void CudaIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
// Compute forces from all groups that didn't have a specified contraction.
for (int i = 0; i < numCopies; i++) {
void* copyToContextArgs[] = {&velocities->getDevicePointer(), &cu.getVelm().getDevicePointer(), &positions->getDevicePointer(),
&cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(copyToContextKernel, copyToContextArgs, cu.getNumAtoms());
context.computeVirtualSites();
Vec3 initialBox[3];
context.getPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
context.updateContextState();
Vec3 finalBox[3];
context.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
if (initialBox[0] != finalBox[0] || initialBox[1] != finalBox[1] || initialBox[2] != finalBox[2])
throw OpenMMException("Standard barostats cannot be used with RPMDIntegrator. Use RPMDMonteCarloBarostat instead.");
context.calcForcesAndEnergy(true, false, groupsNotContracted);
void* copyFromContextArgs[] = {&cu.getForce().getDevicePointer(), &forces->getDevicePointer(), &cu.getVelm().getDevicePointer(),
&velocities->getDevicePointer(), &cu.getPosq().getDevicePointer(), &positions->getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(copyFromContextKernel, copyFromContextArgs, cu.getNumAtoms());
}
// Now loop over contractions and compute forces from them.
for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
int copies = iter->first;
int groupFlags = iter->second;
// Find the contracted positions.
void* contractPosArgs[] = {&positions->getDevicePointer(), &contractedPositions->getDevicePointer()};
cu.executeKernel(positionContractionKernels[copies], contractPosArgs, numParticles*numCopies, workgroupSize);
// Compute forces.
for (int i = 0; i < copies; i++) {
void* copyToContextArgs[] = {&velocities->getDevicePointer(), &cu.getVelm().getDevicePointer(), &contractedPositions->getDevicePointer(),
&cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(copyToContextKernel, copyToContextArgs, cu.getNumAtoms());
context.computeVirtualSites();
context.calcForcesAndEnergy(true, false, groupFlags);
void* copyFromContextArgs[] = {&cu.getForce().getDevicePointer(), &contractedForces->getDevicePointer(), &cu.getVelm().getDevicePointer(),
&velocities->getDevicePointer(), &cu.getPosq().getDevicePointer(), &contractedPositions->getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(copyFromContextKernel, copyFromContextArgs, cu.getNumAtoms());
}
// Apply the forces to the original copies.
void* contractForceArgs[] = {&forces->getDevicePointer(), &contractedForces->getDevicePointer()};
cu.executeKernel(forceContractionKernels[copies], contractForceArgs, numParticles*numCopies, workgroupSize);
}
if (groupsByCopies.size() > 0) {
// Ensure the Context contains the positions from the last copy, since we'll assume that later.
int i = numCopies-1;
void* copyToContextArgs[] = {&velocities->getDevicePointer(), &cu.getVelm().getDevicePointer(), &positions->getDevicePointer(),
&cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(copyToContextKernel, copyToContextArgs, cu.getNumAtoms());
}
}
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) {
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
oldPos = atomCoordinates;
// Loop over steps and execute them.
for (int step = 0; step < numSteps; ) {
if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || context.getLastForceGroups() != forceGroupFlags[step])) {
// Recompute forces and/or energy.
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy) {
energy = e;
context.getEnergyParameterDerivatives(energyParamDerivs);
}
forcesAreValid = true;
}
// Execute the step.
int nextStep = step+1;
switch (stepType[step]) {
case CustomIntegrator::ComputeGlobal: {
uniform = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
gaussian = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
RealOpenMM result = stepExpressions[step][0].evaluate();
globals[stepVariable[step]] = result;
expressionSet.setVariable(stepVariableIndex[step], result);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariableIndex[step] == xIndex)
results = &atomCoordinates;
else if (stepVariableIndex[step] == vIndex)
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariableIndex[step] == perDofVariableIndex[j])
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[step]] = sum;
expressionSet.setVariable(stepVariableIndex[step], sum);
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
break;
}
case CustomIntegrator::IfBlockStart: {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::WhileBlockStart: {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::BlockEnd: {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
break;
}
}
if (invalidatesForces[step])
forcesAreValid = false;
step = nextStep;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
recordChangedParameters(context, globals);
}
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) {
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates;
if (invalidatesForces.size() == 0) {
// Some initialization can't be done in the constructor, since we need a ContextImpl from which to get the list of
// Context parameters. Instead, we do it the first time this method is called.
vector<int> forceGroup;
vector<vector<Lepton::ParsedExpression> > expressions;
CustomIntegratorUtilities::analyzeComputations(context, integrator, expressions, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
stepExpressions.resize(expressions.size());
for (int i = 0; i < numSteps; i++) {
for (int j = 0; j < (int) expressions[i].size(); j++)
stepExpressions[i].push_back(expressions[i][j].createProgram());
if (stepType[i] == CustomIntegrator::BeginWhileBlock)
blockEnd[blockEnd[i]] = i; // Record where to branch back to.
