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Commit 7fb10336 authored by peastman's avatar peastman
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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
--------------------------------------------------------------------------------------- */
ReferenceCustomCompoundBondIxn::~ReferenceCustomCompoundBondIxn( ){
ReferenceCustomCompoundBondIxn::~ReferenceCustomCompoundBondIxn() {
}
/**---------------------------------------------------------------------------------------
......@@ -92,7 +92,7 @@ void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
map<string, double> variables = globalParameters;
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++)
variables[bondParamNames[j]] = bondParameters[bond][j];
calculateOneIxn(bond, atomCoordinates, variables, forces, totalEnergy);
......
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 7fb10336
......@@ -96,7 +96,7 @@ ReferenceCustomDynamics::~ReferenceCustomDynamics() {
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
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();
globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates;
......
platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
View file @ 7fb10336
......@@ -78,7 +78,7 @@ ReferenceCustomExternalIxn::ReferenceCustomExternalIxn(const Lepton::CompiledExp
--------------------------------------------------------------------------------------- */
ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn( ){
ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn() {
// ---------------------------------------------------------------------------------------
......@@ -100,11 +100,11 @@ ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn( ){
--------------------------------------------------------------------------------------- */
void ReferenceCustomExternalIxn::calculateForce( int atomIndex,
void ReferenceCustomExternalIxn::calculateForce(int atomIndex,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* energy ) const {
RealOpenMM* energy) const {
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
--------------------------------------------------------------------------------------- */
ReferenceCustomGBIxn::~ReferenceCustomGBIxn( ){
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;
cutoffDistance = distance;
......@@ -202,8 +202,8 @@ void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, v
else {
// Perform an O(N^2) loop over all atom pairs.
for (int i = 0; i < numAtoms; i++){
for (int j = i+1; j < numAtoms; j++ ){
for (int i = 0; i < numAtoms; i++) {
for (int j = i+1; j < numAtoms; j++) {
if (useExclusions && exclusions[i].find(j) != exclusions[i].end())
continue;
calculateOnePairValue(index, i, j, atomCoordinates, atomParameters, globalParameters, values);
......@@ -274,8 +274,8 @@ void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAto
else {
// Perform an O(N^2) loop over all atom pairs.
for (int i = 0; i < numAtoms; i++){
for (int j = i+1; j < numAtoms; j++ ){
for (int i = 0; i < numAtoms; i++) {
for (int j = i+1; j < numAtoms; j++) {
if (useExclusions && exclusions[i].find(j) != exclusions[i].end())
continue;
calculateOnePairEnergyTerm(index, i, j, atomCoordinates, atomParameters, globalParameters, values, forces, totalEnergy, dEdV);
......@@ -343,8 +343,8 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<RealVec
else {
// Perform an O(N^2) loop over all atom pairs.
for (int i = 0; i < numAtoms; i++){
for (int j = i+1; j < numAtoms; j++ ){
for (int i = 0; i < numAtoms; i++) {
for (int j = i+1; j < numAtoms; j++) {
bool isExcluded = (exclusions[i].find(j) != exclusions[i].end());
calculateOnePairChainRule(i, j, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded);
calculateOnePairChainRule(j, i, atomCoordinates, atomParameters, globalParameters, values, forces, dEdV, isExcluded);
......
platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
View file @ 7fb10336
......@@ -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,
int numDonors = donorAtoms.size();
int numAcceptors = acceptorAtoms.size();
for( int donor = 0; donor < numDonors; donor++ ){
for (int donor = 0; donor < numDonors; donor++) {
// Initialize per-donor parameters.
for (int j = 0; j < (int) donorParamNames.size(); j++)
......@@ -136,7 +136,7 @@ void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates,
// 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()) {
for (int j = 0; j < (int) acceptorParamNames.size(); j++)
variables[acceptorParamNames[j]] = acceptorParameters[acceptor][j];
......
platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.cpp
View file @ 7fb10336
......@@ -103,7 +103,7 @@ ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyP
CustomManyParticleForceImpl::buildFilterArrays(force, numTypes, particleTypes, orderIndex, particleOrder);
}
ReferenceCustomManyParticleIxn::~ReferenceCustomManyParticleIxn( ){
ReferenceCustomManyParticleIxn::~ReferenceCustomManyParticleIxn() {
}
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
--------------------------------------------------------------------------------------- */
ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn( ){
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;
cutoffDistance = distance;
......@@ -119,7 +119,7 @@ void ReferenceCustomNonbondedIxn::setInteractionGroups(const vector<pair<set<int
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::setUseSwitchingFunction( RealOpenMM distance ) {
void ReferenceCustomNonbondedIxn::setUseSwitchingFunction(RealOpenMM distance) {
useSwitch = true;
switchingDistance = 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* 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) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(energyExpression, iter->first), iter->second);
......@@ -244,8 +244,8 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) {
void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) {
// ---------------------------------------------------------------------------------------
......@@ -267,9 +267,9 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (periodic)
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR);
else
ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[jj], atomCoordinates[ii], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex];
if (cutoff && r >= cutoffDistance)
return;
......@@ -289,7 +289,7 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe
energy *= switchValue;
}
}
for( int kk = 0; kk < 3; kk++ ){
for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = -dEdR*deltaR[kk];
forces[ii][kk] += force;
forces[jj][kk] -= force;
......@@ -297,10 +297,10 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe
// accumulate energies
if( totalEnergy || energyByAtom ) {
if( totalEnergy )
if (totalEnergy || energyByAtom) {
if (totalEnergy)
*totalEnergy += energy;
if( energyByAtom ){
if (energyByAtom) {
energyByAtom[ii] += energy;
energyByAtom[jj] += energy;
}
......
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
View file @ 7fb10336
......@@ -61,7 +61,7 @@ ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpre
--------------------------------------------------------------------------------------- */
ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn( ){
ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn() {
// ---------------------------------------------------------------------------------------
......@@ -83,11 +83,11 @@ ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn( ){
--------------------------------------------------------------------------------------- */
void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const {
RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceCustomTorsionIxn::calculateTorsionIxn";
......@@ -135,20 +135,20 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3( crossProduct[0], crossProduct[0] );
RealOpenMM normCross1 = DOT3(crossProduct[0], crossProduct[0]);
RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex];
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[1] = DOT3( deltaR[0], deltaR[1] );
forceFactors[1] = DOT3(deltaR[0], deltaR[1]);
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];
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
internalF[0][ii] = forceFactors[0]*crossProduct[0][ii];
internalF[3][ii] = forceFactors[3]*crossProduct[1][ii];
......@@ -161,7 +161,7 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
// accumulate forces
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
forces[atomAIndex][ii] += internalF[0][ii];
forces[atomBIndex][ii] -= internalF[1][ii];
forces[atomCIndex][ii] -= internalF[2][ii];
......
platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
View file @ 7fb10336
......@@ -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) {
// ---------------------------------------------------------------------------------------
......@@ -68,7 +68,7 @@ ReferenceDynamics::ReferenceDynamics( int numberOfAtoms, RealOpenMM deltaT, Rea
--------------------------------------------------------------------------------------- */
ReferenceDynamics::~ReferenceDynamics( ){
ReferenceDynamics::~ReferenceDynamics() {
// ---------------------------------------------------------------------------------------
......@@ -76,7 +76,7 @@ ReferenceDynamics::~ReferenceDynamics( ){
// ---------------------------------------------------------------------------------------
if( _ownReferenceConstraint ){
if (_ownReferenceConstraint) {
delete _referenceConstraint;
}
}
......@@ -89,7 +89,7 @@ ReferenceDynamics::~ReferenceDynamics( ){
--------------------------------------------------------------------------------------- */
int ReferenceDynamics::getNumberOfAtoms( void ) const {
int ReferenceDynamics::getNumberOfAtoms() 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 {
--------------------------------------------------------------------------------------- */
int ReferenceDynamics::incrementTimeStep( void ){
int ReferenceDynamics::incrementTimeStep() {
// ---------------------------------------------------------------------------------------
......@@ -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 {
--------------------------------------------------------------------------------------- */
void ReferenceDynamics::setDeltaT( RealOpenMM deltaT ) {
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 {
--------------------------------------------------------------------------------------- */
ReferenceConstraintAlgorithm* ReferenceDynamics::getReferenceConstraintAlgorithm( void ) const {
ReferenceConstraintAlgorithm* ReferenceDynamics::getReferenceConstraintAlgorithm() const {
// ---------------------------------------------------------------------------------------
......@@ -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
// delete if own
if( _referenceConstraint && _ownReferenceConstraint ){
if (_referenceConstraint && _ownReferenceConstraint) {
delete _referenceConstraint;
}
......
