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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, 234107 (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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#include "integrators/NVT.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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|
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namespace oopse { |
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namespace OpenMD { |
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|
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NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) { |
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NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), maxIterNum_(4), |
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chiTolerance_(1e-6) { |
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|
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Globals* simParams = info_->getSimParams(); |
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|
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if (!simParams->getUseInitXSstate()) { |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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currSnapshot->setChi(0.0); |
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currSnapshot->setIntegralOfChiDt(0.0); |
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if (!simParams->getUseIntialExtendedSystemState()) { |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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snap->setThermostat(make_pair(0.0, 0.0)); |
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} |
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|
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if (!simParams->haveTargetTemp()) { |
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sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OOPSE_ERROR; |
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simError(); |
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sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OPENMD_ERROR; |
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simError(); |
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} else { |
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targetTemp_ = simParams->getTargetTemp(); |
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targetTemp_ = simParams->getTargetTemp(); |
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} |
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// We must set tauThermostat_. |
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// We must set tauThermostat. |
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|
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if (!simParams->haveTauThermostat()) { |
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sprintf(painCave.errMsg, "If you use the constant temperature\n" |
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"\tintegrator, you must set tauThermostat_.\n"); |
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sprintf(painCave.errMsg, "If you use the constant temperature\n" |
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"\tintegrator, you must set tauThermostat.\n"); |
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|
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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tauThermostat_ = simParams->getTauThermostat(); |
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tauThermostat_ = simParams->getTauThermostat(); |
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} |
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|
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update(); |
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} |
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updateSizes(); |
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} |
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|
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void NVT::doUpdate() { |
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void NVT::doUpdateSizes() { |
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oldVel_.resize(info_->getNIntegrableObjects()); |
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oldJi_.resize(info_->getNIntegrableObjects()); |
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} |
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void NVT::moveA() { |
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oldJi_.resize(info_->getNIntegrableObjects()); |
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} |
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|
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void NVT::moveA() { |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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StuntDouble* sd; |
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Vector3d Tb; |
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Vector3d ji; |
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double mass; |
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RealType mass; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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|
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double chi = currentSnapshot_->getChi(); |
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double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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|
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pair<RealType, RealType> thermostat = snap->getThermostat(); |
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|
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// We need the temperature at time = t for the chi update below: |
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double instTemp = thermo.getTemperature(); |
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RealType instTemp = thermo.getTemperature(); |
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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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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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vel = integrableObject->getVel(); |
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pos = integrableObject->getPos(); |
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frc = integrableObject->getFrc(); |
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for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j)) { |
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mass = integrableObject->getMass(); |
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vel = sd->getVel(); |
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pos = sd->getPos(); |
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frc = sd->getFrc(); |
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|
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// velocity half step (use chi from previous step here): |
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//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi); |
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vel += dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel; |
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mass = sd->getMass(); |
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|
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// velocity half step (use chi from previous step here): |
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vel += dt2 *PhysicalConstants::energyConvert/mass*frc |
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- dt2*thermostat.first*vel; |
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|
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// position whole step |
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//pos[j] += dt * vel[j]; |
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pos += dt * vel; |
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integrableObject->setVel(vel); |
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integrableObject->setPos(pos); |
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sd->setVel(vel); |
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sd->setPos(pos); |
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|
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if (integrableObject->isDirectional()) { |
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if (sd->isDirectional()) { |
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|
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//convert the torque to body frame |
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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//convert the torque to body frame |
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Tb = sd->lab2Body(sd->getTrq()); |
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|
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// get the angular momentum, and propagate a half step |
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// get the angular momentum, and propagate a half step |
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ji = integrableObject->getJ(); |
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ji = sd->getJ(); |
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|
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//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi); |
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ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji; |
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rotAlgo->rotate(integrableObject, ji, dt); |
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ji += dt2*PhysicalConstants::energyConvert*Tb |
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- dt2*thermostat.first *ji; |
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integrableObject->setJ(ji); |
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rotAlgo_->rotate(sd, ji, dt); |
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|
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sd->setJ(ji); |
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} |
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} |
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} |
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} |
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|
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rattle->constraintA(); |
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flucQ_->moveA(); |
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rattle_->constraintA(); |
