dded GB/VI to Cuda platform

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers  = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail 

platforms/reference/src/gbsa/CpuObc.cpp

@@ -632,7 +632,9 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
 
    // cal to Joule conversion
 
-   RealOpenMM conversion = (RealOpenMM)0.4184;  
+   RealOpenMM conversion = (RealOpenMM)(0.4184);  
+//   RealOpenMM conversion = (RealOpenMM)(0.4184/0.987);  
+//fprintf( stderr, "Obc includes .987 XXXXXXXXXXXXXXXXXXXXXXX\n" );
    for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
       inputForces[atomI][0] += conversion*forces[atomI][0];
       inputForces[atomI][1] += conversion*forces[atomI][1];

platforms/reference/tests/TestReferenceGBVIForce.cpp

@@ -368,7 +368,7 @@ int main() {
         testEnergy1();
 */
 //        testSingleParticle();
-        testEnergyTwoParticle();
+//        testEnergyTwoParticle();
         testEnergyEthane();
     }
     catch(const exception& e) {

plugins/freeEnergy/CMakeLists.txt

+#---------------------------------------------------
+# OpenMM FreeEnergy Plugin
+#
+# Creates OpenMM FreeEnergy plugin 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
+#----------------------------------------------------
+
+# On Linux it appears that cmake 2.4 does not work with Cuda cmake rules
+#CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+
+# Does someone at Kitware actually believe that this policy crap
+# might actually make cmake LESS brittle?
+# (Probably the same genius who came up the endif(allthesamecrap) syntax)
+# 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)
+
+# 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 )
+
+# 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})
+
+#INCLUDE(Dart)
+
+SET(LOG TRUE)
+# ----------------------------------------------------------------------------
+IF(LOG)
+   SET(LOG_FILE "CMakeLog.txt" )
+   FILE( WRITE ${LOG_FILE} "In OpenMM Cmake\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)
+
+# ----------------------------------------------------------------------------
+
+# 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_FREE_ENERGY_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
+
+# 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 32 bit binaries, since CUDA doesn't currently work with 64 bit
+#IF (APPLE)
+#   SET (CMAKE_CXX_FLAGS "-arch i386")
+#   SET (CMAKE_C_FLAGS "-arch i386")
+#ENDIF (APPLE)
+#
+#IF(UNIX AND NOT CMAKE_BUILD_TYPE)
+#    SET(CMAKE_BUILD_TYPE Debug 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_FREE_ENERGY_LIBRARY_NAME OpenMMFreeEnergy)
+SET(OPENMM_FREE_ENERGY_MAJOR_VERSION 1)
+SET(OPENMM_FREE_ENERGY_MINOR_VERSION 0)
+SET(OPENMM_FREE_ENERGY_BUILD_VERSION 0)
+
+#SET(OPENMM_COPYRIGHT_YEARS "2009")
+
+# 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_EXE svnversion.exe
+#    PATHS "C:/cygwin/bin"
+#)
+#IF (SVNVERSION_EXE)
+#    EXEC_PROGRAM (${SVNVERSION_EXE}
+#                  ARGS  \"${CMAKE_CURRENT_SOURCE_DIR}\"
+#                  OUTPUT_VARIABLE OPENMM_SVN_REVISION )
+#ELSE (SVNVERSION_EXE) 
+#    FIND_PROGRAM (SVNVERSION svnversion) 
+#    IF (SVNVERSION)
+#        EXEC_PROGRAM (${SVNVERSION}
+#                      ARGS "${CMAKE_CURRENT_SOURCE_DIR}"
+#                      OUTPUT_VARIABLE OPENMM_SVN_REVISION)
+#    ELSE (SVNVERSION)
+#        MESSAGE (STATUS 
+#          "Could not find 'svnversion' executable; 'about' will be wrong. (Cygwin provides one on Windows.)"
+#        )
+#        SET (OPENMM_SVN_REVISION unknown) 
+#    ENDIF (SVNVERSION)
+#ENDIF (SVNVERSION_EXE)
+# Remove colon from build version, for easier placement in directory names
+#STRING(REPLACE ":" "_" OPENMM_SVN_REVISION ${OPENMM_SVN_REVISION})
+
+ADD_DEFINITIONS(-DOPENMM_FREE_ENERGY_LIBRARY_NAME=${OPENMM_FREE_ENERGY_LIBRARY_NAME}
+                -DOPENMM_FREE_ENERGY_MAJOR_VERSION=${OPENMM_FREE_ENERGY_MAJOR_VERSION}
+                -DOPENMM_FREE_ENERGY_MINOR_VERSION=${OPENMM_FREE_ENERGY_MINOR_VERSION}
+		          -DOPENMM_FREE_ENERGY_BUILD_VERSION=${OPENMM_FREE_ENERGY_BUILD_VERSION})
+
+# CMake quotes automatically when building Visual Studio projects but we need
+# to add them ourselves for Linux or Cygwin. Two cases to avoid duplicate quotes
+# in Visual Studio which end up in the binary.
+#
+#IF (${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 FreeEnergy which will be built." FORCE)
+
+SET(SHARED_FREE_ENERGY_TARGET ${OPENMM_FREE_ENERGY_LIBRARY_NAME})
+SET(STATIC_FREE_ENERGY_TARGET ${OPENMM_FREE_ENERGY_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_FREE_ENERGY_TARGET ${SHARED_FREE_ENERGY_TARGET}_d)
+    SET(STATIC_FREE_ENERGY_TARGET ${STATIC_FREE_ENERGY_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_FREE_ENERGY_INCLUDE_DIRS) # start empty
+FOREACH(subdir ${OPENMM_FREE_ENERGY_PLUGIN_SOURCE_SUBDIRS})
+    # append
+    SET(API_FREE_ENERGY_INCLUDE_DIRS ${API_FREE_ENERGY_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_FREE_ENERGY_REL_INCLUDE_FILES)   # start these out empty
+SET(API_FREE_ENERGY_ABS_INCLUDE_FILES)
+
+FOREACH(dir ${API_FREE_ENERGY_INCLUDE_DIRS})
+    FILE(GLOB fullpaths ${dir}/*.h)	# returns full pathnames
+    SET(API_FREE_ENERGY_ABS_INCLUDE_FILES ${API_FREE_ENERGY_ABS_INCLUDE_FILES} ${fullpaths})
+
+    FOREACH(pathname ${fullpaths})
+        GET_FILENAME_COMPONENT(filename ${pathname} NAME)
+        SET(API_FREE_ENERGY_REL_INCLUDE_FILES ${API_FREE_ENERGY_REL_INCLUDE_FILES} ${dir}/${filename})
+    ENDFOREACH(pathname)
+ENDFOREACH(dir)
+
+# collect up source files
+SET(SOURCE_FREE_ENERGY_FILES) # empty
+SET(SOURCE_FREE_ENERGY_INCLUDE_FILES)
+
+FOREACH(subdir ${OPENMM_FREE_ENERGY_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_FREE_ENERGY_FILES         ${SOURCE_FREE_ENERGY_FILES}         ${src_files})   #append
+    SET(SOURCE_FREE_ENERGY_INCLUDE_FILES ${SOURCE_FREE_ENERGY_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)
+
+# ----------------------------------------------------------------------------
+IF(LOG)
+    FILE( APPEND ${LOG_FILE} "SOURCE_FREE_ENERGY_FILES=" ${SOURCE_FREE_ENERGY_FILES} "\n" )
+    FILE( APPEND ${LOG_FILE} "SOURCE_FREE_ENERGY_INCLUDE_FILES=" ${SOURCE_FREE_ENERGY_INCLUDE_FILES} "\n" )
+    FILE( APPEND ${LOG_FILE} "OPENMM_PATH="            ${OPENMM_PATH} "\n" )
+    FILE( APPEND ${LOG_FILE} "CUDA_PATH="              ${CUDA_PATH} "\n" )
+ENDIF(LOG)
+
+# ----------------------------------------------------------------------------
+
+# If API_FREE_ENERGY wrappers are being generated, and add them to the build.
+#SET(OPENMM_BUILD_API_FREE_ENERGY_WRAPPERS OFF CACHE BOOL "Build wrappers for C and Fortran")
+#IF(OPENMM_BUILD_API_FREE_ENERGY_WRAPPERS)
+#    ADD_SUBDIRECTORY(wrappers)
+#    SET(SOURCE_FREE_ENERGY_FILES ${SOURCE_FREE_ENERGY_FILES} wrappers/OpenMMCWrapper.cpp  wrappers/OpenMMFortranWrapper.cpp)
+#    SET_SOURCE_FREE_ENERGY_FILES_PROPERTIES(wrappers/OpenMMCWrapper.cpp wrappers/OpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE)
+#ENDIF(OPENMM_BUILD_API_FREE_ENERGY_WRAPPERS)
+
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
+
+ADD_LIBRARY(${SHARED_FREE_ENERGY_TARGET} SHARED ${SOURCE_FREE_ENERGY_FILES} ${SOURCE_FREE_ENERGY_INCLUDE_FILES} ${API_FREE_ENERGY_ABS_INCLUDE_FILES})
+SET_TARGET_PROPERTIES(${SHARED_FREE_ENERGY_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
+
+ADD_LIBRARY(${STATIC_FREE_ENERGY_TARGET} STATIC ${SOURCE_FREE_ENERGY_FILES} ${SOURCE_FREE_ENERGY_INCLUDE_FILES} ${API_FREE_ENERGY_ABS_INCLUDE_FILES})
+SET_TARGET_PROPERTIES(${STATIC_FREE_ENERGY_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
+
+#IF(OPENMM_BUILD_API_FREE_ENERGY_WRAPPERS)
+#    ADD_DEPENDENCIES(${SHARED_FREE_ENERGY_TARGET} ApiWrappers)
+#    ADD_DEPENDENCIES(${STATIC_FREE_ENERGY_TARGET} ApiWrappers)
+#ENDIF(OPENMM_BUILD_API_FREE_ENERGY_WRAPPERS)
+
+# On Linux need to link to libdl
+FIND_LIBRARY(DL_LIBRARY dl)
+IF(DL_LIBRARY)
+  TARGET_LINK_LIBRARIES(${SHARED_FREE_ENERGY_TARGET} ${DL_LIBRARY})
+  TARGET_LINK_LIBRARIES(${STATIC_FREE_ENERGY_TARGET} ${DL_LIBRARY})
+ENDIF(DL_LIBRARY)
+
+ADD_SUBDIRECTORY(platforms/reference/tests)
+
+# Which hardware platforms to build
+
+SET(OPENMM_BUILD_FREE_ENERGY_CUDA_LIB OFF CACHE BOOL "Build OpenMMFreeEnergyCuda library for Nvidia GPUs")
+
+SET(OPENMM_BUILD_FREE_ENERGY_PATH)
+SET(OPENMM_BUILD_FREE_ENERGY_CUDA_PATH)
+IF(OPENMM_BUILD_FREE_ENERGY_CUDA_LIB)
+    ADD_SUBDIRECTORY(platforms/cuda)
+    SET(OPENMM_BUILD_FREE_ENERGY_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
+    SET(OPENMM_BUILD_FREE_ENERGY_CUDA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
+    SET(OPENMM_FREE_ENERGY_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda)
+ENDIF(OPENMM_BUILD_FREE_ENERGY_CUDA_LIB)
+
+#SET(OPENMM_BUILD_BROOK_LIB OFF CACHE BOOL "Build OpenMMBrook library for ATI GPUs")
+#IF(OPENMM_BUILD_BROOK_LIB)
+#    ADD_SUBDIRECTORY(platforms/brook)
+#ENDIF(OPENMM_BUILD_BROOK_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_FREE_ENERGY_TARGET})
+INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_FREE_ENERGY_TARGET})
+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})
+
+#
+# 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
+#
+
+ENABLE_TESTING()
+
+IF (EXECUTABLE_OUTPUT_PATH)
+  SET (TEST_PATH ${EXECUTABLE_OUTPUT_PATH})
+ELSE (EXECUTABLE_OUTPUT_PATH)
+  SET (TEST_PATH .)
+ENDIF (EXECUTABLE_OUTPUT_PATH)
+
+#INCLUDE(ApiDoxygen.cmake)
+
+#ADD_SUBDIRECTORY(tests)
+#ADD_SUBDIRECTORY(examples)

