Skip to content

GitLab

Commit 77b9b7ba authored by peastman's avatar peastman Committed by GitHub
Browse files

Merge pull request #1534 from saurabhbelsare/master 

Added functions to get per atom lab frame permanent dipoles and per atom total dipole moments for AMOEBA
parents 339167f4 92d86ead
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 672 additions and 234 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ 77b9b7ba
......@@ -370,7 +370,13 @@ public:
* This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.
*/
void setEwaldErrorTolerance(double tol);
/**
* Get the fixed dipole moments of all particles in the global reference frame.
*
* @param context the Context for which to get the fixed dipoles
* @param[out] dipoles the fixed dipole moment of particle i is stored into the i'th element
*/
void getLabFramePermanentDipoles(Context& context, std::vector<Vec3>& dipoles);
/**
* Get the induced dipole moments of all particles.
*
......@@ -379,6 +385,14 @@ public:
*/
void getInducedDipoles(Context& context, std::vector<Vec3>& dipoles);
/**
* Get the total dipole moments (fixed plus induced) of all particles.
*
* @param context the Context for which to get the total dipoles
* @param[out] dipoles the total dipole moment of particle i is stored into the i'th element
*/
void getTotalDipoles(Context& context, std::vector<Vec3>& dipoles);
/**
* Get the electrostatic potential.
*
......
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ 77b9b7ba
......@@ -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
*/
......@@ -348,7 +348,9 @@ 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 getTotalDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
virtual void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) = 0;
......@@ -364,7 +366,7 @@ 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 +391,7 @@ 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 +431,7 @@ 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 +471,7 @@ 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 @ 77b9b7ba
......@@ -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
......@@ -76,13 +76,14 @@ 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 getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getTotalDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential);
......@@ -90,7 +91,7 @@ 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 @ 77b9b7ba
......@@ -147,13 +147,13 @@ 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;
......@@ -183,7 +183,7 @@ 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;
......@@ -250,6 +250,14 @@ void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dip
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getInducedDipoles(getContextImpl(context), dipoles);
}
void AmoebaMultipoleForce::getLabFramePermanentDipoles(Context& context, vector<Vec3>& dipoles) {
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getLabFramePermanentDipoles(getContextImpl(context), dipoles);
}
void AmoebaMultipoleForce::getTotalDipoles(Context& context, vector<Vec3>& dipoles) {
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getTotalDipoles(getContextImpl(context), dipoles);
}
void AmoebaMultipoleForce::getElectrostaticPotential(const std::vector< Vec3 >& inputGrid, Context& context, std::vector< double >& outputElectrostaticPotential) {
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getElectrostaticPotential(getContextImpl(context), inputGrid, outputElectrostaticPotential);
}
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ 77b9b7ba
......@@ -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;
}
......@@ -179,14 +179,22 @@ 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);
}
void AmoebaMultipoleForceImpl::getTotalDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getTotalDipoles(context, dipoles);
