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Commit 7fb10336 authored by peastman's avatar peastman
Browse files

Cleaned up lots of formatting to be more consistent with the rest of OpenMM

parent 1d3ffd7b
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Showing with 219 additions and 219 deletions
platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp
View file @ 7fb10336
...@@ -71,7 +71,7 @@ ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesP ...@@ -71,7 +71,7 @@ ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesP
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomCompoundBondIxn::~ReferenceCustomCompoundBondIxn( ){ ReferenceCustomCompoundBondIxn::~ReferenceCustomCompoundBondIxn() {
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -92,7 +92,7 @@ void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<RealVec>& atomCoord ...@@ -92,7 +92,7 @@ void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
map<string, double> variables = globalParameters; map<string, double> variables = globalParameters;
int numBonds = bondAtoms.size(); int numBonds = bondAtoms.size();
for (int bond = 0; bond < numBonds; bond++){ for (int bond = 0; bond < numBonds; bond++) {
for (int j = 0; j < (int) bondParamNames.size(); j++) for (int j = 0; j < (int) bondParamNames.size(); j++)
variables[bondParamNames[j]] = bondParameters[bond][j]; variables[bondParamNames[j]] = bondParameters[bond][j];
calculateOneIxn(bond, atomCoordinates, variables, forces, totalEnergy); calculateOneIxn(bond, atomCoordinates, variables, forces, totalEnergy);
......
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 7fb10336
...@@ -96,7 +96,7 @@ ReferenceCustomDynamics::~ReferenceCustomDynamics() { ...@@ -96,7 +96,7 @@ ReferenceCustomDynamics::~ReferenceCustomDynamics() {
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates, void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance){ map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance) {
int numSteps = stepType.size(); int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end()); globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates; oldPos = atomCoordinates;
......
platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
View file @ 7fb10336
...@@ -78,7 +78,7 @@ ReferenceCustomExternalIxn::ReferenceCustomExternalIxn(const Lepton::CompiledExp ...@@ -78,7 +78,7 @@ ReferenceCustomExternalIxn::ReferenceCustomExternalIxn(const Lepton::CompiledExp
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn( ){ ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -100,11 +100,11 @@ ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn( ){ ...@@ -100,11 +100,11 @@ ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomExternalIxn::calculateForce( int atomIndex, void ReferenceCustomExternalIxn::calculateForce(int atomIndex,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM* energy ) const { RealOpenMM* energy) const {
static const std::string methodName = "\nReferenceCustomExternalIxn::calculateBondIxn"; static const std::string methodName = "\nReferenceCustomExternalIxn::calculateBondIxn";
......
platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
View file @ 7fb10336
...@@ -85,7 +85,7 @@ ReferenceCustomGBIxn::ReferenceCustomGBIxn(const vector<Lepton::ExpressionProgra ...@@ -85,7 +85,7 @@ ReferenceCustomGBIxn::ReferenceCustomGBIxn(const vector<Lepton::ExpressionProgra
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomGBIxn::~ReferenceCustomGBIxn( ){ ReferenceCustomGBIxn::~ReferenceCustomGBIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -104,7 +104,7 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn( ){ ...@@ -104,7 +104,7 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomGBIxn::setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors ) { void ReferenceCustomGBIxn::setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors) {
cutoff = true; cutoff = true;
cutoffDistance = distance; cutoffDistance = distance;
...@@ -202,8 +202,8 @@ void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, v ...@@ -202,8 +202,8 @@ void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, v
else { else {
// Perform an O(N^2) loop over all atom pairs. // Perform an O(N^2) loop over all atom pairs.
for (int i = 0; i < numAtoms; i++){ for (int i = 0; i < numAtoms; i++) {
for (int j = i+1; j < numAtoms; j++ ){ for (int j = i+1; j < numAtoms; j++) {
if (useExclusions && exclusions[i].find(j) != exclusions[i].end()) if (useExclusions && exclusions[i].find(j) != exclusions[i].end())
continue; continue;
calculateOnePairValue(index, i, j, atomCoordinates, atomParameters, globalParameters, values); calculateOnePairValue(index, i, j, atomCoordinates, atomParameters, globalParameters, values);
...@@ -274,8 +274,8 @@ void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAto ...@@ -274,8 +274,8 @@ void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAto
else { else {
// Perform an O(N^2) loop over all atom pairs. // Perform an O(N^2) loop over all atom pairs.
for (int i = 0; i < numAtoms; i++){ for (int i = 0; i < numAtoms; i++) {
for (int j = i+1; j < numAtoms; j++ ){ for (int j = i+1; j < numAtoms; j++) {
if (useExclusions && exclusions[i].find(j) != exclusions[i].end()) if (useExclusions && exclusions[i].find(j) != exclusions[i].end())
continue; continue;
calculateOnePairEnergyTerm(index, i, j, atomCoordinates, atomParameters, globalParameters, values, forces, totalEnergy, dEdV); calculateOnePairEnergyTerm(index, i, j, atomCoordinates, atomParameters, globalParameters, values, forces, totalEnergy, dEdV);
...@@ -343,8 +343,8 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<RealVec ...@@ -343,8 +343,8 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<RealVec
else { else {
// Perform an O(N^2) loop over all atom pairs. // Perform an O(N^2) loop over all atom pairs.
for (int i = 0; i < numAtoms; i++){ for (int i = 0; i < numAtoms; i++) {
for (int j = i+1; j < numAtoms; j++ ){ for (int j = i+1; j < numAtoms; j++) {
bool isExcluded = (exclusions[i].find(j) != exclusions[i].end()); bool isExcluded = (exclusions[i].find(j) != exclusions[i].end());
calculateOnePairChainRule(i, j, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded); calculateOnePairChainRule(i, j, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded);
calculateOnePairChainRule(j, i, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded); calculateOnePairChainRule(j, i, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded);
......
platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
View file @ 7fb10336
...@@ -64,7 +64,7 @@ ReferenceCustomHbondIxn::ReferenceCustomHbondIxn(const vector<vector<int> >& don ...@@ -64,7 +64,7 @@ ReferenceCustomHbondIxn::ReferenceCustomHbondIxn(const vector<vector<int> >& don
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomHbondIxn::~ReferenceCustomHbondIxn( ){ ReferenceCustomHbondIxn::~ReferenceCustomHbondIxn() {
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -128,7 +128,7 @@ void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, ...@@ -128,7 +128,7 @@ void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates,
int numDonors = donorAtoms.size(); int numDonors = donorAtoms.size();
int numAcceptors = acceptorAtoms.size(); int numAcceptors = acceptorAtoms.size();
for( int donor = 0; donor < numDonors; donor++ ){ for (int donor = 0; donor < numDonors; donor++) {
// Initialize per-donor parameters. // Initialize per-donor parameters.
for (int j = 0; j < (int) donorParamNames.size(); j++) for (int j = 0; j < (int) donorParamNames.size(); j++)
...@@ -136,7 +136,7 @@ void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, ...@@ -136,7 +136,7 @@ void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates,
// loop over atom pairs // loop over atom pairs
for( int acceptor = 0; acceptor < numAcceptors; acceptor++ ){ for (int acceptor = 0; acceptor < numAcceptors; acceptor++) {
if (exclusions[donor].find(acceptor) == exclusions[donor].end()) { if (exclusions[donor].find(acceptor) == exclusions[donor].end()) {
for (int j = 0; j < (int) acceptorParamNames.size(); j++) for (int j = 0; j < (int) acceptorParamNames.size(); j++)
variables[acceptorParamNames[j]] = acceptorParameters[acceptor][j]; variables[acceptorParamNames[j]] = acceptorParameters[acceptor][j];
......
platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.cpp
View file @ 7fb10336
...@@ -103,7 +103,7 @@ ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyP ...@@ -103,7 +103,7 @@ ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyP
CustomManyParticleForceImpl::buildFilterArrays(force, numTypes, particleTypes, orderIndex, particleOrder); CustomManyParticleForceImpl::buildFilterArrays(force, numTypes, particleTypes, orderIndex, particleOrder);
} }
ReferenceCustomManyParticleIxn::~ReferenceCustomManyParticleIxn( ){ ReferenceCustomManyParticleIxn::~ReferenceCustomManyParticleIxn() {
} }
void ReferenceCustomManyParticleIxn::calculateIxn(vector<RealVec>& atomCoordinates, RealOpenMM** particleParameters, void ReferenceCustomManyParticleIxn::calculateIxn(vector<RealVec>& atomCoordinates, RealOpenMM** particleParameters,
......
platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
View file @ 7fb10336
...@@ -72,7 +72,7 @@ ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::CompiledE ...@@ -72,7 +72,7 @@ ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::CompiledE
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn( ){ ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -91,7 +91,7 @@ ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn( ){ ...@@ -91,7 +91,7 @@ ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors ) { void ReferenceCustomNonbondedIxn::setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors) {
cutoff = true; cutoff = true;
cutoffDistance = distance; cutoffDistance = distance;
...@@ -119,7 +119,7 @@ void ReferenceCustomNonbondedIxn::setInteractionGroups(const vector<pair<set<int ...@@ -119,7 +119,7 @@ void ReferenceCustomNonbondedIxn::setInteractionGroups(const vector<pair<set<int
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::setUseSwitchingFunction( RealOpenMM distance ) { void ReferenceCustomNonbondedIxn::setUseSwitchingFunction(RealOpenMM distance) {
useSwitch = true; useSwitch = true;
switchingDistance = distance; switchingDistance = distance;
} }
...@@ -165,10 +165,10 @@ void ReferenceCustomNonbondedIxn::setUseSwitchingFunction( RealOpenMM distance ) ...@@ -165,10 +165,10 @@ void ReferenceCustomNonbondedIxn::setUseSwitchingFunction( RealOpenMM distance )
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<RealVec>& atomCoordinates, void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, vector<set<int> >& exclusions, RealOpenMM** atomParameters, vector<set<int> >& exclusions,
RealOpenMM* fixedParameters, const map<string, double>& globalParameters, vector<RealVec>& forces, RealOpenMM* fixedParameters, const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) { RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) { 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(energyExpression, iter->first), iter->second);
...@@ -244,8 +244,8 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re ...@@ -244,8 +244,8 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& atomCoordinates, vector<RealVec>& forces, void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) { RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -267,9 +267,9 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe ...@@ -267,9 +267,9 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex]; RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (periodic) if (periodic)
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR ); ReferenceForce::getDeltaRPeriodic(atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR);
else else
ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR ); ReferenceForce::getDeltaR(atomCoordinates[jj], atomCoordinates[ii], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex]; RealOpenMM r = deltaR[ReferenceForce::RIndex];
if (cutoff && r >= cutoffDistance) if (cutoff && r >= cutoffDistance)
return; return;
...@@ -289,7 +289,7 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe ...@@ -289,7 +289,7 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe
energy *= switchValue; energy *= switchValue;
} }
} }
for( int kk = 0; kk < 3; kk++ ){ for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = -dEdR*deltaR[kk]; RealOpenMM force = -dEdR*deltaR[kk];
forces[ii][kk] += force; forces[ii][kk] += force;
forces[jj][kk] -= force; forces[jj][kk] -= force;
...@@ -297,10 +297,10 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe ...@@ -297,10 +297,10 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe
// accumulate energies // accumulate energies
if( totalEnergy || energyByAtom ) { if (totalEnergy || energyByAtom) {
if( totalEnergy ) if (totalEnergy)
*totalEnergy += energy; *totalEnergy += energy;
if( energyByAtom ){ if (energyByAtom) {
energyByAtom[ii] += energy; energyByAtom[ii] += energy;
energyByAtom[jj] += energy; energyByAtom[jj] += energy;
} }
......
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
View file @ 7fb10336
...@@ -61,7 +61,7 @@ ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpre ...@@ -61,7 +61,7 @@ ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpre
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn( ){ ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -83,11 +83,11 @@ ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn( ){ ...@@ -83,11 +83,11 @@ ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices, void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceCustomTorsionIxn::calculateTorsionIxn"; static const std::string methodName = "\nReferenceCustomTorsionIxn::calculateTorsionIxn";
...@@ -135,20 +135,20 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices, ...@@ -135,20 +135,20 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
RealOpenMM internalF[4][3]; RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4]; RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3( crossProduct[0], crossProduct[0] ); RealOpenMM normCross1 = DOT3(crossProduct[0], crossProduct[0]);
RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex]; RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex];
forceFactors[0] = (-dEdAngle*normBC)/normCross1; forceFactors[0] = (-dEdAngle*normBC)/normCross1;
RealOpenMM normCross2 = DOT3( crossProduct[1], crossProduct[1] ); RealOpenMM normCross2 = DOT3(crossProduct[1], crossProduct[1]);
forceFactors[3] = (dEdAngle*normBC)/normCross2; forceFactors[3] = (dEdAngle*normBC)/normCross2;
forceFactors[1] = DOT3( deltaR[0], deltaR[1] ); forceFactors[1] = DOT3(deltaR[0], deltaR[1]);
forceFactors[1] /= deltaR[1][ReferenceForce::R2Index]; forceFactors[1] /= deltaR[1][ReferenceForce::R2Index];
forceFactors[2] = DOT3( deltaR[2], deltaR[1] ); forceFactors[2] = DOT3(deltaR[2], deltaR[1]);
forceFactors[2] /= deltaR[1][ReferenceForce::R2Index]; forceFactors[2] /= deltaR[1][ReferenceForce::R2Index];
for( int ii = 0; ii < 3; ii++ ){ for (int ii = 0; ii < 3; ii++) {
internalF[0][ii] = forceFactors[0]*crossProduct[0][ii]; internalF[0][ii] = forceFactors[0]*crossProduct[0][ii];
internalF[3][ii] = forceFactors[3]*crossProduct[1][ii]; internalF[3][ii] = forceFactors[3]*crossProduct[1][ii];
...@@ -161,7 +161,7 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices, ...@@ -161,7 +161,7 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
// accumulate forces // accumulate forces
for( int ii = 0; ii < 3; ii++ ){ for (int ii = 0; ii < 3; ii++) {
forces[atomAIndex][ii] += internalF[0][ii]; forces[atomAIndex][ii] += internalF[0][ii];
forces[atomBIndex][ii] -= internalF[1][ii]; forces[atomBIndex][ii] -= internalF[1][ii];
forces[atomCIndex][ii] -= internalF[2][ii]; forces[atomCIndex][ii] -= internalF[2][ii];
......
platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
View file @ 7fb10336
...@@ -45,7 +45,7 @@ using namespace OpenMM; ...@@ -45,7 +45,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceDynamics::ReferenceDynamics( int numberOfAtoms, RealOpenMM deltaT, RealOpenMM temperature ) : ReferenceDynamics::ReferenceDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM temperature) :
_numberOfAtoms(numberOfAtoms), _deltaT(deltaT), _temperature(temperature) { _numberOfAtoms(numberOfAtoms), _deltaT(deltaT), _temperature(temperature) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -68,7 +68,7 @@ ReferenceDynamics::ReferenceDynamics( int numberOfAtoms, RealOpenMM deltaT, Rea ...@@ -68,7 +68,7 @@ ReferenceDynamics::ReferenceDynamics( int numberOfAtoms, RealOpenMM deltaT, Rea
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceDynamics::~ReferenceDynamics( ){ ReferenceDynamics::~ReferenceDynamics() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -76,7 +76,7 @@ ReferenceDynamics::~ReferenceDynamics( ){ ...@@ -76,7 +76,7 @@ ReferenceDynamics::~ReferenceDynamics( ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
if( _ownReferenceConstraint ){ if (_ownReferenceConstraint) {
delete _referenceConstraint; delete _referenceConstraint;
} }
} }
...@@ -89,7 +89,7 @@ ReferenceDynamics::~ReferenceDynamics( ){ ...@@ -89,7 +89,7 @@ ReferenceDynamics::~ReferenceDynamics( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceDynamics::getNumberOfAtoms( void ) const { int ReferenceDynamics::getNumberOfAtoms() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -108,7 +108,7 @@ int ReferenceDynamics::getNumberOfAtoms( void ) const { ...@@ -108,7 +108,7 @@ int ReferenceDynamics::getNumberOfAtoms( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceDynamics::getTimeStep( void ) const { int ReferenceDynamics::getTimeStep() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -127,7 +127,7 @@ int ReferenceDynamics::getTimeStep( void ) const { ...@@ -127,7 +127,7 @@ int ReferenceDynamics::getTimeStep( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceDynamics::incrementTimeStep( void ){ int ReferenceDynamics::incrementTimeStep() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -146,7 +146,7 @@ int ReferenceDynamics::incrementTimeStep( void ){ ...@@ -146,7 +146,7 @@ int ReferenceDynamics::incrementTimeStep( void ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM ReferenceDynamics::getDeltaT( void ) const { RealOpenMM ReferenceDynamics::getDeltaT() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -163,7 +163,7 @@ RealOpenMM ReferenceDynamics::getDeltaT( void ) const { ...@@ -163,7 +163,7 @@ RealOpenMM ReferenceDynamics::getDeltaT( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceDynamics::setDeltaT( RealOpenMM deltaT ) { void ReferenceDynamics::setDeltaT(RealOpenMM deltaT) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -182,7 +182,7 @@ void ReferenceDynamics::setDeltaT( RealOpenMM deltaT ) { ...@@ -182,7 +182,7 @@ void ReferenceDynamics::setDeltaT( RealOpenMM deltaT ) {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM ReferenceDynamics::getTemperature( void ) const { RealOpenMM ReferenceDynamics::getTemperature() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -201,7 +201,7 @@ RealOpenMM ReferenceDynamics::getTemperature( void ) const { ...@@ -201,7 +201,7 @@ RealOpenMM ReferenceDynamics::getTemperature( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceConstraintAlgorithm* ReferenceDynamics::getReferenceConstraintAlgorithm( void ) const { ReferenceConstraintAlgorithm* ReferenceDynamics::getReferenceConstraintAlgorithm() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -220,7 +220,7 @@ ReferenceConstraintAlgorithm* ReferenceDynamics::getReferenceConstraintAlgorithm ...@@ -220,7 +220,7 @@ ReferenceConstraintAlgorithm* ReferenceDynamics::getReferenceConstraintAlgorithm
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceDynamics::setReferenceConstraintAlgorithm( ReferenceConstraintAlgorithm* referenceConstraint ){ void ReferenceDynamics::setReferenceConstraintAlgorithm(ReferenceConstraintAlgorithm* referenceConstraint) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -230,7 +230,7 @@ void ReferenceDynamics::setReferenceConstraintAlgorithm( ReferenceConstraintAlgo ...@@ -230,7 +230,7 @@ void ReferenceDynamics::setReferenceConstraintAlgorithm( ReferenceConstraintAlgo
// delete if own // delete if own
if( _referenceConstraint && _ownReferenceConstraint ){ if (_referenceConstraint && _ownReferenceConstraint) {
delete _referenceConstraint; delete _referenceConstraint;
} }
......