plugins/freeEnergy/openmmapi/include/OpenMMFreeEnergy.h

+#ifndef OPENMM_FREE_ENERGY_H_
+#define OPENMM_FREE_ENERGY_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) 2009 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/GBVISoftcoreForce.h"
+#include "openmm/GBSAOBCSoftcoreForce.h"
+#include "openmm/NonbondedSoftcoreForce.h"
+
+#endif /*OPENMM_FREE_ENERGY_H_*/

plugins/freeEnergy/openmmapi/include/openmm/GBSAOBCSoftcoreForce.h

+#ifndef OPENMM_FREE_ENERGY_GBSA_OBC_FORCE_FIELD_H_
+#define OPENMM_FREE_ENERGY_GBSA_OBC_FORCE_FIELD_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) 2008-2009 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/Force.h"
+#include <vector>
+#include "openmm/internal/windowsExport.h"
+
+namespace OpenMM {
+
+/**
+ * This class implements an implicit solvation force using the GBSA-OBC model.
+ * <p>
+ * To use this class, create a GBSAOBCSoftcoreForce object, then call addParticle() once for each particle in the
+ * System to define its parameters.  The number of particles for which you define GBSA parameters must
+ * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
+ * try to create a Context.  After a particle has been added, you can modify its force field parameters
+ * by calling setParticleParameters().
+ * <p>
+ * If the System also contains a NonbondedForce, this force will use the cutoffs
+ * and periodic boundary conditions specified in it.
+ */
+
+class OPENMM_EXPORT GBSAOBCSoftcoreForce : public Force {
+public:
+    /*
+     * Create a GBSAOBCSoftcoreForce.
+     */
+    GBSAOBCSoftcoreForce();
+    /**
+     * Get the number of particles in the system.
+     */
+    int getNumParticles() const {
+        return particles.size();
+    }
+    /**
+     * Add the GBSA parameters for a particle.  This should be called once for each particle
+     * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
+     *
+     * @param charge                        the charge of the particle, measured in units of the proton charge
+     * @param radius                        the GBSA radius of the particle, measured in nm
+     * @param scalingFactor                 the OBC scaling factor for the particle
+     * @param nonPolarScalingFactor         the nonpolar scaling factor for the particle (default: 1.0)
+     * @return the index of the particle that was added
+     * @return the index of the particle that was added
+     */
+    int addParticle(double charge, double radius, double scalingFactor, double nonPolarScalingFactor = 1.0);
+    /**
+     * Get the force field parameters for a particle.
+     * 
+     * @param index                  the index of the particle for which to get parameters
+     * @param charge                 the charge of the particle, measured in units of the proton charge
+     * @param radius                 the GBSA radius of the particle, measured in nm
+     * @param scalingFactor          the OBC scaling factor for the particle
+     */
+    void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
+    /**
+     * Get the force field parameters for a particle.
+     * 
+     * @param index                  the index of the particle for which to get parameters
+     * @param charge                 the charge of the particle, measured in units of the proton charge
+     * @param radius                 the GBSA radius of the particle, measured in nm
+     * @param scalingFactor          the OBC scaling factor for the particle
+     * @param nonPolarScalingFactor  the nonpolar scaling factor for the particle
+     */
+    void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor, double& nonPolarScalingFactor) const;
+    /**
+     * Set the force field parameters for a particle.
+     * 
+     * @param index          the index of the particle for which to set parameters
+     * @param charge         the charge of the particle, measured in units of the proton charge
+     * @param radius         the GBSA radius of the particle, measured in nm
+     * @param scalingFactor  the OBC scaling factor for the particle
+     * @param nonPolarScalingFactor  the nonpolar scaling factor for the particle (default: 1.0)
+     */
+    void setParticleParameters(int index, double charge, double radius, double scalingFactor, double nonPolarScalingFactor = 1.0);
+    /**
+     * Get the dielectric constant for the solvent.
+     */
+    double getSolventDielectric() const {
+        return solventDielectric;
+    }
+    /**
+     * Set the dielectric constant for the solvent.
+     */
+    void setSolventDielectric(double dielectric) {
+        solventDielectric = dielectric;
+    }
+    /**
+     * Get the dielectric constant for the solute.
+     */
+    double getSoluteDielectric() const {
+        return soluteDielectric;
+    }
+    /**
+     * Set the dielectric constant for the solute.
+     */
+    void setSoluteDielectric(double dielectric) {
+        soluteDielectric = dielectric;
+    }
+    /**
+     * Get the nonPolarPrefactor.
+     */
+    double getNonPolarPrefactor() const {
+        return nonPolarPrefactor;
+    }
+    /**
+     * Set the nonPolarPrefactor.
+     */
+    void setNonPolarPrefactor(double inputNonPolarPrefactor) {
+        nonPolarPrefactor = inputNonPolarPrefactor;
+    }
+protected:
+    ForceImpl* createImpl();
+private:
+    class ParticleInfo;
+    double solventDielectric, soluteDielectric, nonPolarPrefactor;
+
+// Retarded visual studio compiler complains about being unable to 
+// export private stl class members.
+// This stanza explains that it should temporarily shut up.
+#if defined(_MSC_VER)
+#pragma warning(push)
+#pragma warning(disable:4251)
+#endif
+
+    std::vector<ParticleInfo> particles;
+
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
+};
+
+class GBSAOBCSoftcoreForce::ParticleInfo {
+public:
+    double charge, radius, scalingFactor, nonPolarScalingFactor;
+    ParticleInfo() {
+        charge = radius = scalingFactor = nonPolarScalingFactor = 0.0;
+    }
+    ParticleInfo(double charge, double radius, double scalingFactor, double nonPolarScalingFactor) :
+        charge(charge), radius(radius), scalingFactor(scalingFactor), nonPolarScalingFactor(nonPolarScalingFactor) {
+    }
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_FREE_ENERGY_GBSA_OBC_FORCE_FIELD_H_*/

plugins/freeEnergy/openmmapi/include/openmm/GBVISoftcoreForce.h

+#ifndef OPENMM_GBVI_SOFTCORE_FORCE_FIELD_H_
+#define OPENMM_GBVI_SOFTCORE_FORCE_FIELD_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) 2008-2009 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/Force.h"
+#include <vector>
+#include "openmm/internal/windowsExport.h"
+
+using std::pair;
+
+namespace OpenMM {
+
+/**
+ * This class implements an implicit solvation force using the GB/VI model.
+ * <p>
+ * To use this class, create a GBVISoftcoreForce object, then call addParticle() once for each particle in the
+ * System to define its parameters.  The number of particles for which you define GB/VI parameters must
+ * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
+ * try to create an Context.  After a particle has been added, you can modify its force field parameters
+ * by calling setParticleParameters().
+ * <p>
+ * If the System also contains a NonbondedForce, this force will use the cutoffs
+ * and periodic boundary conditions specified in it.
+ */
+
+class OPENMM_EXPORT GBVISoftcoreForce : public Force {
+public:
+    /** 
+     * This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
+     */
+    enum NonbondedSoftcoreMethod {
+        /**
+         * No cutoff is applied to nonbonded interactions.  The full set of N^2 interactions is computed exactly.
+         * This necessarily means that periodic boundary conditions cannot be used.  This is the default.
+         */
+        NoCutoff = 0,
+        /**
+         * Interactions beyond the cutoff distance are ignored.
+         */
+        CutoffNonPeriodic = 1,
+        /**
+         * Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
+         * each other particle.  Interactions beyond the cutoff distance are ignored.
+         */
+        CutoffPeriodic = 2,
+    };  
+    /** 
+     * This is an enumeration of the different methods that may be used for scaling of the Born radii.
+     */
+    enum BornRadiusScalingSoftcoreMethod {
+        /**
+         * No scaling method is applied.
+         */
+        NoScaling          = 0,
+        /**
+         * Use the method outlined in Proteins 55, 383-394 (2004), Eq. 6
+         */
+        Tanh               = 1,
+        /**
+         * Use quintic spline scaling function
+         */
+        QuinticSpline       = 2 
+    };  
+    /*
+     * Create a GBVISoftcoreForce.
+     */
+    GBVISoftcoreForce();
+    /**
+     * Get the number of particles in the system.
+     */
+    int getNumParticles() const {
+        return particles.size();
+    }
+    /**
+     * Add the GB/VI parameters for a particle.  This should be called once for each particle
+     * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
+     *
+     * @param charge                the charge of the particle, measured in units of the proton charge
+     * @param radius                the GB/VI radius of the particle, measured in nm
+     * @param gamma                 the gamma parameter
+     * @param bornRadiusScaleFactor the Born radius scale factor (used for free energy calculations)
+     */
+    void addParticle(double charge, double radius, double gamma, double bornRadiusScaleFactor = 1.0 );
+    /**
+     * Get the force field parameters for a particle.
+     * 
+     * @param index          the index of the particle for which to get parameters
+     * @param charge         the charge of the particle, measured in units of the proton charge
+     * @param radius         the GBSA radius of the particle, measured in nm
+     * @param gamma          the gamma parameter
+     */
+    void getParticleParameters(int index, double& charge, double& radius, double& gamma) const;
+    /**
+     * Get the force field parameters for a particle.
+     * 
+     * @param index                 the index of the particle for which to get parameters
+     * @param charge                the charge of the particle, measured in units of the proton charge
+     * @param radius                the GBSA radius of the particle, measured in nm
+     * @param gamma                 the gamma parameter
+     * @param bornRadiusScaleFactor the Born radius scale factor (used for free energy calculations)
+     */
+    void getParticleParameters(int index, double& charge, double& radius, double& gamma, double& bornRadiusScaleFactor) const;
+    /**
+     * Set the force field parameters for a particle.
+     * 
+     * @param index                 the index of the particle for which to set parameters
+     * @param charge                the charge of the particle, measured in units of the proton charge
+     * @param radius                the GB/VI radius of the particle, measured in nm
+     * @param gamma                 the gamma parameter
+     * @param bornRadiusScaleFactor the Born radius scale factor (used for free energy calculations)
+     */
+    void setParticleParameters(int index, double charge, double radius, double gamma, double bornRadiusScaleFactor = 1.0 );
+    /**
+     * Add a bond 
+     *
+     * @param particle1 the index of the first particle 
+     * @param particle2 the index of the second particle
+     * @param distance  the distance between the two particles, measured in nm
+     * @return the index of the bond that was added
+     */
+    int addBond(int particle1, int particle2, double distance);
+
+    /** 
+     * Get the parameters defining a bond
+     * 
+     * @param index     the index of the bond for which to get parameters
+     * @param particle1 the index of the first particle involved in the bond
+     * @param particle2 the index of the second particle involved in the bond
+     * @param distance  the distance between the two particles, measured in nm
+     */
+    void getBondParameters(int index, int& particle1, int& particle2, double& distance) const;
+    /**
+     * Set 1-2 bonds
+     * 
+     * @param index          index of the bond for which to set parameters
+     * @param particle1      index of first atom in bond
+     * @param particle2      index of second atom in bond
+     * @param bondLength     bond length
+     */
+    void setBondParameters( int index, int particle1, int particle2, double bondLength);
+    /** 
+     * Get number of bonds
+     * 
+     * @return number of bonds
+     */
+    int getNumBonds( void ) const;
+    /**
+     * Get the dielectric constant for the solvent.
+     */
+    double getSolventDielectric() const {
+        return solventDielectric;
+    }
+    /**
+     * Set the dielectric constant for the solvent.
+     */
+    void setSolventDielectric(double dielectric) {
+        solventDielectric = dielectric;
+    }
+    /**
+     * Get the dielectric constant for the solute.
+     */
+    double getSoluteDielectric() const {
+        return soluteDielectric;
+    }
+    /**
+     * Set the dielectric constant for the solute.
+     */
+    void setSoluteDielectric(double dielectric) {
+        soluteDielectric = dielectric;
+    }
+    /** 
+     * Get the method used for handling long range nonbonded interactions.
+     */
+    NonbondedSoftcoreMethod getNonbondedMethod() const;
+    /** 
+     * Set the method used for handling long range nonbonded interactions.
+     */
+    void setNonbondedMethod(NonbondedSoftcoreMethod method);
+    /** 
+     * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
+     * is NoCutoff, this value will have no effect.
+     */
+    double getCutoffDistance() const;
+    /** 
+     * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
+     * is NoCutoff, this value will have no effect.
+     */
+    void setCutoffDistance(double distance);
+    /** 
+     * Get the method used for scaling Born radii.
+     */
+    BornRadiusScalingSoftcoreMethod getBornRadiusScalingMethod() const;
+    /** 
+     * Set the method used for scaling Born radii.
+     */
+    void setBornRadiusScalingMethod(BornRadiusScalingSoftcoreMethod method);
+    /** 
+     * Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
+     */
+    double getQuinticLowerLimitFactor( void ) const;
+    /** 
+     * Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
+     */
+    void setQuinticLowerLimitFactor(double quinticLowerLimitFactor );
+    /** 
+     * Get the upper limit  used in the quintic spline scaling method (typically 0.5-0.8)
+     */
+    double getQuinticUpperBornRadiusLimit( void ) const;
+    /** 
+     * Set the upper limit used in the quintic spline scaling method (typically 0.008)
+     */
+    void setQuinticUpperBornRadiusLimit(double quinticUpperBornRadiusLimit);
+    /** 
+     * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
+     * is NoCutoff, this value will have no effect.
+     */
+    void getTanhParameters( double& alpha, double& beta, double& gamma) const;
+    /** 
+     * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
+     * is NoCutoff, this value will have no effect.
+     */
+    void setTanhParameters(double alpha, double beta, double gamma);
+protected:
+    ForceImpl* createImpl();
+private:
+    class ParticleInfo;
+
+    NonbondedSoftcoreMethod nonbondedMethod;
+    double cutoffDistance, solventDielectric, soluteDielectric;
+
+    BornRadiusScalingSoftcoreMethod scalingMethod;
+    double alpha, beta, gamma;
+    double quinticLowerLimitFactor, quinticUpperBornRadiusLimit;
+
+    class BondInfo;
+
+// Retarded visual studio compiler complains about being unable to 
+// export private stl class members.
+// This stanza explains that it should temporarily shut up.
+#if defined(_MSC_VER)
+#pragma warning(push)
+#pragma warning(disable:4251)
+#endif
+
+    std::vector<ParticleInfo> particles;
+    std::vector<BondInfo> bonds;
+
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
+};
+
+class GBVISoftcoreForce::ParticleInfo {
+public:
+    double charge, radius, gamma, bornRadiusScaleFactor;
+    ParticleInfo() {
+        charge = radius = gamma = 0.0;
+        bornRadiusScaleFactor = 1.0;
+    }
+    ParticleInfo(double charge, double radius, double gamma, double bornRadiusScaleFactor) :
+        charge(charge), radius(radius), gamma(gamma), bornRadiusScaleFactor(bornRadiusScaleFactor) {
+    }
+};
+
+class GBVISoftcoreForce::BondInfo {
+public:
+    int particle1, particle2;
+    double bondLength;
+    BondInfo() {
+        bondLength     = 0.0;
+        particle1      = -1;
+        particle2      = -1;
+    }
+    BondInfo(int atomIndex1, int atomIndex2, double bondLength) :
+             particle1(atomIndex1), particle2(atomIndex2), bondLength(bondLength) {
+    }
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_GBVI_SOFTCORE_FORCEFIELD_H_*/

