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Commit a381a3ab authored by peastman's avatar peastman
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Merge branch 'master' into gayberne

parents 5ecc8e00 1f7866ad
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Showing with 336 additions and 169 deletions
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
View file @ a381a3ab
......@@ -38,20 +38,19 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false) {
energyTheta = ReferenceForce::getVariablePointer(this->energyExpression, "theta");
forceTheta = ReferenceForce::getVariablePointer(this->forceExpression, "theta");
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters,
const vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false), energyParamDerivExpressions(energyParamDerivExpressions) {
expressionSet.registerExpression(this->energyExpression);
expressionSet.registerExpression(this->forceExpression);
for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
thetaIndex = expressionSet.getVariableIndex("theta");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++) {
energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
forceParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, parameterNames[i]));
}
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpression, iter->first), iter->second);
}
for (int i = 0; i < (int) numParameters; i++)
torsionParamIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
}
/**---------------------------------------------------------------------------------------
......@@ -86,18 +85,10 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceCustomTorsionIxn::calculateTorsionIxn";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
RealOpenMM* totalEnergy, double* energyParamDerivs) {
RealOpenMM deltaR[3][ReferenceForce::LastDeltaRIndex];
for (int i = 0; i < numParameters; i++) {
ReferenceForce::setVariable(energyParams[i], parameters[i]);
ReferenceForce::setVariable(forceParams[i], parameters[i]);
}
for (int i = 0; i < numParameters; i++)
expressionSet.setVariable(torsionParamIndex[i], parameters[i]);
// ---------------------------------------------------------------------------------------
......@@ -130,8 +121,7 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
RealOpenMM dotDihedral;
RealOpenMM signOfAngle;
RealOpenMM angle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2], crossProduct, &dotDihedral, deltaR[0], &signOfAngle, 1);
ReferenceForce::setVariable(energyTheta, angle);
ReferenceForce::setVariable(forceTheta, angle);
expressionSet.setVariable(thetaIndex, angle);
// evaluate delta angle, dE/d(angle)
......@@ -174,6 +164,11 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
forces[atomDIndex][ii] += internalF[3][ii];
}
// Record parameter derivatives.
for (int i = 0; i < energyParamDerivExpressions.size(); i++)
energyParamDerivs[i] += energyParamDerivExpressions[i].evaluate();
// accumulate energies
if (totalEnergy != NULL)
......
platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp
View file @ a381a3ab
......@@ -74,7 +74,7 @@ void ReferenceHarmonicBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
RealOpenMM* totalEnergy, double* energyParamDerivs) {
static const std::string methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
......
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
View file @ a381a3ab
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -81,7 +81,7 @@ ReferenceLJCoulomb14::~ReferenceLJCoulomb14() {
void ReferenceLJCoulomb14::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
RealOpenMM* totalEnergy, double* energyParamDerivs) {
static const std::string methodName = "\nReferenceLJCoulomb14::calculateBondIxn";
......
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @ a381a3ab
......@@ -420,6 +420,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
RealOpenMM totalExclusionEnergy = 0.0f;
const double TWO_OVER_SQRT_PI = 2/sqrt(PI_M);
for (int i = 0; i < numberOfAtoms; i++)
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
if (*iter > i) {
......@@ -446,12 +447,15 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
// accumulate energies
realSpaceEwaldEnergy = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erf(alphaR));
}
else {
realSpaceEwaldEnergy = (RealOpenMM) (alphaEwald*TWO_OVER_SQRT_PI*ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]);
}
totalExclusionEnergy += realSpaceEwaldEnergy;
if (energyByAtom) {
energyByAtom[ii] -= realSpaceEwaldEnergy;
energyByAtom[jj] -= realSpaceEwaldEnergy;
}
totalExclusionEnergy += realSpaceEwaldEnergy;
if (energyByAtom) {
energyByAtom[ii] -= realSpaceEwaldEnergy;
energyByAtom[jj] -= realSpaceEwaldEnergy;
}
}
}
......
platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp
View file @ a381a3ab
......@@ -75,7 +75,7 @@ void ReferenceProperDihedralBond::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
RealOpenMM* totalEnergy, double* energyParamDerivs) {
static const std::string methodName = "\nReferenceProperDihedralBond::calculateBondIxn";
......
platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp
View file @ a381a3ab
......@@ -73,7 +73,7 @@ void ReferenceRbDihedralBond::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
RealOpenMM* totalEnergy, double* energyParamDerivs) {
static const std::string methodName = "\nReferenceRbDihedralBond::calculateBondIxn";
......
platforms/reference/src/SimTKReference/SimTKOpenMMUtilities.cpp
View file @ a381a3ab
......@@ -383,8 +383,11 @@ void SimTKOpenMMUtilities::createCheckpoint(std::ostream& stream) {
void SimTKOpenMMUtilities::loadCheckpoint(std::istream& stream) {
stream.read((char*) &_randomNumberSeed, sizeof(uint32_t));
bool prevInitialized = _randomInitialized;
stream.read((char*) &_randomInitialized, sizeof(bool));
if (_randomInitialized) {
if (!prevInitialized)
init_gen_rand(0, sfmt);
stream.read((char*) &nextGaussianIsValid, sizeof(bool));
stream.read((char*) &nextGaussian, sizeof(RealOpenMM));
sfmt.loadCheckpoint(stream);
......
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ a381a3ab
......@@ -147,11 +147,34 @@ public:
*/
void setCutoffDistance(double distance);
/**
* Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param[out] alpha the separation parameter
* @param[out] nx the number of grid points along the X axis
* @param[out] ny the number of grid points along the Y axis
* @param[out] nz the number of grid points along the Z axis
*/
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
* Set the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @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
* @param nz the number of grid points along the Z axis
*/
void setPMEParameters(double alpha, int nx, int ny, int nz);
/**
* Get the Ewald alpha parameter. If this is 0 (the default), a value is chosen automatically
* based on the Ewald error tolerance.
*
* @return the Ewald alpha parameter
* @deprecated This method exists only for backward compatibility. Use getPMEParameters() instead.
*/
double getAEwald() const;
......@@ -160,6 +183,7 @@ public:
* based on the Ewald error tolerance.
*
* @param aewald alpha parameter
* @deprecated This method exists only for backward compatibility. Use setPMEParameters() instead.
*/
void setAEwald(double aewald);
......@@ -175,6 +199,7 @@ public:
* are chosen automatically based on the Ewald error tolerance.
*
* @return the PME grid dimensions
* @deprecated This method exists only for backward compatibility. Use getPMEParameters() instead.
*/
void getPmeGridDimensions(std::vector<int>& gridDimension) const;
......@@ -183,6 +208,7 @@ public:
* are chosen automatically based on the Ewald error tolerance.
*
* @param gridDimension the PME grid dimensions
* @deprecated This method exists only for backward compatibility. Use setPMEParameters() instead.
*/
void setPmeGridDimensions(const std::vector<int>& gridDimension);
......@@ -344,7 +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.
*
......@@ -353,6 +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.
*
......@@ -408,9 +448,8 @@ private:
NonbondedMethod nonbondedMethod;
PolarizationType polarizationType;
double cutoffDistance;
double aewald;
int pmeBSplineOrder;
std::vector<int> pmeGridDimension;
double alpha;
int pmeBSplineOrder, nx, ny, nz;
int mutualInducedMaxIterations;
std::vector<double> extrapolationCoefficients;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ a381a3ab
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -183,13 +183,34 @@ public:
*/
void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
/**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @return the cutoff distance, measured in nm
*/
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @param distance the cutoff distance, measured in nm
*/
void setCutoffDistance(double distance);
/**
* Set the cutoff distance.
*
* @deprecated This method exists only for backward compatibility. Use setCutoffDistance() instead.
*/
void setCutoff(double cutoff);
/**
* Get the cutoff distance.
*
* @deprecated This method exists only for backward compatibility. Use getCutoffDistance() instead.
*/
double getCutoff() const;
......
