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"platforms/common/src/BondedUtilities.cpp" did not exist on "b33ee3b0420c8eaf117c89a7831ba1b34056170e"
Commit 71d89f7f authored by Peter Eastman's avatar Peter Eastman
Browse files

Eliminated unnecessary copy of the PME grid

parent 5c2569b0
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Inline Side-by-side
Showing with 16 additions and 20 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ 71d89f7f
......@@ -1340,12 +1340,10 @@ CudaCalcNonbondedForceKernel::~CudaCalcNonbondedForceKernel() {
delete exceptionParams;
if (cosSinSums != NULL)
delete cosSinSums;
if (originalPmeGrid != NULL)
delete originalPmeGrid;
if (directPmeGrid != NULL)
delete directPmeGrid;
if (reciprocalPmeGrid != NULL)
delete reciprocalPmeGrid;
if (convolvedPmeGrid != NULL)
delete convolvedPmeGrid;
if (pmeBsplineModuliX != NULL)
delete pmeBsplineModuliX;
if (pmeBsplineModuliY != NULL)
......@@ -1521,11 +1519,10 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
int elementSize = (cu.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
originalPmeGrid = new CudaArray(cu, gridSizeX*gridSizeY*gridSizeZ, cu.getComputeCapability() >= 2.0 ? elementSize : sizeof(long long), "originalPmeGrid");
convolvedPmeGrid = new CudaArray(cu, gridSizeX*gridSizeY*gridSizeZ, elementSize, "convolvedPmeGrid");
directPmeGrid = new CudaArray(cu, gridSizeX*gridSizeY*gridSizeZ, cu.getComputeCapability() >= 2.0 ? elementSize : sizeof(long long), "originalPmeGrid");
reciprocalPmeGrid = new CudaArray(cu, gridSizeX*gridSizeY*(gridSizeZ/2+1), 2*elementSize, "reciprocalPmeGrid");
cu.addAutoclearBuffer(*originalPmeGrid);
cu.addAutoclearBuffer(*directPmeGrid);
pmeBsplineModuliX = new CudaArray(cu, gridSizeX, elementSize, "pmeBsplineModuliX");
pmeBsplineModuliY = new CudaArray(cu, gridSizeY, elementSize, "pmeBsplineModuliY");
......@@ -1660,7 +1657,7 @@ double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeF
void* forcesArgs[] = {&cu.getForce().getDevicePointer(), &cu.getPosq().getDevicePointer(), &cosSinSums->getDevicePointer(), cu.getPeriodicBoxSizePointer()};
cu.executeKernel(ewaldForcesKernel, forcesArgs, cu.getNumAtoms());
}
if (originalPmeGrid != NULL && cu.getContextIndex() == 0 && includeReciprocal) {
if (directPmeGrid != NULL && cu.getContextIndex() == 0 && includeReciprocal) {
void* bsplinesArgs[] = {&cu.getPosq().getDevicePointer(), &pmeBsplineTheta->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(),
cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
int bsplinesSharedSize = cu.ThreadBlockSize*PmeOrder*(cu.getUseDoublePrecision() ? sizeof(double4) : sizeof(float4));
......@@ -1672,19 +1669,19 @@ double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeF
cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
cu.executeKernel(pmeAtomRangeKernel, rangeArgs, cu.getNumAtoms());
void* spreadArgs[] = {&cu.getPosq().getDevicePointer(), &originalPmeGrid->getDevicePointer(), &pmeBsplineTheta->getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
void* spreadArgs[] = {&cu.getPosq().getDevicePointer(), &directPmeGrid->getDevicePointer(), &pmeBsplineTheta->getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
cu.executeKernel(pmeSpreadChargeKernel, spreadArgs, cu.getNumAtoms(), PmeOrder*PmeOrder*PmeOrder);
void* finishSpreadArgs[] = {&originalPmeGrid->getDevicePointer()};
void* finishSpreadArgs[] = {&directPmeGrid->getDevicePointer()};
