Modified softcore equation to conform w/ Shirts and Pande, JCP 122:134508, 2005.

Removed cruft from Cmake file
Modified the way platform is specified in TstFreeEnergyCudaUsingParameterFile.cpp

plugins/freeEnergy/CMakeLists.txt

 #---------------------------------------------------
 # OpenMM FreeEnergy Plugin
 #
-# Creates OpenMM FreeEnergy plugin library, base name=OpenMM.
+# Creates OpenMM FreeEnergy plugin library, base name=OpenMMFreeEnergy.
 # 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
+#   OpenMMFreeEnergy[_d].dll
+#   OpenMMFreeEnergy[_d].lib
+#   OpenMMFreeEnergy_static[_d].lib
 # Unix:
-#   libOpenMM[_d].so
-#   libOpenMM_static[_d].a
+#   libOpenMMFreeEnergy[_d].so
+#   libOpenMMFreeEnergy_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)
@@ -89,43 +40,6 @@ ENDIF(LOG)
 # 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.
 
@@ -134,107 +48,20 @@ 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}
-                -DINCLUDE_FREE_ENERGY_PLUGIN
 		          -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

plugins/freeEnergy/platforms/cuda/src/kernels/kSoftcoreLJ.h

@@ -37,8 +37,7 @@ __device__ float getSoftCoreLJ( float r2, float sig, float  eps, float lambdaI,
 
    float r                         = sqrt(r2);
    float lambda                    = lambdaI < lambdaJ ? lambdaI : lambdaJ;
-   float lambda2                   = lambda*lambda;
-   eps                            *= lambda2*lambda2;
+   eps                            *= lambda;
 
 
     // (r/sig)

plugins/freeEnergy/platforms/cuda/tests/TstFreeEnergyCudaUsingParameterFile.cpp

@@ -3662,56 +3662,6 @@ static int _printIntegratorInfo( Integrator* integrator, FILE* log ){
    return DefaultReturnValue;
 }
 
-/**---------------------------------------------------------------------------------------
-
-   Register forces associated w/ Reference free energy platform
-
-   @param referencePlatform             reference platform
-
-   --------------------------------------------------------------------------------------- */
-
-static void registerFreeEnergyMethodsReferencePlatform( ReferencePlatform& referencePlatform ){
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const char* methodName  = "registerFreeEnergyMethodsReferencePlatform: ";
-
-   // ---------------------------------------------------------------------------------------
-
-#ifdef INCLUDE_FREE_ENERGY_PLUGIN
-   ReferenceFreeEnergyKernelFactory* factory  = new ReferenceFreeEnergyKernelFactory();
-   referencePlatform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
-   referencePlatform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
-   referencePlatform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
-#endif
-
-}
-
-/**---------------------------------------------------------------------------------------
-
-   Register forces associated w/ Cuda free energy platform
-
-   @param cudaPlatform             cuda platform
-
-   --------------------------------------------------------------------------------------- */
-
-static void registerFreeEnergyMethodsCudaPlatform( CudaPlatform& cudaPlatform ){
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const char* methodName  = "registerFreeEnergyMethodsCudaPlatform: ";
-
-   // ---------------------------------------------------------------------------------------
-
-#ifdef INCLUDE_FREE_ENERGY_PLUGIN
-   CudaFreeEnergyKernelFactory* factory  = new CudaFreeEnergyKernelFactory();
-   cudaPlatform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
-   cudaPlatform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
-   cudaPlatform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
-#endif
-
-}
-
 /**---------------------------------------------------------------------------------------
 
    Set the velocities/positions of context2 to those of context1
@@ -3769,25 +3719,12 @@ Context* _getContext( System* system, Context* inputContext, Integrator* inputIn
 
     Context* context;
     ReferencePlatform referencePlatform;
-    registerFreeEnergyMethodsReferencePlatform( referencePlatform );
-
-    CudaPlatform gpuPlatform;
-    registerFreeEnergyMethodsCudaPlatform( gpuPlatform );
 