platforms/reference/src/SimTKReference/ReferenceForce.cpp
View file @ 7fb10336
......@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceForce::ReferenceForce( ){
ReferenceForce::ReferenceForce() {
}
/**---------------------------------------------------------------------------------------
......@@ -48,7 +48,7 @@ ReferenceForce::ReferenceForce( ){
--------------------------------------------------------------------------------------- */
ReferenceForce::~ReferenceForce( ){
ReferenceForce::~ReferenceForce() {
}
/**---------------------------------------------------------------------------------------
......@@ -64,28 +64,28 @@ RealOpenMM ReferenceForce::periodicDifference(RealOpenMM val1, RealOpenMM val2,
}
void ReferenceForce::getDeltaR( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
RealOpenMM* deltaR ){
void ReferenceForce::getDeltaR(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
RealOpenMM* deltaR) {
deltaR[XIndex] = atomCoordinatesJ[0] - atomCoordinatesI[0];
deltaR[YIndex] = atomCoordinatesJ[1] - atomCoordinatesI[1];
deltaR[ZIndex] = atomCoordinatesJ[2] - atomCoordinatesI[2];
deltaR[R2Index] = DOT3( deltaR, deltaR );
deltaR[RIndex] = (RealOpenMM) SQRT( deltaR[R2Index] );
deltaR[R2Index] = DOT3(deltaR, deltaR);
deltaR[RIndex] = (RealOpenMM) SQRT(deltaR[R2Index]);
}
void ReferenceForce::getDeltaRPeriodic( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR ){
void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR) {
deltaR[XIndex] = periodicDifference(atomCoordinatesJ[0], atomCoordinatesI[0], boxSize[0]);
deltaR[YIndex] = periodicDifference(atomCoordinatesJ[1], atomCoordinatesI[1], boxSize[1]);
deltaR[ZIndex] = periodicDifference(atomCoordinatesJ[2], atomCoordinatesI[2], boxSize[2]);
deltaR[R2Index] = DOT3( deltaR, deltaR );
deltaR[RIndex] = (RealOpenMM) SQRT( deltaR[R2Index] );
deltaR[R2Index] = DOT3(deltaR, deltaR);
deltaR[RIndex] = (RealOpenMM) SQRT(deltaR[R2Index]);
}
void ReferenceForce::getDeltaRPeriodic( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealVec* boxVectors, RealOpenMM* deltaR ){
void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealVec* boxVectors, RealOpenMM* deltaR) {
RealVec diff = atomCoordinatesJ-atomCoordinatesI;
diff -= boxVectors[2]*floor(diff[2]/boxVectors[2][2]+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;
--------------------------------------------------------------------------------------- */
ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn( ){
ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn() {
// ---------------------------------------------------------------------------------------
......@@ -55,7 +55,7 @@ ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn( ){
--------------------------------------------------------------------------------------- */
ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn( ){
ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn() {
// ---------------------------------------------------------------------------------------
......@@ -78,11 +78,11 @@ ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn( ){
--------------------------------------------------------------------------------------- */
void ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices,
void ReferenceHarmonicBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const {
RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
......@@ -100,7 +100,7 @@ void ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices,
int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1];
ReferenceForce::getDeltaR( atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
// deltaIdeal = r - r_0
......
