Merge pull request #170 from peastman/master

Prevent segfaults when a simulation blows up

platforms/cpu/src/CpuNonbondedForce.cpp

@@ -383,13 +383,15 @@ void CpuNonbondedForce::calculateDirectIxn(int numberOfAtoms, float* posq, const
                     float r         = sqrtf(r2);
                     float inverseR  = 1/r;
                     float chargeProd = ONE_4PI_EPS0*posq[4*ii+3]*posq[4*jj+3];
+                    float alphaR = alphaEwald*r;
+                    float erfcAlphaR = erfcApprox(alphaR);
                     float dEdR      = (float) (chargeProd * inverseR * inverseR * inverseR);
-                          dEdR      = (float) (dEdR * (1.0f-ewaldScaleFunction(r)));
+                          dEdR      = (float) (dEdR * (1.0f-erfcAlphaR-TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR)));
                     __m128 result = _mm_mul_ps(deltaR, _mm_set1_ps(dEdR));
                     _mm_storeu_ps(forces+4*ii, _mm_sub_ps(_mm_loadu_ps(forces+4*ii), result));
                     _mm_storeu_ps(forces+4*jj, _mm_add_ps(_mm_loadu_ps(forces+4*jj), result));
                     if (includeEnergy)
-                        directEnergy -= chargeProd*inverseR*(1.0f-erfcApprox(alphaEwald*r));
+                        directEnergy -= chargeProd*inverseR*(1.0f-erfcAlphaR);
                 }
             }
     }
@@ -505,8 +507,7 @@ void CpuNonbondedForce::calculateOneEwaldIxn(int ii, int jj, float* forces, doub
     __m128 posJ = _mm_loadu_ps(posq+4*jj);
     float r2;
     getDeltaR(posJ, posI, deltaR, r2, true);
-    if (r2 >= cutoffDistance*cutoffDistance)
-        return;
+    if (r2 < cutoffDistance*cutoffDistance) {
         float r         = sqrtf(r2);
         float inverseR  = 1/r;
         float switchValue = 1, switchDeriv = 0;
@@ -542,6 +543,7 @@ void CpuNonbondedForce::calculateOneEwaldIxn(int ii, int jj, float* forces, doub
             energy += (float) (chargeProd*inverseR*erfcApprox(alphaEwald*r));
             *totalEnergy += energy;
         }
+    }
 }
 
 void CpuNonbondedForce::getDeltaR(const __m128& posI, const __m128& posJ, __m128& deltaR, float& r2, bool periodic) const {

plugins/cpupme/src/CpuPmeKernels.cpp

@@ -93,6 +93,8 @@ static void spreadCharge(int start, int end, float* posq, float* grid, int gridx
         int gridIndexX = _mm_extract_epi32(gridIndex, 0);
         int gridIndexY = _mm_extract_epi32(gridIndex, 1);
         int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
+        if (gridIndexX < 0)
+            return; // This happens when a simulation blows up and coordinates become NaN.
         int zindex[PME_ORDER];
         for (int j = 0; j < PME_ORDER; j++) {
             zindex[j] = gridIndexZ+j;
@@ -288,6 +290,8 @@ static void interpolateForces(int start, int end, float* posq, float* force, flo
         int gridIndexX = _mm_extract_epi32(gridIndex, 0);
         int gridIndexY = _mm_extract_epi32(gridIndex, 1);
         int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
+        if (gridIndexX < 0)
+            return; // This happens when a simulation blows up and coordinates become NaN.
         int zindex[PME_ORDER];
         for (int j = 0; j < PME_ORDER; j++) {
             zindex[j] = gridIndexZ+j;