plugins/freeEnergy/openmmapi/include/openmm/freeEnergyKernels.h

+#ifndef OPENMM_FREE_ENERGY_KERNELS_H_
+#define OPENMM_FREE_ENERGY_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) 2008-2009 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/GBSAOBCSoftcoreForce.h"
+#include "openmm/GBVISoftcoreForce.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/NonbondedSoftcoreForce.h"
+#include "openmm/System.h"
+#include "openmm/KernelImpl.h"
+#include <set>
+#include <string>
+#include <vector>
+
+namespace OpenMM {
+
+/**
+ * This kernel is invoked by GBSAOBCSoftcoreForce to calculate the forces acting on the system and the energy of the system.
+ */
+class CalcGBSAOBCSoftcoreForceKernel : public KernelImpl {
+public:
+    static std::string Name() {
+        return "CalcGBSAOBCSoftcoreForce";
+    }
+    CalcGBSAOBCSoftcoreForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    }
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param force      the GBSAOBCSoftcoreForce this kernel will be used for
+     */
+    virtual void initialize(const System& system, const GBSAOBCSoftcoreForce& force) = 0;
+    /**
+     * Execute the kernel to calculate the forces.
+     * 
+     * @param context    the context in which to execute this kernel
+     */
+    virtual void executeForces(ContextImpl& context) = 0;
+    /**
+     * Execute the kernel to calculate the energy.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @return the potential energy due to the GBSAOBCSoftcoreForce
+     */
+    virtual double executeEnergy(ContextImpl& context) = 0;
+};
+
+/**
+ * This kernel is invoked by NonbondedForce to calculate the forces acting on the system and the energy of the system.
+ */
+class CalcNonbondedSoftcoreForceKernel : public KernelImpl {
+public:
+    enum NonbondedSoftcoreMethod {
+        NoCutoff          = 0,
+        CutoffNonPeriodic = 1,
+        CutoffPeriodic    = 2,
+        Ewald             = 3,
+        PME               = 4
+    };
+    static std::string Name() {
+        return "CalcNonbondedSoftcoreForce";
+    }
+    CalcNonbondedSoftcoreForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    }
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param force      the NonbondedSoftcoreForce this kernel will be used for
+     */
+    virtual void initialize(const System& system, const NonbondedSoftcoreForce& force) = 0;
+    /**
+     * Execute the kernel to calculate the forces.
+     * 
+     * @param context    the context in which to execute this kernel
+     */
+    virtual void executeForces(ContextImpl& context) = 0;
+    /**
+     * Execute the kernel to calculate the energy.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @return the potential energy due to the NonbondedSoftcoreForce
+     */
+    virtual double executeEnergy(ContextImpl& context) = 0;
+};
+
+/**
+ * This kernel is invoked by GBVISoftcoreForce to calculate the forces acting on the system and the energy of the system.
+ */
+class CalcGBVISoftcoreForceKernel : public KernelImpl {
+public:
+    static std::string Name() {
+        return "CalcGBVISoftcoreForce";
+    }
+    CalcGBVISoftcoreForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    }
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system      the System this kernel will be applied to
+     * @param force       the GBVISoftcoreForce this kernel will be used for
+     * @param scaledRadii scaled radii
+     */
+    virtual void initialize(const System& system, const GBVISoftcoreForce& force, const std::vector<double>& scaledRadii) = 0;
+    /**
+     * Execute the kernel to calculate the forces.
+     * 
+     * @param context    the context in which to execute this kernel
+     */
+    virtual void executeForces(ContextImpl& context) = 0;
+    /**
+     * Execute the kernel to calculate the energy.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @return the potential energy due to the GBVISoftcoreForce
+     */
+    virtual double executeEnergy(ContextImpl& context) = 0;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_FREE_ENERGY_KERNELS_H_*/

plugins/freeEnergy/openmmapi/include/openmm/internal/GBSAOBCSoftcoreForceImpl.h

+#ifndef OPENMM_GBSA_OBC_SOFTCORE_FORCE_FIELD_IMPL_H_
+#define OPENMM_GBSA_OBC_SOFTCORE_FORCE_FIELD_IMPL_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 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/internal/ForceImpl.h"
+#include "openmm/GBSAOBCSoftcoreForce.h"
+#include "openmm/Kernel.h"
+#include <string>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of GBSAOBCSoftcoreForce.
+ */
+
+class GBSAOBCSoftcoreForceImpl : public ForceImpl {
+public:
+    GBSAOBCSoftcoreForceImpl(GBSAOBCSoftcoreForce& owner);
+    void initialize(ContextImpl& context);
+    GBSAOBCSoftcoreForce& getOwner() {
+        return owner;
+    }
+    void updateContextState(ContextImpl& context) {
+        // This force field doesn't update the state directly.
+    }
+    void calcForces(ContextImpl& context);
+    double calcEnergy(ContextImpl& context);
+    std::map<std::string, double> getDefaultParameters() {
+        return std::map<std::string, double>(); // This force field doesn't define any parameters.
+    }
+    std::vector<std::string> getKernelNames();
+private:
+    GBSAOBCSoftcoreForce& owner;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_GBSA_OBC_SOFTCORE_FORCE_FIELD_IMPL_H_*/

plugins/freeEnergy/openmmapi/include/openmm/internal/GBVISoftcoreForceImpl.h

+#ifndef OPENMM_GBVI_SOFTCORE_FORCEFIELDIMPL_H_
+#define OPENMM_GBVI_SOFTCORE_FORCEFIELDIMPL_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 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/internal/ForceImpl.h"
+#include "openmm/GBVISoftcoreForce.h"
+#include "openmm/Kernel.h"
+#include <string>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of GBVISoftcoreForce.
+ */
+
+class GBVISoftcoreForceImpl : public ForceImpl {
+public:
+    GBVISoftcoreForceImpl(GBVISoftcoreForce& owner);
+    void initialize(ContextImpl& context);
+    GBVISoftcoreForce& getOwner() {
+        return owner;
+    }
+    
+    // set bond info using HarmonicBond and constraints
+    int getBondsFromForces(ContextImpl& context);
+
+    // calculate scaled radii (Eq. 5 of Labute paper [JCC 29 1693-1698 2008])
+
+    void findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
+                          const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const;
+
+    void updateContextState(ContextImpl& context) {
+        // This force field doesn't update the state directly.
+    }
+    void calcForces(ContextImpl& context);
+    double calcEnergy(ContextImpl& context);
+    std::map<std::string, double> getDefaultParameters() {
+        return std::map<std::string, double>(); // This force field doesn't define any parameters.
+    }
+    std::vector<std::string> getKernelNames();
+private:
+    GBVISoftcoreForce& owner;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_GBVI_SOFTCORE_FORCEFIELDIMPL_H_*/

plugins/freeEnergy/openmmapi/include/openmm/internal/NonbondedSoftcoreForceImpl.h

