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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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platforms/reference/include/ReferenceCustomTorsionIxn.h
View file @ a381a3ab
......@@ -25,7 +25,7 @@
#define __ReferenceCustomTorsionIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/CompiledExpression.h"
#include "openmm/internal/CompiledExpressionSet.h"
namespace OpenMM {
......@@ -34,10 +34,10 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
private:
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyTheta;
double* forceTheta;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
CompiledExpressionSet expressionSet;
std::vector<int> torsionParamIndex;
int thetaIndex;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
......@@ -51,7 +51,8 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomTorsionIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters,
const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);
/**---------------------------------------------------------------------------------------
......@@ -85,7 +86,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferenceHarmonicBondIxn.h
View file @ a381a3ab
......@@ -79,7 +79,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferenceKernels.h
View file @ a381a3ab
......@@ -38,7 +38,6 @@
#include "ReferenceNeighborList.h"
#include "lepton/CompiledExpression.h"
#include "lepton/CustomFunction.h"
#include "lepton/ExpressionProgram.h"
namespace OpenMM {
......@@ -158,6 +157,12 @@ public:
* @param forces on exit, this contains the forces
*/
void getForces(ContextImpl& context, std::vector<Vec3>& forces);
/**
* Get the current derivatives of the energy with respect to context parameters.
*
* @param derivs on exit, this contains the derivatives
*/
void getEnergyParameterDerivatives(ContextImpl& context, std::map<std::string, double>& derivs);
/**
* Get the current periodic box vectors.
*
......@@ -320,7 +325,8 @@ private:
int **bondIndexArray;
RealOpenMM **bondParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames;
bool usePeriodic;
};
......@@ -398,7 +404,8 @@ private:
int **angleIndexArray;
RealOpenMM **angleParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames;
bool usePeriodic;
};
......@@ -551,7 +558,8 @@ private:
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames;
bool usePeriodic;
};
......@@ -648,8 +656,10 @@ private:
std::map<std::string, double> globalParamValues;
std::vector<std::set<int> > exclusions;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames;
std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
std::vector<double> longRangeCoefficientDerivs;
NonbondedMethod nonbondedMethod;
NeighborList* neighborList;
};
......@@ -728,14 +738,16 @@ private:
RealOpenMM **particleParamArray;
RealOpenMM nonbondedCutoff;
std::vector<std::set<int> > exclusions;
std::vector<std::string> particleParameterNames, globalParameterNames, valueNames;
std::vector<Lepton::ExpressionProgram> valueExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions;
std::vector<std::string> particleParameterNames, globalParameterNames, energyParamDerivNames, valueNames;
std::vector<Lepton::CompiledExpression> valueExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueParamDerivExpressions;
std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
std::vector<Lepton::ExpressionProgram> energyExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions;
std::vector<Lepton::CompiledExpression> energyExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyParamDerivExpressions;
std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
NonbondedMethod nonbondedMethod;
NeighborList* neighborList;
......@@ -868,7 +880,7 @@ private:
int numBonds, numParticles;
RealOpenMM **bondParamArray;
ReferenceCustomCentroidBondIxn* ixn;
std::vector<std::string> globalParameterNames;
std::vector<std::string> globalParameterNames, energyParamDerivNames;
bool usePeriodic;
};
......@@ -907,7 +919,7 @@ private:
int numBonds;
RealOpenMM **bondParamArray;
ReferenceCustomCompoundBondIxn* ixn;
std::vector<std::string> globalParameterNames;
std::vector<std::string> globalParameterNames, energyParamDerivNames;
bool usePeriodic;
};
......
platforms/reference/include/ReferenceLJCoulomb14.h
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
......@@ -64,7 +64,7 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferencePlatform.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 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -68,6 +68,7 @@ public:
void* periodicBoxSize;
void* periodicBoxVectors;
void* constraints;
void* energyParameterDerivatives;
};
} // namespace OpenMM
......
platforms/reference/include/ReferenceProperDihedralBond.h
View file @ a381a3ab
......@@ -80,7 +80,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferenceRbDihedralBond.h
View file @ a381a3ab
......@@ -78,7 +78,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/src/ReferenceKernels.cpp
View file @ a381a3ab
......@@ -147,6 +147,11 @@ static ReferenceConstraints& extractConstraints(ContextImpl& context) {
return *(ReferenceConstraints*) data->constraints;
}
static map<string, double>& extractEnergyParameterDerivatives(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *((map<string, double>*) data->energyParameterDerivatives);
}
/**
* Make sure an expression doesn't use any undefined variables.
*/
......@@ -209,6 +214,8 @@ void ReferenceCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context,
}
else
savedForces = forceData;
for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter)
extractEnergyParameterDerivatives(context)[iter->first] = 0;
}
double ReferenceCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
......@@ -274,6 +281,10 @@ void ReferenceUpdateStateDataKernel::getForces(ContextImpl& context, std::vector
forces[i] = Vec3(forceData[i][0], forceData[i][1], forceData[i][2]);
}
void ReferenceUpdateStateDataKernel::getEnergyParameterDerivatives(ContextImpl& context, map<string, double>& derivs) {
derivs = extractEnergyParameterDerivatives(context);
}
void ReferenceUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const {
RealVec* vectors = extractBoxVectors(context);
a = vectors[0];
......@@ -438,6 +449,11 @@ void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const
parameterNames.push_back(force.getPerBondParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string param = force.getEnergyParameterDerivativeName(i);
energyParamDerivNames.push_back(param);
energyParamDerivExpressions.push_back(expression.differentiate(param).createCompiledExpression());
}
set<string> variables;
variables.insert("r");
variables.insert(parameterNames.begin(), parameterNames.end());
......@@ -452,11 +468,15 @@ double ReferenceCalcCustomBondForceKernel::execute(ContextImpl& context, bool in
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomBondIxn bond(energyExpression, forceExpression, parameterNames, globalParameters);
ReferenceCustomBondIxn bond(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
if (usePeriodic)
bond.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, includeEnergy ? &energy : NULL, bond);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
for (int i = 0; i < numBonds; i++)
bond.calculateBondIxn(bondIndexArray[i], posData, bondParamArray[i], forceData, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
for (int i = 0; i < energyParamDerivNames.size(); i++)
energyParamDerivs[energyParamDerivNames[i]] += energyParamDerivValues[i];
return energy;
}
......@@ -563,6 +583,11 @@ void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const
parameterNames.push_back(force.getPerAngleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string param = force.getEnergyParameterDerivativeName(i);
energyParamDerivNames.push_back(param);
energyParamDerivExpressions.push_back(expression.differentiate(param).createCompiledExpression());
}
set<string> variables;
variables.insert("theta");
variables.insert(parameterNames.begin(), parameterNames.end());
......@@ -577,11 +602,15 @@ double ReferenceCalcCustomAngleForceKernel::execute(ContextImpl& context, bool i
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomAngleIxn customAngle(energyExpression, forceExpression, parameterNames, globalParameters);
ReferenceCustomAngleIxn customAngle(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
if (usePeriodic)
customAngle.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, customAngle);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
for (int i = 0; i < numAngles; i++)
customAngle.calculateBondIxn(angleIndexArray[i], posData, angleParamArray[i], forceData, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
for (int i = 0; i < energyParamDerivNames.size(); i++)
energyParamDerivs[energyParamDerivNames[i]] += energyParamDerivValues[i];
return energy;
}
......@@ -824,6 +853,11 @@ void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, con
parameterNames.push_back(force.getPerTorsionParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string param = force.getEnergyParameterDerivativeName(i);
energyParamDerivNames.push_back(param);
energyParamDerivExpressions.push_back(expression.differentiate(param).createCompiledExpression());
}
set<string> variables;
variables.insert("theta");
variables.insert(parameterNames.begin(), parameterNames.end());
......@@ -838,11 +872,15 @@ double ReferenceCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomTorsionIxn customTorsion(energyExpression, forceExpression, parameterNames, globalParameters);
ReferenceCustomTorsionIxn customTorsion(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
if (usePeriodic)
customTorsion.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, customTorsion);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
for (int i = 0; i < numTorsions; i++)
customTorsion.calculateBondIxn(torsionIndexArray[i], posData, torsionParamArray[i], forceData, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
for (int i = 0; i < energyParamDerivNames.size(); i++)
energyParamDerivs[energyParamDerivNames[i]] += energyParamDerivValues[i];
return energy;
}
......@@ -1089,6 +1127,11 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
globalParameterNames.push_back(force.getGlobalParameterName(i));
globalParamValues[force.getGlobalParameterName(i)] = force.getGlobalParameterDefaultValue(i);
}
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string param = force.getEnergyParameterDerivativeName(i);
energyParamDerivNames.push_back(param);
energyParamDerivExpressions.push_back(expression.differentiate(param).createCompiledExpression());
}
set<string> variables;
variables.insert("r");
for (int i = 0; i < numParameters; i++) {
......@@ -1128,7 +1171,7 @@ double ReferenceCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bo
vector<RealVec>& forceData = extractForces(context);
RealVec* boxVectors = extractBoxVectors(context);
RealOpenMM energy = 0;
ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, parameterNames);
ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, parameterNames, energyParamDerivExpressions);
bool periodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff) {
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, extractBoxVectors(context), periodic, nonbondedCutoff, 0.0);
......@@ -1151,15 +1194,22 @@ double ReferenceCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bo
}
if (useSwitchingFunction)
ixn.setUseSwitchingFunction(switchingDistance);
ixn.calculatePairIxn(numParticles, posData, particleParamArray, exclusions, 0, globalParamValues, forceData, 0, includeEnergy ? &energy : NULL);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
ixn.calculatePairIxn(numParticles, posData, particleParamArray, exclusions, 0, globalParamValues, forceData, 0, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
for (int i = 0; i < energyParamDerivNames.size(); i++)
energyParamDerivs[energyParamDerivNames[i]] += energyParamDerivValues[i];
// Add in the long range correction.
