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Commit 5f248e63 authored by Saurabh Belsare's avatar Saurabh Belsare
Browse files

Uncommented all the calculate LabFramePermanentDipoles functions

parent 587ba7f2
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Showing with 70 additions and 70 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ 5f248e63
......@@ -316,13 +316,13 @@ public:
* This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.
*/
void setEwaldErrorTolerance(double tol);
/*
/**
* Get the fixed dipole moments of all particles in the global reference frame.
*
* @param context the Context for which to get the fixed dipoles
* @param[out] dipoles the fixed dipole moment of particle i is stored into the i'th element
*/
// void getLabFramePermanentDipoles(Context& context, std::vector<Vec3>& dipoles);
void getLabFramePermanentDipoles(Context& context, std::vector<Vec3>& dipoles);
/**
* Get the induced dipole moments of all particles.
*
......
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ 5f248e63
......@@ -348,7 +348,7 @@ public:
*/
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
// virtual void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
virtual void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
virtual void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
virtual void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h
View file @ 5f248e63
......@@ -81,7 +81,7 @@ public:
* @param covalentDegree covalent degrees for the CovalentEnd lists
*/
static void getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree);
// void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 5f248e63
......@@ -234,9 +234,9 @@ void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dip
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getInducedDipoles(getContextImpl(context), dipoles);
}
//void AmoebaMultipoleForce::getLabFramePermanentDipoles(Context& context, vector<Vec3>& dipoles) {
// dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getLabFramePermanentDipoles(getContextImpl(context), dipoles);
//}
void AmoebaMultipoleForce::getLabFramePermanentDipoles(Context& context, vector<Vec3>& dipoles) {
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getLabFramePermanentDipoles(getContextImpl(context), dipoles);
}
void AmoebaMultipoleForce::getElectrostaticPotential(const std::vector< Vec3 >& inputGrid, Context& context, std::vector< double >& outputElectrostaticPotential) {
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getElectrostaticPotential(getContextImpl(context), inputGrid, outputElectrostaticPotential);
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ 5f248e63
......@@ -183,9 +183,9 @@ void AmoebaMultipoleForceImpl::getCovalentDegree(const AmoebaMultipoleForce& for
return;
}
//void AmoebaMultipoleForceImpl::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
// kernel.getAs<CalcAmoebaMultipoleForceKernel>().getLabFramePermanentDipoles(context, dipoles);
//}
void AmoebaMultipoleForceImpl::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getLabFramePermanentDipoles(context, dipoles);
}
void AmoebaMultipoleForceImpl::getInducedDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getInducedDipoles(context, dipoles);
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 5f248e63
......@@ -710,24 +710,24 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& con
delete amoebaReferenceMultipoleForce;
}
//void ReferenceCalcAmoebaMultipoleForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& outputDipoles) {
// int numParticles = context.getSystem().getNumParticles();
// outputDipoles.resize(numParticles);
//
// // Create an AmoebaReferenceMultipoleForce to do the calculation.
//
// AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
// vector<RealVec>& posData = extractPositions(context);
//
// // Retrieve the permanent dipoles in the lab frame.
//
// vector<RealVec> labFramePermanentDipoles;
// amoebaReferenceMultipoleForce->calculateLabFramePermanentDipoles(posData, charges, dipoles, quadrupoles, tholes,
// dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, multipoleAtomCovalentInfo, labFramePermanentDipoles);
// for (int i = 0; i < numParticles; i++)
// outputDipoles[i] = labFramePermanentDipoles[i];
// delete amoebaReferenceMultipoleForce;
//}
void ReferenceCalcAmoebaMultipoleForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& outputDipoles) {
int numParticles = context.getSystem().getNumParticles();
outputDipoles.resize(numParticles);
// Create an AmoebaReferenceMultipoleForce to do the calculation.
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
// Retrieve the permanent dipoles in the lab frame.
vector<RealVec> labFramePermanentDipoles;
amoebaReferenceMultipoleForce->calculateLabFramePermanentDipoles(posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, multipoleAtomCovalentInfo, labFramePermanentDipoles);
for (int i = 0; i < numParticles; i++)
outputDipoles[i] = labFramePermanentDipoles[i];
delete amoebaReferenceMultipoleForce;
}
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 5f248e63
......@@ -374,13 +374,13 @@ public:
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/*
/**
* Get the fixed dipole moments of all particles in the global reference frame.
*
* @param context the Context for which to get the fixed dipoles
* @param dipoles the fixed dipole moment of particle i is stored into the i'th element
*/
// void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Calculate the electrostatic potential given vector of grid coordinates.
