| 35 |
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* |
| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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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/LangevinHullForceManager.hpp" |
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namespace OpenMD { |
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|
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– |
|
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LangevinHullDynamics::LangevinHullDynamics(SimInfo* info) : VelocityVerletIntegrator(info){ |
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setForceManager(new LangevinHullForceManager(info)); |
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} |
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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)) { |
| 77 |
> |
|
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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 * PhysicalConstants::energyConvert) * frc; |
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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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// 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 * 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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} //end for(mol = info_->beginMolecule(i)) |
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|
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< |
rattle->constraintA(); |
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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 LangevinHullDynamics::moveB(){ |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
| 120 |
|
Molecule* mol; |
| 121 |
< |
StuntDouble* integrableObject; |
| 121 |
> |
StuntDouble* sd; |
| 122 |
|
Vector3d vel; |
| 123 |
|
Vector3d frc; |
| 124 |
|
Vector3d Tb; |
| 125 |
|
Vector3d ji; |
| 126 |
|
RealType mass; |
| 127 |
|
|
| 128 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 129 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 129 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 128 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 129 |
> |
mol = info_->nextMolecule(i)) { |
| 130 |
|
|
| 131 |
< |
vel =integrableObject->getVel(); |
| 132 |
< |
frc = integrableObject->getFrc(); |
| 133 |
< |
mass = integrableObject->getMass(); |
| 131 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 132 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 133 |
> |
|
| 134 |
> |
vel = sd->getVel(); |
| 135 |
> |
frc = sd->getFrc(); |
| 136 |
> |
mass = sd->getMass(); |
| 137 |
|
|
| 138 |
|
// velocity half step |
| 139 |
|
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
| 140 |
|
|
| 141 |
< |
integrableObject->setVel(vel); |
| 141 |
> |
sd->setVel(vel); |
| 142 |
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|
| 143 |
< |
if (integrableObject->isDirectional()){ |
| 143 |
> |
if (sd->isDirectional()){ |
| 144 |
|
|
| 145 |
|
// get and convert the torque to body frame |
| 146 |
|
|
| 147 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 147 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 148 |
|
|
| 149 |
|
// get the angular momentum, and propagate a half step |
| 150 |
|
|
| 151 |
< |
ji = integrableObject->getJ(); |
| 151 |
> |
ji = sd->getJ(); |
| 152 |
|
|
| 153 |
|
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
| 154 |
|
|
| 155 |
< |
integrableObject->setJ(ji); |
| 155 |
> |
sd->setJ(ji); |
| 156 |
|
} |
| 157 |
|
|
| 158 |
|
|
| 159 |
|
} |
| 160 |
|
} //end for(mol = info_->beginMolecule(i)) |
| 161 |
|
|
| 162 |
< |
|
| 163 |
< |
rattle->constraintB(); |
| 161 |
< |
|
| 162 |
> |
flucQ_->moveB(); |
| 163 |
> |
rattle_->constraintB(); |
| 164 |
|
} |
| 165 |
|
|
| 164 |
– |
|
| 166 |
|
RealType LangevinHullDynamics::calcConservedQuantity() { |
| 167 |
|
return 0.0; |
| 168 |
|
} |
