Merge pull request #109 from peastman/master

Avoid nans when using PME with Drude particles

platforms/cuda/src/kernels/coulombLennardJones.cu

@@ -22,9 +22,11 @@ if ((!isExcluded && r2 < CUTOFF_SQUARED) || needCorrection) {
     if (needCorrection) {
         // Subtract off the part of this interaction that was included in the reciprocal space contribution.
 
+        if (1-erfcAlphaR > 1e-6) {
             tempForce = -prefactor*((1.0f-erfcAlphaR)-alphaR*expAlphaRSqr*TWO_OVER_SQRT_PI);
             tempEnergy += -prefactor*(1.0f-erfcAlphaR);
         }
+    }
     else {
 #if HAS_LENNARD_JONES
         real sig = sigmaEpsilon1.x + sigmaEpsilon2.x;

platforms/opencl/src/kernels/coulombLennardJones.cl

@@ -22,9 +22,11 @@ if ((!isExcluded && r2 < CUTOFF_SQUARED) || needCorrection) {
     if (needCorrection) {
         // Subtract off the part of this interaction that was included in the reciprocal space contribution.
 
+        if (1-erfcAlphaR > 1e-6) {
             tempForce = -prefactor*((1.0f-erfcAlphaR)-alphaR*expAlphaRSqr*TWO_OVER_SQRT_PI);
             tempEnergy += -prefactor*(1.0f-erfcAlphaR);
         }
+    }
     else {
 #if HAS_LENNARD_JONES
         real sig = sigmaEpsilon1.x + sigmaEpsilon2.x;

platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp

@@ -432,6 +432,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
                RealOpenMM r         = deltaR[0][ReferenceForce::RIndex];
                RealOpenMM inverseR  = one/(deltaR[0][ReferenceForce::RIndex]);
                RealOpenMM alphaR    = alphaEwald * r;
+               if (erf(alphaR) > 1e-6) {
                    RealOpenMM dEdR      = (RealOpenMM) (ONE_4PI_EPS0 * atomParameters[ii][QIndex] * atomParameters[jj][QIndex] * inverseR * inverseR * inverseR);
                               dEdR      = (RealOpenMM) (dEdR * (erf(alphaR) - 2 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI ));
 
@@ -454,6 +455,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
                    }
                }
             }
+        }
 
     if( totalEnergy )
         *totalEnergy -= totalExclusionEnergy;