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Commit 4d763c4d authored by Mark Friedrichs's avatar Mark Friedrichs
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Fixed bug in direct PME 

Added diagnostics for handling reorder of atoms
parent 8b8defe8
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Showing with 546 additions and 313 deletions
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 4d763c4d
...@@ -38,7 +38,7 @@ using namespace OpenMM; ...@@ -38,7 +38,7 @@ using namespace OpenMM;
using std::string; using std::string;
using std::vector; using std::vector;
AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(5e-4), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60), AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(1e-4), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60),
mutualInducedTargetEpsilon(1.0e-05), scalingDistanceCutoff(100.0), electricConstant(138.9354558456) { mutualInducedTargetEpsilon(1.0e-05), scalingDistanceCutoff(100.0), electricConstant(138.9354558456) {
} }
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 4d763c4d
...@@ -779,17 +779,15 @@ static void computeAmoebaMultipoleForce( AmoebaCudaData& data ) { ...@@ -779,17 +779,15 @@ static void computeAmoebaMultipoleForce( AmoebaCudaData& data ) {
if( data.getMultipoleForceCount() == 0 ){ if( data.getMultipoleForceCount() == 0 ){
gpuCopyWorkUnit( gpu ); gpuCopyWorkUnit( gpu );
} }
//if( data.getApplyCutoff() && (data.getMultipoleForceCount() % 100) == 0 ){
//gpuReorderAtoms(gpu->gpuContext);
//}
data.incrementMultipoleForceCount(); data.incrementMultipoleForceCount();
data.initializeGpu();
if( 0 && data.getLog() ){ if( 0 && data.getLog() ){
(void) fprintf( data.getLog(), "computeAmoebaMultipoleForce\n" ); (void) fprintf( data.getLog(), "In computeAmoebaMultipoleForce\n" );
(void) fflush( data.getLog()); (void) fflush( data.getLog());
} }
data.initializeGpu();
// calculate Born radii // calculate Born radii
if( data.getHasAmoebaGeneralizedKirkwood() ){ if( data.getHasAmoebaGeneralizedKirkwood() ){
...@@ -974,23 +972,27 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -974,23 +972,27 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
nb.setCutoffDistance(force.getCutoffDistance()); nb.setCutoffDistance(force.getCutoffDistance());
std::vector<int> pmeGridDimension; std::vector<int> pmeGridDimension;
force.getPmeGridDimensions( pmeGridDimension ); force.getPmeGridDimensions( pmeGridDimension );
if( 1 || pmeGridDimension[0] == 0 ){ int pmeParametersSetBasedOnEwaldErrorTolerance;
if( pmeGridDimension[0] == 0 ){
NonbondedForceImpl::calcPMEParameters(system, nb, alpha, xsize, ysize, zsize); NonbondedForceImpl::calcPMEParameters(system, nb, alpha, xsize, ysize, zsize);
/* pmeParametersSetBasedOnEwaldErrorTolerance = 1;
alpha = 5.446;
xsize = 60;
ysize = 48;
zsize = 48;
*/
} else { } else {
alpha = force.getAEwald(); alpha = force.getAEwald();
xsize = pmeGridDimension[0]; xsize = pmeGridDimension[0];
ysize = pmeGridDimension[1]; ysize = pmeGridDimension[1];
zsize = pmeGridDimension[2]; zsize = pmeGridDimension[2];
pmeParametersSetBasedOnEwaldErrorTolerance = 0;
} }
if( data.getLog() ){ if( data.getLog() ){
(void) fprintf( data.getLog(), "AmoebaMultipoleForce: PME parameters tol=%12.3e cutoff=%12.3f alpha=%12.3f [%d %d %d]\n", (void) fprintf( data.getLog(), "AmoebaMultipoleForce: PME parameters tol=%12.3e cutoff=%12.3f alpha=%12.3f [%d %d %d] -",
force.getEwaldErrorTolerance(), force.getCutoffDistance(), alpha, xsize, ysize, zsize ); force.getEwaldErrorTolerance(), force.getCutoffDistance(), alpha, xsize, ysize, zsize );
if( pmeParametersSetBasedOnEwaldErrorTolerance ){
(void) fprintf( data.getLog(), " parameters set based on error tolerance and OpenMM algorithm.\n" );
} else {
double impliedTolerance = alpha*force.getCutoffDistance();
impliedTolerance = 0.5*exp( -(impliedTolerance*impliedTolerance) );
(void) fprintf( data.getLog(), " using input parameters implied tolerance=%12.3e\n", impliedTolerance );
}
(void) fflush( data.getLog() ); (void) fflush( data.getLog() );
} }
gpuSetAmoebaPMEParameters(data.getAmoebaGpu(), (float) alpha, xsize, ysize, zsize); gpuSetAmoebaPMEParameters(data.getAmoebaGpu(), (float) alpha, xsize, ysize, zsize);
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaGpu.cpp
View file @ 4d763c4d
...@@ -3909,6 +3909,33 @@ void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId ...@@ -3909,6 +3909,33 @@ void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId
(void) fclose( filePtr ); (void) fclose( filePtr );
} }
CUDAStream<float>* reorderFloat( amoebaGpuContext amoebaGpu, CUDAStream<float>* arrayToReorder ){
gpuContext gpu = amoebaGpu->gpuContext;
CUDAStream<float>* reorderdArray = new CUDAStream<float>(amoebaGpu->gpuContext->sim.paddedNumberOfAtoms, 1, "TempReorder");
int* order = gpu->psAtomIndex->_pSysData;
for( int ii = 0; ii < gpu->natoms; ii++ ){
reorderdArray->_pSysStream[0][order[ii]] = arrayToReorder->_pSysStream[0][ii];
}
return reorderdArray;
}
