSION
)
SET
(
SHARED_TARGET
${
OPENMM_LIBRARY_NAME
}
)
SET
(
STATIC_TARGET
${
OPENMM_LIBRARY_NAME
}
_static
)
## If no one says otherwise, change the executable path to drop into the same binary
## location as the DLLs so that the test cases will use the just-build DLLs.
IF
(
NOT EXECUTABLE_OUTPUT_PATH
)
SET
(
EXECUTABLE_OUTPUT_PATH
${
PROJECT_BINARY_DIR
}
CACHE INTERNAL
"Single output directory for building all executables."
)
ENDIF
(
NOT EXECUTABLE_OUTPUT_PATH
)
IF
(
NOT LIBRARY_OUTPUT_PATH
)
SET
(
LIBRARY_OUTPUT_PATH
${
PROJECT_BINARY_DIR
}
CACHE INTERNAL
"Single output directory for building all libraries."
)
ENDIF
(
NOT LIBRARY_OUTPUT_PATH
)
SET
(
${
PROJECT_NAME
}
_EXECUTABLE_DIR
${
EXECUTABLE_OUTPUT_PATH
}
/
${
CMAKE_CFG_INTDIR
}
)
SET
(
${
PROJECT_NAME
}
_LIBRARY_DIR
${
LIBRARY_OUTPUT_PATH
}
/
${
CMAKE_CFG_INTDIR
}
)
# 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
)
# used by plugin
SET
(
OPENMM_DIR
${
CMAKE_CURRENT_SOURCE_DIR
}
)
# 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/openmm
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/include/openmm/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 src_files
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/src/*.cpp
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/src/*/*.cpp
)
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
}
)
## Make sure we find these locally before looking in OpenMM/include if
## OpenMM was previously installed there.
INCLUDE_DIRECTORIES
(
BEFORE
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/include
)
ENDFOREACH
(
subdir
)
# If API wrappers are being generated, and add them to the build.
# Java and gccxml are required for API wrappers
FIND_PACKAGE
(
Java
)
MARK_AS_ADVANCED
(
CLEAR JAVA_RUNTIME
)
# One particular location to try first for nightly builds
FIND_PROGRAM
(
GCCXML_PATH gccxml PATH
"C:/Program Files/gccxml_sherm/bin"
)
# In case first attempt fails
FIND_PROGRAM
(
GCCXML_PATH gccxml PATH
/usr/local/bin
"C:/Program Files/gccxml 0.9/bin"
)
IF
(
GCCXML_PATH AND JAVA_RUNTIME AND NOT cmv EQUAL
"2.4"
)
SET
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS ON CACHE BOOL
"Build wrappers for C and Fortran"
)
ELSE
(
GCCXML_PATH AND JAVA_RUNTIME AND NOT cmv EQUAL
"2.4"
)
SET
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS OFF CACHE BOOL
"Build wrappers for C and Fortran"
)
ENDIF
(
GCCXML_PATH AND JAVA_RUNTIME AND NOT cmv EQUAL
"2.4"
)
IF
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS
)
ADD_SUBDIRECTORY
(
wrappers
)
SET
(
SOURCE_FILES
${
SOURCE_FILES
}
wrappers/OpenMMCWrapper.cpp wrappers/OpenMMFortranWrapper.cpp
)
SET_SOURCE_FILES_PROPERTIES
(
wrappers/OpenMMCWrapper.cpp wrappers/OpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE
)
ENDIF
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS
)
INCLUDE_DIRECTORIES
(
BEFORE
${
CMAKE_CURRENT_SOURCE_DIR
}
/src
)
ADD_LIBRARY
(
${
SHARED_TARGET
}
SHARED
${
SOURCE_FILES
}
${
SOURCE_INCLUDE_FILES
}
${
API_ABS_INCLUDE_FILES
}
)
SET_TARGET_PROPERTIES
(
${
SHARED_TARGET
}
PROPERTIES COMPILE_FLAGS
"-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY"
)
SET
(
OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL
"Whether to build static OpenMM libraries"
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
ADD_LIBRARY
(
${
STATIC_TARGET
}
STATIC
${
SOURCE_FILES
}
${
SOURCE_INCLUDE_FILES
}
${
API_ABS_INCLUDE_FILES
}
)
SET_TARGET_PROPERTIES
(
${
STATIC_TARGET
}
PROPERTIES COMPILE_FLAGS
"-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY"
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
IF
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS
)
ADD_DEPENDENCIES
(
${
SHARED_TARGET
}
ApiWrappers
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
ADD_DEPENDENCIES
(
${
STATIC_TARGET
}
ApiWrappers
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
ENDIF
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS
)
# On Linux need to link to libdl
FIND_LIBRARY
(
DL_LIBRARY dl
)
IF
(
DL_LIBRARY
)
TARGET_LINK_LIBRARIES
(
${
SHARED_TARGET
}
${
DL_LIBRARY
}
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
TARGET_LINK_LIBRARIES
(
${
STATIC_TARGET
}
${
DL_LIBRARY
}
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
ENDIF
(
DL_LIBRARY
)
IF
(
WIN32
)
MARK_AS_ADVANCED
(
DL_LIBRARY
)
ENDIF
(
WIN32
)
ADD_SUBDIRECTORY
(
platforms/reference/tests
)
# Which hardware platforms to build
# A bit of tedium because we are using custom FindCUDA files that happen to work...
SET
(
FINDCUDA_DIR
"
${
CMAKE_CURRENT_SOURCE_DIR
}
/cmake_modules/FindCUDA"
)
SET
(
CUDA_BUILD_CUBIN OFF
)
FIND_PACKAGE
(
CUDA QUIET
)
IF
(
CUDA_FOUND
)
IF
(
NOT CUDA_NVCC_FLAGS
)
SET
(
FLAGS
""
)
# Note that cmake will insert semicolons between these item automatically...
SET
(
FLAGS
${
FLAGS
}
-gencode arch=compute_11,code=sm_11
)
SET
(
FLAGS
${
FLAGS
}
-gencode arch=compute_12,code=sm_12
)
SET
(
FLAGS
${
FLAGS
}
-gencode arch=compute_13,code=sm_13
)
SET
(
FLAGS
${
FLAGS
}
-gencode arch=compute_20,code=sm_20
)
SET
(
FLAGS
${
FLAGS
}
-use_fast_math
)
IF
(
MSVC
)
# Unfortunately the variables CUDA_NVCC_FLAGS_RELEASE and CUDA_NVCC_FLAGS_DEBUG
# appear to be unused, at least in CMake 2.6
# Release /MD linkage
set
(
FLAGS
${
FLAGS
}
"-Xcompiler
\"
/MD
\"
-DOPENMMCUDA_BUILDING_SHARED_LIBRARY"
)
ENDIF
(
MSVC
)
SET
(
CUDA_NVCC_FLAGS
"
${
FLAGS
}
"
CACHE STRING
"Semicolon delimit multiple arguments"
)
ENDIF
(
NOT CUDA_NVCC_FLAGS
)
SET
(
OPENMM_BUILD_CUDA_LIB ON CACHE BOOL
"Build OpenMMCuda library for Nvidia GPUs"
)
# I wish I was not hardcoding /MD here
# Avoid strange windows link error with cuda free energy
# plugin by specifying /MD to CUDA_NVCC_FLAGS
MARK_AS_ADVANCED
(
CLEAR CUDA_NVCC_FLAGS
)
IF
(
MSVC
)
# Unfortunately the variables CUDA_NVCC_FLAGS_RELEASE and CUDA_NVCC_FLAGS_DEBUG
# appear to be unused, at least in CMake 2.6
# Release /MD linkage
SET
(
HAS_NVCC_FLAG FALSE
)
IF
(
CUDA_NVCC_FLAGS MATCHES
"-Xcompiler"
)
SET
(
HAS_NVCC_FLAG TRUE
)
ENDIF
(
CUDA_NVCC_FLAGS MATCHES
"-Xcompiler"
)
IF
(
NOT HAS_NVCC_FLAG
)
set
(
new_flags
"-Xcompiler
\"
/MD
\"
-DOPENMMCUDA_BUILDING_SHARED_LIBRARY"
)
if
(
CUDA_NVCC_FLAGS
)
set
(
new_flags
"
${
CUDA_NVCC_FLAGS
}
;
${
new_flags
}
"
)
endif
(
CUDA_NVCC_FLAGS
)
SET
(
CUDA_NVCC_FLAGS
"
${
new_flags
}
"
CACHE STRING
"Semicolon delimit multiple arguments"
FORCE
)
ENDIF
(
NOT HAS_NVCC_FLAG
)
ENDIF
(
MSVC
)
ELSE
(
CUDA_FOUND
)
SET
(
OPENMM_BUILD_CUDA_LIB OFF CACHE BOOL
"Build OpenMMCuda library for Nvidia GPUs"
)
ENDIF
(
CUDA_FOUND
)
IF
(
OPENMM_BUILD_CUDA_LIB
)
ADD_SUBDIRECTORY
(
platforms/cuda
)
ENDIF
(
OPENMM_BUILD_CUDA_LIB
)
MARK_AS_ADVANCED
(
CUDA_VERBOSE_BUILD
)
MARK_AS_ADVANCED
(
CUDA_BUILD_CUBIN
)
MARK_AS_ADVANCED
(
CUDA_BUILD_EMULATION
)
FIND_PACKAGE
(
OpenCL QUIET
)
# Plus the tesla/linux is taking too long on the tests
IF
(
OPENCL_FOUND
)
SET
(
OPENMM_BUILD_OPENCL_LIB ON CACHE BOOL
"Build OpenMMOpenCL library"
)
ELSE
(
OPENCL_FOUND
)
SET
(
OPENMM_BUILD_OPENCL_LIB OFF CACHE BOOL
"Build OpenMMOpenCL library"
)
ENDIF
(
OPENCL_FOUND
)
IF
(
OPENMM_BUILD_OPENCL_LIB
)
ADD_SUBDIRECTORY
(
platforms/opencl
)
ENDIF
(
OPENMM_BUILD_OPENCL_LIB
)
# FreeEnergy plugin
SET
(
OPENMM_BUILD_FREE_ENERGY_PLUGIN ON CACHE BOOL
"Build FreeEnergy plugin"
)
SET
(
OPENMM_BUILD_FREE_ENERGY_PATH
)
IF
(
OPENMM_BUILD_FREE_ENERGY_PLUGIN
)
SET
(
OPENMM_BUILD_FREE_ENERGY_PATH
${
CMAKE_CURRENT_SOURCE_DIR
}
/plugins/freeEnergy
)
# ADD_DEFINITIONS(-DINCLUDE_FREE_ENERGY_PLUGIN)
ADD_SUBDIRECTORY
(
plugins/freeEnergy
)
ENDIF
(
OPENMM_BUILD_FREE_ENERGY_PLUGIN
)
# Amoeba plugin
SET
(
OPENMM_BUILD_AMOEBA_PLUGIN ON CACHE BOOL
"Build Amoeba plugin"
)
SET
(
OPENMM_BUILD_AMOEBA_PATH
)
IF
(
OPENMM_BUILD_AMOEBA_PLUGIN
)
SET
(
OPENMM_BUILD_AMOEBA_PATH
${
CMAKE_CURRENT_SOURCE_DIR
}
/plugins/amoeba
)
ADD_SUBDIRECTORY
(
plugins/amoeba
)
ENDIF
(
OPENMM_BUILD_AMOEBA_PLUGIN
)
INSTALL_TARGETS
(
/lib RUNTIME_DIRECTORY /lib
${
SHARED_TARGET
}
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
INSTALL_TARGETS
(
/lib RUNTIME_DIRECTORY /lib
${
STATIC_TARGET
}
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
FILE
(
GLOB CORE_HEADERS include/*.h */include/*.h
)
FILE
(
GLOB TOP_HEADERS include/openmm/*.h */include/openmm/*.h
)
FILE
(
GLOB INTERNAL_HEADERS include/openmm/internal/*.h */include/openmm/internal/*.h
)
INSTALL_FILES
(
/include FILES
${
CORE_HEADERS
}
)
INSTALL_FILES
(
/include/openmm FILES
${
TOP_HEADERS
}
)
INSTALL_FILES
(
/include/openmm/internal FILES
${
INTERNAL_HEADERS
}
)
# Serialization support
SET
(
OPENMM_BUILD_SERIALIZATION_SUPPORT ON CACHE BOOL
"Whether to build the serialization support library"
)
IF
(
OPENMM_BUILD_SERIALIZATION_SUPPORT
)
ADD_SUBDIRECTORY
(
serialization
)
ENDIF
(
OPENMM_BUILD_SERIALIZATION_SUPPORT
)
# Python wrappers
SET
(
OPENMM_BUILD_PYTHON_WRAPPERS OFF CACHE BOOL
"Build wrappers for Python"
)
IF
(
OPENMM_BUILD_PYTHON_WRAPPERS
)
IF
(
NOT OPENMM_BUILD_SERIALIZATION_SUPPORT
)
MESSAGE
(
SEND_ERROR
"The Python wrappers require that serialization support be built."
