Simplified reference code for accumulating energies

platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.h

@@ -57,17 +57,13 @@ class ReferenceLJCoulomb14 : public ReferenceBondIxn {
          @param atomCoordinates  atom coordinates
          @param parameters       six RB parameters
          @param forces           force array (forces added to current values)
-         @param energiesByBond   energies by bond: energiesByBond[bondIndex]
-         @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
-      
-         @return ReferenceForce::DefaultReturn
+         @param totalEnergy      if not null, the energy will be added to this
             
          --------------------------------------------------------------------------------------- */
       
-      int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+      void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
                             RealOpenMM* parameters, RealOpenMM** forces,
-                            RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
-      
+                            RealOpenMM* totalEnergy ) const;
 
 };
 

platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp

@@ -73,25 +73,15 @@ ReferenceProperDihedralBond::~ReferenceProperDihedralBond( ){
                                          parameters[1] = ideal bond angle in radians
                                          parameters[2] = multiplicity
    @param forces           force array (forces added to current values)
-   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
-   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
-
-   @return ReferenceForce::DefaultReturn
+   @param totalEnergy      if not null, the energy will be added to this
 
    --------------------------------------------------------------------------------------- */
 
-int ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
+void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
                                                    RealOpenMM** atomCoordinates,
                                                    RealOpenMM* parameters,
                                                    RealOpenMM** forces,
-                                                   RealOpenMM* energiesByBond,
-                                                   RealOpenMM* energiesByAtom ) const {
-
-   // ---------------------------------------------------------------------------------------
-
-   // static const char* methodName = "\nReferenceProperDihedralBond::calculateBondIxn";
-
-   // ---------------------------------------------------------------------------------------
+                                                   RealOpenMM* totalEnergy ) const {
 
    static const std::string methodName = "\nReferenceProperDihedralBond::calculateBondIxn";
 
@@ -185,7 +175,6 @@ int ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
 
    // accumulate energies
 
-   updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
-
-   return ReferenceForce::DefaultReturn;
+   if (totalEnergy != NULL)
+       *totalEnergy += energy;
 }

platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.h

@@ -61,17 +61,13 @@ class ReferenceProperDihedralBond : public ReferenceBondIxn {
                                                parameters[1] = ideal bond angle in radians
                                                parameters[2] = multiplicity
          @param forces           force array (forces added to current values)
-         @param energiesByBond   energies by bond: energiesByBond[bondIndex]
-         @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
-      
-         @return ReferenceForce::DefaultReturn
+         @param totalEnergy      if not null, the energy will be added to this
       
          --------------------------------------------------------------------------------------- */
       
-      int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+      void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
                             RealOpenMM* parameters, RealOpenMM** forces,
-                            RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
-      
+                            RealOpenMM* totalEnergy ) const;
 
 };
 

platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp

@@ -71,25 +71,15 @@ ReferenceRbDihedralBond::~ReferenceRbDihedralBond( ){
    @param atomCoordinates  atom coordinates
    @param parameters       six RB parameters
    @param forces           force array (forces added to current values)
-   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
-   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
-
-   @return ReferenceForce::DefaultReturn
+   @param totalEnergy      if not null, the energy will be added to this
 
    --------------------------------------------------------------------------------------- */
 
-int ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
+void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
                                                RealOpenMM** atomCoordinates,
                                                RealOpenMM* parameters,
                                                RealOpenMM** forces,
-                                               RealOpenMM* energiesByBond,
-                                               RealOpenMM* energiesByAtom ) const {
-
-   // ---------------------------------------------------------------------------------------
-
-   // static const char* methodName = "\nReferenceRbDihedralBond::calculateBondIxn";
-
-   // ---------------------------------------------------------------------------------------
+                                               RealOpenMM* totalEnergy ) const {
 
    static const std::string methodName = "\nReferenceRbDihedralBond::calculateBondIxn";
 