}
// Record the variable names and flags for the force and energy in each step.
forceGroupFlags.resize(numSteps, -1);
forceName.resize(numSteps, "f");
energyName.resize(numSteps, "energy");
vector<string> forceGroupName;
vector<string> energyGroupName;
for (int i = 0; i < 32; i++) {
stringstream fname;
fname << "f" << i;
forceGroupName.push_back(fname.str());
stringstream ename;
ename << "energy" << i;
energyGroupName.push_back(ename.str());
}
for (int i = 0; i < numSteps; i++) {
if (needsForces[i] && forceGroup[i] > -1)
forceName[i] = forceGroupName[forceGroup[i]];
if (needsEnergy[i] && forceGroup[i] > -1)
energyName[i] = energyGroupName[forceGroup[i]];
if (forceGroup[i] > -1)
forceGroupFlags[i] = 1<<forceGroup[i];
}
// Build the list of inverse masses.
inverseMasses.resize(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] == 0.0)
inverseMasses[i] = 0.0;
else
inverseMasses[i] = 1.0/masses[i];
}
}
// Loop over steps and execute them.
for (int step = 0; step < numSteps; ) {
if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || context.getLastForceGroups() != forceGroupFlags[step])) {
// Recompute forces and/or energy.
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy)
energy = e;
forcesAreValid = true;
}
globals[energyName[step]] = energy;
// Execute the step.
int nextStep = step+1;
switch (stepType[step]) {
case CustomIntegrator::ComputeGlobal: {
map<string, RealOpenMM> variables = globals;
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
globals[stepVariable[step]] = stepExpressions[step][0].evaluate(variables);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariable[step] == "x")
results = &atomCoordinates;
else if (stepVariable[step] == "v")
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariable[step] == integrator.getPerDofVariableName(j))
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpressions[step][0], forceName[step]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpressions[step][0], forceName[step]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[step]] = sum;
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
break;
}
case CustomIntegrator::BeginIfBlock: {
if (!evaluateCondition(step, globals))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::BeginWhileBlock: {
if (!evaluateCondition(step, globals))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::EndBlock: {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
break;
}
}
if (invalidatesForces[step])
forcesAreValid = false;
step = nextStep;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
recordChangedParameters(context, globals);
}
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){
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates;
if (invalidatesForces.size() == 0) {
// The first time this is called, work out when to recompute forces and energy. First build a
// list of every step that invalidates the forces.
invalidatesForces.resize(numSteps, false);
needsForces.resize(numSteps, false);
needsEnergy.resize(numSteps, false);
forceGroup.resize(numSteps, -2);
forceName.resize(numSteps, "f");
energyName.resize(numSteps, "energy");
set<string> affectsForce;
affectsForce.insert("x");
for (vector<ForceImpl*>::const_iterator iter = context.getForceImpls().begin(); iter != context.getForceImpls().end(); ++iter) {
const map<string, double> params = (*iter)->getDefaultParameters();
for (map<string, double>::const_iterator param = params.begin(); param != params.end(); ++param)
affectsForce.insert(param->first);
}
for (int i = 0; i < numSteps; i++)
invalidatesForces[i] = (stepType[i] == CustomIntegrator::ConstrainPositions || affectsForce.find(stepVariable[i]) != affectsForce.end());
// Make a list of which steps require valid forces or energy to be known.
vector<string> forceGroupName;
vector<string> energyGroupName;
for (int i = 0; i < 32; i++) {
stringstream fname;
fname << "f" << i;
forceGroupName.push_back(fname.str());
stringstream ename;
ename << "energy" << i;
energyGroupName.push_back(ename.str());
}
for (int i = 0; i < numSteps; i++) {
if (stepType[i] == CustomIntegrator::ComputeGlobal || stepType[i] == CustomIntegrator::ComputePerDof || stepType[i] == CustomIntegrator::ComputeSum) {
for (int j = 0; j < stepExpression[i].getNumOperations(); j++) {
const Lepton::Operation& op = stepExpression[i].getOperation(j);
if (op.getId() == Lepton::Operation::VARIABLE) {
if (op.getName() == "energy") {
if (forceGroup[i] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsEnergy[i] = true;
forceGroup[i] = -1;
}
else if (op.getName().substr(0, 6) == "energy") {
for (int k = 0; k < (int) energyGroupName.size(); k++)
if (op.getName() == energyGroupName[k]) {
if (forceGroup[i] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsForces[i] = true;
forceGroup[i] = 1<<k;
energyName[i] = energyGroupName[k];
break;
}
}
else if (op.getName() == "f") {
if (forceGroup[i] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsForces[i] = true;
forceGroup[i] = -1;
}
else if (op.getName()[0] == 'f') {
for (int k = 0; k < (int) forceGroupName.size(); k++)
if (op.getName() == forceGroupName[k]) {
if (forceGroup[i] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsForces[i] = true;
forceGroup[i] = 1<<k;
forceName[i] = forceGroupName[k];
break;
}
}
}
}
}
}
// Build the list of inverse masses.