}
void AmoebaMultipoleForceImpl::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getElectrostaticPotential(context, inputGrid, outputElectrostaticPotential);
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 77b9b7ba
......@@ -1992,6 +1992,27 @@ void CudaCalcAmoebaMultipoleForceKernel::ensureMultipolesValid(ContextImpl& cont
context.calcForcesAndEnergy(false, false, -1);
}
void CudaCalcAmoebaMultipoleForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
ensureMultipolesValid(context);
int numParticles = cu.getNumAtoms();
dipoles.resize(numParticles);
const vector<int>& order = cu.getAtomIndex();
if (cu.getUseDoublePrecision()) {
vector<double> labDipoleVec;
labFrameDipoles->download(labDipoleVec);
for (int i = 0; i < numParticles; i++)
dipoles[order[i]] = Vec3(labDipoleVec[3*i], labDipoleVec[3*i+1], labDipoleVec[3*i+2]);
}
else {
vector<float> labDipoleVec;
labFrameDipoles->download(labDipoleVec);
for (int i = 0; i < numParticles; i++)
dipoles[order[i]] = Vec3(labDipoleVec[3*i], labDipoleVec[3*i+1], labDipoleVec[3*i+2]);
}
}
void CudaCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
ensureMultipolesValid(context);
int numParticles = cu.getNumAtoms();
......@@ -2011,6 +2032,48 @@ void CudaCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& context,
}
}
void CudaCalcAmoebaMultipoleForceKernel::getTotalDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
ensureMultipolesValid(context);
int numParticles = cu.getNumAtoms();
dipoles.resize(numParticles);
const vector<int>& order = cu.getAtomIndex();
if (cu.getUseDoublePrecision()) {
vector<double4> posqVec;
vector<double> labDipoleVec;
vector<double> inducedDipoleVec;
double totalDipoleVecX;
double totalDipoleVecY;
double totalDipoleVecZ;
inducedDipole->download(inducedDipoleVec);
labFrameDipoles->download(labDipoleVec);
cu.getPosq().download(posqVec);
for (int i = 0; i < numParticles; i++) {
totalDipoleVecX = labDipoleVec[3*i] + inducedDipoleVec[3*i];
totalDipoleVecY = labDipoleVec[3*i+1] + inducedDipoleVec[3*i+1];
totalDipoleVecZ = labDipoleVec[3*i+2] + inducedDipoleVec[3*i+2];
dipoles[order[i]] = Vec3(totalDipoleVecX, totalDipoleVecY, totalDipoleVecZ);
}
}
else {
vector<float4> posqVec;
vector<float> labDipoleVec;
vector<float> inducedDipoleVec;
float totalDipoleVecX;
float totalDipoleVecY;
float totalDipoleVecZ;
inducedDipole->download(inducedDipoleVec);
labFrameDipoles->download(labDipoleVec);
cu.getPosq().download(posqVec);
for (int i = 0; i < numParticles; i++) {
totalDipoleVecX = labDipoleVec[3*i] + inducedDipoleVec[3*i];
totalDipoleVecY = labDipoleVec[3*i+1] + inducedDipoleVec[3*i+1];
totalDipoleVecZ = labDipoleVec[3*i+2] + inducedDipoleVec[3*i+2];
dipoles[order[i]] = Vec3(totalDipoleVecX, totalDipoleVecY, totalDipoleVecZ);
}
}
}
void CudaCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const vector<Vec3>& inputGrid, vector<double>& outputElectrostaticPotential) {
ensureMultipolesValid(context);
int numPoints = inputGrid.size();
......@@ -2164,6 +2227,7 @@ void CudaCalcAmoebaMultipoleForceKernel::computeSystemMultipoleMoments(ContextIm
outputMultipoleMoments[12] = 100.0*zzqdp*debye;
}
void CudaCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, vector<double>& outputMultipoleMoments) {
ensureMultipolesValid(context);
if (cu.getUseDoublePrecision())
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ 77b9b7ba
......@@ -328,6 +328,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Get the LabFrame dipole moments of all particles.
*
* @param context the Context for which to get the induced dipoles
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Get the induced dipole moments of all particles.
*
......@@ -335,6 +342,13 @@ public:
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Get the total dipole moments of all particles.
