| 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, 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 |
|
*/ |
| 42 |
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|
| 43 |
|
/** |
| 44 |
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* @file LangevinDynamics.cpp |
| 45 |
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* @author tlin |
| 46 |
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* @date 11/08/2004 |
| 46 |
– |
* @time 15:13am |
| 47 |
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* @version 1.0 |
| 48 |
|
*/ |
| 49 |
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|
| 66 |
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SimInfo::MoleculeIterator i; |
| 67 |
|
Molecule::IntegrableObjectIterator j; |
| 68 |
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Molecule* mol; |
| 69 |
< |
StuntDouble* integrableObject; |
| 69 |
> |
StuntDouble* sd; |
| 70 |
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Vector3d vel; |
| 71 |
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Vector3d pos; |
| 72 |
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Vector3d frc; |
| 74 |
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Vector3d ji; |
| 75 |
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RealType mass; |
| 76 |
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|
| 77 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 78 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 79 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 77 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 78 |
> |
mol = info_->nextMolecule(i)) { |
| 79 |
|
|
| 80 |
< |
vel =integrableObject->getVel(); |
| 81 |
< |
pos = integrableObject->getPos(); |
| 82 |
< |
frc = integrableObject->getFrc(); |
| 83 |
< |
mass = integrableObject->getMass(); |
| 80 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 81 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 82 |
> |
|
| 83 |
> |
vel = sd->getVel(); |
| 84 |
> |
pos = sd->getPos(); |
| 85 |
> |
frc = sd->getFrc(); |
| 86 |
> |
mass = sd->getMass(); |
| 87 |
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|
| 88 |
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// velocity half step |
| 89 |
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vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
| 91 |
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// position whole step |
| 92 |
|
pos += dt * vel; |
| 93 |
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|
| 94 |
< |
integrableObject->setVel(vel); |
| 95 |
< |
integrableObject->setPos(pos); |
| 94 |
> |
sd->setVel(vel); |
| 95 |
> |
sd->setPos(pos); |
| 96 |
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|
| 97 |
< |
if (integrableObject->isDirectional()){ |
| 97 |
> |
if (sd->isDirectional()){ |
| 98 |
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|
| 99 |
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// get and convert the torque to body frame |
| 100 |
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|
| 101 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 101 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 102 |
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|
| 103 |
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// get the angular momentum, and propagate a half step |
| 104 |
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|
| 105 |
< |
ji = integrableObject->getJ(); |
| 105 |
> |
ji = sd->getJ(); |
| 106 |
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|
| 107 |
|
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
| 108 |
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|
| 109 |
< |
rotAlgo->rotate(integrableObject, ji, dt); |
| 109 |
> |
rotAlgo_->rotate(sd, ji, dt); |
| 110 |
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|
| 111 |
< |
integrableObject->setJ(ji); |
| 111 |
> |
sd->setJ(ji); |
| 112 |
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} |
| 113 |
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|
| 114 |
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|
| 115 |
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} |
| 116 |
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} //end for(mol = info_->beginMolecule(i)) |
| 117 |
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|
| 118 |
< |
rattle->constraintA(); |
| 119 |
< |
|
| 118 |
> |
flucQ_->moveA(); |
| 119 |
> |
rattle_->constraintA(); |
| 120 |
|
} |
| 121 |
|
|
| 122 |
|
void LangevinDynamics::moveB(){ |
| 123 |
|
SimInfo::MoleculeIterator i; |
| 124 |
|
Molecule::IntegrableObjectIterator j; |
| 125 |
|
Molecule* mol; |
| 126 |
< |
StuntDouble* integrableObject; |
| 126 |
> |
StuntDouble* sd; |
| 127 |
|
Vector3d vel; |
| 128 |
|
Vector3d frc; |
| 129 |
|
Vector3d Tb; |
| 130 |
|
Vector3d ji; |
| 131 |
|
RealType mass; |
| 132 |
|
|
| 133 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 134 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 133 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 133 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 134 |
> |
mol = info_->nextMolecule(i)) { |
| 135 |
|
|
| 136 |
< |
vel =integrableObject->getVel(); |
| 137 |
< |
frc = integrableObject->getFrc(); |
| 138 |
< |
mass = integrableObject->getMass(); |
| 136 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 137 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 138 |
> |
|
| 139 |
> |
vel = sd->getVel(); |
| 140 |
> |
frc = sd->getFrc(); |
| 141 |
> |
mass = sd->getMass(); |
| 142 |
|
|
| 143 |
|
// velocity half step |
| 144 |
|
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
| 145 |
|
|
| 146 |
< |
integrableObject->setVel(vel); |
| 146 |
> |
sd->setVel(vel); |
| 147 |
|
|
| 148 |
< |
if (integrableObject->isDirectional()){ |
| 148 |
> |
if (sd->isDirectional()){ |
| 149 |
|
|
| 150 |
|
// get and convert the torque to body frame |
| 151 |
|
|
| 152 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 152 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 153 |
|
|
| 154 |
|
// get the angular momentum, and propagate a half step |
| 155 |
|
|
| 156 |
< |
ji = integrableObject->getJ(); |
| 156 |
> |
ji = sd->getJ(); |
| 157 |
|
|
| 158 |
|
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
| 159 |
|
|
| 160 |
< |
integrableObject->setJ(ji); |
| 160 |
> |
sd->setJ(ji); |
| 161 |
|
} |
| 162 |
|
|
| 163 |
|
|
| 164 |
|
} |
| 165 |
|
} //end for(mol = info_->beginMolecule(i)) |
| 166 |
|
|
| 167 |
< |
|
| 168 |
< |
rattle->constraintB(); |
| 165 |
< |
|
| 167 |
> |
flucQ_->moveB(); |
| 168 |
> |
rattle_->constraintB(); |
| 169 |
|
} |
| 170 |
|
|
| 171 |
|
|
