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Commit 454eda76 authored by Saurabh Belsare's avatar Saurabh Belsare
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Added required headers. Still need to actually implement the functions

parent ad966d1c
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plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ 454eda76
......@@ -316,15 +316,6 @@ public:
* This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.
*/
void setEwaldErrorTolerance(double tol);
/**
* Get the induced dipole moments of all particles.
*
* @param context the Context for which to get the induced dipoles
* @param[out] dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(Context& context, std::vector<Vec3>& dipoles);
/**
* Get the fixed dipole moments of all particles in the global reference frame.
*
......@@ -332,6 +323,13 @@ public:
* @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);
/**
* Get the induced dipole moments of all particles.
*
* @param context the Context for which to get the induced dipoles
* @param[out] dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(Context& context, std::vector<Vec3>& dipoles);
/**
* Get the electrostatic potential.
......
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ 454eda76
......@@ -59,7 +59,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the AmoebaBondForce this kernel will be used for
*/
......@@ -99,7 +99,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the AmoebaAngleForce this kernel will be used for
*/
......@@ -139,7 +139,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the AmoebaInPlaneAngleForce this kernel will be used for
*/
......@@ -179,7 +179,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the PiTorsionForce this kernel will be used for
*/
......@@ -219,7 +219,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the StretchBendForce this kernel will be used for
*/
......@@ -259,7 +259,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the OutOfPlaneBendForce this kernel will be used for
*/
......@@ -299,7 +299,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the TorsionTorsionForce this kernel will be used for
*/
......@@ -332,7 +332,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the MultipoleForce this kernel will be used for
*/
......@@ -348,6 +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 getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
virtual void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
......@@ -364,7 +365,7 @@ public:
/**
* Get the parameters being used for PME.
*
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
......@@ -389,7 +390,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the GBSAOBCForce this kernel will be used for
*/
......@@ -429,7 +430,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the GBSAOBCForce this kernel will be used for
*/
......@@ -469,7 +470,7 @@ public:
/**
* Initialize the kernel.
*
*
* @param system the System this kernel will be applied to
* @param force the GBSAOBCForce this kernel will be used for
*/
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h
View file @ 454eda76
......@@ -64,7 +64,7 @@ public:
/**
* Get the CovalentMap for an atom
*
*
* @param force AmoebaMultipoleForce force reference
* @param index the index of the atom for which to set parameters
* @param minCovalentIndex minimum covalent index
......@@ -76,15 +76,13 @@ public:
/**
* Get the covalent degree for the CovalentEnd lists
*
*
* @param force AmoebaMultipoleForce force reference
* @param covalentDegree covalent degrees for the CovalentEnd lists
*/
static void getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree);
void getInducedDipoles(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,
std::vector< double >& outputElectrostaticPotential);
......@@ -92,7 +90,7 @@ public:
void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments);
void updateParametersInContext(ContextImpl& context);
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
private:
const AmoebaMultipoleForce& owner;
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 454eda76
......@@ -69,19 +69,19 @@ void AmoebaMultipoleForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
double AmoebaMultipoleForce::getAEwald() const {
return aewald;
}
void AmoebaMultipoleForce::setAEwald(double inputAewald) {
aewald = inputAewald;
}
int AmoebaMultipoleForce::getPmeBSplineOrder() const {
return pmeBSplineOrder;
}
void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const {
double AmoebaMultipoleForce::getAEwald() const {
return aewald;
}
void AmoebaMultipoleForce::setAEwald(double inputAewald) {
aewald = inputAewald;
}
int AmoebaMultipoleForce::getPmeBSplineOrder() const {
return pmeBSplineOrder;
}
void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const {
if (gridDimension.size() < 3) {
gridDimension.resize(3);
}
......@@ -93,15 +93,15 @@ void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension)
gridDimension[0] = gridDimension[1] = gridDimension[2] = 0;
}
return;
}
}
void AmoebaMultipoleForce::setPmeGridDimensions(const std::vector<int>& gridDimension) {
pmeGridDimension.resize(3);
pmeGridDimension[0] = gridDimension[0];
pmeGridDimension[1] = gridDimension[1];
pmeGridDimension[2] = gridDimension[2];
return;
}
}
void AmoebaMultipoleForce::getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
dynamic_cast<const AmoebaMultipoleForceImpl&>(getImplInContext(context)).getPMEParameters(alpha, nx, ny, nz);
......@@ -131,13 +131,13 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) {
ewaldErrorTol = tol;
}
int AmoebaMultipoleForce::addMultipole(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
int AmoebaMultipoleForce::addMultipole(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
multipoles.push_back(MultipoleInfo(charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity));
return multipoles.size()-1;
}
void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity) const {
charge = multipoles[index].charge;
......@@ -167,7 +167,7 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std
polarity = multipoles[index].polarity;
}
void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole,
void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole,
int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
multipoles[index].charge = charge;
......@@ -230,8 +230,12 @@ void AmoebaMultipoleForce::getCovalentMaps(int index, std::vector< std::vector<i
}
}
void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dipoles) {
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) {
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ 454eda76
......@@ -61,7 +61,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
double cutoff = owner.getCutoffDistance();
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("AmoebaMultipoleForce: The cutoff distance cannot be greater than half the periodic box size.");
}
}
double quadrupoleValidationTolerance = 1.0e-05;
for (int ii = 0; ii < system.getNumParticles(); ii++) {
......@@ -170,7 +170,7 @@ void AmoebaMultipoleForceImpl::getCovalentRange(const AmoebaMultipoleForce& forc
*maxCovalentIndex = covalentList[ii];
}
}
}
}
return;
}
......@@ -179,10 +179,14 @@ void AmoebaMultipoleForceImpl::getCovalentDegree(const AmoebaMultipoleForce& for
const int* CovalentDegrees = AmoebaMultipoleForceImpl::getCovalentDegrees();
for (unsigned int kk = 0; kk < AmoebaMultipoleForce::CovalentEnd; kk++) {
covalentDegree[kk] = CovalentDegrees[kk];
}
}
return;
}
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/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 454eda76
......@@ -35,7 +35,7 @@ using namespace OpenMM;
AmoebaReferenceMultipoleForce::AmoebaReferenceMultipoleForce() :
_nonbondedMethod(NoCutoff),
_numParticles(0),
_numParticles(0),
_electric(138.9354558456),
_dielectric(1.0),
_mutualInducedDipoleConverged(0),
......@@ -51,7 +51,7 @@ AmoebaReferenceMultipoleForce::AmoebaReferenceMultipoleForce() :
AmoebaReferenceMultipoleForce::AmoebaReferenceMultipoleForce(NonbondedMethod nonbondedMethod) :
_nonbondedMethod(nonbondedMethod),
_numParticles(0),
_numParticles(0),
_electric(138.9354558456),
_dielectric(1.0),
_mutualInducedDipoleConverged(0),
......@@ -97,7 +97,7 @@ void AmoebaReferenceMultipoleForce::initialize()
