Mods to allow Born radii to be updated if atomic positions updated off the board

platforms/cuda/src/CudaKernels.cpp

@@ -291,6 +291,7 @@ CudaCalcGBSAOBCForceKernel::~CudaCalcGBSAOBCForceKernel() {
 }
 
 void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCForce& force) {
+
     int numParticles = system.getNumParticles();
     _gpuContext* gpu = data.gpu;
     vector<int> particle(numParticles);
@@ -363,8 +364,6 @@ static void initializeIntegration(const System& system, CudaPlatform::PlatformDa
     gpuBuildExclusionList(gpu);
     gpuBuildOutputBuffers(gpu);
     gpuSetConstants(gpu);
-    kCalculateObcGbsaBornSum(gpu);
-    kReduceObcGbsaBornSum(gpu);
     kClearBornForces(gpu);
     kClearForces(gpu);
     cudaThreadSynchronize();

platforms/cuda/src/CudaStreamFactory.cpp

@@ -42,39 +42,39 @@ StreamImpl* CudaStreamFactory::createStreamImpl(std::string name, int size, Stre
     if (name == "particlePositions") {
         CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
         float padding[] = {100000.0f, 100000.0f, 100000.0f, 0.2f};
-        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psPosq4, 4, padding);
+        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psPosq4, 4, padding, data.gpu);
     }
     if (name == "particleVelocities") {
         CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
         float padding[] = {0.0f, 0.0f, 0.0f, 0.0f};
-        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psVelm4, 4, padding);
+        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psVelm4, 4, padding, data.gpu);
     }
     if (name == "particleForces") {
         CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
         float padding[] = {0.0f, 0.0f, 0.0f, 0.0f};
-        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psForce4, 4, padding);
+        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psForce4, 4, padding, data.gpu);
     }
     switch (type) {
     case Stream::Float:
     case Stream::Double:
-        return new CudaStreamImpl<float1>(name, size, type, platform, 1);
+        return new CudaStreamImpl<float1>(name, size, type, platform, 1, NULL);
     case Stream::Float2:
     case Stream::Double2:
-        return new CudaStreamImpl<float2>(name, size, type, platform, 1);
+        return new CudaStreamImpl<float2>(name, size, type, platform, 1, NULL);
     case Stream::Float3:
     case Stream::Double3:
-        return new CudaStreamImpl<float3>(name, size, type, platform, 1);
+        return new CudaStreamImpl<float3>(name, size, type, platform, 1, NULL);
     case Stream::Float4:
     case Stream::Double4:
-        return new CudaStreamImpl<float4>(name, size, type, platform, 1);
+        return new CudaStreamImpl<float4>(name, size, type, platform, 1, NULL);
     case Stream::Integer:
-        return new CudaStreamImpl<int1>(name, size, type, platform, 1);
+        return new CudaStreamImpl<int1>(name, size, type, platform, 1, NULL);
     case Stream::Integer2:
-        return new CudaStreamImpl<int2>(name, size, type, platform, 1);
+        return new CudaStreamImpl<int2>(name, size, type, platform, 1, NULL);
     case Stream::Integer3:
-        return new CudaStreamImpl<int3>(name, size, type, platform, 1);
+        return new CudaStreamImpl<int3>(name, size, type, platform, 1, NULL);
     case Stream::Integer4:
-        return new CudaStreamImpl<int4>(name, size, type, platform, 1);
+        return new CudaStreamImpl<int4>(name, size, type, platform, 1, NULL);
     }
     throw OpenMMException("Tried to create a Stream with an illegal DataType.");
 }

platforms/cuda/src/CudaStreamImpl.h

@@ -44,8 +44,8 @@ namespace OpenMM {
 template <class T>
 class CudaStreamImpl : public StreamImpl {
 public:
-    CudaStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, int substreams);
-    CudaStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, CUDAStream<T>* stream, int rowOffset, float* padding);
+    CudaStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, int substreams, _gpuContext* gpu);
+    CudaStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, CUDAStream<T>* stream, int rowOffset, float* padding, _gpuContext* gpu);
     ~CudaStreamImpl();
     void loadFromArray(const void* array);
     void saveToArray(void* array);
@@ -55,6 +55,7 @@ public:
 private:
     void initType();
     CUDAStream<T>* stream;
+	 _gpuContext* gpu;
     bool ownStream;
     int width, rowOffset;
     float paddingValues[4];
@@ -62,15 +63,15 @@ private:
 };
 
 template <class T>
-CudaStreamImpl<T>::CudaStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, int substreams) :
-        StreamImpl(name, size, type, platform), stream(new CUDAStream<T>(size, substreams)), ownStream(true) {
+CudaStreamImpl<T>::CudaStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, int substreams, _gpuContext* gpu) :
+        StreamImpl(name, size, type, platform), stream(new CUDAStream<T>(size, substreams)), ownStream(true), gpu(gpu) {
     initType();
     rowOffset = width;
 };
 
 template <class T>
-CudaStreamImpl<T>::CudaStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, CUDAStream<T>* stream, int rowOffset, float* padding) :
-        StreamImpl(name, size, type, platform), stream(stream), rowOffset(rowOffset), ownStream(false) {
+CudaStreamImpl<T>::CudaStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, CUDAStream<T>* stream, int rowOffset, float* padding, _gpuContext* gpu) :
+        StreamImpl(name, size, type, platform), stream(stream), rowOffset(rowOffset), ownStream(false), gpu(gpu) {
     initType();
     for (int i = 0; i < 4; ++i)
         paddingValues[i] = padding[i];
@@ -153,6 +154,13 @@ void CudaStreamImpl<T>::loadFromArray(const void* array) {
         for (int j = 0; j < rowOffset; ++j)
             data[i*rowOffset+j] = paddingValues[j];
     stream->Upload();
+
+	 // VisualStudio compiler did not like stream == gpu->psPosq4 
+	 //if( gpu && stream == gpu->psPosq4 ){
+
+	 if( gpu && getName() == "particlePositions" ){
+	    gpu->bRecalculateBornRadii = true;
+	 }
 }
 
 template <class T>