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Commit 5003591d authored by Peter Eastman's avatar Peter Eastman
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Simplified reference code for accumulating energies

parent b8c624fa
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Showing with 78 additions and 278 deletions
platforms/reference/src/ReferenceKernels.cpp
View file @ 5003591d
......@@ -320,21 +320,17 @@ void ReferenceCalcHarmonicBondForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** forceData = extractForces(context);
ReferenceBondForce refBondForce;
ReferenceHarmonicBondIxn harmonicBond;
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, 0, 0, 0, harmonicBond);
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, 0, harmonicBond);
}
double ReferenceCalcHarmonicBondForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numBonds];
RealOpenMM energy = 0;
ReferenceBondForce refBondForce;
ReferenceHarmonicBondIxn harmonicBond;
for (int i = 0; i < numBonds; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, energyArray, 0, &energy, harmonicBond);
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, &energy, harmonicBond);
disposeRealArray(forceData, context.getSystem().getNumParticles());
delete[] energyArray;
return energy;
}
......@@ -380,24 +376,20 @@ void ReferenceCalcCustomBondForceKernel::executeForces(ContextImpl& context) {
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomBondIxn harmonicBond(energyExpression, forceExpression, parameterNames, globalParameters);
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, 0, 0, 0, harmonicBond);
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, 0, harmonicBond);
}
double ReferenceCalcCustomBondForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numBonds];
RealOpenMM energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomBondIxn harmonicBond(energyExpression, forceExpression, parameterNames, globalParameters);
for (int i = 0; i < numBonds; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, energyArray, 0, &energy, harmonicBond);
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, &energy, harmonicBond);
disposeRealArray(forceData, context.getSystem().getNumParticles());
delete[] energyArray;
return energy;
}
......@@ -427,21 +419,17 @@ void ReferenceCalcHarmonicAngleForceKernel::executeForces(ContextImpl& context)
RealOpenMM** forceData = extractForces(context);
ReferenceBondForce refBondForce;
ReferenceAngleBondIxn angleBond;
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, 0, 0, 0, angleBond);
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, 0, angleBond);
}
double ReferenceCalcHarmonicAngleForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numAngles];
RealOpenMM energy = 0;
ReferenceBondForce refBondForce;
ReferenceAngleBondIxn angleBond;
for (int i = 0; i < numAngles; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, energyArray, 0, &energy, angleBond);
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, &energy, angleBond);
disposeRealArray(forceData, context.getSystem().getNumParticles());
delete[] energyArray;
return energy;
}
......@@ -488,24 +476,20 @@ void ReferenceCalcCustomAngleForceKernel::executeForces(ContextImpl& context) {
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomAngleIxn customAngle(energyExpression, forceExpression, parameterNames, globalParameters);
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, 0, 0, 0, customAngle);
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, 0, customAngle);
}
double ReferenceCalcCustomAngleForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numAngles];
RealOpenMM energy = 0;
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);
for (int i = 0; i < numAngles; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, energyArray, 0, &energy, customAngle);
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, &energy, customAngle);
disposeRealArray(forceData, context.getSystem().getNumParticles());
delete[] energyArray;
return energy;
}
......@@ -537,21 +521,17 @@ void ReferenceCalcPeriodicTorsionForceKernel::executeForces(ContextImpl& context
RealOpenMM** forceData = extractForces(context);
ReferenceBondForce refBondForce;
ReferenceProperDihedralBond periodicTorsionBond;
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, 0, 0, periodicTorsionBond);
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, periodicTorsionBond);
}
double ReferenceCalcPeriodicTorsionForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numTorsions];
RealOpenMM energy = 0;
ReferenceBondForce refBondForce;
ReferenceProperDihedralBond periodicTorsionBond;