_uScale[index++] = 1.0;
}
AmoebaReferenceMultipoleForce::NonbondedMethod AmoebaReferenceMultipoleForce::getNonbondedMethod() const
AmoebaReferenceMultipoleForce::NonbondedMethod AmoebaReferenceMultipoleForce::getNonbondedMethod() const
{
return _nonbondedMethod;
}
......@@ -107,7 +107,7 @@ void AmoebaReferenceMultipoleForce::setNonbondedMethod(AmoebaReferenceMultipoleF
_nonbondedMethod = nonbondedMethod;
}
AmoebaReferenceMultipoleForce::PolarizationType AmoebaReferenceMultipoleForce::getPolarizationType() const
AmoebaReferenceMultipoleForce::PolarizationType AmoebaReferenceMultipoleForce::getPolarizationType() const
{
return _polarizationType;
}
......@@ -117,7 +117,7 @@ void AmoebaReferenceMultipoleForce::setPolarizationType(AmoebaReferenceMultipole
_polarizationType = polarizationType;
}
int AmoebaReferenceMultipoleForce::getMutualInducedDipoleConverged() const
int AmoebaReferenceMultipoleForce::getMutualInducedDipoleConverged() const
{
return _mutualInducedDipoleConverged;
}
......@@ -127,7 +127,7 @@ void AmoebaReferenceMultipoleForce::setMutualInducedDipoleConverged(int mutualIn
_mutualInducedDipoleConverged = mutualInducedDipoleConverged;
}
int AmoebaReferenceMultipoleForce::getMutualInducedDipoleIterations() const
int AmoebaReferenceMultipoleForce::getMutualInducedDipoleIterations() const
{
return _mutualInducedDipoleIterations;
}
......@@ -137,7 +137,7 @@ void AmoebaReferenceMultipoleForce::setMutualInducedDipoleIterations(int mutualI
_mutualInducedDipoleIterations = mutualInducedDipoleIterations;
}
RealOpenMM AmoebaReferenceMultipoleForce::getMutualInducedDipoleEpsilon() const
RealOpenMM AmoebaReferenceMultipoleForce::getMutualInducedDipoleEpsilon() const
{
return _mutualInducedDipoleEpsilon;
}
......@@ -147,7 +147,7 @@ void AmoebaReferenceMultipoleForce::setMutualInducedDipoleEpsilon(RealOpenMM mut
_mutualInducedDipoleEpsilon = mutualInducedDipoleEpsilon;
}
int AmoebaReferenceMultipoleForce::getMaximumMutualInducedDipoleIterations() const
int AmoebaReferenceMultipoleForce::getMaximumMutualInducedDipoleIterations() const
{
return _maximumMutualInducedDipoleIterations;
}
......@@ -157,7 +157,7 @@ void AmoebaReferenceMultipoleForce::setMaximumMutualInducedDipoleIterations(int
_maximumMutualInducedDipoleIterations = maximumMutualInducedDipoleIterations;
}
RealOpenMM AmoebaReferenceMultipoleForce::getMutualInducedDipoleTargetEpsilon() const
RealOpenMM AmoebaReferenceMultipoleForce::getMutualInducedDipoleTargetEpsilon() const
{
return _mutualInducedDipoleTargetEpsilon;
}
......@@ -172,7 +172,7 @@ void AmoebaReferenceMultipoleForce::setupScaleMaps(const vector< vector< vector<
/* Setup for scaling maps:
*
* _scaleMaps[particleIndex][ScaleType] = map, where map[covalentIndex] = scaleFactor
* _scaleMaps[particleIndex][ScaleType] = map, where map[covalentIndex] = scaleFactor
* _maxScaleIndex[particleIndex] = max covalent index for particleIndex
*
* multipoleParticleCovalentInfo[ii][jj], jj =0,1,2,3 contains covalent indices (c12, c13, c14, c15)
......@@ -208,8 +208,8 @@ void AmoebaReferenceMultipoleForce::setupScaleMaps(const vector< vector< vector<
hit = 1;
}
}
}
}
_scaleMaps[ii][P_SCALE][covalentIndex] = hit ? 0.5*_pScale[jj+1] : _pScale[jj+1];
_scaleMaps[ii][M_SCALE][covalentIndex] = _mScale[jj+1];
_maxScaleIndex[ii] = _maxScaleIndex[ii] < covalentIndex ? covalentIndex : _maxScaleIndex[ii];
......@@ -231,7 +231,7 @@ void AmoebaReferenceMultipoleForce::setupScaleMaps(const vector< vector< vector<
}
}
RealOpenMM AmoebaReferenceMultipoleForce::getMultipoleScaleFactor(unsigned int particleI, unsigned int particleJ, ScaleType scaleType) const
RealOpenMM AmoebaReferenceMultipoleForce::getMultipoleScaleFactor(unsigned int particleI, unsigned int particleJ, ScaleType scaleType) const
{
MapIntRealOpenMM scaleMap = _scaleMaps[particleI][scaleType];
......@@ -243,13 +243,13 @@ RealOpenMM AmoebaReferenceMultipoleForce::getMultipoleScaleFactor(unsigned int p
}
}
void AmoebaReferenceMultipoleForce::getDScaleAndPScale(unsigned int particleI, unsigned int particleJ, RealOpenMM& dScale, RealOpenMM& pScale) const
void AmoebaReferenceMultipoleForce::getDScaleAndPScale(unsigned int particleI, unsigned int particleJ, RealOpenMM& dScale, RealOpenMM& pScale) const
{
dScale = getMultipoleScaleFactor(particleI, particleJ, D_SCALE);
pScale = getMultipoleScaleFactor(particleI, particleJ, P_SCALE);
}
void AmoebaReferenceMultipoleForce::getMultipoleScaleFactors(unsigned int particleI, unsigned int particleJ, vector<RealOpenMM>& scaleFactors) const
void AmoebaReferenceMultipoleForce::getMultipoleScaleFactors(unsigned int particleI, unsigned int particleJ, vector<RealOpenMM>& scaleFactors) const
{
scaleFactors[D_SCALE] = getMultipoleScaleFactor(particleI, particleJ, D_SCALE);
scaleFactors[P_SCALE] = getMultipoleScaleFactor(particleI, particleJ, P_SCALE);
......@@ -257,7 +257,7 @@ void AmoebaReferenceMultipoleForce::getMultipoleScaleFactors(unsigned int partic
scaleFactors[U_SCALE] = getMultipoleScaleFactor(particleI, particleJ, U_SCALE);
}
RealOpenMM AmoebaReferenceMultipoleForce::normalizeRealVec(RealVec& vectorToNormalize) const
RealOpenMM AmoebaReferenceMultipoleForce::normalizeRealVec(RealVec& vectorToNormalize) const
{
RealOpenMM norm = SQRT(vectorToNormalize.dot(vectorToNormalize));
if (norm > 0.0) {
......@@ -266,26 +266,26 @@ RealOpenMM AmoebaReferenceMultipoleForce::normalizeRealVec(RealVec& vectorToNorm
return norm;
}
void AmoebaReferenceMultipoleForce::initializeRealOpenMMVector(vector<RealOpenMM>& vectorToInitialize) const
void AmoebaReferenceMultipoleForce::initializeRealOpenMMVector(vector<RealOpenMM>& vectorToInitialize) const
{
RealOpenMM zero = 0.0;
vectorToInitialize.resize(_numParticles);
std::fill(vectorToInitialize.begin(), vectorToInitialize.end(), zero);
}
void AmoebaReferenceMultipoleForce::initializeRealVecVector(vector<RealVec>& vectorToInitialize) const
void AmoebaReferenceMultipoleForce::initializeRealVecVector(vector<RealVec>& vectorToInitialize) const
{
vectorToInitialize.resize(_numParticles);
RealVec zeroVec(0.0, 0.0, 0.0);
std::fill(vectorToInitialize.begin(), vectorToInitialize.end(), zeroVec);
}
void AmoebaReferenceMultipoleForce::copyRealVecVector(const vector<OpenMM::RealVec>& inputVector, vector<OpenMM::RealVec>& outputVector) const
{
void AmoebaReferenceMultipoleForce::copyRealVecVector(const vector<OpenMM::RealVec>& inputVector, vector<OpenMM::RealVec>& outputVector) const
{
outputVector.resize(inputVector.size());
for (unsigned int ii = 0; ii < inputVector.size(); ii++) {
outputVector[ii] = inputVector[ii];
}
}
}
void AmoebaReferenceMultipoleForce::loadParticleData(const vector<RealVec>& particlePositions,
......@@ -295,9 +295,9 @@ void AmoebaReferenceMultipoleForce::loadParticleData(const vector<RealVec>& part
const vector<RealOpenMM>& tholes,
const vector<RealOpenMM>& dampingFactors,
const vector<RealOpenMM>& polarity,
vector<MultipoleParticleData>& particleData) const
vector<MultipoleParticleData>& particleData) const
{
particleData.resize(_numParticles);
for (unsigned int ii = 0; ii < _numParticles; ii++) {
......@@ -343,8 +343,8 @@ void AmoebaReferenceMultipoleForce::zeroFixedMultipoleFields()
}
void AmoebaReferenceMultipoleForce::checkChiralCenterAtParticle(MultipoleParticleData& particleI, int axisType,
MultipoleParticleData& particleZ, MultipoleParticleData& particleX,
MultipoleParticleData& particleY) const
MultipoleParticleData& particleZ, MultipoleParticleData& particleX,
MultipoleParticleData& particleY) const
{
if (axisType == AmoebaMultipoleForce::ZThenX || particleY.particleIndex == -1) {
......@@ -372,7 +372,7 @@ void AmoebaReferenceMultipoleForce::checkChiral(vector<MultipoleParticleData>& p
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector<int>& multipoleAtomZs,
const vector<int>& axisTypes) const
const vector<int>& axisTypes) const
{
for (unsigned int ii = 0; ii < _numParticles; ii++) {
if (multipoleAtomYs[ii] > -1) {
......@@ -388,7 +388,7 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
const MultipoleParticleData& particleZ,
const MultipoleParticleData& particleX,
MultipoleParticleData* particleY,
int axisType) const
int axisType) const
{
// handle case where rotation matrix is identity (e.g. single ion)
......@@ -403,25 +403,25 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
