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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;
using std::string;
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) {
}
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 4d763c4d
......@@ -779,17 +779,15 @@ static void computeAmoebaMultipoleForce( AmoebaCudaData& data ) {
if( data.getMultipoleForceCount() == 0 ){
gpuCopyWorkUnit( gpu );
}
//if( data.getApplyCutoff() && (data.getMultipoleForceCount() % 100) == 0 ){
//gpuReorderAtoms(gpu->gpuContext);
//}
data.incrementMultipoleForceCount();
data.initializeGpu();
if( 0 && data.getLog() ){
(void) fprintf( data.getLog(), "computeAmoebaMultipoleForce\n" );
(void) fprintf( data.getLog(), "In computeAmoebaMultipoleForce\n" );
(void) fflush( data.getLog());
}
data.initializeGpu();
// calculate Born radii
if( data.getHasAmoebaGeneralizedKirkwood() ){
......@@ -974,23 +972,27 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
nb.setCutoffDistance(force.getCutoffDistance());
std::vector<int> pmeGridDimension;
force.getPmeGridDimensions( pmeGridDimension );
if( 1 || pmeGridDimension[0] == 0 ){
int pmeParametersSetBasedOnEwaldErrorTolerance;
if( pmeGridDimension[0] == 0 ){
NonbondedForceImpl::calcPMEParameters(system, nb, alpha, xsize, ysize, zsize);
/*
alpha = 5.446;
xsize = 60;
ysize = 48;
zsize = 48;
*/
pmeParametersSetBasedOnEwaldErrorTolerance = 1;
} else {
alpha = force.getAEwald();
xsize = pmeGridDimension[0];
ysize = pmeGridDimension[1];
zsize = pmeGridDimension[2];
pmeParametersSetBasedOnEwaldErrorTolerance = 0;
}
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 );
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() );
}
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
(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
......@@ -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
// ---------------------------------------------------------------------------------------
array->Download();
int runningIndex = 0;
int orderIndex = 0;
outputVector.resize( numberOfParticles );
for( int ii = 0; ii < numberOfParticles; ii++ ){
if( order ){
orderIndex = order[ii];
} else {
orderIndex = ii;
}
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
}
}
/**---------------------------------------------------------------------------------------
Load contents of arrays into vector
......@@ -3983,10 +4018,12 @@ void cudaLoadCudaFloat2Array( int numberOfParticles, int entriesPerParticle, CUD
@param entriesPerParticle entries/particles array
@param array cuda array
@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
array->Download();
int runningIndex = 0;
int orderIndex;
outputVector.resize( numberOfParticles );
for( int ii = 0; ii < numberOfParticles; ii++ ){
if( order ){
orderIndex = order[runningIndex];
} else {
orderIndex = runningIndex;
}
if( entriesPerParticle > 0 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].x );
outputVector[orderIndex].push_back( array->_pSysStream[0][ii].x );
}
if( entriesPerParticle > 1 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].y );
outputVector[orderIndex].push_back( array->_pSysStream[0][ii].y );
}
if( entriesPerParticle > 2 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].z );
outputVector[orderIndex].push_back( array->_pSysStream[0][ii].z );
}
if( entriesPerParticle > 3 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].w );
outputVector[orderIndex].push_back( array->_pSysStream[0][ii].w );
}
runningIndex++;
}
......@@ -4353,8 +4396,8 @@ void trackMutualInducedIterations( amoebaGpuContext amoebaGpu, int iteration){
}
(void) fflush( amoebaGpu->log );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psVelm4, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psVelm4, outputVector, NULL );
/*
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, 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
int entriesPerAtom2, CUDAStream<float>* array2 );
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 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 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 )
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector);
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector );
}
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaFixedEAndGkFields.cu
View file @ 4d763c4d
......@@ -562,9 +562,9 @@ void cudaComputeAmoebaFixedEAndGkFields( amoebaGpuContext amoebaGpu )
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector);
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psGk_Field, outputVector);
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector, NULL);
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psGk_Field, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaEAndGkField", fileId, outputVector );
}
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaFixedEField.cu
View file @ 4d763c4d
......@@ -307,8 +307,8 @@ void cudaComputeAmoebaFixedEField( amoebaGpuContext amoebaGpu )
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
//cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector);
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaEField", fileId, outputVector );
}
