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#include "integrators/VelocityVerletIntegrator.hpp" |
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namespace oopse { |
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VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) { } |
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> |
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) { |
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dt2 = 0.5 * dt; |
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} |
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { } |
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void VelocityVerletIntegrator::integrate() { |
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double runTime = info_->run_time; |
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void VelocityVerletIntegrator::initialize(){ |
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int calcPot; |
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int calcStress; |
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currSample = 0.0; |
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currStatus = 0.0; |
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currThermal = 0.0; |
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needPotential = false; |
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needStress = false; |
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dt_ = info_->dt; |
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dt2_ = 0.5 * dt_; |
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readyCheck(); |
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// remove center of mass drift velocity (in case we passed in a configuration |
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// that was drifting |
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tStats->removeCOMdrift(); |
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velocitizer_->removeComDrift(); |
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// initialize the forces before the first step |
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calcForce(true, true); |
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calcForce(1, 1); |
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//execute constraint algorithm to make sure at the very beginning the system is constrained |
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if (nConstrained) { |
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constrainA(); |
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calcForce(1, 1); |
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constrainB(); |
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} |
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//if (nConstrained) { |
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// constrainA(); |
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// calcForce(true, true); |
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// constrainB(); |
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//} |
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if (info_->setTemp) { |
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thermalize(); |
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if (needVelocityScaling) { |
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velocitizer_->velocitize(targetScalingTemp); |
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} |
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dumpWriter = createDumpWriter(); |
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statWriter = createStatWriter(); |
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calcPot = 0; |
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calcStress = 0; |
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dumpWriter->writeFrame(); |
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statWriter->writeStat(currentSnapshot_.statData); |
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tStats = new Thermo(info_); |
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statOut = new StatWriter(info_); |
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dumpOut = new DumpWriter(info_); |
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dumpOut->writeDump(info_->getTime()); |
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statOut->writeStat(info_->getTime()); |
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} |
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|
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void VelocityVerletIntegrator::doIntegrate() { |
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "The integrator is ready to go."); |
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MPIcheckPoint(); |
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initialize(); |
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#endif // is_mpi |
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while (currentSnapshot_->getTime() < runTime) { |
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preStep(); |
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while (info_->getTime() < runTime) { |
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difference = info_->getTime() + dt_ - currStatus; |
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integrateStep(); |
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< |
if (difference > 0 || fabs(difference) < 1e - 4) { |
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calcPot = 1; |
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< |
calcStress = 1; |
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> |
info_->incrTime(dt); |
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|
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postStep(); |
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|
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} |
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finalize(); |
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} |
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|
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void VelocityVerletIntegrator::preStep() { |
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double difference = currentSnapshot_->getTime() + dt - currStatus; |
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> |
|
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> |
if (difference > 0 || fabs(difference) < oopse::epsilon) { |
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needPotential = true; |
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> |
needStress = true; |
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} |
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//notify before integrateStep |
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notify() |
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integrateStep(calcPot, calcStress); |
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} |
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|
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void VelocityVerletIntegrator::postStep() { |
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info_->incrTime(dt_); |
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//notify after integratreStep |
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notify(); |
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if (info_->setTemp) { |
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< |
if (info_->getTime() >= currThermal) { |
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< |
thermalize(); |
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> |
if (needVelocityScaling) { |
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> |
if (currentSnapshot_->getTime() >= currThermal) { |
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> |
velocitizer_->velocitize(targetScalingTemp); |
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currThermal += thermalTime; |
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} |
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} |
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< |
if (info_->getTime() >= currSample) { |
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< |
dumpOut->writeDump(info_->getTime()); |
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> |
if (currentSnapshot_->getTime() >= currSample) { |
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> |
dumpWriter->writeFrame(currentSnapshot_->getTime()); |
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currSample += sampleTime; |
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} |
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< |
if (info_->getTime() >= currStatus) { |
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< |
statOut->writeStat(info_->getTime()); |
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< |
calcPot = 0; |
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< |
calcStress = 0; |
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> |
if (currentSnapshot_->getTime() >= currStatus) { |
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> |
statWriter->writeStat(currentSnapshot_.statData); |
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> |
needPotential = false; |
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> |
needStress = false; |
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currStatus += statusTime; |
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} |
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+ |
} |
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– |
if (info_->resetIntegrator) { |
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– |
if (info_->getTime() >= currReset) { |
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– |
this->resetIntegrator(); |
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– |
currReset += resetTime; |
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– |
} |
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} |
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|
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< |
#ifdef IS_MPI |
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> |
void VelocityVerletIntegrator::finalize() { |
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< |
strcpy(checkPointMsg, "successfully took a time step."); |
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< |
MPIcheckPoint(); |
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> |
dumpWriter->writeFrame(); |
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< |
#endif // is_mpi |
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> |
delete dumpWriter; |
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> |
delete statWriter; |
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< |
} |
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< |
|
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< |
dumpOut->writeFinal(info_->getTime()); |
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< |
|
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< |
delete dumpOut; |
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< |
delete statOut; |
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> |
dumpWriter = NULL; |
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> |
statWriter = NULL; |
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> |
|
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} |
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|
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|
void VelocityVerletIntegrator::integrateStep() { |
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|
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moveA(); |
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< |
calcForce(bool needPotential, bool needStress); |
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> |
calcForce(needPotential, needStress); |
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moveB(); |
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} |
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|
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< |
void VelocityVerletIntegrator::thermalize() { |
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< |
|
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< |
if (!info__->have_target_temp) { |
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< |
sprintf(painCave.errMsg, |
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< |
"You can't resample the velocities without a targetTemp!\n"); |
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< |
painCave.isFatal = 1; |
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< |
painCave.severity = OOPSE_ERROR; |
| 162 |
< |
simError(); |
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< |
return; |
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< |
} |
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< |
|
| 154 |
> |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
| 155 |
> |
bool needStress) { |
| 156 |
> |
forceMan_->calcForces(needPotential, needStress) |
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|
} |
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|
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– |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
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– |
bool needStress) { } |
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– |
|
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} //end namespace oopse |
