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Commit 02432980 authored by Mark Friedrichs's avatar Mark Friedrichs
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Obc forces were overwriting input forces instead of being added to input values

parent 248522cb
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Showing with 49 additions and 37 deletions
platforms/reference/src/gbsa/CpuImplicitSolvent.cpp
View file @ 02432980
......@@ -806,6 +806,7 @@ int CpuImplicitSolvent::computeAceNonPolarForce( const ImplicitSolventParameters
const RealOpenMM probeRadius = implicitSolventParameters->getProbeRadius();
const RealOpenMM surfaceAreaFactor = implicitSolventParameters->getPi4Asolv();
const RealOpenMM* atomicRadii = implicitSolventParameters->getAtomicRadii();
int numberOfAtoms = implicitSolventParameters->getNumberOfAtoms();
......
platforms/reference/src/gbsa/CpuObc.cpp
View file @ 02432980
......@@ -316,19 +316,17 @@ if( logFile && atomI == 0 ){
obcChain[atomI] = offsetRadiusI*( alphaObc - two*betaObc*sum + three*gammaObc*sum2 );
obcChain[atomI] = (one - tanhSum*tanhSum)*obcChain[atomI]/radiusI;
/*
if( logFile && atomI >= 0 ){
(void) fprintf( logFile, "\nRRQ %d sum=%12.6e tanhS=%12.6e radI=%.5f %.5f born=%12.6e obc=%12.6e",
/* if( logFile && atomI >= 0 ){
(void) fprintf( logFile, "\nRRQ %d sum %12.6e tanhS %12.6e radI %.5f %.5f born %18.10e obc %12.6e",
atomI, sum, tanhSum, radiusI, offsetRadiusI, bornRadii[atomI], obcChain[atomI] );
} */
}
/*
if( logFile ){
(void) fclose( logFile );
}
*/
*/
return SimTKOpenMMCommon::DefaultReturn;
......@@ -351,7 +349,7 @@ if( logFile && atomI >= 0 ){
--------------------------------------------------------------------------------------- */
int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoordinates,
const RealOpenMM* partialCharges, RealOpenMM** forces ){
const RealOpenMM* partialCharges, RealOpenMM** inputForces ){
// ---------------------------------------------------------------------------------------
......@@ -389,8 +387,13 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
RealOpenMM obcEnergy = zero;
const unsigned int arraySzInBytes = sizeof( RealOpenMM )*numberOfAtoms;
RealOpenMM** forces = (RealOpenMM**) malloc( sizeof( RealOpenMM* )*numberOfAtoms );
RealOpenMM* block = (RealOpenMM*) malloc( sizeof( RealOpenMM )*numberOfAtoms*3 );
memset( block, 0, sizeof( RealOpenMM )*numberOfAtoms*3 );
RealOpenMM* blockPtr = block;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
memset( forces[ii], 0, 3*sizeof( RealOpenMM ) );
forces[ii] = blockPtr;
blockPtr += 3;
}
RealOpenMM* bornForces = getBornForce();
......@@ -474,6 +477,7 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
}
}
//obcEnergy *= getEnergyConversionFactor();
// ---------------------------------------------------------------------------------------
......@@ -596,9 +600,9 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
RealOpenMM conversion = 0.4184;
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
forces[atomI][0] *= conversion;
forces[atomI][1] *= conversion;
forces[atomI][2] *= conversion;
inputForces[atomI][0] += conversion*forces[atomI][0];
inputForces[atomI][1] += conversion*forces[atomI][1];
inputForces[atomI][2] += conversion*forces[atomI][2];
}
setEnergy( obcEnergy*conversion );
......@@ -607,6 +611,9 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
memcpy( bornRadii, bornRadiiTemp, arraySzInBytes );
memcpy( obcChain, obcChainTemp, arraySzInBytes );
free( (char*) block );
