--- trunk/src/integrators/LangevinDynamics.cpp 2008/04/18 16:55:15 1237 +++ trunk/src/integrators/LangevinDynamics.cpp 2013/06/16 15:15:42 1879 @@ -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. @@ -37,21 +28,30 @@ * 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, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ /** * @file LangevinDynamics.cpp * @author tlin * @date 11/08/2004 - * @time 15:13am * @version 1.0 */ #include "integrators/LangevinDynamics.hpp" #include "primitives/Molecule.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" #include "integrators/LDForceManager.hpp" -namespace oopse { +namespace OpenMD { LangevinDynamics::LangevinDynamics(SimInfo* info) : VelocityVerletIntegrator(info){ @@ -66,7 +66,7 @@ namespace oopse { SimInfo::MoleculeIterator i; Molecule::IntegrableObjectIterator j; Molecule* mol; - StuntDouble* integrableObject; + StuntDouble* sd; Vector3d vel; Vector3d pos; Vector3d frc; @@ -74,95 +74,98 @@ namespace oopse { Vector3d ji; 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 (mol = info_->beginMolecule(i); mol != NULL; + mol = info_->nextMolecule(i)) { - vel =integrableObject->getVel(); - pos = integrableObject->getPos(); - frc = integrableObject->getFrc(); - mass = integrableObject->getMass(); + for (sd = mol->beginIntegrableObject(j); sd != NULL; + sd = mol->nextIntegrableObject(j)) { + + vel = sd->getVel(); + pos = sd->getPos(); + frc = sd->getFrc(); + mass = sd->getMass(); // velocity half step - vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc; + vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; // position whole step pos += dt * vel; - integrableObject->setVel(vel); - integrableObject->setPos(pos); + sd->setVel(vel); + sd->setPos(pos); - if (integrableObject->isDirectional()){ + if (sd->isDirectional()){ // get and convert the torque to body frame - Tb = integrableObject->lab2Body(integrableObject->getTrq()); + Tb = sd->lab2Body(sd->getTrq()); // get the angular momentum, and propagate a half step - ji = integrableObject->getJ(); + ji = sd->getJ(); - ji += (dt2 * OOPSEConstant::energyConvert) * Tb; + ji += (dt2 * PhysicalConstants::energyConvert) * Tb; - rotAlgo->rotate(integrableObject, ji, dt); + rotAlgo_->rotate(sd, ji, dt); - integrableObject->setJ(ji); + sd->setJ(ji); } } } //end for(mol = info_->beginMolecule(i)) - rattle->constraintA(); - + flucQ_->moveA(); + rattle_->constraintA(); } void LangevinDynamics::moveB(){ SimInfo::MoleculeIterator i; Molecule::IntegrableObjectIterator j; Molecule* mol; - StuntDouble* integrableObject; + StuntDouble* sd; Vector3d vel; Vector3d frc; Vector3d Tb; Vector3d ji; 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 (mol = info_->beginMolecule(i); mol != NULL; + mol = info_->nextMolecule(i)) { - vel =integrableObject->getVel(); - frc = integrableObject->getFrc(); - mass = integrableObject->getMass(); + for (sd = mol->beginIntegrableObject(j); sd != NULL; + sd = mol->nextIntegrableObject(j)) { + + vel = sd->getVel(); + frc = sd->getFrc(); + mass = sd->getMass(); // velocity half step - vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc; + vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; - integrableObject->setVel(vel); + sd->setVel(vel); - if (integrableObject->isDirectional()){ + if (sd->isDirectional()){ // get and convert the torque to body frame - Tb = integrableObject->lab2Body(integrableObject->getTrq()); + Tb = sd->lab2Body(sd->getTrq()); // get the angular momentum, and propagate a half step - ji = integrableObject->getJ(); + ji = sd->getJ(); - ji += (dt2 * OOPSEConstant::energyConvert) * Tb; + ji += (dt2 * PhysicalConstants::energyConvert) * Tb; - integrableObject->setJ(ji); + sd->setJ(ji); } } } //end for(mol = info_->beginMolecule(i)) - - rattle->constraintB(); - + flucQ_->moveB(); + rattle_->constraintB(); } @@ -170,5 +173,5 @@ namespace oopse { return 0.0; } -} //end namespace oopse +} //end namespace OpenMD