Skip to content

GitLab

Commit cd03350c authored by Peter Eastman's avatar Peter Eastman
Browse files

Lots of cleanup to extrapolated polarization

parent 51f82c02
Show whitespace changes
Inline Side-by-side
Showing with 133 additions and 107 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ cd03350c
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -72,19 +72,24 @@ public:
enum PolarizationType {
/**
* Mutual polarization
* Full mutually induced polarization. The dipoles are iterated until the converge to the accuracy specified
* by getMutualInducedTargetEpsilon().
*/
Mutual = 0,
/**
* Direct polarization
* Direct polarization approximation. The induced dipoles depend only on the fixed multipoles, not on other
* induced dipoles.
*/
Direct = 1,
/**
* Optimized perturbation theory
* Extrapolated perturbation theory approximation. The dipoles are iterated a few times, and then an analytic
* approximation is used to extrapolate to the fully converged values. Call setExtrapolationCoefficients()
* to set the coefficients used for the extrapolation. The default coefficients used in this release are
* [0, -0.3, 0, 1.3], but be aware that those may change in a future release.
*/
OPT = 2
Extrapolated = 2
};
......@@ -305,19 +310,21 @@ public:
void setMutualInducedTargetEpsilon(double inputMutualInducedTargetEpsilon);
/**
* Set the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the perturbation
* theory algorithm for induced dipoles.
* Set the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the extrapolation
* algorithm for induced dipoles.
*
* @param optCoefficients a vector whose mth entry specifies the coefficient for mu_m
* @param coefficients a vector whose mth entry specifies the coefficient for mu_m. The length of this
* vector determines how many iterations are performed.
*
*/
void setOPTCoefficients(const std::vector<double> &OPTFullCoefficientsIn);
void setExtrapolationCoefficients(const std::vector<double> &coefficients);
/**
* Get the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the perturbation
* theory algorithm for induced dipoles.
* Get the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the extrapolation
* algorithm for induced dipoles. In this release, the default values for the coefficients are
* [0, -0.3, 0, 1.3], but be aware that those may change in a future release.
*/
const std::vector<double>& getOPTCoefficients() const;
const std::vector<double>& getExtrapolationCoefficients() const;
/**
* Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces
......@@ -405,7 +412,7 @@ private:
int pmeBSplineOrder;
std::vector<int> pmeGridDimension;
int mutualInducedMaxIterations;
std::vector<double> OPTFullCoefficients;
std::vector<double> extrapolationCoefficients;
double mutualInducedTargetEpsilon;
double scalingDistanceCutoff;
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ cd03350c
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -43,6 +43,10 @@ AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polari
mutualInducedTargetEpsilon(1.0e-02), scalingDistanceCutoff(100.0), electricConstant(138.9354558456), aewald(0.0) {
pmeGridDimension.resize(3);
pmeGridDimension[0] = pmeGridDimension[1] = pmeGridDimension[2];
extrapolationCoefficients.push_back(0.0);
extrapolationCoefficients.push_back(-0.3);
extrapolationCoefficients.push_back(0.0);
extrapolationCoefficients.push_back(1.3);
}
AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod() const {
......@@ -61,19 +65,14 @@ void AmoebaMultipoleForce::setPolarizationType(AmoebaMultipoleForce::Polarizatio
polarizationType = type;
}
void AmoebaMultipoleForce::setOPTCoefficients(const std::vector<double> &OPTFullCoefficientsIn)
{
size_t maxPTOrder = OPTFullCoefficientsIn.size();
OPTFullCoefficients.resize(maxPTOrder);
std::copy(OPTFullCoefficientsIn.begin(), OPTFullCoefficientsIn.end(), OPTFullCoefficients.begin());
void AmoebaMultipoleForce::setExtrapolationCoefficients(const std::vector<double> &coefficients) {
