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Commit 2141605b authored by Mark Friedrichs's avatar Mark Friedrichs
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Added missing lambda factor in second OBC force loop of free energy plugin

parent 39cba8fb
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Showing with 59 additions and 33 deletions
plugins/freeEnergy/platforms/cuda/src/kernels/GpuFreeEnergyCudaKernels.h
View file @ 2141605b
......@@ -153,6 +153,9 @@ void SetCalculateObcGbsaSoftcoreBornSumSim( gpuContext gpu );
extern "C"
void SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsSim( float* nonPolarScalingFactors );
extern "C"
void SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim( float* nonPolarScalingFactors );
// this method and kCalculateObcGbsaSoftcoreForces2() are being
// used until changes in OpenMM version are made
extern "C"
......
plugins/freeEnergy/platforms/cuda/src/kernels/GpuObcGbsaSoftcore.cpp
View file @ 2141605b
......@@ -59,6 +59,7 @@ int GpuObcGbsaSoftcore::setNonPolarScalingFactors( unsigned int particleIndex, f
int GpuObcGbsaSoftcore::upload( gpuContext gpu ){
_psNonPolarScalingFactors->Upload();
SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsSim( getGpuNonPolarScalingFactors() );
SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim( getGpuNonPolarScalingFactors() );
return 0;
}
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.cu
View file @ 2141605b
......@@ -232,6 +232,7 @@ __global__ void kReduceObcGbsaSoftcoreBornSum_kernel()
// Now calculate Born radius and OBC term.
sum *= 0.5f * atom.x;
sum *= gbsaSimDev.pNonPolarScalingFactors[pos];
float sum2 = sum * sum;
float sum3 = sum * sum2;
float tanhSum = tanh(cSim.alphaOBC * sum - cSim.betaOBC * sum2 + cSim.gammaOBC * sum3);
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.cu
View file @ 2141605b
......@@ -34,6 +34,7 @@
using namespace std;
#include "gputypes.h"
#include "GpuObcGbsaSoftcore.h"
struct Atom {
float x;
......@@ -41,14 +42,20 @@ struct Atom {
float z;
float r;
float sr;
float npScale;
float fx;
float fy;
float fz;
float fb;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore {
float* pNonPolarScalingFactors;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore gbsaSimObc2;
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationObcGbsaSoftcore gbsaSimDev;
extern "C"
void SetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
......@@ -58,6 +65,17 @@ void SetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
}
extern "C"
void SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim( float* nonPolarScalingFactors )
{
cudaError_t status;
gbsaSimObc2.pNonPolarScalingFactors = nonPolarScalingFactors;
status = cudaMemcpyToSymbol(gbsaSimDev, &gbsaSimObc2, sizeof(cudaFreeEnergySimulationObcGbsaSoftcore));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim");
//(void) fprintf( stderr, "In SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsObc2Sim\n" );
}
void GetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
{
cudaError_t status;
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.h
View file @ 2141605b
......@@ -55,6 +55,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
float4 apos = cSim.pPosq[i];
float2 a = cSim.pObcData[i];
float fb = cSim.pBornForce[i];
float nonPolarScaleDataI = gbsaSimDev.pNonPolarScalingFactors[i];
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