*
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 5f248e63
......@@ -1819,31 +1819,31 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<RealVec
}
//void AmoebaReferenceMultipoleForce::calculateLabFramePermanentDipoles(const vector<RealVec>& particlePositions,
// const vector<RealOpenMM>& charges,
// const vector<RealOpenMM>& dipoles,
// const vector<RealOpenMM>& quadrupoles,
// const vector<RealOpenMM>& tholes,
// const vector<RealOpenMM>& dampingFactors,
// const vector<RealOpenMM>& polarity,
// const vector<int>& axisTypes,
// const vector<int>& multipoleAtomZs,
// const vector<int>& multipoleAtomXs,
// const vector<int>& multipoleAtomYs,
// const vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
// vector<RealVec>& outputRotatedPermanentDipoles) {
// // setup, including calculating permanent dipoles
//
// vector<MultipoleParticleData> particleData;
// setup(particlePositions, charges, dipoles, quadrupoles, tholes,
// dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
// multipoleAtomCovalentInfo, particleData);
// for (int i = 0; i < _numParticles; i++)
// {
// _labFramePermanentDipole[i] = particleData[i].dipole;
// }
// outputRotatedPermanentDipoles = _labFramePermanentDipole;
//}
void AmoebaReferenceMultipoleForce::calculateLabFramePermanentDipoles(const vector<RealVec>& particlePositions,
const vector<RealOpenMM>& charges,
const vector<RealOpenMM>& dipoles,
const vector<RealOpenMM>& quadrupoles,
const vector<RealOpenMM>& tholes,
const vector<RealOpenMM>& dampingFactors,
const vector<RealOpenMM>& polarity,
const vector<int>& axisTypes,
const vector<int>& multipoleAtomZs,
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
vector<RealVec>& outputRotatedPermanentDipoles) {
// setup, including calculating permanent dipoles
vector<MultipoleParticleData> particleData;
setup(particlePositions, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, particleData);
for (int i = 0; i < _numParticles; i++)
{
_labFramePermanentDipole[i] = particleData[i].dipole;
}
outputRotatedPermanentDipoles = _labFramePermanentDipole;
}
void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments(const vector<RealOpenMM>& masses,
const vector<RealVec>& particlePositions,
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 5f248e63
......@@ -538,19 +538,19 @@ public:
* @param outputMultipoleMoments output multipole moments
*/
// void calculateLabFramePermanentDipoles(const vector<RealVec>& particlePositions,
// const vector<RealOpenMM>& charges,
// const vector<RealOpenMM>& dipoles,
// const vector<RealOpenMM>& quadrupoles,
// const vector<RealOpenMM>& tholes,
// const vector<RealOpenMM>& dampingFactors,
// const vector<RealOpenMM>& polarity,
// const vector<int>& axisTypes,
// const vector<int>& multipoleAtomZs,
// const vector<int>& multipoleAtomXs,
// const vector<int>& multipoleAtomYs,
// const vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
// vector<RealVec>& outputRotatedPermanentDipoles);
void calculateLabFramePermanentDipoles(const vector<RealVec>& particlePositions,
const vector<RealOpenMM>& charges,
const vector<RealOpenMM>& dipoles,
const vector<RealOpenMM>& quadrupoles,
const vector<RealOpenMM>& tholes,
const vector<RealOpenMM>& dampingFactors,
const vector<RealOpenMM>& polarity,
const vector<int>& axisTypes,
const vector<int>& multipoleAtomZs,
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
vector<RealVec>& outputRotatedPermanentDipoles);
/**
* Calculate system multipole moments.
......@@ -1013,7 +1013,7 @@ protected:
*
* @param particleData vector of particle positions and parameters (charge, labFrame dipoles, quadrupoles, ...)
*/
// virtual void calculateLabFramePermanentDipoles(const std::vector<MultipoleParticleData>& particleData);
virtual void calculateLabFramePermanentDipoles(const std::vector<MultipoleParticleData>& particleData);
/**
* Setup:
......@@ -1268,7 +1268,7 @@ private:
*
* @param particleData vector of particle positions and parameters (charge, labFrame dipoles, quadrupoles, ...)
*/
// void calculateLabFramePermanentDipoles(const std::vector<MultipoleParticleData>& particleData);
void calculateLabFramePermanentDipoles(const std::vector<MultipoleParticleData>& particleData);
/**
* Calculate fields due induced dipoles at each site.
......
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