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Commit 4e480ff6 authored by Mark Friedrichs's avatar Mark Friedrichs
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Added tapering function to AMOEBA vdw function; fixed issue w/ zeroing of vdw forces.

parent cb0b20f5
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Showing with 247 additions and 5 deletions
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaGpu.cpp
View file @ 4e480ff6
...@@ -447,7 +447,12 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log ) ...@@ -447,7 +447,12 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
(void) fprintf( log, " vdwSigmaCombiningRule %d\n", amoebaGpu->vdwSigmaCombiningRule); (void) fprintf( log, " vdwSigmaCombiningRule %d\n", amoebaGpu->vdwSigmaCombiningRule);
(void) fprintf( log, " vdwEpsilonCombiningRule %d\n", amoebaGpu->vdwEpsilonCombiningRule); (void) fprintf( log, " vdwEpsilonCombiningRule %d\n", amoebaGpu->vdwEpsilonCombiningRule);
(void) fprintf( log, " vdwUsePBC %d\n", amoebaGpu->amoebaSim.vdwUsePBC); (void) fprintf( log, " vdwUsePBC %d\n", amoebaGpu->amoebaSim.vdwUsePBC);
(void) fprintf( log, " vdwCutoff %15.7e\n", amoebaGpu->amoebaSim.vdwCutoff);
(void) fprintf( log, " vdwCutoff2 %15.7e\n", amoebaGpu->amoebaSim.vdwCutoff2); (void) fprintf( log, " vdwCutoff2 %15.7e\n", amoebaGpu->amoebaSim.vdwCutoff2);
(void) fprintf( log, " vdwTaperCutoff %15.7e\n", amoebaGpu->amoebaSim.vdwTaperCutoff );
if( amoebaGpu->amoebaSim.vdwCutoff > 0.0f ){
(void) fprintf( log, " vdwTaper %8.3f\n", amoebaGpu->amoebaSim.vdwTaperCutoff/amoebaGpu->amoebaSim.vdwCutoff);
}
totalMemory += gpuPrintCudaStreamFloat2( amoebaGpu->psVdwSigmaEpsilon, log ); totalMemory += gpuPrintCudaStreamFloat2( amoebaGpu->psVdwSigmaEpsilon, log );
totalMemory += gpuPrintCudaStreamInt( amoebaGpu->psAmoebaVdwNonReductionID, log ); totalMemory += gpuPrintCudaStreamInt( amoebaGpu->psAmoebaVdwNonReductionID, log );
totalMemory += gpuPrintCudaStreamInt4( amoebaGpu->psAmoebaVdwReductionID, log ); totalMemory += gpuPrintCudaStreamInt4( amoebaGpu->psAmoebaVdwReductionID, log );
...@@ -2243,6 +2248,84 @@ static int decodeCell( int cellCode, unsigned int* x, unsigned int* y, unsigned ...@@ -2243,6 +2248,84 @@ static int decodeCell( int cellCode, unsigned int* x, unsigned int* y, unsigned
return 0; return 0;
} }
static void getVdwTaper( double r, double vdwTaperCoefficients[6], double* taper, double* dtaper ){
double r2 = r*r;
*taper = r*( r2*(vdwTaperCoefficients[5]*r2 +
vdwTaperCoefficients[3]) +
vdwTaperCoefficients[1]) +
( r2*(vdwTaperCoefficients[4]*r2 +
vdwTaperCoefficients[2]) +
vdwTaperCoefficients[0]);
*dtaper = ( r2*(5.0*vdwTaperCoefficients[5]*r2 + 3.0*vdwTaperCoefficients[3]) + vdwTaperCoefficients[1]) +
r*(4.0*vdwTaperCoefficients[4]*r2 + 2.0*vdwTaperCoefficients[2]);
}
static void lookupVdwTaperLinear( float r, double vdwTaperCut, double delta,
std::vector<float>& taperTable, std::vector<float>& dtaperTable, float* taper, float* dtaper ){
//int index = static_cast<int>(floor( (r - vdwTaperCut)/delta));
int index = static_cast<int>(round( (r - vdwTaperCut)/delta));
