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
Show 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: ...@@ -370,7 +370,13 @@ public:
* This can be overridden by explicitly setting an alpha parameter and grid dimensions to use. * This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.
*/ */
void setEwaldErrorTolerance(double tol); 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. * Get the induced dipole moments of all particles.
* *
...@@ -379,6 +385,14 @@ public: ...@@ -379,6 +385,14 @@ public:
*/ */
void getInducedDipoles(Context& context, std::vector<Vec3>& dipoles); 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. * Get the electrostatic potential.
* *
......
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ 77b9b7ba
...@@ -348,7 +348,9 @@ public: ...@@ -348,7 +348,9 @@ public:
*/ */
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0; 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 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, virtual void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) = 0; std::vector< double >& outputElectrostaticPotential) = 0;
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h
View file @ 77b9b7ba
...@@ -81,8 +81,9 @@ public: ...@@ -81,8 +81,9 @@ public:
* @param covalentDegree covalent degrees for the CovalentEnd lists * @param covalentDegree covalent degrees for the CovalentEnd lists
*/ */
static void getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree); 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 getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getTotalDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid, void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential); std::vector< double >& outputElectrostaticPotential);
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 77b9b7ba
...@@ -250,6 +250,14 @@ void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dip ...@@ -250,6 +250,14 @@ void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dip
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getInducedDipoles(getContextImpl(context), 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::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) { void AmoebaMultipoleForce::getElectrostaticPotential(const std::vector< Vec3 >& inputGrid, Context& context, std::vector< double >& outputElectrostaticPotential) {
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getElectrostaticPotential(getContextImpl(context), inputGrid, outputElectrostaticPotential); dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getElectrostaticPotential(getContextImpl(context), inputGrid, outputElectrostaticPotential);
} }
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ 77b9b7ba
...@@ -183,10 +183,18 @@ void AmoebaMultipoleForceImpl::getCovalentDegree(const AmoebaMultipoleForce& for ...@@ -183,10 +183,18 @@ void AmoebaMultipoleForceImpl::getCovalentDegree(const AmoebaMultipoleForce& for
return; return;
} }
void AmoebaMultipoleForceImpl::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getLabFramePermanentDipoles(context, dipoles);
}
void AmoebaMultipoleForceImpl::getInducedDipoles(ContextImpl& context, vector<Vec3>& dipoles) { void AmoebaMultipoleForceImpl::getInducedDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getInducedDipoles(context, 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, void AmoebaMultipoleForceImpl::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) { std::vector< double >& outputElectrostaticPotential) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getElectrostaticPotential(context, inputGrid, 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 ...@@ -1992,6 +1992,27 @@ void CudaCalcAmoebaMultipoleForceKernel::ensureMultipolesValid(ContextImpl& cont
context.calcForcesAndEnergy(false, false, -1); 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) { void CudaCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
ensureMultipolesValid(context); ensureMultipolesValid(context);
int numParticles = cu.getNumAtoms(); int numParticles = cu.getNumAtoms();
...@@ -2011,6 +2032,48 @@ void CudaCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& context, ...@@ -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) { void CudaCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const vector<Vec3>& inputGrid, vector<double>& outputElectrostaticPotential) {
ensureMultipolesValid(context); ensureMultipolesValid(context);
int numPoints = inputGrid.size(); int numPoints = inputGrid.size();
...@@ -2164,6 +2227,7 @@ void CudaCalcAmoebaMultipoleForceKernel::computeSystemMultipoleMoments(ContextIm ...@@ -2164,6 +2227,7 @@ void CudaCalcAmoebaMultipoleForceKernel::computeSystemMultipoleMoments(ContextIm
outputMultipoleMoments[12] = 100.0*zzqdp*debye; outputMultipoleMoments[12] = 100.0*zzqdp*debye;
} }
void CudaCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, vector<double>& outputMultipoleMoments) { void CudaCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, vector<double>& outputMultipoleMoments) {
ensureMultipolesValid(context); ensureMultipolesValid(context);
if (cu.getUseDoublePrecision()) if (cu.getUseDoublePrecision())
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ 77b9b7ba
...@@ -328,6 +328,13 @@ public: ...@@ -328,6 +328,13 @@ public:
* @return the potential energy due to the force * @return the potential energy due to the force
*/ */
double execute(ContextImpl& context, bool includeForces, bool includeEnergy); 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. * Get the induced dipole moments of all particles.
* *
...@@ -335,6 +342,13 @@ public: ...@@ -335,6 +342,13 @@ public:
* @param dipoles the induced dipole moment of particle i is stored into the i'th element * @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/ */
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles); 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 * 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() { ...@@ -2666,6 +2666,76 @@ static void testParticleInducedDipoles() {
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4); 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 // test computation of system multipole moments
static void testSystemMultipoleMoments() { static void testSystemMultipoleMoments() {
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 77b9b7ba
...@@ -735,6 +735,48 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& con ...@@ -735,6 +735,48 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& con
delete amoebaReferenceMultipoleForce; 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, void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) { std::vector< double >& outputElectrostaticPotential) {
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 77b9b7ba
...@@ -381,6 +381,20 @@ public: ...@@ -381,6 +381,20 @@ public:
* @param dipoles the induced dipole moment of particle i is stored into the i'th element * @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/ */
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles); 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. * Calculate the electrostatic potential given vector of grid coordinates.