CUDAStream<float4>* reorderFloat4( amoebaGpuContext amoebaGpu, CUDAStream<float4>* arrayToReorder ){
gpuContext gpu = amoebaGpu->gpuContext;
CUDAStream<float4>* reorderdArray = new CUDAStream<float4>(amoebaGpu->gpuContext->sim.paddedNumberOfAtoms, 1, "TempReorder4");
int* order = gpu->psAtomIndex->_pSysData;
for( int ii = 0; ii < gpu->natoms; ii++ ){
reorderdArray->_pSysStream[0][order[ii]].x = arrayToReorder->_pSysStream[0][ii].x;
reorderdArray->_pSysStream[0][order[ii]].y = arrayToReorder->_pSysStream[0][ii].y;
reorderdArray->_pSysStream[0][order[ii]].z = arrayToReorder->_pSysStream[0][ii].z;
reorderdArray->_pSysStream[0][order[ii]].w = arrayToReorder->_pSysStream[0][ii].w;
}
return reorderdArray;
}
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Load contents of arrays into vector Load contents of arrays into vector
...@@ -3920,7 +3947,9 @@ void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId ...@@ -3920,7 +3947,9 @@ void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void cudaLoadCudaFloatArray( int numberOfParticles, int entriesPerParticle, CUDAStream<float>* array, VectorOfDoubleVectors& outputVector ) void cudaLoadCudaFloatArray( int numberOfParticles, int entriesPerParticle,
CUDAStream<float>* array, VectorOfDoubleVectors& outputVector,
int* order )
{ {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -3929,14 +3958,19 @@ void cudaLoadCudaFloatArray( int numberOfParticles, int entriesPerParticle, CUDA ...@@ -3929,14 +3958,19 @@ void cudaLoadCudaFloatArray( int numberOfParticles, int entriesPerParticle, CUDA
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
array->Download(); array->Download();
int runningIndex = 0; int orderIndex = 0;
outputVector.resize( numberOfParticles ); outputVector.resize( numberOfParticles );
for( int ii = 0; ii < numberOfParticles; ii++ ){ for( int ii = 0; ii < numberOfParticles; ii++ ){
if( order ){
orderIndex = order[ii];
} else {
orderIndex = ii;
}
for( int jj = 0; jj < entriesPerParticle; jj++ ) { for( int jj = 0; jj < entriesPerParticle; jj++ ) {
outputVector[ii].push_back( array->_pSysStream[0][runningIndex++] ); outputVector[orderIndex].push_back( array->_pSysStream[0][entriesPerParticle*ii+jj] );
} }
} }
} }
...@@ -3975,6 +4009,7 @@ void cudaLoadCudaFloat2Array( int numberOfParticles, int entriesPerParticle, CUD ...@@ -3975,6 +4009,7 @@ void cudaLoadCudaFloat2Array( int numberOfParticles, int entriesPerParticle, CUD
} }
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Load contents of arrays into vector Load contents of arrays into vector
...@@ -3983,10 +4018,12 @@ void cudaLoadCudaFloat2Array( int numberOfParticles, int entriesPerParticle, CUD ...@@ -3983,10 +4018,12 @@ void cudaLoadCudaFloat2Array( int numberOfParticles, int entriesPerParticle, CUD
@param entriesPerParticle entries/particles array @param entriesPerParticle entries/particles array
@param array cuda array @param array cuda array
@param outputVector output vector @param outputVector output vector
@param order if set, reorder entries
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void cudaLoadCudaFloat4Array( int numberOfParticles, int entriesPerParticle, CUDAStream<float4>* array, VectorOfDoubleVectors& outputVector ) void cudaLoadCudaFloat4Array( int numberOfParticles, int entriesPerParticle, CUDAStream<float4>* array,
VectorOfDoubleVectors& outputVector, int* order )
{ {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -3996,21 +4033,27 @@ void cudaLoadCudaFloat4Array( int numberOfParticles, int entriesPerParticle, CUD ...@@ -3996,21 +4033,27 @@ void cudaLoadCudaFloat4Array( int numberOfParticles, int entriesPerParticle, CUD
array->Download(); array->Download();
int runningIndex = 0; int runningIndex = 0;
int orderIndex;
outputVector.resize( numberOfParticles ); outputVector.resize( numberOfParticles );
for( int ii = 0; ii < numberOfParticles; ii++ ){ for( int ii = 0; ii < numberOfParticles; ii++ ){
if( order ){
orderIndex = order[runningIndex];
} else {
orderIndex = runningIndex;
}
if( entriesPerParticle > 0 ){ if( entriesPerParticle > 0 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].x ); outputVector[orderIndex].push_back( array->_pSysStream[0][ii].x );
} }
if( entriesPerParticle > 1 ){ if( entriesPerParticle > 1 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].y ); outputVector[orderIndex].push_back( array->_pSysStream[0][ii].y );
} }
if( entriesPerParticle > 2 ){ if( entriesPerParticle > 2 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].z ); outputVector[orderIndex].push_back( array->_pSysStream[0][ii].z );
} }
if( entriesPerParticle > 3 ){ if( entriesPerParticle > 3 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].w ); outputVector[orderIndex].push_back( array->_pSysStream[0][ii].w );
} }
runningIndex++; runningIndex++;
} }
...@@ -4353,8 +4396,8 @@ void trackMutualInducedIterations( amoebaGpuContext amoebaGpu, int iteration){ ...@@ -4353,8 +4396,8 @@ void trackMutualInducedIterations( amoebaGpuContext amoebaGpu, int iteration){
} }