+#ifndef OPENMM_NONBONDED_SOFTCORE_FORCE_IMPL_H_
+#define OPENMM_NONBONDED_SOFTCORE_FORCE_IMPL_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) 2008-2009 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/internal/ForceImpl.h"
+#include "openmm/NonbondedSoftcoreForce.h"
+#include "openmm/Kernel.h"
+#include <utility>
+#include <set>
+#include <string>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of NonbondedSoftcoreForce.
+ */
+
+class NonbondedSoftcoreForceImpl : public ForceImpl {
+public:
+    NonbondedSoftcoreForceImpl(NonbondedSoftcoreForce& owner);
+    ~NonbondedSoftcoreForceImpl();
+    void initialize(ContextImpl& context);
+    NonbondedSoftcoreForce& getOwner() {
+        return owner;
+    }
+    void updateContextState(ContextImpl& context) {
+        // This force field doesn't update the state directly.
+    }
+    void calcForces(ContextImpl& context);
+    double calcEnergy(ContextImpl& context);
+    std::map<std::string, double> getDefaultParameters() {
+        return std::map<std::string, double>(); // This force field doesn't define any parameters.
+    }
+    std::vector<std::string> getKernelNames();
+private:
+    NonbondedSoftcoreForce& owner;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_NONBONDED_SOFTCORE_FORCE_IMPL_H_*/

plugins/freeEnergy/openmmapi/src/GBSAOBCSoftcoreForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2008-2009 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/Force.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/GBSAOBCSoftcoreForce.h"
+#include "openmm/internal/GBSAOBCSoftcoreForceImpl.h"
+
+using namespace OpenMM;
+
+GBSAOBCSoftcoreForce::GBSAOBCSoftcoreForce() : solventDielectric(78.3), soluteDielectric(1.0), nonPolarPrefactor( 0.0054 ){
+}
+
+int GBSAOBCSoftcoreForce::addParticle(double charge, double radius, double scalingFactor, double nonPolarScalingFactor) {
+    particles.push_back(ParticleInfo(charge, radius, scalingFactor, nonPolarScalingFactor));
+    return particles.size()-1;
+}
+
+void GBSAOBCSoftcoreForce::getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const {
+    charge                = particles[index].charge;
+    radius                = particles[index].radius;
+    scalingFactor         = particles[index].scalingFactor;
+}
+
+void GBSAOBCSoftcoreForce::getParticleParameters(int index, double& charge, double& radius, double& scalingFactor, double& nonPolarScalingFactor) const {
+    charge                = particles[index].charge;
+    radius                = particles[index].radius;
+    scalingFactor         = particles[index].scalingFactor;
+    nonPolarScalingFactor = particles[index].nonPolarScalingFactor;
+}
+
+void GBSAOBCSoftcoreForce::setParticleParameters(int index, double charge, double radius, double scalingFactor, double nonPolarScalingFactor) {
+    particles[index].charge                 = charge;
+    particles[index].radius                 = radius;
+    particles[index].scalingFactor          = scalingFactor;
+    particles[index].nonPolarScalingFactor  = nonPolarScalingFactor;
+}
+
+ForceImpl* GBSAOBCSoftcoreForce::createImpl() {
+    return new GBSAOBCSoftcoreForceImpl(*this);
+}

plugins/freeEnergy/openmmapi/src/GBSAOBCSoftcoreForceImpl.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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 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/internal/GBSAOBCSoftcoreForceImpl.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/freeEnergyKernels.h"
+#include <vector>
+
+using namespace OpenMM;
+using std::vector;
+
+GBSAOBCSoftcoreForceImpl::GBSAOBCSoftcoreForceImpl(GBSAOBCSoftcoreForce& owner) : owner(owner) {
+}
+
+void GBSAOBCSoftcoreForceImpl::initialize(ContextImpl& context) {
+    kernel = context.getPlatform().createKernel(CalcGBSAOBCSoftcoreForceKernel::Name(), context);
+    if (owner.getNumParticles() != context.getSystem().getNumParticles())
+        throw OpenMMException("GBSAOBCSoftcoreForce must have exactly as many particles as the System it belongs to.");
+    dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
+}
+
+void GBSAOBCSoftcoreForceImpl::calcForces(ContextImpl& context ) {
+    dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).executeForces(context);
+}
+
+double GBSAOBCSoftcoreForceImpl::calcEnergy(ContextImpl& context) {
+    return dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).executeEnergy(context);
+}
+
+std::vector<std::string> GBSAOBCSoftcoreForceImpl::getKernelNames() {
+    std::vector<std::string> names;
+    names.push_back(CalcGBSAOBCSoftcoreForceKernel::Name());
+    return names;
+}

plugins/freeEnergy/openmmapi/src/GBVISoftcoreForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2008-2009 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/Force.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/GBVISoftcoreForce.h"
+#include "openmm/internal/GBVISoftcoreForceImpl.h"
+#include <sstream>
+
+using namespace OpenMM;
+
+GBVISoftcoreForce::GBVISoftcoreForce() :  nonbondedMethod(NoCutoff), cutoffDistance(1.0), solventDielectric(78.3), soluteDielectric(1.0),
+               scalingMethod(NoScaling), alpha(1.0), beta(0.8), gamma(4.85), quinticLowerLimitFactor(0.8), quinticUpperBornRadiusLimit(5.0) {
+
+}
+
+void GBVISoftcoreForce::addParticle(double charge, double radius, double gamma, double bornRadiusScaleFactor) {
+    particles.push_back(ParticleInfo(charge, radius, gamma, bornRadiusScaleFactor));
+}
+
+void GBVISoftcoreForce::getParticleParameters(int index, double& charge, double& radius, double& gamma ) const {
+    charge = particles[index].charge;
+    radius = particles[index].radius;
+    gamma  = particles[index].gamma;
+}
+
+void GBVISoftcoreForce::getParticleParameters(int index, double& charge, double& radius, double& gamma, double& bornRadiusScaleFactor ) const {
+    charge                = particles[index].charge;
+    radius                = particles[index].radius;
+    gamma                 = particles[index].gamma;
+    bornRadiusScaleFactor = particles[index].bornRadiusScaleFactor;
+}
+
+void GBVISoftcoreForce::setParticleParameters(int index, double charge, double radius, double gamma, double bornRadiusScaleFactor) {
+    particles[index].charge                = charge;
+    particles[index].radius                = radius;
+    particles[index].gamma                 = gamma;
+    particles[index].bornRadiusScaleFactor = bornRadiusScaleFactor;
+}
+
+GBVISoftcoreForce::NonbondedSoftcoreMethod GBVISoftcoreForce::getNonbondedMethod() const {
+    return nonbondedMethod;
+}
+
+void GBVISoftcoreForce::setNonbondedMethod(NonbondedSoftcoreMethod method) {
+    nonbondedMethod = method;
+}
+
+double GBVISoftcoreForce::getCutoffDistance() const {
+    return cutoffDistance;
+}
+
+void GBVISoftcoreForce::setCutoffDistance(double distance) {
+    cutoffDistance = distance;
+}
+
+GBVISoftcoreForce::BornRadiusScalingSoftcoreMethod GBVISoftcoreForce::getBornRadiusScalingMethod( void ) const {
+    return scalingMethod;
+}
+
+void GBVISoftcoreForce::setBornRadiusScalingMethod(BornRadiusScalingSoftcoreMethod method) {
+    scalingMethod = method;
+}
+
+double GBVISoftcoreForce::getQuinticLowerLimitFactor( void ) const {
+    return quinticLowerLimitFactor;
+}
+
+void GBVISoftcoreForce::setQuinticLowerLimitFactor(double inputQuinticLowerLimitFactor ){
+    quinticLowerLimitFactor = inputQuinticLowerLimitFactor;
+}
+
+double GBVISoftcoreForce::getQuinticUpperBornRadiusLimit( void ) const {
+    return quinticUpperBornRadiusLimit;
+}
+
+void GBVISoftcoreForce::setQuinticUpperBornRadiusLimit(double inputQuinticUpperBornRadiusLimit){
+    quinticUpperBornRadiusLimit = inputQuinticUpperBornRadiusLimit;
+}
+
+void GBVISoftcoreForce::getTanhParameters( double& returnAlpha, double& returnBeta, double& returnGamma) const {
+    returnAlpha   = alpha;
+    returnBeta    = beta;
+    returnGamma   = gamma;
+    return;
+}
+
+void GBVISoftcoreForce::setTanhParameters(double inputAlpha, double inputBeta, double inputGamma){
+    alpha   = inputAlpha;
+    beta    = inputBeta;
+    gamma   = inputGamma;
+}
+
+int GBVISoftcoreForce::addBond(int particle1, int particle2, double bondLength) {
+    bonds.push_back(BondInfo(particle1, particle2, bondLength));
+    return bonds.size()-1;
+}
+
+void GBVISoftcoreForce::setBondParameters( int index, int particle1, int particle2, double bondLength) {
+    bonds[index].particle1  = particle1;
+    bonds[index].particle2  = particle2;
+    bonds[index].bondLength = bondLength;
+}
+
+int GBVISoftcoreForce::getNumBonds( void ) const {
+   return (int) bonds.size();
+}
+
+void GBVISoftcoreForce::getBondParameters(int index, int& bondIndex1, int& bondIndex2, double& bondLength) const {
+    bondIndex1 = bonds[index].particle1;
+    bondIndex2 = bonds[index].particle2;
+    bondLength = bonds[index].bondLength;
+}
+
+ForceImpl* GBVISoftcoreForce::createImpl() {
+    return new GBVISoftcoreForceImpl(*this);
+}

