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#include <math.h> |
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|
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#include "primitives/Atom.hpp" |
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#include "primitives/SRI.hpp" |
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#include "primitives/AbstractClasses.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "UseTheForce/ForceFields.hpp" |
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#include "brains/Thermo.hpp" |
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#include "io/ReadWrite.hpp" |
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#include "integrators/Integrator.hpp" |
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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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#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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|
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namespace oopse { |
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|
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// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) { |
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|
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template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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GenericData* data; |
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DoubleGenericData * chiValue; |
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DoubleGenericData * integralOfChidtValue; |
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> |
Globals* simParams = info_->getSimParams(); |
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|
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chiValue = NULL; |
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integralOfChidtValue = NULL; |
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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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} |
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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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} else { |
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targetTemp_ = simParams->getTargetTemp(); |
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} |
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|
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chi = 0.0; |
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have_tau_thermostat = 0; |
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have_target_temp = 0; |
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have_chi_tolerance = 0; |
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integralOfChidt = 0.0; |
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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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|
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if( theInfo->useInitXSstate ){ |
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|
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// retrieve chi and integralOfChidt from simInfo |
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data = info->getProperty(CHIVALUE_ID); |
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if(data){ |
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chiValue = dynamic_cast<DoubleGenericData*>(data); |
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painCave.severity = OOPSE_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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} |
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|
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data = info->getProperty(INTEGRALOFCHIDT_ID); |
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if(data){ |
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integralOfChidtValue = dynamic_cast<DoubleGenericData*>(data); |
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} |
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|
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// chi and integralOfChidt should appear by pair |
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if(chiValue && integralOfChidtValue){ |
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chi = chiValue->getData(); |
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integralOfChidt = integralOfChidtValue->getData(); |
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} |
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} |
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|
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oldVel = new double[3*integrableObjects.size()]; |
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oldJi = new double[3*integrableObjects.size()]; |
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update(); |
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} |
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|
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template<typename T> NVT<T>::~NVT() { |
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delete[] oldVel; |
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delete[] oldJi; |
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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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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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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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|
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template<typename T> void NVT<T>::moveA() { |
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double chi = currentSnapshot_->getChi(); |
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double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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|
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// We need the temperature at time = t for the chi update below: |
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|
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int i, j; |
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DirectionalAtom* dAtom; |
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double Tb[3], ji[3]; |
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double mass; |
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< |
double vel[3], pos[3], frc[3]; |
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> |
double instTemp = thermo.getTemperature(); |
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|
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double instTemp; |
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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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|
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// We need the temperature at time = t for the chi update below: |
