void CpuBondForce::threadComputeForce(ThreadPool& threads, int threadIndex, vector<Vec3>& atomCoordinates, double** parameters, vector<Vec3>& forces,
double* totalEnergy, ReferenceBondIxn& referenceBondIxn) {
vector<int>& bonds = threadBonds[threadIndex];
int numBonds = bonds.size();
for (int i = 0; i < numBonds; i++) {
int bond = bonds[i];
referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy, NULL);
}
}
void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) {
// Have the worker threads compute their forces.
vector<RealOpenMM> threadEnergy(threads->getNumThreads(), 0);
ComputeForceTask task(*this, atomCoordinates, parameters, forces, threadEnergy, totalEnergy, referenceBondIxn);
threads->execute(task);
threads->waitForThreads();
// Compute any "extra" bonds.
for (int i = 0; i < extraBonds.size(); i++) {
int bond = extraBonds[i];
referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy, NULL);
}
// Compute the total energy.
if (totalEnergy != NULL)
for (int i = 0; i < threads->getNumThreads(); i++)
*totalEnergy += threadEnergy[i];
}
void CpuBondForce::calculateForce(vector<Vec3>& atomCoordinates, double** parameters, vector<Vec3>& forces,
double* totalEnergy, ReferenceBondIxn& referenceBondIxn) {
// Have the worker threads compute their forces.
vector<double> threadEnergy(threads->getNumThreads(), 0);
threads->execute([&] (ThreadPool& threads, int threadIndex) {
double* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
});
threads->waitForThreads();
// Compute any "extra" bonds.
for (int i = 0; i < extraBonds.size(); i++) {
int bond = extraBonds[i];
referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy, NULL);
}
// Compute the total energy.
if (totalEnergy != NULL)
for (int i = 0; i < threads->getNumThreads(); i++)
*totalEnergy += threadEnergy[i];
}