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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 |
| 12 |
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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)) |
| 17 |
< |
* |
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* 2. Redistributions of source code must retain the above copyright |
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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. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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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 |
| 14 |
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* documentation and/or other materials provided with the |
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* distribution. |
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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 |
| 30 |
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* such damages. |
| 31 |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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/** |
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* @file NVE.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/NVE.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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|
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namespace oopse { |
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namespace OpenMD { |
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|
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|
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NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){ |
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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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StuntDouble* sd; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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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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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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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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> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j)) { |
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> |
|
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> |
vel = sd->getVel(); |
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pos = sd->getPos(); |
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> |
frc = sd->getFrc(); |
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> |
mass = sd->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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> |
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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> |
sd->setVel(vel); |
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sd->setPos(pos); |
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|
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< |
if (integrableObject->isDirectional()){ |
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> |
if (sd->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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> |
Tb = sd->lab2Body(sd->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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> |
ji = sd->getJ(); |
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|
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< |
ji += (dt2 * OOPSEConstant::energyConvert) * Tb; |
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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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> |
rotAlgo_->rotate(sd, ji, dt); |
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|
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< |
integrableObject->setJ(ji); |
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> |
sd->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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> |
flucQ_->moveA(); |
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> |
rattle_->constraintA(); |
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} |
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|
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void NVE::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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> |
StuntDouble* sd; |
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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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> |
for (mol = info_->beginMolecule(i); mol != NULL; |
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> |
mol = info_->nextMolecule(i)) { |
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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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> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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> |
sd = mol->nextIntegrableObject(j)) { |
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> |
|
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> |
vel = sd->getVel(); |
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> |
frc = sd->getFrc(); |
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> |
mass = sd->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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> |
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
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|
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< |
integrableObject->setVel(vel); |
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> |
sd->setVel(vel); |
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|
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< |
if (integrableObject->isDirectional()){ |
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> |
if (sd->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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> |
Tb = sd->lab2Body(sd->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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> |
ji = sd->getJ(); |
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|
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< |
ji += (dt2 * OOPSEConstant::energyConvert) * Tb; |
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> |
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
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|
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< |
integrableObject->setJ(ji); |
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> |
sd->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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< |
|
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< |
rattle->constraintB(); |
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< |
|
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> |
flucQ_->moveB(); |
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> |
rattle_->constraintB(); |
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} |
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|
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|
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|
RealType NVE::calcConservedQuantity() { |
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< |
return thermo.getTotalE() ; |
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> |
return thermo.getTotalEnergy(); |
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} |
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|
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< |
} //end namespace oopse |
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> |
} //end namespace OpenMD |