platforms/reference/src/SimTKReference/ReferenceForce.cpp
View file @ 7fb10336
...@@ -39,7 +39,7 @@ using namespace OpenMM; ...@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceForce::ReferenceForce( ){ ReferenceForce::ReferenceForce() {
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -48,7 +48,7 @@ ReferenceForce::ReferenceForce( ){ ...@@ -48,7 +48,7 @@ ReferenceForce::ReferenceForce( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceForce::~ReferenceForce( ){ ReferenceForce::~ReferenceForce() {
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -64,28 +64,28 @@ RealOpenMM ReferenceForce::periodicDifference(RealOpenMM val1, RealOpenMM val2, ...@@ -64,28 +64,28 @@ RealOpenMM ReferenceForce::periodicDifference(RealOpenMM val1, RealOpenMM val2,
} }
void ReferenceForce::getDeltaR( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ, void ReferenceForce::getDeltaR(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
RealOpenMM* deltaR ){ RealOpenMM* deltaR) {
deltaR[XIndex] = atomCoordinatesJ[0] - atomCoordinatesI[0]; deltaR[XIndex] = atomCoordinatesJ[0] - atomCoordinatesI[0];
deltaR[YIndex] = atomCoordinatesJ[1] - atomCoordinatesI[1]; deltaR[YIndex] = atomCoordinatesJ[1] - atomCoordinatesI[1];
deltaR[ZIndex] = atomCoordinatesJ[2] - atomCoordinatesI[2]; deltaR[ZIndex] = atomCoordinatesJ[2] - atomCoordinatesI[2];
deltaR[R2Index] = DOT3( deltaR, deltaR ); deltaR[R2Index] = DOT3(deltaR, deltaR);
deltaR[RIndex] = (RealOpenMM) SQRT( deltaR[R2Index] ); deltaR[RIndex] = (RealOpenMM) SQRT(deltaR[R2Index]);
} }
void ReferenceForce::getDeltaRPeriodic( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ, void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR ){ const RealOpenMM* boxSize, RealOpenMM* deltaR) {
deltaR[XIndex] = periodicDifference(atomCoordinatesJ[0], atomCoordinatesI[0], boxSize[0]); deltaR[XIndex] = periodicDifference(atomCoordinatesJ[0], atomCoordinatesI[0], boxSize[0]);
deltaR[YIndex] = periodicDifference(atomCoordinatesJ[1], atomCoordinatesI[1], boxSize[1]); deltaR[YIndex] = periodicDifference(atomCoordinatesJ[1], atomCoordinatesI[1], boxSize[1]);
deltaR[ZIndex] = periodicDifference(atomCoordinatesJ[2], atomCoordinatesI[2], boxSize[2]); deltaR[ZIndex] = periodicDifference(atomCoordinatesJ[2], atomCoordinatesI[2], boxSize[2]);
deltaR[R2Index] = DOT3( deltaR, deltaR ); deltaR[R2Index] = DOT3(deltaR, deltaR);
deltaR[RIndex] = (RealOpenMM) SQRT( deltaR[R2Index] ); deltaR[RIndex] = (RealOpenMM) SQRT(deltaR[R2Index]);
} }
void ReferenceForce::getDeltaRPeriodic( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ, void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealVec* boxVectors, RealOpenMM* deltaR ){ const RealVec* boxVectors, RealOpenMM* deltaR) {
RealVec diff = atomCoordinatesJ-atomCoordinatesI; RealVec diff = atomCoordinatesJ-atomCoordinatesI;
diff -= boxVectors[2]*floor(diff[2]/boxVectors[2][2]+0.5); diff -= boxVectors[2]*floor(diff[2]/boxVectors[2][2]+0.5);
diff -= boxVectors[1]*floor(diff[1]/boxVectors[1][1]+0.5); diff -= boxVectors[1]*floor(diff[1]/boxVectors[1][1]+0.5);
......
platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp
View file @ 7fb10336
...@@ -39,7 +39,7 @@ using namespace OpenMM; ...@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn( ){ ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -55,7 +55,7 @@ ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn( ){ ...@@ -55,7 +55,7 @@ ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn( ){ ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -78,11 +78,11 @@ ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn( ){ ...@@ -78,11 +78,11 @@ ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices, void ReferenceHarmonicBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn"; static const std::string methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
...@@ -100,7 +100,7 @@ void ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices, ...@@ -100,7 +100,7 @@ void ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices,
int atomAIndex = atomIndices[0]; int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1]; int atomBIndex = atomIndices[1];
ReferenceForce::getDeltaR( atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR ); ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
// deltaIdeal = r - r_0 // deltaIdeal = r - r_0
......
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
View file @ 7fb10336
...@@ -39,7 +39,7 @@ using namespace OpenMM; ...@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceLJCoulomb14::ReferenceLJCoulomb14( ) { ReferenceLJCoulomb14::ReferenceLJCoulomb14() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -55,7 +55,7 @@ ReferenceLJCoulomb14::ReferenceLJCoulomb14( ) { ...@@ -55,7 +55,7 @@ ReferenceLJCoulomb14::ReferenceLJCoulomb14( ) {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceLJCoulomb14::~ReferenceLJCoulomb14( ){ ReferenceLJCoulomb14::~ReferenceLJCoulomb14() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -80,9 +80,9 @@ ReferenceLJCoulomb14::~ReferenceLJCoulomb14( ){ ...@@ -80,9 +80,9 @@ ReferenceLJCoulomb14::~ReferenceLJCoulomb14( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>& atomCoordinates, void ReferenceLJCoulomb14::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, vector<RealVec>& forces, RealOpenMM* parameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceLJCoulomb14::calculateBondIxn"; static const std::string methodName = "\nReferenceLJCoulomb14::calculateBondIxn";
...@@ -112,7 +112,7 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>& ...@@ -112,7 +112,7 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>&
int atomAIndex = atomIndices[0]; int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1]; int atomBIndex = atomIndices[1];
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] ); ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index]; RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]); RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
...@@ -120,13 +120,13 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>& ...@@ -120,13 +120,13 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>&
sig2 *= sig2; sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2; RealOpenMM sig6 = sig2*sig2*sig2;
RealOpenMM dEdR = parameters[1]*( twelve*sig6 - six )*sig6; RealOpenMM dEdR = parameters[1]*(twelve*sig6 - six)*sig6;
dEdR += (RealOpenMM) (ONE_4PI_EPS0*parameters[2]*inverseR); dEdR += (RealOpenMM) (ONE_4PI_EPS0*parameters[2]*inverseR);
dEdR *= inverseR*inverseR; dEdR *= inverseR*inverseR;
// accumulate forces // accumulate forces
for( int ii = 0; ii < 3; ii++ ){ for (int ii = 0; ii < 3; ii++) {
RealOpenMM force = dEdR*deltaR[0][ii]; RealOpenMM force = dEdR*deltaR[0][ii];
forces[atomAIndex][ii] += force; forces[atomAIndex][ii] += force;
forces[atomBIndex][ii] -= force; forces[atomBIndex][ii] -= force;
...@@ -135,5 +135,5 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>& ...@@ -135,5 +135,5 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>&
// accumulate energies // accumulate energies
if (totalEnergy != NULL) if (totalEnergy != NULL)
*totalEnergy += parameters[1]*( sig6 - one )*sig6 + (ONE_4PI_EPS0*parameters[2]*inverseR); *totalEnergy += parameters[1]*(sig6 - one)*sig6 + (ONE_4PI_EPS0*parameters[2]*inverseR);
} }
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @ 7fb10336
...@@ -48,7 +48,7 @@ using namespace OpenMM; ...@@ -48,7 +48,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceLJCoulombIxn::ReferenceLJCoulombIxn( ) : cutoff(false), useSwitch(false), periodic(false), ewald(false), pme(false) { ReferenceLJCoulombIxn::ReferenceLJCoulombIxn() : cutoff(false), useSwitch(false), periodic(false), ewald(false), pme(false) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -64,7 +64,7 @@ ReferenceLJCoulombIxn::ReferenceLJCoulombIxn( ) : cutoff(false), useSwitch(false ...@@ -64,7 +64,7 @@ ReferenceLJCoulombIxn::ReferenceLJCoulombIxn( ) : cutoff(false), useSwitch(false
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){ ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -84,7 +84,7 @@ ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){ ...@@ -84,7 +84,7 @@ ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceLJCoulombIxn::setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric ) { void ReferenceLJCoulombIxn::setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric) {
cutoff = true; cutoff = true;
cutoffDistance = distance; cutoffDistance = distance;
...@@ -101,7 +101,7 @@ ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){ ...@@ -101,7 +101,7 @@ ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceLJCoulombIxn::setUseSwitchingFunction( RealOpenMM distance ) { void ReferenceLJCoulombIxn::setUseSwitchingFunction(RealOpenMM distance) {
useSwitch = true; useSwitch = true;
switchingDistance = distance; switchingDistance = distance;
} }
...@@ -210,16 +210,16 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -210,16 +210,16 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
// ************************************************************************************** // **************************************************************************************
if (includeReciprocal) { if (includeReciprocal) {
for( int atomID = 0; atomID < numberOfAtoms; atomID++ ){ for (int atomID = 0; atomID < numberOfAtoms; atomID++) {
RealOpenMM selfEwaldEnergy = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[atomID][QIndex]*atomParameters[atomID][QIndex] * alphaEwald/SQRT_PI); RealOpenMM selfEwaldEnergy = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[atomID][QIndex]*atomParameters[atomID][QIndex] * alphaEwald/SQRT_PI);
totalSelfEwaldEnergy -= selfEwaldEnergy; totalSelfEwaldEnergy -= selfEwaldEnergy;
if( energyByAtom ){ if (energyByAtom) {
energyByAtom[atomID] -= selfEwaldEnergy; energyByAtom[atomID] -= selfEwaldEnergy;
} }
} }
} }
if( totalEnergy ){ if (totalEnergy) {
*totalEnergy += totalSelfEwaldEnergy; *totalEnergy += totalSelfEwaldEnergy;
} }
...@@ -238,11 +238,11 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -238,11 +238,11 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