     if( platformName.compare( "ReferencePlatform" ) == 0 ){
-       context = new Context( *system, *inputIntegrator, referencePlatform );
+       context = new Context( *system, *inputIntegrator, Platform::getPlatform("Reference") );
     } else {
-       gpuPlatform.setPropertyDefaultValue( "CudaDevice", deviceId );
-       context = new Context( *system, *inputIntegrator, gpuPlatform );
-       if( log ){
-          (void) fprintf( log, "OpenMM Platform: %s\n", context->getPlatform().getName().c_str() ); (void) fflush( log );
-          const vector<string>& properties = gpuPlatform.getPropertyNames();
-          for (unsigned int i = 0; i < properties.size(); i++) {
-              fprintf( log, "%s: %s\n", properties[i].c_str(), gpuPlatform.getPropertyValue(*context, properties[i]).c_str());
-          }    
+       context                    = new Context( *system, *inputIntegrator, Platform::getPlatform("Cuda") );
     }
-    }
-
     if( log ){
        (void) fprintf( log, "%s Using Platform: %s device=%s\n", idString.c_str(), context->getPlatform().getName().c_str(), deviceId.c_str() );
        (void) fflush( log );
@@ -5030,11 +4967,8 @@ void testReferenceCudaForces( std::string parameterFileName, MapStringInt& force
       (void) fflush( log );
    }   
 
-   ReferencePlatform referencePlatform;
-   registerFreeEnergyMethodsReferencePlatform( referencePlatform );
-
-   CudaPlatform cudaPlatform;
-   registerFreeEnergyMethodsCudaPlatform( cudaPlatform );
+   Platform& referencePlatform         =  Platform::getPlatform("Reference");
+   Platform& cudaPlatform              = Platform::getPlatform("Cuda");;
 
    double parameterKineticEnergy, parameterPotentialEnergy;
 
@@ -5627,14 +5561,12 @@ void testEnergyForcesConsistent( std::string parameterFileName, MapStringInt& fo
 
    if( platformInclude == 1 ){
 
-      CudaPlatform cudaPlatform;
-
       if( log ){
          (void) fprintf( log, "%s Testing cuda platform\n", methodName.c_str() );
          (void) fflush( log );
       }   
 
-      registerFreeEnergyMethodsCudaPlatform( cudaPlatform );
+      Platform& cudaPlatform              = Platform::getPlatform( "Cuda");;
 
       Context* cudaContext                = testSetup( parameterFileName, forceMap,  cudaPlatform,
                                                          parameterForces2, &parameterKineticEnergy, &parameterPotentialEnergy,
@@ -5644,8 +5576,7 @@ void testEnergyForcesConsistent( std::string parameterFileName, MapStringInt& fo
 
    } else {
 
-      ReferencePlatform referencePlatform;
-      registerFreeEnergyMethodsReferencePlatform( referencePlatform );
+      Platform& referencePlatform         =  Platform::getPlatform( "Reference");
 
       if( log ){
          (void) fprintf( log, "%s Testing reference platform\n", methodName.c_str() );
@@ -5683,9 +5614,7 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM
       (void) fflush( log );
    }   
 
-   //CudaPlatform cudaPlatform;
-   ReferencePlatform referencePlatform;
-   registerFreeEnergyMethodsReferencePlatform( referencePlatform );
+   Platform& referencePlatform         =  Platform::getPlatform( "Reference");
 
    double parameterKineticEnergy, parameterPotentialEnergy;
 
@@ -5854,6 +5783,7 @@ int main( int numberOfArguments, char* argv[] ){
    }
 
    std::string parameterFileName            = defaultParameterFileName;
+   std::string pluginDirectoryName          = Platform::getDefaultPluginsDirectory();
    MapStringInt forceMap;
    initializeForceMap( forceMap, 0 );
    int logFileNameIndex                     = -1;
@@ -5970,6 +5900,7 @@ int main( int numberOfArguments, char* argv[] ){
          (void) fprintf( log, "no summary file\n" );
       }
 
+      (void) fprintf( log, "pluginDirectoryName         %s\n", pluginDirectoryName.c_str() );
       (void) fprintf( log, "checkEnergyForceConsistent  %d\n", checkEnergyForceConsistent );
       (void) fprintf( log, "checkEnergyConservation     %d\n", checkEnergyConservation );
       (void) fprintf( log, "checkInputForces            %d\n", checkInputForces );
@@ -5985,6 +5916,8 @@ int main( int numberOfArguments, char* argv[] ){
       (void) fflush( log );
    }
 
+   Platform::loadPluginsFromDirectory(pluginDirectoryName);
+
    // check forces
 
    if( checkForces ){

plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.cpp

@@ -966,8 +966,7 @@ calculateOneLJIxn( one/r, sig, eps, &dEdROrig, &E_Orig );
 
     // soft-core LJ energy = lambda*4*eps*[ 1/{alphaLJ*(1-lambda) + (r/sig)**6}**2 - 1/{alphaLJ*(1-lambda) + (r/sig)**6} ]
 
-    eps                                *= POW( lambda, four );
-
+    eps                                *= lambda;
     RealOpenMM sig2                     = r/sig;
                sig2                    *= sig2;
     RealOpenMM sig6                     = sig2*sig2*sig2;