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ a381a3ab
......@@ -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 @ a381a3ab
......@@ -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 @ a381a3ab
......@@ -40,9 +40,7 @@ using std::string;
using std::vector;
AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polarizationType(Mutual), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(1e-4), mutualInducedMaxIterations(60),
mutualInducedTargetEpsilon(1.0e-02), scalingDistanceCutoff(100.0), electricConstant(138.9354558456), aewald(0.0) {
pmeGridDimension.resize(3);
pmeGridDimension[0] = pmeGridDimension[1] = pmeGridDimension[2];
mutualInducedTargetEpsilon(1.0e-02), scalingDistanceCutoff(100.0), electricConstant(138.9354558456), alpha(0.0), nx(0), ny(0), nz(0) {
extrapolationCoefficients.push_back(-0.154);
extrapolationCoefficients.push_back(0.017);
extrapolationCoefficients.push_back(0.658);
......@@ -81,12 +79,26 @@ void AmoebaMultipoleForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
void AmoebaMultipoleForce::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
alpha = this->alpha;
nx = this->nx;
ny = this->ny;
nz = this->nz;
}
void AmoebaMultipoleForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
this->alpha = alpha;
this->nx = nx;
this->ny = ny;
this->nz = nz;
}
double AmoebaMultipoleForce::getAEwald() const {
return aewald;
return alpha;
}
void AmoebaMultipoleForce::setAEwald(double inputAewald) {
aewald = inputAewald;
alpha = inputAewald;
}
int AmoebaMultipoleForce::getPmeBSplineOrder() const {
......@@ -94,26 +106,18 @@ int AmoebaMultipoleForce::getPmeBSplineOrder() const {
}
void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const {
if (gridDimension.size() < 3) {
if (gridDimension.size() < 3)
gridDimension.resize(3);
}
if (pmeGridDimension.size() > 2) {
gridDimension[0] = pmeGridDimension[0];
gridDimension[1] = pmeGridDimension[1];
gridDimension[2] = pmeGridDimension[2];
} else {
gridDimension[0] = gridDimension[1] = gridDimension[2] = 0;
}
return;
gridDimension[0] = nx;
gridDimension[1] = ny;
gridDimension[2] = nz;
}
void AmoebaMultipoleForce::setPmeGridDimensions(const std::vector<int>& gridDimension) {
pmeGridDimension.resize(3);
pmeGridDimension[0] = gridDimension[0];
pmeGridDimension[1] = gridDimension[1];
pmeGridDimension[2] = gridDimension[2];
return;
}
nx = gridDimension[0];
ny = gridDimension[1];
nz = gridDimension[2];
}
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);
......@@ -143,13 +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;
......@@ -179,7 +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;
......@@ -246,6 +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 @ a381a3ab
......@@ -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/openmmapi/src/AmoebaVdwForce.cpp
View file @ a381a3ab
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -102,12 +102,20 @@ void AmoebaVdwForce::getParticleExclusions(int particleIndex, std::vector< int >
}
void AmoebaVdwForce::setCutoff(double inputCutoff) {
double AmoebaVdwForce::getCutoffDistance() const {
return cutoff;
}
void AmoebaVdwForce::setCutoffDistance(double inputCutoff) {
cutoff = inputCutoff;
}
void AmoebaVdwForce::setCutoff(double inputCutoff) {
setCutoffDistance(inputCutoff);
}
double AmoebaVdwForce::getCutoff() const {
return cutoff;
return getCutoffDistance();
}
AmoebaVdwForce::NonbondedMethod AmoebaVdwForce::getNonbondedMethod() const {
......
plugins/amoeba/openmmapi/src/AmoebaVdwForceImpl.cpp
View file @ a381a3ab
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -62,7 +62,7 @@ void AmoebaVdwForceImpl::initialize(ContextImpl& context) {
if (owner.getNonbondedMethod() == AmoebaVdwForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoff();
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("AmoebaVdwForce: The cutoff distance cannot be greater than half the periodic box size.");
}
......@@ -103,7 +103,7 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
}
// Compute the VdW tapering coefficients. Mostly copied from amoebaCudaGpu.cpp.