if( index > taperTable.size()-1 ){
*taper = *dtaper = 0.0f;
} else {
float slope = (taperTable[index+1] - taperTable[index])/delta;
float intercept = taperTable[index+1] - slope*(delta*static_cast<float>(index+1));
*taper = slope*(r-vdwTaperCut) + intercept;
slope = (dtaperTable[index+1] - dtaperTable[index])/delta;
intercept = dtaperTable[index+1] - slope*(delta*static_cast<float>(index+1));
*dtaper = slope*(r-vdwTaperCut) + intercept;
//fprintf( stderr, "TaperTest: %3d r=%15.7e m=%15.7e b=%15.7e taper=%15.7e %15.7e\n", index, r, slope, intercept, *taper, *dtaper );
}
}
static void lookupVdwTaper( float r, double vdwTaperCut, double delta,
std::vector<float>& taperTable, std::vector<float>& dtaperTable, float* taper, float* dtaper ){
int index = static_cast<int>(round( (r - vdwTaperCut)/delta));
if( index > taperTable.size()-2 ){
*taper = *dtaper = 0.0f;
} else if( index == 0){
*taper = 1.0f;
*dtaper = 0.0f;
} else {
float x = r-vdwTaperCut;
float x0 = delta*static_cast<float>(index-1);
float y0 = taperTable[index-1];
float x1 = x0 + delta;
float y1 = taperTable[index];
float x2 = x1 + delta;
float y2 = taperTable[index+1];
*taper = y0*( (x-x1)*(x-x2)/((x0-x1)*(x0-x2))) +
y1*( (x-x0)*(x-x2)/((x1-x0)*(x1-x2))) +
y2*( (x-x0)*(x-x1)/((x2-x0)*(x2-x1)));
y0 = dtaperTable[index-1];
y1 = dtaperTable[index];
y2 = dtaperTable[index+1];
*dtaper = y0*( (x-x1)*(x-x2)/((x0-x1)*(x0-x2))) +
y1*( (x-x0)*(x-x2)/((x1-x0)*(x1-x2))) +
y2*( (x-x0)*(x-x1)/((x2-x0)*(x2-x1)));
//fprintf( stderr, "TaperTest: %3d r=%15.7e x=%15.7e x0=%15.7e x1=%15.7e x2=%15.7e V=%15.7e %15.7e\n",
// index, r, x, x0, x1, x2, *taper, *dtaper );
}
}
extern "C" extern "C"
void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu, void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
const std::vector<int>& indexIVs, const std::vector<int>& indexIVs,
...@@ -2265,9 +2348,86 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu, ...@@ -2265,9 +2348,86 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
unsigned int particles = sigmas.size(); unsigned int particles = sigmas.size();
amoebaGpu->amoebaSim.vdwUsePBC = usePBC; amoebaGpu->amoebaSim.vdwUsePBC = usePBC;
amoebaGpu->amoebaSim.vdwCutoff = cutoff;
amoebaGpu->amoebaSim.vdwCutoff2 = cutoff*cutoff; amoebaGpu->amoebaSim.vdwCutoff2 = cutoff*cutoff;
double vdwTaper = 0.90f;
if( vdwTaper < 1.0 ){
double vdwTaperCoefficients[6];
double vdwCut = cutoff;
double vdwTaperCut = vdwTaper*cutoff;
amoebaGpu->amoebaSim.vdwTaperCutoff = vdwTaperCut;
amoebaGpu->amoebaSim.vdwTaperCutoff2 = vdwTaperCut*vdwTaperCut;
double vdwCut2 = vdwCut*vdwCut;
double vdwCut3 = vdwCut2*vdwCut;
double vdwCut4 = vdwCut2*vdwCut2;
double vdwCut5 = vdwCut2*vdwCut3;
double vdwCut6 = vdwCut3*vdwCut3;
double vdwCut7 = vdwCut3*vdwCut4;
double vdwTaperCut2 = vdwTaperCut*vdwTaperCut;
double vdwTaperCut3 = vdwTaperCut2*vdwTaperCut;
double vdwTaperCut4 = vdwTaperCut2*vdwTaperCut2;
double vdwTaperCut5 = vdwTaperCut2*vdwTaperCut3;
double vdwTaperCut6 = vdwTaperCut3*vdwTaperCut3;
double vdwTaperCut7 = vdwTaperCut3*vdwTaperCut4;