inverseMasses.resize(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] == 0.0)
inverseMasses[i] = 0.0;
else
inverseMasses[i] = 1.0/masses[i];
}
}
// Loop over steps and execute them.
for (int i = 0; i < numSteps; i++) {
if ((needsForces[i] || needsEnergy[i]) && (!forcesAreValid || context.getLastForceGroups() != forceGroup[i])) {
// Recompute forces and or energy. Figure out what is actually needed
// between now and the next time they get invalidated again.
bool computeForce = false, computeEnergy = false;
for (int j = i; ; j++) {
if (needsForces[j])
computeForce = true;
if (needsEnergy[j])
computeEnergy = true;
if (invalidatesForces[j])
break;
if (j == numSteps-1)
j = -1;
if (j == i-1)
break;
}
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroup[i]);
if (computeEnergy)
energy = e;
forcesAreValid = true;
}
globals[energyName[i]] = energy;
// Execute the step.
switch (stepType[i]) {
case CustomIntegrator::ComputeGlobal: {
map<string, RealOpenMM> variables = globals;
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
globals[stepVariable[i]] = stepExpression[i].evaluate(variables);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariable[i] == "x")
results = &atomCoordinates;
else if (stepVariable[i] == "v")
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariable[i] == integrator.getPerDofVariableName(j))
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[i]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpression[i], forceName[i]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpression[i], forceName[i]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[i]] = sum;
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
}
}
if (invalidatesForces[i])
forcesAreValid = false;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
recordChangedParameters(context, globals);
}
void ReferenceIntegrateRPMDStepKernel::computeForces(ContextImpl& context, const RPMDIntegrator& integrator) {
const int totalCopies = positions.size();
const int numParticles = positions[0].size();
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& f = extractForces(context);
// Compute forces from all groups that didn't have a specified contraction.
for (int i = 0; i < totalCopies; i++) {
pos = positions[i];
vel = velocities[i];
context.computeVirtualSites();
Vec3 initialBox[3];
context.getPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
context.updateContextState();
Vec3 finalBox[3];
context.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
if (initialBox[0] != finalBox[0] || initialBox[1] != finalBox[1] || initialBox[2] != finalBox[2]) {
// A barostat was applied during updateContextState(). Adjust the particle positions in all the
// other copies to match this one.
for (int j = 0; j < numParticles; j++) {
Vec3 delta = pos[j]-positions[i][j];
for (int k = 0; k < totalCopies; k++)
if (k != i)
positions[k][j] += delta;
}
}
positions[i] = pos;
velocities[i] = vel;
context.calcForcesAndEnergy(true, false, groupsNotContracted);
forces[i] = f;
}
// Now loop over contractions and compute forces from them.
for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
int copies = iter->first;
int groupFlags = iter->second;
fftpack* shortFFT = contractionFFT[copies];
// Find the contracted positions.
vector<t_complex> q(totalCopies);
const RealOpenMM scale1 = 1.0/totalCopies;
for (int particle = 0; particle < numParticles; particle++) {
for (int component = 0; component < 3; component++) {
// Transform to the frequency domain, set high frequency components to zero, and transform back.
for (int k = 0; k < totalCopies; k++)
q[k] = t_complex(positions[k][particle][component], 0.0);
fftpack_exec_1d(fft, FFTPACK_FORWARD, &q[0], &q[0]);
if (copies > 1) {
int start = (copies+1)/2;
int end = totalCopies-copies+start;
for (int k = end; k < totalCopies; k++)
q[k-(totalCopies-copies)] = q[k];
fftpack_exec_1d(shortFFT, FFTPACK_BACKWARD, &q[0], &q[0]);
}
for (int k = 0; k < copies; k++)
contractedPositions[k][particle][component] = scale1*q[k].re;
}
}
// Compute forces.
for (int i = 0; i < copies; i++) {
pos = contractedPositions[i];
context.computeVirtualSites();
context.calcForcesAndEnergy(true, false, groupFlags);
contractedForces[i] = f;
}
// Apply the forces to the original copies.
const RealOpenMM scale2 = 1.0/copies;
for (int particle = 0; particle < numParticles; particle++) {
for (int component = 0; component < 3; component++) {
// Transform to the frequency domain, pad with zeros, and transform back.
for (int k = 0; k < copies; k++)
q[k] = t_complex(contractedForces[k][particle][component], 0.0);
if (copies > 1)
fftpack_exec_1d(shortFFT, FFTPACK_FORWARD, &q[0], &q[0]);
int start = (copies+1)/2;
int end = totalCopies-copies+start;
for (int k = end; k < totalCopies; k++)
q[k] = q[k-(totalCopies-copies)];
for (int k = start; k < end; k++)
q[k] = t_complex(0, 0);
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &q[0], &q[0]);
for (int k = 0; k < totalCopies; k++)
forces[k][particle][component] += scale2*q[k].re;
}
}
}
}