)
ENDIF
(
NOT OPENMM_BUILD_SERIALIZATION_SUPPORT
)
IF
(
NOT OPENMM_BUILD_FREE_ENERGY_PLUGIN
)
MESSAGE
(
SEND_ERROR
"The Python wrappers require that the free energy plugin be built."
)
ENDIF
(
NOT OPENMM_BUILD_FREE_ENERGY_PLUGIN
)
IF
(
NOT OPENMM_BUILD_AMOEBA_PLUGIN
)
MESSAGE
(
SEND_ERROR
"The Python wrappers require that the AMOEBA plugin be built."
)
ENDIF
(
NOT OPENMM_BUILD_AMOEBA_PLUGIN
)
ADD_SUBDIRECTORY
(
wrappers/python
)
ENDIF
(
OPENMM_BUILD_PYTHON_WRAPPERS
)
#
# Allow automated build and dashboard.
#
# redundant INCLUDE(Dart) statement
# 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
#
ENABLE_TESTING
()
IF
(
EXECUTABLE_OUTPUT_PATH
)
SET
(
TEST_PATH
${
EXECUTABLE_OUTPUT_PATH
}
)
ELSE
(
EXECUTABLE_OUTPUT_PATH
)
SET
(
TEST_PATH .
)
ENDIF
(
EXECUTABLE_OUTPUT_PATH
)
# Build and install documentation
find_package
(
Doxygen QUIET
)
mark_as_advanced
(
CLEAR DOXYGEN_EXECUTABLE
)
IF
(
DOXYGEN_EXECUTABLE
)
SET
(
DOXY_CONFIG
"
${
CMAKE_CURRENT_BINARY_DIR
}
/Doxyfile"
)
CONFIGURE_FILE
(
${
CMAKE_CURRENT_SOURCE_DIR
}
/docs/Doxyfile.in
${
DOXY_CONFIG
}
@ONLY
)
FILE
(
GLOB_RECURSE OPENMM_INCLUDES
"openmm/include/*.h"
)
FILE
(
GLOB_RECURSE OLLA_INCLUDES
"olla/include/*.h"
)
ADD_CUSTOM_COMMAND
(
OUTPUT
"
${
CMAKE_CURRENT_BINARY_DIR
}
/html/index.html"
COMMAND
${
DOXYGEN_EXECUTABLE
}
${
DOXY_CONFIG
}
DEPENDS
${
OPENMM_INCLUDES
}
${
OLLA_INCLUDES
}
WORKING_DIRECTORY
"
${
CMAKE_CURRENT_BINARY_DIR
}
"
COMMENT
"Generating API documentation using Doxygen"
)
ADD_CUSTOM_TARGET
(
DoxygenApiDocs
DEPENDS
"
${
CMAKE_CURRENT_BINARY_DIR
}
/html/index.html"
COMMENT
"Generating API documentation using Doxygen"
SOURCES
"
${
CMAKE_CURRENT_SOURCE_DIR
}
/docs/Doxyfile.in"
${
OPENMM_INCLUDES
}
${
OLLA_INCLUDES
}
)
FILE
(
MAKE_DIRECTORY
"
${
PROJECT_BINARY_DIR
}
/html/"
)
INSTALL
(
DIRECTORY
"
${
PROJECT_BINARY_DIR
}
/html/"
DESTINATION
"docs/api/"
)
INSTALL
(
FILES
"docs/API Reference.html"
DESTINATION
"docs/"
)
set
(
OPENMM_GENERATE_API_DOCS OFF CACHE BOOL
"Whether to create API documentation using Doxygen"
)
if
(
OPENMM_GENERATE_API_DOCS
)
ADD_CUSTOM_TARGET
(
GenerateDoxygenApiDocs ALL
DEPENDS
"
${
CMAKE_CURRENT_BINARY_DIR
}
/html/index.html"
COMMENT
"Generating API documentation using Doxygen"
SOURCES
"
${
CMAKE_CURRENT_SOURCE_DIR
}
/docs/Doxyfile.in"
${
OPENMM_INCLUDES
}
${
OLLA_INCLUDES
}
)
endif
(
OPENMM_GENERATE_API_DOCS
)
ENDIF
(
DOXYGEN_EXECUTABLE
)
install
(
FILES docs/UsersGuide/OpenMMUsersGuide.pdf
DESTINATION docs/
)
FILE
(
GLOB LICENSE_FILES
"docs/licenses/*.txt"
)
install
(
FILES
${
LICENSE_FILES
}
DESTINATION licenses/
)
ADD_SUBDIRECTORY
(
tests
)
ADD_SUBDIRECTORY
(
examples
)
ENDIF
(
NOT cmv EQUAL
"2.4"
)
# This whole file...
#---------------------------------------------------
# OpenMM
#
# Creates OpenMM library, base name=OpenMM.
# Default libraries are shared & optimized. Variants
# are created for static (_static) and debug (_d).
#
# Windows:
# OpenMM[_d].dll
# OpenMM[_d].lib
# OpenMM_static[_d].lib
# Unix:
# libOpenMM[_d].so
# libOpenMM_static[_d].a
#----------------------------------------------------
# Don't create a new project name if this is part of a mega-build from the
# parent directory
IF
(
NOT PROJECT_NAME
)
PROJECT
(
OpenMM
)
ENDIF
(
NOT PROJECT_NAME
)
CMAKE_MINIMUM_REQUIRED
(
VERSION 2.8
)
#SET(CMAKE_VERBOSE_MAKEFILE 1)
# CMake 2.4 on dart server only needs to know about Dart
INCLUDE
(
Dart
)
MARK_AS_ADVANCED
(
DART_ROOT
)
# Avoid dart server problem with cmake 2.4 --cmb
set
(
cmv
"
${
CMAKE_MAJOR_VERSION
}
.
${
CMAKE_MINOR_VERSION
}
"
)
IF
(
NOT cmv EQUAL
"2.4"
)
# This whole file...
# We have custom cmake modules for FindOpenMM and running python tests
SET
(
CMAKE_MODULE_PATH
${
CMAKE_MODULE_PATH
}
"
${
CMAKE_SOURCE_DIR
}
/cmake_modules"
)
# Older cmake versions do not have cmake_policy command
# Cmake 2.4.5, the default cmake on red hat linux, has the
# cmake_policy command, but it does not work
# "if(POLICY ..." does not work with cmake 2.4.[56] on red hat
# (cmake 2.4.7 is OK)
if
(
COMMAND cmake_policy
)
if
(
CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5
)
cmake_policy
(
SET CMP0003 NEW
)
cmake_policy
(
SET CMP0005 NEW
)
endif
(
CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5
)
if
(
CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2
)
cmake_policy
(
SET CMP0011 NEW
)
endif
(
CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2
)
endif
(
COMMAND cmake_policy
)
# Where to install
IF
(
${
CMAKE_C_COMPILER
}
MATCHES
"gcc"
)
IF
(
NOT OPENMM_INSTALL_PREFIX
)
SET
(
OPENMM_INSTALL_PREFIX
"/usr/local/openmm"
CACHE PATH
"Where to install OpenMM"
)
ENDIF
(
NOT OPENMM_INSTALL_PREFIX
)
ELSE
(
${
CMAKE_C_COMPILER
}
MATCHES
"gcc"
)
IF
(
NOT OPENMM_INSTALL_PREFIX
)
SET
(
OPENMM_INSTALL_PREFIX
"$ENV{ProgramFiles}/OpenMM"
CACHE PATH
"Where to install OpenMM"
)
ENDIF
(
NOT OPENMM_INSTALL_PREFIX
)
ENDIF
(
${
CMAKE_C_COMPILER
}
MATCHES
"gcc"
)
MARK_AS_ADVANCED
(
OPENMM_INSTALL_PREFIX
)