RealVec vectorX = particleX.position - particleI.position;
normalizeRealVec(vectorZ);
// branch based on axis type
if (axisType == AmoebaMultipoleForce::Bisector) {
// bisector
// dx = dx1 + dx2 (in TINKER code)
normalizeRealVec(vectorX);
vectorZ += vectorX;
normalizeRealVec(vectorZ);
} else if (axisType == AmoebaMultipoleForce::ZBisect) {
// z-bisect
// dx = dx1 + dx2 (in TINKER code)
normalizeRealVec(vectorX);
vectorY = particleY->position - particleI.position;
......@@ -429,13 +429,13 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
vectorX += vectorY;
normalizeRealVec(vectorX);
} else if (axisType == AmoebaMultipoleForce::ThreeFold) {
// 3-fold
// dx = dx1 + dx2 + dx3 (in TINKER code)
normalizeRealVec(vectorX);
vectorY = particleY->position - particleI.position;
......@@ -443,15 +443,15 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
vectorZ += vectorX + vectorY;
normalizeRealVec(vectorZ);
} else if (axisType == AmoebaMultipoleForce::ZOnly) {
// z-only
vectorX = RealVec(0.1, 0.1, 0.1);
}
RealOpenMM dot = vectorZ.dot(vectorX);
vectorX -= vectorZ*dot;
......@@ -461,7 +461,7 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
RealVec rotationMatrix[3];
rotationMatrix[0] = vectorX;
rotationMatrix[1] = vectorY;
rotationMatrix[2] = vectorZ;
rotationMatrix[2] = vectorZ;
RealVec labDipole;
for (int ii = 0; ii < 3; ii++) {
......@@ -471,7 +471,7 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
}
}
particleI.dipole = labDipole;
RealOpenMM mPole[3][3];
RealOpenMM rPole[3][3] = { { 0.0, 0.0, 0.0 },
{ 0.0, 0.0, 0.0 },
......@@ -488,7 +488,7 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
mPole[2][0] = particleI.quadrupole[QXZ];
mPole[2][1] = particleI.quadrupole[QYZ];
mPole[2][2] = particleI.quadrupole[QZZ];
for (int ii = 0; ii < 3; ii++) {
for (int jj = ii; jj < 3; jj++) {
for (int kk = 0; kk < 3; kk++) {
......@@ -498,7 +498,7 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
}
}
}
particleI.quadrupole[QXX] = rPole[0][0];
particleI.quadrupole[QXY] = rPole[0][1];
particleI.quadrupole[QXZ] = rPole[0][2];
......@@ -636,7 +636,7 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrix(vector<MultipoleParticle
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector<int>& multipoleAtomZs,
const vector<int>& axisTypes) const
const vector<int>& axisTypes) const
{
for (unsigned int ii = 0; ii < _numParticles; ii++) {
......@@ -649,19 +649,19 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrix(vector<MultipoleParticle
void AmoebaReferenceMultipoleForce::getAndScaleInverseRs(RealOpenMM dampI, RealOpenMM dampJ,
RealOpenMM tholeI, RealOpenMM tholeJ,
RealOpenMM r, vector<RealOpenMM>& rrI) const
RealOpenMM r, vector<RealOpenMM>& rrI) const
{
RealOpenMM rI = 1.0/r;
RealOpenMM r2I = rI*rI;
rrI[0] = rI*r2I;
RealOpenMM constantFactor = 3.0;
for (unsigned int ii = 1; ii < rrI.size(); ii++) {
for (unsigned int ii = 1; ii < rrI.size(); ii++) {
rrI[ii] = constantFactor*rrI[ii-1]*r2I;
constantFactor += 2.0;
}
RealOpenMM damp = dampI*dampJ;
if (damp != 0.0) {
RealOpenMM pgamma = tholeI < tholeJ ? tholeI : tholeJ;
......@@ -669,7 +669,7 @@ void AmoebaReferenceMultipoleForce::getAndScaleInverseRs(RealOpenMM dampI, RealO
ratio = ratio*ratio*ratio;
damp = -pgamma*ratio;
if (damp > -50.0) {
if (damp > -50.0) {
RealOpenMM dampExp = EXP(damp);
rrI[0] *= 1.0 - dampExp;
......@@ -683,7 +683,7 @@ void AmoebaReferenceMultipoleForce::getAndScaleInverseRs(RealOpenMM dampI, RealO
void AmoebaReferenceMultipoleForce::calculateFixedMultipoleFieldPairIxn(const MultipoleParticleData& particleI,
const MultipoleParticleData& particleJ,
RealOpenMM dScale, RealOpenMM pScale)
RealOpenMM dScale, RealOpenMM pScale)
{
if (particleI.particleIndex == particleJ.particleIndex)
......@@ -693,9 +693,9 @@ void AmoebaReferenceMultipoleForce::calculateFixedMultipoleFieldPairIxn(const Mu
RealOpenMM r = SQRT(deltaR.dot(deltaR));
vector<RealOpenMM> rrI(3);
// get scaling factors, if needed
getAndScaleInverseRs(particleI.dampingFactor, particleJ.dampingFactor, particleI.thole, particleJ.thole, r, rrI);
RealOpenMM rr3 = rrI[0];
......@@ -710,8 +710,8 @@ void AmoebaReferenceMultipoleForce::calculateFixedMultipoleFieldPairIxn(const Mu
qDotDelta[1] = deltaR[0]*particleJ.quadrupole[QXY] + deltaR[1]*particleJ.quadrupole[QYY] + deltaR[2]*particleJ.quadrupole[QYZ];
qDotDelta[2] = deltaR[0]*particleJ.quadrupole[QXZ] + deltaR[1]*particleJ.quadrupole[QYZ] + deltaR[2]*particleJ.quadrupole[QZZ];
RealOpenMM dipoleDelta = particleJ.dipole.dot(deltaR);
RealOpenMM qdpoleDelta = qDotDelta.dot(deltaR);
RealOpenMM dipoleDelta = particleJ.dipole.dot(deltaR);
RealOpenMM qdpoleDelta = qDotDelta.dot(deltaR);
RealOpenMM factor = rr3*particleJ.charge - rr5*dipoleDelta + rr7*qdpoleDelta;
RealVec field = deltaR*factor + particleJ.dipole*rr3 - qDotDelta*rr5_2;
......@@ -719,17 +719,17 @@ void AmoebaReferenceMultipoleForce::calculateFixedMultipoleFieldPairIxn(const Mu
unsigned int particleIndex = particleI.particleIndex;
_fixedMultipoleField[particleIndex] -= field*dScale;
_fixedMultipoleFieldPolar[particleIndex] -= field*pScale;
// field at particle J due multipoles at particle I
qDotDelta[0] = deltaR[0]*particleI.quadrupole[QXX] + deltaR[1]*particleI.quadrupole[QXY] + deltaR[2]*particleI.quadrupole[QXZ];
qDotDelta[1] = deltaR[0]*particleI.quadrupole[QXY] + deltaR[1]*particleI.quadrupole[QYY] + deltaR[2]*particleI.quadrupole[QYZ];
qDotDelta[2] = deltaR[0]*particleI.quadrupole[QXZ] + deltaR[1]*particleI.quadrupole[QYZ] + deltaR[2]*particleI.quadrupole[QZZ];
dipoleDelta = particleI.dipole.dot(deltaR);
qdpoleDelta = qDotDelta.dot(deltaR);
dipoleDelta = particleI.dipole.dot(deltaR);
qdpoleDelta = qDotDelta.dot(deltaR);
factor = rr3*particleI.charge + rr5*dipoleDelta + rr7*qdpoleDelta;
field = deltaR*factor - particleI.dipole*rr3 - qDotDelta*rr5_2;
particleIndex = particleJ.particleIndex;
_fixedMultipoleField[particleIndex] += field*dScale;
......@@ -748,7 +748,7 @@ void AmoebaReferenceMultipoleForce::calculateFixedMultipoleField(const vector<Mu
for (unsigned int jj = ii; jj < _numParticles; jj++) {
// if site jj is less than max covalent scaling index then get/apply scaling constants
// otherwise add unmodified field and fieldPolar to particle fields
// otherwise add unmodified field and fieldPolar to particle fields
RealOpenMM dScale, pScale;
if (jj <= _maxScaleIndex[ii]) {
......@@ -775,13 +775,13 @@ void AmoebaReferenceMultipoleForce::initializeInducedDipoles(vector<UpdateInduce
}
}
void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxn(unsigned int particleI,
void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxn(unsigned int particleI,
unsigned int particleJ,
RealOpenMM rr3,
RealOpenMM rr5,
const RealVec& deltaR,
const vector<RealVec>& inducedDipole,
vector<RealVec>& field) const
vector<RealVec>& field) const
{
RealOpenMM dDotDelta = rr5*(inducedDipole[particleJ].dot(deltaR));
......@@ -790,7 +790,7 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxn(unsigned int p
field[particleJ] += inducedDipole[particleI]*rr3 + deltaR*dDotDelta;
}
void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const MultipoleParticleData& particleI,
void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const MultipoleParticleData& particleI,
const MultipoleParticleData& particleJ,
vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleFields)
{
......@@ -801,13 +801,13 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const Multipo
RealVec deltaR = particleJ.position - particleI.position;
RealOpenMM r = SQRT(deltaR.dot(deltaR));
vector<RealOpenMM> rrI(2);
getAndScaleInverseRs(particleI.dampingFactor, particleJ.dampingFactor,
particleI.thole, particleJ.thole, r, rrI);
RealOpenMM rr3 = -rrI[0];
RealOpenMM rr5 = rrI[1];
for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++) {
calculateInducedDipolePairIxn(particleI.particleIndex, particleJ.particleIndex, rr3, rr5, deltaR,
*updateInducedDipoleFields[ii].inducedDipoles, updateInducedDipoleFields[ii].inducedDipoleField);
......@@ -816,13 +816,13 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const Multipo
void AmoebaReferenceMultipoleForce::calculateInducedDipoleFields(const vector<MultipoleParticleData>& particleData, vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleFields) {
// Initialize the fields to zero.
