void NVE::moveA(){
SimInfo::MoleculeIterator i;
Molecule::IntegrableObjectIterator j;
Molecule* mol;
StuntDouble* sd;
Vector3d vel;
Vector3d pos;
Vector3d frc;
Vector3d Tb;
Vector3d ji;
RealType mass;
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
vel = sd->getVel();
pos = sd->getPos();
frc = sd->getFrc();
mass = sd->getMass();
// velocity half step
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
// position whole step
pos += dt * vel;
sd->setVel(vel);
sd->setPos(pos);
if (sd->isDirectional()){
// get and convert the torque to body frame
Tb = sd->lab2Body(sd->getTrq());
// get the angular momentum, and propagate a half step
ji = sd->getJ();
ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
rotAlgo_->rotate(sd, ji, dt);
sd->setJ(ji);
}
}
}
flucQ_->moveA();
rattle_->constraintA();
}
void NPT::moveA() {
SimInfo::MoleculeIterator i;
Molecule::IntegrableObjectIterator j;
Molecule* mol;
StuntDouble* sd;
Vector3d Tb, ji;
RealType mass;
Vector3d vel;
Vector3d pos;
Vector3d frc;
Vector3d sc;
int index;
thermostat = snap->getThermostat();
loadEta();
instaTemp =thermo.getTemperature();
press = thermo.getPressureTensor();
instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
instaVol =thermo.getVolume();
Vector3d COM = thermo.getCom();
//evolve velocity half step
calcVelScale();
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
vel = sd->getVel();
frc = sd->getFrc();
mass = sd->getMass();
getVelScaleA(sc, vel);
// velocity half step (use chi from previous step here):
vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc;
sd->setVel(vel);
if (sd->isDirectional()) {
// get and convert the torque to body frame
Tb = sd->lab2Body(sd->getTrq());
// get the angular momentum, and propagate a half step
ji = sd->getJ();
ji += dt2*PhysicalConstants::energyConvert * Tb
- dt2*thermostat.first* ji;
rotAlgo_->rotate(sd, ji, dt);
sd->setJ(ji);
}
}
}
// evolve chi and eta half step
thermostat.first += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
evolveEtaA();
//calculate the integral of chidt
thermostat.second += dt2 * thermostat.first;
flucQ_->moveA();
index = 0;
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
oldPos[index++] = sd->getPos();
}
}
//the first estimation of r(t+dt) is equal to r(t)
for(int k = 0; k < maxIterNum_; k++) {
index = 0;
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
vel = sd->getVel();
pos = sd->getPos();
this->getPosScale(pos, COM, index, sc);
pos = oldPos[index] + dt * (vel + sc);
sd->setPos(pos);
++index;
}
}
rattle_->constraintA();
}
// Scale the box after all the positions have been moved:
this->scaleSimBox();
snap->setThermostat(thermostat);
saveEta();
}
void NPT::moveB(void) {
SimInfo::MoleculeIterator i;
Molecule::IntegrableObjectIterator j;
Molecule* mol;
StuntDouble* sd;
int index;
Vector3d Tb;
Vector3d ji;
Vector3d sc;
Vector3d vel;
Vector3d frc;
RealType mass;
thermostat = snap->getThermostat();
RealType oldChi = thermostat.first;
RealType prevChi;
loadEta();
//save velocity and angular momentum
index = 0;
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
oldVel[index] = sd->getVel();
if (sd->isDirectional())
oldJi[index] = sd->getJ();
++index;
}
}
// do the iteration:
instaVol =thermo.getVolume();
for(int k = 0; k < maxIterNum_; k++) {
instaTemp =thermo.getTemperature();
instaPress =thermo.getPressure();
// evolve chi another half step using the temperature at t + dt/2
prevChi = thermostat.first;
thermostat.first = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;
//evolve eta
this->evolveEtaB();
this->calcVelScale();
index = 0;
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
frc = sd->getFrc();
mass = sd->getMass();
getVelScaleB(sc, index);
// velocity half step
vel = oldVel[index]
+ dt2*PhysicalConstants::energyConvert/mass* frc
- dt2*sc;
sd->setVel(vel);
if (sd->isDirectional()) {
// get and convert the torque to body frame
Tb = sd->lab2Body(sd->getTrq());
ji = oldJi[index]
+ dt2*PhysicalConstants::energyConvert*Tb
- dt2*thermostat.first*oldJi[index];
sd->setJ(ji);
}
++index;
}
}
rattle_->constraintB();
if ((fabs(prevChi - thermostat.first) <= chiTolerance) &&
this->etaConverged())
break;
}
//calculate integral of chidt
thermostat.second += dt2 * thermostat.first;
snap->setThermostat(thermostat);
flucQ_->moveB();
saveEta();
}
void ThermoIntegrationForceManager::calcForces(){
Snapshot* curSnapshot;
SimInfo::MoleculeIterator mi;
Molecule* mol;
Molecule::IntegrableObjectIterator ii;
StuntDouble* sd;
Vector3d frc;
Vector3d trq;
Mat3x3d tempTau;
// perform the standard calcForces first
ForceManager::calcForces();
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
// now scale forces and torques of all the sds
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
for (sd = mol->beginIntegrableObject(ii); sd != NULL;
sd = mol->nextIntegrableObject(ii)) {
frc = sd->getFrc();
frc *= factor_;
sd->setFrc(frc);
if (sd->isDirectional()){
trq = sd->getTrq();
trq *= factor_;
sd->setTrq(trq);
}
}
}
// set rawPotential to be the unmodulated potential
lrPot_ = curSnapshot->getLongRangePotential();
curSnapshot->setRawPotential(lrPot_);
// modulate the potential and update the snapshot
lrPot_ *= factor_;
curSnapshot->setLongRangePotential(lrPot_);
// scale the pressure tensor
tempTau = curSnapshot->getStressTensor();
tempTau *= factor_;
curSnapshot->setStressTensor(tempTau);
// now, on to the applied restraining potentials (if needed):
RealType restPot_local = 0.0;
RealType vHarm_local = 0.0;
if (simParam->getUseRestraints()) {
// do restraints from RestraintForceManager:
restPot_local = doRestraints(1.0 - factor_);
vHarm_local = getUnscaledPotential();
}
#ifdef IS_MPI
RealType restPot;
MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1,
MPI::REALTYPE, MPI::SUM);
MPI::COMM_WORLD.Allreduce(&vHarm_local, &vHarm_, 1,
MPI::REALTYPE, MPI::SUM);
lrPot_ += restPot;
#else
lrPot_ += restPot_local;
vHarm_ = vHarm_local;
#endif
// give the final values to stats
curSnapshot->setLongRangePotential(lrPot_);
curSnapshot->setRestraintPotential(vHarm_);
}