*
* @param context the Context for which to get the induced dipoles
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getTotalDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Execute the kernel to calculate the electrostatic potential
*
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ 77b9b7ba
......@@ -2666,6 +2666,76 @@ static void testParticleInducedDipoles() {
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test querying particle lab frame permanent dipoles
static void testParticleLabFramePermanentDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getLabFramePermanentDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.00876454250, -2.04310718E-06, -0.00227593519);
expectedDipole[1] = Vec3(0.000780382180, -0.00432882849, 0.00236926761);
expectedDipole[2] = Vec3(0.000801345883, 0.00431830946, 0.00238143437);
expectedDipole[3] = Vec3(-0.00109746996, 1.16087953e-5, -0.00487407492);
expectedDipole[4] = Vec3(0.00203814102, -2.26554196e-5, 0.00882284298);
expectedDipole[5] = Vec3(-0.00239443187, 0.00432388648, 0.000729303209);
expectedDipole[6] = Vec3(0.00491086743, 2.86430963e-6, -0.000918996348);
expectedDipole[7] = Vec3(-0.00239301946, -0.00432743976, 0.000712674115);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test querying particle total dipoles (fixed + induced)
static void testParticleTotalDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getTotalDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.0119356307, -1.11302433e-6, -0.00296793872);
expectedDipole[1] = Vec3(8.60636211e-4, -0.00460821816, 0.00241705344);
expectedDipole[2] = Vec3(8.80646403e-4, 0.00459728769, 0.00243013245);
expectedDipole[3] = Vec3(-0.00123822377, 1.31555550e-5, -0.00558185336);
expectedDipole[4] = Vec3(0.00399455556, -2.27511931e-5, 0.00955607952);
expectedDipole[5] = Vec3(-0.00157302682, 0.00354892386, 3.40921137e-4);
expectedDipole[6] = Vec3(0.00952428069, 2.14171505e-6, -6.68945865e-4);
expectedDipole[7] = Vec3(-0.00157252460, -0.00355015528, 3.27055162e-4);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test computation of system multipole moments
static void testSystemMultipoleMoments() {
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 77b9b7ba
......@@ -735,6 +735,48 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& con
delete amoebaReferenceMultipoleForce;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& outputDipoles) {
int numParticles = context.getSystem().getNumParticles();
outputDipoles.resize(numParticles);
// Create an AmoebaReferenceMultipoleForce to do the calculation.
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
// Retrieve the permanent dipoles in the lab frame.
vector<RealVec> labFramePermanentDipoles;
amoebaReferenceMultipoleForce->calculateLabFramePermanentDipoles(posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, multipoleAtomCovalentInfo, labFramePermanentDipoles);
for (int i = 0; i < numParticles; i++)
outputDipoles[i] = labFramePermanentDipoles[i];
delete amoebaReferenceMultipoleForce;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getTotalDipoles(ContextImpl& context, vector<Vec3>& outputDipoles) {
int numParticles = context.getSystem().getNumParticles();
outputDipoles.resize(numParticles);
// Create an AmoebaReferenceMultipoleForce to do the calculation.
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
// Retrieve the permanent dipoles in the lab frame.
vector<RealVec> totalDipoles;
amoebaReferenceMultipoleForce->calculateTotalDipoles(posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, multipoleAtomCovalentInfo, totalDipoles);
for (int i = 0; i < numParticles; i++)
outputDipoles[i] = totalDipoles[i];
delete amoebaReferenceMultipoleForce;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) {
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 77b9b7ba
......@@ -381,6 +381,20 @@ public:
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Get the fixed dipole moments of all particles in the global reference frame.
*
* @param context the Context for which to get the fixed dipoles
* @param dipoles the fixed dipole moment of particle i is stored into the i'th element
*/
void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Get the total dipole moments of all particles in the global reference frame.
*
* @param context the Context for which to get the fixed dipoles
* @param dipoles the fixed dipole moment of particle i is stored into the i'th element
*/
void getTotalDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Calculate the electrostatic potential given vector of grid coordinates.
*
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 77b9b7ba
......@@ -533,6 +533,75 @@ public:
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputInducedDipoles);
/**
* Calculate particle permanent dipoles rotated in the lab frame.
*
* @param masses particle masses
* @param particlePositions Cartesian coordinates of particles
* @param charges scalar charges for each particle
* @param dipoles molecular frame dipoles for each particle
* @param quadrupoles molecular frame quadrupoles for each particle
* @param tholes Thole factors for each particle
* @param dampingFactors dampling factors for each particle
* @param polarity polarity for each particle
* @param axisTypes axis type (Z-then-X, ...) for each particle
* @param multipoleAtomZs indicies of particle specifying the molecular frame z-axis for each particle
* @param multipoleAtomXs indicies of particle specifying the molecular frame x-axis for each particle
* @param multipoleAtomYs indicies of particle specifying the molecular frame y-axis for each particle
* @param multipoleAtomCovalentInfo covalent info needed to set scaling factors
* @param outputMultipoleMoments output multipole moments
*/
void calculateLabFramePermanentDipoles(const std::vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles,
const std::vector<RealOpenMM>& tholes,
const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputRotatedPermanentDipoles);
/**
* Calculate particle total dipoles.
