Fixed uninitialized memory access (#3399)

platforms/common/src/kernels/nonbondedParameters.cc

@@ -15,7 +15,7 @@ KERNEL void computeParameters(GLOBAL mixed* RESTRICT energyBuffer, int includeSe
     
     for (int i = GLOBAL_ID; i < numAtoms; i += GLOBAL_SIZE) {
         float4 params = baseParticleParams[i];
-#ifdef HAS_OFFSETS
+#ifdef HAS_PARTICLE_OFFSETS
         int start = particleOffsetIndices[i], end = particleOffsetIndices[i+1];
         for (int j = start; j < end; j++) {
             float4 offset = particleParamOffsets[j];
@@ -47,7 +47,7 @@ KERNEL void computeParameters(GLOBAL mixed* RESTRICT energyBuffer, int includeSe
 #ifdef HAS_EXCEPTIONS
     for (int i = GLOBAL_ID; i < numExceptions; i += GLOBAL_SIZE) {
         float4 params = baseExceptionParams[i];
-#ifdef HAS_OFFSETS
+#ifdef HAS_EXCEPTION_OFFSETS
         int start = exceptionOffsetIndices[i], end = exceptionOffsetIndices[i+1];
         for (int j = start; j < end; j++) {
             float4 offset = exceptionParamOffsets[j];

platforms/cuda/src/CudaKernels.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -670,6 +670,10 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
     hasOffsets = (force.getNumParticleParameterOffsets() > 0 || force.getNumExceptionParameterOffsets() > 0);
     if (hasOffsets)
         paramsDefines["HAS_OFFSETS"] = "1";
+    if (force.getNumParticleParameterOffsets() > 0)
+        paramsDefines["HAS_PARTICLE_OFFSETS"] = "1";
+    if (force.getNumExceptionParameterOffsets() > 0)
+        paramsDefines["HAS_EXCEPTION_OFFSETS"] = "1";
     if (usePosqCharges)
         paramsDefines["USE_POSQ_CHARGES"] = "1";
     if (doLJPME)

platforms/opencl/src/OpenCLKernels.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -675,6 +675,10 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
     hasOffsets = (force.getNumParticleParameterOffsets() > 0 || force.getNumExceptionParameterOffsets() > 0);
     if (hasOffsets)
         paramsDefines["HAS_OFFSETS"] = "1";
+    if (force.getNumParticleParameterOffsets() > 0)
+        paramsDefines["HAS_PARTICLE_OFFSETS"] = "1";
+    if (force.getNumExceptionParameterOffsets() > 0)
+        paramsDefines["HAS_EXCEPTION_OFFSETS"] = "1";
     if (usePosqCharges)
         paramsDefines["USE_POSQ_CHARGES"] = "1";
     if (doLJPME)