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Commit e7c3e2af authored by Mark Friedrichs's avatar Mark Friedrichs
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Removed unused accessors

parent a3bbd5aa
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Showing with 24 additions and 29 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ e7c3e2af
......@@ -893,7 +893,8 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
std::vector<int> minCovalentIndices(numMultipoles);
std::vector<int> minCovalentPolarizationIndices(numMultipoles);
float scalingDistanceCutoff = static_cast<float>(force.getScalingDistanceCutoff());
//float scalingDistanceCutoff = static_cast<float>(force.getScalingDistanceCutoff());
float scalingDistanceCutoff = 50.0f;
std::vector<AmoebaMultipoleForce::CovalentType> covalentList;
covalentList.push_back( AmoebaMultipoleForce::Covalent12 );
......@@ -970,11 +971,6 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
}
int polarizationType = static_cast<int>(force.getPolarizationType());
int iterativeMethod = static_cast<int>(force.getMutualInducedIterationMethod());
if( iterativeMethod != 0 && polarizationType == 0 ){
throw OpenMMException("Iterative method for mutual induced dipoles not recognized.\n");
}
int nonbondedMethod = static_cast<int>(force.getNonbondedMethod());
if( nonbondedMethod != 0 && nonbondedMethod != 1 ){
throw OpenMMException("AmoebaMultipoleForce nonbonded method not recognized.\n");
......@@ -987,13 +983,11 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
gpuSetAmoebaMultipoleParameters(data.getAmoebaGpu(), charges, dipoles, quadrupoles, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
tholes, scalingDistanceCutoff, dampingFactors, polarity,
multipoleAtomCovalentInfo, covalentDegree, minCovalentIndices, minCovalentPolarizationIndices, (maxCovalentRange+2),
static_cast<int>(force.getMutualInducedIterationMethod()),
force.getMutualInducedMaxIterations(),
0, force.getMutualInducedMaxIterations(),
static_cast<float>( force.getMutualInducedTargetEpsilon()),
nonbondedMethod, polarizationType,
static_cast<float>( force.getCutoffDistance()),
static_cast<float>( force.getAEwald()),
static_cast<float>( force.getElectricConstant()) );
static_cast<float>( force.getAEwald()) );
if (nonbondedMethod == AmoebaMultipoleForce::PME) {
double alpha;
int xsize, ysize, zsize;
......@@ -1098,7 +1092,7 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& syst
gpuSetAmoebaGrycukParameters( data.getAmoebaGpu(), static_cast<float>(force.getSoluteDielectric() ),
static_cast<float>( force.getSolventDielectric() ),
static_cast<float>( force.getDielectricOffset() ), radius, scale, charge,
radius, scale, charge,
force.getIncludeCavityTerm(),
static_cast<float>( force.getProbeRadius() ),
static_cast<float>( force.getSurfaceAreaFactor() ) );
......@@ -1107,7 +1101,7 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& syst
gpuSetAmoebaObcParameters( data.getAmoebaGpu(), static_cast<float>(force.getSoluteDielectric() ),
static_cast<float>( force.getSolventDielectric() ),
static_cast<float>( force.getDielectricOffset() ), radius, scale, charge,
radius, scale, charge,
force.getIncludeCavityTerm(),
static_cast<float>( force.getProbeRadius() ),
static_cast<float>( force.getSurfaceAreaFactor() ) );
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaGpu.cpp
View file @ e7c3e2af
......@@ -1699,7 +1699,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector<int>& covalentDegree,
const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
int mutualInducedIterativeMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
int nonbondedMethod, int polarizationType, float cutoffDistance, float alphaEwald, float electricConstant ) {
int nonbondedMethod, int polarizationType, float cutoffDistance, float alphaEwald ) {