# It seems that on linux and mac, everything is trying to be installed in /usr/local/openmm
# But if every install target is prefixed with /openmm/, on Windows the install files
# end up in C:/Program Files/OpenMM/openmm/ which is ugly.
# Better to set CMAKE_INSTALL_PREFIX to /usr/local/openmm and leave /openmm/ off the
# install target names. Plus, the user now has the opportunity to install into /usr/local/
# if she so chooses. --cmb
IF
(
${
CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT
}
)
SET
(
CMAKE_INSTALL_PREFIX
${
OPENMM_INSTALL_PREFIX
}
CACHE PATH
"Where to install OpenMM"
FORCE
)
ENDIF
(
${
CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT
}
)
# 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 . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs platforms/reference libraries/validate
)
IF
(
WIN32
)
SET
(
OPENMM_SOURCE_SUBDIRS
${
OPENMM_SOURCE_SUBDIRS
}
libraries/pthreads
)
ADD_CUSTOM_TARGET
(
PthreadsLibraries ALL
)
FILE
(
GLOB PTHREADS_LIBRARIES libraries/pthreads/lib/*.dll libraries/pthreads/lib/*.lib
)
FOREACH
(
lib
${
PTHREADS_LIBRARIES
}
)
ADD_CUSTOM_COMMAND
(
TARGET PthreadsLibraries COMMAND
${
CMAKE_COMMAND
}
ARGS -E copy
${
lib
}
"
${
CMAKE_CURRENT_BINARY_DIR
}
/
${
CMAKE_CFG_INTDIR
}
"
)
INSTALL
(
FILES
${
lib
}
DESTINATION
"lib/"
)
ENDFOREACH
(
lib
)
LINK_DIRECTORIES
(
"
${
CMAKE_CURRENT_BINARY_DIR
}
/
${
CMAKE_CFG_INTDIR
}
"
)
SET
(
PTHREADS_LIB pthreadVC2
)
ELSE
(
WIN32
)
SET
(
PTHREADS_LIB pthread
)
ENDIF
(
WIN32
)
# The build system will set ARCH64 for 64 bit builds, which require
# use of the lib64/ library directories rather than lib/.
#SET( ARCH64 OFF CACHE BOOL "ON for 64bit builds, OFF for 32bit builds")
#MARK_AS_ADVANCED( ARCH64 )
#IF (ARCH64)
# SET(LIB64 64)
#ELSE (ARCH64)
# SET(LIB64) # nothing
#ENDIF (ARCH64)
IF
(
CMAKE_SIZEOF_VOID_P EQUAL 8
)
SET
(
LIB64 64
)
ELSE
(
CMAKE_SIZEOF_VOID_P EQUAL 8
)
SET
(
LIB64
)
ENDIF
(
CMAKE_SIZEOF_VOID_P EQUAL 8
)
# Build universal binaries compatible with OS X 10.5
IF
(
APPLE AND NOT CMAKE_OSX_DEPLOYMENT_TARGET
)
SET
(
CMAKE_OSX_ARCHITECTURES
"i386;x86_64"
CACHE STRING
"The processor architectures to build for"
FORCE
)
SET
(
CMAKE_OSX_DEPLOYMENT_TARGET
"10.5"
CACHE STRING
"The minimum version of OS X to support"
FORCE
)
SET
(
CMAKE_OSX_SYSROOT
"/Developer/SDKs/MacOSX10.5.sdk"
CACHE STRING
"The SDK to build against"
FORCE
)
ENDIF
(
APPLE AND NOT CMAKE_OSX_DEPLOYMENT_TARGET
)
IF
(
UNIX AND NOT CMAKE_BUILD_TYPE
)
SET
(
CMAKE_BUILD_TYPE Release CACHE STRING
"Debug or Release build"
FORCE
)
ENDIF
(
UNIX AND NOT CMAKE_BUILD_TYPE
)
IF
(
NOT CMAKE_CXX_FLAGS_DEBUG
)
SET
(
CMAKE_CXX_FLAGS_DEBUG
"-g"
CACHE STRING
"To use when CMAKE_BUILD_TYPE=Debug"
FORCE
)
ENDIF
(
NOT CMAKE_CXX_FLAGS_DEBUG
)
IF
(
NOT CMAKE_CXX_FLAGS_RELEASE
)
SET
(
CMAKE_CXX_FLAGS_RELEASE
"-O3 -DNDEBUG"
CACHE STRING
"To use when CMAKE_BUILD_TYPE=Release"
FORCE
)
ENDIF
(
NOT CMAKE_CXX_FLAGS_RELEASE
)
# 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_LIBRARY_NAME OpenMM
)
SET
(
OPENMM_MAJOR_VERSION 1
)
SET
(
OPENMM_MINOR_VERSION 0
)
SET
(
OPENMM_BUILD_VERSION 0
)
SET
(
OPENMM_COPYRIGHT_YEARS
"2008"
)
# underbar separated list of dotted authors, no spaces or commas
SET
(
OPENMM_AUTHORS
"Peter.Eastman"
)
# Get the subversion revision number if we can
# It's possible that WIN32 installs use svnversion through cygwin
# so we'll try for both svnversion.exe and svnversion. Note that
# this will result in warnings if all you have is Tortoise without
# Cygwin, and your "about" string will say "unknown" rather than
# providing the SVN version of the source.
FIND_PROGRAM
(
SVNVERSION_PROGRAM svnversion
PATHS
"C:/cygwin/bin"
)
IF
(
SVNVERSION_PROGRAM
)
EXEC_PROGRAM
(
${
SVNVERSION_PROGRAM
}
ARGS \"
${
CMAKE_CURRENT_SOURCE_DIR
}
\"
OUTPUT_VARIABLE OPENMM_SVN_REVISION
)
ELSE
(
SVNVERSION_PROGRAM
)
MESSAGE
(
STATUS
"Could not find 'svnversion' executable; 'about' will be wrong. (Cygwin provides one on Windows.)"
)
SET
(
OPENMM_SVN_REVISION unknown
)
ENDIF
(
SVNVERSION_PROGRAM
)
# Remove colon from build version, for easier placement in directory names
STRING
(
REPLACE
":"
"_"
OPENMM_SVN_REVISION
${
OPENMM_SVN_REVISION
}
)
SET
(
OPENMM_SVN_REVISION
"
${
OPENMM_SVN_REVISION
}
"
CACHE STRING
"subversion repository revision of OpenMM"
FORCE
)
ADD_DEFINITIONS
(
-DOPENMM_LIBRARY_NAME=
${
OPENMM_LIBRARY_NAME
}
-DOPENMM_MAJOR_VERSION=
${
OPENMM_MAJOR_VERSION
}
-DOPENMM_MINOR_VERSION=
${
OPENMM_MINOR_VERSION
}
-DOPENMM_BUILD_VERSION=
${
OPENMM_BUILD_VERSION
}
)
# CMake quotes automatically when building Visual Studio projects but we need
# to add them ourselves for Linux or Cygwin. Two cases to avoid duplicate quotes
# in Visual Studio which end up in the binary.
IF
(
${
CMAKE_GENERATOR
}
MATCHES
"Visual Studio"
)
SET
(
NEED_QUOTES FALSE
)
ELSE
(
${
CMAKE_GENERATOR
}
MATCHES
"Visual Studio"
)
SET
(
NEED_QUOTES TRUE
)
ENDIF
(
${
CMAKE_GENERATOR
}
MATCHES
"Visual Studio"
)
##TODO: doesn't work without quotes in nightly build
SET
(
NEED_QUOTES TRUE
)
IF
(
NEED_QUOTES
)
ADD_DEFINITIONS
(
-DOPENMM_SVN_REVISION=
"
${
OPENMM_SVN_REVISION
}
"
-DOPENMM_COPYRIGHT_YEARS=
"
${
OPENMM_COPYRIGHT_YEARS
}
"
-DOPENMM_AUTHORS=
"
${
OPENMM_AUTHORS
}
"
)
ELSE
(
NEED_QUOTES
)
ADD_DEFINITIONS
(
-DOPENMM_SVN_REVISION=
${
OPENMM_SVN_REVISION
}
-DOPENMM_COPYRIGHT_YEARS=
${
OPENMM_COPYRIGHT_YEARS
}
-DOPENMM_AUTHORS=
${
OPENMM_AUTHORS
}
)
ENDIF
(
NEED_QUOTES
)
# -DOPENMM_TYPE has to be defined in the target subdirectories.
# -Dsimbody_EXPORTS defined automatically when Windows DLL build is being done.
# Report the version number to the CMake UI
SET
(
OPENMM_VERSION
"
${
OPENMM_MAJOR_VERSION
}
.
${
OPENMM_MINOR_VERSION
}
.
${
OPENMM_BUILD_VERSION
}
"
CACHE STRING
"This is the version of OpenMM which will be built."
FORCE
)
# We don't actually use this version for anything yet
MARK_AS_ADVANCED
(
OPENMM_VERSION
)
SET
(
SHARED_TARGET
${
OPENMM_LIBRARY_NAME
}
)
SET
(
STATIC_TARGET
${
OPENMM_LIBRARY_NAME
}
_static
)
## If no one says otherwise, change the executable path to drop into the same binary
## location as the DLLs so that the test cases will use the just-build DLLs.
IF
(
NOT EXECUTABLE_OUTPUT_PATH
)
SET
(
EXECUTABLE_OUTPUT_PATH
${
PROJECT_BINARY_DIR
}
CACHE INTERNAL
"Single output directory for building all executables."
)
ENDIF
(
NOT EXECUTABLE_OUTPUT_PATH
)
IF
(
NOT LIBRARY_OUTPUT_PATH
)
SET
(
LIBRARY_OUTPUT_PATH
${
PROJECT_BINARY_DIR
}
CACHE INTERNAL
"Single output directory for building all libraries."