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|
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// Finally, evolve chi a half step (just like a velocity) using |
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// temperature at time t, not time t+dt/2 |
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|
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chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
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integralOfChidt += chi * dt2; |
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thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0) |
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/ (tauThermostat_ * tauThermostat_); |
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thermostat.second += thermostat.first * dt2; |
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|
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currentSnapshot_->setChi(chi); |
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currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
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} |
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snap->setThermostat(thermostat); |
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} |
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|
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void NVT::moveB() { |
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> |
void NVT::moveB() { |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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StuntDouble* sd; |
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|
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Vector3d Tb; |
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Vector3d ji; |
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Vector3d vel; |
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Vector3d frc; |
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double mass; |
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double instTemp; |
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RealType mass; |
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RealType instTemp; |
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int index; |
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// Set things up for the iteration: |
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|
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< |
double chi = currentSnapshot_->getChi(); |
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double oldChi = chi; |
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double prevChi; |
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< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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> |
pair<RealType, RealType> thermostat = snap->getThermostat(); |
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RealType oldChi = thermostat.first; |
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RealType prevChi; |
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|
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index = 0; |
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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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oldVel_[index] = integrableObject->getVel(); |
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oldJi_[index] = integrableObject->getJ(); |
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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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|
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< |
++index; |
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} |
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|
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> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j)) { |
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> |
|
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oldVel_[index] = sd->getVel(); |
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> |
|
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> |
if (sd->isDirectional()) |
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> |
oldJi_[index] = sd->getJ(); |
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> |
|
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> |
++index; |
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> |
} |
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} |
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|
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// do the iteration: |
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|
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for(int k = 0; k < maxIterNum_; k++) { |
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< |
index = 0; |
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< |
instTemp = thermo.getTemperature(); |
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> |
index = 0; |
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> |
instTemp = thermo.getTemperature(); |
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|
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< |
// evolve chi another half step using the temperature at t + dt/2 |
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> |
// evolve chi another half step using the temperature at t + dt/2 |
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|
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< |
prevChi = chi; |
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< |
chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
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> |
prevChi = thermostat.first; |
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> |
thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) |
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> |
/ (tauThermostat_ * tauThermostat_); |
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|
|
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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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> |
for (mol = info_->beginMolecule(i); mol != NULL; |
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> |
mol = info_->nextMolecule(i)) { |
| 212 |
> |
|
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> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 214 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 215 |
|
|
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< |
frc = integrableObject->getFrc(); |
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< |
vel = integrableObject->getVel(); |
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> |
frc = sd->getFrc(); |
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> |
mass = sd->getMass(); |
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|
|
| 219 |
< |
mass = integrableObject->getMass(); |
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> |
// velocity half step |
| 220 |
|
|
| 221 |
< |
// velocity half step |
| 222 |
< |
//for(j = 0; j < 3; j++) |
| 223 |
< |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi); |
| 215 |
< |
vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index]; |
| 221 |
> |
vel = oldVel_[index] |
| 222 |
> |
+ dt2/mass*PhysicalConstants::energyConvert * frc |
| 223 |
> |
- dt2*thermostat.first*oldVel_[index]; |
| 224 |
|
|
| 225 |
< |
integrableObject->setVel(vel); |
| 225 |
> |
sd->setVel(vel); |
| 226 |
|
|
| 227 |
< |
if (integrableObject->isDirectional()) { |
| 227 |
> |
if (sd->isDirectional()) { |
| 228 |
|
|
| 229 |
< |
// get and convert the torque to body frame |
| 229 |
> |
// get and convert the torque to body frame |
| 230 |
|
|
| 231 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 231 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 232 |
|
|
| 233 |
< |
//for(j = 0; j < 3; j++) |
| 234 |
< |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi); |
| 227 |
< |
ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
| 233 |
> |
ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb |
| 234 |
> |
- dt2*thermostat.first *oldJi_[index]; |
| 235 |
|
|
| 236 |
< |
integrableObject->setJ(ji); |
| 237 |
< |
} |
| 236 |
> |
sd->setJ(ji); |
| 237 |
> |
} |
| 238 |
|
|
| 239 |
|
|
| 240 |
< |
++index; |
| 241 |
< |
} |
| 242 |
< |
} |
| 240 |
> |
++index; |
| 241 |
> |
} |
| 242 |
> |
} |
| 243 |
|
|
| 244 |
+ |
rattle_->constraintB(); |
| 245 |
|
|
| 246 |
< |
rattle->constraintB(); |
| 246 |
> |
if (fabs(prevChi - thermostat.first) <= chiTolerance_) |
| 247 |
> |
break; |
| 248 |
|
|
| 240 |
– |
if (fabs(prevChi - chi) <= chiTolerance_) |
| 241 |
– |
break; |
| 242 |
– |
|
| 249 |
|
} |
| 250 |
|
|
| 251 |
< |
integralOfChidt += dt2 * chi; |
| 251 |
> |
flucQ_->moveB(); |
| 252 |
|
|
| 253 |
< |
currentSnapshot_->setChi(chi); |
| 254 |
< |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 255 |
< |
} |
| 253 |
> |
thermostat.second += dt2 * thermostat.first; |
| 254 |
> |
snap->setThermostat(thermostat); |
| 255 |
> |
} |
| 256 |
|
|
| 257 |
+ |
void NVT::resetIntegrator() { |
| 258 |
+ |
snap->setThermostat(make_pair(0.0, 0.0)); |
| 259 |
+ |
} |
| 260 |
+ |
|
| 261 |
+ |
RealType NVT::calcConservedQuantity() { |
| 262 |
|
|
| 263 |
< |
double NVT::calcConservedQuantity() { |
| 264 |
< |
|
| 265 |
< |
double chi = currentSnapshot_->getChi(); |
| 266 |
< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 267 |
< |
double conservedQuantity; |
| 268 |
< |
double fkBT; |
| 258 |
< |
double Energy; |
| 259 |
< |
double thermostat_kinetic; |
| 260 |
< |
double thermostat_potential; |
| 263 |
> |
pair<RealType, RealType> thermostat = snap->getThermostat(); |
| 264 |
> |
RealType conservedQuantity; |
| 265 |
> |
RealType fkBT; |
| 266 |
> |
RealType Energy; |
| 267 |
> |
RealType thermostat_kinetic; |
| 268 |
> |
RealType thermostat_potential; |
| 269 |
|
|
| 270 |
< |
fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_; |
| 270 |
> |
fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_; |
| 271 |
|
|
| 272 |
< |
Energy = thermo.getTotalE(); |
| 272 |
> |
Energy = thermo.getTotalEnergy(); |
| 273 |
|
|
| 274 |
< |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
| 274 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert); |
| 275 |
|
|
| 276 |
< |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
| 276 |
> |
thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert; |
| 277 |
|
|
| 278 |
|
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 279 |
|
|
| 280 |
|
return conservedQuantity; |
| 281 |
< |
} |
| 281 |
> |
} |
| 282 |
|
|
| 283 |
|
|
| 284 |
< |
}//end namespace oopse |
| 284 |
> |
}//end namespace OpenMD |
