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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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#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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namespace oopse { |
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namespace OpenMD { |
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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), chiTolerance_ (1e-6), maxIterNum_(4) { |
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Globals* simParams = info_->getSimParams(); |
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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* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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currSnapshot->setChi(0.0); |
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currSnapshot->setIntegralOfChiDt(0.0); |
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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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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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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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update(); |
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} |
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} |
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void NVT::doUpdate() { |
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void NVT::doUpdate() { |
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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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} |
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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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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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double chi = currentSnapshot_->getChi(); |
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double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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RealType chi = currentSnapshot_->getChi(); |
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RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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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 (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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vel = integrableObject->getVel(); |
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pos = integrableObject->getPos(); |
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mass = integrableObject->getMass(); |
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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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//vel[j] += dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - vel[j]*chi); |
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vel += dt2 *PhysicalConstants::energyConvert/mass*frc - dt2*chi*vel; |
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// position whole step |
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//pos[j] += dt * vel[j]; |
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if (integrableObject->isDirectional()) { |
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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 = integrableObject->lab2Body(integrableObject->getTrq()); |
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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 = integrableObject->getJ(); |
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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[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi); |
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ji += dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *ji; |
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rotAlgo->rotate(integrableObject, ji, dt); |
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integrableObject->setJ(ji); |
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integrableObject->setJ(ji); |
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} |
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} |
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} |
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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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} |
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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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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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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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RealType chi = currentSnapshot_->getChi(); |
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RealType oldChi = chi; |
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RealType prevChi; |
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RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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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 (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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++index; |
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} |
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++index; |
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} |
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} |
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// do the iteration: |
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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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// 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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prevChi = chi; |
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chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
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prevChi = chi; |
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chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
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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; 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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frc = integrableObject->getFrc(); |
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vel = integrableObject->getVel(); |
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frc = integrableObject->getFrc(); |
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vel = integrableObject->getVel(); |
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mass = integrableObject->getMass(); |
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mass = integrableObject->getMass(); |
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// velocity half step |
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//for(j = 0; j < 3; j++) |
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// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi); |
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vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index]; |
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// velocity half step |
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//for(j = 0; j < 3; j++) |
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// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - oldVel_[3*i + j]*chi); |
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vel = oldVel_[index] + dt2/mass*PhysicalConstants::energyConvert * frc - dt2*chi*oldVel_[index]; |
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integrableObject->setVel(vel); |
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integrableObject->setVel(vel); |
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if (integrableObject->isDirectional()) { |
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if (integrableObject->isDirectional()) { |
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// get and convert the torque to body frame |
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// get and convert the torque to body frame |
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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|
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< |
//for(j = 0; j < 3; j++) |
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< |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi); |
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ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
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> |
//for(j = 0; j < 3; j++) |
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> |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi_[3*i+j]*chi); |
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ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *oldJi_[index]; |
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|
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integrableObject->setJ(ji); |
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} |
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integrableObject->setJ(ji); |
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} |
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++index; |
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} |
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} |
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++index; |
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} |
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> |
} |
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rattle->constraintB(); |
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> |
rattle->constraintB(); |
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< |
if (fabs(prevChi - chi) <= chiTolerance_) |
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break; |
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> |
if (fabs(prevChi - chi) <= chiTolerance_) |
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break; |
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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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> |
} |
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|
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void NVT::resetIntegrator() { |
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currentSnapshot_->setChi(0.0); |
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currentSnapshot_->setIntegralOfChiDt(0.0); |
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} |
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|
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RealType NVT::calcConservedQuantity() { |
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|
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< |
double NVT::calcConservedQuantity() { |
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< |
|
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< |
double chi = currentSnapshot_->getChi(); |
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< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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< |
double conservedQuantity; |
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< |
double fkBT; |
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< |
double Energy; |
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< |
double thermostat_kinetic; |
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< |
double thermostat_potential; |
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> |
RealType chi = currentSnapshot_->getChi(); |
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> |
RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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> |
RealType conservedQuantity; |
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> |
RealType fkBT; |
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> |
RealType Energy; |
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> |
RealType thermostat_kinetic; |
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> |
RealType thermostat_potential; |
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|
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< |
fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_; |
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> |
fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_; |
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|
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Energy = thermo.getTotalE(); |
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|
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< |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
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> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * PhysicalConstants::energyConvert); |
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|
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< |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
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> |
thermostat_potential = fkBT * integralOfChidt / PhysicalConstants::energyConvert; |
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|
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
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|
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return conservedQuantity; |
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< |
} |
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> |
} |
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|
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< |
}//end namespace oopse |
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> |
}//end namespace OpenMD |