for (int i = 0; i < numTorsions; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, energyArray, 0, &energy, periodicTorsionBond);
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, &energy, periodicTorsionBond);
disposeRealArray(forceData, context.getSystem().getNumParticles());
delete[] energyArray;
return energy;
}
......@@ -586,21 +566,17 @@ void ReferenceCalcRBTorsionForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** forceData = extractForces(context);
ReferenceBondForce refBondForce;
ReferenceRbDihedralBond rbTorsionBond;
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, 0, 0, rbTorsionBond);
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, rbTorsionBond);
}
double ReferenceCalcRBTorsionForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numTorsions];
RealOpenMM energy = 0;
ReferenceBondForce refBondForce;
ReferenceRbDihedralBond rbTorsionBond;
for (int i = 0; i < numTorsions; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, energyArray, 0, &energy, rbTorsionBond);
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, &energy, rbTorsionBond);
disposeRealArray(forceData, context.getSystem().getNumParticles());
delete[] energyArray;
return energy;
}
......@@ -690,24 +666,20 @@ void ReferenceCalcCustomTorsionForceKernel::executeForces(ContextImpl& context)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomTorsionIxn customTorsion(energyExpression, forceExpression, parameterNames, globalParameters);
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, 0, 0, customTorsion);
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, customTorsion);
}
double ReferenceCalcCustomTorsionForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numTorsions];
RealOpenMM energy = 0;
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);
for (int i = 0; i < numTorsions; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, energyArray, 0, &energy, customTorsion);
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, &energy, customTorsion);
disposeRealArray(forceData, context.getSystem().getNumParticles());
delete[] energyArray;
return energy;
}
......@@ -812,7 +784,7 @@ void ReferenceCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, 0);
ReferenceBondForce refBondForce;
ReferenceLJCoulomb14 nonbonded14;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, 0, 0, nonbonded14);
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, nonbonded14);
}
double ReferenceCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
......@@ -836,12 +808,8 @@ double ReferenceCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, &energy);
ReferenceBondForce refBondForce;
ReferenceLJCoulomb14 nonbonded14;
RealOpenMM* energyArray = new RealOpenMM[num14];
for (int i = 0; i < num14; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, energyArray, 0, &energy, nonbonded14);
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, &energy, nonbonded14);
disposeRealArray(forceData, numParticles);
delete[] energyArray;
if (periodic || ewald || pme) {
RealOpenMM* boxSize = extractBoxSize(context);
energy += dispersionCoefficient/(boxSize[0]*boxSize[1]*boxSize[2]);
......
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp
View file @ 5003591d
......@@ -117,27 +117,15 @@ int ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, Rea
@param parameters parameters: parameters[0] = ideal bond length
parameters[1] = bond k (includes factor of 2)
@param forces force array (forces added)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
void ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
RealOpenMM** atomCoordinates,
RealOpenMM* parameters,
RealOpenMM** forces,
RealOpenMM* energiesByBond,
RealOpenMM* energiesByAtom ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceAngleBondIxn::calculateBondIxn";
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nReferenceAngleBondIxn::calculateBondIxn";
RealOpenMM* totalEnergy ) const {
// constants -- reduce Visual Studio warnings regarding conversions between float & double
......@@ -200,7 +188,6 @@ int ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
// accumulate energies
updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
return ReferenceForce::DefaultReturn;
if (totalEnergy != NULL)
*totalEnergy += energy;
}
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.h
View file @ 5003591d
......@@ -77,16 +77,13 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
@param parameters parameters: parameters[0] = ideal bond length
parameters[1] = bond k (includes factor of 2)
@param forces force array (forces added)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
RealOpenMM* totalEnergy ) const;
};
......
