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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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#include "utils/StringUtils.hpp" |
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namespace oopse { |
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VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
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VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
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dt2 = 0.5 * dt; |
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rotAlgo = new DLM(); |
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rattle = new Rattle(info); |
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} |
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|
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
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} |
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|
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
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delete rotAlgo; |
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delete rattle; |
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} |
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|
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void VelocityVerletIntegrator::initialize(){ |
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|
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} |
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|
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void VelocityVerletIntegrator::initialize(){ |
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|
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forceMan_->init(); |
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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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// initialize the forces before the first step |
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calcForce(true, true); |
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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 (info_->getNGlobalConstraints() > 0) { |
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rattle->constraintA(); |
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calcForce(true, true); |
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rattle->constraintB(); |
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info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot |
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rattle->constraintA(); |
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calcForce(true, true); |
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rattle->constraintB(); |
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info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot |
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} |
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|
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if (needVelocityScaling) { |
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velocitizer_->velocitize(targetScalingTemp); |
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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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eorWriter = createEorWriter(); |
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|
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statWriter = createStatWriter(); |
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|
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dumpWriter->writeDump(); |
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eorWriter->writeDump(); |
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|
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if (simParams->getUseSolidThermInt()) { |
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restWriter = createRestWriter(); |
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restWriter->writeZangle(); |
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} |
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|
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dumpWriter->writeDumpAndEor(); |
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|
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|
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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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|
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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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currThermal = thermalTime + currentSnapshot_->getTime(); |
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if (needReset) { |
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currReset = resetTime + currentSnapshot_->getTime(); |
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} |
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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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|
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} |
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|
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void VelocityVerletIntegrator::doIntegrate() { |
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|
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|
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initialize(); |
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|
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|
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while (currentSnapshot_->getTime() < runTime) { |
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preStep(); |
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integrateStep(); |
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postStep(); |
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preStep(); |
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integrateStep(); |
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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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} |
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void VelocityVerletIntegrator::preStep() { |
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double difference = currentSnapshot_->getTime() + dt - currStatus; |
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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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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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std::cout << currentSnapshot_->getTime()<< ": \n"; |
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} |
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|
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} |
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void VelocityVerletIntegrator::postStep() { |
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|
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void VelocityVerletIntegrator::postStep() { |
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//save snapshot |
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info_->getSnapshotManager()->advance(); |
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|
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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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|
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if (currentSnapshot_->getTime() >= currSample) { |
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dumpWriter->writeDumpAndEor(); |
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|
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if (simParams->getUseSolidThermInt()) |
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restWriter->writeZangle(); |
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|
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currSample += sampleTime; |
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} |
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|
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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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|
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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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//save snapshot |
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info_->getSnapshotManager()->advance(); |
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if (needReset && currentSnapshot_->getTime() >= currReset) { |
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resetIntegrator(); |
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currReset += resetTime; |
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} |
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|
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} |
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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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if (currentSnapshot_->getTime() >= currSample) { |
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dumpWriter->writeDump(); |
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eorWriter->writeDump(); |
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currSample += sampleTime; |
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} |
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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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|
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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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} |
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|
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void VelocityVerletIntegrator::finalize() { |
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|
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dumpWriter->writeDump(); |
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eorWriter->writeDump(); |
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|
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void VelocityVerletIntegrator::finalize() { |
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dumpWriter->writeEor(); |
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|
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if (simParams->getUseSolidThermInt()) { |
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restWriter->writeZangle(); |
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delete restWriter; |
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restWriter = NULL; |
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} |
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delete dumpWriter; |
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delete eorWriter; |
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delete statWriter; |
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|
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dumpWriter = NULL; |
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eorWriter = 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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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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} |
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|
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void VelocityVerletIntegrator::calcForce(bool needPotential, |
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bool needStress) { |
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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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DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
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return new DumpWriter(info_, info_->getDumpFileName()); |
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} |
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DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
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return new DumpWriter(info_); |
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} |
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|
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DumpWriter* VelocityVerletIntegrator::createEorWriter() { |
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return new DumpWriter(info_, getPrefix(info_->getDumpFileName()) + ".eor"); |
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} |
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StatWriter* VelocityVerletIntegrator::createStatWriter() { |
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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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std::string statFileFormatString = simParams->getStatFileFormat(); |
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StatsBitSet mask = parseStatFileFormat(statFileFormatString); |
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|
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// if solidThermInt is true, add extra information to the statfile |
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if (simParams->getUseSolidThermInt()){ |
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mask.set(Stats::VRAW); |
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mask.set(Stats::VHARM); |
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} |
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|
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if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){ |
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mask.set(Stats::PRESSURE_TENSOR_X); |
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mask.set(Stats::PRESSURE_TENSOR_Y); |
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mask.set(Stats::PRESSURE_TENSOR_Z); |
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} |
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|
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return new StatWriter(info_->getStatFileName(), mask); |
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} |
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RestWriter* VelocityVerletIntegrator::createRestWriter(){ |
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return new RestWriter(info_); |
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} |
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|
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|
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} //end namespace oopse |