(void) fflush( amoebaGpu->log ); (void) fflush( amoebaGpu->log );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psVelm4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psVelm4, outputVector, NULL );
/* /*
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector );
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaKernels.h
View file @ 4d763c4d
...@@ -147,9 +147,9 @@ extern void cudaWriteFloat1AndFloat1ArraysToFile( int numberOfAtoms, char* fname ...@@ -147,9 +147,9 @@ extern void cudaWriteFloat1AndFloat1ArraysToFile( int numberOfAtoms, char* fname
int entriesPerAtom2, CUDAStream<float>* array2 ); int entriesPerAtom2, CUDAStream<float>* array2 );
extern void readFile( std::string fileName, StringVectorVector& fileContents ); extern void readFile( std::string fileName, StringVectorVector& fileContents );
extern void cudaLoadCudaFloatArray( int numberOfParticles, int entriesPerParticle, CUDAStream<float>* array, VectorOfDoubleVectors& outputVector ); extern void cudaLoadCudaFloatArray( int numberOfParticles, int entriesPerParticle, CUDAStream<float>* array, VectorOfDoubleVectors& outputVector, int* order );
extern void cudaLoadCudaFloat2Array( int numberOfParticles, int entriesPerParticle, CUDAStream<float2>* array, VectorOfDoubleVectors& outputVector ); extern void cudaLoadCudaFloat2Array( int numberOfParticles, int entriesPerParticle, CUDAStream<float2>* array, VectorOfDoubleVectors& outputVector );
extern void cudaLoadCudaFloat4Array( int numberOfParticles, int entriesPerParticle, CUDAStream<float4>* array, VectorOfDoubleVectors& outputVector ); extern void cudaLoadCudaFloat4Array( int numberOfParticles, int entriesPerParticle, CUDAStream<float4>* array, VectorOfDoubleVectors& outputVector, int* order );
extern void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId, VectorOfDoubleVectors& outputVector ); extern void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId, VectorOfDoubleVectors& outputVector );
extern void kClearFloat( amoebaGpuContext amoebaGpu, unsigned int entries, CUDAStream<float>* fieldToClear ); extern void kClearFloat( amoebaGpuContext amoebaGpu, unsigned int entries, CUDAStream<float>* fieldToClear );
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaElectrostatic.cu
View file @ 4d763c4d
...@@ -947,9 +947,9 @@ void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu ) ...@@ -947,9 +947,9 @@ void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu )
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector );
} }
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaFixedEAndGkFields.cu
View file @ 4d763c4d
...@@ -562,9 +562,9 @@ void cudaComputeAmoebaFixedEAndGkFields( amoebaGpuContext amoebaGpu ) ...@@ -562,9 +562,9 @@ void cudaComputeAmoebaFixedEAndGkFields( amoebaGpuContext amoebaGpu )
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector, NULL);
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psGk_Field, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psGk_Field, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaEAndGkField", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaEAndGkField", fileId, outputVector );
} }
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaFixedEField.cu
View file @ 4d763c4d
...@@ -307,8 +307,8 @@ void cudaComputeAmoebaFixedEField( amoebaGpuContext amoebaGpu ) ...@@ -307,8 +307,8 @@ void cudaComputeAmoebaFixedEField( amoebaGpuContext amoebaGpu )
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
//cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); //cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaEField", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaEField", fileId, outputVector );
} }
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.cu
View file @ 4d763c4d
...@@ -1748,10 +1748,10 @@ static void kReduceToBornForcePrefactor( amoebaGpuContext amoebaGpu ) ...@@ -1748,10 +1748,10 @@ static void kReduceToBornForcePrefactor( amoebaGpuContext amoebaGpu )
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( amoebaGpu->gpuContext->natoms, 3, amoebaGpu->gpuContext->psPosq4, outputVector ); cudaLoadCudaFloat4Array( amoebaGpu->gpuContext->natoms, 3, amoebaGpu->gpuContext->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( amoebaGpu->gpuContext->natoms, 1, amoebaGpu->gpuContext->psBornRadii, outputVector ); cudaLoadCudaFloatArray( amoebaGpu->gpuContext->natoms, 1, amoebaGpu->gpuContext->psBornRadii, outputVector, NULL );
cudaLoadCudaFloat2Array( amoebaGpu->gpuContext->natoms, 2, amoebaGpu->gpuContext->psObcData, outputVector ); cudaLoadCudaFloat2Array( amoebaGpu->gpuContext->natoms, 2, amoebaGpu->gpuContext->psObcData, outputVector, NULL );
cudaLoadCudaFloatArray( amoebaGpu->gpuContext->natoms, 1, amoebaGpu->gpuContext->psBornForce, outputVector ); cudaLoadCudaFloatArray( amoebaGpu->gpuContext->natoms, 1, amoebaGpu->gpuContext->psBornForce, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaBornForce", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaBornForce", fileId, outputVector );