)
ENDIF
(
NOT LIBRARY_OUTPUT_PATH
)
SET
(
${
PROJECT_NAME
}
_EXECUTABLE_DIR
${
EXECUTABLE_OUTPUT_PATH
}
/
${
CMAKE_CFG_INTDIR
}
)
SET
(
${
PROJECT_NAME
}
_LIBRARY_DIR
${
LIBRARY_OUTPUT_PATH
}
/
${
CMAKE_CFG_INTDIR
}
)
# 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
)
# used by plugin
SET
(
OPENMM_DIR
${
CMAKE_CURRENT_SOURCE_DIR
}
)
# 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/openmm
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/include/openmm/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 src_files
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/src/*.cpp
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/src/*/*.cpp
)
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
}
)
## Make sure we find these locally before looking in OpenMM/include if
## OpenMM was previously installed there.
INCLUDE_DIRECTORIES
(
BEFORE
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/include
)
ENDFOREACH
(
subdir
)
# If API wrappers are being generated, and add them to the build.
# Java and gccxml are required for API wrappers
FIND_PACKAGE
(
Java
)
MARK_AS_ADVANCED
(
CLEAR JAVA_RUNTIME
)
# One particular location to try first for nightly builds
FIND_PROGRAM
(
GCCXML_PATH gccxml PATH
"C:/Program Files/gccxml_sherm/bin"
)
# In case first attempt fails
FIND_PROGRAM
(
GCCXML_PATH gccxml PATH
/usr/local/bin
"C:/Program Files/gccxml 0.9/bin"
)
IF
(
GCCXML_PATH AND JAVA_RUNTIME AND NOT cmv EQUAL
"2.4"
)
SET
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS ON CACHE BOOL
"Build wrappers for C and Fortran"
)
ELSE
(
GCCXML_PATH AND JAVA_RUNTIME AND NOT cmv EQUAL
"2.4"
)
SET
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS OFF CACHE BOOL
"Build wrappers for C and Fortran"
)
ENDIF
(
GCCXML_PATH AND JAVA_RUNTIME AND NOT cmv EQUAL
"2.4"
)
IF
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS
)
ADD_SUBDIRECTORY
(
wrappers
)
SET
(
SOURCE_FILES
${
SOURCE_FILES
}
wrappers/OpenMMCWrapper.cpp wrappers/OpenMMFortranWrapper.cpp
)
SET_SOURCE_FILES_PROPERTIES
(
wrappers/OpenMMCWrapper.cpp wrappers/OpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE
)
ENDIF
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS
)
INCLUDE_DIRECTORIES
(
BEFORE
${
CMAKE_CURRENT_SOURCE_DIR
}
/src
)
ADD_LIBRARY
(
${
SHARED_TARGET
}
SHARED
${
SOURCE_FILES
}
${
SOURCE_INCLUDE_FILES
}
${
API_ABS_INCLUDE_FILES
}
)
SET_TARGET_PROPERTIES
(
${
SHARED_TARGET
}
PROPERTIES COMPILE_FLAGS
"-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY"
)
SET
(
OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL
"Whether to build static OpenMM libraries"
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
ADD_LIBRARY
(
${
STATIC_TARGET
}
STATIC
${
SOURCE_FILES
}
${
SOURCE_INCLUDE_FILES
}
${
API_ABS_INCLUDE_FILES
}
)
SET_TARGET_PROPERTIES
(
${
STATIC_TARGET
}
PROPERTIES COMPILE_FLAGS
"-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY"
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
IF
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS
)
ADD_DEPENDENCIES
(
${
SHARED_TARGET
}
ApiWrappers
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
ADD_DEPENDENCIES
(
${
STATIC_TARGET
}
ApiWrappers
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
ENDIF
(
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS
)
# On Linux need to link to libdl
FIND_LIBRARY
(
DL_LIBRARY dl
)
IF
(
DL_LIBRARY
)
TARGET_LINK_LIBRARIES
(
${
SHARED_TARGET
}
${
DL_LIBRARY
}
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
TARGET_LINK_LIBRARIES
(
${
STATIC_TARGET
}
${
DL_LIBRARY
}
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
ENDIF
(
DL_LIBRARY
)
IF
(
WIN32
)
MARK_AS_ADVANCED
(
DL_LIBRARY
)
ENDIF
(
WIN32
)
ADD_SUBDIRECTORY
(
platforms/reference/tests
)
# Which hardware platforms to build
# A bit of tedium because we are using custom FindCUDA files that happen to work...
SET
(
FINDCUDA_DIR
"
${
CMAKE_CURRENT_SOURCE_DIR
}
/cmake_modules/FindCUDA"
)
SET
(
CUDA_BUILD_CUBIN OFF
)
FIND_PACKAGE
(
CUDA QUIET
)
IF
(
CUDA_FOUND
)
IF
(
NOT CUDA_NVCC_FLAGS
)
SET
(
FLAGS
""
)
# Note that cmake will insert semicolons between these item automatically...
SET
(
FLAGS
${
FLAGS
}
-gencode arch=compute_11,code=sm_11
)
SET
(
FLAGS
${
FLAGS
}
-gencode arch=compute_12,code=sm_12
)
SET
(
FLAGS
${
FLAGS
}
-gencode arch=compute_13,code=sm_13
)
SET
(
FLAGS
${
FLAGS
}
-gencode arch=compute_20,code=sm_20
)
SET
(
FLAGS
${
FLAGS
}
-use_fast_math
)
IF
(
MSVC
)
# Unfortunately the variables CUDA_NVCC_FLAGS_RELEASE and CUDA_NVCC_FLAGS_DEBUG
# appear to be unused, at least in CMake 2.6
# Release /MD linkage
set
(
FLAGS
${
FLAGS
}
"-Xcompiler
\"
/MD
\"
-DOPENMMCUDA_BUILDING_SHARED_LIBRARY"
)
ENDIF
(
MSVC
)
SET
(
CUDA_NVCC_FLAGS
"
${
FLAGS
}
"
CACHE STRING
"Semicolon delimit multiple arguments"
)
ENDIF
(
NOT CUDA_NVCC_FLAGS
)
SET
(
OPENMM_BUILD_CUDA_LIB ON CACHE BOOL
"Build OpenMMCuda library for Nvidia GPUs"
)
# I wish I was not hardcoding /MD here
# Avoid strange windows link error with cuda free energy
# plugin by specifying /MD to CUDA_NVCC_FLAGS
MARK_AS_ADVANCED
(
CLEAR CUDA_NVCC_FLAGS
)
IF
(
MSVC
)
# Unfortunately the variables CUDA_NVCC_FLAGS_RELEASE and CUDA_NVCC_FLAGS_DEBUG
# appear to be unused, at least in CMake 2.6
# Release /MD linkage
SET
(
HAS_NVCC_FLAG FALSE
)
IF
(
CUDA_NVCC_FLAGS MATCHES
"-Xcompiler"
)
SET
(
HAS_NVCC_FLAG TRUE
)
ENDIF
(
CUDA_NVCC_FLAGS MATCHES
"-Xcompiler"
)
IF
(
NOT HAS_NVCC_FLAG
)
set
(
new_flags
"-Xcompiler
\"
/MD
\"
-DOPENMMCUDA_BUILDING_SHARED_LIBRARY"
)
if
(
CUDA_NVCC_FLAGS
)
set
(
new_flags
"
${
CUDA_NVCC_FLAGS
}
;
${
new_flags
}
"
)
endif
(
CUDA_NVCC_FLAGS
)
SET
(
CUDA_NVCC_FLAGS
"
${
new_flags
}
"
CACHE STRING
"Semicolon delimit multiple arguments"
FORCE
)
ENDIF
(
NOT HAS_NVCC_FLAG
)
ENDIF
(
MSVC
)
ELSE
(
CUDA_FOUND
)
SET
(
OPENMM_BUILD_CUDA_LIB OFF CACHE BOOL
"Build OpenMMCuda library for Nvidia GPUs"
)
ENDIF
(
CUDA_FOUND
)
IF
(
OPENMM_BUILD_CUDA_LIB
)
ADD_SUBDIRECTORY
(
platforms/cuda
)
ENDIF
(
OPENMM_BUILD_CUDA_LIB
)
MARK_AS_ADVANCED
(
CUDA_VERBOSE_BUILD
)
MARK_AS_ADVANCED
(
CUDA_BUILD_CUBIN
)
MARK_AS_ADVANCED
(
CUDA_BUILD_EMULATION
)
FIND_PACKAGE
(
OpenCL QUIET
)
# Plus the tesla/linux is taking too long on the tests
IF
(
OPENCL_FOUND
)
SET
(
OPENMM_BUILD_OPENCL_LIB ON CACHE BOOL
"Build OpenMMOpenCL library"
)
ELSE
(
OPENCL_FOUND
)
SET
(
OPENMM_BUILD_OPENCL_LIB OFF CACHE BOOL
"Build OpenMMOpenCL library"
)
ENDIF
(
OPENCL_FOUND
)
IF
(
OPENMM_BUILD_OPENCL_LIB
)
ADD_SUBDIRECTORY
(
platforms/opencl
)
ENDIF
(
OPENMM_BUILD_OPENCL_LIB
)
# FreeEnergy plugin
SET
(
OPENMM_BUILD_FREE_ENERGY_PLUGIN ON CACHE BOOL
"Build FreeEnergy plugin"
)
SET
(
OPENMM_BUILD_FREE_ENERGY_PATH
)
IF
(
OPENMM_BUILD_FREE_ENERGY_PLUGIN
)
SET
(
OPENMM_BUILD_FREE_ENERGY_PATH
${
CMAKE_CURRENT_SOURCE_DIR
}
/plugins/freeEnergy
)
# ADD_DEFINITIONS(-DINCLUDE_FREE_ENERGY_PLUGIN)
ADD_SUBDIRECTORY
(
plugins/freeEnergy
)
ENDIF
(
OPENMM_BUILD_FREE_ENERGY_PLUGIN
)
# Amoeba plugin
SET
(
OPENMM_BUILD_AMOEBA_PLUGIN ON CACHE BOOL
"Build Amoeba plugin"
)
SET
(
OPENMM_BUILD_AMOEBA_PATH
)
IF
(
OPENMM_BUILD_AMOEBA_PLUGIN
)
SET
(
OPENMM_BUILD_AMOEBA_PATH
${
CMAKE_CURRENT_SOURCE_DIR
}
/plugins/amoeba
)
ADD_SUBDIRECTORY
(
plugins/amoeba
)
ENDIF
(
OPENMM_BUILD_AMOEBA_PLUGIN
)
# RPMD plugin
SET
(
OPENMM_BUILD_RPMD_PLUGIN ON CACHE BOOL
"Build RPMD plugin"
)
SET
(
OPENMM_BUILD_RPMD_PATH
)
IF
(
OPENMM_BUILD_RPMD_PLUGIN
)
SET
(
OPENMM_BUILD_RPMD_PATH
${
CMAKE_CURRENT_SOURCE_DIR
}
/plugins/rpmd
)
ADD_SUBDIRECTORY
(
plugins/rpmd
)
ENDIF
(
OPENMM_BUILD_RPMD_PLUGIN
)
INSTALL_TARGETS
(
/lib RUNTIME_DIRECTORY /lib
${
SHARED_TARGET
}
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
INSTALL_TARGETS
(
/lib RUNTIME_DIRECTORY /lib
${
STATIC_TARGET
}
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
FILE
(
GLOB CORE_HEADERS include/*.h */include/*.h
)
FILE
(
GLOB TOP_HEADERS include/openmm/*.h */include/openmm/*.h
)
FILE
(
GLOB INTERNAL_HEADERS include/openmm/internal/*.h */include/openmm/internal/*.h
)
INSTALL_FILES
(
/include FILES
${
CORE_HEADERS
}
)
INSTALL_FILES
(
/include/openmm FILES
${
TOP_HEADERS
}
)
INSTALL_FILES
(
/include/openmm/internal FILES
${
INTERNAL_HEADERS
}
)
# Serialization support
SET
(
OPENMM_BUILD_SERIALIZATION_SUPPORT ON CACHE BOOL
"Whether to build the serialization support library"
)
IF
(
OPENMM_BUILD_SERIALIZATION_SUPPORT
)
ADD_SUBDIRECTORY
(
serialization
)
ENDIF
(
OPENMM_BUILD_SERIALIZATION_SUPPORT
)
# Python wrappers
SET
(
OPENMM_BUILD_PYTHON_WRAPPERS OFF CACHE BOOL
"Build wrappers for Python"
)
IF
(
OPENMM_BUILD_PYTHON_WRAPPERS
)
IF
(
NOT OPENMM_BUILD_SERIALIZATION_SUPPORT
)
MESSAGE
(
SEND_ERROR
"The Python wrappers require that serialization support be built."