charges[i] = atomParameters[i][QIndex]; charges[i] = atomParameters[i][QIndex];
pme_exec(pmedata,atomCoordinates,forces,charges,periodicBoxVectors,&recipEnergy); pme_exec(pmedata,atomCoordinates,forces,charges,periodicBoxVectors,&recipEnergy);
if( totalEnergy ) if (totalEnergy)
*totalEnergy += recipEnergy; *totalEnergy += recipEnergy;
if( energyByAtom ) if (energyByAtom)
for(int n = 0; n < numberOfAtoms; n++) for (int n = 0; n < numberOfAtoms; n++)
energyByAtom[n] += recipEnergy; energyByAtom[n] += recipEnergy;
pme_destroy(pmedata); pme_destroy(pmedata);
...@@ -267,16 +267,16 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -267,16 +267,16 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
if (kmax < 1) if (kmax < 1)
throw OpenMMException("kmax for Ewald summation < 1"); throw OpenMMException("kmax for Ewald summation < 1");
for(int i = 0; (i < numberOfAtoms); i++) { for (int i = 0; (i < numberOfAtoms); i++) {
for(int m = 0; (m < 3); m++) for (int m = 0; (m < 3); m++)
EIR(0, i, m) = d_complex(1,0); EIR(0, i, m) = d_complex(1,0);
for(int m=0; (m<3); m++) for (int m=0; (m<3); m++)
EIR(1, i, m) = d_complex(cos(atomCoordinates[i][m]*recipBoxSize[m]), EIR(1, i, m) = d_complex(cos(atomCoordinates[i][m]*recipBoxSize[m]),
sin(atomCoordinates[i][m]*recipBoxSize[m])); sin(atomCoordinates[i][m]*recipBoxSize[m]));
for(int j=2; (j<kmax); j++) for (int j=2; (j<kmax); j++)
for(int m=0; (m<3); m++) for (int m=0; (m<3); m++)
EIR(j, i, m) = EIR(j-1, i, m) * EIR(1, i, m); EIR(j, i, m) = EIR(j-1, i, m) * EIR(1, i, m);
} }
...@@ -285,40 +285,40 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -285,40 +285,40 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
int lowry = 0; int lowry = 0;
int lowrz = 1; int lowrz = 1;
for(int rx = 0; rx < numRx; rx++) { for (int rx = 0; rx < numRx; rx++) {
RealOpenMM kx = rx * recipBoxSize[0]; RealOpenMM kx = rx * recipBoxSize[0];
for(int ry = lowry; ry < numRy; ry++) { for (int ry = lowry; ry < numRy; ry++) {
RealOpenMM ky = ry * recipBoxSize[1]; RealOpenMM ky = ry * recipBoxSize[1];
if(ry >= 0) { if (ry >= 0) {
for(int n = 0; n < numberOfAtoms; n++) for (int n = 0; n < numberOfAtoms; n++)
tab_xy[n] = EIR(rx, n, 0) * EIR(ry, n, 1); tab_xy[n] = EIR(rx, n, 0) * EIR(ry, n, 1);
} }
else { else {
for(int n = 0; n < numberOfAtoms; n++) for (int n = 0; n < numberOfAtoms; n++)
tab_xy[n]= EIR(rx, n, 0) * conj (EIR(-ry, n, 1)); tab_xy[n]= EIR(rx, n, 0) * conj (EIR(-ry, n, 1));
} }
for (int rz = lowrz; rz < numRz; rz++) { for (int rz = lowrz; rz < numRz; rz++) {
if( rz >= 0) { if (rz >= 0) {
for( int n = 0; n < numberOfAtoms; n++) for (int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = atomParameters[n][QIndex] * (tab_xy[n] * EIR(rz, n, 2)); tab_qxyz[n] = atomParameters[n][QIndex] * (tab_xy[n] * EIR(rz, n, 2));
} }
else { else {
for( int n = 0; n < numberOfAtoms; n++) for (int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = atomParameters[n][QIndex] * (tab_xy[n] * conj(EIR(-rz, n, 2))); tab_qxyz[n] = atomParameters[n][QIndex] * (tab_xy[n] * conj(EIR(-rz, n, 2)));
} }
RealOpenMM cs = 0.0f; RealOpenMM cs = 0.0f;
RealOpenMM ss = 0.0f; RealOpenMM ss = 0.0f;
for( int n = 0; n < numberOfAtoms; n++) { for (int n = 0; n < numberOfAtoms; n++) {
cs += tab_qxyz[n].real(); cs += tab_qxyz[n].real();
ss += tab_qxyz[n].imag(); ss += tab_qxyz[n].imag();
} }
...@@ -327,21 +327,21 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -327,21 +327,21 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
RealOpenMM k2 = kx * kx + ky * ky + kz * kz; RealOpenMM k2 = kx * kx + ky * ky + kz * kz;
RealOpenMM ak = exp(k2*factorEwald) / k2; RealOpenMM ak = exp(k2*factorEwald) / k2;
for(int n = 0; n < numberOfAtoms; n++) { for (int n = 0; n < numberOfAtoms; n++) {
RealOpenMM force = ak * (cs * tab_qxyz[n].imag() - ss * tab_qxyz[n].real()); RealOpenMM force = ak * (cs * tab_qxyz[n].imag() - ss * tab_qxyz[n].real());
forces[n][0] += 2 * recipCoeff * force * kx ; forces[n][0] += 2 * recipCoeff * force * kx ;
forces[n][1] += 2 * recipCoeff * force * ky ; forces[n][1] += 2 * recipCoeff * force * ky ;
forces[n][2] += 2 * recipCoeff * force * kz ; forces[n][2] += 2 * recipCoeff * force * kz ;
} }
recipEnergy = recipCoeff * ak * ( cs * cs + ss * ss); recipEnergy = recipCoeff * ak * (cs * cs + ss * ss);
totalRecipEnergy += recipEnergy; totalRecipEnergy += recipEnergy;
if( totalEnergy ) if (totalEnergy)
*totalEnergy += recipEnergy; *totalEnergy += recipEnergy;
if( energyByAtom ) if (energyByAtom)
for(int n = 0; n < numberOfAtoms; n++) for (int n = 0; n < numberOfAtoms; n++)
energyByAtom[n] += recipEnergy; energyByAtom[n] += recipEnergy;
lowrz = 1 - numRz; lowrz = 1 - numRz;
...@@ -366,7 +366,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -366,7 +366,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
int jj = pair.second; int jj = pair.second;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex]; RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR[0] ); ReferenceForce::getDeltaRPeriodic(atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR[0]);
RealOpenMM r = deltaR[0][ReferenceForce::RIndex]; RealOpenMM r = deltaR[0][ReferenceForce::RIndex];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]); RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM switchValue = 1, switchDeriv = 0; RealOpenMM switchValue = 1, switchDeriv = 0;
...@@ -379,14 +379,14 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -379,14 +379,14 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
RealOpenMM dEdR = (RealOpenMM) (ONE_4PI_EPS0 * atomParameters[ii][QIndex] * atomParameters[jj][QIndex] * inverseR * inverseR * inverseR); RealOpenMM dEdR = (RealOpenMM) (ONE_4PI_EPS0 * atomParameters[ii][QIndex] * atomParameters[jj][QIndex] * inverseR * inverseR * inverseR);
dEdR = (RealOpenMM) (dEdR * (erfc(alphaR) + 2 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI )); dEdR = (RealOpenMM) (dEdR * (erfc(alphaR) + 2 * alphaR * exp (- alphaR * alphaR) / SQRT_PI));
RealOpenMM sig = atomParameters[ii][SigIndex] + atomParameters[jj][SigIndex]; RealOpenMM sig = atomParameters[ii][SigIndex] + atomParameters[jj][SigIndex];
RealOpenMM sig2 = inverseR*sig; RealOpenMM sig2 = inverseR*sig;
sig2 *= sig2; sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2; RealOpenMM sig6 = sig2*sig2*sig2;
RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex]; RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex];
dEdR += switchValue*eps*( twelve*sig6 - six )*sig6*inverseR*inverseR; dEdR += switchValue*eps*(twelve*sig6 - six)*sig6*inverseR*inverseR;
vdwEnergy = eps*(sig6-one)*sig6; vdwEnergy = eps*(sig6-one)*sig6;
if (useSwitch) { if (useSwitch) {
dEdR -= vdwEnergy*switchDeriv*inverseR; dEdR -= vdwEnergy*switchDeriv*inverseR;
...@@ -395,7 +395,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -395,7 +395,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
// accumulate forces // accumulate forces
for( int kk = 0; kk < 3; kk++ ){ for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = dEdR*deltaR[0][kk]; RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] += force; forces[ii][kk] += force;
forces[jj][kk] -= force; forces[jj][kk] -= force;
...@@ -408,14 +408,14 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -408,14 +408,14 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
totalVdwEnergy += vdwEnergy; totalVdwEnergy += vdwEnergy;
totalRealSpaceEwaldEnergy += realSpaceEwaldEnergy; totalRealSpaceEwaldEnergy += realSpaceEwaldEnergy;
if( energyByAtom ){ if (energyByAtom) {
energyByAtom[ii] += realSpaceEwaldEnergy + vdwEnergy; energyByAtom[ii] += realSpaceEwaldEnergy + vdwEnergy;
energyByAtom[jj] += realSpaceEwaldEnergy + vdwEnergy; energyByAtom[jj] += realSpaceEwaldEnergy + vdwEnergy;
} }
} }
if( totalEnergy ) if (totalEnergy)
*totalEnergy += totalRealSpaceEwaldEnergy + totalVdwEnergy; *totalEnergy += totalRealSpaceEwaldEnergy + totalVdwEnergy;
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum. // Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
...@@ -428,17 +428,17 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -428,17 +428,17 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
int jj = *iter; int jj = *iter;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex]; RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR[0] ); ReferenceForce::getDeltaR(atomCoordinates[jj], atomCoordinates[ii], deltaR[0]);
RealOpenMM r = deltaR[0][ReferenceForce::RIndex]; RealOpenMM r = deltaR[0][ReferenceForce::RIndex];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]); RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM alphaR = alphaEwald * r; RealOpenMM alphaR = alphaEwald * r;
if (erf(alphaR) > 1e-6) { if (erf(alphaR) > 1e-6) {
RealOpenMM dEdR = (RealOpenMM) (ONE_4PI_EPS0 * atomParameters[ii][QIndex] * atomParameters[jj][QIndex] * inverseR * inverseR * inverseR); RealOpenMM dEdR = (RealOpenMM) (ONE_4PI_EPS0 * atomParameters[ii][QIndex] * atomParameters[jj][QIndex] * inverseR * inverseR * inverseR);
dEdR = (RealOpenMM) (dEdR * (erf(alphaR) - 2 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI )); dEdR = (RealOpenMM) (dEdR * (erf(alphaR) - 2 * alphaR * exp (- alphaR * alphaR) / SQRT_PI));
// accumulate forces // accumulate forces
for( int kk = 0; kk < 3; kk++ ){ for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = dEdR*deltaR[0][kk]; RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] -= force; forces[ii][kk] -= force;
forces[jj][kk] += force; forces[jj][kk] += force;
...@@ -449,7 +449,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -449,7 +449,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
realSpaceEwaldEnergy = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erf(alphaR)); realSpaceEwaldEnergy = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erf(alphaR));
totalExclusionEnergy += realSpaceEwaldEnergy; totalExclusionEnergy += realSpaceEwaldEnergy;
if( energyByAtom ){ if (energyByAtom) {
energyByAtom[ii] -= realSpaceEwaldEnergy; energyByAtom[ii] -= realSpaceEwaldEnergy;
energyByAtom[jj] -= realSpaceEwaldEnergy; energyByAtom[jj] -= realSpaceEwaldEnergy;
} }