* *
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 77b9b7ba
...@@ -1943,6 +1943,64 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<RealVec ...@@ -1943,6 +1943,64 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<RealVec
outputInducedDipoles = _inducedDipole; outputInducedDipoles = _inducedDipole;
} }
void AmoebaReferenceMultipoleForce::calculateLabFramePermanentDipoles(const vector<RealVec>& particlePositions,
const vector<RealOpenMM>& charges,
const vector<RealOpenMM>& dipoles,
const vector<RealOpenMM>& quadrupoles,
const vector<RealOpenMM>& tholes,
const vector<RealOpenMM>& dampingFactors,
const vector<RealOpenMM>& polarity,
const vector<int>& axisTypes,
const vector<int>& multipoleAtomZs,
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
vector<RealVec>& outputRotatedPermanentDipoles) {
// setup, including calculating permanent dipoles
vector<MultipoleParticleData> particleData;
setup(particlePositions, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, particleData);
outputRotatedPermanentDipoles.resize(_numParticles);
for (int i = 0; i < _numParticles; i++)
{
outputRotatedPermanentDipoles[i] = particleData[i].dipole;
}
}
void AmoebaReferenceMultipoleForce::calculateTotalDipoles(const vector<RealVec>& particlePositions,
const vector<RealOpenMM>& charges,
const vector<RealOpenMM>& dipoles,
const vector<RealOpenMM>& quadrupoles,
const vector<RealOpenMM>& tholes,
const vector<RealOpenMM>& dampingFactors,
const vector<RealOpenMM>& polarity,
const vector<int>& axisTypes,
const vector<int>& multipoleAtomZs,
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
vector<RealVec>& outputTotalDipoles) {
// setup, including calculating permanent dipoles
vector<MultipoleParticleData> particleData;
setup(particlePositions, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, particleData);
outputTotalDipoles.resize(_numParticles);
for (int i = 0; i < _numParticles; i++)
{
for (int j = 0; j < 3; j++)
{
outputTotalDipoles[i][j] = particleData[i].dipole[j] + _inducedDipole[i][j];
}
}
}
void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments(const vector<RealOpenMM>& masses, void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments(const vector<RealOpenMM>& masses,
const vector<RealVec>& particlePositions, const vector<RealVec>& particlePositions,
const vector<RealOpenMM>& charges, const vector<RealOpenMM>& charges,
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 77b9b7ba
...@@ -533,6 +533,75 @@ public: ...@@ -533,6 +533,75 @@ public:
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputInducedDipoles); 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. * Calculate system multipole moments.
* *
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp
View file @ 77b9b7ba
...@@ -2587,6 +2587,76 @@ static void testParticleInducedDipoles() { ...@@ -2587,6 +2587,76 @@ static void testParticleInducedDipoles() {
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4); 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 // test computation of system multipole moments
static void testSystemMultipoleMoments() { static void testSystemMultipoleMoments() {
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 77b9b7ba
...@@ -124,6 +124,8 @@ NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'), ...@@ -124,6 +124,8 @@ NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
('AmoebaMultipoleForce', 'setCovalentMap', 'covalentAtoms'), ('AmoebaMultipoleForce', 'setCovalentMap', 'covalentAtoms'),
('AmoebaMultipoleForce', 'getElectrostaticPotential', 'context'), ('AmoebaMultipoleForce', 'getElectrostaticPotential', 'context'),
('AmoebaMultipoleForce', 'getInducedDipoles', 'context'), ('AmoebaMultipoleForce', 'getInducedDipoles', 'context'),
('AmoebaMultipoleForce', 'getLabFramePermanentDipoles', 'context'),
('AmoebaMultipoleForce', 'getTotalDipoles', 'context'),
] ]
# SWIG assumes the target language shadow class owns the C++ class # SWIG assumes the target language shadow class owns the C++ class
...@@ -274,6 +276,8 @@ UNITS = { ...@@ -274,6 +276,8 @@ UNITS = {
#("AmoebaMultipoleForce", "getElectrostaticPotential") : ( ('unit.kilojoule_per_mole'), ()), #("AmoebaMultipoleForce", "getElectrostaticPotential") : ( ('unit.kilojoule_per_mole'), ()),
("AmoebaMultipoleForce", "getElectrostaticPotential") : ( None, ()), ("AmoebaMultipoleForce", "getElectrostaticPotential") : ( None, ()),
("AmoebaMultipoleForce", "getInducedDipoles") : ( None, ()), ("AmoebaMultipoleForce", "getInducedDipoles") : ( None, ()),
("AmoebaMultipoleForce", "getLabFramePermanentDipoles") : ( None, ()),
("AmoebaMultipoleForce", "getTotalDipoles") : ( None, ()),
("AmoebaMultipoleForce", "getSystemMultipoleMoments") : ( None, ()), ("AmoebaMultipoleForce", "getSystemMultipoleMoments") : ( None, ()),
("AmoebaOutOfPlaneBendForce", "getNumOutOfPlaneBends") : ( 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