| 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). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 67 |
|
SimInfo::MoleculeIterator i; |
| 68 |
|
Molecule::IntegrableObjectIterator j; |
| 69 |
|
Molecule* mol; |
| 70 |
< |
StuntDouble* integrableObject; |
| 70 |
> |
StuntDouble* sd; |
| 71 |
|
Vector3d vel; |
| 72 |
|
Vector3d pos; |
| 73 |
|
Vector3d frc; |
| 75 |
|
Vector3d ji; |
| 76 |
|
RealType mass; |
| 77 |
|
|
| 78 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 79 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 79 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 78 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 79 |
> |
mol = info_->nextMolecule(i)) { |
| 80 |
|
|
| 81 |
< |
vel =integrableObject->getVel(); |
| 82 |
< |
pos = integrableObject->getPos(); |
| 83 |
< |
frc = integrableObject->getFrc(); |
| 84 |
< |
mass = integrableObject->getMass(); |
| 81 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 82 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 83 |
> |
|
| 84 |
> |
vel = sd->getVel(); |
| 85 |
> |
pos = sd->getPos(); |
| 86 |
> |
frc = sd->getFrc(); |
| 87 |
> |
mass = sd->getMass(); |
| 88 |
|
|
| 89 |
|
// velocity half step |
| 90 |
|
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
| 92 |
|
// position whole step |
| 93 |
|
pos += dt * vel; |
| 94 |
|
|
| 95 |
< |
integrableObject->setVel(vel); |
| 96 |
< |
integrableObject->setPos(pos); |
| 95 |
> |
sd->setVel(vel); |
| 96 |
> |
sd->setPos(pos); |
| 97 |
|
|
| 98 |
< |
if (integrableObject->isDirectional()){ |
| 98 |
> |
if (sd->isDirectional()){ |
| 99 |
|
|
| 100 |
|
// get and convert the torque to body frame |
| 101 |
|
|
| 102 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 102 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 103 |
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|
| 104 |
|
// get the angular momentum, and propagate a half step |
| 105 |
|
|
| 106 |
< |
ji = integrableObject->getJ(); |
| 106 |
> |
ji = sd->getJ(); |
| 107 |
|
|
| 108 |
|
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
| 109 |
|
|
| 110 |
< |
rotAlgo->rotate(integrableObject, ji, dt); |
| 110 |
> |
rotAlgo_->rotate(sd, ji, dt); |
| 111 |
|
|
| 112 |
< |
integrableObject->setJ(ji); |
| 112 |
> |
sd->setJ(ji); |
| 113 |
|
} |
| 114 |
|
|
| 115 |
|
|
| 116 |
|
} |
| 117 |
|
} //end for(mol = info_->beginMolecule(i)) |
| 118 |
|
|
| 119 |
< |
rattle->constraintA(); |
| 120 |
< |
|
| 119 |
> |
flucQ_->moveA(); |
| 120 |
> |
rattle_->constraintA(); |
| 121 |
|
} |
| 122 |
|
|
| 123 |
|
void LangevinDynamics::moveB(){ |
| 124 |
|
SimInfo::MoleculeIterator i; |
| 125 |
|
Molecule::IntegrableObjectIterator j; |
| 126 |
|
Molecule* mol; |
| 127 |
< |
StuntDouble* integrableObject; |
| 127 |
> |
StuntDouble* sd; |
| 128 |
|
Vector3d vel; |
| 129 |
|
Vector3d frc; |
| 130 |
|
Vector3d Tb; |
| 131 |
|
Vector3d ji; |
| 132 |
|
RealType mass; |
| 133 |
|
|
| 134 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 135 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 133 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 134 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 135 |
> |
mol = info_->nextMolecule(i)) { |
| 136 |
|
|
| 137 |
< |
vel =integrableObject->getVel(); |
| 138 |
< |
frc = integrableObject->getFrc(); |
| 139 |
< |
mass = integrableObject->getMass(); |
| 137 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 138 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 139 |
> |
|
| 140 |
> |
vel = sd->getVel(); |
| 141 |
> |
frc = sd->getFrc(); |
| 142 |
> |
mass = sd->getMass(); |
| 143 |
|
|
| 144 |
|
// velocity half step |
| 145 |
|
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
| 146 |
|
|
| 147 |
< |
integrableObject->setVel(vel); |
| 147 |
> |
sd->setVel(vel); |
| 148 |
|
|
| 149 |
< |
if (integrableObject->isDirectional()){ |
| 149 |
> |
if (sd->isDirectional()){ |
| 150 |
|
|
| 151 |
|
// get and convert the torque to body frame |
| 152 |
|
|
| 153 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 153 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 154 |
|
|
| 155 |
|
// get the angular momentum, and propagate a half step |
| 156 |
|
|
| 157 |
< |
ji = integrableObject->getJ(); |
| 157 |
> |
ji = sd->getJ(); |
| 158 |
|
|
| 159 |
|
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
| 160 |
|
|
| 161 |
< |
integrableObject->setJ(ji); |
| 161 |
> |
sd->setJ(ji); |
| 162 |
|
} |
| 163 |
|
|
| 164 |
|
|
| 165 |
|
} |
| 166 |
|
} //end for(mol = info_->beginMolecule(i)) |
| 167 |
|
|
| 168 |
< |
|
| 169 |
< |
rattle->constraintB(); |
| 165 |
< |
|
| 168 |
> |
flucQ_->moveB(); |
| 169 |
> |
rattle_->constraintB(); |
| 170 |
|
} |
| 171 |
|
|
| 172 |
|
|
