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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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/** |
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* @file LangevinDynamics.cpp |
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* @author tlin |
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* @date 11/08/2004 |
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* @time 15:13am |
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* @version 1.0 |
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*/ |
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|
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#include "integrators/SMIPDynamics.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "integrators/SMIPDForceManager.hpp" |
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namespace oopse { |
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|
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|
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SMIPDynamics::SMIPDynamics(SimInfo* info) : VelocityVerletIntegrator(info){ |
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setForceManager(new SMIPDForceManager(info)); |
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|
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// Langevin Dynamics Force Manager needs to know about the half-time step |
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// size to get convergence on the friction forces: |
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dynamic_cast<SMIPDForceManager*>(forceMan_)->setDt2(dt2); |
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|
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} |
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|
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void SMIPDynamics::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 vel; |
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Vector3d pos; |
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Vector3d frc; |
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Vector3d Tb; |
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Vector3d ji; |
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RealType mass; |
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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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|
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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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mass = integrableObject->getMass(); |
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|
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// velocity half step |
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vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc; |
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|
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// position whole step |
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pos += dt * vel; |
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|
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integrableObject->setVel(vel); |
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integrableObject->setPos(pos); |
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|
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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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|
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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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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ji = integrableObject->getJ(); |
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|
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ji += (dt2 * OOPSEConstant::energyConvert) * Tb; |
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|
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rotAlgo->rotate(integrableObject, ji, dt); |
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|
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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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} //end for(mol = info_->beginMolecule(i)) |
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|
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rattle->constraintA(); |
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|
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} |
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|
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void SMIPDynamics::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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Vector3d vel; |
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Vector3d frc; |
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Vector3d Tb; |
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Vector3d ji; |
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RealType mass; |
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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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|
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vel =integrableObject->getVel(); |
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frc = integrableObject->getFrc(); |
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mass = integrableObject->getMass(); |
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|
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// velocity half step |
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vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc; |
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|
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integrableObject->setVel(vel); |
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|
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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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|
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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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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ji = integrableObject->getJ(); |
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|
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ji += (dt2 * OOPSEConstant::energyConvert) * Tb; |
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|
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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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} //end for(mol = info_->beginMolecule(i)) |
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|
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|
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rattle->constraintB(); |
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|
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} |
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|
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|
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RealType SMIPDynamics::calcConservedQuantity() { |
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return 0.0; |
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} |
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|
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} //end namespace oopse |
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|
