--- trunk/src/integrators/NVE.cpp 2005/01/12 22:41:40 246 +++ trunk/src/integrators/NVE.cpp 2009/11/25 20:02:06 1390 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,28 +28,37 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ - /** - * @file NVE.cpp - * @author tlin - * @date 11/08/2004 - * @time 15:13am - * @version 1.0 - */ +/** + * @file NVE.cpp + * @author tlin + * @date 11/08/2004 + * @time 15:13am + * @version 1.0 + */ #include "integrators/NVE.hpp" #include "primitives/Molecule.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" -namespace oopse { +namespace OpenMD { -NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){ + NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){ -} + } -void NVE::moveA(){ + void NVE::moveA(){ SimInfo::MoleculeIterator i; Molecule::IntegrableObjectIterator j; Molecule* mol; @@ -68,52 +68,52 @@ void NVE::moveA(){ Vector3d frc; Vector3d Tb; Vector3d ji; - double mass; + RealType mass; for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { - for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(j)) { + for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(j)) { - vel =integrableObject->getVel(); - pos = integrableObject->getPos(); - frc = integrableObject->getFrc(); - mass = integrableObject->getMass(); + vel =integrableObject->getVel(); + pos = integrableObject->getPos(); + frc = integrableObject->getFrc(); + mass = integrableObject->getMass(); - // velocity half step - vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc; + // velocity half step + vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; - // position whole step - pos += dt * vel; + // position whole step + pos += dt * vel; - integrableObject->setVel(vel); - integrableObject->setPos(pos); + integrableObject->setVel(vel); + integrableObject->setPos(pos); - if (integrableObject->isDirectional()){ + if (integrableObject->isDirectional()){ - // get and convert the torque to body frame + // get and convert the torque to body frame - Tb = integrableObject->lab2Body(integrableObject->getTrq()); + Tb = integrableObject->lab2Body(integrableObject->getTrq()); - // get the angular momentum, and propagate a half step + // get the angular momentum, and propagate a half step - ji = integrableObject->getJ(); + ji = integrableObject->getJ(); - ji += (dt2 * OOPSEConstant::energyConvert) * Tb; + ji += (dt2 * PhysicalConstants::energyConvert) * Tb; - rotAlgo->rotate(integrableObject, ji, dt); + rotAlgo->rotate(integrableObject, ji, dt); - integrableObject->setJ(ji); - } + integrableObject->setJ(ji); + } - } + } } //end for(mol = info_->beginMolecule(i)) rattle->constraintA(); -} + } -void NVE::moveB(){ + void NVE::moveB(){ SimInfo::MoleculeIterator i; Molecule::IntegrableObjectIterator j; Molecule* mol; @@ -122,48 +122,48 @@ void NVE::moveB(){ Vector3d frc; Vector3d Tb; Vector3d ji; - double mass; + RealType mass; for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { - for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(j)) { + for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(j)) { - vel =integrableObject->getVel(); - frc = integrableObject->getFrc(); - mass = integrableObject->getMass(); + vel =integrableObject->getVel(); + frc = integrableObject->getFrc(); + mass = integrableObject->getMass(); - // velocity half step - vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc; + // velocity half step + vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; - integrableObject->setVel(vel); + integrableObject->setVel(vel); - if (integrableObject->isDirectional()){ + if (integrableObject->isDirectional()){ - // get and convert the torque to body frame + // get and convert the torque to body frame - Tb = integrableObject->lab2Body(integrableObject->getTrq()); + Tb = integrableObject->lab2Body(integrableObject->getTrq()); - // get the angular momentum, and propagate a half step + // get the angular momentum, and propagate a half step - ji = integrableObject->getJ(); + ji = integrableObject->getJ(); - ji += (dt2 * OOPSEConstant::energyConvert) * Tb; + ji += (dt2 * PhysicalConstants::energyConvert) * Tb; - integrableObject->setJ(ji); - } + integrableObject->setJ(ji); + } - } + } } //end for(mol = info_->beginMolecule(i)) rattle->constraintB(); -} + } -double NVE::calcConservedQuantity() { - return thermo.getTotalE(); -} + RealType NVE::calcConservedQuantity() { + return thermo.getTotalE() ; + } -} //end namespace oopse +} //end namespace OpenMD