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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. 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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* 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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* |
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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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* 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] Vardeman & Gezelter, in progress (2009). |
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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/PhysicalConstants.hpp" |
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#include "integrators/SMIPDForceManager.hpp" |
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namespace OpenMD { |
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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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|
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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 * PhysicalConstants::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 * PhysicalConstants::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 * PhysicalConstants::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 * PhysicalConstants::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 OpenMD |
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|