(void) fprintf( amoebaGpu->log, "kReduceToBornForcePrefactor: exiting.\n" ); (void) fprintf( amoebaGpu->log, "kReduceToBornForcePrefactor: exiting.\n" );
(void) fprintf( stderr, "kReduceToBornForcePrefactor: exiting.\n" ); (void) fflush( stderr ); (void) fprintf( stderr, "kReduceToBornForcePrefactor: exiting.\n" ); (void) fflush( stderr );
...@@ -2069,8 +2069,8 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu ) ...@@ -2069,8 +2069,8 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu )
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector );
} }
...@@ -2113,8 +2113,8 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu ) ...@@ -2113,8 +2113,8 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu )
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodForce, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaKirkwoodForce", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaKirkwoodForce", fileId, outputVector );
} }
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff.cu
View file @ 4d763c4d
...@@ -1215,9 +1215,9 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu ) ...@@ -1215,9 +1215,9 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu )
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodEDiffForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodEDiffForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector );
} }
...@@ -1260,8 +1260,8 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu ) ...@@ -1260,8 +1260,8 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu )
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodEDiffForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodEDiffForce, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaKirkwoodEDiffForce", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaKirkwoodEDiffForce", fileId, outputVector );
} }
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMapTorques.cu
View file @ 4d763c4d
...@@ -829,8 +829,8 @@ void cudaComputeAmoebaMapTorques( amoebaGpuContext amoebaGpu, CUDAStream<float>* ...@@ -829,8 +829,8 @@ void cudaComputeAmoebaMapTorques( amoebaGpuContext amoebaGpu, CUDAStream<float>*
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector );
} }
#endif #endif
...@@ -1031,9 +1031,9 @@ void cudaComputeAmoebaMapTorquesAndAddTotalForce( amoebaGpuContext amoebaGpu, ...@@ -1031,9 +1031,9 @@ void cudaComputeAmoebaMapTorquesAndAddTotalForce( amoebaGpuContext amoebaGpu,
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
//cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); //cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 4, gpu->psForce4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 4, gpu->psForce4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, psForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, psForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, psTorque, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector );
} }
#endif #endif
...@@ -1123,9 +1123,9 @@ void cudaComputeAmoebaMapTorquesAndAddTotalForce2( amoebaGpuContext amoebaGpu, ...@@ -1123,9 +1123,9 @@ void cudaComputeAmoebaMapTorquesAndAddTotalForce2( amoebaGpuContext amoebaGpu,
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
//cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); //cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 4, gpu->psForce4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 4, gpu->psForce4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector );
} }
#endif #endif
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedAndGkFields.cu
View file @ 4d763c4d
...@@ -925,9 +925,9 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe ...@@ -925,9 +925,9 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaMI_GK", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaMI_GK", fileId, outputVector );
} }
#endif #endif
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedField.cu
View file @ 4d763c4d
...@@ -594,8 +594,8 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu ...@@ -594,8 +594,8 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
// cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); // cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaMI", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaMI", fileId, outputVector );
} }
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.h
View file @ 4d763c4d
...@@ -43,7 +43,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)( ...@@ -43,7 +43,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
){ ){
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
int maxPullIndex = 2; int maxPullIndex = 7;
float4 pullBack[12]; float4 pullBack[12];
#endif #endif
...@@ -56,6 +56,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)( ...@@ -56,6 +56,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
unsigned int end = (warp+1)*numWorkUnits/totalWarps; unsigned int end = (warp+1)*numWorkUnits/totalWarps;
unsigned int lasty = 0xFFFFFFFF; unsigned int lasty = 0xFFFFFFFF;
float totalEnergy = 0.0f; float totalEnergy = 0.0f;