)
ENDIF
(
NOT OPENMM_BUILD_SERIALIZATION_SUPPORT
)
IF
(
NOT OPENMM_BUILD_FREE_ENERGY_PLUGIN
)
MESSAGE
(
SEND_ERROR
"The Python wrappers require that the free energy plugin be built."
)
ENDIF
(
NOT OPENMM_BUILD_FREE_ENERGY_PLUGIN
)
IF
(
NOT OPENMM_BUILD_AMOEBA_PLUGIN
)
MESSAGE
(
SEND_ERROR
"The Python wrappers require that the AMOEBA plugin be built."
)
ENDIF
(
NOT OPENMM_BUILD_AMOEBA_PLUGIN
)
ADD_SUBDIRECTORY
(
wrappers/python
)
ENDIF
(
OPENMM_BUILD_PYTHON_WRAPPERS
)
#
# Allow automated build and dashboard.
#
# redundant INCLUDE(Dart) statement
# 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
#
ENABLE_TESTING
()
IF
(
EXECUTABLE_OUTPUT_PATH
)
SET
(
TEST_PATH
${
EXECUTABLE_OUTPUT_PATH
}
)
ELSE
(
EXECUTABLE_OUTPUT_PATH
)
SET
(
TEST_PATH .
)
ENDIF
(
EXECUTABLE_OUTPUT_PATH
)
# Build and install documentation
find_package
(
Doxygen QUIET
)
mark_as_advanced
(
CLEAR DOXYGEN_EXECUTABLE
)
IF
(
DOXYGEN_EXECUTABLE
)
SET
(
DOXY_CONFIG
"
${
CMAKE_CURRENT_BINARY_DIR
}
/Doxyfile"
)
CONFIGURE_FILE
(
${
CMAKE_CURRENT_SOURCE_DIR
}
/docs/Doxyfile.in
${
DOXY_CONFIG
}
@ONLY
)
FILE
(
GLOB_RECURSE OPENMM_INCLUDES
"openmm/include/*.h"
)
FILE
(
GLOB_RECURSE OLLA_INCLUDES
"olla/include/*.h"
)
ADD_CUSTOM_COMMAND
(
OUTPUT
"
${
CMAKE_CURRENT_BINARY_DIR
}
/html/index.html"
COMMAND
${
DOXYGEN_EXECUTABLE
}
${
DOXY_CONFIG
}
DEPENDS
${
OPENMM_INCLUDES
}
${
OLLA_INCLUDES
}
WORKING_DIRECTORY
"
${
CMAKE_CURRENT_BINARY_DIR
}
"
COMMENT
"Generating API documentation using Doxygen"
)
ADD_CUSTOM_TARGET
(
DoxygenApiDocs
DEPENDS
"
${
CMAKE_CURRENT_BINARY_DIR
}
/html/index.html"
COMMENT
"Generating API documentation using Doxygen"
SOURCES
"
${
CMAKE_CURRENT_SOURCE_DIR
}
/docs/Doxyfile.in"
${
OPENMM_INCLUDES
}
${
OLLA_INCLUDES
}
)
FILE
(
MAKE_DIRECTORY
"
${
PROJECT_BINARY_DIR
}
/html/"
)
INSTALL
(
DIRECTORY
"
${
PROJECT_BINARY_DIR
}
/html/"
DESTINATION
"docs/api/"
)
INSTALL
(
FILES
"docs/API Reference.html"
DESTINATION
"docs/"
)
set
(
OPENMM_GENERATE_API_DOCS OFF CACHE BOOL
"Whether to create API documentation using Doxygen"
)
if
(
OPENMM_GENERATE_API_DOCS
)
ADD_CUSTOM_TARGET
(
GenerateDoxygenApiDocs ALL
DEPENDS
"
${
CMAKE_CURRENT_BINARY_DIR
}
/html/index.html"
COMMENT
"Generating API documentation using Doxygen"
SOURCES
"
${
CMAKE_CURRENT_SOURCE_DIR
}
/docs/Doxyfile.in"
${
OPENMM_INCLUDES
}
${
OLLA_INCLUDES
}
)
endif
(
OPENMM_GENERATE_API_DOCS
)
ENDIF
(
DOXYGEN_EXECUTABLE
)
install
(
FILES docs/UsersGuide/OpenMMUsersGuide.pdf
DESTINATION docs/
)
FILE
(
GLOB LICENSE_FILES
"docs/licenses/*.txt"
)
install
(
FILES
${
LICENSE_FILES
}
DESTINATION licenses/
)
ADD_SUBDIRECTORY
(
tests
)
ADD_SUBDIRECTORY
(
examples
)
ENDIF
(
NOT cmv EQUAL
"2.4"
)
# This whole file...
platforms/reference/src/SimTKReference/fftpack.h
View file @
18a837c0
...
...
@@ -32,10 +32,34 @@ extern "C" {
#endif
typedef
struct
{
RealOpenMM
re
;
RealOpenMM
im
;
}
t_complex
;
class
t_complex
{
public:
RealOpenMM
re
;
RealOpenMM
im
;
t_complex
()
:
re
(
0.0
),
im
(
0.0
)
{
}
t_complex
(
RealOpenMM
re
,
RealOpenMM
im
)
:
re
(
re
),
im
(
im
)
{
}
t_complex
(
const
t_complex
&
c
)
:
re
(
c
.
re
),
im
(
c
.
im
)
{
}
t_complex
operator
*
(
RealOpenMM
r
)
{
return
t_complex
(
re
*
r
,
im
*
r
);
}
t_complex
operator
+
(
const
t_complex
&
c
)
const
{
return
t_complex
(
re
+
c
.
re
,
im
+
c
.
im
);
}
t_complex
operator
-
(
const
t_complex
&
c
)
const
{
return
t_complex
(
re
-
c
.
re
,
im
-
c
.
im
);
}
t_complex
operator
+=
(
const
t_complex
&
c
)
{
re
+=
c
.
re
;
im
+=
c
.
im
;
}
t_complex
operator
-=
(
const
t_complex
&
c
)
{
re
-=
c
.
re
;
im
-=
c
.
im
;
}
};
/*! \brief Datatype for FFT setup
...
...
