Units of nonPolarPrefactor are now kJ/mol/nm^2 (were kcal/mol/A^2)

Changed ReferenceFreeEnergyPlatform name to ReferenceFreeEnergy
Removed references to ParameterFileName in GB/VI

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

@@ -135,7 +135,7 @@ public:
         return nonPolarPrefactor;
     }
     /**
-     * Set the nonPolarPrefactor.
+     * Set the nonPolarPrefactor; units are kJ/mol/nm^2
      */
     void setNonPolarPrefactor(double inputNonPolarPrefactor) {
         nonPolarPrefactor = inputNonPolarPrefactor;

plugins/freeEnergy/openmmapi/src/GBSAOBCSoftcoreForce.cpp

@@ -36,7 +36,9 @@
 
 using namespace OpenMM;
 
-GBSAOBCSoftcoreForce::GBSAOBCSoftcoreForce() : solventDielectric(78.3), soluteDielectric(1.0), nonPolarPrefactor( 0.0054 ){
+// units of nonPolarPrefactor are now kJ/mol/nm^2
+
+GBSAOBCSoftcoreForce::GBSAOBCSoftcoreForce() : solventDielectric(78.3), soluteDielectric(1.0), nonPolarPrefactor( 2.25936 ){
 }
 
 int GBSAOBCSoftcoreForce::addParticle(double charge, double radius, double scalingFactor, double nonPolarScalingFactor) {

plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernels.cpp

@@ -512,6 +512,7 @@ void CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System& syst
         charge[i]                 = static_cast<float>( particleCharge);
         nonPolarScalingFactors[i] = static_cast<float>( particleNonPolarScalingFactor);
     }
+
     gpuObcGbsaSoftcore = gpuSetObcSoftcoreParameters(gpu, static_cast<float>( force.getSoluteDielectric()),
                                                      static_cast<float>( force.getSolventDielectric()),
                                                      static_cast<float>( force.getNonPolarPrefactor()),

plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.cu

@@ -265,7 +265,7 @@ GpuObcGbsaSoftcore* gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDiele
     GpuObcGbsaSoftcore* gpuObcGbsaSoftcore = new GpuObcGbsaSoftcore();
     gpuObcGbsaSoftcore->initializeNonPolarScalingFactors( gpu->sim.paddedNumberOfAtoms );
 
-    gpu->sim.surfaceAreaFactor             =  -6.0f*PI*4.0f*nonPolarPrefactor*1000.0f*0.4184f;
+    gpu->sim.surfaceAreaFactor             =  -6.0f*PI*4.0f*nonPolarPrefactor;
     for (unsigned int i = 0; i < atoms; i++)
     {
             (*gpu->psObcData)[i].x = radius[i] - dielectricOffset;

plugins/freeEnergy/platforms/reference/include/ReferenceFreeEnergyPlatform.h

@@ -45,7 +45,7 @@ public:
 //    class PlatformData;
     ReferenceFreeEnergyPlatform();
     const std::string& getName() const {
-        static const std::string name = "ReferenceFreeEnergyPlatform";
+        static const std::string name = "ReferenceFreeEnergy";
         return name;
     }
 #if 0

plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernels.cpp

@@ -334,7 +334,13 @@ void ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System&
 
     obcParameters->setSolventDielectric( static_cast<RealOpenMM>(force.getSolventDielectric()) );
     obcParameters->setSoluteDielectric(  static_cast<RealOpenMM>(force.getSoluteDielectric()) );
-    obcParameters->setNonPolarPrefactor( static_cast<RealOpenMM>(force.getNonPolarPrefactor()) );
+
+    // nonPolarPrefactor is in units of kJ/mol/nm^2 convert to kcal/mol/A^2 
+    // to be consistent w/ polar part of OBC calculation
+
+    RealOpenMM nonPolarPrefactor =  static_cast<RealOpenMM>(force.getNonPolarPrefactor());
+    nonPolarPrefactor           /= static_cast<RealOpenMM>(418.4);
+    obcParameters->setNonPolarPrefactor( nonPolarPrefactor );
 
     // If there is a NonbondedForce in this system, use it to initialize cutoffs and periodic boundary conditions.
 

plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.cpp

@@ -38,8 +38,6 @@ extern "C" {
 }
 #endif
 
-const std::string GBVISoftcoreParameters::ParameterFileName = std::string( "params.agb" );
-
 /**---------------------------------------------------------------------------------------
 
    GBVISoftcoreParameters:

plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.h

@@ -34,8 +34,6 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
 
    public:
 
-       static const std::string ParameterFileName;
-
     /** 
      * This is an enumeration of the different methods that may be used for scaling of the Born radii.
      */

plugins/freeEnergy/platforms/reference/src/gbsa/ObcSoftcoreParameters.cpp

@@ -118,7 +118,7 @@ ObcSoftcoreParameters::ObcSoftcoreParameters( int numberOfAtoms, ObcSoftcorePara
    _nonPolarScaleFactors         = NULL;
 
 
-   _nonPolarPreFactor            = 0.054;
+   _nonPolarPreFactor            = 2.25936;
 
    setObcTypeParameters( obcType );