float4 forceTorqueEnergy[3];
float scalingFactors[LastScalingIndex]; float scalingFactors[LastScalingIndex];
...@@ -90,10 +91,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)( ...@@ -90,10 +91,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
localParticle.torque[1] = 0.0f; localParticle.torque[1] = 0.0f;
localParticle.torque[2] = 0.0f; localParticle.torque[2] = 0.0f;
scalingFactors[PScaleIndex] = 1.0f;
scalingFactors[DScaleIndex] = 1.0f;
scalingFactors[UScaleIndex] = 1.0f; scalingFactors[UScaleIndex] = 1.0f;
scalingFactors[MScaleIndex] = 1.0f;
if (x == y) // Handle diagonals uniquely at 50% efficiency if (x == y) // Handle diagonals uniquely at 50% efficiency
{ {
...@@ -116,9 +114,6 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)( ...@@ -116,9 +114,6 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
for (unsigned int j = 0; j < GRID; j++) for (unsigned int j = 0; j < GRID; j++)
{ {
float force[3];
float3 torque[2];
unsigned int atomJ = y + j; unsigned int atomJ = y + j;
// set scale factors // set scale factors
...@@ -132,9 +127,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)( ...@@ -132,9 +127,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
// force // force
float energy; calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[j], scalingFactors, forceTorqueEnergy
calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[j],
scalingFactors, force, torque, &energy
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, pullBack , pullBack
#endif #endif
...@@ -143,28 +136,25 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)( ...@@ -143,28 +136,25 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
// nan*0.0 = nan not 0.0, so explicitly exclude (atomI == atomJ) contribution // nan*0.0 = nan not 0.0, so explicitly exclude (atomI == atomJ) contribution
// by setting match flag // by setting match flag
unsigned int mask = ( (atomI == atomJ) || (atomI >= cAmoebaSim.numberOfAtoms) || (atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1; if( (atomI != atomJ) && (atomI < cAmoebaSim.numberOfAtoms) && (atomJ < cAmoebaSim.numberOfAtoms) )
{
// add to field at atomI the field due atomJ's charge/dipole/quadrupole localParticle.force[0] += forceTorqueEnergy[0].x;
localParticle.force[1] += forceTorqueEnergy[0].y;
localParticle.force[2] += forceTorqueEnergy[0].z;
localParticle.force[0] += mask ? force[0] : 0.0f; localParticle.torque[0] += forceTorqueEnergy[1].x;
localParticle.force[1] += mask ? force[1] : 0.0f; localParticle.torque[1] += forceTorqueEnergy[1].y;
localParticle.force[2] += mask ? force[2] : 0.0f; localParticle.torque[2] += forceTorqueEnergy[1].z;
localParticle.torque[0] += mask ? torque[0].x : 0.0f; // energy for each diagonal-block ixn included twice, hence factor of 0.5
localParticle.torque[1] += mask ? torque[0].y : 0.0f;
localParticle.torque[2] += mask ? torque[0].z : 0.0f;
totalEnergy += mask ? 0.5*energy : 0.0f; totalEnergy += 0.5*forceTorqueEnergy[0].w;
}
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
/* if( atomI == targetAtom || atomJ == targetAtom ){
energy = mask ? 0.5*energy : 0.0f;
if( atomI < 200 && (fabs( energy ) > 1.0e+8 || energy != energy) ){
debugSetup( atomI, atomJ, debugArray, pullBack );
} */
if( atomI == targetAtom ){ unsigned int mask = ( (atomI == atomJ) || (atomI >= cAmoebaSim.numberOfAtoms) || (atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1;
unsigned int index = (atomI == targetAtom) ? atomJ : atomI; unsigned int index = (atomI == targetAtom) ? atomJ : atomI;
float blockId = 1.0f; float blockId = 1.0f;
...@@ -174,23 +164,24 @@ if( atomI == targetAtom ){ ...@@ -174,23 +164,24 @@ if( atomI == targetAtom ){
debugArray[index].w = blockId; debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? force[0] : 0.0f; debugArray[index].x = mask ? forceTorqueEnergy[0].x : 0.0f;
debugArray[index].y = mask ? force[1] : 0.0f; debugArray[index].y = mask ? forceTorqueEnergy[0].y : 0.0f;
debugArray[index].z = mask ? force[2] : 0.0f; debugArray[index].z = mask ? forceTorqueEnergy[0].z : 0.0f;
debugArray[index].w = blockId; debugArray[index].w = mask ? forceTorqueEnergy[0].w : 0.0f;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? torque[0].x : 0.0f; debugArray[index].x = mask ? forceTorqueEnergy[1].x : 0.0f;
debugArray[index].y = mask ? torque[0].y : 0.0f; debugArray[index].y = mask ? forceTorqueEnergy[1].y : 0.0f;
debugArray[index].z = mask ? torque[0].z : 0.0f; debugArray[index].z = mask ? forceTorqueEnergy[1].z : 0.0f;
debugArray[index].w = mask ? energy : 0.0f; float offsetF = (float)(3*(x + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms));
debugArray[index].w = offsetF;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? torque[0].x : 0.0f; debugArray[index].x = mask ? forceTorqueEnergy[2].x : 0.0f;
debugArray[index].y = mask ? torque[0].y : 0.0f; debugArray[index].y = mask ? forceTorqueEnergy[2].y : 0.0f;
debugArray[index].z = mask ? torque[0].z : 0.0f; debugArray[index].z = mask ? forceTorqueEnergy[2].z : 0.0f;
