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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), maxIterNum_(4) { |
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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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DoubleData * chiValue; |
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DoubleData * 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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|
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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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|
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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<DoubleData*>(data); |
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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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|
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data = info->getProperty(INTEGRALOFCHIDT_ID); |
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if(data){ |
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integralOfChidtValue = dynamic_cast<DoubleData*>(data); |
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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 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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} |
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// We must set tauThermostat_. |
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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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} |
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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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template<typename T> void NVT<T>::moveA() { |
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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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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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update(); |
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} |
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|
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double instTemp; |
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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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// We need the temperature at time = t for the chi update below: |
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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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instTemp = tStats->getTemperature(); |
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double instTemp = thermo.getTemperature(); |
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|
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for( i=0; i < integrableObjects.size(); i++ ){ |
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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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integrableObjects[i]->getVel( vel ); |
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integrableObjects[i]->getPos( pos ); |
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integrableObjects[i]->getFrc( frc ); |
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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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mass = integrableObjects[i]->getMass(); |
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mass = integrableObject->getMass(); |
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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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// 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]->setVel( vel ); |
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integrableObjects[i]->setPos( pos ); |
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integrableObject->setVel(vel); |
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integrableObject->setPos(pos); |
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|
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if( integrableObjects[i]->isDirectional() ){ |
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if (integrableObject->isDirectional()) { |
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|
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// get and convert the torque to body frame |
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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]->getTrq( Tb ); |
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integrableObjects[i]->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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|
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// get the angular momentum, and propagate a half step |
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ji = integrableObject->getJ(); |
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|
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integrableObjects[i]->getJ( ji ); |
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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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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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integrableObject->setJ(ji); |
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} |
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} |
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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 |
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// temperature at time t, not time t+dt/2 |
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|
|
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< |
//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n"; |
153 |
< |
|
154 |
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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 |
|
|
156 |
< |
} |
156 |
> |
currentSnapshot_->setChi(chi); |
157 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
158 |
> |
} |
159 |
|
|
160 |
< |
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; |
166 |
< |
double oldChi, prevChi; |
167 |
< |
|
168 |
< |
// Set things up for the iteration: |
169 |
< |
|
170 |
< |
oldChi = chi; |
171 |
< |
|
172 |
< |
for( i=0; i < integrableObjects.size(); i++ ){ |
173 |
< |
|
141 |
< |
integrableObjects[i]->getVel( vel ); |
142 |
< |
|
143 |
< |
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]; |
160 |
> |
void NVT::moveB() { |
161 |
> |
SimInfo::MoleculeIterator i; |
162 |
> |
Molecule::IntegrableObjectIterator j; |
163 |
> |
Molecule* mol; |
164 |
> |
StuntDouble* integrableObject; |
165 |
> |
|
166 |
> |
Vector3d Tb; |
167 |
> |
Vector3d ji; |
168 |
> |
Vector3d vel; |
169 |
> |
Vector3d frc; |
170 |
> |
double mass; |
171 |
> |
double instTemp; |
172 |
> |
int index; |
173 |
> |
// Set things up for the iteration: |
174 |
|
|
175 |
+ |
double chi = currentSnapshot_->getChi(); |
176 |
+ |
double oldChi = chi; |
177 |
+ |
double prevChi; |
178 |
+ |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
179 |
+ |
|
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(); |
186 |
+ |
|
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 ); |
233 |
> |
++index; |
234 |
> |
} |
235 |
|
} |
193 |
– |
} |
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; |
247 |
> |
currentSnapshot_->setChi(chi); |
248 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
249 |
|
} |
250 |
|
|
251 |
< |
// We must set tauThermostat. |
252 |
< |
|
253 |
< |
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; |
251 |
> |
void NVT::resetIntegrator() { |
252 |
> |
currentSnapshot_->setChi(0.0); |
253 |
> |
currentSnapshot_->setIntegralOfChiDt(0.0); |
254 |
|
} |
255 |
+ |
|
256 |
+ |
double NVT::calcConservedQuantity() { |
257 |
|
|
258 |
< |
if (!have_chi_tolerance) { |
259 |
< |
sprintf( painCave.errMsg, |
260 |
< |
"In NVT integrator: setting chi tolerance to 1e-6\n"); |
261 |
< |
chiTolerance = 1e-6; |
262 |
< |
have_chi_tolerance = 1; |
263 |
< |
painCave.severity = OOPSE_INFO; |
264 |
< |
painCave.isFatal = 0; |
265 |
< |
simError(); |
266 |
< |
} |
258 |
> |
double chi = currentSnapshot_->getChi(); |
259 |
> |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
260 |
> |
double conservedQuantity; |
261 |
> |
double fkBT; |
262 |
> |
double Energy; |
263 |
> |
double thermostat_kinetic; |
264 |
> |
double thermostat_potential; |
265 |
> |
|
266 |
> |
fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_; |
267 |
|
|
268 |
< |
return 1; |
268 |
> |
Energy = thermo.getTotalE(); |
269 |
|
|
270 |
< |
} |
270 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
271 |
|
|
272 |
< |
template<typename T> double NVT<T>::getConservedQuantity(void){ |
272 |
> |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
273 |
|
|
274 |
< |
double conservedQuantity; |
258 |
< |
double fkBT; |
259 |
< |
double Energy; |
260 |
< |
double thermostat_kinetic; |
261 |
< |
double thermostat_potential; |
274 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
275 |
|
|
276 |
< |
fkBT = (double)(info->ndf) * kB * targetTemp; |
276 |
> |
return conservedQuantity; |
277 |
> |
} |
278 |
|
|
265 |
– |
Energy = tStats->getTotalE(); |
279 |
|
|
280 |
< |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
268 |
< |
(2.0 * eConvert); |
269 |
< |
|
270 |
< |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
271 |
< |
|
272 |
< |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
273 |
< |
|
274 |
< |
return conservedQuantity; |
275 |
< |
} |
276 |
< |
|
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]; |
281 |
< |
|
282 |
< |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
283 |
< |
parameters += buffer; |
284 |
< |
|
285 |
< |
return parameters; |
286 |
< |
} |
280 |
> |
}//end namespace oopse |