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Commit b292cfcd authored by Mark Friedrichs's avatar Mark Friedrichs
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One of loops in reference GBSA/OBC code was missing tests for periodic bndy conditions, cutoff, ...

parent e1656dcb
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Showing with 26 additions and 13 deletions
platforms/reference/src/gbsa/CpuObc.cpp
View file @ b292cfcd
...@@ -527,12 +527,18 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo ...@@ -527,12 +527,18 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
if( atomJ != atomI ){ if( atomJ != atomI ){
RealOpenMM deltaX = atomCoordinates[atomJ][0] - atomCoordinates[atomI][0]; RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
RealOpenMM deltaY = atomCoordinates[atomJ][1] - atomCoordinates[atomI][1]; if (_obcParameters->getPeriodic())
RealOpenMM deltaZ = atomCoordinates[atomJ][2] - atomCoordinates[atomI][2]; ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance())
continue;
RealOpenMM r2 = deltaX*deltaX + deltaY*deltaY + deltaZ*deltaZ; RealOpenMM deltaX = deltaR[ReferenceForce::XIndex];
RealOpenMM r = SQRT( r2 ); RealOpenMM deltaY = deltaR[ReferenceForce::YIndex];
RealOpenMM deltaZ = deltaR[ReferenceForce::ZIndex];
RealOpenMM r = deltaR[ReferenceForce::RIndex];
// radius w/ dielectric offset applied // radius w/ dielectric offset applied
...@@ -969,6 +975,7 @@ FILE* logFile = NULL; ...@@ -969,6 +975,7 @@ FILE* logFile = NULL;
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR ); ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance()) if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance())
continue; continue;
RealOpenMM r2 = deltaR[ReferenceForce::R2Index]; RealOpenMM r2 = deltaR[ReferenceForce::R2Index];
RealOpenMM deltaX = deltaR[ReferenceForce::XIndex]; RealOpenMM deltaX = deltaR[ReferenceForce::XIndex];
RealOpenMM deltaY = deltaR[ReferenceForce::YIndex]; RealOpenMM deltaY = deltaR[ReferenceForce::YIndex];
...@@ -1131,12 +1138,18 @@ for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){ ...@@ -1131,12 +1138,18 @@ for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
if( atomJ != atomI ){ if( atomJ != atomI ){
RealOpenMM deltaX = atomCoordinates[atomJ][0] - atomCoordinates[atomI][0]; RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
RealOpenMM deltaY = atomCoordinates[atomJ][1] - atomCoordinates[atomI][1]; if (_obcParameters->getPeriodic())
RealOpenMM deltaZ = atomCoordinates[atomJ][2] - atomCoordinates[atomI][2]; ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance())
continue;
RealOpenMM r2 = deltaX*deltaX + deltaY*deltaY + deltaZ*deltaZ; RealOpenMM deltaX = deltaR[ReferenceForce::XIndex];
RealOpenMM r = SQRT( r2 ); RealOpenMM deltaY = deltaR[ReferenceForce::YIndex];
RealOpenMM deltaZ = deltaR[ReferenceForce::ZIndex];
RealOpenMM r = deltaR[ReferenceForce::RIndex];
// radius w/ dielectric offset applied // radius w/ dielectric offset applied
......
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