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Commit 82d0ec38 authored by Mark Friedrichs's avatar Mark Friedrichs
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Added code Amoeba Reference platform to handle polarization type = direct

parent 06089c9a
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Showing with 32 additions and 14 deletions
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 82d0ec38
......@@ -445,6 +445,7 @@ double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& contex
ReferenceCalcAmoebaMultipoleForceKernel::ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, System& system) :
CalcAmoebaMultipoleForceKernel(name, platform), system(system) {
}
ReferenceCalcAmoebaMultipoleForceKernel::~ReferenceCalcAmoebaMultipoleForceKernel() {
......@@ -521,6 +522,12 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
if( nonbondedMethod != 0 && nonbondedMethod != 1 ){
throw OpenMMException("AmoebaMultipoleForce nonbonded method not recognized.\n");
}
polarizationType = static_cast<int>(force.getPolarizationType());
if( polarizationType != 0 && polarizationType != 1 ){
throw OpenMMException("AmoebaMultipoleForce polarization type not recognized.\n");
}
}
double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -535,7 +542,7 @@ double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bo
charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes,
multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, forceData);
multipoleAtomCovalentInfo, polarizationType, forceData);
return static_cast<double>(energy);
}
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 82d0ec38
......@@ -386,6 +386,7 @@ public:
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numMultipoles;
int polarizationType;
std::vector<RealOpenMM> charges;
std::vector<RealOpenMM> dipoles;
std::vector<RealOpenMM> quadrupoles;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 82d0ec38
......@@ -945,7 +945,7 @@ void AmoebaReferenceMultipoleForce::updateInducedDipole( MultipoleParticleData&
}
}
void AmoebaReferenceMultipoleForce::calculateNoCutoffInducedDipoles( std::vector<MultipoleParticleData>& particleData ){
void AmoebaReferenceMultipoleForce::calculateNoCutoffInducedDipoles( int polarizationType, std::vector<MultipoleParticleData>& particleData ){
// ---------------------------------------------------------------------------------------
......@@ -984,6 +984,10 @@ void AmoebaReferenceMultipoleForce::calculateNoCutoffInducedDipoles( std::vector
particleData[ii].inducedDipolePolar[2] = particleData[ii].fieldPolar[2];
}
if( polarizationType == 1 ){
return;
}
std::vector<RealOpenMM> field( numParticles*3 );
std::vector<RealOpenMM> fieldPolar( numParticles*3 );
......@@ -1037,7 +1041,8 @@ void AmoebaReferenceMultipoleForce::calculateNoCutoffInducedDipoles( std::vector
return;
}
RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn( const MultipoleParticleData& particleI,
RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn( int polarizationType,
const MultipoleParticleData& particleI,
const MultipoleParticleData& particleK,
RealOpenMM* scalingFactors, std::vector<RealVec>& forces,
std::vector<Vec3>& torque ) const {
......@@ -1075,6 +1080,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn(
RealOpenMM gl[9],gli[7],glip[7];
RealOpenMM sc[10],sci[8],scip[8];
RealOpenMM gf[7],gfi[6],gti[6];
RealOpenMM gfd, fdir[3];
RealOpenMM delta[3];
getDelta( particleI, particleK, delta );
......@@ -1455,8 +1461,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn(
// correction to convert mutual to direct polarization force
/*
if( poltyp .eq. 'DIRECT'){
if( polarizationType == 1 ){
gfd = 0.5 * (rr5*scip[1]*scale3i
- rr7*(scip[2]*sci[3]+sci[2]*scip[3])*scale5i);
temp5 = 0.5 * rr5 * scale5i;
......@@ -1473,7 +1478,6 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn(
ftm2i[1] = ftm2i[1] - fdir[1] + findmp[1];
ftm2i[2] = ftm2i[2] - fdir[2] + findmp[2];
}
*/
// intermediate terms for induced torque on multipoles
......@@ -1925,6 +1929,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
int polarizationType,
std::vector<RealVec>& forces ) const {
// ---------------------------------------------------------------------------------------
......@@ -1977,7 +1982,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v
getScaleFactors( ii, jj, scaleFactors);
}
energy += calculateNoCutoffElectrostaticPairIxn( particleData[ii], particleData[jj], scaleFactors, forces, torques );
energy += calculateNoCutoffElectrostaticPairIxn( polarizationType, particleData[ii], particleData[jj], scaleFactors, forces, torques );
if( jj <= _maxScaleIndex[ii] ){
for( unsigned int kk = 0; kk < LAST_SCALE_TYPE_INDEX; kk++ ){
......@@ -2049,7 +2054,8 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( const
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
std::vector<RealVec>& forces ){
int polarizationType,
std::vector<RealVec>& forces ){
// ---------------------------------------------------------------------------------------
......@@ -2133,11 +2139,11 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( const
// get induced dipoles
calculateNoCutoffInducedDipoles( particleData );
calculateNoCutoffInducedDipoles( polarizationType, particleData );
// check if induced dipoles converged
if( !getMutualInducedDipoleConverged() ){
if( !getMutualInducedDipoleConverged() && polarizationType == 0 ){
std::stringstream message;
message << "Induced dipoles did not converge: ";
message << " iterations=" << getMutualInducedDipoleIterations();
......@@ -2145,7 +2151,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( const
throw OpenMMException(message.str());
}
RealOpenMM energy = calculateNoCutoffElectrostatic( particleData, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, forces );
RealOpenMM energy = calculateNoCutoffElectrostatic( particleData, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, polarizationType, forces );
return energy;
......@@ -2164,6 +2170,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy(
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo,
int polarizationType,
std::vector<RealVec>& forces ){
......@@ -2171,7 +2178,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy(
if( getNonbondedMethod() == NoCutoff || 1 ){
return calculateNoCutoffForceAndEnergy( particlePositions, charges, dipoles, quadrupoles, tholes, dampingFactors,
polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, forces );
polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, polarizationType, forces );
}
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 82d0ec38
......@@ -215,6 +215,7 @@ public:
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
int polarizationType,
std::vector<OpenMM::RealVec>& forces );
......@@ -456,13 +457,13 @@ private:
const std::vector<RealOpenMM>& fieldPolar,
RealOpenMM& epsilonD, RealOpenMM& epsilonP ) const;
void calculateNoCutoffInducedDipoles( std::vector<MultipoleParticleData>& particleData );
void calculateNoCutoffInducedDipoles( int polarizationType, std::vector<MultipoleParticleData>& particleData );
void calculateInducedDipoleField( std::vector<MultipoleParticleData>& particleData,
std::vector<RealOpenMM>& field,
std::vector<RealOpenMM>& fieldPolar ) const;
RealOpenMM calculateNoCutoffElectrostaticPairIxn( const MultipoleParticleData& particleI,
RealOpenMM calculateNoCutoffElectrostaticPairIxn( int polarizationType, const MultipoleParticleData& particleI,
const MultipoleParticleData& particleK,
RealOpenMM* scalingFactors, std::vector<OpenMM::RealVec>& forces, std::vector<Vec3>& torque ) const;
......@@ -495,6 +496,7 @@ private:
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
int polarizationType,
std::vector<OpenMM::RealVec>& forces ) const;
/**---------------------------------------------------------------------------------------
......@@ -526,6 +528,7 @@ private:
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
int polarizationType,
std::vector<OpenMM::RealVec>& forces );
};
......
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