RealVec zeroVec(0.0, 0.0, 0.0);
for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++)
std::fill(updateInducedDipoleFields[ii].inducedDipoleField.begin(), updateInducedDipoleFields[ii].inducedDipoleField.end(), zeroVec);
// Add fields from all induced dipoles.
for (unsigned int ii = 0; ii < particleData.size(); ii++)
for (unsigned int jj = ii; jj < particleData.size(); jj++)
calculateInducedDipolePairIxns(particleData[ii], particleData[jj], updateInducedDipoleFields);
......@@ -832,7 +832,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::updateInducedDipoleFields(const vector
vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleFields)
{
// Calculate the fields coming from induced dipoles.
calculateInducedDipoleFields(particleData, updateInducedDipoleFields);
// Update the induced dipoles and calculate the convergence factor, maxEpsilon
......@@ -843,7 +843,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::updateInducedDipoleFields(const vector
*updateInducedDipoleFields[kk].fixedMultipoleField,
updateInducedDipoleFields[kk].inducedDipoleField,
*updateInducedDipoleFields[kk].inducedDipoles);
maxEpsilon = epsilon > maxEpsilon ? epsilon : maxEpsilon;
}
......@@ -878,11 +878,11 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesBySOR(const vector<Mult
// loop until (1) induced dipoles are converged or
// (2) iterations == max iterations or
// (3) convergence factor (spsilon) increases
// (3) convergence factor (spsilon) increases
while (!done) {
RealOpenMM epsilon = updateInducedDipoleFields(particleData, updateInducedDipoleField);
RealOpenMM epsilon = updateInducedDipoleFields(particleData, updateInducedDipoleField);
epsilon = _polarSOR*_debye*SQRT(epsilon/(static_cast<RealOpenMM>(_numParticles)));
if (epsilon < getMutualInducedDipoleTargetEpsilon()) {
......@@ -907,11 +907,11 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesByDIIS(const vector<Mul
int maxPrevious = 20;
for (int iteration = 0; ; iteration++) {
// Compute the field from the induced dipoles.
calculateInducedDipoleFields(particleData, updateInducedDipoleField);
calculateInducedDipoleFields(particleData, updateInducedDipoleField);
// Record the current dipoles and the errors in them.
RealOpenMM maxEpsilon = 0;
prevErrors.push_back(vector<RealVec>());
prevErrors.back().resize(_numParticles);
......@@ -933,9 +933,9 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesByDIIS(const vector<Mul
maxEpsilon = epsilon;
}
maxEpsilon = _debye*SQRT(maxEpsilon/_numParticles);
// Decide whether to stop or continue iterating.
if (maxEpsilon < getMutualInducedDipoleTargetEpsilon())
setMutualInducedDipoleConverged(true);
if (maxEpsilon < getMutualInducedDipoleTargetEpsilon() || iteration == getMaximumMutualInducedDipoleIterations()) {
......@@ -943,9 +943,9 @@ void AmoebaReferenceMultipoleForce::convergeInduceDipolesByDIIS(const vector<Mul
setMutualInducedDipoleIterations(iteration);
return;
}
// Select the new dipoles.
if (prevErrors.size() > maxPrevious) {
prevErrors.erase(prevErrors.begin());
for (int k = 0; k < numFields; k++)
......@@ -972,9 +972,9 @@ void AmoebaReferenceMultipoleForce::computeDIISCoefficients(const vector<vector<
coefficients[0] = 1;
return;
}
// Create the DIIS matrix.
int rank = steps+1;
Array2D<double> b(rank, rank);
b[0][0] = 0;
......@@ -987,9 +987,9 @@ void AmoebaReferenceMultipoleForce::computeDIISCoefficients(const vector<vector<
sum += prevErrors[i][k].dot(prevErrors[j][k]);
b[i+1][j+1] = b[j+1][i+1] = sum;
}
// Solve using SVD. Since the right hand side is (-1, 0, 0, 0, ...), this is simpler than the general case.
JAMA::SVD<double> svd(b);
Array2D<double> u, v;
svd.getU(u);
......@@ -1002,7 +1002,7 @@ void AmoebaReferenceMultipoleForce::computeDIISCoefficients(const vector<vector<
for (int j = 0; j < effectiveRank; j++)
d -= u[0][j]*v[i][j]/s[j];
coefficients[i-1] = d;
}
}
}
void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<MultipoleParticleData>& particleData)
......@@ -1014,12 +1014,12 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<Multipo
calculateFixedMultipoleField(particleData);
// initialize inducedDipoles
// if polarization type is 'Direct', then return after initializing; otherwise
// if polarization type is 'Direct', then return after initializing; otherwise
// converge induced dipoles.
for (unsigned int ii = 0; ii < _numParticles; ii++) {
_fixedMultipoleField[ii] *= particleData[ii].polarity;
_fixedMultipoleFieldPolar[ii] *= particleData[ii].polarity;
_fixedMultipoleFieldPolar[ii] *= particleData[ii].polarity;
}
_inducedDipole.resize(_numParticles);
......@@ -1045,7 +1045,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostaticPairIxn(const Mu
const MultipoleParticleData& particleK,
const vector<RealOpenMM>& scalingFactors,
vector<RealVec>& forces,
vector<RealVec>& torque) const
vector<RealVec>& torque) const
{
unsigned int iIndex = particleI.particleIndex;
unsigned int kIndex = particleK.particleIndex;
......@@ -1438,9 +1438,9 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForceForParticle(const MultipoleP
const MultipoleParticleData& particleV,
MultipoleParticleData* particleW,
int axisType, const Vec3& torque,
vector<RealVec>& forces) const
vector<RealVec>& forces) const
{
static const int U = 0;
static const int V = 1;
static const int W = 2;
......@@ -1454,17 +1454,17 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForceForParticle(const MultipoleP
static const int VS = 10;
static const int WS = 11;
static const int LastVectorIndex = 12;
static const int X = 0;
static const int Y = 1;
static const int Z = 2;
static const int I = 3;
RealOpenMM norms[LastVectorIndex];
RealOpenMM angles[LastVectorIndex][2];
// ---------------------------------------------------------------------------------------
// get coordinates of this atom and the z & x axis atoms
// compute the vector between the atoms and 1/sqrt(d2), d2 is distance between
// this atom and the axis atom
......@@ -1486,12 +1486,12 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForceForParticle(const MultipoleP
vectorW = vectorU.cross(vectorV);
}
norms[W] = normalizeRealVec(vectorW);
RealVec vectorUV, vectorUW, vectorVW;
vectorUV = vectorV.cross(vectorU);
vectorUW = vectorW.cross(vectorU);
vectorVW = vectorW.cross(vectorV);
norms[UV] = normalizeRealVec(vectorUV);
norms[UW] = normalizeRealVec(vectorUW);
norms[VW] = normalizeRealVec(vectorVW);
......@@ -1501,7 +1501,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForceForParticle(const MultipoleP
angles[UV][0] = vectorU.dot(vectorV);
angles[UV][1] = SQRT(1.0 - angles[UV][0]*angles[UV][0]);
angles[UW][0] = vectorU.dot(vectorW);
angles[UW][1] = SQRT(1.0 - angles[UW][0]*angles[UW][0]);
......@@ -1515,26 +1515,26 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForceForParticle(const MultipoleP
dphi *= -1.0;
// branch based on axis type
if (axisType == AmoebaMultipoleForce::ZThenX || axisType == AmoebaMultipoleForce::Bisector) {
RealOpenMM factor1;
RealOpenMM factor2;
RealOpenMM factor3;
RealOpenMM factor4;
RealOpenMM half = 0.5;
factor1 = dphi[V]/(norms[U]*angles[UV][1]);
factor2 = dphi[W]/(norms[U]);
factor3 = -dphi[U]/(norms[V]*angles[UV][1]);
