Fixes uninitialized bits occurring in the PaddedNumAtoms regions by properly...

Fixes uninitialized bits occurring in the PaddedNumAtoms regions by properly constructing them. This should hopefully get rid of some of the NaN errors we've been seeing.

platforms/opencl/src/OpenCLContext.cpp

@@ -871,9 +871,9 @@ void OpenCLContext::validateMolecules() {
     vector<mm_int4> newCellOffsets(numAtoms);
     if (useDoublePrecision) {
         vector<mm_double4> oldPosq(paddedNumAtoms);
-        vector<mm_double4> newPosq(paddedNumAtoms);
+        vector<mm_double4> newPosq(paddedNumAtoms, mm_double4(0,0,0,0));
         vector<mm_double4> oldVelm(paddedNumAtoms);
-        vector<mm_double4> newVelm(paddedNumAtoms);
+        vector<mm_double4> newVelm(paddedNumAtoms, mm_double4(0,0,0,0));
         posq->download(oldPosq);
         velm->download(oldVelm);
         for (int i = 0; i < numAtoms; i++) {
@@ -887,11 +887,11 @@ void OpenCLContext::validateMolecules() {
     }
     else if (useMixedPrecision) {
         vector<mm_float4> oldPosq(paddedNumAtoms);
-        vector<mm_float4> newPosq(paddedNumAtoms);
+        vector<mm_float4> newPosq(paddedNumAtoms, mm_float4(0,0,0,0));
         vector<mm_float4> oldPosqCorrection(paddedNumAtoms);
-        vector<mm_float4> newPosqCorrection(paddedNumAtoms);
+        vector<mm_float4> newPosqCorrection(paddedNumAtoms, mm_float4(0,0,0,0));
         vector<mm_double4> oldVelm(paddedNumAtoms);
-        vector<mm_double4> newVelm(paddedNumAtoms);
+        vector<mm_double4> newVelm(paddedNumAtoms, mm_double4(0,0,0,0));
         posq->download(oldPosq);
         velm->download(oldVelm);
         for (int i = 0; i < numAtoms; i++) {
@@ -907,9 +907,9 @@ void OpenCLContext::validateMolecules() {
     }
     else {
         vector<mm_float4> oldPosq(paddedNumAtoms);
-        vector<mm_float4> newPosq(paddedNumAtoms);
+        vector<mm_float4> newPosq(paddedNumAtoms, mm_float4(0,0,0,0));
         vector<mm_float4> oldVelm(paddedNumAtoms);
-        vector<mm_float4> newVelm(paddedNumAtoms);
+        vector<mm_float4> newVelm(paddedNumAtoms, mm_float4(0,0,0,0));
         posq->download(oldPosq);
         velm->download(oldVelm);
         for (int i = 0; i < numAtoms; i++) {
@@ -981,9 +981,9 @@ void OpenCLContext::reorderAtomsImpl(bool enforcePeriodic) {
     // Loop over each group of identical molecules and reorder them.
 
     vector<int> originalIndex(numAtoms);
-    vector<Real4> newPosq(paddedNumAtoms);
-    vector<Real4> newPosqCorrection(paddedNumAtoms);
-    vector<Mixed4> newVelm(paddedNumAtoms);
+    vector<Real4> newPosq(paddedNumAtoms, Real4(0,0,0,0));
+    vector<Real4> newPosqCorrection(paddedNumAtoms, Real4(0,0,0,0));
+    vector<Mixed4> newVelm(paddedNumAtoms, Mixed4(0,0,0,0));
     vector<mm_int4> newCellOffsets(numAtoms);
     for (int group = 0; group < (int) moleculeGroups.size(); group++) {
         // Find the center of each molecule.

platforms/opencl/src/OpenCLKernels.cpp

@@ -1376,9 +1376,9 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
 
     int numParticles = force.getNumParticles();
     sigmaEpsilon = OpenCLArray::create<mm_float2>(cl, cl.getPaddedNumAtoms(), "sigmaEpsilon");
-    vector<mm_float4> posqf(cl.getPaddedNumAtoms());
-    vector<mm_double4> posqd(cl.getPaddedNumAtoms());
-    vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms());
+    vector<mm_float4> posqf(cl.getPaddedNumAtoms(), mm_float4(0,0,0,0));
+    vector<mm_double4> posqd(cl.getPaddedNumAtoms(), mm_double4(0,0,0,0));
+    vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms(), mm_float2(0,0));
     vector<vector<int> > exclusionList(numParticles);
     double sumSquaredCharges = 0.0;
     hasCoulomb = false;
@@ -1761,7 +1761,7 @@ void OpenCLCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& contex
     posq.download(cl.getPinnedBuffer());
     mm_float4* posqf = (mm_float4*) cl.getPinnedBuffer();
     mm_double4* posqd = (mm_double4*) cl.getPinnedBuffer();
-    vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms());
+    vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms(), mm_float2(0,0));
     double sumSquaredCharges = 0.0;
     const vector<cl_int>& order = cl.getAtomIndex();
     for (int i = 0; i < force.getNumParticles(); i++) {
@@ -2042,7 +2042,7 @@ void OpenCLCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOB
     }
     vector<mm_float4> posqf(cl.getPaddedNumAtoms());
     vector<mm_double4> posqd(cl.getPaddedNumAtoms());
-    vector<mm_float2> paramsVector(cl.getPaddedNumAtoms());
+    vector<mm_float2> paramsVector(cl.getPaddedNumAtoms(), mm_float2(1,1));
     const double dielectricOffset = 0.009;
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge, radius, scalingFactor;
@@ -2202,7 +2202,7 @@ void OpenCLCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context,
     mm_float4* posqf = (mm_float4*) cl.getPinnedBuffer();
     mm_double4* posqd = (mm_double4*) cl.getPinnedBuffer();
     posq.download(cl.getPinnedBuffer());
-    vector<mm_float2> paramsVector(cl.getPaddedNumAtoms());
+    vector<mm_float2> paramsVector(cl.getPaddedNumAtoms(), mm_float2(1,1));
     const double dielectricOffset = 0.009;
     for (int i = 0; i < numParticles; i++) {
         double charge, radius, scalingFactor;