extrapolationCoefficients = coefficients;
}
const std::vector<double> & AmoebaMultipoleForce::getOPTCoefficients() const
{
return OPTFullCoefficients;
const std::vector<double> & AmoebaMultipoleForce::getExtrapolationCoefficients() const {
return extrapolationCoefficients;
}
double AmoebaMultipoleForce::getCutoffDistance() const {
return cutoffDistance;
}
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ cd03350c
......@@ -565,8 +565,8 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
if (polarizationType == AmoebaMultipoleForce::Mutual) {
mutualInducedMaxIterations = force.getMutualInducedMaxIterations();
mutualInducedTargetEpsilon = force.getMutualInducedTargetEpsilon();
} else if (polarizationType == AmoebaMultipoleForce::OPT) {
OPTFullCoefficients = force.getOPTCoefficients();
} else if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
extrapolationCoefficients = force.getExtrapolationCoefficients();
}
// PME
......@@ -669,9 +669,9 @@ AmoebaReferenceMultipoleForce* ReferenceCalcAmoebaMultipoleForceKernel::setupAmo
amoebaReferenceMultipoleForce->setMaximumMutualInducedDipoleIterations(mutualInducedMaxIterations);
} else if (polarizationType == AmoebaMultipoleForce::Direct) {
amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::Direct);
} else if (polarizationType == AmoebaMultipoleForce::OPT) {
amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::OPT);
amoebaReferenceMultipoleForce->setOPTCoefficients(OPTFullCoefficients);
} else if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::Extrapolated);
amoebaReferenceMultipoleForce->setExtrapolationCoefficients(extrapolationCoefficients);
} else {
throw OpenMMException("Polarization type not recognzied.");
}
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ cd03350c
......@@ -432,7 +432,7 @@ private:
int mutualInducedMaxIterations;
RealOpenMM mutualInducedTargetEpsilon;
std::vector<double> OPTFullCoefficients;
std::vector<double> extrapolationCoefficients;
bool usePme;
RealOpenMM alphaEwald;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ cd03350c
......@@ -161,16 +161,15 @@ RealOpenMM AmoebaReferenceMultipoleForce::getMutualInducedDipoleTargetEpsilon()
return _mutualInducedDipoleTargetEpsilon;
}
void AmoebaReferenceMultipoleForce::setOPTCoefficients(const std::vector<RealOpenMM> &OPTFullCoefficients)
void AmoebaReferenceMultipoleForce::setExtrapolationCoefficients(const std::vector<RealOpenMM> &coefficients)
{
_maxPTOrder = OPTFullCoefficients.size(); // This accounts for the zero-based counting; actual highest order is 1 less
_OPTFullCoefficients.resize(_maxPTOrder);
_OPTPartCoefficients.resize(_maxPTOrder);
std::copy(OPTFullCoefficients.begin(), OPTFullCoefficients.end(), _OPTFullCoefficients.begin());
for(int i = 0; i < _maxPTOrder; ++i){
_OPTPartCoefficients[i] = 0.0;
for(int j = i; j < _maxPTOrder; ++j)
_OPTPartCoefficients[i] += _OPTFullCoefficients[j];
_maxPTOrder = coefficients.size(); // This accounts for the zero-based counting; actual highest order is 1 less
_extrapolationCoefficients = coefficients;
_extPartCoefficients.resize(_maxPTOrder);
for (int i = 0; i < _maxPTOrder; ++i) {
_extPartCoefficients[i] = 0.0;
for (int j = i; j < _maxPTOrder; ++j)
_extPartCoefficients[i] += _extrapolationCoefficients[j];
}
}
......@@ -568,7 +567,7 @@ void AmoebaReferenceMultipoleForce::formQIRotationMatrix(const RealVec& iPositio
{
RealVec vectorZ = (deltaR)/r;
RealVec vectorX(vectorZ);
if ((iPosition[1] != jPosition[1]) || (iPosition[2] != jPosition[2])){
if ((iPosition[1] != jPosition[1]) || (iPosition[2] != jPosition[2])) {
vectorX[0] += 1.0;
}else{
vectorX[1] += 1.0;
......@@ -813,8 +812,8 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const Multipo
RealVec deltaR = particleJ.position - particleI.position;
RealOpenMM r = SQRT(deltaR.dot(deltaR));
vector<RealOpenMM> rrI(2);
// If we're using the OPT algorithm, we need to compute the field gradient, so ask for one more rrI value.
