Fixed some Valgrind warnings

platforms/cuda/src/CudaKernels.cpp

@@ -223,7 +223,7 @@ void CudaCalcCustomBondForceKernel::initialize(const System& system, const Custo
     }
     gpuSetCustomBondParameters(data.gpu, particle1, particle2, params, force.getEnergyFunction(), paramNames, globalParamNames);
     if (globalParamValues.size() > 0)
-        SetCustomBondGlobalParams(&globalParamValues[0]);
+        SetCustomBondGlobalParams(globalParamValues);
 }
 
 void CudaCalcCustomBondForceKernel::executeForces(ContextImpl& context) {
@@ -246,7 +246,7 @@ void CudaCalcCustomBondForceKernel::updateGlobalParams(ContextImpl& context) {
         globalParamValues[i] = value;
     }
     if (changed)
-        SetCustomBondGlobalParams(&globalParamValues[0]);
+        SetCustomBondGlobalParams(globalParamValues);
 }
 
 CudaCalcHarmonicAngleForceKernel::~CudaCalcHarmonicAngleForceKernel() {
@@ -514,7 +514,7 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
     }
     gpuSetCustomNonbondedParameters(gpu, parameters, exclusionList, method, (float) force.getCutoffDistance(), force.getEnergyFunction(), paramNames, globalParamNames);
     if (globalParamValues.size() > 0)
-        SetCustomNonbondedGlobalParams(&globalParamValues[0]);
+        SetCustomNonbondedGlobalParams(globalParamValues);
 }
 
 void CudaCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context) {
@@ -535,7 +535,7 @@ void CudaCalcCustomNonbondedForceKernel::updateGlobalParams(ContextImpl& context
         globalParamValues[i] = value;
     }
     if (changed)
-        SetCustomNonbondedGlobalParams(&globalParamValues[0]);
+        SetCustomNonbondedGlobalParams(globalParamValues);
 }
 
 CudaCalcGBSAOBCForceKernel::~CudaCalcGBSAOBCForceKernel() {
@@ -613,7 +613,7 @@ void CudaCalcCustomExternalForceKernel::initialize(const System& system, const C
     }
     gpuSetCustomExternalParameters(data.gpu, particle, params, force.getEnergyFunction(), paramNames, globalParamNames);
     if (globalParamValues.size() > 0)
-        SetCustomExternalGlobalParams(&globalParamValues[0]);
+        SetCustomExternalGlobalParams(globalParamValues);
 }
 
 void CudaCalcCustomExternalForceKernel::executeForces(ContextImpl& context) {
@@ -636,7 +636,7 @@ void CudaCalcCustomExternalForceKernel::updateGlobalParams(ContextImpl& context)
         globalParamValues[i] = value;
     }
     if (changed)
-        SetCustomExternalGlobalParams(&globalParamValues[0]);
+        SetCustomExternalGlobalParams(globalParamValues);
 }
 
 static void initializeIntegration(const System& system, CudaPlatform::PlatformData& data, const Integrator& integrator) {

platforms/cuda/src/kernels/cudaKernels.h

@@ -113,10 +113,10 @@ extern void SetRandomSim(gpuContext gpu);
 extern void GetRandomSim(gpuContext gpu);
 extern void SetCustomBondForceExpression(const Expression<128>& expression);
 extern void SetCustomBondEnergyExpression(const Expression<128>& expression);
-extern void SetCustomBondGlobalParams(float* paramValues);
+extern void SetCustomBondGlobalParams(const std::vector<float>&  paramValues);
 extern void SetCustomExternalForceExpressions(const Expression<128>& expressionX, const Expression<128>& expressionY, const Expression<128>& expressionZ);
 extern void SetCustomExternalEnergyExpression(const Expression<128>& expression);
-extern void SetCustomExternalGlobalParams(float* paramValues);
+extern void SetCustomExternalGlobalParams(const std::vector<float>& paramValues);
 extern void SetCustomNonbondedForceExpression(const Expression<128>& expression);
 extern void SetCustomNonbondedEnergyExpression(const Expression<128>& expression);
-extern void SetCustomNonbondedGlobalParams(float* paramValues);
+extern void SetCustomNonbondedGlobalParams(const std::vector<float>& paramValues);

platforms/cuda/src/kernels/gpu.cpp

@@ -1863,7 +1863,8 @@ void* gpuInit(int numAtoms, unsigned int device, bool useBlockingSync)
     for (int i = 0; i < MAX_TABULATED_FUNCTIONS; i++)
         gpu->tabulatedFunctions[i].coefficients = NULL;
     gpu->sim.customExpressionStackSize = 0;
-
+    gpu->sim.customBonds = 0;
+    
     // Initialize output buffer before reading parameters
     gpu->pOutputBufferCounter       = new unsigned int[gpu->sim.paddedNumberOfAtoms];
     memset(gpu->pOutputBufferCounter, 0, gpu->sim.paddedNumberOfAtoms * sizeof(unsigned int));

platforms/cuda/src/kernels/kCalculateCustomBondForces.cu

@@ -70,10 +70,10 @@ void SetCustomBondEnergyExpression(const Expression<128>& expression)
     RTERROR(status, "SetCustomBondEnergyExpression: cudaMemcpyToSymbol failed");
 }
 
-void SetCustomBondGlobalParams(float* paramValues)
+void SetCustomBondGlobalParams(const vector<float>& paramValues)
 {
     cudaError_t status;
-    status = cudaMemcpyToSymbol(globalParams, paramValues, sizeof(globalParams));
+    status = cudaMemcpyToSymbol(globalParams, &paramValues[0], paramValues.size()*sizeof(float));
     RTERROR(status, "SetCustomBondGlobalParams: cudaMemcpyToSymbol failed");
 }
 

platforms/cuda/src/kernels/kCalculateCustomExternalForces.cu

@@ -74,10 +74,10 @@ void SetCustomExternalEnergyExpression(const Expression<128>& expression)
     RTERROR(status, "SetCustomExternalEnergyExpression: cudaMemcpyToSymbol failed");
 }
 
-void SetCustomExternalGlobalParams(float* paramValues)
+void SetCustomExternalGlobalParams(const vector<float>& paramValues)
 {
     cudaError_t status;
-    status = cudaMemcpyToSymbol(globalParams, paramValues, sizeof(globalParams));
+    status = cudaMemcpyToSymbol(globalParams, &paramValues[0], paramValues.size()*sizeof(float));
     RTERROR(status, "SetCustomExternalGlobalParams: cudaMemcpyToSymbol failed");
 }
 

platforms/cuda/src/kernels/kCalculateCustomNonbondedForces.cu

@@ -83,10 +83,10 @@ void SetCustomNonbondedEnergyExpression(const Expression<128>& expression)
     RTERROR(status, "SetCustomNonbondedEnergyExpression: cudaMemcpyToSymbol failed");
 }
 
-void SetCustomNonbondedGlobalParams(float* paramValues)
+void SetCustomNonbondedGlobalParams(const vector<float>& paramValues)
 {
     cudaError_t status;
-    status = cudaMemcpyToSymbol(globalParams, paramValues, sizeof(globalParams));
+    status = cudaMemcpyToSymbol(globalParams, &paramValues[0], paramValues.size()*sizeof(float));
     RTERROR(status, "SetCustomNonbondedGlobalParams: cudaMemcpyToSymbol failed");
 }