...@@ -457,7 +457,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec> ...@@ -457,7 +457,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
} }
} }
if( totalEnergy ) if (totalEnergy)
*totalEnergy -= totalExclusionEnergy; *totalEnergy -= totalExclusionEnergy;
} }
...@@ -499,10 +499,10 @@ void ReferenceLJCoulombIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>& ...@@ -499,10 +499,10 @@ void ReferenceLJCoulombIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>&
} }
} }
else { else {
for( int ii = 0; ii < numberOfAtoms; ii++ ){ for (int ii = 0; ii < numberOfAtoms; ii++) {
// loop over atom pairs // loop over atom pairs
for( int jj = ii+1; jj < numberOfAtoms; jj++ ) for (int jj = ii+1; jj < numberOfAtoms; jj++)
if (exclusions[jj].find(ii) == exclusions[jj].end()) if (exclusions[jj].find(ii) == exclusions[jj].end())
calculateOneIxn(ii, jj, atomCoordinates, atomParameters, forces, energyByAtom, totalEnergy); calculateOneIxn(ii, jj, atomCoordinates, atomParameters, forces, energyByAtom, totalEnergy);
} }
...@@ -523,9 +523,9 @@ void ReferenceLJCoulombIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>& ...@@ -523,9 +523,9 @@ void ReferenceLJCoulombIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>&
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& atomCoordinates, void ReferenceLJCoulombIxn::calculateOneIxn(int ii, int jj, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, vector<RealVec>& forces, RealOpenMM** atomParameters, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const { RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -552,9 +552,9 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at ...@@ -552,9 +552,9 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
// get deltaR, R2, and R between 2 atoms // get deltaR, R2, and R between 2 atoms
if (periodic) if (periodic)
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR[0] ); ReferenceForce::getDeltaRPeriodic(atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR[0]);
else else
ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR[0] ); ReferenceForce::getDeltaR(atomCoordinates[jj], atomCoordinates[ii], deltaR[0]);
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index]; RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]); RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
...@@ -573,7 +573,7 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at ...@@ -573,7 +573,7 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
RealOpenMM sig6 = sig2*sig2*sig2; RealOpenMM sig6 = sig2*sig2*sig2;
RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex]; RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex];
RealOpenMM dEdR = switchValue*eps*( twelve*sig6 - six )*sig6; RealOpenMM dEdR = switchValue*eps*(twelve*sig6 - six)*sig6;
if (cutoff) if (cutoff)
dEdR += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR-2.0f*krf*r2)); dEdR += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR-2.0f*krf*r2));
else else
...@@ -591,7 +591,7 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at ...@@ -591,7 +591,7 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
// accumulate forces // accumulate forces
for( int kk = 0; kk < 3; kk++ ){ for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = dEdR*deltaR[0][kk]; RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] += force; forces[ii][kk] += force;
forces[jj][kk] -= force; forces[jj][kk] -= force;
...@@ -599,9 +599,9 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at ...@@ -599,9 +599,9 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
// accumulate energies // accumulate energies
if( totalEnergy ) if (totalEnergy)
*totalEnergy += energy; *totalEnergy += energy;
if( energyByAtom ){ if (energyByAtom) {
energyByAtom[ii] += energy; energyByAtom[ii] += energy;
energyByAtom[jj] += energy; energyByAtom[jj] += energy;
} }
......
platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp
View file @ 7fb10336
...@@ -43,9 +43,9 @@ using namespace OpenMM; ...@@ -43,9 +43,9 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceLincsAlgorithm::ReferenceLincsAlgorithm( int numberOfConstraints, ReferenceLincsAlgorithm::ReferenceLincsAlgorithm(int numberOfConstraints,
int** atomIndices, int** atomIndices,
RealOpenMM* distance ){ RealOpenMM* distance) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -69,7 +69,7 @@ ReferenceLincsAlgorithm::ReferenceLincsAlgorithm( int numberOfConstraints, ...@@ -69,7 +69,7 @@ ReferenceLincsAlgorithm::ReferenceLincsAlgorithm( int numberOfConstraints,
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceLincsAlgorithm::getNumberOfConstraints( void ) const { int ReferenceLincsAlgorithm::getNumberOfConstraints() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -88,7 +88,7 @@ int ReferenceLincsAlgorithm::getNumberOfConstraints( void ) const { ...@@ -88,7 +88,7 @@ int ReferenceLincsAlgorithm::getNumberOfConstraints( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceLincsAlgorithm::getNumTerms( void ) const { int ReferenceLincsAlgorithm::getNumTerms() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -105,7 +105,7 @@ int ReferenceLincsAlgorithm::getNumTerms( void ) const { ...@@ -105,7 +105,7 @@ int ReferenceLincsAlgorithm::getNumTerms( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceLincsAlgorithm::setNumTerms( int terms ){ void ReferenceLincsAlgorithm::setNumTerms(int terms) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -218,9 +218,9 @@ void ReferenceLincsAlgorithm::updateAtomPositions(int numberOfAtoms, vector<Real ...@@ -218,9 +218,9 @@ void ReferenceLincsAlgorithm::updateAtomPositions(int numberOfAtoms, vector<Real
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceLincsAlgorithm::apply( int numberOfAtoms, vector<RealVec>& atomCoordinates, int ReferenceLincsAlgorithm::apply(int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP, vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses ){ vector<RealOpenMM>& inverseMasses) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -235,7 +235,7 @@ int ReferenceLincsAlgorithm::apply( int numberOfAtoms, vector<RealVec>& atomCoor ...@@ -235,7 +235,7 @@ int ReferenceLincsAlgorithm::apply( int numberOfAtoms, vector<RealVec>& atomCoor
if (_numberOfConstraints == 0) if (_numberOfConstraints == 0)
return SimTKOpenMMCommon::DefaultReturn; return SimTKOpenMMCommon::DefaultReturn;
if( !_hasInitialized ) if (!_hasInitialized)
initialize(numberOfAtoms, inverseMasses); initialize(numberOfAtoms, inverseMasses);
// Calculate the direction of each constraint, along with the initial RHS and solution vectors. // Calculate the direction of each constraint, along with the initial RHS and solution vectors.
......
platforms/reference/src/SimTKReference/ReferenceMonteCarloBarostat.cpp
View file @ 7fb10336
...@@ -49,7 +49,7 @@ ReferenceMonteCarloBarostat::ReferenceMonteCarloBarostat(int numAtoms, const vec ...@@ -49,7 +49,7 @@ ReferenceMonteCarloBarostat::ReferenceMonteCarloBarostat(int numAtoms, const vec
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceMonteCarloBarostat::~ReferenceMonteCarloBarostat( ) { ReferenceMonteCarloBarostat::~ReferenceMonteCarloBarostat() {
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceNeighborList.cpp
View file @ 7fb10336
...@@ -45,12 +45,12 @@ void OPENMM_EXPORT computeNeighborListNaive( ...@@ -45,12 +45,12 @@ void OPENMM_EXPORT computeNeighborListNaive(
for (AtomIndex atomJ = atomI + 1; atomJ < (AtomIndex) nAtoms; ++atomJ) for (AtomIndex atomJ = atomI + 1; atomJ < (AtomIndex) nAtoms; ++atomJ)
{ {
double pairDistanceSquared = compPairDistanceSquared(atomLocations[atomI], atomLocations[atomJ], periodicBoxVectors, usePeriodic); double pairDistanceSquared = compPairDistanceSquared(atomLocations[atomI], atomLocations[atomJ], periodicBoxVectors, usePeriodic);
if ( (pairDistanceSquared <= maxDistanceSquared) && (pairDistanceSquared >= minDistanceSquared)) if ((pairDistanceSquared <= maxDistanceSquared) && (pairDistanceSquared >= minDistanceSquared))
if (exclusions[atomI].find(atomJ) == exclusions[atomI].end()) if (exclusions[atomI].find(atomJ) == exclusions[atomI].end())
{ {
neighborList.push_back( AtomPair(atomI, atomJ) ); neighborList.push_back(AtomPair(atomI, atomJ));
if (reportSymmetricPairs) if (reportSymmetricPairs)
neighborList.push_back( AtomPair(atomI, atomJ) ); neighborList.push_back(AtomPair(atomI, atomJ));
} }
} }
} }
...@@ -199,9 +199,9 @@ public: ...@@ -199,9 +199,9 @@ public:
// Ignore exclusions. // Ignore exclusions.
if (exclusions[atomI].find(atomJ) != exclusions[atomI].end()) continue; if (exclusions[atomI].find(atomJ) != exclusions[atomI].end()) continue;
neighbors.push_back( AtomPair(atomI, atomJ) ); neighbors.push_back(AtomPair(atomI, atomJ));
if (reportSymmetricPairs) if (reportSymmetricPairs)
neighbors.push_back( AtomPair(atomJ, atomI) ); neighbors.push_back(AtomPair(atomJ, atomI));
} }
} }
} }
...@@ -228,7 +228,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash( ...@@ -228,7 +228,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash(
double maxDistance, double maxDistance,
double minDistance, double minDistance,
bool reportSymmetricPairs bool reportSymmetricPairs
) )
{ {
neighborList.clear(); neighborList.clear();
...@@ -245,7 +245,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash( ...@@ -245,7 +245,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash(
{ {
// 1) Find other atoms that are close to this one // 1) Find other atoms that are close to this one
const RealVec& location = atomLocations[atomJ]; const RealVec& location = atomLocations[atomJ];
voxelHash.getNeighbors( voxelHash.getNeighbors(
neighborList, neighborList,
VoxelItem(&location, atomJ), VoxelItem(&location, atomJ),
exclusions, exclusions,
......
platforms/reference/src/SimTKReference/ReferencePME.cpp
View file @ 7fb10336
...@@ -77,7 +77,7 @@ struct pme ...@@ -77,7 +77,7 @@ struct pme
* If particle i has coordinates { 0.543 , 6.235 , -0.73 }, we will get: * If particle i has coordinates { 0.543 , 6.235 , -0.73 }, we will get:
* *
* particleindex[i] = { 5 , 62 , 92 } (-0.73 + 10 = 9.27, we always apply PBC for grid calculations!) * particleindex[i] = { 5 , 62 , 92 } (-0.73 + 10 = 9.27, we always apply PBC for grid calculations!)