if (getPolarizationType() == AmoebaReferenceMultipoleForce::OPT)
// If we're using the extrapolation algorithm, we need to compute the field gradient, so ask for one more rrI value.
if (getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated)
rrI.push_back(0.0);
getAndScaleInverseRs(particleI.dampingFactor, particleJ.dampingFactor,
......@@ -826,7 +825,7 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const Multipo
for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++) {
calculateInducedDipolePairIxn(particleI.particleIndex, particleJ.particleIndex, rr3, rr5, deltaR,
*updateInducedDipoleFields[ii].inducedDipoles, updateInducedDipoleFields[ii].inducedDipoleField);
if (getPolarizationType() == AmoebaReferenceMultipoleForce::OPT){
if (getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated) {
// Compute and store the field gradient for later use.
RealOpenMM dx = deltaR[0];
RealOpenMM dy = deltaR[1];
......@@ -959,13 +958,7 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesBySOR(const vector<Mult
}
void AmoebaReferenceMultipoleForce::convergeInduceDipolesByOPT(const vector<MultipoleParticleData>& particleData, vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleField) {
if (_OPTFullCoefficients.empty()){
std::stringstream message;
message << "An OPT calcultion was requested, but setOPTCoefficients() was not called.";
throw OpenMMException(message.str());
}
void AmoebaReferenceMultipoleForce::convergeInduceDipolesByExtrapolation(const vector<MultipoleParticleData>& particleData, vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleField) {
_ptDipoleD.clear();
_ptDipoleP.clear();
......@@ -975,7 +968,7 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesByOPT(const vector<Mult
// Start by storing the direct dipoles as PT0
vector<RealVec> thisDipoleD;
vector<RealVec> thisDipoleP;
for(int atom = 0; atom < _numParticles; ++atom){
for (int atom = 0; atom < _numParticles; ++atom) {
thisDipoleD.push_back((*fieldD.inducedDipoles)[atom]);
thisDipoleP.push_back((*fieldP.inducedDipoles)[atom]);
}
......@@ -988,13 +981,13 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesByOPT(const vector<Mult
fieldP.inducedDipoleFieldGradient.resize(_numParticles);
// Recursively apply alpha.Tau to the µ_(n) components to generate µ_(n+1), and store the result
for(int order = 1; order < _maxPTOrder; ++order){
for (int order = 1; order < _maxPTOrder; ++order) {
std::fill(fieldD.inducedDipoleFieldGradient.begin(), fieldD.inducedDipoleFieldGradient.end(), zeros);
std::fill(fieldP.inducedDipoleFieldGradient.begin(), fieldP.inducedDipoleFieldGradient.end(), zeros);
calculateInducedDipoleFields(particleData, updateInducedDipoleField);
vector<RealVec> thisDipoleD;
vector<RealVec> thisDipoleP;
for(int atom = 0; atom < _numParticles; ++atom){
for (int atom = 0; atom < _numParticles; ++atom) {
(*fieldD.inducedDipoles)[atom] = fieldD.inducedDipoleField[atom] * particleData[atom].polarity;
(*fieldP.inducedDipoles)[atom] = fieldP.inducedDipoleField[atom] * particleData[atom].polarity;
thisDipoleD.push_back((*fieldD.inducedDipoles)[atom]);
......@@ -1004,8 +997,8 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesByOPT(const vector<Mult
_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){
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];
}
......@@ -1019,16 +1012,16 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesByOPT(const vector<Mult
std::fill(_inducedDipole.begin(), _inducedDipole.end(), zeroVec);
std::fill(_inducedDipolePolar.begin(), _inducedDipolePolar.end(), zeroVec);
for(int order = 0; order < _maxPTOrder; ++order){
for(int atom = 0; atom < _numParticles; ++atom){
_inducedDipole[atom] += _ptDipoleD[order][atom] * _OPTPartCoefficients[order];
_inducedDipolePolar[atom] += _ptDipoleP[order][atom] * _OPTPartCoefficients[order];
