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Commit 1a3caae0 authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Continue PME

parent e3196201
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Showing with 225 additions and 45 deletions
plugins/amoeba/openmmapi/include/AmoebaMultipoleForce.h
View file @ 1a3caae0
......@@ -127,6 +127,34 @@ public:
*/
void setAEwald(double aewald);
/**
* Get the B-spline order parameter
*
* @return the B-spline order parameter
*/
int getPmeBSplineOrder( ) const;
/**
* Set the B-spline order parameter
*
* @param the B-spline order parameter
*/
void setPmeBSplineOrder(int inputBSplineOrder);
/**
* Get the PME grid dimensions
*
* @return the PME grid dimensions
*/
void getPmeGridDimensions( std::vector<int>& gridDimension ) const;
/**
* Set the PME grid dimensions
*
* @param the PME grid dimensions
*/
void setPmeGridDimensions( const std::vector<int>& gridDimension );
/**
* Add multipole-related info for a particle
*
......@@ -294,6 +322,8 @@ private:
AmoebaNonbondedMethod nonbondedMethod;
double cutoffDistance;
double aewald;
int pmeBSplineOrder;
std::vector<int> pmeGridDimension;
MutualInducedIterationMethod mutualInducedIterationMethod;
int mutualInducedMaxIterations;
double mutualInducedTargetEpsilon;
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 1a3caae0
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), ewaldErrorTol(5e-4), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60),
AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(5e-4), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60),
mutualInducedTargetEpsilon(1.0e-05), scalingDistanceCutoff(100.0), electricConstant(138.9354558456) {
}
......@@ -64,6 +64,36 @@ void AmoebaMultipoleForce::setAEwald(double inputAewald ) {
aewald = inputAewald;
}
int AmoebaMultipoleForce::getPmeBSplineOrder( void ) const {
return pmeBSplineOrder;
}
void AmoebaMultipoleForce::setPmeBSplineOrder(int inputBSplineOrder) {
pmeBSplineOrder = inputBSplineOrder;
}
void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension ) const {
if( gridDimension.size() < 3 ){
gridDimension.resize(3);
}
if( pmeGridDimension.size() > 2 ){
gridDimension[0] = pmeGridDimension[0];
gridDimension[1] = pmeGridDimension[1];
gridDimension[2] = pmeGridDimension[2];
} else {
gridDimension[0] = gridDimension[1] = gridDimension[2] = 0;
}
return;
}
void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDimension ) {
pmeGridDimension.resize(3);
pmeGridDimension[0] = gridDimension[0];
pmeGridDimension[1] = gridDimension[1];
pmeGridDimension[2] = gridDimension[2];
return;
}
AmoebaMultipoleForce::MutualInducedIterationMethod AmoebaMultipoleForce::getMutualInducedIterationMethod( void ) const {
return mutualInducedIterationMethod;
}
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 1a3caae0
......@@ -597,7 +597,16 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
NonbondedForce nb;
nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
nb.setCutoffDistance(force.getCutoffDistance());
NonbondedForceImpl::calcPMEParameters(system, nb, alpha, xsize, ysize, zsize);
std::vector<int> pmeGridDimension;
force.getPmeGridDimensions( pmeGridDimension );
if( 1 || pmeGridDimension[0] == 0 ){
NonbondedForceImpl::calcPMEParameters(system, nb, alpha, xsize, ysize, zsize);
} else {
alpha = force.getAEwald();
xsize = pmeGridDimension[0];
ysize = pmeGridDimension[1];
zsize = pmeGridDimension[2];
}
gpuSetAmoebaPMEParameters(data.getAmoebaGpu(), (float) alpha, xsize, ysize, zsize);
}
......