*
* @param masses particle masses
* @param particlePositions Cartesian coordinates of particles
* @param charges scalar charges for each particle
* @param dipoles molecular frame dipoles for each particle
* @param quadrupoles molecular frame quadrupoles for each particle
* @param tholes Thole factors for each particle
* @param dampingFactors dampling factors for each particle
* @param polarity polarity for each particle
* @param axisTypes axis type (Z-then-X, ...) for each particle
* @param multipoleAtomZs indicies of particle specifying the molecular frame z-axis for each particle
* @param multipoleAtomXs indicies of particle specifying the molecular frame x-axis for each particle
* @param multipoleAtomYs indicies of particle specifying the molecular frame y-axis for each particle
* @param multipoleAtomCovalentInfo covalent info needed to set scaling factors
* @param outputMultipoleMoments output multipole moments
*/
void calculateTotalDipoles(const std::vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles,
const std::vector<RealOpenMM>& tholes,
const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputRotatedPermanentDipoles);
/**
* Calculate system multipole moments.
*
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp
View file @ 77b9b7ba
......@@ -2587,6 +2587,76 @@ static void testParticleInducedDipoles() {
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test querying particle lab frame permanent dipoles
static void testParticleLabFramePermanentDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getLabFramePermanentDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.00876454250, -2.04310718E-06, -0.00227593519);
expectedDipole[1] = Vec3(0.000780382180, -0.00432882849, 0.00236926761);
expectedDipole[2] = Vec3(0.000801345883, 0.00431830946, 0.00238143437);
expectedDipole[3] = Vec3(-0.00109746996, 1.16087953e-5, -0.00487407492);
expectedDipole[4] = Vec3(0.00203814102, -2.26554196e-5, 0.00882284298);
expectedDipole[5] = Vec3(-0.00239443187, 0.00432388648, 0.000729303209);
expectedDipole[6] = Vec3(0.00491086743, 2.86430963e-6, -0.000918996348);
expectedDipole[7] = Vec3(-0.00239301946, -0.00432743976, 0.000712674115);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test querying particle total dipoles (fixed + induced)
static void testParticleTotalDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getTotalDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.0119356307, -1.11302433e-6, -0.00296793872);
expectedDipole[1] = Vec3(8.60636211e-4, -0.00460821816, 0.00241705344);
expectedDipole[2] = Vec3(8.80646403e-4, 0.00459728769, 0.00243013245);
expectedDipole[3] = Vec3(-0.00123822377, 1.31555550e-5, -0.00558185336);
expectedDipole[4] = Vec3(0.00399455556, -2.27511931e-5, 0.00955607952);
expectedDipole[5] = Vec3(-0.00157302682, 0.00354892386, 3.40921137e-4);
expectedDipole[6] = Vec3(0.00952428069, 2.14171505e-6, -6.68945865e-4);
expectedDipole[7] = Vec3(-0.00157252460, -0.00355015528, 3.27055162e-4);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test computation of system multipole moments
static void testSystemMultipoleMoments() {
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 77b9b7ba
......@@ -124,6 +124,8 @@ NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
('AmoebaMultipoleForce', 'setCovalentMap', 'covalentAtoms'),
('AmoebaMultipoleForce', 'getElectrostaticPotential', 'context'),
('AmoebaMultipoleForce', 'getInducedDipoles', 'context'),
('AmoebaMultipoleForce', 'getLabFramePermanentDipoles', 'context'),
('AmoebaMultipoleForce', 'getTotalDipoles', 'context'),
]
# SWIG assumes the target language shadow class owns the C++ class
......@@ -274,6 +276,8 @@ UNITS = {
#("AmoebaMultipoleForce", "getElectrostaticPotential") : ( ('unit.kilojoule_per_mole'), ()),
("AmoebaMultipoleForce", "getElectrostaticPotential") : ( None, ()),
("AmoebaMultipoleForce", "getInducedDipoles") : ( None, ()),
("AmoebaMultipoleForce", "getLabFramePermanentDipoles") : ( None, ()),
("AmoebaMultipoleForce", "getTotalDipoles") : ( None, ()),
("AmoebaMultipoleForce", "getSystemMultipoleMoments") : ( None, ()),
("AmoebaOutOfPlaneBendForce", "getNumOutOfPlaneBends") : ( None, ()),
......
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