debugArray[index].w = (float) (blockIdx.x * blockDim.x + threadIdx.x); debugArray[index].w = offsetF;
for( int pullIndex = 0; pullIndex < maxPullIndex; pullIndex++ ){ for( int pullIndex = 0; pullIndex < maxPullIndex; pullIndex++ ){
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
...@@ -290,14 +281,11 @@ if( atomI == targetAtom ){ ...@@ -290,14 +281,11 @@ if( atomI == targetAtom ){
for (unsigned int j = 0; j < GRID; j++) for (unsigned int j = 0; j < GRID; j++)
{ {
if ((flags&(1<<j)) != 0) if( (flags & (1<<j) ) != 0)
{ {
unsigned int jIdx = (flags == 0xFFFFFFFF) ? tj : j; unsigned int jIdx = (flags == 0xFFFFFFFF) ? tj : j;
unsigned int atomJ = y + jIdx; unsigned int atomJ = y + jIdx;
float force[3];
float3 torque[2];
// set scale factors // set scale factors
if( bExclusionFlag ) if( bExclusionFlag )
...@@ -309,9 +297,8 @@ if( atomI == targetAtom ){ ...@@ -309,9 +297,8 @@ if( atomI == targetAtom ){
// force // force
float energy;
calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[jIdx], calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[jIdx],
scalingFactors, force, torque, &energy scalingFactors, forceTorqueEnergy
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, pullBack , pullBack
#endif #endif
...@@ -319,41 +306,41 @@ if( atomI == targetAtom ){ ...@@ -319,41 +306,41 @@ if( atomI == targetAtom ){
// check if atoms out-of-bounds // check if atoms out-of-bounds
unsigned int mask = ( (atomI >= cAmoebaSim.numberOfAtoms) || (atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1; if( (atomI < cAmoebaSim.numberOfAtoms) && (atomJ < cAmoebaSim.numberOfAtoms) )
{
// add force and torque to atom I due atom J // add force and torque to atom I due atom J
localParticle.force[0] += mask ? force[0] : 0.0f; localParticle.force[0] += forceTorqueEnergy[0].x;
localParticle.force[1] += mask ? force[1] : 0.0f; localParticle.force[1] += forceTorqueEnergy[0].y;
localParticle.force[2] += mask ? force[2] : 0.0f; localParticle.force[2] += forceTorqueEnergy[0].z;
localParticle.torque[0] += mask ? torque[0].x : 0.0f; totalEnergy += forceTorqueEnergy[0].w;
localParticle.torque[1] += mask ? torque[0].y : 0.0f;
localParticle.torque[2] += mask ? torque[0].z : 0.0f;
totalEnergy += mask ? energy : 0.0f; localParticle.torque[0] += forceTorqueEnergy[1].x;
localParticle.torque[1] += forceTorqueEnergy[1].y;
localParticle.torque[2] += forceTorqueEnergy[1].z;
// add force and torque to atom J due atom I // add force and torque to atom J due atom I
if( flags == 0xFFFFFFFF ){ if( flags == 0xFFFFFFFF ){
psA[jIdx].force[0] -= mask ? force[0] : 0.0f; psA[jIdx].force[0] -= forceTorqueEnergy[0].x;
psA[jIdx].force[1] -= mask ? force[1] : 0.0f; psA[jIdx].force[1] -= forceTorqueEnergy[0].y;
psA[jIdx].force[2] -= mask ? force[2] : 0.0f; psA[jIdx].force[2] -= forceTorqueEnergy[0].z;
psA[jIdx].torque[0] += mask ? torque[1].x : 0.0f; psA[jIdx].torque[0] += forceTorqueEnergy[2].x;
psA[jIdx].torque[1] += mask ? torque[1].y : 0.0f; psA[jIdx].torque[1] += forceTorqueEnergy[2].y;
psA[jIdx].torque[2] += mask ? torque[1].z : 0.0f; psA[jIdx].torque[2] += forceTorqueEnergy[2].z;
} else { } else {
sA[threadIdx.x].tempForce[0] = mask ? 0.0f : force[0]; sA[threadIdx.x].tempForce[0] = forceTorqueEnergy[0].x;
sA[threadIdx.x].tempForce[1] = mask ? 0.0f : force[1]; sA[threadIdx.x].tempForce[1] = forceTorqueEnergy[1].y;
sA[threadIdx.x].tempForce[2] = mask ? 0.0f : force[2]; sA[threadIdx.x].tempForce[2] = forceTorqueEnergy[2].z;
sA[threadIdx.x].tempTorque[0] = mask ? 0.0f : torque[1].x; sA[threadIdx.x].tempTorque[0] = forceTorqueEnergy[2].x;
sA[threadIdx.x].tempTorque[1] = mask ? 0.0f : torque[1].y; sA[threadIdx.x].tempTorque[1] = forceTorqueEnergy[2].y;
sA[threadIdx.x].tempTorque[2] = mask ? 0.0f : torque[1].z; sA[threadIdx.x].tempTorque[2] = forceTorqueEnergy[2].z;
if( tgx % 2 == 0 ){ if( tgx % 2 == 0 ){
sumTempBuffer( sA[threadIdx.x], sA[threadIdx.x+1] ); sumTempBuffer( sA[threadIdx.x], sA[threadIdx.x+1] );
...@@ -379,15 +366,58 @@ if( atomI == targetAtom ){ ...@@ -379,15 +366,58 @@ if( atomI == targetAtom ){
psA[jIdx].torque[2] += sA[threadIdx.x].tempTorque[2] + sA[threadIdx.x+16].tempTorque[2]; psA[jIdx].torque[2] += sA[threadIdx.x].tempTorque[2] + sA[threadIdx.x+16].tempTorque[2];
} }
} }
} } // end of atoms out-of-bounds
} // end of flags&(1<<j block
#ifdef AMOEBA_DEBUG
unsigned int jIdx = (flags == 0xFFFFFFFF) ? tj : j;
unsigned int atomJ = y + jIdx;
unsigned int mask = ( (atomI >= cAmoebaSim.numberOfAtoms) || (atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1;
if( atomI == targetAtom || atomJ == targetAtom ){
unsigned int index = (atomI == targetAtom) ? atomJ : atomI;
debugArray[index].x = (float) atomI;
debugArray[index].y = (float) atomJ;
debugArray[index].z = (float) y;
debugArray[index].w = (flags == 0xFFFFFFFF) ? (float) -141.0f : -151.0f;
index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? forceTorqueEnergy[0].x : 0.0f;
debugArray[index].y = mask ? forceTorqueEnergy[0].y : 0.0f;
debugArray[index].z = mask ? forceTorqueEnergy[0].z : 0.0f;