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.cu
View file @ 4d763c4d
......@@ -1748,10 +1748,10 @@ static void kReduceToBornForcePrefactor( amoebaGpuContext amoebaGpu )
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( amoebaGpu->gpuContext->natoms, 3, amoebaGpu->gpuContext->psPosq4, outputVector );
cudaLoadCudaFloatArray( amoebaGpu->gpuContext->natoms, 1, amoebaGpu->gpuContext->psBornRadii, outputVector );
cudaLoadCudaFloat2Array( amoebaGpu->gpuContext->natoms, 2, amoebaGpu->gpuContext->psObcData, outputVector );
cudaLoadCudaFloatArray( amoebaGpu->gpuContext->natoms, 1, amoebaGpu->gpuContext->psBornForce, outputVector );
cudaLoadCudaFloat4Array( amoebaGpu->gpuContext->natoms, 3, amoebaGpu->gpuContext->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( amoebaGpu->gpuContext->natoms, 1, amoebaGpu->gpuContext->psBornRadii, outputVector, NULL );
cudaLoadCudaFloat2Array( amoebaGpu->gpuContext->natoms, 2, amoebaGpu->gpuContext->psObcData, outputVector, NULL );
cudaLoadCudaFloatArray( amoebaGpu->gpuContext->natoms, 1, amoebaGpu->gpuContext->psBornForce, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaBornForce", fileId, outputVector );
(void) fprintf( amoebaGpu->log, "kReduceToBornForcePrefactor: exiting.\n" );
(void) fprintf( stderr, "kReduceToBornForcePrefactor: exiting.\n" ); (void) fflush( stderr );
......@@ -2069,8 +2069,8 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu )
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodForce, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector);
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector );
}
......@@ -2113,8 +2113,8 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu )
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodForce, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodForce, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaKirkwoodForce", fileId, outputVector );
}
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff.cu
View file @ 4d763c4d
......@@ -1215,9 +1215,9 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu )
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodEDiffForce, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector);
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodEDiffForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaForceTorque", fileId, outputVector );
}
......@@ -1260,8 +1260,8 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu )
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodEDiffForce, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psKirkwoodEDiffForce, outputVector, NULL );
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>*
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector);
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector );
}
#endif
......@@ -1031,9 +1031,9 @@ void cudaComputeAmoebaMapTorquesAndAddTotalForce( amoebaGpuContext amoebaGpu,
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
//cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 4, gpu->psForce4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, psForce, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, psTorque, outputVector);
cudaLoadCudaFloat4Array( gpu->natoms, 4, gpu->psForce4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, psForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector );
}
#endif
......@@ -1123,9 +1123,9 @@ void cudaComputeAmoebaMapTorquesAndAddTotalForce2( amoebaGpuContext amoebaGpu,
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
//cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 4, gpu->psForce4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector);
cudaLoadCudaFloat4Array( gpu->natoms, 4, gpu->psForce4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, NULL);
cudaWriteVectorOfDoubleVectorsToFile( "CudaVacuumElecForce", fileId, outputVector );
}
#endif
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedAndGkFields.cu
View file @ 4d763c4d
......@@ -925,9 +925,9 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaMI_GK", fileId, outputVector );
}
#endif
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedField.cu
View file @ 4d763c4d
......@@ -594,8 +594,8 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
// cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaMI", fileId, outputVector );
}
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.cu
View file @ 4d763c4d
......@@ -152,11 +152,12 @@ __device__ static void calculatePmeSelfTorqueElectrostaticPairIxn_kernel( PmeDir
}
__device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectrostaticParticle& atomI, PmeDirectElectrostaticParticle& atomJ,
float* scalingFactors, float* outputForce, float3 outputTorque[3], float* energy
float* scalingFactors, float4 forceTorqueEnergy[3]
#ifdef AMOEBA_DEBUG
,float4* debugArray
#endif
){
float xr = atomJ.x - atomI.x;
float yr = atomJ.y - atomI.y;
float zr = atomJ.z - atomI.z;
......@@ -210,12 +211,11 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
// calculate the real space error function terms;
float ralpha = cSim.alphaEwald*r;
float bn0 = erfc(ralpha)/r;
float alsq2 = 2.0f*cSim.alphaEwald*cSim.alphaEwald;
float alsq2n = 0.0f;