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ 1a3caae0
......@@ -351,6 +351,7 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
(void) fprintf( log, " pM_ScaleIndices %p\n", amoebaGpu->amoebaSim.pM_ScaleIndices );
(void) fprintf( log, " sqrtPi %15.7e\n", amoebaGpu->amoebaSim.sqrtPi );
(void) fprintf( log, " alpha Ewald %15.7e\n", gpu->sim.alphaEwald );
(void) fprintf( log, " PME grid dimensions %6d %6d %6d\n", gpu->sim.pmeGridSize.x, gpu->sim.pmeGridSize.y, gpu->sim.pmeGridSize.z);
(void) fprintf( log, " cutoffDistance2 %15.7e\n", amoebaGpu->amoebaSim.cutoffDistance2 );
(void) fprintf( log, " electric %15.7e\n", amoebaGpu->amoebaSim.electric );
(void) fprintf( log, " box %15.7e %15.7e %15.7e\n", gpu->sim.periodicBoxSizeX, gpu->sim.periodicBoxSizeY, gpu->sim.periodicBoxSizeZ);
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu
View file @ 1a3caae0
......@@ -6,7 +6,7 @@
#include "amoebaCudaKernels.h"
#include "kCalculateAmoebaCudaUtilities.h"
//#define AMOEBA_DEBUG
#define AMOEBA_DEBUG
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaAmoebaGmxSimulation cAmoebaSim;
......@@ -39,7 +39,7 @@ __launch_bounds__(GT2XX_THREADS_PER_BLOCK, 1)
#else
__launch_bounds__(G8X_THREADS_PER_BLOCK, 1)
#endif
void kReduceDirectSelfFields_kernel( unsigned int fieldComponents, unsigned int outputBuffers, float* fieldIn, float* fieldOut )
static void kReducePmeEFieldPolar_kernel( unsigned int fieldComponents, unsigned int outputBuffers, float* EFieldReciprocal, float* fieldIn, float* fieldOut )
{
unsigned int pos = blockIdx.x * blockDim.x + threadIdx.x;
......@@ -52,7 +52,7 @@ void kReduceDirectSelfFields_kernel( unsigned int fieldComponents, unsigned int
// self-term included here
float totalField = term*cAmoebaSim.pLabFrameDipole[pos];
float totalField = EFieldReciprocal[pos] + term*cAmoebaSim.pLabFrameDipole[pos];
float* pFt = fieldIn + pos;
unsigned int i = outputBuffers;
......@@ -80,19 +80,74 @@ void kReduceDirectSelfFields_kernel( unsigned int fieldComponents, unsigned int
}
}
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(GF1XX_THREADS_PER_BLOCK, 1)
#elif (__CUDA_ARCH__ >= 130)
__launch_bounds__(GT2XX_THREADS_PER_BLOCK, 1)
#else
__launch_bounds__(G8X_THREADS_PER_BLOCK, 1)
#endif
static void kReducePmeEField_kernel( unsigned int fieldComponents, unsigned int outputBuffers, float* fieldIn, float* fieldOut )
{
unsigned int pos = blockIdx.x * blockDim.x + threadIdx.x;
// Reduce field
const float term = (4.0f/3.0f)*(cSim.alphaEwald*cSim.alphaEwald*cSim.alphaEwald)/cAmoebaSim.sqrtPi;
//const float term = 0.0f;
while (pos < fieldComponents)
{
// self-term included here
float totalField = term*cAmoebaSim.pLabFrameDipole[pos];
float* pFt = fieldIn + pos;
unsigned int i = outputBuffers;
while (i >= 4)
{
totalField += pFt[0] + pFt[fieldComponents] + pFt[2*fieldComponents] + pFt[3*fieldComponents];
pFt += fieldComponents*4;
i -= 4;
}
if (i >= 2)
{
totalField += pFt[0] + pFt[fieldComponents];
pFt += fieldComponents*2;
i -= 2;
}
if (i > 0)
{
totalField += pFt[0];
}
fieldOut[pos] += totalField;
pos += gridDim.x * blockDim.x;
}
}
// reduce psWorkArray_3_1 -> EField
// reduce psWorkArray_3_2 -> EFieldPolar
static void kReducePmeDirectE_Fields(amoebaGpuContext amoebaGpu )
{
kReduceDirectSelfFields_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
amoebaGpu->paddedNumberOfAtoms*3, amoebaGpu->outputBuffers,
amoebaGpu->psWorkArray_3_1->_pDevStream[0], amoebaGpu->psE_Field->_pDevStream[0] );
// E_FieldPolar = E_Field (reciprocal) + E_FieldPolar (direct) + self
kReducePmeEFieldPolar_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
amoebaGpu->paddedNumberOfAtoms*3, amoebaGpu->outputBuffers,
amoebaGpu->psE_Field->_pDevStream[0], amoebaGpu->psWorkArray_3_2->_pDevStream[0], amoebaGpu->psE_FieldPolar->_pDevStream[0] );
LAUNCHERROR("kReducePmeE_Fields1");
kReduceDirectSelfFields_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
amoebaGpu->paddedNumberOfAtoms*3, amoebaGpu->outputBuffers,
amoebaGpu->psWorkArray_3_2->_pDevStream[0], amoebaGpu->psE_FieldPolar->_pDevStream[0] );
// E_Field = E_Field (reciprocal) + E_Field (direct) + self
kReducePmeEField_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
amoebaGpu->paddedNumberOfAtoms*3, amoebaGpu->outputBuffers,
amoebaGpu->psWorkArray_3_1->_pDevStream[0], amoebaGpu->psE_Field->_pDevStream[0] );