* particlefraction[i] = { 0.43 , 0.35 , 0.7 } ( this is the fraction of the cell length where the atom is) * particlefraction[i] = { 0.43 , 0.35 , 0.7 } (this is the fraction of the cell length where the atom is)
* *
* (The reason for precaculating / storing these is that it gets a bit more complex for triclinic cells :-) * (The reason for precaculating / storing these is that it gets a bit more complex for triclinic cells :-)
* *
...@@ -108,7 +108,7 @@ pme_calculate_bsplines_moduli(pme_t pme) ...@@ -108,7 +108,7 @@ pme_calculate_bsplines_moduli(pme_t pme)
RealOpenMM sc,ss,arg; RealOpenMM sc,ss,arg;
nmax = 0; nmax = 0;
for(d=0;d<3;d++) for (d=0;d<3;d++)
{ {
nmax = (pme->ngrid[d] > nmax) ? pme->ngrid[d] : nmax; nmax = (pme->ngrid[d] > nmax) ? pme->ngrid[d] : nmax;
pme->bsplines_moduli[d] = (RealOpenMM *) malloc(sizeof(RealOpenMM)*pme->ngrid[d]); pme->bsplines_moduli[d] = (RealOpenMM *) malloc(sizeof(RealOpenMM)*pme->ngrid[d]);
...@@ -125,11 +125,11 @@ pme_calculate_bsplines_moduli(pme_t pme) ...@@ -125,11 +125,11 @@ pme_calculate_bsplines_moduli(pme_t pme)
data[1]=0; data[1]=0;
data[0]=1; data[0]=1;
for(k=3;k<order;k++) for (k=3;k<order;k++)
{ {
div=(RealOpenMM) (1.0/(k-1.0)); div=(RealOpenMM) (1.0/(k-1.0));
data[k-1]=0; data[k-1]=0;
for(l=1;l<(k-1);l++) for (l=1;l<(k-1);l++)
{ {
data[k-l-1]=div*(l*data[k-l-2]+(k-l)*data[k-l-1]); data[k-l-1]=div*(l*data[k-l-2]+(k-l)*data[k-l-1]);
} }
...@@ -138,7 +138,7 @@ pme_calculate_bsplines_moduli(pme_t pme) ...@@ -138,7 +138,7 @@ pme_calculate_bsplines_moduli(pme_t pme)
/* differentiate */ /* differentiate */
ddata[0]=-data[0]; ddata[0]=-data[0];
for(k=1;k<order;k++) for (k=1;k<order;k++)
{ {
ddata[k]=data[k-1]-data[k]; ddata[k]=data[k-1]-data[k];
} }
...@@ -146,29 +146,29 @@ pme_calculate_bsplines_moduli(pme_t pme) ...@@ -146,29 +146,29 @@ pme_calculate_bsplines_moduli(pme_t pme)
div=(RealOpenMM) (1.0/(order-1)); div=(RealOpenMM) (1.0/(order-1));
data[order-1]=0; data[order-1]=0;
for(l=1;l<(order-1);l++) for (l=1;l<(order-1);l++)
{ {
data[order-l-1]=div*(l*data[order-l-2]+(order-l)*data[order-l-1]); data[order-l-1]=div*(l*data[order-l-2]+(order-l)*data[order-l-1]);
} }
data[0]=div*data[0]; data[0]=div*data[0];
for(i=0;i<nmax;i++) for (i=0;i<nmax;i++)
{ {
bsplines_data[i]=0; bsplines_data[i]=0;
} }
for(i=1;i<=order;i++) for (i=1;i<=order;i++)
{ {
bsplines_data[i]=data[i-1]; bsplines_data[i]=data[i-1];
} }
/* Evaluate the actual bspline moduli for X/Y/Z */ /* Evaluate the actual bspline moduli for X/Y/Z */
for(d=0;d<3;d++) for (d=0;d<3;d++)
{ {
ndata = pme->ngrid[d]; ndata = pme->ngrid[d];
for(i=0;i<ndata;i++) for (i=0;i<ndata;i++)
{ {
sc=ss=0; sc=ss=0;
for(j=0;j<ndata;j++) for (j=0;j<ndata;j++)
{ {
arg=(RealOpenMM) ((2.0*M_PI*i*j)/ndata); arg=(RealOpenMM) ((2.0*M_PI*i*j)/ndata);
sc+=bsplines_data[j]*cos(arg); sc+=bsplines_data[j]*cos(arg);
...@@ -176,9 +176,9 @@ pme_calculate_bsplines_moduli(pme_t pme) ...@@ -176,9 +176,9 @@ pme_calculate_bsplines_moduli(pme_t pme)
} }
pme->bsplines_moduli[d][i]=sc*sc+ss*ss; pme->bsplines_moduli[d][i]=sc*sc+ss*ss;
} }
for(i=0;i<ndata;i++) for (i=0;i<ndata;i++)
{ {
if(pme->bsplines_moduli[d][i]<1.0e-7) if (pme->bsplines_moduli[d][i]<1.0e-7)
{ {
pme->bsplines_moduli[d][i]=(pme->bsplines_moduli[d][i-1]+pme->bsplines_moduli[d][i+1])/2; pme->bsplines_moduli[d][i]=(pme->bsplines_moduli[d][i-1]+pme->bsplines_moduli[d][i+1])/2;
} }
...@@ -213,7 +213,7 @@ pme_update_grid_index_and_fraction(pme_t pme, ...@@ -213,7 +213,7 @@ pme_update_grid_index_and_fraction(pme_t pme,
RealOpenMM t; RealOpenMM t;
int ti; int ti;
for(i=0;i<pme->natoms;i++) for (i=0;i<pme->natoms;i++)
{ {
/* Index calculation (Look mom, no conditionals!): /* Index calculation (Look mom, no conditionals!):
* *
...@@ -252,7 +252,7 @@ pme_update_grid_index_and_fraction(pme_t pme, ...@@ -252,7 +252,7 @@ pme_update_grid_index_and_fraction(pme_t pme,
* (And, by adding 100.0 box lengths, we would lose a bit of numerical accuracy here!) * (And, by adding 100.0 box lengths, we would lose a bit of numerical accuracy here!)
*/ */
RealVec coord = atomCoordinates[i]; RealVec coord = atomCoordinates[i];
for(d=0;d<3;d++) for (d=0;d<3;d++)
{ {
t = coord[0]*recipBoxVectors[0][d]+coord[1]*recipBoxVectors[1][d]+coord[2]*recipBoxVectors[2][d]; t = coord[0]*recipBoxVectors[0][d]+coord[1]*recipBoxVectors[1][d]+coord[2]*recipBoxVectors[2][d];
t = (t-floor(t))*pme->ngrid[d]; t = (t-floor(t))*pme->ngrid[d];
...@@ -281,9 +281,9 @@ pme_update_bsplines(pme_t pme) ...@@ -281,9 +281,9 @@ pme_update_bsplines(pme_t pme)
order = pme->order; order = pme->order;
for(i=0; (i<pme->natoms); i++) for (i=0; (i<pme->natoms); i++)
{ {
for(j=0; j<3; j++) for (j=0; j<3; j++)
{ {
/* dr is relative offset from lower cell limit */ /* dr is relative offset from lower cell limit */
dr = pme->particlefraction[i][j]; dr = pme->particlefraction[i][j];
...@@ -294,11 +294,11 @@ pme_update_bsplines(pme_t pme) ...@@ -294,11 +294,11 @@ pme_update_bsplines(pme_t pme)
data[1] = dr; data[1] = dr;
data[0] = 1-dr; data[0] = 1-dr;
for(k=3; k<order; k++) for (k=3; k<order; k++)
{ {
div = (RealOpenMM) (1.0/(k-1.0)); div = (RealOpenMM) (1.0/(k-1.0));
data[k-1] = div*dr*data[k-2]; data[k-1] = div*dr*data[k-2];
for(l=1; l<(k-1); l++) for (l=1; l<(k-1); l++)
{ {
data[k-l-1] = div*((dr+l)*data[k-l-2]+(k-l-dr)*data[k-l-1]); data[k-l-1] = div*((dr+l)*data[k-l-2]+(k-l-dr)*data[k-l-1]);
} }
...@@ -308,7 +308,7 @@ pme_update_bsplines(pme_t pme) ...@@ -308,7 +308,7 @@ pme_update_bsplines(pme_t pme)
/* differentiate */ /* differentiate */
ddata[0] = -data[0]; ddata[0] = -data[0];
for(k=1; k<order; k++) for (k=1; k<order; k++)
{ {
ddata[k] = data[k-1]-data[k]; ddata[k] = data[k-1]-data[k];
} }
...@@ -316,7 +316,7 @@ pme_update_bsplines(pme_t pme) ...@@ -316,7 +316,7 @@ pme_update_bsplines(pme_t pme)
div = (RealOpenMM) (1.0/(order-1)); div = (RealOpenMM) (1.0/(order-1));
data[order-1] = div*dr*data[order-2]; data[order-1] = div*dr*data[order-2];
for(l=1; l<(order-1); l++) for (l=1; l<(order-1); l++)
{ {
data[order-l-1] = div*((dr+l)*data[order-l-2]+(order-l-dr)*data[order-l-1]); data[order-l-1] = div*((dr+l)*data[order-l-2]+(order-l-dr)*data[order-l-1]);
} }
...@@ -343,12 +343,12 @@ pme_grid_spread_charge(pme_t pme, const vector<RealOpenMM>& charges) ...@@ -343,12 +343,12 @@ pme_grid_spread_charge(pme_t pme, const vector<RealOpenMM>& charges)
order = pme->order; order = pme->order;
/* Reset the grid */ /* Reset the grid */
for(i=0;i<pme->ngrid[0]*pme->ngrid[1]*pme->ngrid[2];i++) for (i=0;i<pme->ngrid[0]*pme->ngrid[1]*pme->ngrid[2];i++)
{ {
pme->grid[i].re = pme->grid[i].im = 0; pme->grid[i].re = pme->grid[i].im = 0;
} }
for(i=0;i<pme->natoms;i++) for (i=0;i<pme->natoms;i++)
{ {
q = charges[i]; q = charges[i];
...@@ -380,16 +380,16 @@ pme_grid_spread_charge(pme_t pme, const vector<RealOpenMM>& charges) ...@@ -380,16 +380,16 @@ pme_grid_spread_charge(pme_t pme, const vector<RealOpenMM>& charges)
* 3) When we parallelize things, we only need to communicate in one direction instead of two! * 3) When we parallelize things, we only need to communicate in one direction instead of two!