if (!hasInitializedLongRangeCorrection || (globalParamsChanged && forceCopy != NULL)) {
longRangeCoefficient = CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner());
CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner(), longRangeCoefficient, longRangeCoefficientDerivs);
hasInitializedLongRangeCorrection = true;
}
energy += longRangeCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
double volume = boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2];
energy += longRangeCoefficient/volume;
for (int i = 0; i < longRangeCoefficientDerivs.size(); i++)
energyParamDerivs[energyParamDerivNames[i]] += longRangeCoefficientDerivs[i]/volume;
return energy;
}
......@@ -1181,7 +1231,7 @@ void ReferenceCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImp
// If necessary, recompute the long range correction.
if (forceCopy != NULL) {
longRangeCoefficient = CustomNonbondedForceImpl::calcLongRangeCorrection(force, context.getOwner());
CustomNonbondedForceImpl::calcLongRangeCorrection(force, context.getOwner(), longRangeCoefficient, longRangeCoefficientDerivs);
hasInitializedLongRangeCorrection = true;
*forceCopy = force;
}
......@@ -1310,6 +1360,7 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
valueDerivExpressions.resize(force.getNumComputedValues());
valueGradientExpressions.resize(force.getNumComputedValues());
valueParamDerivExpressions.resize(force.getNumComputedValues());
set<string> particleVariables, pairVariables;
pairVariables.insert("r");
particleVariables.insert("x");
......@@ -1327,21 +1378,26 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
CustomGBForce::ComputationType type;
force.getComputedValueParameters(i, name, expression, type);
Lepton::ParsedExpression ex = Lepton::Parser::parse(expression, functions).optimize();
valueExpressions.push_back(ex.createProgram());
valueExpressions.push_back(ex.createCompiledExpression());
valueTypes.push_back(type);
valueNames.push_back(name);
if (i == 0) {
valueDerivExpressions[i].push_back(ex.differentiate("r").optimize().createProgram());
valueDerivExpressions[i].push_back(ex.differentiate("r").createCompiledExpression());
validateVariables(ex.getRootNode(), pairVariables);
}
else {
valueGradientExpressions[i].push_back(ex.differentiate("x").optimize().createProgram());
valueGradientExpressions[i].push_back(ex.differentiate("y").optimize().createProgram());
valueGradientExpressions[i].push_back(ex.differentiate("z").optimize().createProgram());
valueGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
for (int j = 0; j < i; j++)
valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).optimize().createProgram());
valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).createCompiledExpression());
validateVariables(ex.getRootNode(), particleVariables);
}
for (int j = 0; j < force.getNumEnergyParameterDerivatives(); j++) {
string param = force.getEnergyParameterDerivativeName(j);
energyParamDerivNames.push_back(param);
valueParamDerivExpressions[i].push_back(ex.differentiate(param).createCompiledExpression());
}
particleVariables.insert(name);
pairVariables.insert(name+"1");
pairVariables.insert(name+"2");
......@@ -1351,29 +1407,32 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
energyDerivExpressions.resize(force.getNumEnergyTerms());
energyGradientExpressions.resize(force.getNumEnergyTerms());
energyParamDerivExpressions.resize(force.getNumEnergyTerms());
for (int i = 0; i < force.getNumEnergyTerms(); i++) {
string expression;
CustomGBForce::ComputationType type;
force.getEnergyTermParameters(i, expression, type);
Lepton::ParsedExpression ex = Lepton::Parser::parse(expression, functions).optimize();
energyExpressions.push_back(ex.createProgram());
energyExpressions.push_back(ex.createCompiledExpression());
energyTypes.push_back(type);
if (type != CustomGBForce::SingleParticle)
energyDerivExpressions[i].push_back(ex.differentiate("r").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate("r").createCompiledExpression());
for (int j = 0; j < force.getNumComputedValues(); j++) {
if (type == CustomGBForce::SingleParticle) {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).optimize().createProgram());
energyGradientExpressions[i].push_back(ex.differentiate("x").optimize().createProgram());
energyGradientExpressions[i].push_back(ex.differentiate("y").optimize().createProgram());
energyGradientExpressions[i].push_back(ex.differentiate("z").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
validateVariables(ex.getRootNode(), particleVariables);
}
else {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").createCompiledExpression());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").createCompiledExpression());
validateVariables(ex.getRootNode(), pairVariables);
}
}
for (int j = 0; j < force.getNumEnergyParameterDerivatives(); j++)
energyParamDerivExpressions[i].push_back(ex.differentiate(force.getEnergyParameterDerivativeName(j)).createCompiledExpression());
}
// Delete the custom functions.
......@@ -1386,8 +1445,8 @@ double ReferenceCalcCustomGBForceKernel::execute(ContextImpl& context, bool incl
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
ReferenceCustomGBIxn ixn(valueExpressions, valueDerivExpressions, valueGradientExpressions, valueNames, valueTypes, energyExpressions,
energyDerivExpressions, energyGradientExpressions, energyTypes, particleParameterNames);
ReferenceCustomGBIxn ixn(valueExpressions, valueDerivExpressions, valueGradientExpressions, valueParamDerivExpressions, valueNames, valueTypes,
energyExpressions, energyDerivExpressions, energyGradientExpressions, energyParamDerivExpressions, energyTypes, particleParameterNames);
bool periodic = (nonbondedMethod == CutoffPeriodic);
if (periodic)
ixn.setPeriodic(extractBoxVectors(context));
......@@ -1398,7 +1457,11 @@ double ReferenceCalcCustomGBForceKernel::execute(ContextImpl& context, bool incl
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ixn.calculateIxn(numParticles, posData, particleParamArray, exclusions, globalParameters, forceData, includeEnergy ? &energy : NULL);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
ixn.calculateIxn(numParticles, posData, particleParamArray, exclusions, globalParameters, forceData, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
for (int i = 0; i < energyParamDerivNames.size(); i++)
energyParamDerivs[energyParamDerivNames[i]] += energyParamDerivValues[i];
return energy;
}
......@@ -1708,7 +1771,13 @@ void ReferenceCalcCustomCentroidBondForceKernel::initialize(const System& system
bondParameterNames.push_back(force.getPerBondParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
ixn = new ReferenceCustomCentroidBondIxn(force.getNumGroupsPerBond(), groupAtoms, normalizedWeights, bondGroups, energyExpression, bondParameterNames, distances, angles, dihedrals);
vector<Lepton::CompiledExpression> energyParamDerivExpressions;
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string param = force.getEnergyParameterDerivativeName(i);
energyParamDerivNames.push_back(param);
energyParamDerivExpressions.push_back(energyExpression.differentiate(param).createCompiledExpression());
}
ixn = new ReferenceCustomCentroidBondIxn(force.getNumGroupsPerBond(), groupAtoms, normalizedWeights, bondGroups, energyExpression, bondParameterNames, distances, angles, dihedrals, energyParamDerivExpressions);
// Delete the custom functions.
......@@ -1725,7 +1794,11 @@ double ReferenceCalcCustomCentroidBondForceKernel::execute(ContextImpl& context,
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
if (usePeriodic)
ixn->setPeriodic(extractBoxVectors(context));
ixn->calculatePairIxn(posData, bondParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
ixn->calculatePairIxn(posData, bondParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
for (int i = 0; i < energyParamDerivNames.size(); i++)
energyParamDerivs[energyParamDerivNames[i]] += energyParamDerivValues[i];
return energy;
}
......@@ -1788,7 +1861,13 @@ void ReferenceCalcCustomCompoundBondForceKernel::initialize(const System& system
bondParameterNames.push_back(force.getPerBondParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
ixn = new ReferenceCustomCompoundBondIxn(force.getNumParticlesPerBond(), bondParticles, energyExpression, bondParameterNames, distances, angles, dihedrals);
vector<Lepton::CompiledExpression> energyParamDerivExpressions;
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string param = force.getEnergyParameterDerivativeName(i);
energyParamDerivNames.push_back(param);
energyParamDerivExpressions.push_back(energyExpression.differentiate(param).createCompiledExpression());
}
ixn = new ReferenceCustomCompoundBondIxn(force.getNumParticlesPerBond(), bondParticles, energyExpression, bondParameterNames, distances, angles, dihedrals, energyParamDerivExpressions);
// Delete the custom functions.