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
View file @ 7fb10336
......@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceLJCoulomb14::ReferenceLJCoulomb14( ) {
ReferenceLJCoulomb14::ReferenceLJCoulomb14() {
// ---------------------------------------------------------------------------------------
......@@ -55,7 +55,7 @@ ReferenceLJCoulomb14::ReferenceLJCoulomb14( ) {
--------------------------------------------------------------------------------------- */
ReferenceLJCoulomb14::~ReferenceLJCoulomb14( ){
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* totalEnergy ) const {
RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceLJCoulomb14::calculateBondIxn";
......@@ -112,7 +112,7 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>&
int atomAIndex = atomIndices[0];
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 inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
......@@ -120,13 +120,13 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>&
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 *= inverseR*inverseR;
// accumulate forces
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
RealOpenMM force = dEdR*deltaR[0][ii];
forces[atomAIndex][ii] += force;
forces[atomBIndex][ii] -= force;
......@@ -135,5 +135,5 @@ void ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, vector<RealVec>&
// accumulate energies
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;
--------------------------------------------------------------------------------------- */
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
--------------------------------------------------------------------------------------- */
ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){
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;
cutoffDistance = distance;
......@@ -101,7 +101,7 @@ ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){
--------------------------------------------------------------------------------------- */
void ReferenceLJCoulombIxn::setUseSwitchingFunction( RealOpenMM distance ) {
void ReferenceLJCoulombIxn::setUseSwitchingFunction(RealOpenMM distance) {
useSwitch = true;
switchingDistance = distance;
}
......@@ -210,16 +210,16 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
// **************************************************************************************
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);
totalSelfEwaldEnergy -= selfEwaldEnergy;
if( energyByAtom ){
if (energyByAtom) {
energyByAtom[atomID] -= selfEwaldEnergy;
}
}
}
if( totalEnergy ){
if (totalEnergy) {
*totalEnergy += totalSelfEwaldEnergy;
}
......@@ -238,11 +238,11 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
charges[i] = atomParameters[i][QIndex];
pme_exec(pmedata,atomCoordinates,forces,charges,periodicBoxVectors,&recipEnergy);
if( totalEnergy )
if (totalEnergy)
*totalEnergy += recipEnergy;
if( energyByAtom )
for(int n = 0; n < numberOfAtoms; n++)
if (energyByAtom)
for (int n = 0; n < numberOfAtoms; n++)
energyByAtom[n] += recipEnergy;
pme_destroy(pmedata);
......@@ -267,16 +267,16 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
if (kmax < 1)
throw OpenMMException("kmax for Ewald summation < 1");
for(int i = 0; (i < numberOfAtoms); i++) {
for(int m = 0; (m < 3); m++)
for (int i = 0; (i < numberOfAtoms); i++) {
for (int m = 0; (m < 3); m++)
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]),
sin(atomCoordinates[i][m]*recipBoxSize[m]));
for(int j=2; (j<kmax); j++)
for(int m=0; (m<3); m++)
for (int j=2; (j<kmax); j++)
for (int m=0; (m<3); 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>
int lowry = 0;
int lowrz = 1;
for(int rx = 0; rx < numRx; rx++) {
for (int rx = 0; rx < numRx; rx++) {
RealOpenMM kx = rx * recipBoxSize[0];
for(int ry = lowry; ry < numRy; ry++) {
for (int ry = lowry; ry < numRy; ry++) {
RealOpenMM ky = ry * recipBoxSize[1];
if(ry >= 0) {
for(int n = 0; n < numberOfAtoms; n++)
if (ry >= 0) {
for (int n = 0; n < numberOfAtoms; n++)
tab_xy[n] = EIR(rx, n, 0) * EIR(ry, n, 1);
}
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));
}
for (int rz = lowrz; rz < numRz; rz++) {
if( rz >= 0) {
for( int n = 0; n < numberOfAtoms; n++)
if (rz >= 0) {
for (int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = atomParameters[n][QIndex] * (tab_xy[n] * EIR(rz, n, 2));
}
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)));
}
RealOpenMM cs = 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();
ss += tab_qxyz[n].imag();
}
......@@ -327,21 +327,21 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
RealOpenMM k2 = kx * kx + ky * ky + kz * kz;
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());
forces[n][0] += 2 * recipCoeff * force * kx ;
forces[n][1] += 2 * recipCoeff * force * ky ;
forces[n][2] += 2 * recipCoeff * force * kz ;
}
recipEnergy = recipCoeff * ak * ( cs * cs + ss * ss);
recipEnergy = recipCoeff * ak * (cs * cs + ss * ss);
totalRecipEnergy += recipEnergy;
if( totalEnergy )
if (totalEnergy)
*totalEnergy += recipEnergy;
if( energyByAtom )
for(int n = 0; n < numberOfAtoms; n++)
if (energyByAtom)
for (int n = 0; n < numberOfAtoms; n++)
energyByAtom[n] += recipEnergy;
lowrz = 1 - numRz;
......@@ -366,7 +366,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
int jj = pair.second;
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 inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM switchValue = 1, switchDeriv = 0;
......@@ -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);
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 sig2 = inverseR*sig;
sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2;
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;