*/ */
for(ix=0;ix<order;ix++) for (ix=0;ix<order;ix++)
{ {
/* Calculate index, apply PBC so we spread to index 0/1/2 when a particle is close to the upper limit of the grid */ /* Calculate index, apply PBC so we spread to index 0/1/2 when a particle is close to the upper limit of the grid */
xindex = (x0index + ix) % pme->ngrid[0]; xindex = (x0index + ix) % pme->ngrid[0];
for(iy=0;iy<order;iy++) for (iy=0;iy<order;iy++)
{ {
yindex = (y0index + iy) % pme->ngrid[1]; yindex = (y0index + iy) % pme->ngrid[1];
for(iz=0;iz<order;iz++) for (iz=0;iz<order;iz++)
{ {
/* Can be optimized, but we keep it simple here */ /* Can be optimized, but we keep it simple here */
zindex = (z0index + iz) % pme->ngrid[2]; zindex = (z0index + iz) % pme->ngrid[2];
...@@ -448,21 +448,21 @@ pme_reciprocal_convolution(pme_t pme, ...@@ -448,21 +448,21 @@ pme_reciprocal_convolution(pme_t pme,
maxky = (RealOpenMM) ((ny+1)/2); maxky = (RealOpenMM) ((ny+1)/2);
maxkz = (RealOpenMM) ((nz+1)/2); maxkz = (RealOpenMM) ((nz+1)/2);
for(kx=0;kx<nx;kx++) for (kx=0;kx<nx;kx++)
{ {
/* Calculate frequency. Grid indices in the upper half correspond to negative frequencies! */ /* Calculate frequency. Grid indices in the upper half correspond to negative frequencies! */
mx = (RealOpenMM) ((kx<maxkx) ? kx : (kx-nx)); mx = (RealOpenMM) ((kx<maxkx) ? kx : (kx-nx));
mhx = mx*recipBoxVectors[0][0]; mhx = mx*recipBoxVectors[0][0];
bx = boxfactor*pme->bsplines_moduli[0][kx]; bx = boxfactor*pme->bsplines_moduli[0][kx];
for(ky=0;ky<ny;ky++) for (ky=0;ky<ny;ky++)
{ {
/* Calculate frequency. Grid indices in the upper half correspond to negative frequencies! */ /* Calculate frequency. Grid indices in the upper half correspond to negative frequencies! */
my = (RealOpenMM) ((ky<maxky) ? ky : (ky-ny)); my = (RealOpenMM) ((ky<maxky) ? ky : (ky-ny));
mhy = mx*recipBoxVectors[1][0]+my*recipBoxVectors[1][1]; mhy = mx*recipBoxVectors[1][0]+my*recipBoxVectors[1][1];
by = pme->bsplines_moduli[1][ky]; by = pme->bsplines_moduli[1][ky];
for(kz=0;kz<nz;kz++) for (kz=0;kz<nz;kz++)
{ {
/* If the net charge of the system is 0.0, there will not be any DC (direct current, zero frequency) component. However, /* If the net charge of the system is 0.0, there will not be any DC (direct current, zero frequency) component. However,
* we can still handle charged systems through a charge correction, in which case the DC * we can still handle charged systems through a charge correction, in which case the DC
...@@ -546,7 +546,7 @@ pme_grid_interpolate_force(pme_t pme, ...@@ -546,7 +546,7 @@ pme_grid_interpolate_force(pme_t pme,
/* This is almost identical to the charge spreading routine! */ /* This is almost identical to the charge spreading routine! */
for(i=0;i<pme->natoms;i++) for (i=0;i<pme->natoms;i++)
{ {
fx = fy = fz = 0; fx = fy = fz = 0;
...@@ -570,21 +570,21 @@ pme_grid_interpolate_force(pme_t pme, ...@@ -570,21 +570,21 @@ pme_grid_interpolate_force(pme_t pme,
/* Since we will add order^3 (typically 4*4*4=64) terms to the force on each particle, we use temporary fx/fy/fz /* Since we will add order^3 (typically 4*4*4=64) terms to the force on each particle, we use temporary fx/fy/fz
* variables, and only add it to memory forces[] at the end. * variables, and only add it to memory forces[] at the end.
*/ */
for(ix=0;ix<order;ix++) for (ix=0;ix<order;ix++)
{ {
xindex = (x0index + ix) % pme->ngrid[0]; xindex = (x0index + ix) % pme->ngrid[0];
/* Get both the bspline factor and its derivative with respect to the x coordinate! */ /* Get both the bspline factor and its derivative with respect to the x coordinate! */
tx = thetax[ix]; tx = thetax[ix];
dtx = dthetax[ix]; dtx = dthetax[ix];
for(iy=0;iy<order;iy++) for (iy=0;iy<order;iy++)
{ {
yindex = (y0index + iy) % pme->ngrid[1]; yindex = (y0index + iy) % pme->ngrid[1];
/* bspline + derivative wrt y */ /* bspline + derivative wrt y */
ty = thetay[iy]; ty = thetay[iy];
dty = dthetay[iy]; dty = dthetay[iy];
for(iz=0;iz<order;iz++) for (iz=0;iz<order;iz++)
{ {
/* Can be optimized, but we keep it simple here */ /* Can be optimized, but we keep it simple here */
zindex = (z0index + iz) % pme->ngrid[2]; zindex = (z0index + iz) % pme->ngrid[2];
...@@ -633,7 +633,7 @@ pme_init(pme_t * ppme, ...@@ -633,7 +633,7 @@ pme_init(pme_t * ppme,
pme->ewaldcoeff = ewaldcoeff; pme->ewaldcoeff = ewaldcoeff;
pme->natoms = natoms; pme->natoms = natoms;
for(d=0;d<3;d++) for (d=0;d<3;d++)
{ {
pme->ngrid[d] = ngrid[d]; pme->ngrid[d] = ngrid[d];
pme->bsplines_theta[d] = (RealOpenMM *)malloc(sizeof(RealOpenMM)*pme_order*natoms); pme->bsplines_theta[d] = (RealOpenMM *)malloc(sizeof(RealOpenMM)*pme_order*natoms);
...@@ -712,7 +712,7 @@ pme_destroy(pme_t pme) ...@@ -712,7 +712,7 @@ pme_destroy(pme_t pme)
free(pme->grid); free(pme->grid);
for(d=0;d<3;d++) for (d=0;d<3;d++)
{ {
free(pme->bsplines_moduli[d]); free(pme->bsplines_moduli[d]);
free(pme->bsplines_theta[d]); free(pme->bsplines_theta[d]);
......