for (int order = 0; order < _maxPTOrder; ++order) {
for (int atom = 0; atom < _numParticles; ++atom) {
_inducedDipole[atom] += _ptDipoleD[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){
for (int order = 0; order < _maxPTOrder; ++order) {
for (int atom = 0; atom < _numParticles; ++atom) {
(*fieldD.inducedDipoles)[atom] = _inducedDipole[atom];
(*fieldP.inducedDipoles)[atom] = _inducedDipolePolar[atom];
}
......@@ -1177,10 +1170,10 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<Multipo
// UpdateInducedDipoleFieldStruct contains induced dipole, fixed multipole fields and fields
// due to other induced dipoles at each site
if (getPolarizationType() == AmoebaReferenceMultipoleForce::Mutual){
if (getPolarizationType() == AmoebaReferenceMultipoleForce::Mutual) {
convergeInduceDipolesByDIIS(particleData, updateInducedDipoleField);
}if (getPolarizationType() == AmoebaReferenceMultipoleForce::OPT){
convergeInduceDipolesByOPT(particleData, updateInducedDipoleField);
}if (getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated) {
convergeInduceDipolesByExtrapolation(particleData, updateInducedDipoleField);
}
}
......@@ -1298,7 +1291,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostaticPairIxn(const Mu
// The rInvVec array is defined such that the ith element is R^-i, with the
// dieleectric constant folded in, to avoid conversions later.
rInvVec[1] = prefac * rInv;
for(int i = 2; i < 7; ++i)
for (int i = 2; i < 7; ++i)
rInvVec[i] = rInvVec[i-1] * rInv;
RealOpenMM mScale = scalingFactors[M_SCALE];
......@@ -1504,7 +1497,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostaticPairIxn(const Mu
RealOpenMM fIZ = qiQI[0]*VijR[0];
RealOpenMM fJZ = qiQJ[0]*VjiR[0];
RealOpenMM EIX = 0.0, EIY = 0.0, EIZ = 0.0, EJX = 0.0, EJY = 0.0, EJZ = 0.0;
for(int i = 1; i < 9; ++i){
for (int i = 1; i < 9; ++i) {
energy += 0.5*(qiQI[i]*Vij[i] + qiQJ[i]*Vji[i]);
fIZ += qiQI[i]*VijR[i];
fJZ += qiQJ[i]*VjiR[i];
......@@ -1532,7 +1525,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostaticPairIxn(const Mu
RealOpenMM iEJY = qiUinpJ[0]*Vjip[1] + qiUindJ[0]*Vjid[1] - qiUinpJ[1]*Vjip[0] - qiUindJ[1]*Vjid[0];
// Add in the induced-induced terms, if needed.
if(getPolarizationType() == AmoebaReferenceMultipoleForce::Mutual){
if(getPolarizationType() == AmoebaReferenceMultipoleForce::Mutual) {
// Uind-Uind terms (m=0)
RealOpenMM eCoef = -4.0*rInvVec[3]*uScale*thole_d0;
RealOpenMM dCoef = 6.0*rInvVec[4]*uScale*dthole_d0;
......@@ -1846,13 +1839,13 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Mu
}
}
}
if (getPolarizationType() == AmoebaReferenceMultipoleForce::OPT){
if (getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated) {
RealOpenMM prefac = (_electric/_dielectric);
for (int i = 0; i < _numParticles; i++) {
// Compute the µ(m) T µ(n) force contributions here
for(int l = 0; l < _maxPTOrder-1; ++l) {
for(int m = 0; m < _maxPTOrder-1-l; ++m) {
RealOpenMM p = _OPTPartCoefficients[l+m+1];
for (int l = 0; l < _maxPTOrder-1; ++l) {
for (int m = 0; m < _maxPTOrder-1-l; ++m) {
RealOpenMM p = _extPartCoefficients[l+m+1];
if(std::fabs(p) < 1e-6) continue;
forces[i][0] += 0.5*p*prefac*(_ptDipoleD[l][i][0]*_ptDipoleFieldGradientP[m][6*i+0]
+ _ptDipoleD[l][i][1]*_ptDipoleFieldGradientP[m][6*i+3]
......@@ -6091,7 +6084,7 @@ void AmoebaReferencePmeMultipoleForce::calculateInducedDipoleFields(const vector
calculateReciprocalSpaceInducedDipoleField(updateInducedDipoleFields);
if(getPolarizationType() == AmoebaReferenceMultipoleForce::OPT){
if(getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated) {
// While we have the reciprocal space (fractional coordinate) field gradient available, add it to the real space
// terms computed above, after transforming to Cartesian coordinates. This allows real and reciprocal space
// dipole response force contributions to be computed together.