......@@ -1805,7 +1884,11 @@ double ReferenceCalcCustomCompoundBondForceKernel::execute(ContextImpl& context,
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
if (usePeriodic)
ixn->setPeriodic(extractBoxVectors(context));
ixn->calculatePairIxn(posData, bondParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL);
vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
ixn->calculatePairIxn(posData, bondParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
for (int i = 0; i < energyParamDerivNames.size(); i++)
energyParamDerivs[energyParamDerivNames[i]] += energyParamDerivValues[i];
return energy;
}
......
platforms/reference/src/ReferencePlatform.cpp
View file @ a381a3ab
......@@ -36,6 +36,7 @@
#include "openmm/internal/ContextImpl.h"
#include "SimTKOpenMMRealType.h"
#include "RealVec.h"
#include <map>
#include <vector>
using namespace OpenMM;
......@@ -100,6 +101,7 @@ ReferencePlatform::PlatformData::PlatformData(const System& system) : time(0.0),
periodicBoxSize = new RealVec();
periodicBoxVectors = new RealVec[3];
constraints = new ReferenceConstraints(system);
energyParameterDerivatives = new map<string, double>();
}
ReferencePlatform::PlatformData::~PlatformData() {
......@@ -109,4 +111,5 @@ ReferencePlatform::PlatformData::~PlatformData() {
delete (RealVec*) periodicBoxSize;
delete[] (RealVec*) periodicBoxVectors;
delete (ReferenceConstraints*) constraints;
delete (map<string, double>*) energyParameterDerivatives;
}
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.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
......@@ -129,7 +129,7 @@ void ReferenceAngleBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
RealOpenMM* totalEnergy, double* energyParamDerivs) {
// constants -- reduce Visual Studio warnings regarding conversions between float & double
......
platforms/reference/src/SimTKReference/ReferenceBondForce.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
......@@ -97,7 +97,7 @@ void ReferenceBondForce::calculateForce(int numberOfBonds, int** atomIndices,
// calculate bond ixn
referenceBondIxn.calculateBondIxn(atomIndices[ii], atomCoordinates, parameters[ii],
forces, totalEnergy);
forces, totalEnergy, NULL);
}
}
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
View file @ a381a3ab
/* Portions copyright (c) 2006-2009 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
......@@ -78,7 +78,7 @@ ReferenceBondIxn::~ReferenceBondIxn() {
void ReferenceBondIxn::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
RealOpenMM* totalEnergy, double* energyParamDerivs) {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nReferenceBondIxn::calculateBondIxn";
......
platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.cpp
View file @ a381a3ab
......@@ -207,5 +207,5 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCo
--------------------------------------------------------------------------------------- */
void ReferenceCMAPTorsionIxn::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
RealOpenMM* parameters, vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
}
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
View file @ a381a3ab
......@@ -38,20 +38,19 @@ using namespace std;
--------------------------------------------------------------------------------------- */
ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(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++)
angleParamIndex.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 ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceCustomAngleIxn::calculateAngleIxn";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
RealOpenMM* totalEnergy, double* energyParamDerivs) {
RealOpenMM deltaR[2][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(angleParamIndex[i], parameters[i]);
// ---------------------------------------------------------------------------------------
......@@ -122,14 +113,13 @@ void ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
RealOpenMM dot = DOT3(deltaR[0], deltaR[1]);
RealOpenMM cosine = dot/SQRT((deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]));
RealOpenMM angle;
if (cosine >= one)
angle = zero;
else if (cosine <= -one)
if (cosine >= 1.0)
angle = 0.0;
else if (cosine <= -1.0)
angle = PI_M;
else
angle = ACOS(cosine);
ReferenceForce::setVariable(energyTheta, angle);
ReferenceForce::setVariable(forceTheta, angle);
expressionSet.setVariable(thetaIndex, angle);
// Compute the force and energy, and apply them to the atoms.
......@@ -156,6 +146,11 @@ void ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
}
}
// 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/ReferenceCustomBondIxn.cpp
View file @ a381a3ab
......@@ -39,19 +39,19 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false) {
energyR = ReferenceForce::getVariablePointer(this->energyExpression, "r");
forceR = ReferenceForce::getVariablePointer(this->forceExpression, "r");
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]);
rIndex = expressionSet.getVariableIndex("r");
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++)
bondParamIndex.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);
}
/**---------------------------------------------------------------------------------------
......@@ -86,21 +86,10 @@ void ReferenceCustomBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceCustomBondIxn::calculateBondIxn";
static const int twoI = 2;
static const RealOpenMM zero = 0.0;
static const RealOpenMM two = 2.0;
static const RealOpenMM half = 0.5;
RealOpenMM* totalEnergy, double* energyParamDerivs) {
RealOpenMM deltaR[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(bondParamIndex[i], parameters[i]);
// ---------------------------------------------------------------------------------------
......@@ -113,10 +102,9 @@ void ReferenceCustomBondIxn::calculateBondIxn(int* atomIndices,
else
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
ReferenceForce::setVariable(energyR, deltaR[ReferenceForce::RIndex]);
ReferenceForce::setVariable(forceR, deltaR[ReferenceForce::RIndex]);
expressionSet.setVariable(rIndex, deltaR[ReferenceForce::RIndex]);
RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate();
dEdR = deltaR[ReferenceForce::RIndex] > zero ? (dEdR/deltaR[ReferenceForce::RIndex]) : zero;
dEdR = deltaR[ReferenceForce::RIndex] > 0 ? (dEdR/deltaR[ReferenceForce::RIndex]) : 0;
forces[atomAIndex][0] += dEdR*deltaR[ReferenceForce::XIndex];
forces[atomAIndex][1] += dEdR*deltaR[ReferenceForce::YIndex];
......@@ -126,6 +114,8 @@ void ReferenceCustomBondIxn::calculateBondIxn(int* atomIndices,
forces[atomBIndex][1] -= dEdR*deltaR[ReferenceForce::YIndex];
forces[atomBIndex][2] -= dEdR*deltaR[ReferenceForce::ZIndex];
for (int i = 0; i < energyParamDerivExpressions.size(); i++)
energyParamDerivs[i] += energyParamDerivExpressions[i].evaluate();
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
}
platforms/reference/src/SimTKReference/ReferenceCustomCentroidBondIxn.cpp
View file @ a381a3ab
......@@ -40,23 +40,47 @@ using namespace OpenMM;
ReferenceCustomCentroidBondIxn::ReferenceCustomCentroidBondIxn(int numGroupsPerBond, const vector<vector<int> >& groupAtoms,
const vector<vector<double> >& normalizedWeights, const vector<vector<int> >& bondGroups,
const Lepton::ParsedExpression& energyExpression, const vector<string>& bondParameterNames,
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
groupAtoms(groupAtoms), normalizedWeights(normalizedWeights), bondGroups(bondGroups), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames), usePeriodic(false) {
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals,
const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
groupAtoms(groupAtoms), normalizedWeights(normalizedWeights), bondGroups(bondGroups), energyExpression(energyExpression.createCompiledExpression()),
usePeriodic(false), energyParamDerivExpressions(energyParamDerivExpressions) {
expressionSet.registerExpression(this->energyExpression);
for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
for (int i = 0; i < numGroupsPerBond; i++) {
stringstream xname, yname, zname;
xname << 'x' << (i+1);
yname << 'y' << (i+1);
zname << 'z' << (i+1);
positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(xname.str(), i, 0, energyExpression.differentiate(xname.str()).optimize().createProgram()));
positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).optimize().createProgram()));
positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).optimize().createProgram()));
positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(xname.str(), i, 0, energyExpression.differentiate(xname.str()).createCompiledExpression()));
positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).createCompiledExpression()));
positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).createCompiledExpression()));
}
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomCentroidBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
distanceTerms.push_back(ReferenceCustomCentroidBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomCentroidBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
angleTerms.push_back(ReferenceCustomCentroidBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomCentroidBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
dihedralTerms.push_back(ReferenceCustomCentroidBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (int i = 0; i < positionTerms.size(); i++) {
expressionSet.registerExpression(positionTerms[i].forceExpression);
positionTerms[i].index = expressionSet.getVariableIndex(positionTerms[i].name);
}
for (int i = 0; i < distanceTerms.size(); i++) {
expressionSet.registerExpression(distanceTerms[i].forceExpression);
distanceTerms[i].index = expressionSet.getVariableIndex(distanceTerms[i].name);
}
for (int i = 0; i < angleTerms.size(); i++) {
expressionSet.registerExpression(angleTerms[i].forceExpression);
angleTerms[i].index = expressionSet.getVariableIndex(angleTerms[i].name);
}
for (int i = 0; i < dihedralTerms.size(); i++) {
expressionSet.registerExpression(dihedralTerms[i].forceExpression);
dihedralTerms[i].index = expressionSet.getVariableIndex(dihedralTerms[i].name);
}
numParameters = bondParameterNames.size();
for (int i = 0; i < numParameters; i++)
bondParamIndex.push_back(expressionSet.getVariableIndex(bondParameterNames[i]));
}
ReferenceCustomCentroidBondIxn::~ReferenceCustomCentroidBondIxn() {
......@@ -71,7 +95,7 @@ void ReferenceCustomCentroidBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, RealOpenMM** bondParameters,
const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
RealOpenMM* totalEnergy, double* energyParamDerivs) {
// First compute the center of each group.
......@@ -84,13 +108,14 @@ void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
// Compute the forces on groups.
map<string, double> variables = globalParameters;
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
vector<RealVec> groupForces(numGroups);
int numBonds = bondGroups.size();
for (int bond = 0; bond < numBonds; bond++) {
for (int j = 0; j < (int) bondParamNames.size(); j++)
variables[bondParamNames[j]] = bondParameters[bond][j];
calculateOneIxn(bond, groupCenters, variables, groupForces, totalEnergy);
for (int i = 0; i < numParameters; i++)
expressionSet.setVariable(bondParamIndex[i], bondParameters[bond][i]);
calculateOneIxn(bond, groupCenters, groupForces, totalEnergy, energyParamDerivs);
}
// Apply the forces to the individual atoms.