if (axisType == AmoebaMultipoleForce::Bisector) {
if (axisType == AmoebaMultipoleForce::Bisector) {
factor2 *= half;
factor4 = half*dphi[W]/(norms[V]);
} else {
factor4 = 0.0;
}
for (int ii = 0; ii < 3; ii++) {
double forceU = vectorUV[ii]*factor1 + factor2*vectorUW[ii];
forces[particleU.particleIndex][ii] -= forceU;
......@@ -1547,7 +1547,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForceForParticle(const MultipoleP
} else if (axisType == AmoebaMultipoleForce::ZBisect) {
RealVec vectorR = vectorV + vectorW;
RealVec vectorR = vectorV + vectorW;
RealVec vectorS = vectorU.cross(vectorR);
norms[R] = normalizeRealVec(vectorR);
......@@ -1574,7 +1574,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForceForParticle(const MultipoleP
angles[WS][0] = vectorW.dot(vectorS);
angles[WS][1] = SQRT(1.0 - angles[WS][0]*angles[WS][0]);
RealVec t1 = vectorV - vectorS*angles[VS][0];
RealVec t2 = vectorW - vectorS*angles[WS][0];
......@@ -1656,7 +1656,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForce(vector<MultipoleParticleDat
const vector<int>& multipoleAtomZs,
const vector<int>& axisTypes,
vector<RealVec>& torques,
vector<RealVec>& forces) const
vector<RealVec>& forces) const
{
// map torques to forces
......@@ -1666,7 +1666,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForce(vector<MultipoleParticleDat
mapTorqueToForceForParticle(particleData[ii],
particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]],
multipoleAtomYs[ii] > -1 ? &particleData[multipoleAtomYs[ii]] : NULL,
axisTypes[ii], torques[ii], forces);
axisTypes[ii], torques[ii], forces);
}
}
}
......@@ -1680,7 +1680,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Mu
vector<RealOpenMM> scaleFactors(LAST_SCALE_TYPE_INDEX);
for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) {
scaleFactors[kk] = 1.0;
}
}
// main loop over particle pairs
......@@ -1878,7 +1878,7 @@ void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments(const
}
// convert the quadrupole from traced to traceless form
outputMultipoleMoments.resize(13);
RealOpenMM qave = (xxqdp + yyqdp + zzqdp)/3.0;
outputMultipoleMoments[4] = 0.5*(xxqdp-qave);
......@@ -1901,7 +1901,7 @@ void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments(const
outputMultipoleMoments[7] = outputMultipoleMoments[5];
outputMultipoleMoments[10] = outputMultipoleMoments[6];
outputMultipoleMoments[11] = outputMultipoleMoments[9];
RealOpenMM debye = 4.80321;
outputMultipoleMoments[0] = netchg;
......@@ -1910,16 +1910,16 @@ void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments(const
outputMultipoleMoments[1] = dpl[0];
outputMultipoleMoments[2] = dpl[1];
outputMultipoleMoments[3] = dpl[2];
debye *= 3.0;
for (unsigned int ii = 4; ii < 13; ii++) {
outputMultipoleMoments[ii] *= 100.0*debye;
}
}
RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostaticPotentialForParticleGridPoint(const MultipoleParticleData& particleI, const RealVec& gridPoint) const
RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostaticPotentialForParticleGridPoint(const MultipoleParticleData& particleI, const RealVec& gridPoint) const
{
RealVec deltaR = particleI.position - gridPoint;
getPeriodicDelta(deltaR);
......@@ -1961,7 +1961,7 @@ void AmoebaReferenceMultipoleForce::calculateElectrostaticPotential(const vector
{
// setup, including calculating induced dipoles
// initialize potential
// initialize potential
// calculate contribution of each particle to potential at grid point
// apply prefactor
......@@ -1988,14 +1988,14 @@ void AmoebaReferenceMultipoleForce::calculateElectrostaticPotential(const vector
}
AmoebaReferenceMultipoleForce::UpdateInducedDipoleFieldStruct::UpdateInducedDipoleFieldStruct(vector<OpenMM::RealVec>& inputFixed_E_Field, vector<OpenMM::RealVec>& inputInducedDipoles) :
fixedMultipoleField(&inputFixed_E_Field), inducedDipoles(&inputInducedDipoles) {
fixedMultipoleField(&inputFixed_E_Field), inducedDipoles(&inputInducedDipoles) {
inducedDipoleField.resize(fixedMultipoleField->size());
}
}
AmoebaReferenceGeneralizedKirkwoodMultipoleForce::AmoebaReferenceGeneralizedKirkwoodMultipoleForce(AmoebaReferenceGeneralizedKirkwoodForce* amoebaReferenceGeneralizedKirkwoodForce) :
AmoebaReferenceMultipoleForce(NoCutoff),
_amoebaReferenceGeneralizedKirkwoodForce(amoebaReferenceGeneralizedKirkwoodForce),
_gkc(2.455)
_gkc(2.455)
{
RealOpenMM solventDielectric = _amoebaReferenceGeneralizedKirkwoodForce->getSolventDielectric();
......@@ -2016,33 +2016,33 @@ AmoebaReferenceGeneralizedKirkwoodMultipoleForce::AmoebaReferenceGeneralizedKirk
for (unsigned int ii = 0; ii < _scaledRadii.size(); ii++) {
_scaledRadii[ii] *= _atomicRadii[ii];
}
}
}
AmoebaReferenceGeneralizedKirkwoodMultipoleForce::~AmoebaReferenceGeneralizedKirkwoodMultipoleForce()
{
delete _amoebaReferenceGeneralizedKirkwoodForce;
};
int AmoebaReferenceGeneralizedKirkwoodMultipoleForce::getIncludeCavityTerm() const
{
return _includeCavityTerm;
};
RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::getProbeRadius() const
RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::getProbeRadius() const
{
return _probeRadius;
};
RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::getSurfaceAreaFactor() const
RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::getSurfaceAreaFactor() const
{
return _surfaceAreaFactor;
};
RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::getDielectricOffset() const
RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::getDielectricOffset() const
{
return _dielectricOffset;
};
void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::zeroFixedMultipoleFields()
{
this->AmoebaReferenceMultipoleForce::zeroFixedMultipoleFields();
......@@ -2057,7 +2057,7 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateFixedMultipoleFi
this->AmoebaReferenceMultipoleForce::calculateFixedMultipoleFieldPairIxn(particleI, particleJ, dScale, pScale);
// get deltaR, R2, and R between 2 atoms
RealVec deltaR = particleJ.position - particleI.position;
RealOpenMM r = SQRT(deltaR.dot(deltaR));
RealOpenMM rb2 = _bornRadii[particleI.particleIndex]*_bornRadii[particleJ.particleIndex];
......@@ -2067,36 +2067,36 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateFixedMultipoleFi
RealOpenMM uxi = particleI.dipole[0];
RealOpenMM uyi = particleI.dipole[1];
RealOpenMM uzi = particleI.dipole[2];
RealOpenMM qxxi = particleI.quadrupole[QXX];
RealOpenMM qxyi = particleI.quadrupole[QXY];
RealOpenMM qxzi = particleI.quadrupole[QXZ];
RealOpenMM qyyi = particleI.quadrupole[QYY];
RealOpenMM qyzi = particleI.quadrupole[QYZ];
RealOpenMM qzzi = particleI.quadrupole[QZZ];
RealOpenMM xr = deltaR[0];
RealOpenMM yr = deltaR[1];
RealOpenMM zr = deltaR[2];
RealOpenMM ck = particleJ.charge;
RealOpenMM xr2 = xr*xr;
RealOpenMM yr2 = yr*yr;
RealOpenMM zr2 = zr*zr;
RealOpenMM r2 = xr2 + yr2 + zr2;
RealOpenMM uxk = particleJ.dipole[0];
RealOpenMM uyk = particleJ.dipole[1];
RealOpenMM uzk = particleJ.dipole[2];
RealOpenMM qxxk = particleJ.quadrupole[QXX];
RealOpenMM qxyk = particleJ.quadrupole[QXY];
RealOpenMM qxzk = particleJ.quadrupole[QXZ];
RealOpenMM qyyk = particleJ.quadrupole[QYY];
RealOpenMM qyzk = particleJ.quadrupole[QYZ];