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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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|
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instTemp = tStats->getTemperature(); |
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mass = integrableObject->getMass(); |
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|
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for( i=0; i < integrableObjects.size(); i++ ){ |
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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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> |
|
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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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|
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< |
integrableObjects[i]->getVel( vel ); |
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integrableObjects[i]->getPos( pos ); |
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integrableObjects[i]->getFrc( frc ); |
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integrableObject->setVel(vel); |
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integrableObject->setPos(pos); |
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|
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mass = integrableObjects[i]->getMass(); |
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if (integrableObject->isDirectional()) { |
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|
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for (j=0; j < 3; j++) { |
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// velocity half step (use chi from previous step here): |
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vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi); |
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// position whole step |
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pos[j] += dt * vel[j]; |
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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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|
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integrableObjects[i]->setVel( vel ); |
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integrableObjects[i]->setPos( pos ); |
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// get the angular momentum, and propagate a half step |
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|
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if( integrableObjects[i]->isDirectional() ){ |
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> |
ji = integrableObject->getJ(); |
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|
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// get and convert the torque to body frame |
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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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|
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integrableObjects[i]->getTrq( Tb ); |
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integrableObjects[i]->lab2Body( Tb ); |
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> |
integrableObject->setJ(ji); |
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> |
} |
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} |
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|
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// get the angular momentum, and propagate a half step |
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|
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integrableObjects[i]->getJ( ji ); |
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|
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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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|
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this->rotationPropagation( integrableObjects[i], ji ); |
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|
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integrableObjects[i]->setJ( ji ); |
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|
} |
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< |
} |
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< |
|
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if(nConstrained) |
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< |
constrainA(); |
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> |
|
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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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> |
// Finally, evolve chi a half step (just like a velocity) using |
| 150 |
> |
// temperature at time t, not time t+dt/2 |
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|
|
| 152 |
< |
//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n"; |
| 153 |
< |
|
| 154 |
< |
chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
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< |
integralOfChidt += chi*dt2; |
| 152 |
> |
|
| 153 |
> |
chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
| 154 |
> |
integralOfChidt += chi * dt2; |
| 155 |
|
|
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+ |
currentSnapshot_->setChi(chi); |
| 157 |
+ |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
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|
} |
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|
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< |
template<typename T> void NVT<T>::moveB( void ){ |
| 161 |
< |
int i, j, k; |
| 162 |
< |
double Tb[3], ji[3]; |
| 163 |
< |
double vel[3], frc[3]; |
| 164 |
< |
double mass; |
| 165 |
< |
double instTemp; |
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< |
double oldChi, prevChi; |
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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; |
| 165 |
> |
|
| 166 |
> |
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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> |
int index; |
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> |
// Set things up for the iteration: |
| 174 |
|
|
| 175 |
< |
// Set things up for the iteration: |
| 176 |
< |
|
| 177 |
< |
oldChi = chi; |
| 175 |
> |
double chi = currentSnapshot_->getChi(); |
| 176 |
> |
double oldChi = chi; |
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> |
double prevChi; |
| 178 |
> |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 179 |
|
|
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< |
for( i=0; i < integrableObjects.size(); i++ ){ |
| 180 |
> |
index = 0; |
| 181 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 182 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 183 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 184 |
> |
oldVel_[index] = integrableObject->getVel(); |
| 185 |
> |
oldJi_[index] = integrableObject->getJ(); |