platforms/reference/src/SimTKReference/ReferencePairIxn.cpp
View file @ 7fb10336
...@@ -38,7 +38,7 @@ using namespace OpenMM; ...@@ -38,7 +38,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferencePairIxn::ReferencePairIxn( ){ ReferencePairIxn::ReferencePairIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -54,7 +54,7 @@ ReferencePairIxn::ReferencePairIxn( ){ ...@@ -54,7 +54,7 @@ ReferencePairIxn::ReferencePairIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferencePairIxn::~ReferencePairIxn( ){ ReferencePairIxn::~ReferencePairIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp
View file @ 7fb10336
...@@ -39,7 +39,7 @@ using namespace OpenMM; ...@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceProperDihedralBond::ReferenceProperDihedralBond( ){ ReferenceProperDihedralBond::ReferenceProperDihedralBond() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -55,7 +55,7 @@ ReferenceProperDihedralBond::ReferenceProperDihedralBond( ){ ...@@ -55,7 +55,7 @@ ReferenceProperDihedralBond::ReferenceProperDihedralBond( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceProperDihedralBond::~ReferenceProperDihedralBond( ){ ReferenceProperDihedralBond::~ReferenceProperDihedralBond() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -79,11 +79,11 @@ ReferenceProperDihedralBond::~ReferenceProperDihedralBond( ){ ...@@ -79,11 +79,11 @@ ReferenceProperDihedralBond::~ReferenceProperDihedralBond( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices, void ReferenceProperDihedralBond::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceProperDihedralBond::calculateBondIxn"; static const std::string methodName = "\nReferenceProperDihedralBond::calculateBondIxn";
...@@ -111,9 +111,9 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -111,9 +111,9 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
int atomBIndex = atomIndices[1]; int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2]; int atomCIndex = atomIndices[2];
int atomDIndex = atomIndices[3]; int atomDIndex = atomIndices[3];
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] ); ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1] ); ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR( atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2] ); ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
RealOpenMM dotDihedral; RealOpenMM dotDihedral;
RealOpenMM signOfAngle; RealOpenMM signOfAngle;
...@@ -127,35 +127,35 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -127,35 +127,35 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
// get dihedral angle // get dihedral angle
RealOpenMM dihedralAngle = getDihedralAngleBetweenThreeVectors( deltaR[0], deltaR[1], deltaR[2], RealOpenMM dihedralAngle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2],
crossProduct, &dotDihedral, deltaR[0], crossProduct, &dotDihedral, deltaR[0],
&signOfAngle, hasREntry ); &signOfAngle, hasREntry);
// evaluate delta angle, dE/d(angle) // evaluate delta angle, dE/d(angle)
RealOpenMM deltaAngle = parameters[2]*dihedralAngle - parameters[1]; RealOpenMM deltaAngle = parameters[2]*dihedralAngle - parameters[1];
RealOpenMM sinDeltaAngle = SIN( deltaAngle ); RealOpenMM sinDeltaAngle = SIN(deltaAngle);
RealOpenMM dEdAngle = -parameters[0]*parameters[2]*sinDeltaAngle; RealOpenMM dEdAngle = -parameters[0]*parameters[2]*sinDeltaAngle;
RealOpenMM energy = parameters[0]*(one + COS( deltaAngle ) ); RealOpenMM energy = parameters[0]*(one + COS(deltaAngle));
// compute force // compute force
RealOpenMM internalF[4][3]; RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4]; RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3( crossProduct[0], crossProduct[0] ); RealOpenMM normCross1 = DOT3(crossProduct[0], crossProduct[0]);
RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex]; RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex];
forceFactors[0] = (-dEdAngle*normBC)/normCross1; forceFactors[0] = (-dEdAngle*normBC)/normCross1;
RealOpenMM normCross2 = DOT3( crossProduct[1], crossProduct[1] ); RealOpenMM normCross2 = DOT3(crossProduct[1], crossProduct[1]);
forceFactors[3] = (dEdAngle*normBC)/normCross2; forceFactors[3] = (dEdAngle*normBC)/normCross2;
forceFactors[1] = DOT3( deltaR[0], deltaR[1] ); forceFactors[1] = DOT3(deltaR[0], deltaR[1]);
forceFactors[1] /= deltaR[1][ReferenceForce::R2Index]; forceFactors[1] /= deltaR[1][ReferenceForce::R2Index];
forceFactors[2] = DOT3( deltaR[2], deltaR[1] ); forceFactors[2] = DOT3(deltaR[2], deltaR[1]);
forceFactors[2] /= deltaR[1][ReferenceForce::R2Index]; forceFactors[2] /= deltaR[1][ReferenceForce::R2Index];
for( int ii = 0; ii < 3; ii++ ){ for (int ii = 0; ii < 3; ii++) {
internalF[0][ii] = forceFactors[0]*crossProduct[0][ii]; internalF[0][ii] = forceFactors[0]*crossProduct[0][ii];
internalF[3][ii] = forceFactors[3]*crossProduct[1][ii]; internalF[3][ii] = forceFactors[3]*crossProduct[1][ii];
...@@ -168,7 +168,7 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -168,7 +168,7 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
// accumulate forces // accumulate forces
for( int ii = 0; ii < 3; ii++ ){ for (int ii = 0; ii < 3; ii++) {
forces[atomAIndex][ii] += internalF[0][ii]; forces[atomAIndex][ii] += internalF[0][ii];
forces[atomBIndex][ii] -= internalF[1][ii]; forces[atomBIndex][ii] -= internalF[1][ii];
forces[atomCIndex][ii] -= internalF[2][ii]; forces[atomCIndex][ii] -= internalF[2][ii];
......
platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp
View file @ 7fb10336
...@@ -39,7 +39,7 @@ using namespace OpenMM; ...@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceRbDihedralBond::ReferenceRbDihedralBond( ){ ReferenceRbDihedralBond::ReferenceRbDihedralBond() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -55,7 +55,7 @@ ReferenceRbDihedralBond::ReferenceRbDihedralBond( ){ ...@@ -55,7 +55,7 @@ ReferenceRbDihedralBond::ReferenceRbDihedralBond( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceRbDihedralBond::~ReferenceRbDihedralBond( ){ ReferenceRbDihedralBond::~ReferenceRbDihedralBond() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -77,11 +77,11 @@ ReferenceRbDihedralBond::~ReferenceRbDihedralBond( ){ ...@@ -77,11 +77,11 @@ ReferenceRbDihedralBond::~ReferenceRbDihedralBond( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices, void ReferenceRbDihedralBond::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceRbDihedralBond::calculateBondIxn"; static const std::string methodName = "\nReferenceRbDihedralBond::calculateBondIxn";
...@@ -113,9 +113,9 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -113,9 +113,9 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
int atomBIndex = atomIndices[1]; int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2]; int atomCIndex = atomIndices[2];
int atomDIndex = atomIndices[3]; int atomDIndex = atomIndices[3];
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] ); ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1] ); ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR( atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2] ); ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
RealOpenMM cosPhi; RealOpenMM cosPhi;
RealOpenMM signOfAngle; RealOpenMM signOfAngle;
...@@ -126,13 +126,13 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -126,13 +126,13 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
RealOpenMM* crossProduct[2]; RealOpenMM* crossProduct[2];
crossProduct[0] = crossProductMemory; crossProduct[0] = crossProductMemory;
crossProduct[1] = crossProductMemory + 3; crossProduct[1] = crossProductMemory + 3;
RealOpenMM dihederalAngle = getDihedralAngleBetweenThreeVectors( deltaR[0], deltaR[1], deltaR[2], RealOpenMM dihederalAngle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2],
crossProduct, &cosPhi, deltaR[0], crossProduct, &cosPhi, deltaR[0],
&signOfAngle, hasREntry ); &signOfAngle, hasREntry);
// Gromacs: use polymer convention // Gromacs: use polymer convention
if( dihederalAngle < zero ){ if (dihederalAngle < zero) {
dihederalAngle += PI_M; dihederalAngle += PI_M;
} else { } else {
dihederalAngle -= PI_M; dihederalAngle -= PI_M;
...@@ -141,36 +141,36 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -141,36 +141,36 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
// Ryckaert-Bellemans: // Ryckaert-Bellemans:
// V = sum over i: { C_i*cos( psi )**i }, where psi = phi - PI, // V = sum over i: { C_i*cos(psi)**i }, where psi = phi - PI,
// C_i is ith RB coefficient // C_i is ith RB coefficient
RealOpenMM dEdAngle = zero; RealOpenMM dEdAngle = zero;
RealOpenMM energy = parameters[0]; RealOpenMM energy = parameters[0];
RealOpenMM cosFactor = one; RealOpenMM cosFactor = one;
for( int ii = 1; ii < numberOfParameters; ii++ ){ for (int ii = 1; ii < numberOfParameters; ii++) {
dEdAngle -= ((RealOpenMM) ii)*parameters[ii]*cosFactor; dEdAngle -= ((RealOpenMM) ii)*parameters[ii]*cosFactor;
cosFactor *= cosPhi; cosFactor *= cosPhi;
energy += cosFactor*parameters[ii]; energy += cosFactor*parameters[ii];
} }
dEdAngle *= SIN( dihederalAngle ); dEdAngle *= SIN(dihederalAngle);
RealOpenMM internalF[4][3]; RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4]; RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3( crossProduct[0], crossProduct[0] ); RealOpenMM normCross1 = DOT3(crossProduct[0], crossProduct[0]);
RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex]; RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex];
forceFactors[0] = (-dEdAngle*normBC)/normCross1; forceFactors[0] = (-dEdAngle*normBC)/normCross1;
RealOpenMM normCross2 = DOT3( crossProduct[1], crossProduct[1] ); RealOpenMM normCross2 = DOT3(crossProduct[1], crossProduct[1]);
forceFactors[3] = (dEdAngle*normBC)/normCross2; forceFactors[3] = (dEdAngle*normBC)/normCross2;
forceFactors[1] = DOT3( deltaR[0], deltaR[1] ); forceFactors[1] = DOT3(deltaR[0], deltaR[1]);
forceFactors[1] /= deltaR[1][ReferenceForce::R2Index]; forceFactors[1] /= deltaR[1][ReferenceForce::R2Index];
forceFactors[2] = DOT3( deltaR[2], deltaR[1] ); forceFactors[2] = DOT3(deltaR[2], deltaR[1]);
forceFactors[2] /= deltaR[1][ReferenceForce::R2Index]; forceFactors[2] /= deltaR[1][ReferenceForce::R2Index];
for( int ii = 0; ii < 3; ii++ ){ for (int ii = 0; ii < 3; ii++) {
internalF[0][ii] = forceFactors[0]*crossProduct[0][ii]; internalF[0][ii] = forceFactors[0]*crossProduct[0][ii];
internalF[3][ii] = forceFactors[3]*crossProduct[1][ii]; internalF[3][ii] = forceFactors[3]*crossProduct[1][ii];
...@@ -183,7 +183,7 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -183,7 +183,7 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
// accumulate forces // accumulate forces
for( int ii = 0; ii < 3; ii++ ){ for (int ii = 0; ii < 3; ii++) {
forces[atomAIndex][ii] += internalF[0][ii]; forces[atomAIndex][ii] += internalF[0][ii];
forces[atomBIndex][ii] -= internalF[1][ii]; forces[atomBIndex][ii] -= internalF[1][ii];
forces[atomCIndex][ii] -= internalF[2][ii]; forces[atomCIndex][ii] -= internalF[2][ii];
......
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