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Commit a80b8a02 authored by Mark Friedrichs's avatar Mark Friedrichs
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Fixed problem w/ cavity force

parent a924f45c
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Showing with 101 additions and 10 deletions
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ a80b8a02
......@@ -1899,10 +1899,26 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
gpu->sim.preFactor = -amoebaGpu->amoebaSim.electric*((1.0f/innerDielectric)-(1.0f/solventDielectric));
if( amoebaGpu->log ){
(void) fprintf( amoebaGpu->log,"gpuSetAmoebaObcParameters: cavity=%d dielectricOffset=%15.7e probeRadius=%15.7e surfaceAreaFactor=%15.7e\n",
includeCavityTerm, dielectricOffset, probeRadius, surfaceAreaFactor );
(void) fprintf( amoebaGpu->log," gkc=%12.3f solventDielectric=%15.7e innerDielectric=%15.7e sim.preFactor=%15.7e\n",
amoebaGpu->amoebaSim.gkc, amoebaGpu->amoebaSim.dwater, amoebaGpu->amoebaSim.dielec, gpu->sim.preFactor );
(void) fprintf( amoebaGpu->log," fc=%15.7e fd=%15.7e fq=%15.7e\n",
amoebaGpu->amoebaSim.fc, amoebaGpu->amoebaSim.fq, amoebaGpu->amoebaSim.fq );
(void) fprintf( amoebaGpu->log,"\nRadius (r-off) scl*(r-off) scl\n" );
for (unsigned int i = 0; i < amoebaGpu->paddedNumberOfAtoms && i < 10; i++)
{
(void) fprintf( amoebaGpu->log,"%6d %15.7e %15.7e %15.7e %15.7e\n", i,
radius[i] , (*gpu->psObcData)[i].x, (*gpu->psObcData)[i].y, scale[i] );
}
}
gpuRotationToLabFrameAllocate( amoebaGpu );
gpuFixedEFieldAllocate( amoebaGpu );
gpuElectrostaticAllocate( amoebaGpu );
gpuKirkwoodAllocate( amoebaGpu );
}
static int encodeCell( unsigned int x, unsigned int y ){
......@@ -3764,6 +3780,41 @@ void cudaLoadCudaFloatArray( int numberOfParticles, int entriesPerParticle, CUDA
}
}
/**---------------------------------------------------------------------------------------
Load contents of arrays into vector
@param numberOfParticles number of particles
@param entriesPerParticle entries/particles array
@param array cuda array
@param outputVector output vector
--------------------------------------------------------------------------------------- */
void cudaLoadCudaFloat2Array( int numberOfParticles, int entriesPerParticle, CUDAStream<float2>* array, VectorOfDoubleVectors& outputVector )
{
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "cudaLoadCudaFloat2Array";
// ---------------------------------------------------------------------------------------
array->Download();
int runningIndex = 0;
outputVector.resize( numberOfParticles );
for( int ii = 0; ii < numberOfParticles; ii++ ){
if( entriesPerParticle > 0 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].x );
}
if( entriesPerParticle > 1 ){
outputVector[ii].push_back( array->_pSysStream[0][runningIndex].y );
}
runningIndex++;
}
}
/**---------------------------------------------------------------------------------------
Load contents of arrays into vector
......@@ -3779,7 +3830,7 @@ void cudaLoadCudaFloat4Array( int numberOfParticles, int entriesPerParticle, CUD
{
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "cudaLoadCudaFloatArray";
// static const std::string methodName = "cudaLoadCudaFloat4Array";
// ---------------------------------------------------------------------------------------
......@@ -4089,6 +4140,7 @@ void trackMutualInducedIterations( amoebaGpuContext amoebaGpu, int iteration){
// ---------------------------------------------------------------------------------------
if( amoebaGpu->log == NULL || currentStep > 20000 )return;
//if( amoebaGpu->log == NULL )return;
gpuContext gpu = amoebaGpu->gpuContext;
currentStep++;
......@@ -4117,7 +4169,7 @@ void trackMutualInducedIterations( amoebaGpuContext amoebaGpu, int iteration){
fileId.push_back( currentStep );
}
if( (currentStep % 20) == 0 || fileId[0] > 20 ){