if( cSim.alphaEwald > 0.0f){
if( cSim.alphaEwald > 0.0f ){
alsq2n = 1.0f/(cAmoebaSim.sqrtPi*cSim.alphaEwald);
}
float exp2a = exp(-(ralpha*ralpha));
......@@ -263,7 +263,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
if( damp != 0.0f ){
float pgamma = atomI.thole < atomJ.thole ? atomI.thole : atomJ.thole;
float ratio = r/damp;
damp = -pgamma * ratio*ratio*ratio;
damp = -pgamma*ratio*ratio*ratio;
if( damp > -50.0f ){
float expdamp = exp(damp);
scale3 = 1.0f - expdamp;
......@@ -510,7 +510,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
e = e - (1.0f-scalingFactors[MScaleIndex])*erl;
ei = ei - erli;
*energy = -conversionFactor*(e + ei);
forceTorqueEnergy[0].w = -conversionFactor*(e + ei);
// increment the total intramolecular energy; assumes;
// intramolecular distances are less than half of cell;
......@@ -604,6 +604,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
+ (sci3+scip3)*bn2*dk1
+ gfi4*(qkui1+qkuip1-qiuk1-qiukp1))
+ gfi5*qir1 + gfi6*qkr1;
float ftm2i2 = gfi1*yr + 0.5f*
(gfi2*(atomI.inducedDipole[1]+atomI.inducedDipoleP[1])
+ bn2*(sci4*atomI.inducedDipoleP[1]+scip4*atomI.inducedDipole[1])
......@@ -613,6 +614,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
+ (sci3+scip3)*bn2*dk2
+ gfi4*(qkui2+qkuip2-qiuk2-qiukp2))
+ gfi5*qir2 + gfi6*qkr2;
float ftm2i3 = gfi1*zr + 0.5f*
(gfi2*(atomI.inducedDipole[2]+atomI.inducedDipoleP[2])
+ bn2*(sci4*atomI.inducedDipoleP[2]+scip4*atomI.inducedDipole[2])
......@@ -674,10 +676,13 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
float temp3 = 0.5f * rr3 * ((gli1+gli6)*scalingFactors[PScaleIndex]
+(glip1+glip6)*scalingFactors[DScaleIndex]);
float temp5 = 0.5f * rr5 * ((gli2+gli7)*scalingFactors[PScaleIndex]
+(glip2+glip7)*scalingFactors[DScaleIndex]);
float temp7 = 0.5f * rr7 * (gli3*scalingFactors[PScaleIndex]
+glip3*scalingFactors[DScaleIndex]);
float fridmp1 = temp3*ddsc31 + temp5*ddsc51 + temp7*ddsc71;
float fridmp2 = temp3*ddsc32 + temp5*ddsc52 + temp7*ddsc72;
float fridmp3 = temp3*ddsc33 + temp5*ddsc53 + temp7*ddsc73;
......@@ -692,9 +697,9 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
// modify the forces for partially excluded interactions
ftm2i1 -= fridmp1 - findmp1;
ftm2i2 -= fridmp2 - findmp2;
ftm2i3 -= fridmp3 - findmp3;
ftm2i1 -= (fridmp1 + findmp1);
ftm2i2 -= (fridmp2 + findmp2);
ftm2i3 -= (fridmp3 + findmp3);
// correction to convert mutual to direct polarization force
......@@ -851,18 +856,18 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
// increment gradient due to force and torque on first site;
outputForce[0] = conversionFactor*(ftm21 + ftm2i1);
outputForce[1] = conversionFactor*(ftm22 + ftm2i2);
outputForce[2] = conversionFactor*(ftm23 + ftm2i3);
forceTorqueEnergy[0].x = conversionFactor*(ftm21 + ftm2i1);
forceTorqueEnergy[0].y = conversionFactor*(ftm22 + ftm2i2);
forceTorqueEnergy[0].z = conversionFactor*(ftm23 + ftm2i3);
conversionFactor *= -1.0;
outputTorque[0].x = conversionFactor*(ttm21 + ttm2i1);
outputTorque[1].x = conversionFactor*(ttm22 + ttm2i2);
outputTorque[2].x = conversionFactor*(ttm23 + ttm2i3);
forceTorqueEnergy[1].x = conversionFactor*(ttm21 + ttm2i1);
forceTorqueEnergy[1].y = conversionFactor*(ttm22 + ttm2i2);
forceTorqueEnergy[1].z = conversionFactor*(ttm23 + ttm2i3);
outputTorque[1].x = conversionFactor*(ttm31 + ttm3i1);
outputTorque[1].y = conversionFactor*(ttm32 + ttm3i2);
outputTorque[1].z = conversionFactor*(ttm33 + ttm3i3);
forceTorqueEnergy[2].x = conversionFactor*(ttm31 + ttm3i1);
forceTorqueEnergy[2].y = conversionFactor*(ttm32 + ttm3i2);
forceTorqueEnergy[2].z = conversionFactor*(ttm33 + ttm3i3);
#ifdef AMOEBA_DEBUG
int debugIndex = 0;
......@@ -915,64 +920,103 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
debugArray[debugIndex].z = conversionFactor*ftm23;
debugArray[debugIndex].w = idTracker;
debugIndex++;
*/
idTracker += 1.0;
debugArray[debugIndex].x = e;
debugArray[debugIndex].y = ei;
debugArray[debugIndex].z = erl;
debugArray[debugIndex].w = erli;
debugIndex++;
idTracker += 1.0;
*/
idTracker += 100.0;
debugArray[debugIndex].x = r2;
debugArray[debugIndex].y = cSim.alphaEwald;
debugArray[debugIndex].z = conversionFactor*fridmp3;
debugArray[debugIndex].w = 115.0;
debugArray[debugIndex].z = conversionFactor;
debugArray[debugIndex].w = idTracker;
debugIndex++;
idTracker += 100.0;
debugArray[debugIndex].x = conversionFactor*ftm21;
debugArray[debugIndex].y = conversionFactor*ftm22;
debugArray[debugIndex].z = conversionFactor*ftm23;
debugArray[debugIndex].w = idTracker;
debugIndex++;
idTracker += 1.0;
debugArray[debugIndex].x = conversionFactor*findmp1;
debugArray[debugIndex].y = conversionFactor*findmp2;
debugArray[debugIndex].z = conversionFactor*findmp3;
debugArray[debugIndex].w = cSim.alphaEwald + 1.0f;
idTracker += 100.0;
debugArray[debugIndex].x = conversionFactor*ftm2i1;
debugArray[debugIndex].y = conversionFactor*ftm2i2;
debugArray[debugIndex].z = conversionFactor*ftm2i3;
debugArray[debugIndex].w = idTracker;
debugIndex++;
idTracker += 1.0;
/*
idTracker += 100.0;
debugArray[debugIndex].x = fridmp1;
debugArray[debugIndex].y = fridmp2;
debugArray[debugIndex].z = fridmp3;
debugArray[debugIndex].w = idTracker;
debugIndex++;