// get 5th degree multiplicative switching function coefficients;
double denom = 1.0/(vdwCut-vdwTaperCut);
double denom2 = denom*denom;
denom = denom*denom2*denom2;
vdwTaperCoefficients[0] = vdwCut*vdwCut2 * (vdwCut2-5.0*vdwCut*vdwTaperCut+10.0*vdwTaperCut2)*denom;
vdwTaperCoefficients[1] = -30.0*vdwCut2*vdwTaperCut2*denom;
vdwTaperCoefficients[2] = 30.0*(vdwCut2*vdwTaperCut+vdwCut*vdwTaperCut2)*denom;
vdwTaperCoefficients[3] = -10.0*(vdwCut2+4.0*vdwCut*vdwTaperCut+vdwTaperCut2)*denom;
vdwTaperCoefficients[4] = 15.0*(vdwCut+vdwTaperCut)*denom;
vdwTaperCoefficients[5] = -6.0*denom;
// table
int vdwTableSize = VDW_TAPER_TABLE_SIZE;
double tableDelta = vdwCut - vdwTaperCut;
double tableIncrement = tableDelta/static_cast<double>(vdwTableSize-1);
amoebaGpu->amoebaSim.vdwTaperDelta = static_cast<float>(tableIncrement);
std::vector<float> taper;
std::vector<float> dtaper;
for( unsigned int ii = 0; ii < vdwTableSize; ii ++ ){
double r = vdwTaperCut + static_cast<double>(ii)*tableIncrement;
double taperValue, dtaperValue;
getVdwTaper( r, vdwTaperCoefficients, &taperValue, &dtaperValue );
taper.push_back( static_cast<float>(taperValue) );
dtaper.push_back( static_cast<float>(dtaperValue) );
amoebaGpu->amoebaSim.vdwTaperTable[ii] = taperValue;
amoebaGpu->amoebaSim.vdw_dTaperTable[ii] = dtaperValue;
//fprintf( stderr, "Taper: %3d %15.7e %15.7e %15.7e\n", ii, r, taperValue, dtaperValue );
}
amoebaGpu->amoebaSim.vdwTaperTable[VDW_TAPER_TABLE_SIZE] = 0.0f;
amoebaGpu->amoebaSim.vdw_dTaperTable[VDW_TAPER_TABLE_SIZE] = 0.0f;
if( 0 ){
for( unsigned int ii = 0; ii < vdwTableSize; ii ++ ){
float r = vdwTaperCut + (static_cast<double>(ii)+0.5)*tableIncrement;
float taperValue, dtaperValue;
float taperValueL, dtaperValueL;
double taperValueD, dtaperValueD;
lookupVdwTaperLinear( r, vdwTaperCut, tableIncrement, taper, dtaper, &taperValueL, &dtaperValueL );
lookupVdwTaper( r, vdwTaperCut, tableIncrement, taper, dtaper, &taperValue, &dtaperValue );
getVdwTaper( static_cast<double>(r), vdwTaperCoefficients, &taperValueD, &dtaperValueD );
double diffTaperL = fabs( (taperValueL-taperValueD )/taperValueD);
double diffdTaperL= fabs( (dtaperValueL-dtaperValueD )/dtaperValueD);
double diffTaper = fabs( (taperValue-taperValueD )/taperValueD);
double diffdTaper = fabs( (dtaperValue-dtaperValueD )/dtaperValueD);
fprintf( stderr, "TT: %3d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e\n",
ii, r, diffTaper, diffTaperL, taperValueL, taperValue, taperValueD, diffdTaper, diffdTaperL, dtaperValueL, dtaperValue, dtaperValueD );
}
}
}
// set sigma combining rule flag // sigma combining rule flag
if( vdwSigmaCombiningRule.compare( "ARITHMETIC" ) == 0 ){ if( vdwSigmaCombiningRule.compare( "ARITHMETIC" ) == 0 ){
amoebaGpu->vdwSigmaCombiningRule = 1; amoebaGpu->vdwSigmaCombiningRule = 1;
...@@ -2832,6 +2992,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu, ...@@ -2832,6 +2992,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
const float totalMaxWcaDispersionEnergy, const float totalMaxWcaDispersionEnergy,
