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Commit 49277790 authored by Saurabh Belsare's avatar Saurabh Belsare
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Restructuring the lab frame dipole moments function

parent a8d0f0e1
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Showing with 75 additions and 14 deletions
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 49277790
......@@ -647,20 +647,20 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrix(vector<MultipoleParticle
}
}
void AmoebaReferenceMultipoleForce::applyRotationMatrixPublic(vector<MultipoleParticleData>& particleData,
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector<int>& multipoleAtomZs,
const vector<int>& axisTypes) const
{
for (unsigned int ii = 0; ii < _numParticles; ii++) {
if (multipoleAtomZs[ii] >= 0 && multipoleAtomXs[ii] >= 0) {
applyRotationMatrixToParticle(particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]],
multipoleAtomYs[ii] > -1 ? &particleData[multipoleAtomYs[ii]] : NULL, axisTypes[ii]);
}
}
}
//void AmoebaReferenceMultipoleForce::applyRotationMatrixPublic(vector<MultipoleParticleData>& particleData,
// const vector<int>& multipoleAtomXs,
// const vector<int>& multipoleAtomYs,
// const vector<int>& multipoleAtomZs,
// const vector<int>& axisTypes) const
//{
//
// for (unsigned int ii = 0; ii < _numParticles; ii++) {
// if (multipoleAtomZs[ii] >= 0 && multipoleAtomXs[ii] >= 0) {
// applyRotationMatrixToParticle(particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]],
// multipoleAtomYs[ii] > -1 ? &particleData[multipoleAtomYs[ii]] : NULL, axisTypes[ii]);
// }
// }
//}
void AmoebaReferenceMultipoleForce::getAndScaleInverseRs(RealOpenMM dampI, RealOpenMM dampJ,
RealOpenMM tholeI, RealOpenMM tholeJ,
......@@ -1818,6 +1818,33 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<RealVec
outputInducedDipoles = _inducedDipole;
}
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,
const vector<RealOpenMM>& charges,
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 49277790
......@@ -519,6 +519,39 @@ public:
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputInducedDipoles);
/**
* Calculate particle permanent dipoles rotated in the lab frame.
*
* @param masses particle masses
* @param particlePositions Cartesian coordinates of particles
* @param charges scalar charges for each particle
* @param dipoles molecular frame dipoles for each particle
* @param quadrupoles molecular frame quadrupoles for each particle
* @param tholes Thole factors for each particle
* @param dampingFactors dampling factors for each particle
* @param polarity polarity for each particle
* @param axisTypes axis type (Z-then-X, ...) for each particle
* @param multipoleAtomZs indicies of particle specifying the molecular frame z-axis for each particle
* @param multipoleAtomXs indicies of particle specifying the molecular frame x-axis for each particle
* @param multipoleAtomYs indicies of particle specifying the molecular frame y-axis for each particle
* @param multipoleAtomCovalentInfo covalent info needed to set scaling factors
* @param outputMultipoleMoments output multipole moments
*/
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);
/**
* Calculate system multipole moments.
*
......@@ -669,6 +702,7 @@ protected:
std::vector<RealVec> _fixedMultipoleField;
std::vector<RealVec> _fixedMultipoleFieldPolar;
std::vector<RealVec> _inducedDipole;
std::vector<RealVec> _labFramePermanentDipole;
std::vector<RealVec> _inducedDipolePolar;
int _mutualInducedDipoleConverged;
......
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