if (useSwitch) {
dEdR -= vdwEnergy*switchDeriv*inverseR;
......@@ -395,7 +395,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
// accumulate forces
for( int kk = 0; kk < 3; kk++ ){
for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] += force;
forces[jj][kk] -= force;
......@@ -408,14 +408,14 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
totalVdwEnergy += vdwEnergy;
totalRealSpaceEwaldEnergy += realSpaceEwaldEnergy;
if( energyByAtom ){
if (energyByAtom) {
energyByAtom[ii] += realSpaceEwaldEnergy + vdwEnergy;
energyByAtom[jj] += realSpaceEwaldEnergy + vdwEnergy;
}
}
if( totalEnergy )
if (totalEnergy)
*totalEnergy += totalRealSpaceEwaldEnergy + totalVdwEnergy;
// 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>
int jj = *iter;
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 inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM alphaR = alphaEwald * r;
if (erf(alphaR) > 1e-6) {
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
for( int kk = 0; kk < 3; kk++ ){
for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] -= force;
forces[jj][kk] += force;
......@@ -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));
totalExclusionEnergy += realSpaceEwaldEnergy;
if( energyByAtom ){
if (energyByAtom) {
energyByAtom[ii] -= realSpaceEwaldEnergy;
energyByAtom[jj] -= realSpaceEwaldEnergy;
}
......@@ -457,7 +457,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
}
}
if( totalEnergy )
if (totalEnergy)
*totalEnergy -= totalExclusionEnergy;
}
......@@ -499,10 +499,10 @@ void ReferenceLJCoulombIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>&
}
}
else {
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for (int ii = 0; ii < numberOfAtoms; ii++) {
// 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())
calculateOneIxn(ii, jj, atomCoordinates, atomParameters, forces, energyByAtom, totalEnergy);
}
......@@ -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* energyByAtom, RealOpenMM* totalEnergy ) const {
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const {
// ---------------------------------------------------------------------------------------
......@@ -552,9 +552,9 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
// get deltaR, R2, and R between 2 atoms
if (periodic)
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR[0] );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR[0]);
else
ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR[0] );
ReferenceForce::getDeltaR(atomCoordinates[jj], atomCoordinates[ii], deltaR[0]);
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
......@@ -573,7 +573,7 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
RealOpenMM sig6 = sig2*sig2*sig2;
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)
dEdR += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR-2.0f*krf*r2));
else
......@@ -591,7 +591,7 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
// accumulate forces
for( int kk = 0; kk < 3; kk++ ){
for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] += force;
forces[jj][kk] -= force;
......@@ -599,9 +599,9 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
// accumulate energies
if( totalEnergy )
if (totalEnergy)
*totalEnergy += energy;
if( energyByAtom ){
if (energyByAtom) {
energyByAtom[ii] += energy;
energyByAtom[jj] += energy;
}
......
platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp
View file @ 7fb10336
......@@ -43,9 +43,9 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceLincsAlgorithm::ReferenceLincsAlgorithm( int numberOfConstraints,
int** atomIndices,
RealOpenMM* distance ){
ReferenceLincsAlgorithm::ReferenceLincsAlgorithm(int numberOfConstraints,
int** atomIndices,
RealOpenMM* distance) {
// ---------------------------------------------------------------------------------------
......@@ -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 {
--------------------------------------------------------------------------------------- */
int ReferenceLincsAlgorithm::getNumTerms( void ) const {
int ReferenceLincsAlgorithm::getNumTerms() 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
--------------------------------------------------------------------------------------- */
int ReferenceLincsAlgorithm::apply( int numberOfAtoms, vector<RealVec>& atomCoordinates,
int ReferenceLincsAlgorithm::apply(int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses ){
vector<RealOpenMM>& inverseMasses) {
// ---------------------------------------------------------------------------------------
......@@ -235,7 +235,7 @@ int ReferenceLincsAlgorithm::apply( int numberOfAtoms, vector<RealVec>& atomCoor
if (_numberOfConstraints == 0)
return SimTKOpenMMCommon::DefaultReturn;
if( !_hasInitialized )
if (!_hasInitialized)
initialize(numberOfAtoms, inverseMasses);
// 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
--------------------------------------------------------------------------------------- */
ReferenceMonteCarloBarostat::~ReferenceMonteCarloBarostat( ) {
ReferenceMonteCarloBarostat::~ReferenceMonteCarloBarostat() {
}
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceNeighborList.cpp
View file @ 7fb10336
......@@ -45,12 +45,12 @@ void OPENMM_EXPORT computeNeighborListNaive(
for (AtomIndex atomJ = atomI + 1; atomJ < (AtomIndex) nAtoms; ++atomJ)
{
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())
{
neighborList.push_back( AtomPair(atomI, atomJ) );
neighborList.push_back(AtomPair(atomI, atomJ));
if (reportSymmetricPairs)
neighborList.push_back( AtomPair(atomI, atomJ) );
neighborList.push_back(AtomPair(atomI, atomJ));
}
}
}
......@@ -199,9 +199,9 @@ public:
// Ignore exclusions.