const float epso, const float epsh, const float rmino, const float rminh, const float epso, const float epsh, const float rmino, const float rminh,
const float awater, const float shctd, const float dispoff ) const float awater, const float shctd, const float dispoff )
{ {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaTypes.h
View file @ 4e480ff6
...@@ -164,7 +164,16 @@ struct cudaAmoebaGmxSimulation { ...@@ -164,7 +164,16 @@ struct cudaAmoebaGmxSimulation {
float* pWorkArray_1_2; float* pWorkArray_1_2;
int vdwUsePBC; int vdwUsePBC;
float vdwCutoff;
float vdwCutoff2; float vdwCutoff2;
float vdwTaperCutoff;
float vdwTaperCutoff2;
float vdwTaperDelta;
#define VDW_TAPER_TABLE_SIZE 100
float vdwTaperTable[VDW_TAPER_TABLE_SIZE+1];
float vdw_dTaperTable[VDW_TAPER_TABLE_SIZE+1];
unsigned int amoebaVdwNonReductions; unsigned int amoebaVdwNonReductions;
int* pAmoebaVdwNonReductionID; int* pAmoebaVdwNonReductionID;
unsigned int* pVdwWorkUnit; unsigned int* pVdwWorkUnit;
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaVdw14_7.cu
View file @ 4e480ff6
...@@ -116,6 +116,67 @@ __device__ void getVdw14_7CombindedSigmaEpsilon_kernel( int sigmaCombiningRule, ...@@ -116,6 +116,67 @@ __device__ void getVdw14_7CombindedSigmaEpsilon_kernel( int sigmaCombiningRule,
} }
// lookup table w/ linear interpolation
__device__ void lookupLinearVdwTaper( float r, float* taper, float* dtaper )
{
if( r > (cAmoebaSim.vdwCutoff - cAmoebaSim.vdwTaperDelta) ){
*taper = *dtaper = 0.0f;
} else {
int index = (int) (floor( (r - cAmoebaSim.vdwTaperCutoff)/cAmoebaSim.vdwTaperDelta));
// int index = (int) round( (r - cAmoebaSim.vdwTaperCutoff)/cAmoebaSim.vdwTaperDelta);
float slope = (cAmoebaSim.vdwTaperTable[index+1] - cAmoebaSim.vdwTaperTable[index])/cAmoebaSim.vdwTaperDelta;
float intercept = cAmoebaSim.vdwTaperTable[index+1] - slope*(cAmoebaSim.vdwTaperDelta*static_cast<float>(index+1));
*taper = slope*(r-cAmoebaSim.vdwTaperCutoff) + intercept;
slope = (cAmoebaSim.vdw_dTaperTable[index+1] - cAmoebaSim.vdw_dTaperTable[index])/cAmoebaSim.vdwTaperDelta;
intercept = cAmoebaSim.vdw_dTaperTable[index+1] - slope*(cAmoebaSim.vdwTaperDelta*static_cast<float>(index+1));
*dtaper = slope*(r-cAmoebaSim.vdwTaperCutoff) + intercept;
}
}
// lookup table w/ quadratic interpolation
__device__ void lookupVdwTaper( float r, float* taper, float* dtaper )
{
if( r > (cAmoebaSim.vdwCutoff - 2.0f*cAmoebaSim.vdwTaperDelta) ){
*taper = *dtaper = 0.0f;
} else {
float x = r - cAmoebaSim.vdwTaperCutoff;
// int index = (int) (floor(x)/cAmoebaSim.vdwTaperDelta);
int index = (int) round(x/cAmoebaSim.vdwTaperDelta);
if( index ){
float x0 = cAmoebaSim.vdwTaperDelta*static_cast<float>(index-1);
float y0 = cAmoebaSim.vdwTaperTable[index-1];
float x1 = x0 + cAmoebaSim.vdwTaperDelta;
float y1 = cAmoebaSim.vdwTaperTable[index];
float x2 = x1 + cAmoebaSim.vdwTaperDelta;
float y2 = cAmoebaSim.vdwTaperTable[index+1];
*taper = y0*( (x-x1)*(x-x2)/((x0-x1)*(x0-x2))) +
y1*( (x-x0)*(x-x2)/((x1-x0)*(x1-x2))) +
y2*( (x-x0)*(x-x1)/((x2-x0)*(x2-x1)));
y0 = cAmoebaSim.vdw_dTaperTable[index-1];
y1 = cAmoebaSim.vdw_dTaperTable[index];