RealOpenMM qzzk = particleJ.quadrupole[QZZ];
RealOpenMM expterm = EXP(-r2/(_gkc*rb2));
RealOpenMM expc = expterm/_gkc;
RealOpenMM dexpc = -2.0/(_gkc*rb2);
......@@ -2284,11 +2284,11 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateFixedMultipoleFi
void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateInducedDipolePairGkIxn(const MultipoleParticleData& particleI,
const MultipoleParticleData& particleJ,
const vector<OpenMM::RealVec>& inputFields,
vector<OpenMM::RealVec>& outputFields) const
vector<OpenMM::RealVec>& outputFields) const
{
RealOpenMM a[3][3];
RealVec deltaR = particleJ.position - particleI.position;
RealOpenMM r = SQRT(deltaR.dot(deltaR));
......@@ -2306,7 +2306,7 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateInducedDipolePai
RealOpenMM r2 = xr2 + yr2 + zr2;
RealOpenMM expterm = EXP(-r2/(_gkc*rb2));
RealOpenMM expc = expterm /_gkc;
RealOpenMM expc = expterm /_gkc;
RealOpenMM gf2 = 1.0/(r2+rb2*expterm);
RealOpenMM gf = SQRT(gf2);
......@@ -2317,7 +2317,7 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateInducedDipolePai
RealVec duks = inputFields[jIndex];
// reaction potential auxiliary terms
a[1][0] = -gf3;
a[2][0] = 3.0*gf5;
......@@ -2325,22 +2325,22 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateInducedDipolePai
RealOpenMM expc1 = 1.0 - expc;
a[1][1] = expc1*a[2][0];
// unweighted dipole reaction potential gradient tensor
RealVec gux, guy, guz;
gux[0] = (a[1][0] + xr2*a[1][1]);
gux[1] = xr*yr*a[1][1];
gux[2] = xr*zr*a[1][1];
guy[0] = gux[1];
guy[1] = (a[1][0] + yr2*a[1][1]);
guy[2] = yr*zr*a[1][1];
guz[0] = gux[2];
guz[1] = guy[2];
guz[2] = (a[1][0] + zr2*a[1][1]);
outputFields[iIndex][0] += _fd*duks.dot(gux);
outputFields[iIndex][1] += _fd*duks.dot(guy);
outputFields[iIndex][2] += _fd*duks.dot(guz);
......@@ -2387,8 +2387,8 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateInducedDipoles(c
for (unsigned int ii = 0; ii < _numParticles; ii++) {
_fixedMultipoleField[ii] *= particleData[ii].polarity;
_fixedMultipoleFieldPolar[ii] *= particleData[ii].polarity;
_gkField[ii] *= particleData[ii].polarity;
_fixedMultipoleFieldPolar[ii] *= particleData[ii].polarity;
_gkField[ii] *= particleData[ii].polarity;
_inducedDipole[ii] = _fixedMultipoleField[ii];
_inducedDipolePolar[ii] = _fixedMultipoleFieldPolar[ii];
......@@ -2418,7 +2418,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodPa
const MultipoleParticleData& particleJ,
vector<RealVec>& forces,
vector<RealVec>& torques,
vector<RealOpenMM>& dBorn) const
vector<RealOpenMM>& dBorn) const
{
RealOpenMM e,ei;
......@@ -2469,9 +2469,9 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodPa
szi = _inducedDipoleS[iIndex][2] + _inducedDipolePolarS[iIndex][2];
// decide whether to compute the current interaction
RealVec deltaR = particleJ.position - particleI.position;
RealOpenMM r = SQRT(deltaR.dot(deltaR));
RealOpenMM r = SQRT(deltaR.dot(deltaR));
xr = deltaR[0];
yr = deltaR[1];
......@@ -3863,7 +3863,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateElectrosta
vector<RealOpenMM> scaleFactors(LAST_SCALE_TYPE_INDEX);
for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) {
scaleFactors[kk] = 1.0;
}
}
RealOpenMM eDiffEnergy = 0.0;
for (unsigned int ii = 0; ii < particleData.size(); ii++) {
......@@ -3889,7 +3889,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateElectrosta
}
void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateGrycukChainRulePairIxn(const MultipoleParticleData& particleI, const MultipoleParticleData& particleJ,
const vector<RealOpenMM>& dBorn, vector<RealVec>& forces) const
const vector<RealOpenMM>& dBorn, vector<RealVec>& forces) const
{
unsigned int iIndex = particleI.particleIndex;
unsigned int jIndex = particleJ.particleIndex;
......@@ -3937,7 +3937,7 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateGrycukChainRuleP
uik = r + sk;
uik4 = uik*uik;
uik4 = uik4*uik4;
de -= 0.25*M_PI*(sk2+4.0*sk*r+r2)/ (r2*uik4);
RealOpenMM dbr = term*de/r;
de = dbr*dBorn[iIndex];
......@@ -3946,7 +3946,7 @@ void AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateGrycukChainRuleP
forces[jIndex] += deltaR*de;
}
RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateCavityTermEnergyAndForces(vector<RealOpenMM>& dBorn) const
RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateCavityTermEnergyAndForces(vector<RealOpenMM>& dBorn) const
{
RealOpenMM energy = 0.0;
......@@ -3973,7 +3973,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
const MultipoleParticleData& particleJ,
RealOpenMM pscale, RealOpenMM dscale,
vector<RealVec>& forces,
vector<RealVec>& torques) const
vector<RealVec>& torques) const
{
static const RealOpenMM uscale = 1.0;
......@@ -4022,7 +4022,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
RealOpenMM ddsc7_3 = 0.0;
// apply Thole polarization damping to scale factors
RealOpenMM damp = particleI.dampingFactor*particleJ.dampingFactor;
if (damp != 0.0) {
pgamma = particleJ.thole > particleI.thole ? particleI.thole : particleJ.thole;
......@@ -4059,9 +4059,9 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
psc3 = scale3*pscale;
psc5 = scale5*pscale;
psc7 = scale7*pscale;
// construct auxiliary vectors for permanent terms
RealOpenMM dixr1 = particleI.dipole[1]*zr - particleI.dipole[2]*yr;
RealOpenMM dixr2 = particleI.dipole[2]*xr - particleI.dipole[0]*zr;
RealOpenMM dixr3 = particleI.dipole[0]*yr - particleI.dipole[1]*xr;
......@@ -4087,14 +4087,14 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
RealOpenMM rxqkr3 = xr*qkr2 - yr*qkr1;
// get intermediate variables for permanent energy terms
RealOpenMM sc3 = particleI.dipole[0]*xr + particleI.dipole[1]*yr + particleI.dipole[2]*zr;
RealOpenMM sc4 = particleJ.dipole[0]*xr + particleJ.dipole[1]*yr + particleJ.dipole[2]*zr;
RealOpenMM sc5 = qir1*xr + qir2*yr + qir3*zr;
RealOpenMM sc6 = qkr1*xr + qkr2*yr + qkr3*zr;
// construct auxiliary vectors for induced terms
RealOpenMM dixuk1 = particleI.dipole[1]*_inducedDipoleS[jIndex][2] - particleI.dipole[2]*_inducedDipoleS[jIndex][1];
RealOpenMM dixuk2 = particleI.dipole[2]*_inducedDipoleS[jIndex][0] - particleI.dipole[0]*_inducedDipoleS[jIndex][2];
RealOpenMM dixuk3 = particleI.dipole[0]*_inducedDipoleS[jIndex][1] - particleI.dipole[1]*_inducedDipoleS[jIndex][0];
......@@ -4158,7 +4158,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
RealOpenMM rxqkuip1 = yr*qkuip3 - zr*qkuip2;
RealOpenMM rxqkuip2 = zr*qkuip1 - xr*qkuip3;
RealOpenMM rxqkuip3 = xr*qkuip2 - yr*qkuip1;
// get intermediate variables for induction energy terms
RealOpenMM sci1 = _inducedDipoleS[iIndex][0]*particleJ.dipole[0] + _inducedDipoleS[iIndex][1]*particleJ.dipole[1] +
......@@ -4216,7 +4216,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
RealOpenMM gfi6 = -rr7*(sci3*psc7+scip3*dsc7);
// get the induced force
RealOpenMM ftm2i1 = gfi1*xr + 0.5*
(- rr3*particleJ.charge*(_inducedDipoleS[iIndex][0]*psc3+_inducedDipolePolarS[iIndex][0]*dsc3)
+ rr5*sc4*(_inducedDipoleS[iIndex][0]*psc5+_inducedDipolePolarS[iIndex][0]*dsc5)
......@@ -4231,7 +4231,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
+ 0.5*gfi4*((qkui1-qiuk1)*psc5
+ (qkuip1-qiukp1)*dsc5)
+ gfi5*qir1 + gfi6*qkr1;