debugArray[index].w = mask ? forceTorqueEnergy[0].w : 0.0f;
index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? forceTorqueEnergy[1].x : 0.0f;
debugArray[index].y = mask ? forceTorqueEnergy[1].y : 0.0f;
debugArray[index].z = mask ? forceTorqueEnergy[1].z : 0.0f;
float offsetF = (float)(3*(y + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms));
debugArray[index].w = offsetF;
index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? forceTorqueEnergy[2].x : 0.0f;
debugArray[index].y = mask ? forceTorqueEnergy[2].y : 0.0f;
debugArray[index].z = mask ? forceTorqueEnergy[2].z : 0.0f;
offsetF = (float) (3*(x + tgx + (y >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms));
debugArray[index].w = offsetF;
for( int pullIndex = 0; pullIndex < maxPullIndex; pullIndex++ ){
index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
}
}
#endif
tj = (tj + 1) & (GRID - 1); tj = (tj + 1) & (GRID - 1);
} // end of j-loop } // end of j-loop
// Write results // Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP #ifdef USE_OUTPUT_BUFFER_PER_WARP
float of; float of;
unsigned int offset = 3*(x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms); unsigned int offset = 3*(x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms);
...@@ -441,7 +471,7 @@ if( atomI == targetAtom ){ ...@@ -441,7 +471,7 @@ if( atomI == targetAtom ){
of += sA[threadIdx.x].torque[2]; of += sA[threadIdx.x].torque[2];
outputTorque[offset+2] = of; outputTorque[offset+2] = of;
#else #else
unsigned int offset = 3*(x + tgx + (y >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms); unsigned int offset = 3*(x + tgx + (y >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms);
outputForce[offset] = localParticle.force[0]; outputForce[offset] = localParticle.force[0];
...@@ -462,7 +492,7 @@ if( atomI == targetAtom ){ ...@@ -462,7 +492,7 @@ if( atomI == targetAtom ){
outputTorque[offset+1] = sA[threadIdx.x].torque[1]; outputTorque[offset+1] = sA[threadIdx.x].torque[1];
outputTorque[offset+2] = sA[threadIdx.x].torque[2]; outputTorque[offset+2] = sA[threadIdx.x].torque[2];
#endif #endif
lasty = y; lasty = y;
} // end of pInteractionFlag block } // end of pInteractionFlag block
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu
View file @ 4d763c4d
...@@ -565,9 +565,9 @@ if( fabs(debugArray->_pSysStream[0][jj+3*paddedNumberOfAtoms].x) > 0.0 ){ ...@@ -565,9 +565,9 @@ if( fabs(debugArray->_pSysStream[0][jj+3*paddedNumberOfAtoms].x) > 0.0 ){
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaEField", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaEField", fileId, outputVector );
} }
delete debugArray; delete debugArray;
...@@ -578,9 +578,9 @@ if( fabs(debugArray->_pSysStream[0][jj+3*paddedNumberOfAtoms].x) > 0.0 ){ ...@@ -578,9 +578,9 @@ if( fabs(debugArray->_pSysStream[0][jj+3*paddedNumberOfAtoms].x) > 0.0 ){
std::vector<int> fileId; std::vector<int> fileId;
fileId.push_back( 0 ); fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector, gpu->psAtomIndex->_pSysData);
cudaWriteVectorOfDoubleVectorsToFile( "CudaEField", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaEField", fileId, outputVector );
} }
...@@ -590,4 +590,15 @@ void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu ) ...@@ -590,4 +590,15 @@ void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
{ {
kCalculateAmoebaPMEFixedMultipoles( amoebaGpu ); kCalculateAmoebaPMEFixedMultipoles( amoebaGpu );
cudaComputeAmoebaPmeDirectFixedEField( amoebaGpu ); cudaComputeAmoebaPmeDirectFixedEField( amoebaGpu );
if( 0 ){
gpuContext gpu = amoebaGpu->gpuContext;
std::vector<int> fileId;
fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaEField", fileId, outputVector );
}
} }
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.cu
View file @ 4d763c4d
...@@ -193,6 +193,7 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce ...@@ -193,6 +193,7 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
fields[2].z = 0.0f; fields[2].z = 0.0f;
fields[2].w = 0.0f; fields[2].w = 0.0f;
} }
/*
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
pullBack[0].x = xr; pullBack[0].x = xr;
pullBack[0].y = yr; pullBack[0].y = yr;
...@@ -204,7 +205,6 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce ...@@ -204,7 +205,6 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
pullBack[1].z = bn2; pullBack[1].z = bn2;
pullBack[1].w = exp2a; pullBack[1].w = exp2a;
/*
pullBack[1].x = atomJ.x - atomI.x; pullBack[1].x = atomJ.x - atomI.x;
pullBack[1].y = atomJ.y - atomI.y; pullBack[1].y = atomJ.y - atomI.y;
pullBack[1].z = atomJ.z - atomI.z; pullBack[1].z = atomJ.z - atomI.z;
...@@ -212,8 +212,8 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce ...@@ -212,8 +212,8 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
pullBack[1].x = scale3; pullBack[1].x = scale3;
pullBack[1].y = scale5; pullBack[1].y = scale5;
pullBack[1].z = scale7; pullBack[1].z = scale7;
*/
#endif #endif
*/
} }
// Include versions of the kernels for N^2 calculations. // Include versions of the kernels for N^2 calculations.
