Fixes and minor improvements

platforms/opencl/include/OpenCLKernels.h

@@ -709,7 +709,7 @@ private:
     double ewaldSelfEnergy, dispersionCoefficient, alpha, dispersionAlpha;
     int gridSizeX, gridSizeY, gridSizeZ;
     int dispersionGridSizeX, dispersionGridSizeY, dispersionGridSizeZ;
-    bool hasCoulomb, hasLJ, usePmeQueue, doLJPME, usePosqCharges;
+    bool hasCoulomb, hasLJ, usePmeQueue, doLJPME, usePosqCharges, recomputeParams, hasOffsets;
     NonbondedMethod nonbondedMethod;
     static const int PmeOrder = 5;
 };

platforms/opencl/src/OpenCLKernels.cpp

@@ -1636,6 +1636,8 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         if (cl.getContextIndex() == 0) {
             paramsDefines["INCLUDE_EWALD"] = "1";
             paramsDefines["EWALD_SELF_ENERGY_SCALE"] = cl.doubleToString(ONE_4PI_EPS0*alpha/sqrt(M_PI));
+            for (int i = 0; i < numParticles; i++)
+                ewaldSelfEnergy += baseParticleParamVec[i].x*baseParticleParamVec[i].x*ONE_4PI_EPS0*alpha/sqrt(M_PI);
 
             // Create the reciprocal space kernels.
 
@@ -1675,9 +1677,13 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         if (cl.getContextIndex() == 0) {
             paramsDefines["INCLUDE_EWALD"] = "1";
             paramsDefines["EWALD_SELF_ENERGY_SCALE"] = cl.doubleToString(ONE_4PI_EPS0*alpha/sqrt(M_PI));
+            for (int i = 0; i < numParticles; i++)
+                ewaldSelfEnergy += baseParticleParamVec[i].x*baseParticleParamVec[i].x*ONE_4PI_EPS0*alpha/sqrt(M_PI);
             if (doLJPME) {
                 paramsDefines["INCLUDE_LJPME"] = "1";
                 paramsDefines["LJPME_SELF_ENERGY_SCALE"] = cl.doubleToString(pow(dispersionAlpha, 6)/3.0);
+                for (int i = 0; i < numParticles; i++)
+                    ewaldSelfEnergy += baseParticleParamVec[i].z*pow(baseParticleParamVec[i].y*dispersionAlpha, 6)/3.0;
             }
             pmeDefines["PME_ORDER"] = cl.intToString(PmeOrder);
             pmeDefines["NUM_ATOMS"] = cl.intToString(numParticles);
@@ -1973,6 +1979,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         exceptionOffsetIndices.upload(exceptionOffsetIndicesVec);
     }
     globalParams.initialize(cl, max((int) paramValues.size(), 1), cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float), "globalParams");
+    recomputeParams = true;
     
     // Initialize the kernel for updating parameters.
     
@@ -2143,6 +2150,7 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
         }
     }
     if (paramChanged) {
+        recomputeParams = true;
         if (cl.getUseDoublePrecision())
             globalParams.upload(paramValues);
         else {
@@ -2152,8 +2160,12 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
             globalParams.upload(v);
         }
     }
+    double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
+    if (recomputeParams || hasOffsets) {
         computeParamsKernel.setArg<cl_int>(1, includeEnergy && includeReciprocal);
         cl.executeKernel(computeParamsKernel, cl.getPaddedNumAtoms());
+        energy = 0.0; // The Ewald self energy was computed in the kernel.
+    }
     
     // Do reciprocal space calculations.
     
@@ -2391,7 +2403,6 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
             cl.restoreDefaultQueue();
         }
     }
-    double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
     if (dispersionCoefficient != 0.0 && includeDirect) {
         mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
         energy += dispersionCoefficient/(boxSize.x*boxSize.y*boxSize.z);
@@ -2457,6 +2468,7 @@ void OpenCLCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& contex
     if (force.getUseDispersionCorrection() && cl.getContextIndex() == 0 && (nonbondedMethod == CutoffPeriodic || nonbondedMethod == Ewald || nonbondedMethod == PME))
         dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
     cl.invalidateMolecules(info);
+    recomputeParams = true;
 }
 
 void OpenCLCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {

platforms/opencl/src/kernels/nonbondedParameters.cl

@@ -26,17 +26,17 @@ __kernel void computeParameters(__global mixed* restrict energyBuffer, int inclu
         }
 #endif
 #ifdef USE_POSQ_CHARGES
-        posq[i].w = params[0];
+        posq[i].w = params.x;
 #else
-        charge[i] = params[0];
+        charge[i] = params.x;
 #endif
-        sigmaEpsilon[i] = (float2) (0.5f*params[1], 2*SQRT(params[2]));
+        sigmaEpsilon[i] = (float2) (0.5f*params.y, 2*SQRT(params.z));
 #ifdef INCLUDE_EWALD
-        energy -= EWALD_SELF_ENERGY_SCALE*params[0]*params[0];
+        energy -= EWALD_SELF_ENERGY_SCALE*params.x*params.x;
 #endif
 #ifdef INCLUDE_LJPME
-        real sig3 = params[1]*params[1]*params[1];
-        energy += LJPME_SELF_ENERGY_SCALE*sig3*sig3*params[2];
+        real sig3 = params.y*params.y*params.y;
+        energy += LJPME_SELF_ENERGY_SCALE*sig3*sig3*params.z;
 #endif
     }
 
@@ -55,7 +55,7 @@ __kernel void computeParameters(__global mixed* restrict energyBuffer, int inclu
             params.z += value*offset.z;
         }
 #endif
-        exceptionParams[i] = (float4) ((float) (138.935456f*params[0]), (float) params[1], (float) (4*params[2]), 0);
+        exceptionParams[i] = (float4) ((float) (138.935456f*params.x), (float) params.y, (float) (4*params.z), 0);
     }
 #endif
     if (includeSelfEnergy)