idTracker += 100.0;
debugArray[debugIndex].x = findmp1;
debugArray[debugIndex].y = findmp2;
debugArray[debugIndex].z = findmp3;
debugArray[debugIndex].w = idTracker;
debugIndex++;
*/
idTracker += 100.0;
debugArray[debugIndex].x = conversionFactor*ttm21;
debugArray[debugIndex].y = conversionFactor*ttm22;
debugArray[debugIndex].z = conversionFactor*ttm23;
debugArray[debugIndex].w = idTracker;
debugIndex++;
idTracker += 1.0;
idTracker += 100.0;
debugArray[debugIndex].x = conversionFactor*ttm2i1;
debugArray[debugIndex].y = conversionFactor*ttm2i2;
debugArray[debugIndex].z = conversionFactor*ttm2i3;
debugArray[debugIndex].w = idTracker;
debugIndex++;
idTracker += 100.0;
debugArray[debugIndex].x = conversionFactor*ttm31;
debugArray[debugIndex].y = conversionFactor*ttm32;
debugArray[debugIndex].z = conversionFactor*ttm33;
debugArray[debugIndex].w = idTracker;
debugIndex++;
idTracker += 100.0;
debugArray[debugIndex].x = conversionFactor*ttm3i1;
debugArray[debugIndex].y = conversionFactor*ttm3i2;
debugArray[debugIndex].z = conversionFactor*ttm3i3;
debugArray[debugIndex].w = idTracker;
debugIndex++;
#endif
} else {
outputForce[0] = 0.0f;
outputForce[1] = 0.0f;
outputForce[2] = 0.0f;
forceTorqueEnergy[0].x = 0.0f;
forceTorqueEnergy[0].y = 0.0f;
forceTorqueEnergy[0].z = 0.0f;
outputTorque[0].x = 0.0f;
outputTorque[0].y = 0.0f;
outputTorque[0].z = 0.0f;
forceTorqueEnergy[1].x = 0.0f;
forceTorqueEnergy[1].y = 0.0f;
forceTorqueEnergy[1].z = 0.0f;
outputTorque[1].x = 0.0f;
outputTorque[1].y = 0.0f;
outputTorque[1].z = 0.0f;
forceTorqueEnergy[2].x = 0.0f;
forceTorqueEnergy[2].y = 0.0f;
forceTorqueEnergy[2].z = 0.0f;
*energy = 0.0f;
forceTorqueEnergy[0].w = 0.0f;
#ifdef AMOEBA_DEBUG
for( int ii = 0; ii < 5; ii++ ){
for( int ii = 0; ii < 12; ii++ ){
debugArray[ii].x = 0.0f;
debugArray[ii].y = 0.0f;
debugArray[ii].z = 0.0f;
debugArray[ii].w = (float) (11*ii);
debugArray[ii].w = (float) (-ii);
}
#endif
......@@ -1047,12 +1091,52 @@ static void kReduceForceTorque(amoebaGpuContext amoebaGpu )
amoebaGpu->paddedNumberOfAtoms*3, amoebaGpu->outputBuffers,
amoebaGpu->psWorkArray_3_1->_pDevStream[0], amoebaGpu->psForce->_pDevStream[0] );
LAUNCHERROR("kReducePmeDirectElectrostaticForce");
kReduceFields_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
amoebaGpu->paddedNumberOfAtoms*3, amoebaGpu->outputBuffers,
amoebaGpu->psWorkArray_3_2->_pDevStream[0], amoebaGpu->psTorque->_pDevStream[0] );
LAUNCHERROR("kReducePmeDirectElectrostaticTorque");
}
/**---------------------------------------------------------------------------------------
Zero gpu->psForce4
@param amoebaGpu amoebaGpu context
--------------------------------------------------------------------------------------- */
static void zeroForce( amoebaGpuContext amoebaGpu )
{
gpuContext gpu = amoebaGpu->gpuContext;
for( int ii = 0; ii < amoebaGpu->gpuContext->natoms; ii++ ){
gpu->psForce4->_pSysStream[0][ii].x = 0.0f;
gpu->psForce4->_pSysStream[0][ii].y = 0.0f;
gpu->psForce4->_pSysStream[0][ii].z = 0.0f;
}
gpu->psForce4->Upload();
}
/**---------------------------------------------------------------------------------------
Copy gpu->psForce4 to amoebaGpu->psForce
@param amoebaGpu amoebaGpu context
--------------------------------------------------------------------------------------- */
static void copyForce( amoebaGpuContext amoebaGpu, float conversion )
{
gpuContext gpu = amoebaGpu->gpuContext;
gpu->psForce4->Download();
int indexOffset = 0;
for( int ii = 0; ii < amoebaGpu->gpuContext->natoms; ii++ ){
amoebaGpu->psForce->_pSysStream[0][indexOffset] = conversion*(gpu->psForce4->_pSysStream[0][ii].x);
amoebaGpu->psForce->_pSysStream[0][indexOffset+1] = conversion*(gpu->psForce4->_pSysStream[0][ii].y);
amoebaGpu->psForce->_pSysStream[0][indexOffset+2] = conversion*(gpu->psForce4->_pSysStream[0][ii].z);
indexOffset += 3;
}
amoebaGpu->psForce->Upload();
}
//#define GET_INDUCED_DIPOLE_FROM_FILE
#ifdef GET_INDUCED_DIPOLE_FROM_FILE
#include <stdlib.h>
......@@ -1098,11 +1182,12 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
CUDAStream<float4>* debugArray = new CUDAStream<float4>(paddedNumberOfAtoms*paddedNumberOfAtoms, 1, "DebugArray");
memset( debugArray->_pSysStream[0], 0, sizeof( float )*4*paddedNumberOfAtoms*paddedNumberOfAtoms);
debugArray->Upload();
unsigned int targetAtom = 10;
unsigned int targetAtom = 49;
#endif
#ifdef GET_INDUCED_DIPOLE_FROM_FILE
std::string fileName = "waterInducedDipole.txt";
//std::string fileName = "waterInducedDipole.txt";
std::string fileName = "water_3_MI.txt";
StringVectorVector fileContents;
readFile( fileName, fileContents );
unsigned int offset = 0;
......@@ -1152,7 +1237,7 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
threadsPerBlock, getThreadsPerBlock(amoebaGpu, sizeof(PmeDirectElectrostaticParticle)),
sizeof(PmeDirectElectrostaticParticle) );
(void) fprintf( amoebaGpu->log, "kCalculateAmoebaPmeDirectElectrostaticCutoffForces no warp: numBlocks=%u numThreads=%u bufferPerWarp=%u atm=%u shrd=%u Obuf=%u ixnCt=%u workUnits=%u gpu->nonbond_threads_per_block=%u\n",
(void) fprintf( amoebaGpu->log, "kCalculateAmoebaPmeDirectElectrostaticCutoffForces: numBlocks=%u numThreads=%u bufferPerWarp=%u atm=%u shrd=%u Obuf=%u ixnCt=%u workUnits=%u gpu->nonbond_threads_per_block=%u\n",