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|
|
| 187 |
< |
integrableObjects[i]->getVel( vel ); |
| 188 |
< |
|
| 189 |
< |
for (j=0; j < 3; j++) |
| 144 |
< |
oldVel[3*i + j] = vel[j]; |
| 145 |
< |
|
| 146 |
< |
if( integrableObjects[i]->isDirectional() ){ |
| 147 |
< |
|
| 148 |
< |
integrableObjects[i]->getJ( ji ); |
| 149 |
< |
|
| 150 |
< |
for (j=0; j < 3; j++) |
| 151 |
< |
oldJi[3*i + j] = ji[j]; |
| 152 |
< |
|
| 187 |
> |
++index; |
| 188 |
> |
} |
| 189 |
> |
|
| 190 |
|
} |
| 154 |
– |
} |
| 191 |
|
|
| 192 |
< |
// do the iteration: |
| 192 |
> |
// do the iteration: |
| 193 |
|
|
| 194 |
< |
for (k=0; k < 4; k++) { |
| 194 |
> |
for(int k = 0; k < maxIterNum_; k++) { |
| 195 |
> |
index = 0; |
| 196 |
> |
instTemp = thermo.getTemperature(); |
| 197 |
|
|
| 198 |
< |
instTemp = tStats->getTemperature(); |
| 198 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
| 199 |
|
|
| 200 |
< |
// evolve chi another half step using the temperature at t + dt/2 |
| 200 |
> |
prevChi = chi; |
| 201 |
> |
chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
| 202 |
|
|
| 203 |
< |
prevChi = chi; |
| 204 |
< |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
| 205 |
< |
(tauThermostat*tauThermostat); |
| 203 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 204 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 205 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 206 |
|
|
| 207 |
< |
for( i=0; i < integrableObjects.size(); i++ ){ |
| 207 |
> |
frc = integrableObject->getFrc(); |
| 208 |
> |
vel = integrableObject->getVel(); |
| 209 |
|
|
| 210 |
< |
integrableObjects[i]->getFrc( frc ); |
| 171 |
< |
integrableObjects[i]->getVel(vel); |
| 210 |
> |
mass = integrableObject->getMass(); |
| 211 |
|
|
| 212 |
< |
mass = integrableObjects[i]->getMass(); |
| 212 |
> |
// velocity half step |
| 213 |
> |
//for(j = 0; j < 3; j++) |
| 214 |
> |
// 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]; |
| 216 |
> |
|
| 217 |
> |
integrableObject->setVel(vel); |
| 218 |
|
|
| 219 |
< |
// velocity half step |
| 176 |
< |
for (j=0; j < 3; j++) |
| 177 |
< |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi); |
| 219 |
> |
if (integrableObject->isDirectional()) { |
| 220 |
|
|
| 221 |
< |
integrableObjects[i]->setVel( vel ); |
| 221 |
> |
// get and convert the torque to body frame |
| 222 |
|
|
| 223 |
< |
if( integrableObjects[i]->isDirectional() ){ |
| 223 |
> |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 224 |
|
|
| 225 |
< |
// get and convert the torque to body frame |
| 225 |
> |
//for(j = 0; j < 3; j++) |
| 226 |
> |
// 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]; |
| 228 |
|
|
| 229 |
< |
integrableObjects[i]->getTrq( Tb ); |
| 230 |
< |
integrableObjects[i]->lab2Body( Tb ); |
| 229 |
> |
integrableObject->setJ(ji); |
| 230 |
> |
} |
| 231 |
|
|
| 188 |
– |
for (j=0; j < 3; j++) |
| 189 |
– |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 232 |
|
|
| 233 |
< |
integrableObjects[i]->setJ( ji ); |
| 234 |
< |
} |
| 235 |
< |
} |
| 233 |
> |
++index; |
| 234 |
> |
} |
| 235 |
> |
} |
| 236 |
|
|
| 195 |
– |
if(nConstrained) |
| 196 |
– |
constrainB(); |
| 237 |
|
|
| 238 |
< |
if (fabs(prevChi - chi) <= chiTolerance) break; |
| 199 |
< |
} |
| 238 |
> |
rattle->constraintB(); |
| 239 |
|
|
| 240 |
< |
integralOfChidt += dt2*chi; |
| 241 |
< |
} |
| 240 |
> |
if (fabs(prevChi - chi) <= chiTolerance_) |
| 241 |
> |
break; |
| 242 |
|
|
| 243 |
< |
template<typename T> void NVT<T>::resetIntegrator( void ){ |
| 243 |
> |
} |
| 244 |
|
|
| 245 |
< |
chi = 0.0; |
| 207 |
< |
integralOfChidt = 0.0; |
| 208 |
< |
} |
| 245 |
> |
integralOfChidt += dt2 * chi; |
| 246 |
|
|
| 247 |
< |
template<typename T> int NVT<T>::readyCheck() { |
| 248 |
< |
|
| 212 |
< |
//check parent's readyCheck() first |
| 213 |
< |
if (T::readyCheck() == -1) |
| 214 |
< |
return -1; |
| 215 |
< |
|
| 216 |
< |
// First check to see if we have a target temperature. |
| 217 |
< |
// Not having one is fatal. |
| 218 |
< |
|
| 219 |
< |
if (!have_target_temp) { |
| 220 |
< |
sprintf( painCave.errMsg, |
| 221 |
< |
"You can't use the NVT integrator without a targetTemp!\n" |
| 222 |
< |
); |
| 223 |
< |
painCave.isFatal = 1; |
| 224 |
< |
painCave.severity = OOPSE_ERROR; |
| 225 |
< |
simError(); |
| 226 |
< |
return -1; |
| 227 |
< |
} |
| 228 |
< |
|
| 229 |
< |
// We must set tauThermostat. |
| 230 |
< |
|
| 231 |
< |
if (!have_tau_thermostat) { |
| 232 |
< |
sprintf( painCave.errMsg, |
| 233 |
< |
"If you use the constant temperature\n" |
| 234 |
< |
"\tintegrator, you must set tauThermostat.\n"); |
| 235 |
< |
painCave.severity = OOPSE_ERROR; |
| 236 |
< |
painCave.isFatal = 1; |
| 237 |
< |
simError(); |
| 238 |
< |
return -1; |
| 239 |
< |
} |
| 240 |
< |
|
| 241 |
< |
if (!have_chi_tolerance) { |
| 242 |
< |
sprintf( painCave.errMsg, |
| 243 |
< |
"In NVT integrator: setting chi tolerance to 1e-6\n"); |
| 244 |
< |
chiTolerance = 1e-6; |
| 245 |
< |
have_chi_tolerance = 1; |
| 246 |
< |
painCave.severity = OOPSE_INFO; |
| 247 |
< |
painCave.isFatal = 0; |
| 248 |
< |
simError(); |
| 249 |
< |
} |
| 250 |
< |
|
| 251 |
< |
return 1; |
| 252 |
< |
|
| 247 |
> |
currentSnapshot_->setChi(chi); |
| 248 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 249 |
|
} |
| 250 |
|
|
| 255 |
– |
template<typename T> double NVT<T>::getConservedQuantity(void){ |
| 251 |
|
|
| 252 |
< |
double conservedQuantity; |
| 258 |
< |
double fkBT; |
| 259 |
< |
double Energy; |
| 260 |
< |
double thermostat_kinetic; |
| 261 |
< |
double thermostat_potential; |
| 252 |
> |
double NVT::calcConservedQuantity() { |
| 253 |
|
|
| 254 |
< |
fkBT = (double)(info->ndf) * kB * targetTemp; |
| 254 |
> |
double chi = currentSnapshot_->getChi(); |
| 255 |
> |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 256 |
> |
double conservedQuantity; |
| 257 |
> |
double fkBT; |
| 258 |
> |
double Energy; |
| 259 |
> |
double thermostat_kinetic; |
| 260 |
> |
double thermostat_potential; |
| 261 |
> |
|
| 262 |
> |
fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_; |
| 263 |
|
|
| 264 |
< |
Energy = tStats->getTotalE(); |
| 264 |
> |
Energy = thermo.getTotalE(); |
| 265 |
|
|
| 266 |
< |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 268 |
< |
(2.0 * eConvert); |
| 266 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
| 267 |
|
|
| 268 |
< |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
| 268 |
> |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
| 269 |
|
|
| 270 |
< |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 270 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 271 |
|
|
| 272 |
< |
return conservedQuantity; |
| 272 |
> |
return conservedQuantity; |
| 273 |
|
} |
| 274 |
|
|
| 277 |
– |
template<typename T> string NVT<T>::getAdditionalParameters(void){ |
| 278 |
– |
string parameters; |
| 279 |
– |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 280 |
– |
char buffer[BUFFERSIZE]; |
| 275 |
|
|
| 276 |
< |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 283 |
< |
parameters += buffer; |
| 284 |
< |
|
| 285 |
< |
return parameters; |
| 286 |
< |
} |
| 276 |
> |
}//end namespace oopse |
