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Commit 1589d425 authored by Peter Eastman's avatar Peter Eastman
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Further cleanup to extrapolated polarization

parent cd03350c
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Showing with 48 additions and 67 deletions
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 1589d425
...@@ -959,75 +959,50 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesBySOR(const vector<Mult ...@@ -959,75 +959,50 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesBySOR(const vector<Mult
void AmoebaReferenceMultipoleForce::convergeInduceDipolesByExtrapolation(const vector<MultipoleParticleData>& particleData, vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleField) { void AmoebaReferenceMultipoleForce::convergeInduceDipolesByExtrapolation(const vector<MultipoleParticleData>& particleData, vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleField) {
_ptDipoleD.clear();
_ptDipoleP.clear();
UpdateInducedDipoleFieldStruct& fieldD = updateInducedDipoleField[0];
UpdateInducedDipoleFieldStruct& fieldP = updateInducedDipoleField[1];
// Start by storing the direct dipoles as PT0 // Start by storing the direct dipoles as PT0
vector<RealVec> thisDipoleD;
vector<RealVec> thisDipoleP;
for (int atom = 0; atom < _numParticles; ++atom) {
thisDipoleD.push_back((*fieldD.inducedDipoles)[atom]);
thisDipoleP.push_back((*fieldP.inducedDipoles)[atom]);
}
_ptDipoleD.push_back(thisDipoleD);
_ptDipoleP.push_back(thisDipoleP);
// Make sure there is some storage available for the field derivatives int numFields = updateInducedDipoleField.size();
std::vector<RealOpenMM> zeros(6, 0.0); for (int i = 0; i < numFields; i++) {
fieldD.inducedDipoleFieldGradient.resize(_numParticles); UpdateInducedDipoleFieldStruct& field = updateInducedDipoleField[i];
fieldP.inducedDipoleFieldGradient.resize(_numParticles); field.extrapolatedDipoles->resize(_maxPTOrder);
(*field.extrapolatedDipoles)[0].resize(_numParticles);
for (int atom = 0; atom < _numParticles; ++atom)
(*field.extrapolatedDipoles)[0][atom] = (*field.inducedDipoles)[atom];
field.inducedDipoleFieldGradient.resize(_numParticles);
}
// Recursively apply alpha.Tau to the µ_(n) components to generate µ_(n+1), and store the result // Recursively apply alpha.Tau to the µ_(n) components to generate µ_(n+1), and store the result
vector<RealOpenMM> zeros(6, 0.0);
for (int order = 1; order < _maxPTOrder; ++order) { for (int order = 1; order < _maxPTOrder; ++order) {
std::fill(fieldD.inducedDipoleFieldGradient.begin(), fieldD.inducedDipoleFieldGradient.end(), zeros); for (int i = 0; i < numFields; i++)
std::fill(fieldP.inducedDipoleFieldGradient.begin(), fieldP.inducedDipoleFieldGradient.end(), zeros); std::fill(updateInducedDipoleField[i].inducedDipoleFieldGradient.begin(), updateInducedDipoleField[i].inducedDipoleFieldGradient.end(), zeros);
calculateInducedDipoleFields(particleData, updateInducedDipoleField); calculateInducedDipoleFields(particleData, updateInducedDipoleField);
vector<RealVec> thisDipoleD; for (int i = 0; i < numFields; i++) {
vector<RealVec> thisDipoleP; UpdateInducedDipoleFieldStruct& field = updateInducedDipoleField[i];
for (int atom = 0; atom < _numParticles; ++atom) { (*field.extrapolatedDipoles)[order].resize(_numParticles);
(*fieldD.inducedDipoles)[atom] = fieldD.inducedDipoleField[atom] * particleData[atom].polarity; for (int atom = 0; atom < _numParticles; ++atom) {
(*fieldP.inducedDipoles)[atom] = fieldP.inducedDipoleField[atom] * particleData[atom].polarity; (*field.inducedDipoles)[atom] = field.inducedDipoleField[atom] * particleData[atom].polarity;
thisDipoleD.push_back((*fieldD.inducedDipoles)[atom]); (*field.extrapolatedDipoles)[order][atom] = (*field.inducedDipoles)[atom];
thisDipoleP.push_back((*fieldP.inducedDipoles)[atom]);
}
_ptDipoleD.push_back(thisDipoleD);
_ptDipoleP.push_back(thisDipoleP);
vector<RealOpenMM> fieldGradD(6*_numParticles, 0.0);
vector<RealOpenMM> fieldGradP(6*_numParticles, 0.0);
for (int atom = 0; atom < _numParticles; ++atom) {
for (int component = 0; component < 6; ++component) {