y2 = cAmoebaSim.vdw_dTaperTable[index+1];
*dtaper = y0*( (x-x1)*(x-x2)/((x0-x1)*(x0-x2))) +
y1*( (x-x0)*(x-x2)/((x1-x0)*(x1-x2))) +
y2*( (x-x0)*(x-x1)/((x2-x0)*(x2-x1)));
} else {
*taper = 1.0f;
*dtaper = 0.0f;
}
}
}
__device__ void calculateVdw14_7PairIxn_kernel( float combindedSigma, float combindedEpsilon, __device__ void calculateVdw14_7PairIxn_kernel( float combindedSigma, float combindedEpsilon,
float force[3], float* energy) float force[3], float* energy)
{ {
...@@ -156,10 +217,20 @@ __device__ void calculateVdw14_7PairIxn_kernel( float combindedSigma, float c ...@@ -156,10 +217,20 @@ __device__ void calculateVdw14_7PairIxn_kernel( float combindedSigma, float c
*energy = combindedEpsilon*combindedSigma7*tau7*( (combindedSigma7*gammaHal*rhoInverse) - 2.0f); *energy = combindedEpsilon*combindedSigma7*tau7*( (combindedSigma7*gammaHal*rhoInverse) - 2.0f);
float deltaE = (-7.0f*(dTau*(*energy) + gTau))*rI; float deltaE = (-7.0f*(dTau*(*energy) + gTau))*rI;
if( r > cAmoebaSim.vdwTaperCutoff ){
float taper, dtaper;
lookupVdwTaper( r, &taper, &dtaper );
//lookupLinearVdwTaper( r, &taper, &dtaper );
deltaE = (*energy)*dtaper + deltaE*taper;
*energy *= taper;
}
force[0] *= deltaE; force[0] *= deltaE;
force[1] *= deltaE; force[1] *= deltaE;
force[2] *= deltaE; force[2] *= deltaE;
} }
// perform reduction of force on H's and add to heavy atom partner // perform reduction of force on H's and add to heavy atom partner
...@@ -512,6 +583,7 @@ void kCalculateAmoebaVdw14_7Forces( amoebaGpuContext amoebaGpu, int applyCutoff ...@@ -512,6 +583,7 @@ void kCalculateAmoebaVdw14_7Forces( amoebaGpuContext amoebaGpu, int applyCutoff
threadsPerBlock = std::min(getThreadsPerBlock(amoebaGpu, sizeof(Vdw14_7Particle), gpu->sharedMemoryPerBlock ), maxThreads); threadsPerBlock = std::min(getThreadsPerBlock(amoebaGpu, sizeof(Vdw14_7Particle), gpu->sharedMemoryPerBlock ), maxThreads);
} }
kCalculateAmoebaVdw14_7CopyCoordinates( amoebaGpu, gpu->psPosq4, amoebaGpu->psAmoebaVdwCoordinates ); kCalculateAmoebaVdw14_7CopyCoordinates( amoebaGpu, gpu->psPosq4, amoebaGpu->psAmoebaVdwCoordinates );
kCalculateAmoebaVdw14_7CoordinateReduction( amoebaGpu, amoebaGpu->psAmoebaVdwCoordinates, amoebaGpu->psAmoebaVdwCoordinates ); kCalculateAmoebaVdw14_7CoordinateReduction( amoebaGpu, amoebaGpu->psAmoebaVdwCoordinates, amoebaGpu->psAmoebaVdwCoordinates );
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaVdw14_7.h
View file @ 4e480ff6
...@@ -162,15 +162,15 @@ void METHOD_NAME(kCalculateAmoebaVdw14_7, _kernel)( ...@@ -162,15 +162,15 @@ void METHOD_NAME(kCalculateAmoebaVdw14_7, _kernel)(
} }
// zero shared fields
zeroVdw14_7SharedForce( &(sA[threadIdx.x]) );
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int flags = cSim.pInteractionFlag[pos]; unsigned int flags = cSim.pInteractionFlag[pos];
if (flags == 0) { if (flags == 0) {
} else { } else {
#endif #endif
// zero shared fields
zeroVdw14_7SharedForce( &(sA[threadIdx.x]) );
if( bExclusionFlag ) if( bExclusionFlag )
{ {
......
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