plugins/rpmd/CMakeLists.txt
0 → 100644
View file @
18a837c0
#---------------------------------------------------
# OpenMM RPMD Plugin
#
# Creates OpenMM RPMD plugin library, base name=OpenMMRPMD.
# Default libraries are shared & optimized. Variants
# are created for static (_static) and debug (_d).
#
# Windows:
# OpenMMRPMD[_d].dll
# OpenMMRPMD[_d].lib
# OpenMMRPMD_static[_d].lib
# Unix:
# libOpenMMRPMD[_d].so
# libOpenMMRPMD_static[_d].a
#----------------------------------------------------
#INCLUDE(Dart)
# ----------------------------------------------------------------------------
SET
(
CREATE_SERIALIZABLE_OPENMM_RPMD 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_RPMD_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference
)
SET
(
OPENMM_RPMD_LIBRARY_NAME OpenMMRPMD
)
SET
(
SHARED_RPMD_TARGET
${
OPENMM_RPMD_LIBRARY_NAME
}
)
SET
(
STATIC_RPMD_TARGET
${
OPENMM_RPMD_LIBRARY_NAME
}
_static
)
IF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
SET
(
SHARED_RPMD_SERIALIZABLE_TARGET
${
OPENMM_RPMD_LIBRARY_NAME
}
_serializable
)
ENDIF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
# But on Unix or Cygwin we have to add the suffix manually
IF
(
UNIX AND CMAKE_BUILD_TYPE MATCHES Debug
)
SET
(
SHARED_RPMD_TARGET
${
SHARED_RPMD_TARGET
}
_d
)
SET
(
STATIC_RPMD_TARGET
${
STATIC_RPMD_TARGET
}
_d
)
IF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
SET
(
SHARED_RPMD_SERIALIZABLE_TARGET
${
SHARED_RPMD_SERIALIZABLE_TARGET
}
_d
)
ENDIF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
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_RPMD_INCLUDE_DIRS
)
# start empty
FOREACH
(
subdir
${
OPENMM_RPMD_PLUGIN_SOURCE_SUBDIRS
}
)
# append
SET
(
API_RPMD_INCLUDE_DIRS
${
API_RPMD_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_RPMD_REL_INCLUDE_FILES
)
# start these out empty
SET
(
API_RPMD_ABS_INCLUDE_FILES
)
FOREACH
(
dir
${
API_RPMD_INCLUDE_DIRS
}
)
FILE
(
GLOB fullpaths
${
dir
}
/*.h
)
# returns full pathnames
SET
(
API_RPMD_ABS_INCLUDE_FILES
${
API_RPMD_ABS_INCLUDE_FILES
}
${
fullpaths
}
)
FOREACH
(
pathname
${
fullpaths
}
)
GET_FILENAME_COMPONENT
(
filename
${
pathname
}
NAME
)
SET
(
API_RPMD_REL_INCLUDE_FILES
${
API_RPMD_REL_INCLUDE_FILES
}
${
dir
}
/
${
filename
}
)
ENDFOREACH
(
pathname
)
ENDFOREACH
(
dir
)
# collect up source files
SET
(
SOURCE_RPMD_FILES
)
# empty
SET
(
SOURCE_RPMD_INCLUDE_FILES
)
FOREACH
(
subdir
${
OPENMM_RPMD_PLUGIN_SOURCE_SUBDIRS
}
)
FILE
(
GLOB src_files
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/src/*.cpp
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/src/*/*.cpp
)
FILE
(
GLOB incl_files
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
subdir
}
/src/*.h
)
SET
(
SOURCE_RPMD_FILES
${
SOURCE_RPMD_FILES
}
${
src_files
}
)
#append
SET
(
SOURCE_RPMD_INCLUDE_FILES
${
SOURCE_RPMD_INCLUDE_FILES
}
${
incl_files
}
)
## Make sure we find these locally before looking in OpenMM/include if
## OpenMM was previously installed there.
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_RPMD wrappers are being generated, and add them to the build.
#IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
# ADD_SUBDIRECTORY(wrappers)
# SET(SOURCE_RPMD_FILES ${SOURCE_RPMD_FILES} wrappers/RPMDOpenMMCWrapper.cpp wrappers/RPMDOpenMMFortranWrapper.cpp)
# SET_SOURCE_FILES_PROPERTIES(wrappers/RPMDOpenMMCWrapper.cpp wrappers/RPMDOpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE)
#ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
INCLUDE_DIRECTORIES
(
BEFORE
${
CMAKE_CURRENT_SOURCE_DIR
}
/src
)
ADD_LIBRARY
(
${
SHARED_RPMD_TARGET
}
SHARED
${
SOURCE_RPMD_FILES
}
${
SOURCE_RPMD_INCLUDE_FILES
}
${
API_RPMD_ABS_INCLUDE_FILES
}
)
SET_TARGET_PROPERTIES
(
${
SHARED_RPMD_TARGET
}
PROPERTIES COMPILE_FLAGS
"-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY"
)
#IF( CREATE_SERIALIZABLE_OPENMM_RPMD )
# ADD_LIBRARY(${SHARED_RPMD_SERIALIZABLE_TARGET} SHARED ${SOURCE_RPMD_FILES} ${SOURCE_RPMD_INCLUDE_FILES} ${API_RPMD_ABS_INCLUDE_FILES})
# SET_TARGET_PROPERTIES(${SHARED_RPMD_SERIALIZABLE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_SERIALIZE")
# INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../serialization/include)
#ENDIF( CREATE_SERIALIZABLE_OPENMM_RPMD )
IF
(
OPENMM_BUILD_STATIC_LIB
)
ADD_LIBRARY
(
${
STATIC_RPMD_TARGET
}
STATIC
${
SOURCE_RPMD_FILES
}
${
SOURCE_RPMD_INCLUDE_FILES
}
${
API_RPMD_ABS_INCLUDE_FILES
}
)
SET_TARGET_PROPERTIES
(
${
STATIC_RPMD_TARGET
}
PROPERTIES COMPILE_FLAGS
"-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY"
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
#IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
# ADD_DEPENDENCIES(${SHARED_RPMD_TARGET} RPMDApiWrappers)
# IF( CREATE_SERIALIZABLE_OPENMM_RPMD )
# ADD_DEPENDENCIES(${SHARED_RPMD_SERIALIZABLE_TARGET} RPMDApiWrappers)
# ENDIF( CREATE_SERIALIZABLE_OPENMM_RPMD )
# IF(OPENMM_BUILD_STATIC_LIB)
# ADD_DEPENDENCIES(${STATIC_RPMD_TARGET} RPMDApiWrappers)
# ENDIF(OPENMM_BUILD_STATIC_LIB)
#ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
# ----------------------------------------------------------------------------
# On Linux need to link to libdl
FIND_LIBRARY
(
DL_LIBRARY dl
)
IF
(
DL_LIBRARY
)
TARGET_LINK_LIBRARIES
(
${
SHARED_RPMD_TARGET
}
${
DL_LIBRARY
}
)
IF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
TARGET_LINK_LIBRARIES
(
${
SHARED_RPMD_SERIALIZABLE_TARGET
}
${
DL_LIBRARY
}
)
ENDIF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
TARGET_LINK_LIBRARIES
(
${
STATIC_RPMD_TARGET
}
${
DL_LIBRARY
}
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
ENDIF
(
DL_LIBRARY
)
SET
(
OpenMMLib OpenMM
)
# But on Unix or Cygwin we have to add the suffix manually
IF
(
UNIX AND CMAKE_BUILD_TYPE MATCHES Debug
)
SET
(
OpenMMLib
${
OpenMMLib
}
_d
)
ENDIF
(
UNIX AND CMAKE_BUILD_TYPE MATCHES Debug
)
TARGET_LINK_LIBRARIES
(
${
SHARED_RPMD_TARGET
}
${
SHARED_TARGET
}
)
IF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
TARGET_LINK_LIBRARIES
(
${
SHARED_RPMD_SERIALIZABLE_TARGET
}
${
SHARED_TARGET
}
)
ENDIF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
TARGET_LINK_LIBRARIES
(
${
STATIC_RPMD_TARGET
}
${
STATIC_TARGET
}
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
#ADD_SUBDIRECTORY(platforms/reference/tests)
# Which hardware platforms to build
IF
(
CUDA_FOUND
)
SET
(
OPENMM_BUILD_RPMD_CUDA_LIB ON CACHE BOOL
"Build OpenMMRPMDCuda library for Nvidia GPUs"
)
ELSE
(
CUDA_FOUND
)
SET
(
OPENMM_BUILD_RPMD_CUDA_LIB OFF CACHE BOOL
"Build OpenMMRPMDCuda library for Nvidia GPUs"
)
ENDIF
(
CUDA_FOUND
)
#SET(OPENMM_BUILD_RPMD_PATH)
#SET(OPENMM_BUILD_RPMD_CUDA_PATH)
#IF(OPENMM_BUILD_RPMD_CUDA_LIB)
# ADD_SUBDIRECTORY(platforms/cuda)
# SET(OPENMM_BUILD_RPMD_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
# SET(OPENMM_BUILD_RPMD_CUDA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
# SET(OPENMM_RPMD_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda)
#ENDIF(OPENMM_BUILD_RPMD_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_RPMD_TARGET
}
)
IF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
INSTALL_TARGETS
(
/lib/plugins RUNTIME_DIRECTORY /lib/plugins
${
SHARED_RPMD_SERIALIZABLE_TARGET
}
)
ENDIF
(
CREATE_SERIALIZABLE_OPENMM_RPMD
)
IF
(
OPENMM_BUILD_STATIC_LIB
)
INSTALL_TARGETS
(
/lib RUNTIME_DIRECTORY /lib
${
STATIC_RPMD_TARGET
}
)
ENDIF
(
OPENMM_BUILD_STATIC_LIB
)
FILE
(
GLOB CORE_HEADERS include/*.h */include/*.h
)
FILE
(
GLOB TOP_HEADERS include/openmm/*.h */include/openmm/*.h
)
FILE
(
GLOB INTERNAL_HEADERS include/openmm/internal/*.h */include/openmm/internal/*.h
)
INSTALL_FILES
(
/include FILES
${
CORE_HEADERS
}
)
INSTALL_FILES
(
/include/openmm FILES
${
TOP_HEADERS
}
)
INSTALL_FILES
(
/include/openmm/internal FILES
${
INTERNAL_HEADERS
}
)
#
# Testing
#
ENABLE_TESTING
()
IF
(
EXECUTABLE_OUTPUT_PATH
)
SET
(
TEST_PATH
${
EXECUTABLE_OUTPUT_PATH
}
)
ELSE
(
EXECUTABLE_OUTPUT_PATH
)
SET
(
TEST_PATH .
)
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/rpmd/openmmapi/include/openmm/RPMDIntegrator.h
0 → 100644
View file @
18a837c0
#ifndef OPENMM_RPMDINTEGRATOR_H_
#define OPENMM_RPMDINTEGRATOR_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2011 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Integrator.h"
#include "openmm/Kernel.h"
#include "openmm/State.h"
#include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h"
namespace
OpenMM
{
/**
* This is an Integrator which simulates a System using RPMD dynamics.
*/
class
OPENMM_EXPORT
RPMDIntegrator
:
public
Integrator
{
public:
/**
* Create a RPMDIntegrator.
*
* @param numCopies the number of copies of the system that should be simulated
* @param temperature the temperature of the heat bath (in Kelvin)
* @param frictionCoeff the friction coefficient which couples the system to the heat bath (in inverse picoseconds)
* @param stepSize the step size with which to integrator the system (in picoseconds)
*/
RPMDIntegrator
(
int
numCopies
,
double
temperature
,
double
frictionCoeff
,
double
stepSize
);
/**
* Get the number of copies of the system being simulated.
*/
int
getNumCopies
()
const
{
return
numCopies
;
}
/**
* Get the temperature of the heat bath (in Kelvin).
