The differences in the Ewald energies between the Reference and Cuda platforms...

The differences in the Ewald energies between the Reference and Cuda platforms were traced to roundoff error in the 
computation of the Vdw and Coulomb ixns for the short-range energy contribution (verified using double precision in the sum); the vdw and Coulomb terms are now accumulated separately and then added to the total energy 

platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp

@@ -243,9 +243,10 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
     RealOpenMM TWO_PI                   = 2.0 * PI;
     RealOpenMM recipCoeff               = (RealOpenMM)(4*PI/(periodicBoxSize[0] * periodicBoxSize[1] * periodicBoxSize[2]) /epsilon);
 
-    RealOpenMM selfEwaldEnergy          = 0.0;
+    RealOpenMM totalSelfEwaldEnergy     = 0.0;
     RealOpenMM realSpaceEwaldEnergy     = 0.0;
     RealOpenMM recipEnergy              = 0.0;
+    RealOpenMM totalRecipEnergy         = 0.0;
     RealOpenMM vdwEnergy                = 0.0;
 
 // **************************************************************************************
@@ -253,16 +254,18 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
 // **************************************************************************************
 
     for( int atomID = 0; atomID < numberOfAtoms; atomID++ ){
-        selfEwaldEnergy = atomParameters[atomID][QIndex]*atomParameters[atomID][QIndex] * alphaEwald/SQRT_PI;
-
-        if( totalEnergy )
-              *totalEnergy -= selfEwaldEnergy;
+        RealOpenMM selfEwaldEnergy       = atomParameters[atomID][QIndex]*atomParameters[atomID][QIndex] * alphaEwald/SQRT_PI;
+        totalSelfEwaldEnergy            -= selfEwaldEnergy;
 
         if( energyByAtom ){
            energyByAtom[atomID]         -= selfEwaldEnergy;
         }
     }
 
+    if( totalEnergy ){
+        *totalEnergy += totalSelfEwaldEnergy;
+    }
+
 // **************************************************************************************
 // RECIPROCAL SPACE EWALD ENERGY AND FORCES
 // **************************************************************************************
@@ -333,7 +336,6 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
 
     // calculate reciprocal space energy and forces
 
-
     int lowry = 0;
     int lowrz = 1;
 
@@ -387,6 +389,7 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
           }
 
           recipEnergy       = recipCoeff * ak * ( cs * cs + ss * ss);
+          totalRecipEnergy += recipEnergy;
 
           if( totalEnergy )
              *totalEnergy += recipEnergy;
@@ -408,10 +411,14 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
       SimTKOpenMMLog::printError( message );
   }
 
+
 // **************************************************************************************
 // SHORT-RANGE ENERGY AND FORCES
 // **************************************************************************************
 
+    RealOpenMM totalVdwEnergy            = 0.0f;
+    RealOpenMM totalRealSpaceEwaldEnergy = 0.0f;
+
     for (int i = 0; i < (int) neighborList->size(); i++) {
        OpenMM::AtomPair pair = (*neighborList)[i];
        int ii = pair.first;
@@ -448,8 +455,8 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
        realSpaceEwaldEnergy        = (RealOpenMM) (atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erfc(alphaR));
        vdwEnergy                   = eps*(sig6-one)*sig6;
 
-        if( totalEnergy )
-              *totalEnergy += realSpaceEwaldEnergy + vdwEnergy;
+       totalVdwEnergy             += vdwEnergy;
+       totalRealSpaceEwaldEnergy  += realSpaceEwaldEnergy;
 
         if( energyByAtom ){
            energyByAtom[ii] += realSpaceEwaldEnergy + vdwEnergy;
@@ -458,8 +465,12 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
 
     }
 
+    if( totalEnergy )
+        *totalEnergy += totalRealSpaceEwaldEnergy + totalVdwEnergy;
+
     // Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
 
+    RealOpenMM totalExclusionEnergy = 0.0f;
     for (int i = 0; i < numberOfAtoms; i++)
         for (int j = 1; j <= exclusions[i][0]; j++)
             if (exclusions[i][j] > i) {
@@ -486,17 +497,17 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
 
                realSpaceEwaldEnergy = (RealOpenMM) (atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erf(alphaR));
 
-                if( totalEnergy )
-                      *totalEnergy -= realSpaceEwaldEnergy;
-
+               totalExclusionEnergy += realSpaceEwaldEnergy;
                if( energyByAtom ){
                    energyByAtom[ii] -= realSpaceEwaldEnergy;
                    energyByAtom[jj] -= realSpaceEwaldEnergy;
                }
             }
 
-// ***********************************************************************
+    if( totalEnergy )
+        *totalEnergy -= totalExclusionEnergy;
 
+// ***********************************************************************
 
    return ReferenceForce::DefaultReturn;
 }