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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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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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#include "utils/StringUtils.hpp" |
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#include "utils/ProgressBar.hpp" |
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namespace oopse { |
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namespace OpenMD { |
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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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void VelocityVerletIntegrator::initialize(){ |
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forceMan_->init(); |
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forceMan_->initialize(); |
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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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// remove center of mass drift velocity (in case we passed in a |
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// configuration that was drifting) |
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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(); |
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//execute constraint algorithm to make sure at the very beginning the system is constrained |
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// execute the constraint algorithm to make sure that the system is |
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// constrained at the very beginning |
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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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calcForce(); |
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rattle->constraintB(); |
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//copy the current snapshot to previous snapshot |
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info_->getSnapshotManager()->advance(); |
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} |
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if (needVelocityScaling) { |
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dumpWriter = createDumpWriter(); |
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statWriter = createStatWriter(); |
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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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progressBar = new ProgressBar(); |
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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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if (simParams->getUseRNEMD()) |
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rnemd_->getStarted(); |
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|
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statWriter->writeStat(currentSnapshot_->statData); |
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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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currStatus = statusTime + 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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if (simParams->getUseRNEMD()){ |
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currRNEMD = RNEMD_exchangeTime + 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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void VelocityVerletIntegrator::doIntegrate() { |
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} |
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|
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void VelocityVerletIntegrator::doIntegrate() { |
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initialize(); |
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initialize(); |
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while (currentSnapshot_->getTime() < runTime) { |
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while (currentSnapshot_->getTime() < runTime) { |
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preStep(); |
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preStep(); |
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integrateStep(); |
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integrateStep(); |
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postStep(); |
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} |
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postStep(); |
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} |
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finalize(); |
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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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void VelocityVerletIntegrator::preStep() { |
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RealType difference = currentSnapshot_->getTime() + dt - currStatus; |
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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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if (difference > 0 || fabs(difference) < OpenMD::epsilon) { |
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needPotential = true; |
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needStress = true; |
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} |
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} |
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|
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} |
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void VelocityVerletIntegrator::postStep() { |
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void VelocityVerletIntegrator::postStep() { |
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|
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//save snapshot |
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info_->getSnapshotManager()->advance(); |
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//save snapshot |
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info_->getSnapshotManager()->advance(); |
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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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//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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if (useRNEMD) { |
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if (currentSnapshot_->getTime() >= currRNEMD) { |
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rnemd_->doRNEMD(); |
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currRNEMD += RNEMD_exchangeTime; |
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} |
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rnemd_->collectData(); |
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} |
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if (simParams->getUseSolidThermInt()) |
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restWriter->writeZangle(); |
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if (currentSnapshot_->getTime() >= currSample) { |
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dumpWriter->writeDumpAndEor(); |
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currSample += sampleTime; |
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} |
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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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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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|
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if (simParams->getUseRNEMD()) { |
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rnemd_->getStatus(); |
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} |
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|
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statWriter->writeStat(currentSnapshot_->statData); |
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progressBar->setStatus(currentSnapshot_->getTime(), runTime); |
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progressBar->update(); |
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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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needPotential = false; |
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needStress = false; |
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currStatus += statusTime; |
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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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} |
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void VelocityVerletIntegrator::finalize() { |
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dumpWriter->writeEor(); |
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void VelocityVerletIntegrator::finalize() { |
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dumpWriter->writeEor(); |
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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 statWriter; |
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delete dumpWriter; |
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delete statWriter; |
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dumpWriter = NULL; |
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statWriter = NULL; |
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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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void VelocityVerletIntegrator::integrateStep() { |
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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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moveA(); |
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calcForce(); |
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moveB(); |
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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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void VelocityVerletIntegrator::calcForce() { |
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forceMan_->calcForces(); |
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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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DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
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return new DumpWriter(info_); |
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} |
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StatWriter* VelocityVerletIntegrator::createStatWriter() { |
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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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StatsBitSet mask; |
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mask.set(Stats::TIME); |
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mask.set(Stats::TOTAL_ENERGY); |
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mask.set(Stats::POTENTIAL_ENERGY); |
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mask.set(Stats::KINETIC_ENERGY); |
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mask.set(Stats::TEMPERATURE); |
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mask.set(Stats::PRESSURE); |
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mask.set(Stats::CONSERVED_QUANTITY); |
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mask.set(Stats::VRAW); |
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mask.set(Stats::VHARM); |
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StatWriter* VelocityVerletIntegrator::createStatWriter() { |
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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 we're doing a thermodynamic integration, we'll want the raw |
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// potential as well as the full potential: |
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|
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|
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if (simParams->getUseThermodynamicIntegration()) |
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mask.set(Stats::VRAW); |
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|
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// if we've got restraints turned on, we'll also want a report of the |
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// total harmonic restraints |
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if (simParams->getUseRestraints()){ |
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mask.set(Stats::VHARM); |
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} |
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|
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if (simParams->havePrintPressureTensor() && |
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simParams->getPrintPressureTensor()){ |
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mask.set(Stats::PRESSURE_TENSOR_XX); |
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mask.set(Stats::PRESSURE_TENSOR_XY); |
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mask.set(Stats::PRESSURE_TENSOR_XZ); |
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mask.set(Stats::PRESSURE_TENSOR_YX); |
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mask.set(Stats::PRESSURE_TENSOR_YY); |
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mask.set(Stats::PRESSURE_TENSOR_YZ); |
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mask.set(Stats::PRESSURE_TENSOR_ZX); |
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mask.set(Stats::PRESSURE_TENSOR_ZY); |
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mask.set(Stats::PRESSURE_TENSOR_ZZ); |
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} |
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|
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> |
if (simParams->getAccumulateBoxDipole()) { |
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> |
mask.set(Stats::BOX_DIPOLE_X); |
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mask.set(Stats::BOX_DIPOLE_Y); |
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mask.set(Stats::BOX_DIPOLE_Z); |
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} |
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> |
|
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if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) { |
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if (simParams->getPrintTaggedPairDistance()) { |
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mask.set(Stats::TAGGED_PAIR_DISTANCE); |
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} |
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} |
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> |
|
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if (simParams->getUseRNEMD()) { |
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mask.set(Stats::RNEMD_EXCHANGE_TOTAL); |
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} |
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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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return new StatWriter(info_->getStatFileName()); |
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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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} //end namespace oopse |
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> |
} //end namespace OpenMD |