LAUNCHERROR("kReducePmeE_Fields2");
}
......@@ -318,6 +373,20 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
#define METHOD_NAME(a, b) a##N2ByWarp##b
#include "kCalculateAmoebaCudaPmeFixedEField.h"
/**---------------------------------------------------------------------------------------
Report whether a number is a nan or infinity
@param number number to test
@return 1 if number is nan or infinity; else return 0
--------------------------------------------------------------------------------------- */
static int isNanOrInfinity( double number ){
return (number != number || number == std::numeric_limits<double>::infinity() || number == -std::numeric_limits<double>::infinity()) ? 1 : 0;
}
/**---------------------------------------------------------------------------------------
Compute fixed electric field using PME
......@@ -335,6 +404,7 @@ static void cudaComputeAmoebaPmeDirectFixedEField( amoebaGpuContext amoebaGpu )
gpuContext gpu = amoebaGpu->gpuContext;
#ifdef AMOEBA_DEBUG
static const char* methodName = "computeCudaAmoebaPmeFixedEField";
if( amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "\n%s\n", methodName ); (void) fflush( amoebaGpu->log );
......@@ -347,21 +417,36 @@ static void cudaComputeAmoebaPmeDirectFixedEField( amoebaGpuContext amoebaGpu )
memset( debugArray->_pSysStream[0], 0, sizeof( float )*4*paddedNumberOfAtoms*paddedNumberOfAtoms);
debugArray->Upload();
(*gpu->psInteractionCount)[0] = gpu->sim.workUnits;
gpu->psInteractionCount->Upload();
// print intermediate results for the targetAtom
unsigned int targetAtom = 0;
#endif
//#define SET_ALPHA_EWALD
//#ifdef SET_ALPHA_EWALD
// amoebaGpu->gpuContext->sim.alphaEwald = 5.4459052e+00f;
// (void) fprintf( amoebaGpu->log, "computeCudaAmoebaPmeFixedEField: forceing alphaEwald=%15.7e\n", amoebaGpu->gpuContext->sim.alphaEwald );
// SetCalculateAmoebaCudaPmeFixedEFieldSim(amoebaGpu);
//#endif
int maxPrint = 3002;
amoebaGpu->psE_Field->Download();
(void) fprintf( amoebaGpu->log, "Recip EFields In\n" );
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( amoebaGpu->log, "%5d ", ii);
int indexOffset = ii*3;
// E_Field
int isNan = isNanOrInfinity( amoebaGpu->psE_Field->_pSysStream[0][indexOffset] );
isNan += isNanOrInfinity( amoebaGpu->psE_Field->_pSysStream[0][indexOffset+1] );
isNan += isNanOrInfinity( amoebaGpu->psE_Field->_pSysStream[0][indexOffset+2] );
(void) fprintf( amoebaGpu->log,"E[%16.9e %16.9e %16.9e] %s\n",
amoebaGpu->psE_Field->_pSysStream[0][indexOffset],
amoebaGpu->psE_Field->_pSysStream[0][indexOffset+1],
amoebaGpu->psE_Field->_pSysStream[0][indexOffset+2], (isNan ? "XXX" :"") );
if( ii == maxPrint && (gpu->natoms - maxPrint) > ii ){
ii = gpu->natoms - maxPrint;
}
}
(void) fflush( amoebaGpu->log );
(void) fprintf( amoebaGpu->log, "Recip EFields End\n" );
#endif
kClearFields_3( amoebaGpu, 2 );
......@@ -413,12 +498,10 @@ static void cudaComputeAmoebaPmeDirectFixedEField( amoebaGpuContext amoebaGpu )
sizeof(FixedFieldParticle), sizeof(FixedFieldParticle)*amoebaGpu->nonbondThreadsPerBlock, amoebaGpu->energyOutputBuffers,
(*gpu->psInteractionCount)[0], gpu->sim.workUnits, gpu->bOutputBufferPerWarp );
(void) fflush( amoebaGpu->log );
/*
(void) fprintf( amoebaGpu->log, "Out WorkArray_3_[1,2] paddedNumberOfAtoms=%d\n", amoebaGpu->paddedNumberOfAtoms, amoebaGpu->outputBuffers );
amoebaGpu->psWorkArray_3_1->Download();
amoebaGpu->psWorkArray_3_2->Download();
amoebaGpu->psE_Field->Download();
amoebaGpu->psE_FieldPolar->Download();
(void) fprintf( amoebaGpu->log, "Out WorkArray_3_[1,2] paddedNumberOfAtoms=%d\n", amoebaGpu->paddedNumberOfAtoms, amoebaGpu->outputBuffers );
int maxPrint = 32;
for( int ii = 0; ii < amoebaGpu->paddedNumberOfAtoms; ii++ ){
(void) fprintf( amoebaGpu->log, "%5d ", ii);
......@@ -444,8 +527,9 @@ static void cudaComputeAmoebaPmeDirectFixedEField( amoebaGpuContext amoebaGpu )
}
}
(void) fflush( amoebaGpu->log );
(void) fprintf( amoebaGpu->log, "EFields End\n" );
*/
amoebaGpu->psE_Field->Download();
amoebaGpu->psE_FieldPolar->Download();
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( amoebaGpu->log, "%5d ", ii);
......@@ -520,6 +604,14 @@ static void cudaComputeAmoebaPmeDirectFixedEField( amoebaGpuContext amoebaGpu )
void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
{
cudaComputeAmoebaPmeDirectFixedEField( amoebaGpu );
// zero field?