platforms/reference/src/SimTKReference/ReferenceBondForce.cpp
View file @ 5003591d
......@@ -72,21 +72,15 @@ ReferenceBondForce::~ReferenceBondForce( ){
@param parameters parameters: parameters[bondIndex][*]; contents of array
depend on ixn
@param forces force array (forces added to current values): forces[atomIndex][3]
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@param totalEnergy totalEnergy: sum over { energies[atomIndex] }
@param totalEnergy if not null, the energy will be added to this
@param ReferenceBondIxn ixn to be calculated
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices,
void ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices,
RealOpenMM** atomCoordinates,
RealOpenMM** parameters,
RealOpenMM** forces,
RealOpenMM* energiesByBond,
RealOpenMM* energiesByAtom,
RealOpenMM *totalEnergy,
ReferenceBondIxn& referenceBondIxn ){
......@@ -102,13 +96,7 @@ int ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices,
// calculate bond ixn
referenceBondIxn.calculateBondIxn( atomIndices[ii], atomCoordinates, parameters[ii],
forces, (energiesByBond == NULL ? NULL : energiesByBond + ii), energiesByAtom );
if( energiesByBond != NULL ){
*totalEnergy += energiesByBond[ii];
forces, totalEnergy );
}
}
return ReferenceForce::DefaultReturn;
}
platforms/reference/src/SimTKReference/ReferenceBondForce.h
View file @ 5003591d
......@@ -62,19 +62,14 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
@param parameters parameters: parameters[bondIndex][*]; contents of array
depend on ixn
@param forces force array (forces added to current values): forces[atomIndex][3]
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@param totalEnergy totalEnergy: sum over { energies[atomIndex] }
@param totalEnergy if not null, the energy will be added to this
@param ReferenceBondIxn ixn to be calculated
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculateForce( int numberOfBonds, int** atomIndices,
void calculateForce( int numberOfBonds, int** atomIndices,
RealOpenMM** atomCoordinates,
RealOpenMM** parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom,
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn );
};
......
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
View file @ 5003591d
......@@ -63,42 +63,6 @@ ReferenceBondIxn::~ReferenceBondIxn( ){
}
/**---------------------------------------------------------------------------------------
Update energy
@param energy energy value to update
@param energyByBond ptr to energyByBond accumulator (may be null)
@param numberOfAtomIndices number of atoms in bond
@param atomIndices array of atom indices of size 'numberOfAtomIndices'
@param energyByAtom array of energies by atom (may be null)
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceBondIxn::updateEnergy( RealOpenMM energy, RealOpenMM* energyByBond,
int numberOfAtomIndices, int* atomIndices, RealOpenMM* energyByAtom ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nReferenceBondIxn::updateEnergy";
// ---------------------------------------------------------------------------------------
if( energyByBond ){
*energyByBond += energy;
}
if( energyByAtom ){
for( int ii = 0; ii < numberOfAtomIndices; ii++ ){
energyByAtom[atomIndices[ii]] += energy;
}
}
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate Bond Ixn -- virtual method -- does nothing
......@@ -107,22 +71,19 @@ int ReferenceBondIxn::updateEnergy( RealOpenMM energy, RealOpenMM* energyByBond,
@param atomCoordinates atom coordinates
@param parameters parameters
@param forces force array (forces added)
@param energyByBond bond energy
@param energy atom energy
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int ReferenceBondIxn::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
void ReferenceBondIxn::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energyByBond, RealOpenMM* energyByAtom ) const {
RealOpenMM* totalEnergy ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nReferenceBondIxn::calculateBondIxn";
// ---------------------------------------------------------------------------------------
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceBondIxn.h
View file @ 5003591d
......@@ -59,32 +59,13 @@ class OPENMM_EXPORT ReferenceBondIxn {
@param atomCoordinates atom coordinates
@param parameters parameters
@param forces force array (forces added)
@param energyByBond bond energy
@param energy atom energy
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
virtual int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
virtual void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energyByBond, RealOpenMM* energyByAtom ) const;
/**---------------------------------------------------------------------------------------
Update energy
@param energy energy value to update
@param energyByBond ptr to energyByBond accumulator (may be null)
@param numberOfAtomIndices number of atoms in bond
@param atomIndices array of atom indices of size 'numberOfAtomIndices'
@param energyByAtom array of energies by atom (may be null)
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int updateEnergy( RealOpenMM energy, RealOpenMM* energyByBond,
int numberOfAtomIndices, int* atomIndices, RealOpenMM* energyByAtom ) const;
RealOpenMM* totalEnergy ) const;
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.cpp
View file @ 5003591d
......@@ -188,7 +188,6 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, RealOpenMM** atomCoordi
--------------------------------------------------------------------------------------- */