......@@ -6109,8 +6102,8 @@ void AmoebaReferencePmeMultipoleForce::calculateInducedDipoleFields(const vector
};
RealOpenMM Exx = 0.0, Eyy = 0.0, Ezz = 0.0, Exy = 0.0, Exz = 0.0, Eyz = 0.0;
for(int k = 0; k < 3; ++k){
for(int l = 0; l < 3; ++l){
for (int k = 0; k < 3; ++k) {
for (int l = 0; l < 3; ++l) {
Exx += fracToCart[0][k] * EmatD[k][l] * fracToCart[0][l];
Eyy += fracToCart[1][k] * EmatD[k][l] * fracToCart[1][l];
Ezz += fracToCart[2][k] * EmatD[k][l] * fracToCart[2][l];
......@@ -6133,8 +6126,8 @@ void AmoebaReferencePmeMultipoleForce::calculateInducedDipoleFields(const vector
};
Exx = 0.0; Eyy = 0.0; Ezz = 0.0; Exy = 0.0; Exz = 0.0; Eyz = 0.0;
for(int k = 0; k < 3; ++k){
for(int l = 0; l < 3; ++l){
for (int k = 0; k < 3; ++k) {
for (int l = 0; l < 3; ++l) {
Exx += fracToCart[0][k] * EmatP[k][l] * fracToCart[0][l];
Eyy += fracToCart[1][k] * EmatP[k][l] * fracToCart[1][l];
Ezz += fracToCart[2][k] * EmatP[k][l] * fracToCart[2][l];
......@@ -6260,7 +6253,7 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons
calculateDirectInducedDipolePairIxn(particleI.particleIndex, particleJ.particleIndex, preFactor1, preFactor2, deltaR,
*updateInducedDipoleFields[ii].inducedDipoles,
updateInducedDipoleFields[ii].inducedDipoleField);
if (getPolarizationType() == AmoebaReferenceMultipoleForce::OPT){
if (getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated) {
// Compute and store the field gradient for later use.
RealOpenMM dx = deltaR[0];
RealOpenMM dy = deltaR[1];
......@@ -6468,13 +6461,13 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
// The rInvVec array is defined such that the ith element is R^-i, with the
// dieleectric constant folded in, to avoid conversions later.
rInvVec[1] = prefac * rInv;
for(int i = 2; i < 7; ++i)
for (int i = 2; i < 7; ++i)
rInvVec[i] = rInvVec[i-1] * rInv;
// The alpharVec array is defined such that the ith element is (alpha R)^i,
// where kappa (alpha in OpenMM parlance) is the Ewald attenuation parameter.