*
* @return the temperature of the heat bath, measured in Kelvin
*/
double
getTemperature
()
const
{
return
temperature
;
}
/**
* Set the temperature of the heat bath (in Kelvin).
*
* @param temp the temperature of the heat bath, measured in Kelvin
*/
void
setTemperature
(
double
temp
)
{
temperature
=
temp
;
}
/**
* Get the friction coefficient which determines how strongly the system is coupled to
* the heat bath (in inverse ps).
*
* @return the friction coefficient, measured in 1/ps
*/
double
getFriction
()
const
{
return
friction
;
}
/**
* Set the friction coefficient which determines how strongly the system is coupled to
* the heat bath (in inverse ps).
*
* @param coeff the friction coefficient, measured in 1/ps
*/
void
setFriction
(
double
coeff
)
{
friction
=
coeff
;
}
/**
* Get the random number seed. See setRandomNumberSeed() for details.
*/
int
getRandomNumberSeed
()
const
{
return
randomNumberSeed
;
}
/**
* Set the random number seed. The precise meaning of this parameter is undefined, and is left up
* to each Platform to interpret in an appropriate way. It is guaranteed that if two simulations
* are run with different random number seeds, the sequence of random forces will be different. On
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*/
void
setRandomNumberSeed
(
int
seed
)
{
randomNumberSeed
=
seed
;
}
/**
* Set the positions of all particles in one copy of the system.
*
* @param copy the index of the copy for which to set positions
* @param positions the positions of all particles in the system
*/
void
setPositions
(
int
copy
,
const
std
::
vector
<
Vec3
>&
positions
);
/**
* Get the velocities of all particles in one copy of the system.
*
* @param copy the index of the copy for which to set velocities
* @param velocities the velocities of all particles in the system
*/
void
setVelocities
(
int
copy
,
const
std
::
vector
<
Vec3
>&
velocities
);
/**
* Get a State object recording the current state information about one copy of the system.
*
* @param copy the index of the copy for which to retrieve state information
* @param types the set of data types which should be stored in the State object. This
* should be a union of DataType values, e.g. (State::Positions | State::Velocities).
*/
State
getState
(
int
copy
,
int
types
);
/**
* Advance a simulation through time by taking a series of time steps.
*
* @param steps the number of time steps to take
*/
void
step
(
int
steps
);
protected:
/**
* This will be called by the Context when it is created. It informs the Integrator
* of what context it will be integrating, and gives it a chance to do any necessary initialization.
* It will also get called again if the application calls reinitialize() on the Context.
*/
void
initialize
(
ContextImpl
&
context
);
/**
* Get the names of all Kernels used by this Integrator.
*/
std
::
vector
<
std
::
string
>
getKernelNames
();
private:
double
temperature
,
friction
;
int
numCopies
,
randomNumberSeed
;
ContextImpl
*
context
;
Context
*
owner
;
Kernel
kernel
;
};
}
// namespace OpenMM
#endif
/*OPENMM_RPMDINTEGRATOR_H_*/
plugins/rpmd/openmmapi/include/openmm/RpmdKernels.h
0 → 100644
View file @
18a837c0
#ifndef RPMD_KERNELS_H_
#define RPMD_KERNELS_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/RPMDIntegrator.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/Vec3.h"
#include <string>
#include <vector>
namespace
OpenMM
{
/**
* This kernel is invoked by RPMDIntegrator to take one time step, and to get and
* set the state of system copies.
*/
class
IntegrateRPMDStepKernel
:
public
KernelImpl
{
public:
static
std
::
string
Name
()
{
return
"IntegrateRPMDStep"
;
}
IntegrateRPMDStepKernel
(
std
::
string
name
,
const
Platform
&
platform
)
:
KernelImpl
(
name
,
platform
)
{
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the RPMDIntegrator this kernel will be used for
*/
virtual
void
initialize
(
const
System
&
system
,
const
RPMDIntegrator
&
integrator
)
=
0
;
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the RPMDIntegrator this kernel is being used for
*/
virtual
void
execute
(
ContextImpl
&
context
,
const
RPMDIntegrator
&
integrator
)
=
0
;
/**
* Get the positions of all particles in one copy of the system.
*/
virtual
void
setPositions
(
int
copy
,
const
std
::
vector
<
Vec3
>&
positions
)
=
0
;
/**
* Get the velocities of all particles in one copy of the system.
*/
virtual
void
setVelocities
(
int
copy
,
const
std
::
vector
<
Vec3
>&
velocities
)
=
0
;
/**
* Copy positions and velocities for one copy into the context.
*/
virtual
void
copyToContext
(
int
copy
,
ContextImpl
&
context
)
const
=
0
;
};
}
// namespace OpenMM
#endif
/*RPMD_KERNELS_H_*/
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
0 → 100644
View file @
18a837c0
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2011 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/RPMDIntegrator.h"
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/RPMDKernels.h"
#include <ctime>
#include <string>
using
namespace
OpenMM
;
using
std
::
string
;
using
std
::
vector
;
RPMDIntegrator
::
RPMDIntegrator
(
int
numCopies
,
double
temperature
,
double
frictionCoeff
,
double
stepSize
)
:
owner
(
NULL
),
numCopies
(
numCopies
)
{
setTemperature
(
temperature
);
setFriction
(
frictionCoeff
);
setStepSize
(
stepSize
);
setConstraintTolerance
(
1e-4
);
setRandomNumberSeed
((
int
)
time
(
NULL
));
}
void
RPMDIntegrator
::
initialize
(
ContextImpl
&
contextRef
)
{
if
(
owner
!=
NULL
&&
&
contextRef
.
getOwner
()
!=
owner
)
throw
OpenMMException
(
"This Integrator is already bound to a context"
);
context
=
&
contextRef
;
owner
=
&
contextRef
.
getOwner
();
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateRPMDStepKernel
::
Name
(),
contextRef
);
dynamic_cast
<
IntegrateRPMDStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
}
vector
<
string
>
RPMDIntegrator
::
getKernelNames
()
{
std
::
vector
<
std
::
string
>
names
;
names
.
push_back
(
IntegrateRPMDStepKernel
::
Name
());
return
names
;
}
void
RPMDIntegrator
::
setPositions
(
int
copy
,
const
vector
<
Vec3
>&
positions
)
{
dynamic_cast
<
IntegrateRPMDStepKernel
&>
(
kernel
.
getImpl
()).
setPositions
(
copy
,
positions
);
}
void
RPMDIntegrator
::
setVelocities
(
int
copy
,
const
vector
<
Vec3
>&
velocities
)
{
dynamic_cast
<
IntegrateRPMDStepKernel
&>
(
kernel
.
getImpl
()).
setVelocities
(
copy
,
velocities
);
}
State
RPMDIntegrator
::
getState
(
int
copy
,
int
types
)
{
dynamic_cast
<
const
IntegrateRPMDStepKernel
&>
(
kernel
.
getImpl
()).
copyToContext
(
copy
,
*
context
);
return
context
->
getOwner
().
getState
(
types
);
}
void
RPMDIntegrator
::
step
(
int
steps
)
{
for
(
int
i
=
0
;
i
<
steps
;
++
i
)
{
context
->
updateContextState
();
context
->
calcForcesAndEnergy
(
true
,
false
);
dynamic_cast
<
IntegrateRPMDStepKernel
&>
(
kernel
.
getImpl
()).
execute
(
*
context
,
*
this
);
}
}
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
0 → 100644
View file @
18a837c0
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ReferenceRpmdKernels.h"
#include "openmm/internal/ContextImpl.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
using
namespace
OpenMM
;
using
namespace
std
;
static
vector
<
RealVec
>&
extractPositions
(
ContextImpl
&
context
)
{
ReferencePlatform
::
PlatformData
*
data
=
reinterpret_cast
<
ReferencePlatform
::
PlatformData
*>
(
context
.
getPlatformData
());
return
*
((
vector
<
RealVec
>*
)
data
->
positions
);
}
static
vector
<
RealVec
>&
extractVelocities
(
ContextImpl
&
context
)
{
ReferencePlatform
::
PlatformData
*
data
=
reinterpret_cast
<
ReferencePlatform
::
PlatformData
*>
(
context
.
getPlatformData
());
return
*
((
vector
<
RealVec
>*
)
data
->
velocities
);
}
static
vector
<
RealVec
>&
extractForces
(
ContextImpl
&
context
)
{
ReferencePlatform
::
PlatformData
*
data
=
reinterpret_cast
<
ReferencePlatform
::
PlatformData
*>
(
context
.
getPlatformData
());
return
*
((
vector
<
RealVec
>*
)
data
->
forces
);
}
ReferenceIntegrateRPMDStepKernel
::~
ReferenceIntegrateRPMDStepKernel
()
{
if
(
fft
!=
NULL
)
fftpack_destroy
(
fft
);
}
void
ReferenceIntegrateRPMDStepKernel
::
initialize
(
const
System
&
system
,
const
RPMDIntegrator
&
integrator
)
{
int
numCopies
=
integrator
.
getNumCopies
();
int
numParticles
=
system
.
getNumParticles
();
positions
.
resize
(
numCopies
);
velocities
.
resize
(
numCopies
);
forces
.
resize
(
numCopies
);
for
(
int
i
=
0
;
i
<
numCopies
;
i
++
)
{
positions
[
i
].
resize
(
numParticles
);
velocities
[
i
].
resize
(
numParticles
);
forces
[
i
].
resize
(
numParticles
);
}
fftpack_init_1d
(
&
fft
,
numParticles
);
SimTKOpenMMUtilities
::
setRandomNumberSeed
((
unsigned
int
)
integrator
.
getRandomNumberSeed
());
}
void
ReferenceIntegrateRPMDStepKernel
::
execute
(
ContextImpl
&
context
,
const
RPMDIntegrator
&
integrator
)
{
int
numCopies
=
positions
.
size
();
int
numParticles
=
positions
[
0
].
size
();
vector
<
RealVec
>&
pos
=
extractPositions
(
context
);
vector
<
RealVec
>&
vel
=
extractVelocities
(
context
);
vector
<
RealVec
>&
f
=
extractForces
(
context
);
if
(
!
hasSetPosition
)
{
// Initialize the positions from the context.