amoebaGpu->nonbondBlocks, threadsPerBlock, amoebaGpu->bOutputBufferPerWarp,
sizeof(PmeDirectElectrostaticParticle), (sizeof(PmeDirectElectrostaticParticle))*threadsPerBlock,
amoebaGpu->energyOutputBuffers, (*gpu->psInteractionCount)[0], gpu->sim.workUnits, gpu->sim.nonbond_threads_per_block );
......@@ -1173,9 +1258,6 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
} else {
// gpu->sim.pInteractingWorkUnit,
// amoebaGpu->psWorkUnit->_pDevStream[0],
kCalculateAmoebaPmeDirectElectrostaticCutoffForces_kernel<<<amoebaGpu->nonbondBlocks, threadsPerBlock, sizeof(PmeDirectElectrostaticParticle)*threadsPerBlock>>>(
gpu->sim.pInteractingWorkUnit,
amoebaGpu->psWorkArray_3_1->_pDevStream[0],
......@@ -1196,11 +1278,12 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
amoebaGpu->psTorque->Download();
debugArray->Download();
(void) fprintf( amoebaGpu->log, "Finished PmeDirectElectrostatic kernel execution\n" ); (void) fflush( amoebaGpu->log );
int maxPrint = 5;
float conversion = 1.0f/41.84f;
float forceSum[3] = { 0.0f, 0.0f, 0.0f};
(void) fprintf( amoebaGpu->log, "Finished PmeDirectElectrostatic kernel execution conversion=%.5f\n", conversion ); (void) fflush( amoebaGpu->log );
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( amoebaGpu->log, "%5d ", ii);
......@@ -1230,6 +1313,7 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
}
}
(void) fflush( amoebaGpu->log );
/*
gpu->psEnergy->Download();
double energy = 0.0;
for( unsigned int ii = 0; ii < gpu->sim.energyOutputBuffers; ii++ ){
......@@ -1240,36 +1324,41 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
}
}
(void) fprintf( amoebaGpu->log,"Force sums: [%16.9e %16.9e %16.9e] Energy=%16.9e\n", forceSum[0], forceSum[1], forceSum[2], energy );
if( 0 ){
(void) fprintf( amoebaGpu->log,"DebugElecAll\n" );
int paddedNumberOfAtoms = amoebaGpu->gpuContext->sim.paddedNumberOfAtoms;
for( int jj = 0; jj < gpu->natoms*gpu->natoms; jj++ ){
if( fabs( debugArray->_pSysStream[0][jj].w - 111.0 ) < 1.0e-04 ){
int debugIndex = jj;
(void) fprintf( amoebaGpu->log,"%8d [%16.9e %16.9e %16.9e %16.9e] Enr11\n", jj,
debugArray->_pSysStream[0][debugIndex].x, debugArray->_pSysStream[0][debugIndex].y,
debugArray->_pSysStream[0][debugIndex].z, debugArray->_pSysStream[0][debugIndex].w );
debugIndex += paddedNumberOfAtoms;
(void) fprintf( amoebaGpu->log,"%8d [%16.9e %16.9e %16.9e %16.9e] Enr12\n", jj,
debugArray->_pSysStream[0][debugIndex].x, debugArray->_pSysStream[0][debugIndex].y,
debugArray->_pSysStream[0][debugIndex].z, debugArray->_pSysStream[0][debugIndex].w );
}
}
}
(void) fprintf( amoebaGpu->log,"\n" );
*/
if( 0 ){
(void) fprintf( amoebaGpu->log,"DebugElec\n" );
int paddedNumberOfAtoms = amoebaGpu->gpuContext->sim.paddedNumberOfAtoms;
float torqueSum0[3] = { 0.0f, 0.0f, 0.0f};
float torqueSum1[3] = { 0.0f, 0.0f, 0.0f};
int offset0 = 7*paddedNumberOfAtoms;
int offset1 = 8*paddedNumberOfAtoms;
int offset2 = 7*paddedNumberOfAtoms;
int offset3 = 8*paddedNumberOfAtoms;
for( int jj = 0; jj < gpu->natoms; jj++ ){
int debugIndex = jj;
for( int kk = 0; kk < 6; kk++ ){
(void) fprintf( amoebaGpu->log,"%5d %5d [%16.9e %16.9e %16.9e %16.9e] E11\n", targetAtom, jj,
if( fabs( debugArray->_pSysStream[0][debugIndex+5*paddedNumberOfAtoms].y ) < 1.0e-10 )continue;
if( jj != targetAtom ){
torqueSum0[0] += debugArray->_pSysStream[0][debugIndex+offset0].x + debugArray->_pSysStream[0][debugIndex+offset1].x;
torqueSum0[1] += debugArray->_pSysStream[0][debugIndex+offset0].y + debugArray->_pSysStream[0][debugIndex+offset1].y;
torqueSum0[2] += debugArray->_pSysStream[0][debugIndex+offset0].z + debugArray->_pSysStream[0][debugIndex+offset1].z;
torqueSum1[0] += debugArray->_pSysStream[0][debugIndex+offset2].x + debugArray->_pSysStream[0][debugIndex+offset3].x;
torqueSum1[1] += debugArray->_pSysStream[0][debugIndex+offset2].y + debugArray->_pSysStream[0][debugIndex+offset3].y;
torqueSum1[2] += debugArray->_pSysStream[0][debugIndex+offset2].z + debugArray->_pSysStream[0][debugIndex+offset3].z;
}
if( jj == 2 ){
offset0 += 2*paddedNumberOfAtoms;
offset1 += 2*paddedNumberOfAtoms;
}
for( int kk = 0; kk < 12; kk++ ){
(void) fprintf( amoebaGpu->log,"%5d %5d %5d [%16.9e %16.9e %16.9e %16.9e] E11\n", targetAtom, jj, kk,
debugArray->_pSysStream[0][debugIndex].x, debugArray->_pSysStream[0][debugIndex].y,
debugArray->_pSysStream[0][debugIndex].z, debugArray->_pSysStream[0][debugIndex].w );
debugIndex += paddedNumberOfAtoms;
}
(void) fprintf( amoebaGpu->log,"%5d %5d [%16.9e %16.9e %16.9e] [%16.9e %16.9e %16.9e] Sum\n", targetAtom, jj,
torqueSum0[0], torqueSum0[1], torqueSum0[2], torqueSum1[0], torqueSum1[1], torqueSum1[2]);
(void) fprintf( amoebaGpu->log,"\n" );
}
}
......@@ -1279,9 +1368,9 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector);
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psTorque, outputVector, gpu->psAtomIndex->_pSysData);
cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeDirectForceTorque", fileId, outputVector );
}
......@@ -1291,8 +1380,16 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