......@@ -102,31 +127,24 @@ void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
}
void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>& groupCenters,
map<string, double>& variables, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nReferenceCustomCentroidBondIxn::calculateOneIxn";
// ---------------------------------------------------------------------------------------
vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
// Compute all of the variables the energy can depend on.
const vector<int>& groups = bondGroups[bond];
for (int i = 0; i < (int) positionTerms.size(); i++) {
const PositionTermInfo& term = positionTerms[i];
variables[term.name] = groupCenters[groups[term.group]][term.component];
expressionSet.setVariable(term.index, groupCenters[groups[term.group]][term.component]);
}
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
computeDelta(groups[term.g1], groups[term.g2], term.delta, groupCenters);
variables[term.name] = term.delta[ReferenceForce::RIndex];
expressionSet.setVariable(term.index, term.delta[ReferenceForce::RIndex]);
}
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
computeDelta(groups[term.g1], groups[term.g2], term.delta1, groupCenters);
computeDelta(groups[term.g3], groups[term.g2], term.delta2, groupCenters);
variables[term.name] = computeAngle(term.delta1, term.delta2);
expressionSet.setVariable(term.index, computeAngle(term.delta1, term.delta2));
}
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
......@@ -135,21 +153,21 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
computeDelta(groups[term.g4], groups[term.g3], term.delta3, groupCenters);
RealOpenMM dotDihedral, signOfDihedral;
RealOpenMM* crossProduct[] = {term.cross1, term.cross2};
variables[term.name] = getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1);
expressionSet.setVariable(term.index, getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1));
}
// Apply forces based on individual particle coordinates.
for (int i = 0; i < (int) positionTerms.size(); i++) {
const PositionTermInfo& term = positionTerms[i];
forces[groups[term.group]][term.component] -= term.forceExpression.evaluate(variables);
forces[groups[term.group]][term.component] -= term.forceExpression.evaluate();
}
// Apply forces based on distances.
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]));
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]));
for (int i = 0; i < 3; i++) {
RealOpenMM force = -dEdR*term.delta[i];
forces[groups[term.g1]][i] -= force;
......@@ -161,7 +179,7 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
......@@ -188,7 +206,7 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(term.cross1, term.cross1);
......@@ -218,7 +236,12 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
// Add the energy
if (totalEnergy)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
// Compute derivatives of the energy.
for (int i = 0; i < energyParamDerivExpressions.size(); i++)
energyParamDerivs[i] += energyParamDerivExpressions[i].evaluate();
}
void ReferenceCustomCentroidBondIxn::computeDelta(int group1, int group2, RealOpenMM* delta, vector<RealVec>& groupCenters) const {
......
platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp
View file @ a381a3ab
......@@ -45,23 +45,47 @@ using namespace OpenMM;
ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesPerBond, const vector<vector<int> >& bondAtoms,
const Lepton::ParsedExpression& energyExpression, const vector<string>& bondParameterNames,
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
bondAtoms(bondAtoms), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames), usePeriodic(false) {
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals,
const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
bondAtoms(bondAtoms), energyExpression(energyExpression.createCompiledExpression()), usePeriodic(false),
energyParamDerivExpressions(energyParamDerivExpressions) {
expressionSet.registerExpression(this->energyExpression);
for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
for (int i = 0; i < numParticlesPerBond; i++) {
stringstream xname, yname, zname;
xname << 'x' << (i+1);
yname << 'y' << (i+1);
zname << 'z' << (i+1);
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(xname.str(), i, 0, energyExpression.differentiate(xname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(xname.str(), i, 0, energyExpression.differentiate(xname.str()).createCompiledExpression()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).createCompiledExpression()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).createCompiledExpression()));
}
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomCompoundBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
distanceTerms.push_back(ReferenceCustomCompoundBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomCompoundBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
angleTerms.push_back(ReferenceCustomCompoundBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomCompoundBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
dihedralTerms.push_back(ReferenceCustomCompoundBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (int i = 0; i < particleTerms.size(); i++) {
expressionSet.registerExpression(particleTerms[i].forceExpression);
particleTerms[i].index = expressionSet.getVariableIndex(particleTerms[i].name);
}
for (int i = 0; i < distanceTerms.size(); i++) {
expressionSet.registerExpression(distanceTerms[i].forceExpression);
distanceTerms[i].index = expressionSet.getVariableIndex(distanceTerms[i].name);
}
for (int i = 0; i < angleTerms.size(); i++) {
expressionSet.registerExpression(angleTerms[i].forceExpression);
angleTerms[i].index = expressionSet.getVariableIndex(angleTerms[i].name);
}
for (int i = 0; i < dihedralTerms.size(); i++) {
expressionSet.registerExpression(dihedralTerms[i].forceExpression);
dihedralTerms[i].index = expressionSet.getVariableIndex(dihedralTerms[i].name);
}
numParameters = bondParameterNames.size();
for (int i = 0; i < numParameters; i++)
bondParamIndex.push_back(expressionSet.getVariableIndex(bondParameterNames[i]));
}
/**---------------------------------------------------------------------------------------
......@@ -94,14 +118,14 @@ void ReferenceCustomCompoundBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, RealOpenMM** bondParameters,
const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
map<string, double> variables = globalParameters;
RealOpenMM* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
int numBonds = bondAtoms.size();
for (int bond = 0; bond < numBonds; bond++) {
for (int j = 0; j < (int) bondParamNames.size(); j++)
variables[bondParamNames[j]] = bondParameters[bond][j];
calculateOneIxn(bond, atomCoordinates, variables, forces, totalEnergy);
for (int i = 0; i < numParameters; i++)
expressionSet.setVariable(bondParamIndex[i], bondParameters[bond][i]);
calculateOneIxn(bond, atomCoordinates, forces, totalEnergy, energyParamDerivs);
}
}
......@@ -111,7 +135,6 @@ void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
@param bond the index of the bond
@param atomCoordinates atom coordinates
@param variables the values of variables that may appear in expressions
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
......@@ -119,31 +142,24 @@ void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
--------------------------------------------------------------------------------------- */
void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>& atomCoordinates,
map<string, double>& variables, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nReferenceCustomCompoundBondIxn::calculateOneIxn";
// ---------------------------------------------------------------------------------------
vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
// Compute all of the variables the energy can depend on.
const vector<int>& atoms = bondAtoms[bond];
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
variables[term.name] = atomCoordinates[atoms[term.atom]][term.component];
expressionSet.setVariable(term.index, atomCoordinates[atoms[term.atom]][term.component]);
}
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
computeDelta(atoms[term.p1], atoms[term.p2], term.delta, atomCoordinates);
variables[term.name] = term.delta[ReferenceForce::RIndex];
expressionSet.setVariable(term.index, term.delta[ReferenceForce::RIndex]);
}
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
computeDelta(atoms[term.p1], atoms[term.p2], term.delta1, atomCoordinates);
computeDelta(atoms[term.p3], atoms[term.p2], term.delta2, atomCoordinates);
variables[term.name] = computeAngle(term.delta1, term.delta2);
expressionSet.setVariable(term.index, computeAngle(term.delta1, term.delta2));
}
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
......@@ -152,21 +168,21 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
computeDelta(atoms[term.p4], atoms[term.p3], term.delta3, atomCoordinates);
RealOpenMM dotDihedral, signOfDihedral;
RealOpenMM* crossProduct[] = {term.cross1, term.cross2};
variables[term.name] = getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1);
expressionSet.setVariable(term.index,getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1));
}
// Apply forces based on individual particle coordinates.
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
forces[atoms[term.atom]][term.component] -= term.forceExpression.evaluate(variables);
forces[atoms[term.atom]][term.component] -= term.forceExpression.evaluate();
}
// Apply forces based on distances.
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]));
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]));
for (int i = 0; i < 3; i++) {
RealOpenMM force = -dEdR*term.delta[i];
forces[atoms[term.p1]][i] -= force;
......@@ -178,7 +194,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
......@@ -205,7 +221,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(term.cross1, term.cross1);
......@@ -235,7 +251,12 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
// Add the energy
if (totalEnergy)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
// Compute derivatives of the energy.
for (int i = 0; i < energyParamDerivExpressions.size(); i++)
energyParamDerivs[i] += energyParamDerivExpressions[i].evaluate();
}
void ReferenceCustomCompoundBondIxn::computeDelta(int atom1, int atom2, RealOpenMM* delta, vector<RealVec>& atomCoordinates) const {
......