alphaRVec[1] = _alphaEwald * r;
for(int i = 2; i < 8; ++i)
for (int i = 2; i < 8; ++i)
alphaRVec[i] = alphaRVec[i-1] * alphaRVec[1];
RealOpenMM erfAlphaR = erf(alphaRVec[1]);
......@@ -6487,7 +6480,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
int doubleFactorial = 1, facCount = 1;
RealOpenMM tmp = alphaRVec[1];
bVec[1] = -erfAlphaR;
for(int i=2; i < 5; ++i){
for (int i=2; i < 5; ++i) {
bVec[i] = bVec[i-1] + tmp * X / (RealOpenMM)(doubleFactorial);
facCount = facCount + 2;
doubleFactorial = doubleFactorial * facCount;
......@@ -6692,7 +6685,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
RealOpenMM fIZ = qiQI[0]*VijR[0];
RealOpenMM fJZ = qiQJ[0]*VjiR[0];
RealOpenMM EIX = 0.0, EIY = 0.0, EIZ = 0.0, EJX = 0.0, EJY = 0.0, EJZ = 0.0;
for(int i = 1; i < 9; ++i){
for (int i = 1; i < 9; ++i) {
energy += 0.5*(qiQI[i]*Vij[i] + qiQJ[i]*Vji[i]);
fIZ += qiQI[i]*VijR[i];
fJZ += qiQJ[i]*VjiR[i];
......@@ -6801,14 +6794,14 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculateElectrostatic(const vector
energy += calculatePmeSelfEnergy(particleData);
// Now that both the direct and reciprocal space contributions have been added, we can compute the dipole
// response contributions to the forces, if we're using the OPT polarization algorithm.
if (getPolarizationType() == AmoebaReferenceMultipoleForce::OPT){
// response contributions to the forces, if we're using the extrapolated polarization algorithm.
if (getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated) {
RealOpenMM prefac = (_electric/_dielectric);
for (int i = 0; i < _numParticles; i++) {
// Compute the µ(m) T µ(n) force contributions here
for(int l = 0; l < _maxPTOrder-1; ++l) {
for(int m = 0; m < _maxPTOrder-1-l; ++m) {
RealOpenMM p = _OPTPartCoefficients[l+m+1];
for (int l = 0; l < _maxPTOrder-1; ++l) {
for (int m = 0; m < _maxPTOrder-1-l; ++m) {
RealOpenMM p = _extPartCoefficients[l+m+1];
if(std::fabs(p) < 1e-6) continue;
forces[i][0] += 0.5*p*prefac*(_ptDipoleD[l][i][0]*_ptDipoleFieldGradientP[m][6*i+0]
+ _ptDipoleD[l][i][1]*_ptDipoleFieldGradientP[m][6*i+3]
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ cd03350c
......@@ -351,9 +351,9 @@ public:
Direct = 1,
/**
* Optimized perturbation theory
* Extrapolated perturbation theory
*/
OPT = 2
Extrapolated = 2
};
/**
......@@ -428,13 +428,13 @@ public:
RealOpenMM getMutualInducedDipoleEpsilon() const;
/**
* Set the coefficients for the µ_0, µ_1, µ_2, µ_n terms in the pertubation
* Set the coefficients for the µ_0, µ_1, µ_2, µ_n terms in the extrapolation
* theory algorithm for induced dipoles
*
* @param optCoefficients a vector whose mth entry specifies the coefficient for µ_m
*
*/
void setOPTCoefficients(const std::vector<RealOpenMM> &OPTFullCoefficients);
void setExtrapolationCoefficients(const std::vector<RealOpenMM> &coefficients);
/**
* Set the target epsilon for converging mutual induced dipoles.
......@@ -677,8 +677,8 @@ protected:
int _mutualInducedDipoleIterations;
int _maximumMutualInducedDipoleIterations;
int _maxPTOrder;
std::vector<RealOpenMM> _OPTFullCoefficients;
std::vector<RealOpenMM> _OPTPartCoefficients;
std::vector<RealOpenMM> _extrapolationCoefficients;
std::vector<RealOpenMM> _extPartCoefficients;
RealOpenMM _mutualInducedDipoleEpsilon;
RealOpenMM _mutualInducedDipoleTargetEpsilon;
RealOpenMM _polarSOR;
......@@ -945,12 +945,12 @@ protected:
virtual void calculateInducedDipoleFields(const std::vector<MultipoleParticleData>& particleData,
std::vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleFields);
/**
* Calculated induced dipoles using Optimized Perturbation Theory.
* Calculated induced dipoles using extrapolated perturbation theory.
*
* @param particleData vector of particle positions and parameters (charge, labFrame dipoles, quadrupoles, ...)