plugins/freeEnergy/openmmapi/src/GBVISoftcoreForceImpl.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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 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/internal/GBVISoftcoreForceImpl.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/freeEnergyKernels.h"
+#include "openmm/kernels.h"
+#include <vector>
+#include <cmath>
+#include <cstdio>
+#include <sstream>
+
+using namespace OpenMM;
+using std::vector;
+
+GBVISoftcoreForceImpl::GBVISoftcoreForceImpl(GBVISoftcoreForce& owner) : owner(owner) {
+}
+
+void GBVISoftcoreForceImpl::initialize(ContextImpl& context) {
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "GBVISoftcoreForceImpl::initialize";
+
+// ---------------------------------------------------------------------------------------
+
+    kernel                    = context.getPlatform().createKernel(CalcGBVISoftcoreForceKernel::Name(), context);
+    System& system            = context.getSystem();
+    int     numberOfParticles = owner.getNumParticles();
+
+    // validate number of particles consistent
+
+    if( numberOfParticles != system.getNumParticles() ){
+        throw OpenMMException("GBVISoftcoreForce must have exactly as many particles as the System it belongs to.");
+    }
+
+    // load 1-2 atom pairs along w/ bond distance using HarmonicBondForce & constraints
+    // if numberOfBonds < 1, indicating they were not set by the user
+
+    if( owner.getNumBonds() < 1 ){
+        getBondsFromForces( context );
+    }   
+    int numberOfBonds = owner.getNumBonds();
+
+    std::vector< std::vector<int> > bondIndices;
+    bondIndices.resize( numberOfBonds );
+
+    std::vector<double> bondLengths;
+    bondLengths.resize( numberOfBonds );
+double maxBond = -1.0;
+    for (int i = 0; i < numberOfBonds; i++) {
+        int particle1, particle2;
+        double bondLength;
+        owner.getBondParameters(i, particle1, particle2, bondLength);
+        if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
+            std::stringstream msg;
+            msg << "GBVISoftcoreForce: Illegal particle index: ";
+            msg << particle1;
+            throw OpenMMException(msg.str());
+        }
+        if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
+            std::stringstream msg;
+            msg << "GBVISoftcoreForce: Illegal particle index: ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+if( maxBond < bondLength ) maxBond = bondLength;
+        if (bondLength < 0.0 ) {
+            std::stringstream msg;
+            msg << "GBVISoftcoreForce: negative bondlength: ";
+            msg << bondLength;
+            throw OpenMMException(msg.str());
+        }
+        bondIndices[i].push_back( particle1 ); 
+        bondIndices[i].push_back( particle2 );
+        bondLengths[i] = bondLength;
+    }
+
+fprintf( stderr, "%s MaxBond=%14.6e\n", methodName.c_str(), maxBond );
+
+    vector<double> scaledRadii;
+    scaledRadii.resize(numberOfParticles);
+    findScaledRadii( numberOfParticles, bondIndices, bondLengths, scaledRadii);
+
+    dynamic_cast<CalcGBVISoftcoreForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner, scaledRadii);
+}
+
+int GBVISoftcoreForceImpl::getBondsFromForces(ContextImpl& context) {
+
+// ---------------------------------------------------------------------------------------
+
+   //static const std::string methodName      = "GBVISoftcoreForceImpl::getBondsFromForces";
+
+// ---------------------------------------------------------------------------------------
+
+    // load 1-2 atom pairs along w/ bond distance using HarmonicBondForce & constraints
+    
+    System& system            = context.getSystem();
+    for (int i = 0; i < system.getNumForces(); i++) {
+        if (dynamic_cast<HarmonicBondForce*>(&system.getForce(i)) != NULL) {
+            const HarmonicBondForce& force = dynamic_cast<const HarmonicBondForce&>(system.getForce(i));
+            for (int j = 0; j < force.getNumBonds(); ++j) {
+                int particle1, particle2;
+                double length, k;
+                force.getBondParameters(j, particle1, particle2, length, k); 
+                owner.addBond( particle1, particle2, length );
+            }
+            break;
+        }
+    }
+
+    // Also treat constrained distances as bonds if mass of one particle is < (2.0 + epsilon) (~2=deuterium) 
+
+    for (int j = 0; j < system.getNumConstraints(); j++) {
+        int particle1, particle2;
+        double distance;
+        system.getConstraintParameters(j, particle1, particle2, distance);
+        if( system.getParticleMass( particle1 ) < 2.1 || system.getParticleMass( particle2 ) < 2.1 ){
+            owner.addBond( particle1, particle2, distance );
+        }
+    }
+
+}
+
+#define GBVIDebug 0
+
+void GBVISoftcoreForceImpl::findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
+                                             const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const {
+
+// ---------------------------------------------------------------------------------------
+
+   //static const std::string methodName      = "GBVISoftcoreForceImpl::findScaledRadii";
+
+// ---------------------------------------------------------------------------------------
+
+    // load 1-2 indicies for each atom 
+
+    std::vector<std::vector<int> > bonded12(numberOfParticles);
+
+    for (int i = 0; i < (int) bondIndices.size(); ++i) {
+        bonded12[bondIndices[i][0]].push_back(i);
+        bonded12[bondIndices[i][1]].push_back(i);
+    }
+
+    int errors = 0;
+
+    // compute scaled radii (Eq. 5 of Labute paper [JCC 29 p. 1693-1698 2008])
+
+    for (int j = 0; j < (int) bonded12.size(); ++j){
+
+        double charge;
+        double gamma;
+        double radiusJ;
+        double scaledRadiusJ;
+     
+        owner.getParticleParameters(j, charge, radiusJ, gamma); 
+
+        if(  bonded12[j].size() == 0 ){
+//            (void) fprintf( stderr, "Warning GBVISoftcoreForceImpl::findScaledRadii atom %d has no covalent bonds; using atomic radius=%.3f.\n", j, radiusJ );
+            scaledRadiusJ = radiusJ;
+//             errors++;
+        } else {
+
+            double rJ2    = radiusJ*radiusJ;
+    
+            // loop over bonded neighbors of atom j, applying Eq. 5 in Labute
+
+            scaledRadiusJ = 0.0;
+            for (int i = 0; i < (int) bonded12[j].size(); ++i){
+    
+               int index            = bonded12[j][i];
+               int bondedAtomIndex  = (j == bondIndices[index][0]) ? bondIndices[index][1] : bondIndices[index][0];
+              
+               double radiusI;
+               owner.getParticleParameters(bondedAtomIndex, charge, radiusI, gamma); 
+               double rI2           = radiusI*radiusI;
+    
+               double a_ij          = (radiusI - bondLengths[index]);
+                      a_ij         *= a_ij;
+                      a_ij          = (rJ2 - a_ij)/(2.0*bondLengths[index]);
+    
+               double a_ji          = radiusJ - bondLengths[index];
+                      a_ji         *= a_ji;
+                      a_ji          = (rI2 - a_ji)/(2.0*bondLengths[index]);
+    
+               scaledRadiusJ       += a_ij*a_ij*(3.0*radiusI - a_ij) + a_ji*a_ji*( 3.0*radiusJ - a_ji );
+            }
+    
+#if GBVIDebug
+//(void) fprintf( stderr, "j=%d rJ=%12.4f scaledRadiusJRaw==%12.4f", j, radiusJ, scaledRadiusJ );
+#endif
+            scaledRadiusJ  = (radiusJ*radiusJ*radiusJ) - 0.125*scaledRadiusJ; 
+
+#if GBVIDebug
+//(void) fprintf( stderr, " scRJInt=%12.4f\n", scaledRadiusJ );
+#endif
+            if( scaledRadiusJ > 0.0 ){
+                scaledRadiusJ  = 0.95*pow( scaledRadiusJ, (1.0/3.0) );
+            } else {
+                scaledRadiusJ  = 0.0;
+            }
+        }
+        scaledRadii[j] = scaledRadiusJ;
+
+    }
+
+    // abort if errors
+
+    if( errors ){
+        throw OpenMMException("GBVISoftcoreForceImpl::findScaledRadii errors -- aborting");
+    }
+
+#if GBVIDebug
+    (void) fprintf( stderr, "                  R              q          gamma   scaled radii no. bnds\n" );
+    double totalQ = 0.0;
+    for( int i = 0; i < (int) scaledRadii.size(); i++ ){
+
+        double charge;
+        double gamma;
+        double radiusI;
+     
+        owner.getParticleParameters(i, charge, radiusI, gamma); 
+        totalQ += charge;
+        (void) fprintf( stderr, "%4d %14.5e %14.5e %14.5e %14.5e %d\n", i, radiusI, charge, gamma, scaledRadii[i], (int) bonded12[i].size() );
+    }
+    (void) fprintf( stderr, "Total charge=%e\n", totalQ );
+    (void) fflush( stderr );
+#endif
+#undef GBVIDebug
+
+}
+
+void GBVISoftcoreForceImpl::calcForces(ContextImpl& context) {
+    dynamic_cast<CalcGBVISoftcoreForceKernel&>(kernel.getImpl()).executeForces(context);
+}
+
+double GBVISoftcoreForceImpl::calcEnergy(ContextImpl& context) {
+    return dynamic_cast<CalcGBVISoftcoreForceKernel&>(kernel.getImpl()).executeEnergy(context);
+}
+
+std::vector<std::string> GBVISoftcoreForceImpl::getKernelNames() {
+    std::vector<std::string> names;
+    names.push_back(CalcGBVISoftcoreForceKernel::Name());
+    return names;
+}

plugins/freeEnergy/openmmapi/src/NonbondedSoftcoreForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2008-2009 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/Force.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/NonbondedSoftcoreForce.h"
+#include "openmm/internal/NonbondedSoftcoreForceImpl.h"
+#include <cmath>
+#include <map>
+#include <sstream>
+#include <utility>
+
+using namespace OpenMM;
+using std::map;
+using std::pair;
+using std::set;
+using std::string;
+using std::stringstream;
+using std::vector;
+
+NonbondedSoftcoreForce::NonbondedSoftcoreForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0),  rfDielectric(78.3), ewaldErrorTol(1e-4), softCoreLJLambda(1.0) {
+}
+
+NonbondedSoftcoreForce::NonbondedSoftcoreMethod NonbondedSoftcoreForce::getNonbondedMethod() const {
+    return nonbondedMethod;
+}
+
+void NonbondedSoftcoreForce::setNonbondedMethod(NonbondedSoftcoreMethod method) {
+    nonbondedMethod = method;
+}
+
+double NonbondedSoftcoreForce::getCutoffDistance() const {
+    return cutoffDistance;
+}
+
+void NonbondedSoftcoreForce::setCutoffDistance(double distance) {
+    cutoffDistance = distance;
+}
+
+double NonbondedSoftcoreForce::getSoftCoreLJLambda( void ) const {
+    return softCoreLJLambda;
+}
+
+void NonbondedSoftcoreForce::setSoftCoreLJLambda(double lambda) {
+    softCoreLJLambda = lambda;
+}
+
+double NonbondedSoftcoreForce::getReactionFieldDielectric( void ) const {
+    return rfDielectric;
+}
+
+void NonbondedSoftcoreForce::setReactionFieldDielectric(double dielectric) {
+    rfDielectric = dielectric;
+}
+
+double NonbondedSoftcoreForce::getEwaldErrorTolerance( void ) const {
+    return ewaldErrorTol;
+}
+
+void NonbondedSoftcoreForce::setEwaldErrorTolerance(double tol)
+{
+    ewaldErrorTol = tol;
+}
+
+int NonbondedSoftcoreForce::addParticle(double charge, double sigma, double epsilon, double softcoreLJLambda) {
+    particles.push_back(ParticleInfo(charge, sigma, epsilon, softcoreLJLambda));
+    return particles.size()-1;
+}
+
+void NonbondedSoftcoreForce::getParticleParameters(int index, double& charge, double& sigma, double& epsilon) const {
+    charge   = particles[index].charge;
+    sigma    = particles[index].sigma;
+    epsilon  = particles[index].epsilon;
+}
+
+void NonbondedSoftcoreForce::getParticleParameters(int index, double& charge, double& sigma, double& epsilon, double& softcoreLJLambda) const {
+    charge           = particles[index].charge;
+    sigma            = particles[index].sigma;
+    epsilon          = particles[index].epsilon;
+    softcoreLJLambda = particles[index].softcoreLJLambda;
+}
+
+void NonbondedSoftcoreForce::setParticleParameters(int index, double charge, double sigma, double epsilon, double softcoreLJLambda) {
+    particles[index].charge            = charge;
+    particles[index].sigma             = sigma;
+    particles[index].epsilon           = epsilon;
+    particles[index].softcoreLJLambda  = softcoreLJLambda;
+}
+
+int NonbondedSoftcoreForce::addException(int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace, double softcoreLJLambda ) {
+    map<pair<int, int>, int>::iterator iter = exceptionMap.find(pair<int, int>(particle1, particle2));
+    int newIndex;
+    if (iter == exceptionMap.end())
+        iter = exceptionMap.find(pair<int, int>(particle2, particle1));
+    if (iter != exceptionMap.end()) {
+        if (!replace) {
+            stringstream msg;
+            msg << "NonbondedSoftcoreForce: There is already an exception for particles ";
+            msg << particle1;
+            msg << " and ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+        exceptions[iter->second] = ExceptionInfo(particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda);
+        newIndex = iter->second;
+        exceptionMap.erase(iter->first);
+    }
+    else {
+        exceptions.push_back(ExceptionInfo(particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda));
+        newIndex = exceptions.size()-1;
+    }
+    exceptionMap[pair<int, int>(particle1, particle2)] = newIndex;
+    return newIndex;
+}
+void NonbondedSoftcoreForce::getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon ) const {
+    particle1        = exceptions[index].particle1;
+    particle2        = exceptions[index].particle2;
+    chargeProd       = exceptions[index].chargeProd;
+    sigma            = exceptions[index].sigma;
+    epsilon          = exceptions[index].epsilon;
+}
+
+void NonbondedSoftcoreForce::getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon, double& softcoreLJLambda ) const {
+    particle1        = exceptions[index].particle1;
+    particle2        = exceptions[index].particle2;
+    chargeProd       = exceptions[index].chargeProd;
+    sigma            = exceptions[index].sigma;
+    epsilon          = exceptions[index].epsilon;
+    softcoreLJLambda = exceptions[index].softcoreLJLambda;
+}
+
+void NonbondedSoftcoreForce::setExceptionParameters(int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon, double softcoreLJLambda) {
+    exceptions[index].particle1           = particle1;
+    exceptions[index].particle2           = particle2;
+    exceptions[index].chargeProd          = chargeProd;
+    exceptions[index].sigma               = sigma;
+    exceptions[index].epsilon             = epsilon;
+    exceptions[index].softcoreLJLambda    = softcoreLJLambda;
+}
+
+ForceImpl* NonbondedSoftcoreForce::createImpl() {
+    return new NonbondedSoftcoreForceImpl(*this);
+}
+
+void NonbondedSoftcoreForce::createExceptionsFromBonds(const vector<pair<int, int> >& bonds, double coulomb14Scale, double lj14Scale) {
+
+    // Find particles separated by 1, 2, or 3 bonds.
+
+    vector<set<int> > exclusions(particles.size());
+    vector<set<int> > bonded12(exclusions.size());
+    for (int i = 0; i < (int) bonds.size(); ++i) {
+        bonded12[bonds[i].first].insert(bonds[i].second);
+        bonded12[bonds[i].second].insert(bonds[i].first);
+    }
+    for (int i = 0; i < (int) exclusions.size(); ++i)
+        addExclusionsToSet(bonded12, exclusions[i], i, i, 2);
+
+    // Find particles separated by 1 or 2 bonds and create the exceptions.
+
+    for (int i = 0; i < (int) exclusions.size(); ++i) {
+        set<int> bonded13;
+        addExclusionsToSet(bonded12, bonded13, i, i, 1);
+        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
+            if (*iter < i) {
+                if (bonded13.find(*iter) == bonded13.end()) {
+                    // This is a 1-4 interaction.
+
+                    const ParticleInfo& particle1 = particles[*iter];
+                    const ParticleInfo& particle2 = particles[i];
+                    const double chargeProd = coulomb14Scale*particle1.charge*particle2.charge;
+                    const double sigma = 0.5*(particle1.sigma+particle2.sigma);
+                    const double epsilon = lj14Scale*std::sqrt(particle1.epsilon*particle2.epsilon);
+                    addException(*iter, i, chargeProd, sigma, epsilon);
+                }
+                else {
+                    // This interaction should be completely excluded.
+
+                    addException(*iter, i, 0.0, 1.0, 0.0);
+                }
+            }
+    }
+}
+
+void NonbondedSoftcoreForce::addExclusionsToSet(const vector<set<int> >& bonded12, set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const {
+    for (set<int>::const_iterator iter = bonded12[fromParticle].begin(); iter != bonded12[fromParticle].end(); ++iter) {
+        if (*iter != baseParticle)
+            exclusions.insert(*iter);
+        if (currentLevel > 0)
+            addExclusionsToSet(bonded12, exclusions, baseParticle, *iter, currentLevel-1);
+    }
+}