(void) fprintf( amoebaGpu->log, "step=%d fileId=%d\n", currentStep, fileId[0] );
(void) fprintf( amoebaGpu->log, "step=%d fileId=%d iterations=%d\n", currentStep, fileId[0], iteration );
}
(void) fflush( amoebaGpu->log );
VectorOfDoubleVectors outputVector;
......@@ -4129,7 +4181,7 @@ void trackMutualInducedIterations( amoebaGpuContext amoebaGpu, int iteration){
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipoleS, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolarS,outputVector );
*/
cudaWriteVectorOfDoubleVectorsToFile( "CudaMIT", fileId, outputVector );
cudaWriteVectorOfDoubleVectorsToFile( "CudaMI", fileId, outputVector );
int nansPresent = isNanOrInfinity( amoebaGpu->mutualInducedCurrentEpsilon );
if( nansPresent == 0 ){
for( int ii = 0; ii < gpu->natoms && nansPresent == 0; ii++ ){
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaKernels.h
View file @ a80b8a02
......@@ -140,6 +140,7 @@ extern void cudaWriteFloat1AndFloat1ArraysToFile( int numberOfAtoms, char* fname
extern void readFile( std::string fileName, StringVectorVector& fileContents );
extern void cudaLoadCudaFloatArray( int numberOfParticles, int entriesPerParticle, CUDAStream<float>* 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 cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId, VectorOfDoubleVectors& outputVector );
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.cu
View file @ a80b8a02
......@@ -4,6 +4,7 @@
#include "amoebaGpuTypes.h"
#include "amoebaCudaKernels.h"
#include "cudaKernels.h"
#include "kCalculateAmoebaCudaUtilities.h"
#include "kCalculateAmoebaCudaKirkwoodParticle.h"
extern void kCalculateObcGbsaForces2(gpuContext gpu);
......@@ -1805,9 +1806,9 @@ void kReduceToBornForcePrefactorAndSASA_kernel( unsigned int fieldComponents, un
totalForce += saTerm / bornRadius;
totalForce *= bornRadius * bornRadius * obcChain;
energy += saTerm;
fieldOut[pos] = totalForce;
fieldOut[pos] = totalForce*bornRadius*bornRadius*obcChain;
energy += saTerm;
pos += gridDim.x * blockDim.x;
}
......@@ -1830,11 +1831,48 @@ static void kReduceToBornForcePrefactor( amoebaGpuContext amoebaGpu )
{
if( amoebaGpu->includeObcCavityTerm ){
kReduceToBornForcePrefactorAndSASA_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
amoebaGpu->paddedNumberOfAtoms, amoebaGpu->outputBuffers,
amoebaGpu->psWorkArray_1_1->_pDevStream[0],
amoebaGpu->psWorkArray_1_2->_pDevStream[0],
amoebaGpu->gpuContext->psBornForce->_pDevStream[0] );
#ifdef AMOEBA_DEBUG
if( amoebaGpu->log ){
// kClearEnergy() should be called prior to kReduceToBornForcePrefactorAndSASA_kernel
double energy = kReduceEnergy( amoebaGpu->gpuContext );
amoebaGpu->gpuContext->psBornForce->Download();
amoebaGpu->gpuContext->psObcData->Download();
amoebaGpu->gpuContext->psBornRadii->Download();
(void) fprintf( amoebaGpu->log, "Born force w/ cavity energy=%15.7e.\n", energy ); (void) fflush( amoebaGpu->log );
for( int ii = 0; ii < amoebaGpu->gpuContext->natoms; ii++ ){
(void) fprintf( amoebaGpu->log, "%5d ", ii);
(void) fprintf( amoebaGpu->log,"bF %16.9e obc=%16.9e bR=%16.9e\n",
amoebaGpu->gpuContext->psBornForce->_pSysStream[0][ii],
amoebaGpu->gpuContext->psObcData->_pSysStream[0][ii].x,
amoebaGpu->gpuContext->psBornRadii->_pSysStream[0][ii] );
}
(void) fflush( amoebaGpu->log );
if( 1 ){
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 );
cudaWriteVectorOfDoubleVectorsToFile( "CudaBornForce", fileId, outputVector );
(void) fprintf( amoebaGpu->log, "kReduceToBornForcePrefactor: exiting.\n" );
(void) fprintf( stderr, "kReduceToBornForcePrefactor: exiting.\n" ); (void) fflush( stderr );
exit(0);
}
}
#endif
} else {
kReduceToBornForcePrefactor_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
amoebaGpu->paddedNumberOfAtoms, amoebaGpu->outputBuffers,
......
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