@@ -200,7 +190,6 @@ int ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
 
    // accumulate energies
 
-   updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
-
-   return ReferenceForce::DefaultReturn;
+   if (totalEnergy != NULL)
+       *totalEnergy += energy;
 }

platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.h

@@ -59,17 +59,13 @@ class ReferenceRbDihedralBond : public ReferenceBondIxn {
          @param atomCoordinates  atom coordinates
          @param parameters       six RB parameters
          @param forces           force array (forces added to current values)
-         @param energiesByBond   energies by bond: energiesByBond[bondIndex]
-         @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
-      
-         @return ReferenceForce::DefaultReturn
+         @param totalEnergy      if not null, the energy will be added to this
             
          --------------------------------------------------------------------------------------- */
       
-      int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+      void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
                             RealOpenMM* parameters, RealOpenMM** forces,
-                            RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
-      
+                            RealOpenMM* totalEnergy ) const;
 
 };
 

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

@@ -259,7 +259,7 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::executeForces(ContextI
     ReferenceFreeEnergyLJCoulomb14Softcore nonbonded14;
     if (nonbondedMethod == CutoffNonPeriodic || nonbondedMethod == CutoffPeriodic)
         nonbonded14.setUseCutoff(nonbondedCutoff, rfDielectric);
-    refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, 0, 0, nonbonded14);
+    refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, nonbonded14);
 }
 
 double ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::executeEnergy(ContextImpl& context) {
@@ -289,12 +289,8 @@ double ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::executeEnergy(Contex
     if (nonbondedMethod == CutoffNonPeriodic || nonbondedMethod == CutoffPeriodic)
         nonbonded14.setUseCutoff(nonbondedCutoff, rfDielectric);
 
-    RealOpenMM* energyArray = new RealOpenMM[num14];
-    for (int i = 0; i < num14; ++i)
-        energyArray[i] = 0;
-    refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, energyArray, 0, &energy, nonbonded14);
+    refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, &energy, nonbonded14);
     disposeRealArray(forceData, numParticles);
-    delete[] energyArray;
 
     return energy;
 }

plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.cpp

@@ -140,23 +140,13 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::getDerivedParameters( RealOpenMM c6,
 										parameters[1]= c6*c6/c12      (4*epsilon)
 										parameters[2]= epsfac*q1*q2
    @param forces           force array (forces added to current values)
-   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
-   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
-
-   @return ReferenceForce::DefaultReturn
+   @param totalEnergy      if not null, the energy will be added to this
 
    --------------------------------------------------------------------------------------- */
 
-int ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+void ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
                                                                RealOpenMM* parameters, RealOpenMM** forces,
-                                                               RealOpenMM* energiesByBond,
-                                                               RealOpenMM* energiesByAtom ) const {
-
-   // ---------------------------------------------------------------------------------------
-
-   // static const char* methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn";
-
-   // ---------------------------------------------------------------------------------------
+                                                               RealOpenMM* totalEnergy ) const {
 
    static const std::string methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn";
 
@@ -193,7 +183,7 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices,
    ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] );  
 
    if (cutoff && deltaR[0][ReferenceForce::RIndex] > cutoffDistance)
-       return ReferenceForce::DefaultReturn;
+       return;
    RealOpenMM r2        = deltaR[0][ReferenceForce::R2Index];
    RealOpenMM inverseR  = one/(deltaR[0][ReferenceForce::RIndex]);
 
@@ -229,7 +219,8 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices,
 
    // accumulate energies
 
-   updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
+   if (totalEnergy != NULL)
+       *totalEnergy += energy;
 
    // debug 
 
@@ -283,8 +274,6 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices,
 
       //SimTKOpenMMLog::printMessage( message );
    }   
-
-   return ReferenceForce::DefaultReturn;
 }
 
   /**---------------------------------------------------------------------------------------

plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.h

@@ -98,16 +98,13 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
          @param atomCoordinates  atom coordinates
          @param parameters       six RB parameters
          @param forces           force array (forces added to current values)
-         @param energiesByBond   energies by bond: energiesByBond[bondIndex]
-         @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
-      
-         @return ReferenceForce::DefaultReturn
+         @param totalEnergy      if not null, the energy will be added to this
             
          --------------------------------------------------------------------------------------- */
       
-      int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+      void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
                             RealOpenMM* parameters, RealOpenMM** forces,
-                            RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
+                            RealOpenMM* totalEnergy ) const;
       
         /**---------------------------------------------------------------------------------------