// ---------------------------------------------------------------------------------------
......@@ -1743,7 +1743,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
}
amoebaGpu->amoebaSim.sqrtPi = std::sqrt( 3.14159265358f );
amoebaGpu->amoebaSim.electric = electricConstant;
amoebaGpu->amoebaSim.electric = 138.9354558456f;
amoebaGpu->gpuContext->sim.alphaEwald = alphaEwald;
amoebaGpu->gpuContext->sim.nonbondedCutoff = cutoffDistance;
......@@ -2078,14 +2078,14 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
}
extern "C"
void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectric, float solventDielectric, float dielectricOffset,
void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectric, float solventDielectric,
const std::vector<float>& radius, const std::vector<float>& scale, const std::vector<float>& charge,
int includeCavityTerm, float probeRadius, float surfaceAreaFactor )
{
gpuContext gpu = amoebaGpu->gpuContext;
int paddedNumberOfAtoms = gpu->sim.paddedNumberOfAtoms;
gpu->sim.dielectricOffset = dielectricOffset;
gpu->sim.dielectricOffset = 0.009f;
amoebaGpu->includeObcCavityTerm = includeCavityTerm;
gpu->sim.probeRadius = probeRadius;
gpu->sim.surfaceAreaFactor = surfaceAreaFactor;
......@@ -2093,7 +2093,7 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
for (unsigned int i = 0; i < particles; i++)
{
(*gpu->psObcData)[i].x = radius[i] - dielectricOffset;
(*gpu->psObcData)[i].x = radius[i] - gpu->sim.dielectricOffset;
(*gpu->psObcData)[i].y = scale[i] * (*gpu->psObcData)[i].x;
(*gpu->psPosq4)[i].w = charge[i];
}
......@@ -2122,7 +2122,7 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
if( amoebaGpu->log ){
(void) fprintf( amoebaGpu->log,"gpuSetAmoebaObcParameters: cavity=%d dielectricOffset=%15.7e probeRadius=%15.7e surfaceAreaFactor=%15.7e\n",
includeCavityTerm, dielectricOffset, probeRadius, surfaceAreaFactor );
includeCavityTerm, gpu->sim.dielectricOffset, probeRadius, surfaceAreaFactor );
(void) fprintf( amoebaGpu->log," gkc=%12.3f solventDielectric=%15.7e innerDielectric=%15.7e sim.preFactor=%15.7e\n",
amoebaGpu->amoebaSim.gkc, amoebaGpu->amoebaSim.dwater, amoebaGpu->amoebaSim.dielec, gpu->sim.preFactor );
(void) fprintf( amoebaGpu->log," fc=%15.7e fd=%15.7e fq=%15.7e\n",
......@@ -2143,14 +2143,13 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
}
extern "C"
void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu, float innerDielectric, float solventDielectric, float dielectricOffset,
void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu, float innerDielectric, float solventDielectric,
const std::vector<float>& radius, const std::vector<float>& scale, const std::vector<float>& charge,
int includeCavityTerm, float probeRadius, float surfaceAreaFactor )
{
gpuContext gpu = amoebaGpu->gpuContext;
int paddedNumberOfAtoms = gpu->sim.paddedNumberOfAtoms;
gpu->sim.dielectricOffset = dielectricOffset;
amoebaGpu->includeObcCavityTerm = includeCavityTerm;
gpu->sim.probeRadius = probeRadius;
gpu->sim.surfaceAreaFactor = surfaceAreaFactor;
......@@ -2191,8 +2190,8 @@ void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu, float innerDielec
if( amoebaGpu->log ){
unsigned int maxPrint = MAX_PARAMETER_PRINT;
unsigned int maxIndex = particles;
(void) fprintf( amoebaGpu->log,"gpuSetAmoebaGrycukParameters: cavity=%d dielectricOffset=%15.7e probeRadius=%15.7e surfaceAreaFactor=%15.7e\n",
includeCavityTerm, dielectricOffset, probeRadius, surfaceAreaFactor );
(void) fprintf( amoebaGpu->log,"gpuSetAmoebaGrycukParameters: cavity=%d probeRadius=%15.7e surfaceAreaFactor=%15.7e\n",
includeCavityTerm, probeRadius, surfaceAreaFactor );
(void) fprintf( amoebaGpu->log," gkc=%12.3f solventDielectric=%15.7e innerDielectric=%15.7e sim.preFactor=%15.7e\n",