int ReferenceCMAPTorsionIxn::calculateBondIxn(int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces, RealOpenMM* energyByBond, RealOpenMM* energyByAtom) const {
return ReferenceForce::DefaultReturn;
void ReferenceCMAPTorsionIxn::calculateBondIxn(int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces, RealOpenMM* totalEnergy) const {
}
platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.h
View file @ 5003591d
......@@ -84,9 +84,9 @@ public:
--------------------------------------------------------------------------------------- */
int calculateBondIxn(int* atomIndices, RealOpenMM** atomCoordinates,
void calculateBondIxn(int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energyByBond, RealOpenMM* energyByAtom) const;
RealOpenMM* totalEnergy) const;
// ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
View file @ 5003591d
......@@ -74,25 +74,15 @@ ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn( ){
@param atomCoordinates atom coordinates
@param parameters parameters values
@param forces force array (forces added to input values)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn;
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int ReferenceCustomAngleIxn::calculateBondIxn( int* atomIndices,
void ReferenceCustomAngleIxn::calculateBondIxn( int* atomIndices,
RealOpenMM** atomCoordinates,
RealOpenMM* parameters,
RealOpenMM** forces,
RealOpenMM* energiesByBond,
RealOpenMM* energiesByAtom ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomAngleIxn::calculateAngleIxn";
// ---------------------------------------------------------------------------------------
RealOpenMM* totalEnergy ) const {
static const std::string methodName = "\nReferenceCustomAngleIxn::calculateAngleIxn";
......@@ -156,8 +146,7 @@ int ReferenceCustomAngleIxn::calculateBondIxn( int* atomIndices,
// accumulate energies
updateEnergy(energy, energiesByBond, 3, atomIndices, energiesByAtom);
return ReferenceForce::DefaultReturn;
if (totalEnergy != NULL)
*totalEnergy += energy;
}
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.h
View file @ 5003591d
......@@ -64,14 +64,13 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
@param atomCoordinates atom coordinates
@param parameters parameter values
@param forces force array (forces added)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
RealOpenMM* totalEnergy) const;
};
......
platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
View file @ 5003591d
......@@ -75,25 +75,15 @@ ReferenceCustomBondIxn::~ReferenceCustomBondIxn( ){
@param atomCoordinates atom coordinates
@param parameters parameters values
@param forces force array (forces added to input values)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn;
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
RealOpenMM** atomCoordinates,
RealOpenMM* parameters,
RealOpenMM** forces,
RealOpenMM* energiesByBond,
RealOpenMM* energiesByAtom ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomBondIxn::calculateBondIxn";
// ---------------------------------------------------------------------------------------
RealOpenMM* totalEnergy ) const {
static const std::string methodName = "\nReferenceCustomBondIxn::calculateBondIxn";
......@@ -127,8 +117,6 @@ int ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
forces[atomBIndex][1] -= dEdR*deltaR[ReferenceForce::YIndex];
forces[atomBIndex][2] -= dEdR*deltaR[ReferenceForce::ZIndex];
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate(variables);
updateEnergy( energy, energiesByBond, twoI, atomIndices, energiesByAtom );
return ReferenceForce::DefaultReturn;
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
}
platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.h
View file @ 5003591d
......@@ -65,14 +65,13 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
@param atomCoordinates atom coordinates
@param parameters parameter values
@param forces force array (forces added)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
RealOpenMM* totalEnergy ) const;
};
......
platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
View file @ 5003591d
......@@ -79,22 +79,14 @@ ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn( ){
@param forces force array (forces added to input values)
@param energy energy is added to this
@return ReferenceForce::DefaultReturn;
--------------------------------------------------------------------------------------- */
int ReferenceCustomExternalIxn::calculateForce( int atomIndex,
void ReferenceCustomExternalIxn::calculateForce( int atomIndex,
RealOpenMM** atomCoordinates,
RealOpenMM* parameters,
RealOpenMM** forces,
RealOpenMM* energy ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomExternalIxn::calculateBondIxn";
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nReferenceCustomExternalIxn::calculateBondIxn";
map<string, double> variables = globalParameters;
......@@ -111,6 +103,4 @@ int ReferenceCustomExternalIxn::calculateForce( int atomIndex,
forces[atomIndex][2] -= (RealOpenMM) forceExpressionZ.evaluate(variables);
if (energy != NULL)
*energy += (RealOpenMM) energyExpression.evaluate(variables);
return ReferenceForce::DefaultReturn;
}
platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.h
View file @ 5003591d
......@@ -72,7 +72,7 @@ class ReferenceCustomExternalIxn {
--------------------------------------------------------------------------------------- */
int calculateForce( int atomIndex, RealOpenMM** atomCoordinates,
void calculateForce( int atomIndex, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces, RealOpenMM* energy ) const;
......