if (exclusions[atomI].find(atomJ) != exclusions[atomI].end()) continue;
neighbors.push_back( AtomPair(atomI, atomJ) );
neighbors.push_back(AtomPair(atomI, atomJ));
if (reportSymmetricPairs)
neighbors.push_back( AtomPair(atomJ, atomI) );
neighbors.push_back(AtomPair(atomJ, atomI));
}
}
}
......@@ -228,7 +228,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash(
double maxDistance,
double minDistance,
bool reportSymmetricPairs
)
)
{
neighborList.clear();
......@@ -245,7 +245,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash(
{
// 1) Find other atoms that are close to this one
const RealVec& location = atomLocations[atomJ];
voxelHash.getNeighbors(
voxelHash.getNeighbors(
neighborList,
VoxelItem(&location, atomJ),
exclusions,
......
platforms/reference/src/SimTKReference/ReferencePME.cpp
View file @ 7fb10336
......@@ -77,7 +77,7 @@ struct pme
* 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!)
* 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 :-)
*
......@@ -108,7 +108,7 @@ pme_calculate_bsplines_moduli(pme_t pme)
RealOpenMM sc,ss,arg;
nmax = 0;
for(d=0;d<3;d++)
for (d=0;d<3;d++)
{
nmax = (pme->ngrid[d] > nmax) ? pme->ngrid[d] : nmax;
pme->bsplines_moduli[d] = (RealOpenMM *) malloc(sizeof(RealOpenMM)*pme->ngrid[d]);
......@@ -125,11 +125,11 @@ pme_calculate_bsplines_moduli(pme_t pme)
data[1]=0;
data[0]=1;
for(k=3;k<order;k++)
for (k=3;k<order;k++)
{
div=(RealOpenMM) (1.0/(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]);
}
......@@ -138,7 +138,7 @@ pme_calculate_bsplines_moduli(pme_t pme)
/* differentiate */
ddata[0]=-data[0];
for(k=1;k<order;k++)
for (k=1;k<order;k++)
{
ddata[k]=data[k-1]-data[k];
}
......@@ -146,29 +146,29 @@ pme_calculate_bsplines_moduli(pme_t pme)
div=(RealOpenMM) (1.0/(order-1));
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[0]=div*data[0];
for(i=0;i<nmax;i++)
for (i=0;i<nmax;i++)
{
bsplines_data[i]=0;
}
for(i=1;i<=order;i++)
for (i=1;i<=order;i++)
{
bsplines_data[i]=data[i-1];
}
/* 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];
for(i=0;i<ndata;i++)
for (i=0;i<ndata;i++)
{
sc=ss=0;
for(j=0;j<ndata;j++)
for (j=0;j<ndata;j++)
{
arg=(RealOpenMM) ((2.0*M_PI*i*j)/ndata);
sc+=bsplines_data[j]*cos(arg);
......@@ -176,9 +176,9 @@ pme_calculate_bsplines_moduli(pme_t pme)
}
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;
}
......@@ -213,7 +213,7 @@ pme_update_grid_index_and_fraction(pme_t pme,
RealOpenMM t;
int ti;
for(i=0;i<pme->natoms;i++)
for (i=0;i<pme->natoms;i++)
{
/* Index calculation (Look mom, no conditionals!):
*
......@@ -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!)
