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Commit ebdb2ef3 authored by Peter Eastman's avatar Peter Eastman
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Updated to use new API

parent c742d7ff
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Showing with 6 additions and 6 deletions
plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernels.cpp
View file @ ebdb2ef3
...@@ -294,7 +294,7 @@ void CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const System& sy ...@@ -294,7 +294,7 @@ void CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const System& sy
exclusionList[exclusions[i].second].push_back(exclusions[i].first); exclusionList[exclusions[i].second].push_back(exclusions[i].first);
} }
Vec3 boxVectors[3]; Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]); system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
gpuSetPeriodicBoxSize(gpu, static_cast<float>(boxVectors[0][0] ), static_cast<float>(boxVectors[1][1] ), static_cast<float>(boxVectors[2][2] )); gpuSetPeriodicBoxSize(gpu, static_cast<float>(boxVectors[0][0] ), static_cast<float>(boxVectors[1][1] ), static_cast<float>(boxVectors[2][2] ));
CudaNonbondedMethod method = NO_CUTOFF; CudaNonbondedMethod method = NO_CUTOFF;
if (force.getNonbondedMethod() != NonbondedSoftcoreForce::NoCutoff) { if (force.getNonbondedMethod() != NonbondedSoftcoreForce::NoCutoff) {
......
plugins/freeEnergy/platforms/cuda/tests/TstFreeEnergyCudaUsingParameterFile.cpp
View file @ ebdb2ef3
...@@ -3321,9 +3321,9 @@ Integrator* readParameterFile( const std::string& inputParameterFile, MapStringI ...@@ -3321,9 +3321,9 @@ Integrator* readParameterFile( const std::string& inputParameterFile, MapStringI
boxIndex++; boxIndex++;
} }
} }
system.setPeriodicBoxVectors( box[0], box[1], box[2] ); system.setDefaultPeriodicBoxVectors( box[0], box[1], box[2] );
Vec3 a, b, c; Vec3 a, b, c;
system.getPeriodicBoxVectors( a, b, c); system.getDefaultPeriodicBoxVectors( a, b, c);
if( log ){ if( log ){
(void) fprintf( log, "Box [%14.7f %14.7f %14.7f]\n [%14.7f %14.7f %14.7f]\n [%14.7f %14.7f %14.7f]\n", (void) fprintf( log, "Box [%14.7f %14.7f %14.7f]\n [%14.7f %14.7f %14.7f]\n [%14.7f %14.7f %14.7f]\n",
a[0], a[1], a[2], b[0], b[1], b[2], c[0], c[1], c[2] ); a[0], a[1], a[2], b[0], b[1], b[2], c[0], c[1], c[2] );
......
plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernels.cpp
View file @ ebdb2ef3
...@@ -177,7 +177,7 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const Syste ...@@ -177,7 +177,7 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const Syste
//softCoreLJLambda = (RealOpenMM) force.getSoftCoreLJLambda(); //softCoreLJLambda = (RealOpenMM) force.getSoftCoreLJLambda();
Vec3 boxVectors[3]; Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]); system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0]; periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1]; periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2]; periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
...@@ -351,7 +351,7 @@ void ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System& ...@@ -351,7 +351,7 @@ void ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System&
obcParameters->setUseCutoff(static_cast<RealOpenMM>(nonbonded->getCutoffDistance())); obcParameters->setUseCutoff(static_cast<RealOpenMM>(nonbonded->getCutoffDistance()));
if (nonbonded->getNonbondedMethod() == NonbondedForce::CutoffPeriodic) { if (nonbonded->getNonbondedMethod() == NonbondedForce::CutoffPeriodic) {
Vec3 boxVectors[3]; Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]); system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3]; RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0]; periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1]; periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
...@@ -427,7 +427,7 @@ void ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::initialize(const System& sy ...@@ -427,7 +427,7 @@ void ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::initialize(const System& sy
gBVIParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance())); gBVIParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance()));
if (force.getNonbondedMethod() == GBVISoftcoreForce::CutoffPeriodic) { if (force.getNonbondedMethod() == GBVISoftcoreForce::CutoffPeriodic) {
Vec3 boxVectors[3]; Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]); system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3]; RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0]; periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1]; periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
......
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