RealOpenMM ftm2i2 = gfi1*yr + 0.5*
(- rr3*particleJ.charge*(_inducedDipoleS[iIndex][1]*psc3+_inducedDipolePolarS[iIndex][1]*dsc3)
+ rr5*sc4*(_inducedDipoleS[iIndex][1]*psc5+_inducedDipolePolarS[iIndex][1]*dsc5)
......@@ -4261,7 +4261,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
+ 0.5*gfi4*((qkui3-qiuk3)*psc5
+ (qkuip3-qiukp3)*dsc5)
+ gfi5*qir3 + gfi6*qkr3;
// intermediate values needed for partially excluded interactions
RealOpenMM fridmp1 = 0.5*(rr3*((gli1+gli6)*pscale
......@@ -4283,7 +4283,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
+ rr7*(gli3*pscale+glip3*dscale)*ddsc7_3);
// get the induced-induced derivative terms
RealOpenMM findmp1 = 0.5*uscale*(scip2*rr3*ddsc3_1
- rr5*ddsc5_1*(sci3*scip4+scip3*sci4));
......@@ -4309,12 +4309,12 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
ftm2i1 -= fdir1 - findmp1;
ftm2i2 -= fdir2 - findmp2;
ftm2i3 -= fdir3 - findmp3;
}
// now perform the torque calculation
// intermediate terms for torque between multipoles i and j
RealOpenMM gti2 = 0.5*(sci4*psc5+scip4*dsc5)*rr5;
RealOpenMM gti3 = 0.5*(sci3*psc5+scip3*dsc5)*rr5;
RealOpenMM gti4 = gfi4;
......@@ -4346,7 +4346,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
RealOpenMM ttm3i3 = -rr3*(dkxui3*psc3+dkxuip3*dsc3)*0.5
+ gti3*dkxr3 - gti4*((uixqkr3+rxqkui3)*psc5
+(uixqkrp3+rxqkuip3)*dsc5)*0.5 - gti6*rxqkr3;
// update force and torque
RealVec force, torqueI, torqueJ;
......@@ -4610,7 +4610,7 @@ RealOpenMM AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateKirkwoodED
+ gti3*dkxr3 - gti4*((uixqkr3+rxqkui3)*psc5
+(uixqkrp3+rxqkuip3)*dsc5)*0.5 - gti6*rxqkr3;
// update force and torque
// update force and torque
force[0] += ftm2i1;
force[1] += ftm2i2;
......@@ -4635,13 +4635,13 @@ const RealOpenMM AmoebaReferencePmeMultipoleForce::SQRT_PI = 1.77245385091;
AmoebaReferencePmeMultipoleForce::AmoebaReferencePmeMultipoleForce() :
AmoebaReferenceMultipoleForce(PME),
_cutoffDistance(1.0), _cutoffDistanceSquared(1.0),
_pmeGridSize(0), _totalGridSize(0), _alphaEwald(0.0)
_pmeGridSize(0), _totalGridSize(0), _alphaEwald(0.0)
{
_fftplan = NULL;
_pmeGrid = NULL;
_pmeGridDimensions = IntVec(-1, -1, -1);
}
}
AmoebaReferencePmeMultipoleForce::~AmoebaReferencePmeMultipoleForce()
{
......@@ -4652,19 +4652,19 @@ AmoebaReferencePmeMultipoleForce::~AmoebaReferencePmeMultipoleForce()
delete _pmeGrid;
}
};
RealOpenMM AmoebaReferencePmeMultipoleForce::getCutoffDistance() const
RealOpenMM AmoebaReferencePmeMultipoleForce::getCutoffDistance() const
{
return _cutoffDistance;
};
void AmoebaReferencePmeMultipoleForce::setCutoffDistance(RealOpenMM cutoffDistance)
{
_cutoffDistance = cutoffDistance;
_cutoffDistanceSquared = cutoffDistance*cutoffDistance;
};
RealOpenMM AmoebaReferencePmeMultipoleForce::getAlphaEwald() const
RealOpenMM AmoebaReferencePmeMultipoleForce::getAlphaEwald() const
{
return _alphaEwald;
};
......@@ -4674,7 +4674,7 @@ void AmoebaReferencePmeMultipoleForce::setAlphaEwald(RealOpenMM alphaEwald)
_alphaEwald = alphaEwald;
};
void AmoebaReferencePmeMultipoleForce::getPmeGridDimensions(vector<int>& pmeGridDimensions) const
void AmoebaReferencePmeMultipoleForce::getPmeGridDimensions(vector<int>& pmeGridDimensions) const
{
pmeGridDimensions.resize(3);
......@@ -4687,7 +4687,7 @@ void AmoebaReferencePmeMultipoleForce::getPmeGridDimensions(vector<int>& pmeGrid
void AmoebaReferencePmeMultipoleForce::setPmeGridDimensions(vector<int>& pmeGridDimensions)
{
if ((pmeGridDimensions[0] == _pmeGridDimensions[0]) &&
if ((pmeGridDimensions[0] == _pmeGridDimensions[0]) &&
(pmeGridDimensions[1] == _pmeGridDimensions[1]) &&
(pmeGridDimensions[2] == _pmeGridDimensions[2]))
return;
......@@ -4761,9 +4761,9 @@ void AmoebaReferencePmeMultipoleForce::initializePmeGrid()
for (int jj = 0; jj < _totalGridSize; jj++) {
_pmeGrid[jj].re = _pmeGrid[jj].im = 0.0;
}
}
}
void AmoebaReferencePmeMultipoleForce::getPeriodicDelta(RealVec& deltaR) const
void AmoebaReferencePmeMultipoleForce::getPeriodicDelta(RealVec& deltaR) const
{
deltaR -= _periodicBoxVectors[2]*FLOOR(deltaR[2]*_recipBoxVectors[2][2]+0.5);
deltaR -= _periodicBoxVectors[1]*FLOOR(deltaR[1]*_recipBoxVectors[1][1]+0.5);
......@@ -4773,8 +4773,8 @@ void AmoebaReferencePmeMultipoleForce::getPeriodicDelta(RealVec& deltaR) const
void AmoebaReferencePmeMultipoleForce::getDampedInverseDistances(const MultipoleParticleData& particleI,
const MultipoleParticleData& particleJ,
RealOpenMM dscale, RealOpenMM pscale, RealOpenMM r,
RealVec& dampedDInverseDistances,
RealVec& dampedPInverseDistances) const
RealVec& dampedDInverseDistances,
RealVec& dampedPInverseDistances) const
{
RealVec scaleFactor = RealVec(1.0, 1.0, 1.0);
......@@ -4792,8 +4792,8 @@ void AmoebaReferencePmeMultipoleForce::getDampedInverseDistances(const Multipole
scaleFactor[0] = 1.0 - expdamp;
scaleFactor[1] = 1.0 - expdamp*(1.0-damp);
scaleFactor[2] = 1.0 - expdamp*(1.0-damp+(0.6f*damp*damp));
}
}
}
}
RealVec dampedDScale = scaleFactor*dscale;
RealOpenMM r2 = r*r;
......@@ -4808,7 +4808,7 @@ void AmoebaReferencePmeMultipoleForce::getDampedInverseDistances(const Multipole
dampedPInverseDistances = dampedDInverseDistances;
} else {
RealVec dampedPScale = scaleFactor*pscale;
dampedPInverseDistances[0] = (1.0-dampedPScale[0])/r3;
dampedPInverseDistances[0] = (1.0-dampedPScale[0])/r3;
dampedPInverseDistances[1] = 3.0*(1.0-dampedPScale[1])/r5;
dampedPInverseDistances[2] = 15.0*(1.0-dampedPScale[2])/r7;
}
......@@ -4976,7 +4976,7 @@ void AmoebaReferencePmeMultipoleForce::calculateFixedMultipoleFieldPairIxn(const
RealVec qj = RealVec(qxJ.dot(deltaR), qyJ.dot(deltaR), qzJ.dot(deltaR));
RealOpenMM qjr = qj.dot(deltaR);
RealVec fim = qj*(2.0*bn2) - particleJ.dipole*bn1 - deltaR*(bn1*particleJ.charge - bn2*djr+bn3*qjr);
RealVec fjm = qi*(-2.0*bn2) - particleI.dipole*bn1 + deltaR*(bn1*particleI.charge + bn2*dir+bn3*qir);
......@@ -5105,7 +5105,7 @@ void AmoebaReferencePmeMultipoleForce::computeBSplinePoint(vector<RealOpenMM4>&
/**
* Compute b-spline coefficients.
*/
void AmoebaReferencePmeMultipoleForce::computeAmoebaBsplines(const vector<MultipoleParticleData>& particleData)
void AmoebaReferencePmeMultipoleForce::computeAmoebaBsplines(const vector<MultipoleParticleData>& particleData)
{
// get the B-spline coefficients for each multipole site
......@@ -5127,7 +5127,7 @@ void AmoebaReferencePmeMultipoleForce::computeAmoebaBsplines(const vector<Multip
_thetai[jj][ii*AMOEBA_PME_ORDER+kk] = thetaiTemp[kk];
}
}
// Record the grid point.
_iGrid[ii] = igrid;
......@@ -5136,7 +5136,7 @@ void AmoebaReferencePmeMultipoleForce::computeAmoebaBsplines(const vector<Multip
void AmoebaReferencePmeMultipoleForce::transformMultipolesToFractionalCoordinates(const vector<MultipoleParticleData>& particleData) {
// Build matrices for transforming the dipoles and quadrupoles.
RealVec a[3];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
......@@ -5172,7 +5172,7 @@ void AmoebaReferencePmeMultipoleForce::transformMultipolesToFractionalCoordinate
void AmoebaReferencePmeMultipoleForce::transformPotentialToCartesianCoordinates(const vector<RealOpenMM>& fphi, vector<RealOpenMM>& cphi) const {
// Build a matrix for transforming the potential.