plugins/freeEnergy/openmmapi/src/NonbondedSoftcoreForceImpl.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2008-2009 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/OpenMMException.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/NonbondedSoftcoreForceImpl.h"
+#include "openmm/freeEnergyKernels.h"
+#include <sstream>
+
+using namespace OpenMM;
+using std::pair;
+using std::vector;
+using std::set;
+using std::stringstream;
+
+NonbondedSoftcoreForceImpl::NonbondedSoftcoreForceImpl(NonbondedSoftcoreForce& owner) : owner(owner) {
+}
+
+NonbondedSoftcoreForceImpl::~NonbondedSoftcoreForceImpl() {
+}
+
+void NonbondedSoftcoreForceImpl::initialize(ContextImpl& context) {
+
+    kernel = context.getPlatform().createKernel(CalcNonbondedSoftcoreForceKernel::Name(), context);
+
+    // Check for errors in the specification of exceptions.
+
+    System& system = context.getSystem();
+    if (owner.getNumParticles() != system.getNumParticles())
+        throw OpenMMException("NonbondedSoftcoreForce must have exactly as many particles as the System it belongs to.");
+    vector<set<int> > exceptions(owner.getNumParticles());
+    for (int i = 0; i < owner.getNumExceptions(); i++) {
+        int particle1, particle2;
+        double chargeProd, sigma, epsilon, softcoreLJLambda;
+        owner.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda);
+        if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
+            stringstream msg;
+            msg << "NonbondedSoftcoreForce: Illegal particle index for an exception: ";
+            msg << particle1;
+            throw OpenMMException(msg.str());
+        }
+        if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
+            stringstream msg;
+            msg << "NonbondedSoftcoreForce: Illegal particle index for an exception: ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+        if (exceptions[particle1].count(particle2) > 0 || exceptions[particle2].count(particle1) > 0) {
+            stringstream msg;
+            msg << "NonbondedSoftcoreForce: Multiple exceptions are specified for particles ";
+            msg << particle1;
+            msg << " and ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+        exceptions[particle1].insert(particle2);
+        exceptions[particle2].insert(particle1);
+    }
+    dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
+}
+
+void NonbondedSoftcoreForceImpl::calcForces(ContextImpl& context ) {
+    dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).executeForces(context);
+}
+
+double NonbondedSoftcoreForceImpl::calcEnergy(ContextImpl& context) {
+    return dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).executeEnergy(context);
+}
+
+std::vector<std::string> NonbondedSoftcoreForceImpl::getKernelNames() {
+    std::vector<std::string> names;
+    names.push_back(CalcNonbondedSoftcoreForceKernel::Name());
+    return names;
+}

plugins/freeEnergy/platforms/cuda/CMakeLists.txt

+#---------------------------------------------------
+# OpenMMFreeEnergy CUDA Platform
+#
+# Creates OpenMM library, base name=OpenMMFreeEnergyCuda.
+# Default libraries are shared & optimized. Variants
+# are created for static (_static) and debug (_d).
+#
+# Windows:
+#   OpenMMFreeEnergyCuda[_d].dll
+#   OpenMMFreeEnergyCuda[_d].lib
+#   OpenMMFreeEnergyCuda_static[_d].lib
+# Unix:
+#   libOpenMMFreeEnergyCuda[_d].so
+#   libOpenMMFreeEnergyCuda_static[_d].a
+#----------------------------------------------------
+
+# ----------------------------------------------------------------------------
+# logging
+
+SET(LOG TRUE)
+   
+IF(LOG)
+   SET(LOG_FILE "CMakeLog.txt" )
+   FILE( WRITE ${LOG_FILE} "In plugins/freeEnergy/platforms/cuda\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)
+
+# ----------------------------------------------------------------------------
+
+SUBDIRS (tests)
+
+# 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_FREE_ENERGY_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(OPENMMCUDA_LIBRARY_NAME OpenMMFreeEnergyCuda)
+
+SET(SHARED_TARGET ${OPENMMCUDA_LIBRARY_NAME})
+SET(STATIC_TARGET ${OPENMMCUDA_LIBRARY_NAME}_static)
+
+# Ensure that debug libraries have "_d" appended to their names.
+# CMake gets this right on Windows automatically with this definition.
+IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+    SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
+ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+
+# But on Unix or Cygwin we have to add the suffix manually
+IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(SHARED_TARGET ${SHARED_TARGET}_d)
+    SET(STATIC_TARGET ${STATIC_TARGET}_d)
+ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+
+# These are all the places to search for header files which are
+# to be part of the API.
+SET(API_FREE_ENERGY_INCLUDE_DIRS) # start empty
+FOREACH(subdir ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS})
+    # append
+    SET(API_FREE_ENERGY_INCLUDE_DIRS ${API_FREE_ENERGY_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_FREE_ENERGY_SOURCE_SUBDIRS"  ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS} )
+   LOG_DIR( ${LOG_FILE} "API_FREE_ENERGY_INCLUDE_DIRS"       ${API_FREE_ENERGY_INCLUDE_DIRS} )
+   LOG_DIR( ${LOG_FILE} "CMAKE_CURRENT_SOURCE_DIR"           ${CMAKE_CURRENT_SOURCE_DIR} )
+   MESSAGE("\nIn0 OpenMM free/cuda: OPENMM_BUILD_FREE_ENERGY_PATH=" ${OPENMM_BUILD_FREE_ENERGY_PATH} " XXX " ${CMAKE_CURRENT_SOURCE_DIR} )
+ENDIF(LOG)
+## ----------------------------------------------------------------------------
+
+# We'll need both *relative* path names, starting with their API_FREE_ENERGY_INCLUDE_DIRS,
+# and absolute pathnames.
+SET(API_FREE_ENERGY_REL_INCLUDE_FILES)   # start these out empty
+SET(API_FREE_ENERGY_ABS_INCLUDE_FILES)
+
+FOREACH(dir ${API_FREE_ENERGY_INCLUDE_DIRS})
+    FILE(GLOB fullpaths ${dir}/*.h)	# returns full pathnames
+    SET(API_FREE_ENERGY_ABS_INCLUDE_FILES ${API_FREE_ENERGY_ABS_INCLUDE_FILES} ${fullpaths})
+
+    FOREACH(pathname ${fullpaths})
+        GET_FILENAME_COMPONENT(filename ${pathname} NAME)
+        SET(API_FREE_ENERGY_REL_INCLUDE_FILES ${API_FREE_ENERGY_REL_INCLUDE_FILES} ${dir}/${filename})
+    ENDFOREACH(pathname)
+ENDFOREACH(dir)
+
+## ----------------------------------------------------------------------------
+IF(LOG)
+   LOG_DIR( ${LOG_FILE} "API_FREE_ENERGY_REL_INCLUDE_FILES" ${API_FREE_ENERGY_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_FREE_ENERGY_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})
+    LOG_DIR( ${LOG_FILE} "Adding include dir: " ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include )
+    INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
+ENDFOREACH(subdir)
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/include)
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src)
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src/kernels)
+
+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)
+
+SET(FINDCUDA_DIR ${CMAKE_CURRENT_SOURCE_DIR}/cuda-cmake)
+
+SUBDIRS (sharedTarget staticTarget)

plugins/freeEnergy/platforms/cuda/cuda-cmake/CudaDependency.cmake

+
+#  For more information, please see: http://software.sci.utah.edu
+#
+#  The MIT License
+#
+#  Copyright (c) 2007
+#  Scientific Computing and Imaging Institute, University of Utah
+#
+#  License for the specific language governing rights and limitations under
+#  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 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.
+
+# This code is based on the Manta swig/python wrapper dependency checking code.
+# -- Abe Stephens
+
+#####################################################################
+## CUDA_INCLUDE_NVCC_DEPENDENCIES
+##
+
+# So we want to try and include the dependency file if it exists.  If
+# it doesn't exist then we need to create an empty one, so we can
+# include it.
+
+# If it does exist, then we need to check to see if all the files it
+# depends on exist.  If they don't then we should clear the dependency
+# file and regenerate it later.  This covers the case where a header
+# file has disappeared or moved.
+
+MACRO(CUDA_INCLUDE_NVCC_DEPENDENCIES dependency_file)
+  SET(CUDA_NVCC_DEPEND)
+  SET(CUDA_NVCC_DEPEND_REGENERATE)
+
+  # Include the dependency file.  Create it first if it doesn't exist
+  # for make files except for IDEs (see below).  The INCLUDE puts a
+  # dependency that will force CMake to rerun and bring in the new info
+  # when it changes.  DO NOT REMOVE THIS (as I did and spent a few hours
+  # figuring out why it didn't work.
+  IF(${CMAKE_MAKE_PROGRAM} MATCHES "make")
+    IF(NOT EXISTS ${dependency_file})
+      CONFIGURE_FILE(
+        ${FINDCUDA_DIR}/empty.depend.in
+        ${dependency_file} IMMEDIATE)
+    ENDIF(NOT EXISTS ${dependency_file})
+    # Always include this file to force CMake to run again next
+    # invocation and rebuild the dependencies.
+    INCLUDE(${dependency_file})
+  ELSE(${CMAKE_MAKE_PROGRAM} MATCHES "make")
+    # for IDE generators like MS dev only include the depend files
+    # if they exist.   This is to prevent ecessive reloading of
+    # workspaces after each build.   This also means
+    # that the depends will not be correct until cmake
+    # is run once after the build has completed once.
+    # the depend files are created in the wrap tcl/python sections
+    # when the .xml file is parsed.
+    INCLUDE(${dependency_file} OPTIONAL)
+  ENDIF(${CMAKE_MAKE_PROGRAM} MATCHES "make")
+
+  # Now we need to verify the existence of all the included files
+  # here.  If they aren't there we need to just blank this variable and
+  # make the file regenerate again.
+  IF(CUDA_NVCC_DEPEND)
+    FOREACH(f ${CUDA_NVCC_DEPEND})
+      IF(EXISTS ${f})
+      ELSE(EXISTS ${f})
+        SET(CUDA_NVCC_DEPEND_REGENERATE 1)
+      ENDIF(EXISTS ${f})
+    ENDFOREACH(f)
+  ELSE(CUDA_NVCC_DEPEND)
+    # No dependencies, so regenerate the file.
+    SET(CABLE_NVCC_DEPEND_REGENERATE 1)
+  ENDIF(CUDA_NVCC_DEPEND)
+
+  # No incoming dependencies, so we need to generate them.  Make the
+  # output depend on the dependency file itself, which should cause the
+  # rule to re-run.
+  IF(CUDA_NVCC_DEPEND_REGENERATE)
+    SET(CUDA_NVCC_DEPEND ${dependency_file})
+    # Force CMake to run again next build
+    CONFIGURE_FILE(
+      ${FINDCUDA_DIR}/empty.depend.in
+      ${dependency_file} IMMEDIATE)
+  ENDIF(CUDA_NVCC_DEPEND_REGENERATE)
+      
+ENDMACRO(CUDA_INCLUDE_NVCC_DEPENDENCIES)
\ No newline at end of file

plugins/freeEnergy/platforms/cuda/cuda-cmake/FindCuda.cmake

+###############################################################################
+#  For more information, please see: http://software.sci.utah.edu
+#
+#  The MIT License
+#
+#  Copyright (c) 2007-2008
+#  Scientific Computing and Imaging Institute, University of Utah
+#
+#  License for the specific language governing rights and limitations under
+#  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 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.
+#
+# This script locates the Nvidia Compute Unified Driver Architecture (CUDA) 
+# tools. It should work on linux, windows, and mac and should be reasonably 
+# up to date with cuda releases.
+#
+# The script will prompt the user to specify CUDA_INSTALL_PREFIX if the 
+# prefix cannot be determined by the location of nvcc in the system path. To
+# use a different installed version of the toolkit set the environment variable
+# CUDA_BIN_PATH before running cmake (e.g. CUDA_BIN_PATH=/usr/local/cuda1.0 
+# instead of the default /usr/local/cuda).
+#
+# Set CUDA_BUILD_TYPE to "Device" or "Emulation" mode.
+# _DEVICEEMU is defined in "Emulation" mode.
+#
+# Set CUDA_BUILD_CUBIN to "ON" or "OFF" to enable and extra compilation pass
+# with the -cubin option in Device mode. The output is parsed and register, 
+# shared memory usage is printed during build. Default ON.
+# 
+# The script creates the following macros:
+# CUDA_INCLUDE_DIRECTORIES( path0 path1 ... )
+# -- Sets the directories that should be passed to nvcc 
+#    (e.g. nvcc -Ipath0 -Ipath1 ... ). These paths usually contain other .cu 
+#    files.
+# 
+# CUDA_ADD_LIBRARY( cuda_target file0 file1 ... )
+# -- Creates a shared library "cuda_target" which contains all of the source 
+#    (*.c, *.cc, etc.) specified and all of the nvcc'ed .cu files specified.
+#    All of the specified source files and generated .cpp files are compiled 
+#    using the standard CMake compiler, so the normal INCLUDE_DIRECTORIES, 
+#    LINK_DIRECTORIES, and TARGET_LINK_LIBRARIES can be used to affect their
+#    build and link.
+#
+# CUDA_ADD_EXECUTABLE( cuda_target file0 file1 ... )
+# -- Same as CUDA_ADD_LIBRARY except that an exectuable is created.
+#
+# CUDA_COMPILE( cuda_files file0 file1 ... )
+# -- Returns a list of build commands in the first argument to be used with 
+#    ADD_LIBRARY or ADD_EXECUTABLE.
+# 
+# The script defines the following variables:
+#
+# ( Note CUDA_ADD_* macros setup cuda/cut library dependencies automatically. 
+# These variables are only needed if a cuda API call must be made from code in 
+# a outside library or executable. )
+#
+# CUDA_INCLUDE         -- Include directory for cuda headers.
+# CUDA_TARGET_LINK     -- Cuda RT library. 
+# CUDA_CUT_INCLUDE     -- Include directory for cuda SDK headers (cutil.h).   
+# CUDA_CUT_TARGET_LINK -- SDK libraries.
+# CUDA_NVCC_FLAGS      -- Additional NVCC command line arguments. NOTE: 
+#                         multiple arguments must be semi-colon delimited 
+#                         e.g. --compiler-options;-Wall
+# CUBLAS_TARGET_LINK-- cublas library name.
+# CUFFT_TARGET_LINK -- cubfft library name.
+# 
+# The nvcc flag "--host-compilation;c++" should be used if functions declared
+# as __host__ contain C++ code.
+#
+# It might be necessary to set CUDA_INSTALL_PATH manually on certain platforms,
+# or to use a cuda runtime not installed in the default location. In newer 
+# versions of the toolkit the cuda library is included with the graphics 
+# driver- be sure that the driver version matches what is needed by the cuda 
+# runtime version.
+# 
+# -- Abe Stephens SCI Institute -- http://www.sci.utah.edu/~abe/FindCuda.html
+###############################################################################
+
+# FindCuda.cmake
+CMAKE_MINIMUM_REQUIRED(VERSION 2.4)
+
+INCLUDE(${FINDCUDA_DIR}/CudaDependency.cmake)
+
+###############################################################################
+###############################################################################
+# Locate CUDA, Set Build Type, etc.
+###############################################################################
+###############################################################################
+
+# Parse CUDA build type.
+IF (NOT CUDA_BUILD_TYPE)
+  SET(CUDA_BUILD_TYPE "Device" CACHE STRING "Cuda build type: Emulation or Device")
+ENDIF(NOT CUDA_BUILD_TYPE)
+
+# Emulation if the card isn't present.
+IF (CUDA_BUILD_TYPE MATCHES "Emulation")
+  # Emulation.
+  SET(nvcc_flags --device-emulation -D_DEVICEEMU -g)
+ELSE(CUDA_BUILD_TYPE MATCHES "Emulation")
+  # Device present.
+  SET(nvcc_flags "")
+ENDIF(CUDA_BUILD_TYPE MATCHES "Emulation")
+
+SET(CUDA_BUILD_CUBIN TRUE CACHE BOOL "Generate and parse .cubin files in Device mode.")
+SET(CUDA_NVCC_FLAGS "-maxrregcount=32;-use_fast_math;-O0;-arch=sm_11" CACHE STRING "Semi-colon delimit multiple arguments.")
+
+# Search for the cuda distribution.
+IF(NOT CUDA_INSTALL_PREFIX)
+  FIND_PATH(CUDA_INSTALL_PREFIX
+    NAMES nvcc nvcc.exe
+    PATHS /usr/local/cuda C:/CUDA
+    PATH_SUFFIXES bin
+    ENV CUDA_BIN_PATH
+    DOC "Toolkit location."
+    )
+  IF (CUDA_INSTALL_PREFIX) 
+    STRING(REGEX REPLACE "[/\\\\]?bin[/\\\\]?$" "" CUDA_INSTALL_PREFIX ${CUDA_INSTALL_PREFIX})
+  ENDIF(CUDA_INSTALL_PREFIX)
+  IF (NOT EXISTS ${CUDA_INSTALL_PREFIX})
+    MESSAGE(FATAL_ERROR "Specify CUDA_INSTALL_PREFIX")
+  ENDIF (NOT EXISTS ${CUDA_INSTALL_PREFIX})
+ENDIF (NOT CUDA_INSTALL_PREFIX)
+
+# CUDA_NVCC
+IF (NOT CUDA_NVCC)
+  FIND_PROGRAM(CUDA_NVCC 
+    nvcc
+    PATHS ${CUDA_INSTALL_PREFIX}/bin $ENV{CUDA_BIN_PATH}
+    )
+  IF(NOT CUDA_NVCC)
+    MESSAGE(FATAL_ERROR "Could not find nvcc")
+  ELSE(NOT CUDA_NVCC)
+    MARK_AS_ADVANCED(CUDA_NVCC)
+  ENDIF(NOT CUDA_NVCC)
+ENDIF(NOT CUDA_NVCC)
+
+# CUDA_NVCC_INCLUDE_ARGS
+# IF (NOT FOUND_CUDA_NVCC_INCLUDE)
+  FIND_PATH(FOUND_CUDA_NVCC_INCLUDE
+    device_functions.h # Header included in toolkit
+    PATHS ${CUDA_INSTALL_PREFIX}/include 
+          $ENV{CUDA_INC_PATH}
+    )
+  
+  IF(NOT FOUND_CUDA_NVCC_INCLUDE)
+    MESSAGE(FATAL_ERROR "Could not find Cuda headers")
+  ELSE(NOT FOUND_CUDA_NVCC_INCLUDE)
+    # Set the initial include dir.
+    SET (CUDA_NVCC_INCLUDE_ARGS "-I"${FOUND_CUDA_NVCC_INCLUDE})
+	SET (CUDA_INCLUDE ${FOUND_CUDA_NVCC_INCLUDE})
+
+    MARK_AS_ADVANCED(
+      FOUND_CUDA_NVCC_INCLUDE
+      CUDA_NVCC_INCLUDE_ARGS
+      )
+  ENDIF(NOT FOUND_CUDA_NVCC_INCLUDE)
+  
+# ENDIF(NOT FOUND_CUDA_NVCC_INCLUDE)
+
+  
+# CUDA_TARGET_LINK
+IF (NOT CUDA_TARGET_LINK)
+
+  FIND_LIBRARY(FOUND_CUDART
+    cudart
+    PATHS ${CUDA_INSTALL_PREFIX}/lib $ENV{CUDA_LIB_PATH}
+    DOC "\"cudart\" library"
+    )
+  
+  # Check to see if cudart library was found.
+  IF(NOT FOUND_CUDART)
+    MESSAGE(FATAL_ERROR "Could not find cudart library (cudart)")
+  ENDIF(NOT FOUND_CUDART)  
+
+  # 1.1 toolkit on linux doesn't appear to have a separate library on 
+  # some platforms.
+  FIND_LIBRARY(FOUND_CUDA
+    cuda
+    PATHS ${CUDA_INSTALL_PREFIX}/lib
+    DOC "\"cuda\" library (older versions only)."
+    NO_DEFAULT_PATH
+    NO_CMAKE_ENVIRONMENT_PATH
+    NO_CMAKE_PATH
+    NO_SYSTEM_ENVIRONMENT_PATH
+    NO_CMAKE_SYSTEM_PATH
+    )
+
+  # Add cuda library to the link line only if it is found.
+  IF (FOUND_CUDA)
+    SET(CUDA_TARGET_LINK ${FOUND_CUDA})
+  ENDIF(FOUND_CUDA)
+
+  # Always add cudart to the link line.
+  IF(FOUND_CUDART)
+    SET(CUDA_TARGET_LINK
+      ${CUDA_TARGET_LINK} ${FOUND_CUDART}
+      )
+    MARK_AS_ADVANCED(
+      CUDA_TARGET_LINK 
+      CUDA_LIB
+      FOUND_CUDA
+      FOUND_CUDART
+      )
+  ELSE(FOUND_CUDART)
+    MESSAGE(FATAL_ERROR "Could not find cuda libraries.")
+  ENDIF(FOUND_CUDART)
+  
+ENDIF(NOT CUDA_TARGET_LINK)
+
+# CUDA_CUT_INCLUDE
+IF(NOT CUDA_CUT_INCLUDE)
+  FIND_PATH(FOUND_CUT_INCLUDE
+    cutil.h
+    PATHS ${CUDA_INSTALL_PREFIX}/local/NVSDK0.2/common/inc
+          ${CUDA_INSTALL_PREFIX}/NVSDK0.2/common/inc
+          ${CUDA_INSTALL_PREFIX}/NV_CUDA_SDK/common/inc
+          $ENV{HOME}/NVIDIA_CUDA_SDK/common/inc
+          $ENV{HOME}/NVIDIA_CUDA_SDK_MACOSX/common/inc
+          $ENV{NVSDKCUDA_ROOT}/common/inc
+    DOC "Location of cutil.h"
+    )
+  IF(FOUND_CUT_INCLUDE)
+    SET(CUDA_CUT_INCLUDE ${FOUND_CUT_INCLUDE})
+    MARK_AS_ADVANCED(
+      FOUND_CUT_INCLUDE
+      )
+  ENDIF(FOUND_CUT_INCLUDE)
+ENDIF(NOT CUDA_CUT_INCLUDE)
+
+
+# CUDA_CUT_TARGET_LINK
+IF(NOT CUDA_CUT_TARGET_LINK)
+  FIND_LIBRARY(FOUND_CUT
+    cutil
+    cutil32
+    PATHS ${CUDA_INSTALL_PREFIX}/local/NVSDK0.2/lib