amoebaGpu->amoebaSim.gkc, amoebaGpu->amoebaSim.dwater, amoebaGpu->amoebaSim.dielec, gpu->sim.preFactor );
(void) fprintf( amoebaGpu->log," fc=%15.7e fd=%15.7e fq=%15.7e\n",
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaGpuTypes.h
View file @ e7c3e2af
......@@ -280,16 +280,16 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector<int>& covalentDegree,
const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
int mutualInducedIterationMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
int nonbondedMethod, int polarizationType, float cutoffDistance, float alphaEwald, float electricConstant );
int nonbondedMethod, int polarizationType, float cutoffDistance, float alphaEwald );
extern "C"
void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu , float innerDielectric, float solventDielectric, float dielectricOffset,
void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu , float innerDielectric, float solventDielectric,
const std::vector<float>& radius, const std::vector<float>& scale, const std::vector<float>& charge,
int includeCavityTerm, float probeRadius, float surfaceAreaFactor);
extern "C"
void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu , float innerDielectric, float solventDielectric, float dielectricOffset,
void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu , float innerDielectric, float solventDielectric,
const std::vector<float>& radius, const std::vector<float>& scale, const std::vector<float>& charge,
int includeCavityTerm, float probeRadius, float surfaceAreaFactor);
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ e7c3e2af
......@@ -2216,7 +2216,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
multipoleForce->setNonbondedMethod( AmoebaMultipoleForce::PME );
multipoleForce->setCutoffDistance( cutoffDistance );
multipoleForce->setAEwald( aewald );
multipoleForce->setPmeBSplineOrder( bsOrder );
//multipoleForce->setPmeBSplineOrder( bsOrder );
multipoleForce->setPmeGridDimensions( grid );
system.setDefaultPeriodicBoxVectors( Vec3(box[0], 0.0, 0.0), Vec3(0.0, box[1], 0.0), Vec3(0.0, 0.0, box[2]) );
} else {
......@@ -2334,7 +2334,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
multipoleForce->setAEwald( multipoleForce->getAEwald()/AngstromToNm );
multipoleForce->setCutoffDistance( multipoleForce->getCutoffDistance()*AngstromToNm );
multipoleForce->setScalingDistanceCutoff( multipoleForce->getScalingDistanceCutoff()*AngstromToNm );
//multipoleForce->setScalingDistanceCutoff( multipoleForce->getScalingDistanceCutoff()*AngstromToNm );
Vec3 a,b,c;
system.getDefaultPeriodicBoxVectors( a, b, c);
......@@ -2374,9 +2374,11 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
}
} else {
/*
float electricConstant = static_cast<float>(multipoleForce->getElectricConstant());
electricConstant /= static_cast<float>(AngstromToNm*CalToJoule);
multipoleForce->setElectricConstant( electricConstant );
*/
}
// diagnostics
......@@ -2597,7 +2599,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
// convert to OpenMM units
if( useOpenMMUnits ){
gbsaObcForce->setDielectricOffset( 0.009 );
//gbsaObcForce->setDielectricOffset( 0.009 );
for( int ii = 0; ii < gbsaObcForce->getNumParticles(); ii++ ){
double charge, radius, scalingFactor;
gbsaObcForce->getParticleParameters( ii, charge, radius, scalingFactor );
......@@ -2605,7 +2607,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
gbsaObcForce->setParticleParameters( ii, charge, radius, scalingFactor );
}
} else {
gbsaObcForce->setDielectricOffset( 0.09 );
//gbsaObcForce->setDielectricOffset( 0.09 );
gbsaObcForce->setProbeRadius( 1.4 );
double surfaceAreaFactor = gbsaObcForce->getSurfaceAreaFactor( );
surfaceAreaFactor *= (AngstromToNm*AngstromToNm)/CalToJoule;
......
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