fieldGradD[6*atom + component] = fieldD.inducedDipoleFieldGradient[atom][component];
fieldGradP[6*atom + component] = fieldP.inducedDipoleFieldGradient[atom][component];
} }
vector<RealOpenMM> fieldGrad(6*_numParticles, 0.0);
for (int atom = 0; atom < _numParticles; ++atom)
for (int component = 0; component < 6; ++component)
fieldGrad[6*atom + component] = field.inducedDipoleFieldGradient[atom][component];
field.extrapolatedDipoleFieldGradient->push_back(fieldGrad);
} }
_ptDipoleFieldGradientD.push_back(fieldGradD);
_ptDipoleFieldGradientP.push_back(fieldGradP);
} }
// Take a linear combination of the µ_(n) components to form the total dipole // Take a linear combination of the µ_(n) components to form the total dipole
RealVec zeroVec(0.0, 0.0, 0.0);
std::fill(_inducedDipole.begin(), _inducedDipole.end(), zeroVec); for (int i = 0; i < numFields; i++) {
std::fill(_inducedDipolePolar.begin(), _inducedDipolePolar.end(), zeroVec); UpdateInducedDipoleFieldStruct& field = updateInducedDipoleField[i];
*field.inducedDipoles = vector<RealVec>(_numParticles, RealVec());
for (int order = 0; order < _maxPTOrder; ++order) { for (int order = 0; order < _maxPTOrder; ++order)
for (int atom = 0; atom < _numParticles; ++atom) { for (int atom = 0; atom < _numParticles; ++atom)
_inducedDipole[atom] += _ptDipoleD[order][atom] * _extPartCoefficients[order]; (*field.inducedDipoles)[atom] += (*field.extrapolatedDipoles)[order][atom] * _extPartCoefficients[order];
_inducedDipolePolar[atom] += _ptDipoleP[order][atom] * _extPartCoefficients[order];
}
}
// Copy the combined dipoles over to compute the field
for (int order = 0; order < _maxPTOrder; ++order) {
for (int atom = 0; atom < _numParticles; ++atom) {
(*fieldD.inducedDipoles)[atom] = _inducedDipole[atom];
(*fieldP.inducedDipoles)[atom] = _inducedDipolePolar[atom];
}
} }
calculateInducedDipoleFields(particleData, updateInducedDipoleField); calculateInducedDipoleFields(particleData, updateInducedDipoleField);
setMutualInducedDipoleConverged(true); setMutualInducedDipoleConverged(true);
} }
...@@ -1158,8 +1133,8 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<Multipo ...@@ -1158,8 +1133,8 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<Multipo
_inducedDipole.resize(_numParticles); _inducedDipole.resize(_numParticles);
_inducedDipolePolar.resize(_numParticles); _inducedDipolePolar.resize(_numParticles);
vector<UpdateInducedDipoleFieldStruct> updateInducedDipoleField; vector<UpdateInducedDipoleFieldStruct> updateInducedDipoleField;
updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_fixedMultipoleField, _inducedDipole)); updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_fixedMultipoleField, _inducedDipole, _ptDipoleD, _ptDipoleFieldGradientD));
updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_fixedMultipoleFieldPolar, _inducedDipolePolar)); updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_fixedMultipoleFieldPolar, _inducedDipolePolar, _ptDipoleP, _ptDipoleFieldGradientP));
initializeInducedDipoles(updateInducedDipoleField); initializeInducedDipoles(updateInducedDipoleField);
...@@ -2156,8 +2131,8 @@ void AmoebaReferenceMultipoleForce::calculateElectrostaticPotential(const vector ...@@ -2156,8 +2131,8 @@ void AmoebaReferenceMultipoleForce::calculateElectrostaticPotential(const vector
} }
} }
AmoebaReferenceMultipoleForce::UpdateInducedDipoleFieldStruct::UpdateInducedDipoleFieldStruct(vector<OpenMM::RealVec>& inputFixed_E_Field, vector<OpenMM::RealVec>& inputInducedDipoles) : AmoebaReferenceMultipoleForce::UpdateInducedDipoleFieldStruct::UpdateInducedDipoleFieldStruct(vector<OpenMM::RealVec>& inputFixed_E_Field, vector<OpenMM::RealVec>& inputInducedDipoles, vector<vector<RealVec> >& extrapolatedDipoles, vector<vector<RealOpenMM> >& extrapolatedDipoleFieldGradient) :
fixedMultipoleField(&inputFixed_E_Field), inducedDipoles(&inputInducedDipoles) { fixedMultipoleField(&inputFixed_E_Field), inducedDipoles(&inputInducedDipoles), extrapolatedDipoles(&extrapolatedDipoles), extrapolatedDipoleFieldGradient(&extrapolatedDipoleFieldGradient) {
inducedDipoleField.resize(fixedMultipoleField->size()); inducedDipoleField.resize(fixedMultipoleField->size());