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ a381a3ab
......@@ -36,6 +36,28 @@
using namespace std;
using namespace OpenMM;
using namespace Lepton;
class ReferenceCustomDynamics::DerivFunction : public CustomFunction {
public:
DerivFunction(map<string, double>& energyParamDerivs, const string& param) : energyParamDerivs(energyParamDerivs), param(param) {
}
int getNumArguments() const {
return 0;
}
double evaluate(const double* arguments) const {
return energyParamDerivs[param];
}
double evaluateDerivative(const double* arguments, const int* derivOrder) const {
return 0;
}
CustomFunction* clone() const {
return new DerivFunction(energyParamDerivs, param);
}
private:
map<string, double>& energyParamDerivs;
string param;
};
/**---------------------------------------------------------------------------------------
......@@ -56,7 +78,7 @@ ReferenceCustomDynamics::ReferenceCustomDynamics(int numberOfAtoms, const Custom
string expression;
integrator.getComputationStep(i, stepType[i], stepVariable[i], expression);
}
kineticEnergyExpression = Lepton::Parser::parse(integrator.getKineticEnergyExpression()).optimize().createCompiledExpression();
kineticEnergyExpression = Parser::parse(integrator.getKineticEnergyExpression()).optimize().createCompiledExpression();
expressionSet.registerExpression(kineticEnergyExpression);
kineticEnergyNeedsForce = false;
if (kineticEnergyExpression.getVariables().find("f") != kineticEnergyExpression.getVariables().end())
......@@ -78,13 +100,13 @@ void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<RealOpenMM
int numSteps = stepType.size();
vector<int> forceGroup;
vector<vector<Lepton::ParsedExpression> > expressions;
vector<vector<ParsedExpression> > expressions;
CustomIntegratorUtilities::analyzeComputations(context, integrator, expressions, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
stepExpressions.resize(expressions.size());
for (int i = 0; i < numSteps; i++) {
stepExpressions[i].resize(expressions[i].size());
for (int j = 0; j < (int) expressions[i].size(); j++) {
stepExpressions[i][j] = expressions[i][j].createCompiledExpression();
stepExpressions[i][j] = ParsedExpression(replaceDerivFunctions(expressions[i][j].getRootNode(), context)).createCompiledExpression();
expressionSet.registerExpression(stepExpressions[i][j]);
}
if (stepType[i] == CustomIntegrator::WhileBlockStart)
......@@ -141,6 +163,22 @@ void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<RealOpenMM
stepVariableIndex.push_back(expressionSet.getVariableIndex(stepVariable[i]));
}
ExpressionTreeNode ReferenceCustomDynamics::replaceDerivFunctions(const ExpressionTreeNode& node, ContextImpl& context) {
const Operation& op = node.getOperation();
if (op.getId() == Operation::CUSTOM && op.getName() == "deriv") {
string param = node.getChildren()[1].getOperation().getName();
if (context.getParameters().find(param) == context.getParameters().end())
throw OpenMMException("The second argument to deriv() must be a context parameter");
return ExpressionTreeNode(new Operation::Custom("deriv", new DerivFunction(energyParamDerivs, param)));
}
else {
vector<ExpressionTreeNode> children;
for (int i = 0; i < (int) node.getChildren().size(); i++)
children.push_back(replaceDerivFunctions(node.getChildren()[i], context));
return ExpressionTreeNode(op.clone(), children);
}
}
/**---------------------------------------------------------------------------------------
Update -- driver routine for performing Custom dynamics update of coordinates
......@@ -178,8 +216,10 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy)
if (computeEnergy) {
energy = e;
context.getEnergyParameterDerivatives(energyParamDerivs);
}
forcesAreValid = true;
}
expressionSet.setVariable(energyVariableIndex[step], energy);
......@@ -266,7 +306,7 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
void ReferenceCustomDynamics::computePerDof(int numberOfAtoms, vector<RealVec>& results, const vector<RealVec>& atomCoordinates,
const vector<RealVec>& velocities, const vector<RealVec>& forces, const vector<RealOpenMM>& masses,
const vector<vector<RealVec> >& perDof, const Lepton::CompiledExpression& expression, int forceIndex) {
const vector<vector<RealVec> >& perDof, const CompiledExpression& expression, int forceIndex) {
// Loop over all degrees of freedom.
for (int i = 0; i < numberOfAtoms; i++) {
......
platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
View file @ a381a3ab
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -42,38 +42,62 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceCustomGBIxn::ReferenceCustomGBIxn(const vector<Lepton::ExpressionProgram>& valueExpressions,
const vector<vector<Lepton::ExpressionProgram> > valueDerivExpressions,
const vector<vector<Lepton::ExpressionProgram> > valueGradientExpressions,
ReferenceCustomGBIxn::ReferenceCustomGBIxn(const vector<Lepton::CompiledExpression>& valueExpressions,
const vector<vector<Lepton::CompiledExpression> > valueDerivExpressions,
const vector<vector<Lepton::CompiledExpression> > valueGradientExpressions,
const vector<vector<Lepton::CompiledExpression> > valueParamDerivExpressions,
const vector<string>& valueNames,
const vector<OpenMM::CustomGBForce::ComputationType>& valueTypes,
const vector<Lepton::ExpressionProgram>& energyExpressions,
const vector<vector<Lepton::ExpressionProgram> > energyDerivExpressions,
const vector<vector<Lepton::ExpressionProgram> > energyGradientExpressions,
const vector<Lepton::CompiledExpression>& energyExpressions,
const vector<vector<Lepton::CompiledExpression> > energyDerivExpressions,
const vector<vector<Lepton::CompiledExpression> > energyGradientExpressions,
const vector<vector<Lepton::CompiledExpression> > energyParamDerivExpressions,
const vector<OpenMM::CustomGBForce::ComputationType>& energyTypes,
const vector<string>& parameterNames) :
cutoff(false), periodic(false), valueExpressions(valueExpressions), valueDerivExpressions(valueDerivExpressions), valueGradientExpressions(valueGradientExpressions),
valueNames(valueNames), valueTypes(valueTypes), energyExpressions(energyExpressions), energyDerivExpressions(energyDerivExpressions), energyGradientExpressions(energyGradientExpressions),
energyTypes(energyTypes), paramNames(parameterNames) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomGBIxn::ReferenceCustomGBIxn";
// ---------------------------------------------------------------------------------------
for (int i = 0; i < (int) paramNames.size(); i++) {
cutoff(false), periodic(false), valueExpressions(valueExpressions), valueDerivExpressions(valueDerivExpressions), valueGradientExpressions(valueGradientExpressions), valueParamDerivExpressions(valueParamDerivExpressions),
valueTypes(valueTypes), energyExpressions(energyExpressions), energyDerivExpressions(energyDerivExpressions), energyGradientExpressions(energyGradientExpressions), energyParamDerivExpressions(energyParamDerivExpressions),
energyTypes(energyTypes) {
for (int i = 0; i < this->valueExpressions.size(); i++)
expressionSet.registerExpression(this->valueExpressions[i]);
for (int i = 0; i < this->valueDerivExpressions.size(); i++)
for (int j = 0; j < this->valueDerivExpressions[i].size(); j++)
expressionSet.registerExpression(this->valueDerivExpressions[i][j]);
for (int i = 0; i < this->valueGradientExpressions.size(); i++)
for (int j = 0; j < this->valueGradientExpressions[i].size(); j++)
expressionSet.registerExpression(this->valueGradientExpressions[i][j]);
for (int i = 0; i < this->valueParamDerivExpressions.size(); i++)
for (int j = 0; j < this->valueParamDerivExpressions[i].size(); j++)
expressionSet.registerExpression(this->valueParamDerivExpressions[i][j]);
for (int i = 0; i < this->energyExpressions.size(); i++)
expressionSet.registerExpression(this->energyExpressions[i]);
for (int i = 0; i < this->energyDerivExpressions.size(); i++)
for (int j = 0; j < this->energyDerivExpressions[i].size(); j++)
expressionSet.registerExpression(this->energyDerivExpressions[i][j]);
for (int i = 0; i < this->energyGradientExpressions.size(); i++)
for (int j = 0; j < this->energyGradientExpressions[i].size(); j++)
expressionSet.registerExpression(this->energyGradientExpressions[i][j]);
for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
for (int j = 0; j < this->energyParamDerivExpressions[i].size(); j++)
expressionSet.registerExpression(this->energyParamDerivExpressions[i][j]);
rIndex = expressionSet.getVariableIndex("r");
xIndex = expressionSet.getVariableIndex("x");
yIndex = expressionSet.getVariableIndex("y");
zIndex = expressionSet.getVariableIndex("z");
for (int i = 0; i < (int) parameterNames.size(); i++) {
paramIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
for (int j = 1; j < 3; j++) {
stringstream name;
name << paramNames[i] << j;
particleParamNames.push_back(name.str());
name << parameterNames[i] << j;
particleParamIndex.push_back(expressionSet.getVariableIndex(name.str()));
}
}
for (int i = 0; i < (int) valueNames.size(); i++) {
valueIndex.push_back(expressionSet.getVariableIndex(valueNames[i]));
for (int j = 1; j < 3; j++) {
stringstream name;
name << valueNames[i] << j;
particleValueNames.push_back(name.str());
particleValueIndex.push_back(expressionSet.getVariableIndex(name.str()));
}
}
}
......@@ -85,13 +109,6 @@ ReferenceCustomGBIxn::ReferenceCustomGBIxn(const vector<Lepton::ExpressionProgra
--------------------------------------------------------------------------------------- */
ReferenceCustomGBIxn::~ReferenceCustomGBIxn() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomGBIxn::~ReferenceCustomGBIxn";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -135,55 +152,73 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn() {
void ReferenceCustomGBIxn::calculateIxn(int numberOfAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const vector<set<int> >& exclusions, map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
RealOpenMM* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
// Initialize arrays for storing values.
int numValues = valueTypes.size();
int numDerivs = valueParamDerivExpressions[0].size();
values.resize(numValues);
dEdV.resize(numValues, vector<RealOpenMM>(numberOfAtoms, 0.0));
dValuedParam.resize(numValues);
for (int i = 0; i < numValues; i++)
dValuedParam[i].resize(numDerivs, vector<RealOpenMM>(numberOfAtoms, 0.0));
// First calculate the computed values.
int numValues = valueTypes.size();
vector<vector<RealOpenMM> > values(numValues);
for (int valueIndex = 0; valueIndex < numValues; valueIndex++) {
if (valueTypes[valueIndex] == OpenMM::CustomGBForce::SingleParticle)
calculateSingleParticleValue(valueIndex, numberOfAtoms, atomCoordinates, values, globalParameters, atomParameters);
calculateSingleParticleValue(valueIndex, numberOfAtoms, atomCoordinates, atomParameters);
else if (valueTypes[valueIndex] == OpenMM::CustomGBForce::ParticlePair)
calculateParticlePairValue(valueIndex, numberOfAtoms, atomCoordinates, atomParameters, values, globalParameters, exclusions, true);
calculateParticlePairValue(valueIndex, numberOfAtoms, atomCoordinates, atomParameters, exclusions, true);
else
calculateParticlePairValue(valueIndex, numberOfAtoms, atomCoordinates, atomParameters, values, globalParameters, exclusions, false);
calculateParticlePairValue(valueIndex, numberOfAtoms, atomCoordinates, atomParameters, exclusions, false);
}
// Now calculate the energy and its derivates.