*/
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 = (t-floor(t))*pme->ngrid[d];
......@@ -281,9 +281,9 @@ pme_update_bsplines(pme_t pme)
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 = pme->particlefraction[i][j];
......@@ -294,11 +294,11 @@ pme_update_bsplines(pme_t pme)
data[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));
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]);
}
......@@ -308,7 +308,7 @@ pme_update_bsplines(pme_t pme)
/* differentiate */
ddata[0] = -data[0];
for(k=1; k<order; k++)
for (k=1; k<order; k++)
{
ddata[k] = data[k-1]-data[k];
}
......@@ -316,7 +316,7 @@ pme_update_bsplines(pme_t pme)
div = (RealOpenMM) (1.0/(order-1));
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]);
}
......@@ -343,12 +343,12 @@ pme_grid_spread_charge(pme_t pme, const vector<RealOpenMM>& charges)
order = pme->order;
/* 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;
}
for(i=0;i<pme->natoms;i++)
for (i=0;i<pme->natoms;i++)
{
q = charges[i];
......@@ -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!
*/
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 */
xindex = (x0index + ix) % pme->ngrid[0];
for(iy=0;iy<order;iy++)
for (iy=0;iy<order;iy++)
{
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 */
zindex = (z0index + iz) % pme->ngrid[2];
......@@ -448,21 +448,21 @@ pme_reciprocal_convolution(pme_t pme,
maxky = (RealOpenMM) ((ny+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! */
mx = (RealOpenMM) ((kx<maxkx) ? kx : (kx-nx));
mhx = mx*recipBoxVectors[0][0];
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! */
my = (RealOpenMM) ((ky<maxky) ? ky : (ky-ny));
mhy = mx*recipBoxVectors[1][0]+my*recipBoxVectors[1][1];
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,
* 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,
/* 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;
......@@ -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
* 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];
/* Get both the bspline factor and its derivative with respect to the x coordinate! */
tx = thetax[ix];
dtx = dthetax[ix];
for(iy=0;iy<order;iy++)
for (iy=0;iy<order;iy++)
{
yindex = (y0index + iy) % pme->ngrid[1];
/* bspline + derivative wrt y */
ty = thetay[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 */
zindex = (z0index + iz) % pme->ngrid[2];
......@@ -633,7 +633,7 @@ pme_init(pme_t * ppme,
pme->ewaldcoeff = ewaldcoeff;
pme->natoms = natoms;
for(d=0;d<3;d++)
for (d=0;d<3;d++)
{
pme->ngrid[d] = ngrid[d];
pme->bsplines_theta[d] = (RealOpenMM *)malloc(sizeof(RealOpenMM)*pme_order*natoms);
......@@ -712,7 +712,7 @@ pme_destroy(pme_t pme)
free(pme->grid);
for(d=0;d<3;d++)
for (d=0;d<3;d++)
{
free(pme->bsplines_moduli[d]);
free(pme->bsplines_theta[d]);
......
platforms/reference/src/SimTKReference/ReferencePairIxn.cpp
View file @ 7fb10336
......@@ -38,7 +38,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferencePairIxn::ReferencePairIxn( ){
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;
--------------------------------------------------------------------------------------- */
ReferenceProperDihedralBond::ReferenceProperDihedralBond( ){
ReferenceProperDihedralBond::ReferenceProperDihedralBond() {
// ---------------------------------------------------------------------------------------
......@@ -55,7 +55,7 @@ ReferenceProperDihedralBond::ReferenceProperDihedralBond( ){
--------------------------------------------------------------------------------------- */
ReferenceProperDihedralBond::~ReferenceProperDihedralBond( ){
ReferenceProperDihedralBond::~ReferenceProperDihedralBond() {
// ---------------------------------------------------------------------------------------
......@@ -79,11 +79,11 @@ ReferenceProperDihedralBond::~ReferenceProperDihedralBond( ){
--------------------------------------------------------------------------------------- */
void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
void ReferenceProperDihedralBond::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const {
RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceProperDihedralBond::calculateBondIxn";
......@@ -111,9 +111,9 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2];
int atomDIndex = atomIndices[3];
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] );
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1] );
ReferenceForce::getDeltaR( atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2] );
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
RealOpenMM dotDihedral;
RealOpenMM signOfAngle;
......@@ -127,35 +127,35 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
// get dihedral angle
RealOpenMM dihedralAngle = getDihedralAngleBetweenThreeVectors( deltaR[0], deltaR[1], deltaR[2],
crossProduct, &dotDihedral, deltaR[0],
&signOfAngle, hasREntry );
RealOpenMM dihedralAngle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2],
crossProduct, &dotDihedral, deltaR[0],
&signOfAngle, hasREntry);
// evaluate delta angle, dE/d(angle)
RealOpenMM deltaAngle = parameters[2]*dihedralAngle - parameters[1];
RealOpenMM sinDeltaAngle = SIN( deltaAngle );
RealOpenMM sinDeltaAngle = SIN(deltaAngle);
RealOpenMM dEdAngle = -parameters[0]*parameters[2]*sinDeltaAngle;
RealOpenMM energy = parameters[0]*(one + COS( deltaAngle ) );
RealOpenMM energy = parameters[0]*(one + COS(deltaAngle));
// compute force
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3( crossProduct[0], crossProduct[0] );
RealOpenMM normCross1 = DOT3(crossProduct[0], crossProduct[0]);
RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex];
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[1] = DOT3( deltaR[0], deltaR[1] );
forceFactors[1] = DOT3(deltaR[0], deltaR[1]);
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];
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
internalF[0][ii] = forceFactors[0]*crossProduct[0][ii];
internalF[3][ii] = forceFactors[3]*crossProduct[1][ii];
......@@ -168,7 +168,7 @@ void ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
// accumulate forces
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
forces[atomAIndex][ii] += internalF[0][ii];
forces[atomBIndex][ii] -= internalF[1][ii];
forces[atomCIndex][ii] -= internalF[2][ii];
......
platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp
View file @ 7fb10336
......@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceRbDihedralBond::ReferenceRbDihedralBond( ){
ReferenceRbDihedralBond::ReferenceRbDihedralBond() {
// ---------------------------------------------------------------------------------------
......@@ -55,7 +55,7 @@ ReferenceRbDihedralBond::ReferenceRbDihedralBond( ){
--------------------------------------------------------------------------------------- */
ReferenceRbDihedralBond::~ReferenceRbDihedralBond( ){
ReferenceRbDihedralBond::~ReferenceRbDihedralBond() {
// ---------------------------------------------------------------------------------------
......@@ -77,11 +77,11 @@ ReferenceRbDihedralBond::~ReferenceRbDihedralBond( ){
--------------------------------------------------------------------------------------- */
void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
void ReferenceRbDihedralBond::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const {
RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceRbDihedralBond::calculateBondIxn";
......@@ -113,9 +113,9 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2];
int atomDIndex = atomIndices[3];
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] );
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1] );
ReferenceForce::getDeltaR( atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2] );
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
RealOpenMM cosPhi;
RealOpenMM signOfAngle;
......@@ -126,13 +126,13 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
RealOpenMM* crossProduct[2];
crossProduct[0] = crossProductMemory;
crossProduct[1] = crossProductMemory + 3;
RealOpenMM dihederalAngle = getDihedralAngleBetweenThreeVectors( deltaR[0], deltaR[1], deltaR[2],
crossProduct, &cosPhi, deltaR[0],
&signOfAngle, hasREntry );
RealOpenMM dihederalAngle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2],
crossProduct, &cosPhi, deltaR[0],
&signOfAngle, hasREntry);
// Gromacs: use polymer convention
if( dihederalAngle < zero ){
if (dihederalAngle < zero) {
dihederalAngle += PI_M;
} else {
dihederalAngle -= PI_M;
......@@ -141,36 +141,36 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
// 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
RealOpenMM dEdAngle = zero;
RealOpenMM energy = parameters[0];
RealOpenMM cosFactor = one;
for( int ii = 1; ii < numberOfParameters; ii++ ){
for (int ii = 1; ii < numberOfParameters; ii++) {
dEdAngle -= ((RealOpenMM) ii)*parameters[ii]*cosFactor;
cosFactor *= cosPhi;
energy += cosFactor*parameters[ii];
}
dEdAngle *= SIN( dihederalAngle );
dEdAngle *= SIN(dihederalAngle);
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3( crossProduct[0], crossProduct[0] );
RealOpenMM normCross1 = DOT3(crossProduct[0], crossProduct[0]);
RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex];
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[1] = DOT3( deltaR[0], deltaR[1] );
forceFactors[1] = DOT3(deltaR[0], deltaR[1]);
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];
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
internalF[0][ii] = forceFactors[0]*crossProduct[0][ii];
internalF[3][ii] = forceFactors[3]*crossProduct[1][ii];
......@@ -183,7 +183,7 @@ void ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
// accumulate forces
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
forces[atomAIndex][ii] += internalF[0][ii];
forces[atomBIndex][ii] -= internalF[1][ii];
forces[atomCIndex][ii] -= internalF[2][ii];
......
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