......@@ -72,6 +73,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
sA[threadIdx.x].r = a.x;
sA[threadIdx.x].sr = a.y;
sA[threadIdx.x].fb = fb;
sA[threadIdx.x].npScale = nonPolarScaleDataI;
for (unsigned int j = (tgx+1)&(GRID-1); j != tgx; j = (j+1)&(GRID-1))
{
......@@ -105,6 +107,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
float term = 0.125f *
(1.000f + psA[j].sr * psA[j].sr * r2Inverse) * t3 +
0.250f * t1 * r2Inverse;
term *= psA[j].npScale*nonPolarScaleDataI;
float dE = fb * term;
#if defined USE_PERIODIC
......@@ -151,6 +154,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pObcData[j];
sA[threadIdx.x].fb = cSim.pBornForce[j];
sA[threadIdx.x].npScale = gbsaSimDev.pNonPolarScalingFactors[j];
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
......@@ -208,6 +212,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
float term = 0.125f *
(1.000f + psA[tj].sr * psA[tj].sr * r2Inverse) * t3J +
0.250f * t1J * r2Inverse;
term *= psA[tj].npScale*nonPolarScaleDataI;
float dE = fb * term;
#if defined USE_PERIODIC
......@@ -235,6 +240,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
term = 0.125f *
(1.000f + sr2 * r2Inverse) * t3I +
0.250f * t1I * r2Inverse;
term *= psA[tj].npScale*nonPolarScaleDataI;
dE = psA[tj].fb * term;
float rj = psA[tj].r;
......@@ -306,6 +312,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
float term = 0.125f *
(1.000f + psA[j].sr * psA[j].sr * r2Inverse) * t3J +
0.250f * t1J * r2Inverse;
term *= psA[j].npScale*nonPolarScaleDataI;
float dE = fb * term;
#if defined USE_PERIODIC
......@@ -333,6 +340,7 @@ __global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned
term = 0.125f *
(1.000f + sr2 * r2Inverse) * t3I +
0.250f * t1I * r2Inverse;
term *= psA[j].npScale*nonPolarScaleDataI;
dE = psA[j].fb * term;
float rj = psA[j].r;
......
plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.cpp
View file @ 2141605b
......@@ -241,7 +241,7 @@ void CpuObcSoftcore::computeBornRadii( vector<RealVec>& atomCoordinates, std::v
//FILE* logFile = SimTKOpenMMLog::getSimTKOpenMMLogFile( );
//FILE* logFile = NULL;
//FILE* logFile = fopen( "bR", "w" );
//FILE* logFile = fopen( "bRSoft", "w" );
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
......@@ -290,22 +290,13 @@ void CpuObcSoftcore::computeBornRadii( vector<RealVec>& atomCoordinates, std::v
term += two*( radiusIInverse - l_ij);
}
sum += nonPolarScaleFactors[atomJ]*term;
/*
if( logFile && atomI == 0 ){
(void) fprintf( logFile, "\nRR %d %d r=%.4f rads[%.6f %.6f] scl=[%.3f %.3f] sum=%12.6e %12.6e %12.6e %12.6e",
atomI, atomJ, r, offsetRadiusI, offsetRadiusJ, scaledRadiusFactor[atomI], scaledRadiusFactor[atomJ], 0.5f*sum,
l_ij, u_ij, term );
}
*/
}
}
}
// OBC-specific code (Eqs. 6-8 in paper)
sum *= half*offsetRadiusI;
sum *= nonPolarScaleFactors[atomI]*half*offsetRadiusI;
RealOpenMM sum2 = sum*sum;
RealOpenMM sum3 = sum*sum2;
RealOpenMM tanhSum = TANH( alphaObc*sum - betaObc*sum2 + gammaObc*sum3 );
......@@ -317,7 +308,7 @@ if( logFile && atomI == 0 ){
#if 0
if( logFile && atomI >= 0 ){
(void) fprintf( logFile, "\nRRQ %d sum %12.6e tanhS %12.6e radI %.5f %.5f born %18.10e obc %12.6e",
(void) fprintf( logFile, "RRQ %d sum %12.6e tanhS %12.6e radI %.5f %.5f born %18.10e obc %12.6e\n",
atomI, sum, tanhSum, radiusI, offsetRadiusI, bornRadii[atomI], obcChain[atomI] );
}
#endif
......@@ -327,8 +318,15 @@ if( logFile && atomI >= 0 ){