vector<vector<RealOpenMM> > dEdV(numValues, vector<RealOpenMM>(numberOfAtoms, (RealOpenMM) 0));
for (int termIndex = 0; termIndex < (int) energyExpressions.size(); termIndex++) {
if (energyTypes[termIndex] == OpenMM::CustomGBForce::SingleParticle)
calculateSingleParticleEnergyTerm(termIndex, numberOfAtoms, atomCoordinates, values, globalParameters, atomParameters, forces, totalEnergy, dEdV);
calculateSingleParticleEnergyTerm(termIndex, numberOfAtoms, atomCoordinates, atomParameters, forces, totalEnergy, energyParamDerivs);
else if (energyTypes[termIndex] == OpenMM::CustomGBForce::ParticlePair)
calculateParticlePairEnergyTerm(termIndex, numberOfAtoms, atomCoordinates, atomParameters, values, globalParameters, exclusions, true, forces, totalEnergy, dEdV);
calculateParticlePairEnergyTerm(termIndex, numberOfAtoms, atomCoordinates, atomParameters, exclusions, true, forces, totalEnergy, energyParamDerivs);
else
calculateParticlePairEnergyTerm(termIndex, numberOfAtoms, atomCoordinates, atomParameters, values, globalParameters, exclusions, false, forces, totalEnergy, dEdV);
calculateParticlePairEnergyTerm(termIndex, numberOfAtoms, atomCoordinates, atomParameters, exclusions, false, forces, totalEnergy, energyParamDerivs);
}
// Apply the chain rule to evaluate forces.
calculateChainRuleForces(numberOfAtoms, atomCoordinates, atomParameters, values, globalParameters, exclusions, forces, dEdV);
calculateChainRuleForces(numberOfAtoms, atomCoordinates, atomParameters, exclusions, forces, energyParamDerivs);
}
void ReferenceCustomGBIxn::calculateSingleParticleValue(int index, int numAtoms, vector<RealVec>& atomCoordinates, vector<vector<RealOpenMM> >& values,
const map<string, double>& globalParameters, RealOpenMM** atomParameters) const {
void ReferenceCustomGBIxn::calculateSingleParticleValue(int index, int numAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters) {
values[index].resize(numAtoms);
map<string, double> variables = globalParameters;
for (int i = 0; i < numAtoms; i++) {
variables["x"] = atomCoordinates[i][0];
variables["y"] = atomCoordinates[i][1];
variables["z"] = atomCoordinates[i][2];
for (int j = 0; j < (int) paramNames.size(); j++)
variables[paramNames[j]] = atomParameters[i][j];
expressionSet.setVariable(xIndex, atomCoordinates[i][0]);
expressionSet.setVariable(yIndex, atomCoordinates[i][1]);
expressionSet.setVariable(zIndex, atomCoordinates[i][2]);
for (int j = 0; j < (int) paramIndex.size(); j++)
expressionSet.setVariable(paramIndex[j], atomParameters[i][j]);
for (int j = 0; j < index; j++)
variables[valueNames[j]] = values[j][i];
values[index][i] = (RealOpenMM) valueExpressions[index].evaluate(variables);
expressionSet.setVariable(valueIndex[j], values[j][i]);
values[index][i] = (RealOpenMM) valueExpressions[index].evaluate();
// Calculate derivatives with respect to parameters.
for (int j = 0; j < valueParamDerivExpressions[index].size(); j++)
dValuedParam[index][j][i] += valueParamDerivExpressions[index][j].evaluate();
for (int j = 0; j < index; j++) {
RealOpenMM dVdV = valueDerivExpressions[index][j].evaluate();
for (int k = 0; k < valueParamDerivExpressions[index].size(); k++)
dValuedParam[index][k][i] += dVdV*dValuedParam[j][k][i];
}
}
}
void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
vector<vector<RealOpenMM> >& values, const map<string, double>& globalParameters, const vector<set<int> >& exclusions, bool useExclusions) const {
const vector<set<int> >& exclusions, bool useExclusions) {
values[index].resize(numAtoms);
for (int i = 0; i < numAtoms; i++)
values[index][i] = (RealOpenMM) 0.0;
......@@ -194,8 +229,8 @@ void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, v
OpenMM::AtomPair pair = (*neighborList)[i];
if (useExclusions && exclusions[pair.first].find(pair.second) != exclusions[pair.first].end())
continue;
calculateOnePairValue(index, pair.first, pair.second, atomCoordinates, atomParameters, globalParameters, values);
calculateOnePairValue(index, pair.second, pair.first, atomCoordinates, atomParameters, globalParameters, values);
calculateOnePairValue(index, pair.first, pair.second, atomCoordinates, atomParameters);
calculateOnePairValue(index, pair.second, pair.first, atomCoordinates, atomParameters);
}
}
else {
......@@ -205,15 +240,14 @@ void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, v
for (int j = i+1; j < numAtoms; j++) {
if (useExclusions && exclusions[i].find(j) != exclusions[i].end())
continue;
calculateOnePairValue(index, i, j, atomCoordinates, atomParameters, globalParameters, values);
calculateOnePairValue(index, j, i, atomCoordinates, atomParameters, globalParameters, values);
calculateOnePairValue(index, i, j, atomCoordinates, atomParameters);
calculateOnePairValue(index, j, i, atomCoordinates, atomParameters);
}
}
}
}
void ReferenceCustomGBIxn::calculateOnePairValue(int index, int atom1, int atom2, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const map<string, double>& globalParameters, vector<vector<RealOpenMM> >& values) const {
void ReferenceCustomGBIxn::calculateOnePairValue(int index, int atom1, int atom2, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (periodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom2], atomCoordinates[atom1], periodicBoxVectors, deltaR);
......@@ -222,44 +256,53 @@ void ReferenceCustomGBIxn::calculateOnePairValue(int index, int atom1, int atom2
RealOpenMM r = deltaR[ReferenceForce::RIndex];
if (cutoff && r >= cutoffDistance)
return;
map<string, double> variables = globalParameters;
for (int i = 0; i < (int) paramNames.size(); i++) {
variables[particleParamNames[i*2]] = atomParameters[atom1][i];
variables[particleParamNames[i*2+1]] = atomParameters[atom2][i];
for (int i = 0; i < (int) paramIndex.size(); i++) {
expressionSet.setVariable(particleParamIndex[i*2], atomParameters[atom1][i]);
expressionSet.setVariable(particleParamIndex[i*2+1], atomParameters[atom2][i]);
}
variables["r"] = r;
expressionSet.setVariable(rIndex, r);
for (int i = 0; i < index; i++) {
variables[particleValueNames[i*2]] = values[i][atom1];
variables[particleValueNames[i*2+1]] = values[i][atom2];
expressionSet.setVariable(particleValueIndex[i*2], values[i][atom1]);
expressionSet.setVariable(particleValueIndex[i*2+1], values[i][atom2]);
}
values[index][atom1] += (RealOpenMM) valueExpressions[index].evaluate(variables);
values[index][atom1] += (RealOpenMM) valueExpressions[index].evaluate();
// Calculate derivatives with respect to parameters.
for (int i = 0; i < valueParamDerivExpressions[index].size(); i++)
dValuedParam[index][i][atom1] += valueParamDerivExpressions[index][i].evaluate();
}
void ReferenceCustomGBIxn::calculateSingleParticleEnergyTerm(int index, int numAtoms, vector<RealVec>& atomCoordinates, const vector<vector<RealOpenMM> >& values,
const map<string, double>& globalParameters, RealOpenMM** atomParameters, vector<RealVec>& forces, RealOpenMM* totalEnergy,
vector<vector<RealOpenMM> >& dEdV) const {
map<string, double> variables = globalParameters;
void ReferenceCustomGBIxn::calculateSingleParticleEnergyTerm(int index, int numAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
for (int i = 0; i < numAtoms; i++) {
variables["x"] = atomCoordinates[i][0];
variables["y"] = atomCoordinates[i][1];
variables["z"] = atomCoordinates[i][2];
for (int j = 0; j < (int) paramNames.size(); j++)
variables[paramNames[j]] = atomParameters[i][j];
for (int j = 0; j < (int) valueNames.size(); j++)
variables[valueNames[j]] = values[j][i];
expressionSet.setVariable(xIndex, atomCoordinates[i][0]);
expressionSet.setVariable(yIndex, atomCoordinates[i][1]);
expressionSet.setVariable(zIndex, atomCoordinates[i][2]);
for (int j = 0; j < (int) paramIndex.size(); j++)
expressionSet.setVariable(paramIndex[j], atomParameters[i][j]);
for (int j = 0; j < valueIndex.size(); j++)
expressionSet.setVariable(valueIndex[j], values[j][i]);
// Compute energy and force.