+          ${CUDA_INSTALL_PREFIX}/NVSDK0.2/lib
+          ${CUDA_INSTALL_PREFIX}/NV_CUDA_SDK/lib
+          $ENV{HOME}/NVIDIA_CUDA_SDK/lib
+          $ENV{HOME}/NVIDIA_CUDA_SDK_MACOSX/lib
+          $ENV{NVSDKCUDA_ROOT}/common/lib
+    NO_DEFAULT_PATH
+    NO_CMAKE_ENVIRONMENT_PATH
+    NO_CMAKE_PATH
+    NO_SYSTEM_ENVIRONMENT_PATH
+    NO_CMAKE_SYSTEM_PATH
+    DOC "Location of cutil library"
+    )
+  IF(FOUND_CUT)
+    SET(CUDA_CUT_TARGET_LINK ${FOUND_CUT})
+    MARK_AS_ADVANCED(
+      FOUND_CUT
+      )
+  ENDIF(FOUND_CUT)
+
+# Add variables for cufft and cublas target link
+FIND_LIBRARY(FOUND_CUFFTEMU
+  cufftemu
+  PATHS ${CUDA_INSTALL_PREFIX}/lib $ENV{CUDA_LIB_PATH}
+  DOC "\"cufftemu\" library"
+  )
+FIND_LIBRARY(FOUND_CUBLASEMU
+  cublasemu
+  PATHS ${CUDA_INSTALL_PREFIX}/lib $ENV{CUDA_LIB_PATH}
+  DOC "\"cublasemu\" library"
+  )
+FIND_LIBRARY(FOUND_CUFFT
+  cufft
+  PATHS ${CUDA_INSTALL_PREFIX}/lib $ENV{CUDA_LIB_PATH}
+  DOC "\"cufft\" library"
+  )
+FIND_LIBRARY(FOUND_CUBLAS
+  cublas
+  PATHS ${CUDA_INSTALL_PREFIX}/lib $ENV{CUDA_LIB_PATH}
+  DOC "\"cublas\" library"
+  )
+
+IF (CUDA_BUILD_TYPE MATCHES "Emulation")
+  SET(CUFFT_TARGET_LINK  ${FOUND_CUFFTEMU})
+  SET(CUBLAS_TARGET_LINK ${FOUND_CUBLASEMU})
+ELSE(CUDA_BUILD_TYPE MATCHES "Emulation")
+  SET(CUFFT_TARGET_LINK  ${FOUND_CUFFT})
+  SET(CUBLAS_TARGET_LINK ${FOUND_CUBLAS})
+ENDIF(CUDA_BUILD_TYPE MATCHES "Emulation")
+
+
+
+
+ENDIF(NOT CUDA_CUT_TARGET_LINK)
+
+
+###############################################################################
+# Add include directories to pass to the nvcc command.
+MACRO(CUDA_INCLUDE_DIRECTORIES)
+  FOREACH(dir ${ARGN})
+    SET(CUDA_NVCC_INCLUDE_ARGS ${CUDA_NVCC_INCLUDE_ARGS} -I${dir})
+  ENDFOREACH(dir ${ARGN})
+ENDMACRO(CUDA_INCLUDE_DIRECTORIES)
+
+
+##############################################################################
+##############################################################################
+# This helper macro populates the following variables and setups up custom commands and targets to
+# invoke the nvcc compiler. The compiler is invoked once with -M to generate a dependency file and
+# a second time with -cuda to generate a .cpp file
+# ${target_srcs}
+# ${cuda_cu_sources}
+##############################################################################
+##############################################################################
+
+MACRO(CUDA_add_custom_commands cuda_target)
+
+  SET(target_srcs "")
+  SET(cuda_cu_sources "")
+
+  # Iterate over the macro arguments and create custom
+  # commands for all the .cu files.
+  FOREACH(file ${ARGN})
+    IF(${file} MATCHES ".*\\.cu$")
+    
+    # Add a custom target to generate a c file.
+    SET(generated_file  "${CMAKE_BINARY_DIR}/src/cuda/${file}_${cuda_target}_generated.cpp")
+    SET(generated_target "${file}_target")
+    
+    FILE(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/src/cuda)
+
+    SET(source_file ${CMAKE_CURRENT_SOURCE_DIR}/../${file})
+
+    # MESSAGE("${CUDA_NVCC} ${source_file} ${CUDA_NVCC_FLAGS} ${nvcc_flags} -cuda -o ${generated_file} ${CUDA_NVCC_INCLUDE_ARGS}")
+    
+    # Bring in the dependencies.  Creates a variable CUDA_NVCC_DEPEND
+	SET(cmake_dependency_file "${generated_file}.depend")
+	CUDA_INCLUDE_NVCC_DEPENDENCIES(${cmake_dependency_file})
+	SET(NVCC_generated_dependency_file "${generated_file}.NVCC-depend")
+
+
+	# Build the NVCC made dependency file
+  IF (CUDA_BUILD_TYPE MATCHES "Device" AND CUDA_BUILD_CUBIN)
+    SET(NVCC_generated_cubin_file "${generated_file}.NVCC-cubin.txt")
+	  ADD_CUSTOM_COMMAND(
+
+      # Generate the .cubin output.
+      OUTPUT ${NVCC_generated_cubin_file}
+      COMMAND ${CUDA_NVCC}
+      ARGS ${source_file} 
+      ${CUDA_NVCC_FLAGS}
+      ${nvcc_flags}
+      -DNVCC
+      -cubin
+      -o ${NVCC_generated_cubin_file} 
+      ${CUDA_NVCC_INCLUDE_ARGS}
+
+      # Execute the parser script.
+      COMMAND  ${CMAKE_COMMAND}
+      ARGS 
+      -D input_file="${NVCC_generated_cubin_file}"
+      -P "${FINDCUDA_DIR}/parse_cubin.cmake"
+
+
+      # MAIN_DEPENDENCY ${source_file}
+      DEPENDS ${source_file}
+      DEPENDS ${CUDA_NVCC_DEPEND}
+
+
+
+	    COMMENT "Building (${CUDA_BUILD_TYPE}) NVCC -cubin File: ${NVCC_generated_cubin_file}\n"
+      )
+  ELSE (CUDA_BUILD_TYPE MATCHES "Device" AND CUDA_BUILD_CUBIN)
+    # Depend on something that will exist.
+    SET(NVCC_generated_cubin_file "${source_file}")
+  ENDIF (CUDA_BUILD_TYPE MATCHES "Device"AND CUDA_BUILD_CUBIN)
+
+	# Build the NVCC made dependency file
+	ADD_CUSTOM_COMMAND(
+      OUTPUT ${NVCC_generated_dependency_file}
+      COMMAND ${CUDA_NVCC}
+      ARGS ${source_file} 
+           ${CUDA_NVCC_FLAGS}
+           ${nvcc_flags}
+           -DNVCC
+           -M
+           -o ${NVCC_generated_dependency_file} 
+           ${CUDA_NVCC_INCLUDE_ARGS}
+      # MAIN_DEPENDENCY ${source_file}
+      DEPENDS ${source_file}
+      DEPENDS ${CUDA_NVCC_DEPEND}
+	  COMMENT "Building (${CUDA_BUILD_TYPE}) NVCC Dependency File: ${NVCC_generated_dependency_file}\n"
+    )
+    
+    # Build the CMake readible dependency file
+	ADD_CUSTOM_COMMAND(
+	  OUTPUT ${cmake_dependency_file}
+      COMMAND ${CMAKE_COMMAND}
+      ARGS 
+      -D input_file="${NVCC_generated_dependency_file}"
+      -D output_file="${cmake_dependency_file}"
+      -P "${FINDCUDA_DIR}/make2cmake.cmake"
+      MAIN_DEPENDENCY ${NVCC_generated_dependency_file}
+      COMMENT "Converting NVCC dependency to CMake (${cmake_dependency_file})"
+    )
+
+    ADD_CUSTOM_COMMAND(
+      OUTPUT ${generated_file}
+      MAIN_DEPENDENCY ${source_file} 
+      DEPENDS ${CUDA_NVCC_DEPEND}
+      DEPENDS ${cmake_dependency_file}
+      DEPENDS ${NVCC_generated_cubin_file}
+      COMMAND ${CUDA_NVCC} 
+      ARGS ${source_file} 
+           ${CUDA_NVCC_FLAGS}
+           ${nvcc_flags}
+			  ${CUDA_NVCC_BUILD_FLAGS}
+           -DNVCC
+           --keep
+           -cuda -o ${generated_file} 
+           ${CUDA_NVCC_INCLUDE_ARGS}
+       COMMENT "Building (${CUDA_BUILD_TYPE}) NVCC ${source_file}: ${generated_file}\n"
+      )
+    	
+    SET(cuda_cu_sources ${cuda_cu_sources} ${source_file})
+
+    # Add the generated file name to the source list.
+    SET(target_srcs ${target_srcs} ${generated_file})
+    
+    ELSE(${file} MATCHES ".*\\.cu$")
+  
+    # Otherwise add the file name to the source list.
+    SET(target_srcs ${target_srcs} ${file})
+  
+    ENDIF(${file} MATCHES ".*\\.cu$")
+  ENDFOREACH(file)
+
+ENDMACRO(CUDA_add_custom_commands)
+
+###############################################################################
+###############################################################################
+# ADD LIBRARY
+###############################################################################
+###############################################################################
+MACRO(CUDA_ADD_LIBRARY cuda_target)
+
+  # Create custom commands and targets for each file.
+  CUDA_add_custom_commands( ${cuda_target} ${ARGN} )  
+  
+  # Add the library.
+  ADD_LIBRARY(${cuda_target}
+    ${target_srcs}
+    ${cuda_cu_sources}
+    )
+
+  TARGET_LINK_LIBRARIES(${cuda_target}
+    ${CUDA_TARGET_LINK}
+    )
+
+ENDMACRO(CUDA_ADD_LIBRARY cuda_target)
+
+
+###############################################################################
+###############################################################################
+# ADD EXECUTABLE
+###############################################################################
+###############################################################################
+MACRO(CUDA_ADD_EXECUTABLE cuda_target)
+  
+  # Create custom commands and targets for each file.
+  CUDA_add_custom_commands( ${cuda_target} ${ARGN} )
+  
+  # Add the library.
+  ADD_EXECUTABLE(${cuda_target}
+    ${target_srcs}
+    ${cuda_cu_sources}
+    )
+
+  TARGET_LINK_LIBRARIES(${cuda_target}
+    ${CUDA_TARGET_LINK}
+    )
+
+
+ENDMACRO(CUDA_ADD_EXECUTABLE cuda_target)
+
+###############################################################################
+###############################################################################
+# ADD EXECUTABLE
+###############################################################################
+###############################################################################
+MACRO(CUDA_COMPILE file_variable)
+  
+  # Create custom commands and targets for each file.
+  CUDA_add_custom_commands( cuda_compile ${ARGN} )
+  
+  SET(file_variable ${target_srcs} ${cuda_cu_sources})
+
+ENDMACRO(CUDA_COMPILE)