Avoid uninitialized memory

platforms/cuda/src/CudaContext.cpp

@@ -827,9 +827,9 @@ void CudaContext::validateMolecules() {
     vector<int4> newCellOffsets(numAtoms);
     if (useDoublePrecision) {
         vector<double4> oldPosq(paddedNumAtoms);
-        vector<double4> newPosq(paddedNumAtoms);
+        vector<double4> newPosq(paddedNumAtoms, make_double4(0, 0, 0, 0));
         vector<double4> oldVelm(paddedNumAtoms);
-        vector<double4> newVelm(paddedNumAtoms);
+        vector<double4> newVelm(paddedNumAtoms, make_double4(0, 0, 0, 0));
         posq->download(oldPosq);
         velm->download(oldVelm);
         for (int i = 0; i < numAtoms; i++) {
@@ -843,11 +843,11 @@ void CudaContext::validateMolecules() {
     }
     else if (useMixedPrecision) {
         vector<float4> oldPosq(paddedNumAtoms);
-        vector<float4> newPosq(paddedNumAtoms);
+        vector<float4> newPosq(paddedNumAtoms, make_float4(0, 0, 0, 0));
         vector<float4> oldPosqCorrection(paddedNumAtoms);
-        vector<float4> newPosqCorrection(paddedNumAtoms);
+        vector<float4> newPosqCorrection(paddedNumAtoms, make_float4(0, 0, 0, 0));
         vector<double4> oldVelm(paddedNumAtoms);
-        vector<double4> newVelm(paddedNumAtoms);
+        vector<double4> newVelm(paddedNumAtoms, make_double4(0, 0, 0, 0));
         posq->download(oldPosq);
         velm->download(oldVelm);
         for (int i = 0; i < numAtoms; i++) {
@@ -863,9 +863,9 @@ void CudaContext::validateMolecules() {
     }
     else {
         vector<float4> oldPosq(paddedNumAtoms);
-        vector<float4> newPosq(paddedNumAtoms);
+        vector<float4> newPosq(paddedNumAtoms, make_float4(0, 0, 0, 0));
         vector<float4> oldVelm(paddedNumAtoms);
-        vector<float4> newVelm(paddedNumAtoms);
+        vector<float4> newVelm(paddedNumAtoms, make_float4(0, 0, 0, 0));
         posq->download(oldPosq);
         velm->download(oldVelm);
         for (int i = 0; i < numAtoms; i++) {
@@ -905,9 +905,9 @@ template <class Real, class Real4, class Mixed, class Mixed4>
 void CudaContext::reorderAtomsImpl(bool enforcePeriodic) {
     // Find the range of positions and the number of bins along each axis.
 
-    vector<Real4> oldPosq(paddedNumAtoms);
-    vector<Real4> oldPosqCorrection(paddedNumAtoms);
-    vector<Mixed4> oldVelm(paddedNumAtoms);
+    vector<Real4> oldPosq(paddedNumAtoms, (Real4) {0, 0, 0, 0});
+    vector<Real4> oldPosqCorrection(paddedNumAtoms, (Real4) {0, 0, 0, 0});
+    vector<Mixed4> oldVelm(paddedNumAtoms, (Mixed4) {0, 0, 0, 0});
     posq->download(oldPosq);
     velm->download(oldVelm);
     if (useMixedPrecision)

platforms/cuda/src/CudaKernels.cpp

@@ -1409,7 +1409,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
     CudaArray& posq = cu.getPosq();
     float4* posqf = (float4*) cu.getPinnedBuffer();
     double4* posqd = (double4*) cu.getPinnedBuffer();
-    vector<float2> sigmaEpsilonVector(cu.getPaddedNumAtoms());
+    vector<float2> sigmaEpsilonVector(cu.getPaddedNumAtoms(), make_float2(0, 0));
     vector<vector<int> > exclusionList(numParticles);
     double sumSquaredCharges = 0.0;
     hasCoulomb = false;
@@ -1747,7 +1747,7 @@ void CudaCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context,
     posq.download(cu.getPinnedBuffer());
     float4* posqf = (float4*) cu.getPinnedBuffer();
     double4* posqd = (double4*) cu.getPinnedBuffer();
-    vector<float2> sigmaEpsilonVector(cu.getPaddedNumAtoms());
+    vector<float2> sigmaEpsilonVector(cu.getPaddedNumAtoms(), make_float2(0, 0));
     double sumSquaredCharges = 0.0;
     const vector<int>& order = cu.getAtomIndex();
     for (int i = 0; i < force.getNumParticles(); i++) {
@@ -2026,7 +2026,7 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
     CudaArray& posq = cu.getPosq();
     float4* posqf = (float4*) cu.getPinnedBuffer();
     double4* posqd = (double4*) cu.getPinnedBuffer();
-    vector<float2> paramsVector(cu.getPaddedNumAtoms());
+    vector<float2> paramsVector(cu.getPaddedNumAtoms(), make_float2(1, 1));
     const double dielectricOffset = 0.009;
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge, radius, scalingFactor;
@@ -2144,7 +2144,7 @@ void CudaCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, c
     float4* posqf = (float4*) cu.getPinnedBuffer();
     double4* posqd = (double4*) cu.getPinnedBuffer();
     posq.download(cu.getPinnedBuffer());
-    vector<float2> paramsVector(cu.getPaddedNumAtoms());
+    vector<float2> paramsVector(cu.getPaddedNumAtoms(), make_float2(1, 1));
     const double dielectricOffset = 0.009;
     for (int i = 0; i < numParticles; i++) {
         double charge, radius, scalingFactor;