if (cu.getUseDoublePrecision() || cu.getComputeCapability() < 2.0) {
void* finishSpreadArgs[] = {&originalPmeGrid->getDevicePointer()};
cu.executeKernel(pmeFinishSpreadChargeKernel, finishSpreadArgs, originalPmeGrid->getSize());
void* finishSpreadArgs[] = {&directPmeGrid->getDevicePointer()};
cu.executeKernel(pmeFinishSpreadChargeKernel, finishSpreadArgs, directPmeGrid->getSize());
}
if (cu.getUseDoublePrecision())
cufftExecD2Z(fftForward, (double*) originalPmeGrid->getDevicePointer(), (double2*) reciprocalPmeGrid->getDevicePointer());
cufftExecD2Z(fftForward, (double*) directPmeGrid->getDevicePointer(), (double2*) reciprocalPmeGrid->getDevicePointer());
else
cufftExecR2C(fftForward, (float*) originalPmeGrid->getDevicePointer(), (float2*) reciprocalPmeGrid->getDevicePointer());
cufftExecR2C(fftForward, (float*) directPmeGrid->getDevicePointer(), (float2*) reciprocalPmeGrid->getDevicePointer());
if (includeEnergy) {
void* computeEnergyArgs[] = {&reciprocalPmeGrid->getDevicePointer(), &cu.getEnergyBuffer().getDevicePointer(), &pmeBsplineModuliX->getDevicePointer(), &pmeBsplineModuliY->getDevicePointer(), &pmeBsplineModuliZ->getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
......@@ -1695,12 +1692,12 @@ double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeF
cu.executeKernel(pmeConvolutionKernel, convolutionArgs, cu.getNumAtoms());
if (cu.getUseDoublePrecision())
cufftExecZ2D(fftBackward, (double2*) reciprocalPmeGrid->getDevicePointer(), (double*) convolvedPmeGrid->getDevicePointer());
cufftExecZ2D(fftBackward, (double2*) reciprocalPmeGrid->getDevicePointer(), (double*) directPmeGrid->getDevicePointer());
else
cufftExecC2R(fftBackward, (float2*) reciprocalPmeGrid->getDevicePointer(), (float*) convolvedPmeGrid->getDevicePointer());
cufftExecC2R(fftBackward, (float2*) reciprocalPmeGrid->getDevicePointer(), (float*) directPmeGrid->getDevicePointer());
void* interpolateArgs[] = {&cu.getPosq().getDevicePointer(), &cu.getForce().getDevicePointer(), &convolvedPmeGrid->getDevicePointer(),
void* interpolateArgs[] = {&cu.getPosq().getDevicePointer(), &cu.getForce().getDevicePointer(), &directPmeGrid->getDevicePointer(),
cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
cu.executeKernel(pmeInterpolateForceKernel, interpolateArgs, cu.getNumAtoms());
......
platforms/cuda/src/CudaKernels.h
View file @ 71d89f7f
......@@ -556,7 +556,7 @@ private:
class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
CudaCalcNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcNonbondedForceKernel(name, platform),
cu(cu), hasInitializedFFT(false), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), originalPmeGrid(NULL), reciprocalPmeGrid(NULL), convolvedPmeGrid(NULL),
cu(cu), hasInitializedFFT(false), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), directPmeGrid(NULL), reciprocalPmeGrid(NULL),
pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeBsplineTheta(NULL), pmeBsplineDTheta(NULL),
pmeAtomRange(NULL), pmeAtomGridIndex(NULL), sort(NULL) {
}
......@@ -602,9 +602,8 @@ private:
CudaArray* sigmaEpsilon;
CudaArray* exceptionParams;
CudaArray* cosSinSums;
CudaArray* originalPmeGrid;
CudaArray* directPmeGrid;
CudaArray* reciprocalPmeGrid;
CudaArray* convolvedPmeGrid;
CudaArray* pmeBsplineModuliX;
CudaArray* pmeBsplineModuliY;
CudaArray* pmeBsplineModuliZ;
......
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