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
View file @ 5003591d
......@@ -74,25 +74,15 @@ ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn( ){
@param atomCoordinates atom coordinates
@param parameters parameters values
@param forces force array (forces added to input values)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn;
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
RealOpenMM** atomCoordinates,
RealOpenMM* parameters,
RealOpenMM** forces,
RealOpenMM* energiesByBond,
RealOpenMM* energiesByAtom ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomTorsionIxn::calculateTorsionIxn";
// ---------------------------------------------------------------------------------------
RealOpenMM* totalEnergy ) const {
static const std::string methodName = "\nReferenceCustomTorsionIxn::calculateTorsionIxn";
......@@ -133,7 +123,6 @@ int ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
// evaluate delta angle, dE/d(angle)
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate(variables);
RealOpenMM dEdAngle = (RealOpenMM) forceExpression.evaluate(variables);
// compute force
......@@ -175,8 +164,7 @@ int ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
// accumulate energies
updateEnergy( energy, energiesByBond, 4, atomIndices, energiesByAtom );
return ReferenceForce::DefaultReturn;
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
}
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.h
View file @ 5003591d
......@@ -64,14 +64,13 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
@param atomCoordinates atom coordinates
@param parameters parameter values
@param forces force array (forces added)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
RealOpenMM* totalEnergy ) const;
};
......
platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp
View file @ 5003591d
......@@ -72,25 +72,15 @@ ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn( ){
@param parameters parameters: parameters[0] = ideal bond length
parameters[1] = bond k
@param forces force array (forces added to input values)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn;
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices,
void ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices,
RealOpenMM** atomCoordinates,
RealOpenMM* parameters,
RealOpenMM** forces,
RealOpenMM* energiesByBond,
RealOpenMM* energiesByAtom ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
// ---------------------------------------------------------------------------------------
RealOpenMM* totalEnergy ) const {
static const std::string methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
......@@ -129,8 +119,6 @@ int ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices,
forces[atomBIndex][1] -= dEdR*deltaR[ReferenceForce::YIndex];
forces[atomBIndex][2] -= dEdR*deltaR[ReferenceForce::ZIndex];
RealOpenMM energy = half*parameters[1]*deltaIdeal2;
updateEnergy( energy, energiesByBond, twoI, atomIndices, energiesByAtom );
return ReferenceForce::DefaultReturn;
if (totalEnergy != NULL)
*totalEnergy += half*parameters[1]*deltaIdeal2;
}
platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.h
View file @ 5003591d
......@@ -60,15 +60,13 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
@param parameters parameters: parameters[0] = ideal bond length
parameters[1] = bond k
@param forces force array (forces added)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
RealOpenMM* totalEnergy ) const;
};
......
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
View file @ 5003591d
......@@ -74,23 +74,13 @@ ReferenceLJCoulomb14::~ReferenceLJCoulomb14( ){
parameters[1]= c6*c6/c12 (4*epsilon)
parameters[2]= epsfac*q1*q2
@param forces force array (forces added to current values)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn
@param totalEnergy if not null, the energy will be added to this
--------------------------------------------------------------------------------------- */
int ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond,
RealOpenMM* energiesByAtom ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceLJCoulomb14::calculateBondIxn";
// ---------------------------------------------------------------------------------------
RealOpenMM* totalEnergy ) const {
static const std::string methodName = "\nReferenceLJCoulomb14::calculateBondIxn";
......@@ -140,12 +130,8 @@ int ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, RealOpenMM** atomC
forces[atomBIndex][ii] -= force;
}
RealOpenMM energy = parameters[1]*( sig6 - one )*sig6;
energy += (RealOpenMM) (ONE_4PI_EPS0*parameters[2]*inverseR);
// accumulate energies
updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
return ReferenceForce::DefaultReturn;
if (totalEnergy != NULL)
*totalEnergy += parameters[1]*( sig6 - one )*sig6 + (ONE_4PI_EPS0*parameters[2]*inverseR);
}
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