cudaComputeAmoebaMapTorquesAndAddTotalForce( amoebaGpu, amoebaGpu->psTorque, amoebaGpu->psForce, gpu->psForce4 );
}
if( 0 ){
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
copyForce( amoebaGpu, -1.0f/41.84f );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeDirectForce", fileId, outputVector );
}
}
/**---------------------------------------------------------------------------------------
Compute Amoeba electrostatic force & torque using PME
......@@ -1303,6 +1400,55 @@ void cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpuContext amoebaGpu )
void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu )
{
if( 0 ){
gpuContext gpu = amoebaGpu->gpuContext;
std::vector<int> fileId;
zeroForce( amoebaGpu );
kCalculateAmoebaPMEInducedDipoleForces( amoebaGpu );
copyForce( amoebaGpu, -1.0f/41.84 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeRecipForce", fileId, outputVector );
zeroForce( amoebaGpu );
}
if( 0 ){
gpuContext gpu = amoebaGpu->gpuContext;
std::vector<int> fileId;
zeroForce( amoebaGpu );
cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpu );
copyForce( amoebaGpu, -1.0f/41.84f );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "yCudaPmeDirectForce", fileId, outputVector );
zeroForce( amoebaGpu );
}
if( 0 ){
gpuContext gpu = amoebaGpu->gpuContext;
std::vector<int> fileId;
zeroForce( amoebaGpu );
cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpu );
kCalculateAmoebaPMEInducedDipoleForces( amoebaGpu );
copyForce( amoebaGpu, -1.0f/41.84f );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeForce", fileId, outputVector );
}
if( 0 ){
gpuContext gpu = amoebaGpu->gpuContext;
std::vector<int> fileId;
copyForce( amoebaGpu, -1.0f/41.84f );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psForce, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaPrePmeForce", fileId, outputVector );
}
//zeroForce( amoebaGpu );
cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpu );
kCalculateAmoebaPMEInducedDipoleForces( amoebaGpu );
}
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.h
View file @ 4d763c4d
......@@ -43,7 +43,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
){
#ifdef AMOEBA_DEBUG
int maxPullIndex = 2;
int maxPullIndex = 7;
float4 pullBack[12];
#endif
......@@ -56,6 +56,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
unsigned int lasty = 0xFFFFFFFF;
float totalEnergy = 0.0f;
float4 forceTorqueEnergy[3];
float scalingFactors[LastScalingIndex];
......@@ -90,10 +91,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
localParticle.torque[1] = 0.0f;
localParticle.torque[2] = 0.0f;
scalingFactors[PScaleIndex] = 1.0f;
scalingFactors[DScaleIndex] = 1.0f;
scalingFactors[UScaleIndex] = 1.0f;
scalingFactors[MScaleIndex] = 1.0f;
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
......@@ -116,9 +114,6 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
for (unsigned int j = 0; j < GRID; j++)
{
float force[3];
float3 torque[2];
unsigned int atomJ = y + j;
// set scale factors
......@@ -132,9 +127,7 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
// force
float energy;
calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[j],
scalingFactors, force, torque, &energy
calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[j], scalingFactors, forceTorqueEnergy
#ifdef AMOEBA_DEBUG
, pullBack
#endif
......@@ -143,28 +136,25 @@ void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
// nan*0.0 = nan not 0.0, so explicitly exclude (atomI == atomJ) contribution
// by setting match flag
unsigned int mask = ( (atomI == atomJ) || (atomI >= cAmoebaSim.numberOfAtoms) || (atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1;
// add to field at atomI the field due atomJ's charge/dipole/quadrupole
if( (atomI != atomJ) && (atomI < cAmoebaSim.numberOfAtoms) && (atomJ < cAmoebaSim.numberOfAtoms) )
{
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.force[1] += mask ? force[1] : 0.0f;
localParticle.force[2] += mask ? force[2] : 0.0f;
localParticle.torque[0] += forceTorqueEnergy[1].x;
localParticle.torque[1] += forceTorqueEnergy[1].y;
localParticle.torque[2] += forceTorqueEnergy[1].z;
localParticle.torque[0] += mask ? torque[0].x : 0.0f;
localParticle.torque[1] += mask ? torque[0].y : 0.0f;
localParticle.torque[2] += mask ? torque[0].z : 0.0f;
// energy for each diagonal-block ixn included twice, hence factor of 0.5
totalEnergy += mask ? 0.5*energy : 0.0f;
totalEnergy += 0.5*forceTorqueEnergy[0].w;
}
#ifdef AMOEBA_DEBUG
/*
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 || atomJ == targetAtom ){
if( atomI == targetAtom ){
unsigned int mask = ( (atomI == atomJ) || (atomI >= cAmoebaSim.numberOfAtoms) || (atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1;
unsigned int index = (atomI == targetAtom) ? atomJ : atomI;
float blockId = 1.0f;
......@@ -174,23 +164,24 @@ if( atomI == targetAtom ){
debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? force[0] : 0.0f;
debugArray[index].y = mask ? force[1] : 0.0f;
debugArray[index].z = mask ? force[2] : 0.0f;
debugArray[index].w = blockId;
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 ? torque[0].x : 0.0f;
debugArray[index].y = mask ? torque[0].y : 0.0f;
debugArray[index].z = mask ? torque[0].z : 0.0f;