for
(
int
i
=
0
;
i
<
numCopies
;
i
++
)
for
(
int
j
=
0
;
j
<
numParticles
;
j
++
)
positions
[
i
][
j
]
=
pos
[
j
];
hasSetPosition
=
true
;
}
if
(
!
hasSetVelocity
)
{
// Initialize the velocities from the context.
for
(
int
i
=
0
;
i
<
numCopies
;
i
++
)
for
(
int
j
=
0
;
j
<
numParticles
;
j
++
)
velocities
[
i
][
j
]
=
vel
[
j
];
hasSetVelocity
=
true
;
}
// Loop over copies and compute the force on each one.
for
(
int
i
=
0
;
i
<
numCopies
;
i
++
)
{
pos
=
positions
[
i
];
vel
=
velocities
[
i
];
context
.
calcForcesAndEnergy
(
true
,
false
);
forces
[
i
]
=
f
;
}
// Update velocities.
const
RealOpenMM
dt
=
integrator
.
getStepSize
();
const
System
&
system
=
context
.
getSystem
();
for
(
int
i
=
0
;
i
<
numCopies
;
i
++
)
for
(
int
j
=
0
;
j
<
numParticles
;
j
++
)
velocities
[
i
][
j
]
+=
forces
[
i
][
j
]
*
(
dt
/
system
.
getParticleMass
(
j
));
// Evolve the free ring polymer by transforming to the frequency domain.
vector
<
t_complex
>
p
(
numCopies
);
vector
<
t_complex
>
q
(
numCopies
);
const
RealOpenMM
scale
=
1.0
/
sqrt
(
numCopies
);
const
RealOpenMM
hbar
=
1.054571628e-34
*
AVOGADRO
/
1000
;
const
RealOpenMM
nkT
=
numCopies
*
BOLTZ
*
integrator
.
getTemperature
();
const
RealOpenMM
twown
=
2.0
*
nkT
/
hbar
;
for
(
int
particle
=
0
;
particle
<
numParticles
;
particle
++
)
{
for
(
int
component
=
0
;
component
<
3
;
component
++
)
{
for
(
int
k
=
0
;
k
<
numCopies
;
k
++
)
{
q
[
k
]
=
t_complex
(
scale
*
positions
[
k
][
particle
][
component
],
0.0
);
p
[
k
]
=
t_complex
(
scale
*
velocities
[
k
][
particle
][
component
]
*
system
.
getParticleMass
(
particle
),
0.0
);
}
fftpack_exec_1d
(
fft
,
FFTPACK_FORWARD
,
&
q
[
0
],
&
q
[
0
]);
fftpack_exec_1d
(
fft
,
FFTPACK_FORWARD
,
&
p
[
0
],
&
p
[
0
]);
q
[
0
]
+=
p
[
0
]
*
(
dt
/
system
.
getParticleMass
(
particle
));
for
(
int
k
=
1
;
k
<
numCopies
;
k
++
)
{
const
RealOpenMM
wk
=
twown
*
sin
(
k
*
M_PI
/
numCopies
);
const
RealOpenMM
wt
=
wk
*
dt
;
const
RealOpenMM
sinwt2
=
sin
(
wt
/
2
);
const
RealOpenMM
wm
=
wk
*
system
.
getParticleMass
(
particle
);
const
t_complex
pprime
=
p
[
k
]
-
q
[
k
]
*
2.0
*
wm
*
sinwt2
;
// Advance momentum from t-dt/2 to t+dt/2
q
[
k
]
=
p
[
k
]
*
(
2.0
*
sinwt2
/
wm
)
+
q
[
k
]
*
(
1.0
-
4.0
*
sinwt2
*
sinwt2
);
// Advance position from t to t+dt
p
[
k
]
=
pprime
;
}
fftpack_exec_1d
(
fft
,
FFTPACK_BACKWARD
,
&
q
[
0
],
&
q
[
0
]);
fftpack_exec_1d
(
fft
,
FFTPACK_BACKWARD
,
&
p
[
0
],
&
p
[
0
]);
for
(
int
k
=
0
;
k
<
numCopies
;
k
++
)
{
positions
[
k
][
particle
][
component
]
=
scale
*
q
[
k
].
re
;
velocities
[
k
][
particle
][
component
]
=
scale
*
p
[
k
].
re
/
system
.
getParticleMass
(
particle
);
}
}
}
// Apply the PILE-L thermostat.
const
RealOpenMM
c1_0
=
exp
(
-
dt
*
integrator
.
getFriction
());
const
RealOpenMM
c2_0
=
sqrt
(
1.0
-
c1_0
*
c1_0
);
for
(
int
particle
=
0
;
particle
<
numParticles
;
particle
++
)
{
const
RealOpenMM
localc3
=
c2_0
*
sqrt
(
system
.
getParticleMass
(
particle
));
for
(
int
component
=
0
;
component
<
3
;
component
++
)
{
for
(
int
k
=
0
;
k
<
numCopies
;
k
++
)
p
[
k
]
=
t_complex
(
scale
*
velocities
[
k
][
particle
][
component
]
*
system
.
getParticleMass
(
particle
),
0.0
);
fftpack_exec_1d
(
fft
,
FFTPACK_FORWARD
,
&
p
[
0
],
&
p
[
0
]);
// Apply a local Langevin thermostat to the centroid mode.
p
[
0
].
re
=
p
[
0
].
re
*
c1_0
+
localc3
*
SimTKOpenMMUtilities
::
getNormallyDistributedRandomNumber
();
// Use critical damping white noise for the remaining modes.
for
(
int
k
=
1
;
k
<
numCopies
/
2
;
k
++
)
{
const
bool
isCenter
=
(
numCopies
%
2
==
0
&&
k
==
numCopies
/
2
);
const
RealOpenMM
wk
=
twown
*
sin
(
k
*
M_PI
/
numCopies
);
const
RealOpenMM
c1
=
exp
(
-
2.0
*
wk
*
dt
);
const
RealOpenMM
c2
=
sqrt
((
1.0
-
c1
*
c1
)
/
2
)
*
(
isCenter
?
sqrt
(
2.0
)
:
1.0
);
const
RealOpenMM
c3
=
c2
*
sqrt
(
system
.
getParticleMass
(
particle
)
*
nkT
);
RealOpenMM
rand1
=
c3
*
SimTKOpenMMUtilities
::
getNormallyDistributedRandomNumber
();
RealOpenMM
rand2
=
(
isCenter
?
0.0
:
c3
*
SimTKOpenMMUtilities
::
getNormallyDistributedRandomNumber
());
p
[
k
]
=
p
[
k
]
*
c1
+
t_complex
(
rand1
,
rand2
);
if
(
k
<
numCopies
-
k
)
p
[
numCopies
-
k
]
=
p
[
numCopies
-
k
]
*
c1
+
t_complex
(
rand1
,
-
rand2
);
}
fftpack_exec_1d
(
fft
,
FFTPACK_BACKWARD
,
&
p
[
0
],
&
p
[
0
]);
for
(
int
k
=
0
;
k
<
numCopies
;
k
++
)
velocities
[
k
][
particle
][
component
]
=
scale
*
p
[
k
].
re
/
system
.
getParticleMass
(
particle
);
}
}
}
void
ReferenceIntegrateRPMDStepKernel
::
setPositions
(
int
copy
,
const
vector
<
Vec3
>&
pos
)
{
int
numParticles
=
positions
[
copy
].
size
();
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
positions
[
copy
][
i
]
=
pos
[
i
];
hasSetPosition
=
true
;
}
void
ReferenceIntegrateRPMDStepKernel
::
setVelocities
(
int
copy
,
const
vector
<
Vec3
>&
vel
)
{
int
numParticles
=
velocities
[
copy
].
size
();
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
velocities
[
copy
][
i
]
=
vel
[
i
];
hasSetVelocity
=
true
;
}
void
ReferenceIntegrateRPMDStepKernel
::
copyToContext
(
int
copy
,
ContextImpl
&
context
)
const
{
extractPositions
(
context
)
=
positions
[
copy
];
extractVelocities
(
context
)
=
velocities
[
copy
];
}
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.h
0 → 100644
View file @
18a837c0
#ifndef REFERENCE_RPMD_KERNELS_H_
#define REFERENCE_RPMD_KERNELS_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ReferencePlatform.h"
#include "openmm/RpmdKernels.h"
#include "SimTKUtilities/RealVec.h"
#include "SimTKReference/fftpack.h"
namespace
OpenMM
{
/**
* This kernel is invoked by RPMDIntegrator to take one time step, and to get and
* set the state of system copies.
*/
class
ReferenceIntegrateRPMDStepKernel
:
public
IntegrateRPMDStepKernel
{
public:
ReferenceIntegrateRPMDStepKernel
(
std
::
string
name
,
const
Platform
&
platform
)
:
IntegrateRPMDStepKernel
(
name
,
platform
),
fft
(
NULL
),
hasSetPosition
(
false
),
hasSetVelocity
(
false
)
{
}
~
ReferenceIntegrateRPMDStepKernel
();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the RPMDIntegrator this kernel will be used for
*/
void
initialize
(
const
System
&
system
,
const
RPMDIntegrator
&
integrator
);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the RPMDIntegrator this kernel is being used for
*/
void
execute
(
ContextImpl
&
context
,
const
RPMDIntegrator
&
integrator
);
/**
* Get the positions of all particles in one copy of the system.
*/
void
setPositions
(
int
copy
,
const
std
::
vector
<
Vec3
>&
positions
);
/**
* Get the velocities of all particles in one copy of the system.
*/
void
setVelocities
(
int
copy
,
const
std
::
vector
<
Vec3
>&
velocities
);
/**
* Copy positions and velocities for one copy into the context.
*/
void
copyToContext
(
int
copy
,
ContextImpl
&
context
)
const
;
private:
std
::
vector
<
std
::
vector
<
RealVec
>
>
positions
;
std
::
vector
<
std
::
vector
<
RealVec
>
>
velocities
;
std
::
vector
<
std
::
vector
<
RealVec
>
>
forces
;
fftpack
*
fft
;
bool
hasSetPosition
,
hasSetVelocity
;
};
}
// namespace OpenMM
#endif
/*REFERENCE_RPMD_KERNELS_H_*/
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