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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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* non-exclusive, royalty free, license to use, modify and |
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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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* 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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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|
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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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#include "utils/StringUtils.hpp" |
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|
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namespace oopse { |
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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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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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forceMan_->init(); |
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|
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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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|
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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 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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//copy the current snapshot to previous snapshot |
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info_->getSnapshotManager()->advance(); |
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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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} |
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|
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dumpWriter = createDumpWriter(); |
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|
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statWriter = createStatWriter(); |
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|
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dumpWriter->writeDumpAndEor(); |
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|
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if (simParams->getUseSolidThermInt()) { |
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restWriter = createRestWriter(); |
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restWriter->writeZAngFile(); |
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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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currSample = sampleTime + 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_swapTime + 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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initialize(); |
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|
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while (currentSnapshot_->getTime() < runTime) { |
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|
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preStep(); |
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|
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integrateStep(); |
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|
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postStep(); |
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|
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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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|
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void VelocityVerletIntegrator::preStep() { |
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RealType 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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} |
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|
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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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|
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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 (useRNEMD) { |
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if (currentSnapshot_->getTime() >= currRNEMD) { |
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rnemd_->doSwap(); |
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currRNEMD += RNEMD_swapTime; |
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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->writeZAngFile(); |
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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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if (simParams->getUseRNEMD()) |
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rnemd_->getStatus(); |
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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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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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|
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if (simParams->getUseSolidThermInt()) { |
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restWriter->writeZAngFile(); |
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delete restWriter; |
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restWriter = NULL; |
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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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} |
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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(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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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_); |
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} |
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|
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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 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() && |
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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_SWAP_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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|
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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 |