double cutoff = force.getCutoff();
double cutoff = force.getCutoffDistance();
double vdwTaper = 0.90; // vdwTaper is a scaling factor, it is not a distance.
double c0 = 0.0;
double c1 = 0.0;
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ a381a3ab
......@@ -1146,11 +1146,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
coefficients << cu.doubleToString(sum);
}
defines["EXTRAPOLATION_COEFFICIENTS_SUM"] = coefficients.str();
alpha = force.getAEwald();
if (usePME) {
vector<int> pmeGridDimension;
force.getPmeGridDimensions(pmeGridDimension);
if (pmeGridDimension[0] == 0 || alpha == 0.0) {
int nx, ny, nz;
force.getPMEParameters(alpha, nx, ny, nz);
if (nx == 0 || alpha == 0.0) {
NonbondedForce nb;
nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
nb.setCutoffDistance(force.getCutoffDistance());
......@@ -1159,9 +1158,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
gridSizeY = CudaFFT3D::findLegalDimension(gridSizeY);
gridSizeZ = CudaFFT3D::findLegalDimension(gridSizeZ);
} else {
gridSizeX = CudaFFT3D::findLegalDimension(pmeGridDimension[0]);
gridSizeY = CudaFFT3D::findLegalDimension(pmeGridDimension[1]);
gridSizeZ = CudaFFT3D::findLegalDimension(pmeGridDimension[2]);
gridSizeX = CudaFFT3D::findLegalDimension(nx);
gridSizeY = CudaFFT3D::findLegalDimension(ny);
gridSizeZ = CudaFFT3D::findLegalDimension(nz);
}
defines["EWALD_ALPHA"] = cu.doubleToString(alpha);
defines["SQRT_PI"] = cu.doubleToString(sqrt(M_PI));
......@@ -1993,6 +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();
......@@ -2012,6 +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();
......@@ -2165,6 +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())
......@@ -2601,15 +2664,15 @@ void CudaCalcAmoebaVdwForceKernel::initialize(const System& system, const Amoeba
replacements["EPSILON_COMBINING_RULE"] = "4";
else
throw OpenMMException("Illegal combining rule for sigma: "+sigmaCombiningRule);
double cutoff = force.getCutoff();
double cutoff = force.getCutoffDistance();
double taperCutoff = cutoff*0.9;
replacements["CUTOFF_DISTANCE"] = cu.doubleToString(force.getCutoff());
replacements["CUTOFF_DISTANCE"] = cu.doubleToString(force.getCutoffDistance());
replacements["TAPER_CUTOFF"] = cu.doubleToString(taperCutoff);
replacements["TAPER_C3"] = cu.doubleToString(10/pow(taperCutoff-cutoff, 3.0));
replacements["TAPER_C4"] = cu.doubleToString(15/pow(taperCutoff-cutoff, 4.0));
replacements["TAPER_C5"] = cu.doubleToString(6/pow(taperCutoff-cutoff, 5.0));
bool useCutoff = (force.getNonbondedMethod() != AmoebaVdwForce::NoCutoff);
nonbonded->addInteraction(useCutoff, useCutoff, true, force.getCutoff(), exclusions,
nonbonded->addInteraction(useCutoff, useCutoff, true, force.getCutoffDistance(), exclusions,
cu.replaceStrings(CudaAmoebaKernelSources::amoebaVdwForce2, replacements), 0);
// Create the other kernels.
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ a381a3ab
......@@ -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/src/kernels/multipoleElectrostatics.cu
View file @ a381a3ab
......@@ -488,6 +488,8 @@ extern "C" __global__ void computeElectrostatics(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -508,34 +510,31 @@ extern "C" __global__ void computeElectrostatics(
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu
View file @ a381a3ab
......@@ -592,6 +592,8 @@ extern "C" __global__ void computeFixedField(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -612,34 +614,31 @@ extern "C" __global__ void computeFixedField(
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleInducedField.cu
View file @ a381a3ab
......@@ -454,6 +454,8 @@ extern "C" __global__ void computeInducedField(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -474,34 +476,31 @@ extern "C" __global__ void computeInducedField(
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
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