RealVec a[3];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
......@@ -5194,9 +5194,9 @@ void AmoebaReferencePmeMultipoleForce::transformPotentialToCartesianCoordinates(
b[i][j] += a[index1[i]][index2[j]]*a[index2[i]][index1[j]];
}
}
// Transform the potential.
for (int i = 0; i < _numParticles; i++) {
cphi[10*i] = fphi[20*i];
cphi[10*i+1] = a[0][0]*fphi[20*i+1] + a[0][1]*fphi[20*i+2] + a[0][2]*fphi[20*i+3];
......@@ -5210,18 +5210,18 @@ void AmoebaReferencePmeMultipoleForce::transformPotentialToCartesianCoordinates(
}
}
void AmoebaReferencePmeMultipoleForce::spreadFixedMultipolesOntoGrid(const vector<MultipoleParticleData>& particleData)
void AmoebaReferencePmeMultipoleForce::spreadFixedMultipolesOntoGrid(const vector<MultipoleParticleData>& particleData)
{
transformMultipolesToFractionalCoordinates(particleData);
// Clear the grid.
for (int gridIndex = 0; gridIndex < _totalGridSize; gridIndex++)
_pmeGrid[gridIndex] = t_complex(0, 0);
// Loop over atoms and spread them on the grid.
for (int atomIndex = 0; atomIndex < _numParticles; atomIndex++) {
RealOpenMM atomCharge = _transformed[atomIndex].charge;
RealVec atomDipole = RealVec(_transformed[atomIndex].dipole[0],
......@@ -5405,19 +5405,19 @@ void AmoebaReferencePmeMultipoleForce::computeFixedPotentialFromGrid()
void AmoebaReferencePmeMultipoleForce::spreadInducedDipolesOnGrid(const vector<RealVec>& inputInducedDipole,
const vector<RealVec>& inputInducedDipolePolar) {
// Create the matrix to convert from Cartesian to fractional coordinates.
RealVec cartToFrac[3];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
cartToFrac[j][i] = _pmeGridDimensions[j]*_recipBoxVectors[i][j];
// Clear the grid.
for (int gridIndex = 0; gridIndex < _totalGridSize; gridIndex++)
_pmeGrid[gridIndex] = t_complex(0, 0);
// Loop over atoms and spread them on the grid.
for (int atomIndex = 0; atomIndex < _numParticles; atomIndex++) {
RealVec inducedDipole = RealVec(inputInducedDipole[atomIndex][0]*cartToFrac[0][0] + inputInducedDipole[atomIndex][1]*cartToFrac[0][1] + inputInducedDipole[atomIndex][2]*cartToFrac[0][2],
inputInducedDipole[atomIndex][0]*cartToFrac[1][0] + inputInducedDipole[atomIndex][1]*cartToFrac[1][1] + inputInducedDipole[atomIndex][2]*cartToFrac[1][2],
......@@ -5432,7 +5432,7 @@ void AmoebaReferencePmeMultipoleForce::spreadInducedDipolesOnGrid(const vector<R
int y = (gridPoint[1]+iy) % _pmeGridDimensions[1];
for (int iz = 0; iz < AMOEBA_PME_ORDER; iz++) {
int z = (gridPoint[2]+iz) % _pmeGridDimensions[2];
RealOpenMM4 t = _thetai[0][atomIndex*AMOEBA_PME_ORDER+ix];
RealOpenMM4 u = _thetai[1][atomIndex*AMOEBA_PME_ORDER+iy];
RealOpenMM4 v = _thetai[2][atomIndex*AMOEBA_PME_ORDER+iz];
......@@ -5654,7 +5654,7 @@ void AmoebaReferencePmeMultipoleForce::computeInducedPotentialFromGrid()
}
RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceFixedMultipoleForceAndEnergy(const vector<MultipoleParticleData>& particleData,
vector<RealVec>& forces, vector<RealVec>& torques) const
vector<RealVec>& forces, vector<RealVec>& torques) const
{
RealOpenMM multipole[10];
const int deriv1[] = {1, 4, 7, 8, 10, 15, 17, 13, 14, 19};
......@@ -5734,7 +5734,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceFixedMultipol
*/
RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceInducedDipoleForceAndEnergy(AmoebaReferenceMultipoleForce::PolarizationType polarizationType,
const vector<MultipoleParticleData>& particleData,
vector<RealVec>& forces, vector<RealVec>& torques) const
vector<RealVec>& forces, vector<RealVec>& torques) const
{
RealOpenMM multipole[10];
......@@ -5820,7 +5820,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceInducedDipole
f[0] += (inducedDipole[k]+inducedDipolePolar[k])*_phi[20*i+j1];
f[1] += (inducedDipole[k]+inducedDipolePolar[k])*_phi[20*i+j2];
f[2] += (inducedDipole[k]+inducedDipolePolar[k])*_phi[20*i+j3];
if (polarizationType == AmoebaReferenceMultipoleForce::Mutual)
{
f[0] += (inducedDipole[k]*_phip[10*i+j1] + inducedDipolePolar[k]*_phid[10*i+j1]);
......@@ -5899,13 +5899,13 @@ void AmoebaReferencePmeMultipoleForce::calculateInducedDipoleFields(const vector
vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleFields)
{
// Initialize the fields to zero.
RealVec zeroVec(0.0, 0.0, 0.0);
for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++)
std::fill(updateInducedDipoleFields[ii].inducedDipoleField.begin(), updateInducedDipoleFields[ii].inducedDipoleField.end(), zeroVec);
// Add fields from direct space interactions.
for (unsigned int ii = 0; ii < particleData.size(); ii++) {
for (unsigned int jj = ii + 1; jj < particleData.size(); jj++) {
calculateDirectInducedDipolePairIxns(particleData[ii], particleData[jj], updateInducedDipoleFields);
......@@ -5916,7 +5916,7 @@ void AmoebaReferencePmeMultipoleForce::calculateInducedDipoleFields(const vector
calculateReciprocalSpaceInducedDipoleField(updateInducedDipoleFields);
// self ixn
// self ixn
RealOpenMM term = (4.0/3.0)*(_alphaEwald*_alphaEwald*_alphaEwald)/SQRT_PI;
for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++) {
......@@ -5924,7 +5924,7 @@ void AmoebaReferencePmeMultipoleForce::calculateInducedDipoleFields(const vector
vector<RealVec>& field = updateInducedDipoleFields[ii].inducedDipoleField;
for (unsigned int jj = 0; jj < particleData.size(); jj++) {
field[jj] += inducedDipoles[jj]*term;
}
}
}
}
......@@ -5932,7 +5932,7 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxn(unsig
RealOpenMM preFactor1, RealOpenMM preFactor2,
const RealVec& delta,
const vector<RealVec>& inducedDipole,
vector<RealVec>& field) const
vector<RealVec>& field) const
{
// field at i due induced dipole at j
......@@ -5952,7 +5952,7 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons
{
// compute the real space portion of the Ewald summation
RealOpenMM uscale = 1.0;
RealVec deltaR = particleJ.position - particleI.position;
......@@ -6013,10 +6013,10 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons
calculateDirectInducedDipolePairIxn(particleI.particleIndex, particleJ.particleIndex, preFactor1, preFactor2, deltaR,
*updateInducedDipoleFields[ii].inducedDipoles,
updateInducedDipoleFields[ii].inducedDipoleField);
}
}
}
RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeSelfEnergy(const vector<MultipoleParticleData>& particleData) const
RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeSelfEnergy(const vector<MultipoleParticleData>& particleData) const
{
RealOpenMM cii = 0.0;
RealOpenMM dii = 0.0;
......@@ -6044,7 +6044,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeSelfEnergy(const vector
}
void AmoebaReferencePmeMultipoleForce::calculatePmeSelfTorque(const vector<MultipoleParticleData>& particleData,
vector<RealVec>& torques) const
vector<RealVec>& torques) const
{
RealOpenMM term = (2.0/3.0)*(_electric/_dielectric)*(_alphaEwald*_alphaEwald*_alphaEwald)/SQRT_PI;
for (unsigned int ii = 0; ii < _numParticles; ii++) {
......@@ -6058,11 +6058,11 @@ void AmoebaReferencePmeMultipoleForce::calculatePmeSelfTorque(const vector<Multi
}
}
RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPairIxn(const MultipoleParticleData& particleI,
RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPairIxn(const MultipoleParticleData& particleI,
const MultipoleParticleData& particleJ,
const vector<RealOpenMM>& scalingFactors,
vector<RealVec>& forces,
vector<RealVec>& torques) const
vector<RealVec>& torques) const
{
unsigned int iIndex = particleI.particleIndex;
......@@ -6483,7 +6483,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculateElectrostatic(const vector
vector<RealOpenMM> scaleFactors(LAST_SCALE_TYPE_INDEX);
for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) {
scaleFactors[kk] = 1.0;
}
}
// loop over particle pairs for direct space interactions
......@@ -6508,6 +6508,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculateElectrostatic(const vector
energy += computeReciprocalSpaceInducedDipoleForceAndEnergy(getPolarizationType(), particleData, forces, torques);
energy += computeReciprocalSpaceFixedMultipoleForceAndEnergy(particleData, forces, torques);
energy += calculatePmeSelfEnergy(particleData);
return energy;
}
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