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpressions[index].evaluate(variables);
for (int j = 0; j < (int) valueNames.size(); j++)
dEdV[j][i] += (RealOpenMM) energyDerivExpressions[index][j].evaluate(variables);
forces[i][0] -= (RealOpenMM) energyGradientExpressions[index][0].evaluate(variables);
forces[i][1] -= (RealOpenMM) energyGradientExpressions[index][1].evaluate(variables);
forces[i][2] -= (RealOpenMM) energyGradientExpressions[index][2].evaluate(variables);
*totalEnergy += (RealOpenMM) energyExpressions[index].evaluate();
for (int j = 0; j < (int) valueIndex.size(); j++)
dEdV[j][i] += (RealOpenMM) energyDerivExpressions[index][j].evaluate();
forces[i][0] -= (RealOpenMM) energyGradientExpressions[index][0].evaluate();
forces[i][1] -= (RealOpenMM) energyGradientExpressions[index][1].evaluate();
forces[i][2] -= (RealOpenMM) energyGradientExpressions[index][2].evaluate();
// Compute derivatives with respect to parameters.
for (int k = 0; k < energyParamDerivExpressions[index].size(); k++)
energyParamDerivs[k] += energyParamDerivExpressions[index][k].evaluate();
}
}
void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const vector<vector<RealOpenMM> >& values, const map<string, double>& globalParameters, const vector<set<int> >& exclusions, bool useExclusions,
vector<RealVec>& forces, RealOpenMM* totalEnergy, vector<vector<RealOpenMM> >& dEdV) const {
const vector<set<int> >& exclusions, bool useExclusions, vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
if (cutoff) {
// Loop over all pairs in the neighbor list.
......@@ -267,7 +310,7 @@ void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAto
OpenMM::AtomPair pair = (*neighborList)[i];
if (useExclusions && exclusions[pair.first].find(pair.second) != exclusions[pair.first].end())
continue;
calculateOnePairEnergyTerm(index, pair.first, pair.second, atomCoordinates, atomParameters, globalParameters, values, forces, totalEnergy, dEdV);
calculateOnePairEnergyTerm(index, pair.first, pair.second, atomCoordinates, atomParameters, forces, totalEnergy, energyParamDerivs);
}
}
else {
......@@ -277,15 +320,14 @@ void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAto
for (int j = i+1; j < numAtoms; j++) {
if (useExclusions && exclusions[i].find(j) != exclusions[i].end())
continue;
calculateOnePairEnergyTerm(index, i, j, atomCoordinates, atomParameters, globalParameters, values, forces, totalEnergy, dEdV);
calculateOnePairEnergyTerm(index, i, j, atomCoordinates, atomParameters, forces, totalEnergy, energyParamDerivs);
}
}
}
}
void ReferenceCustomGBIxn::calculateOnePairEnergyTerm(int index, int atom1, int atom2, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const map<string, double>& globalParameters, const vector<vector<RealOpenMM> >& values, vector<RealVec>& forces, RealOpenMM* totalEnergy,
vector<vector<RealOpenMM> >& dEdV) const {
vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
// Compute the displacement.
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
......@@ -299,44 +341,47 @@ void ReferenceCustomGBIxn::calculateOnePairEnergyTerm(int index, int atom1, int
// Record variables for evaluating expressions.
map<string, double> variables = globalParameters;
for (int i = 0; i < (int) paramNames.size(); i++) {
variables[particleParamNames[i*2]] = atomParameters[atom1][i];
variables[particleParamNames[i*2+1]] = atomParameters[atom2][i];
for (int i = 0; i < (int) paramIndex.size(); i++) {
expressionSet.setVariable(particleParamIndex[i*2], atomParameters[atom1][i]);
expressionSet.setVariable(particleParamIndex[i*2+1], atomParameters[atom2][i]);
}
variables["r"] = r;
for (int i = 0; i < (int) valueNames.size(); i++) {
variables[particleValueNames[i*2]] = values[i][atom1];
variables[particleValueNames[i*2+1]] = values[i][atom2];
expressionSet.setVariable(rIndex, r);
for (int i = 0; i < (int) valueIndex.size(); i++) {
expressionSet.setVariable(particleValueIndex[i*2], values[i][atom1]);
expressionSet.setVariable(particleValueIndex[i*2+1], values[i][atom2]);
}
// Evaluate the energy and its derivatives.
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpressions[index].evaluate(variables);
RealOpenMM dEdR = (RealOpenMM) energyDerivExpressions[index][0].evaluate(variables);
*totalEnergy += (RealOpenMM) energyExpressions[index].evaluate();
RealOpenMM dEdR = (RealOpenMM) energyDerivExpressions[index][0].evaluate();
dEdR *= 1/r;
for (int i = 0; i < 3; i++) {
forces[atom1][i] -= dEdR*deltaR[i];
forces[atom2][i] += dEdR*deltaR[i];
}
for (int i = 0; i < (int) valueNames.size(); i++) {
dEdV[i][atom1] += (RealOpenMM) energyDerivExpressions[index][2*i+1].evaluate(variables);
dEdV[i][atom2] += (RealOpenMM) energyDerivExpressions[index][2*i+2].evaluate(variables);
for (int i = 0; i < (int) valueIndex.size(); i++) {
dEdV[i][atom1] += (RealOpenMM) energyDerivExpressions[index][2*i+1].evaluate();
dEdV[i][atom2] += (RealOpenMM) energyDerivExpressions[index][2*i+2].evaluate();
}
// Compute derivatives with respect to parameters.
for (int i = 0; i < energyParamDerivExpressions[index].size(); i++)
energyParamDerivs[i] += energyParamDerivExpressions[index][i].evaluate();
}
void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const vector<vector<RealOpenMM> >& values, const map<string, double>& globalParameters,
const vector<set<int> >& exclusions, vector<RealVec>& forces, vector<vector<RealOpenMM> >& dEdV) const {
const vector<set<int> >& exclusions, vector<RealVec>& forces, double* energyParamDerivs) {
if (cutoff) {
// Loop over all pairs in the neighbor list.
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
bool isExcluded = (exclusions[pair.first].find(pair.second) != exclusions[pair.first].end());
calculateOnePairChainRule(pair.first, pair.second, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded);
calculateOnePairChainRule(pair.second, pair.first, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded);
calculateOnePairChainRule(pair.first, pair.second, atomCoordinates, atomParameters, forces, isExcluded);
calculateOnePairChainRule(pair.second, pair.first, atomCoordinates, atomParameters, forces, isExcluded);
}
}
else {
......@@ -345,45 +390,50 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<RealVec
for (int i = 0; i < numAtoms; i++) {
for (int j = i+1; j < numAtoms; j++) {
bool isExcluded = (exclusions[i].find(j) != exclusions[i].end());
calculateOnePairChainRule(i, j, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded);
calculateOnePairChainRule(j, i, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded);
calculateOnePairChainRule(i, j, atomCoordinates, atomParameters, forces, isExcluded);
calculateOnePairChainRule(j, i, atomCoordinates, atomParameters, forces, isExcluded);
}
}
}
// Compute chain rule terms for computed values that depend explicitly on particle coordinates.
map<string, double> variables = globalParameters;
for (int i = 0; i < numAtoms; i++) {
variables["x"] = atomCoordinates[i][0];
variables["y"] = atomCoordinates[i][1];
variables["z"] = atomCoordinates[i][2];
expressionSet.setVariable(xIndex, atomCoordinates[i][0]);
expressionSet.setVariable(yIndex, atomCoordinates[i][1]);
expressionSet.setVariable(zIndex, atomCoordinates[i][2]);
vector<RealOpenMM> dVdX(valueDerivExpressions.size(), 0.0);
vector<RealOpenMM> dVdY(valueDerivExpressions.size(), 0.0);
vector<RealOpenMM> dVdZ(valueDerivExpressions.size(), 0.0);
for (int j = 0; j < (int) paramNames.size(); j++)
variables[paramNames[j]] = atomParameters[i][j];
for (int j = 1; j < (int) valueNames.size(); j++) {
variables[valueNames[j-1]] = values[j-1][i];
for (int j = 0; j < (int) paramIndex.size(); j++)
expressionSet.setVariable(paramIndex[j], atomParameters[i][j]);
for (int j = 1; j < (int) valueIndex.size(); j++) {
expressionSet.setVariable(valueIndex[j-1], values[j-1][i]);
for (int k = 1; k < j; k++) {
RealOpenMM dVdV = (RealOpenMM) valueDerivExpressions[j][k].evaluate(variables);
RealOpenMM dVdV = (RealOpenMM) valueDerivExpressions[j][k].evaluate();
dVdX[j] += dVdV*dVdX[k];
dVdY[j] += dVdV*dVdY[k];
dVdZ[j] += dVdV*dVdZ[k];
}
dVdX[j] += (RealOpenMM) valueGradientExpressions[j][0].evaluate(variables);
dVdY[j] += (RealOpenMM) valueGradientExpressions[j][1].evaluate(variables);
dVdZ[j] += (RealOpenMM) valueGradientExpressions[j][2].evaluate(variables);
dVdX[j] += (RealOpenMM) valueGradientExpressions[j][0].evaluate();
dVdY[j] += (RealOpenMM) valueGradientExpressions[j][1].evaluate();
dVdZ[j] += (RealOpenMM) valueGradientExpressions[j][2].evaluate();
forces[i][0] -= dEdV[j][i]*dVdX[j];
forces[i][1] -= dEdV[j][i]*dVdY[j];
forces[i][2] -= dEdV[j][i]*dVdZ[j];
}
}
// Compute chain rule terms for derivatives with respect to parameters.
for (int i = 0; i < numAtoms; i++)
for (int j = 0; j < (int) valueIndex.size(); j++)
for (int k = 0; k < dValuedParam[j].size(); k++)
energyParamDerivs[k] += dEdV[j][i]*dValuedParam[j][k][i];
}
void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const map<string, double>& globalParameters, const vector<vector<RealOpenMM> >& values, vector<RealVec>& forces,
vector<vector<RealOpenMM> >& dEdV, bool isExcluded) const {
vector<RealVec>& forces, bool isExcluded) {
// Compute the displacement.