} }
...@@ -2575,10 +2550,10 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateInducedDipoles(c ...@@ -2575,10 +2550,10 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateInducedDipoles(c
} }
vector<UpdateInducedDipoleFieldStruct> updateInducedDipoleField; vector<UpdateInducedDipoleFieldStruct> updateInducedDipoleField;
updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_fixedMultipoleField, _inducedDipole)); updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_fixedMultipoleField, _inducedDipole, _ptDipoleD, _ptDipoleFieldGradientD));
updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_fixedMultipoleFieldPolar, _inducedDipolePolar)); updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_fixedMultipoleFieldPolar, _inducedDipolePolar, _ptDipoleP, _ptDipoleFieldGradientP));
updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_gkField, _inducedDipoleS)); updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(_gkField, _inducedDipoleS, _ptDipoleDS, _ptDipoleFieldGradientDS));
updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(gkFieldPolar, _inducedDipolePolarS)); updateInducedDipoleField.push_back(UpdateInducedDipoleFieldStruct(gkFieldPolar, _inducedDipolePolarS, _ptDipolePS, _ptDipoleFieldGradientPS));
convergeInduceDipolesByDIIS(particleData, updateInducedDipoleField); convergeInduceDipolesByDIIS(particleData, updateInducedDipoleField);
} }
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 1589d425
...@@ -638,9 +638,11 @@ protected: ...@@ -638,9 +638,11 @@ protected:
* Helper class used in calculating induced dipoles * Helper class used in calculating induced dipoles
*/ */
struct UpdateInducedDipoleFieldStruct { struct UpdateInducedDipoleFieldStruct {
UpdateInducedDipoleFieldStruct(std::vector<OpenMM::RealVec>& inputFixed_E_Field, std::vector<OpenMM::RealVec>& inputInducedDipoles); UpdateInducedDipoleFieldStruct(std::vector<OpenMM::RealVec>& inputFixed_E_Field, std::vector<OpenMM::RealVec>& inputInducedDipoles, std::vector<std::vector<RealVec> >& extrapolatedDipoles, std::vector<std::vector<RealOpenMM> >& extrapolatedDipoleFieldGradient);
std::vector<OpenMM::RealVec>* fixedMultipoleField; std::vector<OpenMM::RealVec>* fixedMultipoleField;
std::vector<OpenMM::RealVec>* inducedDipoles; std::vector<OpenMM::RealVec>* inducedDipoles;
std::vector<std::vector<RealVec> >* extrapolatedDipoles;
std::vector<std::vector<RealOpenMM> >* extrapolatedDipoleFieldGradient;
std::vector<OpenMM::RealVec> inducedDipoleField; std::vector<OpenMM::RealVec> inducedDipoleField;
std::vector<std::vector<RealOpenMM> > inducedDipoleFieldGradient; std::vector<std::vector<RealOpenMM> > inducedDipoleFieldGradient;
}; };
...@@ -666,8 +668,8 @@ protected: ...@@ -666,8 +668,8 @@ protected:
std::vector<RealVec> _fixedMultipoleFieldPolar; std::vector<RealVec> _fixedMultipoleFieldPolar;
std::vector<RealVec> _inducedDipole; std::vector<RealVec> _inducedDipole;
std::vector<RealVec> _inducedDipolePolar; std::vector<RealVec> _inducedDipolePolar;
std::vector< std::vector<RealVec> > _ptDipoleP; std::vector<std::vector<RealVec> > _ptDipoleP;
std::vector< std::vector<RealVec> > _ptDipoleD; std::vector<std::vector<RealVec> > _ptDipoleD;
std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientP; std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientP;
std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientD; std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientD;
...@@ -1223,6 +1225,10 @@ private: ...@@ -1223,6 +1225,10 @@ private:
std::vector<RealVec> _gkField; std::vector<RealVec> _gkField;
std::vector<RealVec> _inducedDipoleS; std::vector<RealVec> _inducedDipoleS;
std::vector<RealVec> _inducedDipolePolarS; std::vector<RealVec> _inducedDipolePolarS;
std::vector<std::vector<RealVec> > _ptDipolePS;
std::vector<std::vector<RealVec> > _ptDipoleDS;
std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientPS;
std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientDS;
int _includeCavityTerm; int _includeCavityTerm;
RealOpenMM _probeRadius; RealOpenMM _probeRadius;
......
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