free( (char*) forces );
return SimTKOpenMMCommon::DefaultReturn;
}
......@@ -821,18 +828,24 @@ int CpuObc::writeForceLoop( int numberOfAtoms, const IntVector& chunkSizes,
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
std::stringstream line;
line << (atomI+1) << " ";
char buffer[128];
(void) sprintf( buffer, "%4d ", atomI );
line << buffer;
int index = 0;
for( RealOpenMMPtrPtrVectorCI ii = realRealOpenMMVector.begin(); ii != realRealOpenMMVector.end(); ii++ ){
RealOpenMM** forces = *ii;
SimTKOpenMMUtilities::formatRealStringStream( line, forces[atomI], chunks[index++] );
line << " ";
(void) sprintf( buffer, "%11.5f %11.5f %11.5f ", forces[atomI][0], forces[atomI][1], forces[atomI][2] );
line << buffer;
// SimTKOpenMMUtilities::formatRealStringStream( line, forces[atomI], chunks[index++] );
// line << " ";
}
for( RealOpenMMPtrVectorCI ii = realVector.begin(); ii != realVector.end(); ii++ ){
RealOpenMM* array = *ii;
line << array[atomI] << " ";
(void) sprintf( buffer, "%11.5f ", array[atomI] );
line << buffer;
}
lineVector.push_back( line.str() );
......@@ -914,6 +927,7 @@ FILE* logFile = NULL;
memset( forces[ii], 0, 3*sizeof( RealOpenMM ) );
}
RealOpenMM* bornForces = getBornForce();
memset( bornForces, 0, arraySzInBytes );
......@@ -1002,8 +1016,6 @@ FILE* logFile = NULL;
obcEnergy += Gpol;
bornForces[atomI] += dGpol_dalpha2_ij*bornRadii[atomJ];
/*
if( logFile ){
//if( logFile && (atomI == -1 || atomJ == -1) ){
// (void) fprintf( logFile, "\nWWX %d %d F[%.6e %.6e %.6e] bF=[%.6e %.6e] Gpl[%.6e %.6e %.6e] rb[%6.4f %7.4f] rs[%6.4f %7.4f] ",
// atomI, atomJ,
......@@ -1012,17 +1024,15 @@ if( logFile ){
// Gpol,dGpol_dr,dGpol_dalpha2_ij,
// bornRadii[atomI],bornRadii[atomJ],atomicRadii[atomI],atomicRadii[atomJ] );
//
(void) fprintf( logFile, "\nWWX %d %d %.1f r2=%.4f q=%.2f bF=[%.6e %.6e] Gpl[%.6e %.6e %.6e] rb[%.5f %.5f] add[%.6e %.6e] ",
atomI, atomJ, preFactor, r2, partialCharges[atomJ],
bornForces[atomI], bornForces[atomJ],
Gpol,dGpol_dr,dGpol_dalpha2_ij,
bornRadii[atomI], bornRadii[atomJ],
dGpol_dalpha2_ij*bornRadii[atomJ], dGpol_dalpha2_ij*bornRadii[atomI] );
}
*/
// (void) fprintf( logFile, "\nWWX %d %d %.1f r2=%.4f q=%.2f bF=[%.6e %.6e] Gpl[%.6e %.6e %.6e] rb[%.5f %.5f] add[%.6e %.6e] ",
// atomI, atomJ, preFactor, r2, partialCharges[atomJ],
// bornForces[atomI], bornForces[atomJ],
// Gpol,dGpol_dr,dGpol_dalpha2_ij,
// bornRadii[atomI], bornRadii[atomJ],
// dGpol_dalpha2_ij*bornRadii[atomJ], dGpol_dalpha2_ij*bornRadii[atomI] );
//}
}
}
if( logFile ){
......@@ -1033,7 +1043,8 @@ if( logFile ){
}
}
if( 0 ){
if( 1 ){
std::string outputFileName = "Loop1Cpu.txt";
CpuObc::writeForceLoop1( numberOfAtoms, forces, bornForces, outputFileName );
/*
......@@ -1070,7 +1081,7 @@ if( logFile ){
bornForces[atomI] *= bornRadii[atomI]*bornRadii[atomI]*obcChain[atomI];
}
if( 0 ){
if( 1 ){
std::string outputFileName = "PostLoop1Cpu.txt";
......@@ -1081,9 +1092,9 @@ if( logFile ){
realPtrPtrVector.push_back( forces );
RealOpenMMPtrVector realPtrVector;
realPtrVector.push_back( obcChain );
realPtrVector.push_back( bornRadii );
realPtrVector.push_back( bornForces );
realPtrVector.push_back( obcChain );
CpuObc::writeForceLoop( numberOfAtoms, chunkVector, realPtrPtrVector, realPtrVector, outputFileName );
}
......@@ -1211,7 +1222,7 @@ if( logFile && atomI >= 0 ){
}
setEnergy( obcEnergy*conversion );
if( 0 ){
if( 1 ){
std::string outputFileName = "Loop2Cpu.txt";
......
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