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
......@@ -397,14 +447,13 @@ void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, vecto
// Record variables for evaluating expressions.
map<string, double> variables = globalParameters;
for (int i = 0; i < (int) paramNames.size(); i++) {
variables[particleParamNames[i*2]] = atomParameters[atom1][i];
variables[particleParamNames[i*2+1]] = atomParameters[atom2][i];
for (int i = 0; i < (int) paramIndex.size(); i++) {
expressionSet.setVariable(particleParamIndex[i*2], atomParameters[atom1][i]);
expressionSet.setVariable(particleParamIndex[i*2+1], atomParameters[atom2][i]);
}
variables["r"] = r;
variables[particleValueNames[0]] = values[0][atom1];
variables[particleValueNames[1]] = values[0][atom2];
expressionSet.setVariable(rIndex, r);
expressionSet.setVariable(particleValueIndex[0], values[0][atom1]);
expressionSet.setVariable(particleValueIndex[1], values[0][atom2]);
// Evaluate the derivative of each parameter with respect to position and apply forces.
......@@ -415,24 +464,23 @@ void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, vecto
vector<RealOpenMM> dVdR1(valueDerivExpressions.size(), 0.0);
vector<RealOpenMM> dVdR2(valueDerivExpressions.size(), 0.0);
if (!isExcluded || valueTypes[0] != OpenMM::CustomGBForce::ParticlePair) {
dVdR1[0] = (RealOpenMM) valueDerivExpressions[0][0].evaluate(variables);;
dVdR1[0] = (RealOpenMM) valueDerivExpressions[0][0].evaluate();
dVdR2[0] = -dVdR1[0];
for (int i = 0; i < 3; i++) {
forces[atom1][i] -= dEdV[0][atom1]*dVdR1[0]*deltaR[i];
forces[atom2][i] -= dEdV[0][atom1]*dVdR2[0]*deltaR[i];
}
}
variables = globalParameters;
for (int i = 0; i < (int) paramNames.size(); i++)
variables[paramNames[i]] = atomParameters[atom1][i];
variables[valueNames[0]] = values[0][atom1];
for (int i = 1; i < (int) valueNames.size(); i++) {
variables[valueNames[i]] = values[i][atom1];
variables["x"] = atomCoordinates[atom1][0];
variables["y"] = atomCoordinates[atom1][1];
variables["z"] = atomCoordinates[atom1][2];
for (int i = 0; i < (int) paramIndex.size(); i++)
expressionSet.setVariable(paramIndex[i], atomParameters[atom1][i]);
expressionSet.setVariable(valueIndex[0], values[0][atom1]);
for (int i = 1; i < (int) valueIndex.size(); i++) {
expressionSet.setVariable(valueIndex[i], values[i][atom1]);
expressionSet.setVariable(xIndex, atomCoordinates[atom1][0]);
expressionSet.setVariable(yIndex, atomCoordinates[atom1][1]);
expressionSet.setVariable(zIndex, atomCoordinates[atom1][2]);
for (int j = 0; j < i; j++) {
RealOpenMM dVdV = (RealOpenMM) valueDerivExpressions[i][j].evaluate(variables);
RealOpenMM dVdV = (RealOpenMM) valueDerivExpressions[i][j].evaluate();
dVdR1[i] += dVdV*dVdR1[j];
dVdR2[i] += dVdV*dVdR2[j];
}
......
platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
View file @ a381a3ab
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -44,23 +44,20 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames) :
cutoff(false), useSwitch(false), periodic(false), energyExpression(energyExpression), forceExpression(forceExpression), paramNames(parameterNames) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn";
// ---------------------------------------------------------------------------------------
energyR = ReferenceForce::getVariablePointer(this->energyExpression, "r");
forceR = ReferenceForce::getVariablePointer(this->forceExpression, "r");
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames,
const vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
cutoff(false), useSwitch(false), periodic(false), energyExpression(energyExpression), forceExpression(forceExpression),
paramNames(parameterNames), energyParamDerivExpressions(energyParamDerivExpressions) {
expressionSet.registerExpression(this->energyExpression);
expressionSet.registerExpression(this->forceExpression);
for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
rIndex = expressionSet.getVariableIndex("r");
for (int i = 0; i < (int) paramNames.size(); i++) {
for (int j = 1; j < 3; j++) {
stringstream name;
name << paramNames[i] << j;
energyParticleParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, name.str()));
forceParticleParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, name.str()));
particleParamIndex.push_back(expressionSet.getVariableIndex(name.str()));
}
}
}
......@@ -167,12 +164,10 @@ void ReferenceCustomNonbondedIxn::setUseSwitchingFunction(RealOpenMM distance) {
void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, vector<set<int> >& exclusions,
RealOpenMM* fixedParameters, const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) {
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(forceExpression, iter->first), iter->second);
}
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
if (interactionGroups.size() > 0) {
// The user has specified interaction groups, so compute only the requested interactions.
......@@ -186,12 +181,10 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
if (*atom1 > *atom2 && set1.find(*atom2) != set1.end() && set2.find(*atom1) != set2.end())
continue; // Both atoms are in both sets, so skip duplicate interactions.
for (int j = 0; j < (int) paramNames.size(); j++) {
ReferenceForce::setVariable(energyParticleParams[j*2], atomParameters[*atom1][j]);
ReferenceForce::setVariable(energyParticleParams[j*2+1], atomParameters[*atom2][j]);
ReferenceForce::setVariable(forceParticleParams[j*2], atomParameters[*atom1][j]);
ReferenceForce::setVariable(forceParticleParams[j*2+1], atomParameters[*atom2][j]);
expressionSet.setVariable(particleParamIndex[j*2], atomParameters[*atom1][j]);
expressionSet.setVariable(particleParamIndex[j*2+1], atomParameters[*atom2][j]);
}
calculateOneIxn(*atom1, *atom2, atomCoordinates, forces, energyByAtom, totalEnergy);
calculateOneIxn(*atom1, *atom2, atomCoordinates, forces, energyByAtom, totalEnergy, energyParamDerivs);
}
}
}
......@@ -202,12 +195,10 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
for (int j = 0; j < (int) paramNames.size(); j++) {
ReferenceForce::setVariable(energyParticleParams[j*2], atomParameters[pair.first][j]);
ReferenceForce::setVariable(energyParticleParams[j*2+1], atomParameters[pair.second][j]);
ReferenceForce::setVariable(forceParticleParams[j*2], atomParameters[pair.first][j]);
ReferenceForce::setVariable(forceParticleParams[j*2+1], atomParameters[pair.second][j]);
expressionSet.setVariable(particleParamIndex[j*2], atomParameters[pair.first][j]);
expressionSet.setVariable(particleParamIndex[j*2+1], atomParameters[pair.second][j]);
}
calculateOneIxn(pair.first, pair.second, atomCoordinates, forces, energyByAtom, totalEnergy);
calculateOneIxn(pair.first, pair.second, atomCoordinates, forces, energyByAtom, totalEnergy, energyParamDerivs);
}
}
else {
......@@ -217,12 +208,10 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
for (int jj = ii+1; jj < numberOfAtoms; jj++) {
if (exclusions[jj].find(ii) == exclusions[jj].end()) {
for (int j = 0; j < (int) paramNames.size(); j++) {
ReferenceForce::setVariable(energyParticleParams[j*2], atomParameters[ii][j]);
ReferenceForce::setVariable(energyParticleParams[j*2+1], atomParameters[jj][j]);
ReferenceForce::setVariable(forceParticleParams[j*2], atomParameters[ii][j]);
ReferenceForce::setVariable(forceParticleParams[j*2+1], atomParameters[jj][j]);
expressionSet.setVariable(particleParamIndex[j*2], atomParameters[ii][j]);
expressionSet.setVariable(particleParamIndex[j*2+1], atomParameters[jj][j]);
}
calculateOneIxn(ii, jj, atomCoordinates, forces, energyByAtom, totalEnergy);
calculateOneIxn(ii, jj, atomCoordinates, forces, energyByAtom, totalEnergy, energyParamDerivs);
}
}
}
......@@ -244,24 +233,7 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nReferenceCustomNonbondedIxn::calculateOneIxn";
// ---------------------------------------------------------------------------------------
// constants -- reduce Visual Studio warnings regarding conversions between float & double
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
static const RealOpenMM three = 3.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM twelve = 12.0;
static const RealOpenMM oneM = -1.0;
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, double* energyParamDerivs) {
// get deltaR, R2, and R between 2 atoms
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
......@@ -275,14 +247,14 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec
// accumulate forces
ReferenceForce::setVariable(energyR, r);
ReferenceForce::setVariable(forceR, r);
expressionSet.setVariable(rIndex, r);
RealOpenMM dEdR = (RealOpenMM) (forceExpression.evaluate()/(deltaR[ReferenceForce::RIndex]));
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate();
RealOpenMM switchValue = 1.0;
if (useSwitch) {
if (r > switchingDistance) {
RealOpenMM t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
RealOpenMM switchValue = 1+t*t*t*(-10+t*(15-t*6));
switchValue = 1+t*t*t*(-10+t*(15-t*6));
RealOpenMM switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
dEdR = switchValue*dEdR + energy*switchDeriv/r;
energy *= switchValue;
......@@ -293,6 +265,8 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec
forces[ii][kk] += force;
forces[jj][kk] -= force;
}
for (int i = 0; i < energyParamDerivExpressions.size(); i++)
energyParamDerivs[i] += switchValue*energyParamDerivExpressions[i].evaluate();
// accumulate energies
......
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