debugArray[index].w = mask ? energy : 0.0f;
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*(x + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms));
debugArray[index].w = offsetF;
index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? torque[0].x : 0.0f;
debugArray[index].y = mask ? torque[0].y : 0.0f;
debugArray[index].z = mask ? torque[0].z : 0.0f;
debugArray[index].w = (float) (blockIdx.x * blockDim.x + threadIdx.x);
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;
debugArray[index].w = offsetF;
for( int pullIndex = 0; pullIndex < maxPullIndex; pullIndex++ ){
index += cAmoebaSim.paddedNumberOfAtoms;
......@@ -290,14 +281,11 @@ if( atomI == targetAtom ){
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 atomJ = y + jIdx;
float force[3];
float3 torque[2];
// set scale factors
if( bExclusionFlag )
......@@ -309,9 +297,8 @@ if( atomI == targetAtom ){
// force
float energy;
calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[jIdx],
scalingFactors, force, torque, &energy
scalingFactors, forceTorqueEnergy
#ifdef AMOEBA_DEBUG
, pullBack
#endif
......@@ -319,41 +306,41 @@ if( atomI == targetAtom ){
// 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
localParticle.force[0] += mask ? force[0] : 0.0f;
localParticle.force[1] += mask ? force[1] : 0.0f;
localParticle.force[2] += mask ? force[2] : 0.0f;
localParticle.force[0] += forceTorqueEnergy[0].x;
localParticle.force[1] += forceTorqueEnergy[0].y;
localParticle.force[2] += forceTorqueEnergy[0].z;
localParticle.torque[0] += mask ? torque[0].x : 0.0f;
localParticle.torque[1] += mask ? torque[0].y : 0.0f;
localParticle.torque[2] += mask ? torque[0].z : 0.0f;
totalEnergy += forceTorqueEnergy[0].w;
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
if( flags == 0xFFFFFFFF ){
psA[jIdx].force[0] -= mask ? force[0] : 0.0f;
psA[jIdx].force[1] -= mask ? force[1] : 0.0f;
psA[jIdx].force[2] -= mask ? force[2] : 0.0f;
psA[jIdx].force[0] -= forceTorqueEnergy[0].x;
psA[jIdx].force[1] -= forceTorqueEnergy[0].y;
psA[jIdx].force[2] -= forceTorqueEnergy[0].z;
psA[jIdx].torque[0] += mask ? torque[1].x : 0.0f;
psA[jIdx].torque[1] += mask ? torque[1].y : 0.0f;
psA[jIdx].torque[2] += mask ? torque[1].z : 0.0f;
psA[jIdx].torque[0] += forceTorqueEnergy[2].x;
psA[jIdx].torque[1] += forceTorqueEnergy[2].y;
psA[jIdx].torque[2] += forceTorqueEnergy[2].z;
} else {
sA[threadIdx.x].tempForce[0] = mask ? 0.0f : force[0];
sA[threadIdx.x].tempForce[1] = mask ? 0.0f : force[1];
sA[threadIdx.x].tempForce[2] = mask ? 0.0f : force[2];
sA[threadIdx.x].tempForce[0] = forceTorqueEnergy[0].x;
sA[threadIdx.x].tempForce[1] = forceTorqueEnergy[1].y;
sA[threadIdx.x].tempForce[2] = forceTorqueEnergy[2].z;
sA[threadIdx.x].tempTorque[0] = mask ? 0.0f : torque[1].x;
sA[threadIdx.x].tempTorque[1] = mask ? 0.0f : torque[1].y;
sA[threadIdx.x].tempTorque[2] = mask ? 0.0f : torque[1].z;
sA[threadIdx.x].tempTorque[0] = forceTorqueEnergy[2].x;
sA[threadIdx.x].tempTorque[1] = forceTorqueEnergy[2].y;
sA[threadIdx.x].tempTorque[2] = forceTorqueEnergy[2].z;
if( tgx % 2 == 0 ){
sumTempBuffer( sA[threadIdx.x], sA[threadIdx.x+1] );
......@@ -379,15 +366,58 @@ if( atomI == targetAtom ){
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);
} // end of j-loop
// Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP
#ifdef USE_OUTPUT_BUFFER_PER_WARP
float of;
unsigned int offset = 3*(x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms);
......@@ -441,7 +471,7 @@ if( atomI == targetAtom ){
of += sA[threadIdx.x].torque[2];
outputTorque[offset+2] = of;
#else
#else
unsigned int offset = 3*(x + tgx + (y >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms);
outputForce[offset] = localParticle.force[0];
......@@ -462,7 +492,7 @@ if( atomI == targetAtom ){
outputTorque[offset+1] = sA[threadIdx.x].torque[1];
outputTorque[offset+2] = sA[threadIdx.x].torque[2];
#endif
#endif
lasty = y;
} // 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 ){
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, 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 );
}
delete debugArray;
......@@ -578,9 +578,9 @@ if( fabs(debugArray->_pSysStream[0][jj+3*paddedNumberOfAtoms].x) > 0.0 ){
std::vector<int> fileId;
fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_Field, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psE_FieldPolar, 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 );
}
......@@ -590,4 +590,15 @@ void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
{
kCalculateAmoebaPMEFixedMultipoles( 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
fields[2].z = 0.0f;
fields[2].w = 0.0f;
}
/*
#ifdef AMOEBA_DEBUG
pullBack[0].x = xr;
pullBack[0].y = yr;
......@@ -204,7 +205,6 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
pullBack[1].z = bn2;
pullBack[1].w = exp2a;
/*
pullBack[1].x = atomJ.x - atomI.x;
pullBack[1].y = atomJ.y - atomI.y;
pullBack[1].z = atomJ.z - atomI.z;
......@@ -212,8 +212,8 @@ __device__ void calculatePmeDirectMutualInducedFieldPairIxn_kernel( MutualInduce
pullBack[1].x = scale3;
pullBack[1].y = scale5;
pullBack[1].z = scale7;
*/
#endif
*/
}
// Include versions of the kernels for N^2 calculations.