...@@ -385,8 +385,7 @@ static void cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply( amoebaGpuConte ...@@ -385,8 +385,7 @@ static void cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply( amoebaGpuConte
static const char* methodName = "cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply"; static const char* methodName = "cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply";
static int iteration = 1; static int iteration = 1;
if( 1 && amoebaGpu->log ){ if( 1 && amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "%s: scalingDistanceCutoff=%.5f\n", (void) fprintf( amoebaGpu->log, "%s\n", methodName );
methodName, amoebaGpu->scalingDistanceCutoff );
(void) fflush( amoebaGpu->log ); (void) fflush( amoebaGpu->log );
} }
int paddedNumberOfAtoms = amoebaGpu->gpuContext->sim.paddedNumberOfAtoms; int paddedNumberOfAtoms = amoebaGpu->gpuContext->sim.paddedNumberOfAtoms;
...@@ -748,9 +747,9 @@ static void cudaComputeAmoebaPmeMutualInducedFieldBySOR( amoebaGpuContext amoeba ...@@ -748,9 +747,9 @@ static void cudaComputeAmoebaPmeMutualInducedFieldBySOR( amoebaGpuContext amoeba
std::vector<int> fileId; std::vector<int> fileId;
fileId.push_back( iteration ); fileId.push_back( iteration );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeMI", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeMI", fileId, outputVector );
} }
...@@ -780,9 +779,9 @@ fflush( amoebaGpu->log ); ...@@ -780,9 +779,9 @@ fflush( amoebaGpu->log );
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); //cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeMI", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeMI", fileId, outputVector );
} }
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.h
View file @ 4d763c4d
...@@ -122,6 +122,7 @@ void METHOD_NAME(kCalculateAmoebaPmeMutualInducedField, _kernel)( ...@@ -122,6 +122,7 @@ void METHOD_NAME(kCalculateAmoebaPmeMutualInducedField, _kernel)(
fieldPolarSum[1] += mask ? ijField[1].z : 0.0f; fieldPolarSum[1] += mask ? ijField[1].z : 0.0f;
fieldPolarSum[2] += mask ? ijField[2].z : 0.0f; fieldPolarSum[2] += mask ? ijField[2].z : 0.0f;
/*
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( atomI == targetAtom || (y+j) == targetAtom ){ if( atomI == targetAtom || (y+j) == targetAtom ){
unsigned int index = atomI == targetAtom ? (y+j) : atomI; unsigned int index = atomI == targetAtom ? (y+j) : atomI;
...@@ -173,7 +174,6 @@ if( atomI == targetAtom || (y+j) == targetAtom ){ ...@@ -173,7 +174,6 @@ if( atomI == targetAtom || (y+j) == targetAtom ){
debugArray[index].z = ijField[indexJ+1][2]; debugArray[index].z = ijField[indexJ+1][2];
debugArray[index].w = flag; debugArray[index].w = flag;
/*
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
...@@ -189,10 +189,10 @@ if( atomI == targetAtom || (y+j) == targetAtom ){ ...@@ -189,10 +189,10 @@ if( atomI == targetAtom || (y+j) == targetAtom ){
debugArray[index].y = scaleMask.x & mask ? 1.0f : -1.0f; debugArray[index].y = scaleMask.x & mask ? 1.0f : -1.0f;
debugArray[index].z = scaleMask.y & mask ? 1.0f : -1.0f; debugArray[index].z = scaleMask.y & mask ? 1.0f : -1.0f;
debugArray[index].w = + 10.0f; debugArray[index].w = + 10.0f;
*/
} }
#endif #endif
*/
} }
// Write results // Write results
...@@ -308,6 +308,7 @@ if( atomI == targetAtom || (y+j) == targetAtom ){ ...@@ -308,6 +308,7 @@ if( atomI == targetAtom || (y+j) == targetAtom ){
} }
/*
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( atomI == targetAtom || (y+jIdx) == targetAtom ){ if( atomI == targetAtom || (y+jIdx) == targetAtom ){
unsigned int index = atomI == targetAtom ? (y+jIdx) : atomI; unsigned int index = atomI == targetAtom ? (y+jIdx) : atomI;
...@@ -360,6 +361,7 @@ if( atomI == targetAtom || (y+jIdx) == targetAtom ){ ...@@ -360,6 +361,7 @@ if( atomI == targetAtom || (y+jIdx) == targetAtom ){
debugArray[index].w = flag; debugArray[index].w = flag;
} }
#endif #endif
*/
} }
tj = (tj + 1) & (GRID - 1); tj = (tj + 1) & (GRID - 1);
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaRotateFrame.cu
View file @ 4d763c4d
...@@ -528,8 +528,8 @@ void cudaComputeAmoebaLabFrameMoments( amoebaGpuContext amoebaGpu ) ...@@ -528,8 +528,8 @@ void cudaComputeAmoebaLabFrameMoments( amoebaGpuContext amoebaGpu )
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( particles, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( particles, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( particles, 9, amoebaGpu->psRotationMatrix, outputVector ); cudaLoadCudaFloatArray( particles, 9, amoebaGpu->psRotationMatrix, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaRotationMatrices", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaRotationMatrices", fileId, outputVector );
} }
if( 0 ){ if( 0 ){
...@@ -539,9 +539,9 @@ void cudaComputeAmoebaLabFrameMoments( amoebaGpuContext amoebaGpu ) ...@@ -539,9 +539,9 @@ void cudaComputeAmoebaLabFrameMoments( amoebaGpuContext amoebaGpu )
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( particles, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( particles, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( particles, 3, amoebaGpu->psLabFrameDipole, outputVector ); cudaLoadCudaFloatArray( particles, 3, amoebaGpu->psLabFrameDipole, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( particles, 9, amoebaGpu->psLabFrameQuadrupole, outputVector ); cudaLoadCudaFloatArray( particles, 9, amoebaGpu->psLabFrameQuadrupole, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaRotatedMoments", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaRotatedMoments", fileId, outputVector );
} }
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaVdw14_7.cu
View file @ 4d763c4d
...@@ -715,8 +715,8 @@ void kCalculateAmoebaVdw14_7Forces( amoebaGpuContext amoebaGpu, int applyCutoff ...@@ -715,8 +715,8 @@ void kCalculateAmoebaVdw14_7Forces( amoebaGpuContext amoebaGpu, int applyCutoff
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloat4Array( gpu->natoms, 3, psTempForce, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, psTempForce, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaVdw", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaVdw", fileId, outputVector );
delete psTempForce; delete psTempForce;
//exit(0); //exit(0);
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaWcaDispersion.cu
View file @ 4d763c4d
...@@ -631,8 +631,8 @@ void kCalculateAmoebaWcaDispersionForces( amoebaGpuContext amoebaGpu ) ...@@ -631,8 +631,8 @@ void kCalculateAmoebaWcaDispersionForces( amoebaGpuContext amoebaGpu )
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, psTempForce, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, psTempForce, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaWca", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaWca", fileId, outputVector );
delete psTempForce; delete psTempForce;
//exit(0); //exit(0);
......
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