/*
* Verlet MD NVE integrator step
*
* This method implements the algorithm:
*
* vm(n) = v(n) + 0.5*a(n)*dt
* x(n+1) = x(n) + vm(n)*dt
*
* calculate acceleration a(n+1)
*
* v(n+1) = vm(n) + 0.5*a(n+1)*dt
*
* where x is position, v is velocity, and a is acceleration.
*/
void NveVvIntegrator::step()
{
Vector dv;
Vector dr;
System::MoleculeIterator molIter;
double prefactor;
int iSpecies, nSpecies;
nSpecies = simulation().nSpecies();
// 1st half velocity Verlet, loop over atoms
#if USE_ITERATOR
Molecule::AtomIterator atomIter;
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
atomIter->velocity() += dv;
dr.multiply(atomIter->velocity(), dt_);
atomIter->position() += dr;
}
}
}
#else
Atom* atomPtr;
int ia;
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (ia=0; ia < molIter->nAtom(); ++ia) {
atomPtr = &molIter->atom(ia);
prefactor = prefactors_[atomPtr->typeId()];
dv.multiply(atomPtr->force(), prefactor);
atomPtr->velocity() += dv;
dr.multiply(atomPtr->velocity(), dt_);
atomPtr->position() += dr;
}
}
}
#endif
system().calculateForces();
// 2nd half velocity Verlet, loop over atoms
#if USE_ITERATOR
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
atomIter->velocity() += dv;
}
}
}
#else
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter)
{
for (ia=0; ia < molIter->nAtom(); ++ia) {
atomPtr = &molIter->atom(ia);
prefactor = prefactors_[atomPtr->typeId()];
dv.multiply(atomPtr->force(), prefactor);
atomPtr->velocity() += dv;
}
}
}
#endif
#ifndef INTER_NOPAIR
if (!system().pairPotential().isPairListCurrent()) {
system().pairPotential().buildPairList();
}
#endif
}
/*
* Nose-Hoover integrator step.
*
* This implements a reversible Velocity-Verlet MD NVT integrator step.
*
* Reference: Winkler, Kraus, and Reineker, J. Chem. Phys. 102, 9018 (1995).
*/
void NvtNhIntegrator::step()
{
Vector dv;
Vector dr;
System::MoleculeIterator molIter;
double dtHalf = 0.5*dt_;
double prefactor;
double factor;
Molecule::AtomIterator atomIter;
int iSpecies, nSpecies;
int nAtom;
T_target_ = energyEnsemblePtr_->temperature();
nSpecies = simulation().nSpecies();
nAtom = system().nAtom();
factor = exp(-dtHalf*(xi_ + xiDot_*dtHalf));
// 1st half velocity Verlet, loop over atoms
for (iSpecies = 0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
molIter->begin(atomIter);
for ( ; atomIter.notEnd(); ++atomIter) {
atomIter->velocity() *= factor;
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
//dv.multiply(atomIter->force(), dtHalf);
atomIter->velocity() += dv;
dr.multiply(atomIter->velocity(), dt_);
atomIter->position() += dr;
}
}
}
// First half of update of xi_
xi_ += xiDot_*dtHalf;
#ifndef INTER_NOPAIR
// Rebuild the pair list if necessary
if (!system().pairPotential().isPairListCurrent()) {
system().pairPotential().buildPairList();
}
#endif
system().calculateForces();
// 2nd half velocity Verlet, loop over atoms
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
atomIter->velocity() += dv;
atomIter->velocity() *=factor;
}
}
}
// Update xiDot and complete update of xi_
T_kinetic_ = system().kineticEnergy()*2.0/double(3*nAtom);
xiDot_ = (T_kinetic_/T_target_ -1.0)*nuT_*nuT_;
xi_ += xiDot_*dtHalf;
}