......@@ -385,8 +385,7 @@ static void cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply( amoebaGpuConte
static const char* methodName = "cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply";
static int iteration = 1;
if( 1 && amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "%s: scalingDistanceCutoff=%.5f\n",
methodName, amoebaGpu->scalingDistanceCutoff );
(void) fprintf( amoebaGpu->log, "%s\n", methodName );
(void) fflush( amoebaGpu->log );
}
int paddedNumberOfAtoms = amoebaGpu->gpuContext->sim.paddedNumberOfAtoms;
......@@ -748,9 +747,9 @@ static void cudaComputeAmoebaPmeMutualInducedFieldBySOR( amoebaGpuContext amoeba
std::vector<int> fileId;
fileId.push_back( iteration );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeMI", fileId, outputVector );
}
......@@ -780,9 +779,9 @@ fflush( amoebaGpu->log );
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector );
//cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaPmeMI", fileId, outputVector );
}
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.h
View file @ 4d763c4d
......@@ -122,6 +122,7 @@ void METHOD_NAME(kCalculateAmoebaPmeMutualInducedField, _kernel)(
fieldPolarSum[1] += mask ? ijField[1].z : 0.0f;
fieldPolarSum[2] += mask ? ijField[2].z : 0.0f;
/*
#ifdef AMOEBA_DEBUG
if( atomI == targetAtom || (y+j) == targetAtom ){
unsigned int index = atomI == targetAtom ? (y+j) : atomI;
......@@ -173,7 +174,6 @@ if( atomI == targetAtom || (y+j) == targetAtom ){
debugArray[index].z = ijField[indexJ+1][2];
debugArray[index].w = flag;
/*
index += cAmoebaSim.paddedNumberOfAtoms;
index += cAmoebaSim.paddedNumberOfAtoms;
......@@ -189,10 +189,10 @@ if( atomI == targetAtom || (y+j) == targetAtom ){
debugArray[index].y = scaleMask.x & mask ? 1.0f : -1.0f;
debugArray[index].z = scaleMask.y & mask ? 1.0f : -1.0f;
debugArray[index].w = + 10.0f;
*/
}
#endif
*/
}
// Write results
......@@ -308,6 +308,7 @@ if( atomI == targetAtom || (y+j) == targetAtom ){
}
/*
#ifdef AMOEBA_DEBUG
if( atomI == targetAtom || (y+jIdx) == targetAtom ){
unsigned int index = atomI == targetAtom ? (y+jIdx) : atomI;
......@@ -360,6 +361,7 @@ if( atomI == targetAtom || (y+jIdx) == targetAtom ){
debugArray[index].w = flag;
}
#endif
*/
}
tj = (tj + 1) & (GRID - 1);
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaRotateFrame.cu
View file @ 4d763c4d
......@@ -528,8 +528,8 @@ void cudaComputeAmoebaLabFrameMoments( amoebaGpuContext amoebaGpu )
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( particles, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( particles, 9, amoebaGpu->psRotationMatrix, outputVector );
cudaLoadCudaFloat4Array( particles, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( particles, 9, amoebaGpu->psRotationMatrix, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaRotationMatrices", fileId, outputVector );
}
if( 0 ){
......@@ -539,9 +539,9 @@ void cudaComputeAmoebaLabFrameMoments( amoebaGpuContext amoebaGpu )
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( particles, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( particles, 3, amoebaGpu->psLabFrameDipole, outputVector );
cudaLoadCudaFloatArray( particles, 9, amoebaGpu->psLabFrameQuadrupole, outputVector );
cudaLoadCudaFloat4Array( particles, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( particles, 3, amoebaGpu->psLabFrameDipole, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloatArray( particles, 9, amoebaGpu->psLabFrameQuadrupole, outputVector, gpu->psAtomIndex->_pSysData );
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
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, psTempForce, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, gpu->psAtomIndex->_pSysData );
cudaLoadCudaFloat4Array( gpu->natoms, 3, psTempForce, outputVector, gpu->psAtomIndex->_pSysData );
cudaWriteVectorOfDoubleVectorsToFile( "CudaVdw", fileId, outputVector );
delete psTempForce;
//exit(0);
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaWcaDispersion.cu
View file @ 4d763c4d
......@@ -631,8 +631,8 @@ void kCalculateAmoebaWcaDispersionForces( amoebaGpuContext amoebaGpu )
std::vector<int> fileId;
//fileId.push_back( 0 );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, psTempForce, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector, NULL );
cudaLoadCudaFloatArray( gpu->natoms, 3, psTempForce, outputVector, NULL );
cudaWriteVectorOfDoubleVectorsToFile( "CudaWca", fileId, outputVector );
delete psTempForce;
//exit(0);
......
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