unsigned int offset = 3*amoebaGpu->paddedNumberOfAtoms*sizeof( float );
memset( amoebaGpu->psE_Field->_pSysStream[0], 0, offset );
amoebaGpu->psE_Field->Upload();
kCalculateAmoebaPMEFixedMultipoleField( amoebaGpu );
cudaComputeAmoebaPmeDirectFixedEField( amoebaGpu );
}
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ 1a3caae0
......@@ -1985,21 +1985,33 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
// load in parameters
int numberOfMultipoles = atoi( tokens[1].c_str() );
unsigned int tokenIndex = 1;
int numberOfMultipoles = atoi( tokens[tokenIndex++].c_str() );
int usePme = 0;
int bsOrder = 0;
std::vector<int> grid(3,0);
double aewald = 0.0;
double cutoffDistance = 0.0;
double box[3] = { 10.0, 10.0, 10.0 };
std::vector<double> box(3,10.0);
// usePme, aewald, cutoffDistance added w/ Version 1
if( version > 0 ){
usePme = atoi( tokens[2].c_str() );
aewald = atof( tokens[3].c_str() );
cutoffDistance = atof( tokens[4].c_str() );
box[0] = atof( tokens[5].c_str() );
box[1] = atof( tokens[6].c_str() );
box[2] = atof( tokens[7].c_str() );
usePme = atoi( tokens[tokenIndex++].c_str() );
aewald = atof( tokens[tokenIndex++].c_str() );
cutoffDistance = atof( tokens[tokenIndex++].c_str() );
box[0] = atof( tokens[tokenIndex++].c_str() );
box[1] = atof( tokens[tokenIndex++].c_str() );
box[2] = atof( tokens[tokenIndex++].c_str() );
//double electric = atof( tokens[tokenIndex++].c_str() );
tokenIndex++;
bsOrder = atoi( tokens[tokenIndex++].c_str() );
grid[0] = atoi( tokens[tokenIndex++].c_str() );
grid[1] = atoi( tokens[tokenIndex++].c_str() );
grid[2] = atoi( tokens[tokenIndex++].c_str() );
}
if( usePme ){
......@@ -2009,6 +2021,8 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
}
multipoleForce->setCutoffDistance( cutoffDistance );
multipoleForce->setAEwald( aewald );
multipoleForce->setPmeBSplineOrder( bsOrder );
multipoleForce->setPmeGridDimensions( grid );
system.setDefaultPeriodicBoxVectors( Vec3(box[0], 0.0, 0.0), Vec3(0.0, box[1], 0.0), Vec3(0.0, 0.0, box[2]) );
if( log ){
(void) fprintf( log, "%s number of MultipoleParameter terms=%d usePme=%d aewald=%15.7e cutoffDistance=%12.4f\n",
......@@ -3605,15 +3619,19 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
readVec3( filePtr, tokens, forces[AMOEBA_GK_FORCE], &lineCount, field, log );
} else if( field == "AmoebaGkAndCavityForce" ){
readVec3( filePtr, tokens, forces[AMOEBA_GK_CAVITY_FORCE], &lineCount, field, log );
} else if( field == "AmoebaGk_A_ForceAndTorque" ||
field == "AmoebaGk_A_Force" ||
field == "AmoebaSurfaceParameters" ||
field == "AmoebaGk_A_DrB" ||
field == "AmoebaDBorn" ||
field == "AmoebaBorn1Force" ||
field == "AmoebaBornForce" ||
field == "AmoebaGkEdiffForceAndTorque" ||
field == "AmoebaGkEdiffForce" ){
} else if( field == "AmoebaGk_A_ForceAndTorque" ||
field == "AmoebaGk_A_Force" ||
field == "AmoebaSurfaceParameters" ||
field == "AmoebaGk_A_DrB" ||
field == "AmoebaDBorn" ||
field == "AmoebaBorn1Force" ||
field == "AmoebaBornForce" ||
field == "AmoebaGkEdiffForceAndTorque" ||
field == "AmoebaGkEdiffForce" ||
field == "PmeDirectForceAndTorqueOutLoop" ||
field == "PmeDirectForceIncludingMappedTorqueOutLoop" ||
field == "PmeDirectForceTorqueInLoop"
){
std::vector< std::vector<double> > vectorOfDoubleVectors;
readVectorOfDoubleVectors( filePtr, tokens, vectorOfDoubleVectors, &lineCount, field, log );
supplementary[field] = vectorOfDoubleVectors;
......
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