#if 0
if( logFile ){
(void) fclose( logFile );
logFile = fopen( "bRSoftJ", "w" );
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
(void) fprintf( logFile, "%6d %18.10e %18.10e\n",
atomI, bornRadii[atomI], obcChain[atomI] );
}
(void) fclose( logFile );
}
#endif
}
/**---------------------------------------------------------------------------------------
......@@ -476,6 +474,8 @@ void CpuObcSoftcore::computeBornEnergyForces( vector<RealOpenMM>& bornRadii, vec
computeAceNonPolarForce( obcSoftcoreParameters, bornRadii, &obcEnergy, bornForces );
}
const RealOpenMM* nonPolarScaleFactors = obcSoftcoreParameters->getNonPolarScaleFactors();
// ---------------------------------------------------------------------------------------
// first main loop
......@@ -492,32 +492,28 @@ void CpuObcSoftcore::computeBornEnergyForces( vector<RealOpenMM>& bornRadii, vec
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
if (_obcSoftcoreParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcSoftcoreParameters->getCutoffDistance())
continue;
RealOpenMM r2 = deltaR[ReferenceForce::R2Index];
RealOpenMM deltaX = deltaR[ReferenceForce::XIndex];
RealOpenMM deltaY = deltaR[ReferenceForce::YIndex];
RealOpenMM deltaZ = deltaR[ReferenceForce::ZIndex];
RealOpenMM r2 = deltaR[ReferenceForce::R2Index];
RealOpenMM deltaX = deltaR[ReferenceForce::XIndex];
RealOpenMM deltaY = deltaR[ReferenceForce::YIndex];
RealOpenMM deltaZ = deltaR[ReferenceForce::ZIndex];
// 3 FLOP
RealOpenMM alpha2_ij = bornRadii[atomI]*bornRadii[atomJ];
RealOpenMM D_ij = r2/(four*alpha2_ij);
RealOpenMM alpha2_ij = bornRadii[atomI]*bornRadii[atomJ];
RealOpenMM D_ij = r2/(four*alpha2_ij);
RealOpenMM expTerm = EXP( -D_ij );
RealOpenMM denominator2 = r2 + alpha2_ij*expTerm;
RealOpenMM denominator = SQRT( denominator2 );
// exp + 2 + sqrt FLOP
// charges are assumed to be scaled on input so nonPolarScaleFactor is not needed
RealOpenMM expTerm = EXP( -D_ij );
RealOpenMM denominator2 = r2 + alpha2_ij*expTerm;
RealOpenMM denominator = SQRT( denominator2 );
// 6 FLOP
//RealOpenMM nonPolarScaleFactor = atomI != atomJ ? nonPolarScaleFactors[atomI]*nonPolarScaleFactors[atomJ] : nonPolarScaleFactors[atomI];
RealOpenMM Gpol = (partialChargeI*partialCharges[atomJ])/denominator;
RealOpenMM dGpol_dr = -Gpol*( one - fourth*expTerm )/denominator2;
RealOpenMM Gpol = (partialChargeI*partialCharges[atomJ])/denominator;
// Gpol *= nonPolarScaleFactor;
// 5 FLOP
RealOpenMM dGpol_dalpha2_ij = -half*Gpol*expTerm*( one + D_ij )/denominator2;
RealOpenMM dGpol_dalpha2_ij = -half*Gpol*expTerm*( one + D_ij )/denominator2;
// 11 FLOP
RealOpenMM dGpol_dr = -Gpol*( one - fourth*expTerm )/denominator2;
if( atomI != atomJ ){
......@@ -547,8 +543,6 @@ void CpuObcSoftcore::computeBornEnergyForces( vector<RealOpenMM>& bornRadii, vec
}
}
//obcEnergy *= getEnergyConversionFactor();
// ---------------------------------------------------------------------------------------
// second main loop
......@@ -630,6 +624,7 @@ void CpuObcSoftcore::computeBornEnergyForces( vector<RealOpenMM>& bornRadii, vec
RealOpenMM r2Inverse = rInverse*rInverse;
RealOpenMM t3 = eighth*(one + scaledRadiusJ2*r2Inverse)*(l_ij2 - u_ij2) + fourth*LN( u_ij/l_ij )*r2Inverse;
t3 *= nonPolarScaleFactors[atomI]*nonPolarScaleFactors[atomJ];
RealOpenMM de = bornForces[atomI]*t3*rInverse;
......
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