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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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/** |
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* @file VelocityVerletIntegrator.cpp |
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* @author tlin |
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* @date 11/09/2004 |
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* @time 16:16am |
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* @version 1.0 |
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*/ |
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|
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/** |
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* @file VelocityVerletIntegrator.cpp |
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* @author tlin |
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* @date 11/09/2004 |
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* @time 16:16am |
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* @version 1.0 |
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*/ |
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|
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#include "integrators/VelocityVerletIntegrator.hpp" |
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#include "integrators/DLM.hpp" |
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namespace oopse { |
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|
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VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo* info){ |
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|
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VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
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rotAlgo = new DLM(); |
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dt2 = 0.5 * dt; |
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} |
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
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|
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
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delete rotAlgo; |
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} |
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|
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void VelocityVerletIntegrator::integrate() { |
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void VelocityVerletIntegrator::initialize(){ |
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|
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} |
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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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velocitizer_->removeComDrift(); |
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|
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void VelocityVerletIntegrator::integrateStep() { |
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// initialize the forces before the first step |
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calcForce(true, true); |
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|
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} |
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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(true, true); |
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// constrainB(); |
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//} |
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|
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void VelocityVerletIntegrator::moveA() { |
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if (needVelocityScaling) { |
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velocitizer_->velocitize(targetScalingTemp); |
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} |
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|
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dumpWriter = createDumpWriter(); |
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statWriter = createStatWriter(); |
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} |
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dumpWriter->writeDump(); |
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void VelocityVerletIntegrator::moveB() { |
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//save statistics, before writeStat, we must save statistics |
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thermo.saveStat(); |
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saveConservedQuantity(); |
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statWriter->writeStat(currentSnapshot_->statData); |
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|
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currSample = sampleTime + currentSnapshot_->getTime(); |
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currStatus = statusTime + currentSnapshot_->getTime();; |
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currThermal = thermalTime + + currentSnapshot_->getTime(); |
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needPotential = false; |
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needStress = false; |
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|
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} |
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|
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void VelocityVerletIntegrator::doIntegrate() { |
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void VelocityVerletIntegrator::thermalize() { |
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} |
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initialize(); |
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void VelocityVerletIntegrator::velocitize() { |
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Vector3d aVel; |
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Vector3d aJ; |
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Mat3x3d I; |
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int l, m, n; // velocity randomizer loop counts |
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Vector3d vdrift; |
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double vbar; |
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const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
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double av2; |
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double kebar; |
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double temperature; |
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while (currentSnapshot_->getTime() < runTime) { |
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|
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preStep(); |
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std::vector<Molecule*>::iterator i; |
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std::vector<StuntDouble*>::iterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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gaussianSPRNG gaussStream(info_->getSeed()); |
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integrateStep(); |
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|
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postStep(); |
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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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); |
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painCave.isFatal = 1; |
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painCave.severity = OOPSE_ERROR; |
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simError(); |
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return; |
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} |
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temperature = info_->target_temp; |
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|
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kebar = kb * temperature * info_->getNdfRaw() / ( 2.0 * info_->getNdf()); |
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|
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finalize(); |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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// uses equipartition theory to solve for vbar in angstrom/fs |
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} |
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av2 = 2.0 * kebar / integrableObject->getMass(); |
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vbar = sqrt( av2 ); |
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// picks random velocities from a gaussian distribution |
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// centered on vbar |
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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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for (int k=0; k<3; k++) { |
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aVel[k] = vbar * gaussStream.getGaussian(); |
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} |
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|
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integrableObject->setVel( aVel ); |
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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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if(integrableObject->isDirectional()){ |
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} |
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I = integrableObject->getI(); |
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void VelocityVerletIntegrator::postStep() { |
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if (integrableObject->isLinear()) { |
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//save snapshot |
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info_->getSnapshotManager()->advance(); |
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l= integrableObject->linearAxis(); |
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m = (l+1)%3; |
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n = (l+2)%3; |
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//increase time |
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currentSnapshot_->increaseTime(dt); |
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|
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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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aJ[l] = 0.0; |
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vbar = sqrt( 2.0 * kebar * I(m, m) ); |
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aJ[m] = vbar * gaussStream.getGaussian(); |
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vbar = sqrt( 2.0 * kebar * I(n, n) ); |
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aJ[n] = vbar * gaussStream.getGaussian(); |
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if (currentSnapshot_->getTime() >= currSample) { |
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dumpWriter->writeDump(); |
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currSample += sampleTime; |
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} |
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} else { |
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if (currentSnapshot_->getTime() >= currStatus) { |
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//save statistics, before writeStat, we must save statistics |
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thermo.saveStat(); |
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saveConservedQuantity(); |
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statWriter->writeStat(currentSnapshot_->statData); |
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for (int k = 0 ; k < 3; k++) { |
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vbar = sqrt( 2.0 * kebar * I(k, k) ); |
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aJ[k] = vbar * gaussStream.getGaussian(); |
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} |
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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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} // else isLinear |
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|
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} |
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integrableObject->setJ( aJ ); |
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}//isDirectional |
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} |
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}//end for (mol = beginMolecule(i); ...) |
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void VelocityVerletIntegrator::finalize() { |
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// Get the Center of Mass drift velocity. |
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vdrift = info_->getComVel(); |
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|
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// Corrects for the center of mass drift. |
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// sums all the momentum and divides by total mass. |
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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dumpWriter->writeDump(); |
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aVel = integrableObject->getVel(); |
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aVel -= vdrift; |
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integrableObject->setVel( aVel ); |
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} |
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} |
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delete dumpWriter; |
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delete statWriter; |
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|
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dumpWriter = NULL; |
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statWriter = NULL; |
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} |
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void VelocityVerletIntegrator::calcForce(int needPotential, int needStress){ |
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void VelocityVerletIntegrator::integrateStep() { |
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|
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moveA(); |
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calcForce(needPotential, needStress); |
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moveB(); |
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} |
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void VelocityVerletIntegrator::velocitize() { |
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|
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void VelocityVerletIntegrator::calcForce(bool needPotential, |
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bool needStress) { |
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forceMan_->calcForces(needPotential, needStress); |
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} |
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|
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void removeComDrift(){ |
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DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
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return new DumpWriter(info_, info_->getDumpFileName()); |
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} |
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StatWriter* VelocityVerletIntegrator::createStatWriter() { |
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return new StatWriter(info_->getStatFileName()); |
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} |
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|
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|
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} //end namespace oopse |