* @param updateInducedDipoleFields vector of UpdateInducedDipoleFieldStruct containing input induced dipoles and output fields
*/
void convergeInduceDipolesByOPT(const std::vector<MultipoleParticleData>& particleData,
void convergeInduceDipolesByExtrapolation(const std::vector<MultipoleParticleData>& particleData,
std::vector<UpdateInducedDipoleFieldStruct>& calculateInducedDipoleField);
/**
* Converge induced dipoles.
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPTPolarization.cpp
View file @ cd03350c
......@@ -319,13 +319,13 @@ static void testWaterDimerExPTPolarizationTriclinicPME() {
Vec3(0.2, 2.0, 0.0),
Vec3(0.1, 0.5, 2.0));
amoebaMultipoleForce->setNonbondedMethod(AmoebaMultipoleForce::PME);
amoebaMultipoleForce->setPolarizationType(AmoebaMultipoleForce::OPT);
amoebaMultipoleForce->setPolarizationType(AmoebaMultipoleForce::Extrapolated);
std::vector<double> coefs;
coefs.push_back(0.0); // The mu_0 coefficient
coefs.push_back(-0.3); // The mu_1 coefficient
coefs.push_back(0.0); // The mu_2 coefficient
coefs.push_back(1.3); // The mu_3 coefficient
amoebaMultipoleForce->setOPTCoefficients(coefs);
amoebaMultipoleForce->setExtrapolationCoefficients(coefs);
amoebaMultipoleForce->setCutoffDistance(9.0*OpenMM::NmPerAngstrom);
amoebaMultipoleForce->setAEwald(4);
amoebaMultipoleForce->setEwaldErrorTolerance(1.0e-06);
......@@ -368,13 +368,13 @@ static void testWaterDimerExPTPolarizationTriclinicPMENoPolGroups() {
Vec3(0.2, 2.0, 0.0),
Vec3(0.1, 0.5, 2.0));
amoebaMultipoleForce->setNonbondedMethod(AmoebaMultipoleForce::PME);
amoebaMultipoleForce->setPolarizationType(AmoebaMultipoleForce::OPT);
amoebaMultipoleForce->setPolarizationType(AmoebaMultipoleForce::Extrapolated);
std::vector<double> coefs;
coefs.push_back(0.0); // The mu_0 coefficient
coefs.push_back(-0.3); // The mu_1 coefficient
coefs.push_back(0.0); // The mu_2 coefficient
coefs.push_back(1.3); // The mu_3 coefficient
amoebaMultipoleForce->setOPTCoefficients(coefs);
amoebaMultipoleForce->setExtrapolationCoefficients(coefs);
amoebaMultipoleForce->setCutoffDistance(9.0*OpenMM::NmPerAngstrom);
amoebaMultipoleForce->setAEwald(4);
amoebaMultipoleForce->setEwaldErrorTolerance(1.0e-06);
......@@ -415,13 +415,13 @@ static void testWaterDimerExPTPolarizationNoCutoff() {
vector<Vec3> coords = setupWaterDimer(system, amoebaMultipoleForce, true);
amoebaMultipoleForce->setNonbondedMethod(AmoebaMultipoleForce::NoCutoff);
amoebaMultipoleForce->setPolarizationType(AmoebaMultipoleForce::OPT);
amoebaMultipoleForce->setPolarizationType(AmoebaMultipoleForce::Extrapolated);
std::vector<double> coefs;
coefs.push_back(0.0); // The mu_0 coefficient
coefs.push_back(-0.3); // The mu_1 coefficient
coefs.push_back(0.0); // The mu_2 coefficient
coefs.push_back(1.3); // The mu_3 coefficient
amoebaMultipoleForce->setOPTCoefficients(coefs);
amoebaMultipoleForce->setExtrapolationCoefficients(coefs);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
......@@ -456,13 +456,13 @@ static void testWaterDimerExPTPolarizationNoCutoffNoPolGroups() {
vector<Vec3> coords = setupWaterDimer(system, amoebaMultipoleForce, false);
amoebaMultipoleForce->setNonbondedMethod(AmoebaMultipoleForce::NoCutoff);
amoebaMultipoleForce->setPolarizationType(AmoebaMultipoleForce::OPT);
amoebaMultipoleForce->setPolarizationType(AmoebaMultipoleForce::Extrapolated);
std::vector<double> coefs;
coefs.push_back(0.0); // The mu_0 coefficient
coefs.push_back(-0.3); // The mu_1 coefficient
coefs.push_back(0.0); // The mu_2 coefficient
coefs.push_back(1.3); // The mu_3 coefficient
amoebaMultipoleForce->setOPTCoefficients(coefs);
amoebaMultipoleForce->setExtrapolationCoefficients(coefs);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
......@@ -492,7 +492,6 @@ static void testWaterDimerExPTPolarizationNoCutoffNoPolGroups() {
int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestReferenceAmoebaPTPolarization running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
/*
......
plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp
View file @ cd03350c
......@@ -68,7 +68,7 @@ void loadCovalentMap(const SerializationNode& map, std::vector< int >& covalentM
}
void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
node.setIntProperty("version", 3);
const AmoebaMultipoleForce& force = *reinterpret_cast<const AmoebaMultipoleForce*>(object);
node.setIntProperty("nonbondedMethod", force.getNonbondedMethod());
......@@ -88,6 +88,14 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
SerializationNode& gridDimensionsNode = node.createChildNode("MultipoleParticleGridDimension");
gridDimensionsNode.setIntProperty("d0", gridDimensions[0]).setIntProperty("d1", gridDimensions[1]).setIntProperty("d2", gridDimensions[2]);
SerializationNode& coefficients = node.createChildNode("ExtrapolationCoefficients");
vector<double> coeff = force.getExtrapolationCoefficients();
for (int i = 0; i < coeff.size(); i++) {
stringstream key;
key << "c" << i;
coefficients.setDoubleProperty(key.str(), coeff[i]);
}
std::vector<std::string> covalentTypes;
getCovalentTypes(covalentTypes);
......@@ -124,16 +132,16 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
}
void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") > 2)
int version = node.getIntProperty("version");
if (version < 0 || version > 3)
throw OpenMMException("Unsupported version number");
AmoebaMultipoleForce* force = new AmoebaMultipoleForce();
try {
force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
if (node.getIntProperty("version") == 2) {
if (version >= 2)
force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));
}
//force->setPmeBSplineOrder(node.getIntProperty("pmeBSplineOrder"));
//force->setMutualInducedIterationMethod(static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty("mutualInducedIterationMethod")));
force->setMutualInducedMaxIterations(node.getIntProperty("mutualInducedMaxIterations"));
......@@ -151,6 +159,18 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d2"));
force->setPmeGridDimensions(gridDimensions);
if (version >= 3) {
const SerializationNode& coefficients = node.getChildNode("ExtrapolationCoefficients");
vector<double> coeff;
for (int i = 0; ; i++) {
stringstream key;
key << "c" << i;
if (coefficients.getProperties().find(key.str()) == coefficients.getProperties().end())
break;
coeff.push_back(coefficients.getDoubleProperty(key.str()));
}
force->setExtrapolationCoefficients(coeff);
}
std::vector<std::string> covalentTypes;
getCovalentTypes(covalentTypes);
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp
View file @ cd03350c
......@@ -75,6 +75,12 @@ void testSerialization() {
//force1.setElectricConstant(138.93);
force1.setEwaldErrorTolerance(1.0e-05);
vector<double> coeff;
coeff.push_back(0.0);
coeff.push_back(-0.1);
coeff.push_back(1.1);
force1.setExtrapolationCoefficients(coeff);
std::vector<std::string> covalentTypes;
getCovalentTypes(covalentTypes);
......@@ -125,6 +131,8 @@ void testSerialization() {
ASSERT_EQUAL(gridDimension1[jj], gridDimension2[jj]);
}
ASSERT_EQUAL_CONTAINERS(force1.getExtrapolationCoefficients(), force2.getExtrapolationCoefficients());
ASSERT_EQUAL(force1.getNumMultipoles(), force2.getNumMultipoles());
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumMultipoles()); ii++) {
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment