| 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). |
| 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 |
|
*/ |
| 95 |
|
std::map<std::string, HydroProp*> hydroPropMap; |
| 96 |
|
|
| 97 |
|
Molecule* mol; |
| 98 |
< |
StuntDouble* integrableObject; |
| 98 |
> |
StuntDouble* sd; |
| 99 |
|
SimInfo::MoleculeIterator i; |
| 100 |
|
Molecule::IntegrableObjectIterator j; |
| 101 |
|
bool needHydroPropFile = false; |
| 102 |
|
|
| 103 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
| 104 |
|
mol = info->nextMolecule(i)) { |
| 105 |
< |
for (integrableObject = mol->beginIntegrableObject(j); |
| 106 |
< |
integrableObject != NULL; |
| 107 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 105 |
> |
|
| 106 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 107 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 108 |
|
|
| 109 |
< |
if (integrableObject->isRigidBody()) { |
| 110 |
< |
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 109 |
> |
if (sd->isRigidBody()) { |
| 110 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 111 |
|
if (rb->getNumAtoms() > 1) needHydroPropFile = true; |
| 112 |
|
} |
| 113 |
|
|
| 130 |
|
|
| 131 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
| 132 |
|
mol = info->nextMolecule(i)) { |
| 133 |
– |
for (integrableObject = mol->beginIntegrableObject(j); |
| 134 |
– |
integrableObject != NULL; |
| 135 |
– |
integrableObject = mol->nextIntegrableObject(j)) { |
| 133 |
|
|
| 134 |
< |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 134 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 135 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 136 |
> |
|
| 137 |
> |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType()); |
| 138 |
|
if (iter != hydroPropMap.end()) { |
| 139 |
|
hydroProps_.push_back(iter->second); |
| 140 |
|
} else { |
| 141 |
|
sprintf( painCave.errMsg, |
| 142 |
< |
"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str()); |
| 142 |
> |
"Can not find resistance tensor for atom [%s]\n", sd->getType().c_str()); |
| 143 |
|
painCave.severity = OPENMD_ERROR; |
| 144 |
|
painCave.isFatal = 1; |
| 145 |
|
simError(); |
| 151 |
|
std::map<std::string, HydroProp*> hydroPropMap; |
| 152 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
| 153 |
|
mol = info->nextMolecule(i)) { |
| 154 |
< |
for (integrableObject = mol->beginIntegrableObject(j); |
| 155 |
< |
integrableObject != NULL; |
| 156 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 154 |
> |
|
| 155 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 156 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 157 |
> |
|
| 158 |
|
Shape* currShape = NULL; |
| 159 |
|
|
| 160 |
< |
if (integrableObject->isAtom()){ |
| 161 |
< |
Atom* atom = static_cast<Atom*>(integrableObject); |
| 160 |
> |
if (sd->isAtom()){ |
| 161 |
> |
Atom* atom = static_cast<Atom*>(sd); |
| 162 |
|
AtomType* atomType = atom->getAtomType(); |
| 163 |
|
GayBerneAdapter gba = GayBerneAdapter(atomType); |
| 164 |
|
if (gba.isGayBerne()) { |
| 200 |
|
|
| 201 |
|
|
| 202 |
|
HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp()); |
| 203 |
< |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 203 |
> |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType()); |
| 204 |
|
if (iter != hydroPropMap.end()) |
| 205 |
|
hydroProps_.push_back(iter->second); |
| 206 |
|
else { |
| 207 |
|
currHydroProp->complete(); |
| 208 |
< |
hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp)); |
| 208 |
> |
hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(sd->getType(), currHydroProp)); |
| 209 |
|
hydroProps_.push_back(currHydroProp); |
| 210 |
|
} |
| 211 |
+ |
delete currShape; |
| 212 |
|
} |
| 213 |
|
} |
| 214 |
|
} |
| 236 |
|
SimInfo::MoleculeIterator i; |
| 237 |
|
Molecule::IntegrableObjectIterator j; |
| 238 |
|
Molecule* mol; |
| 239 |
< |
StuntDouble* integrableObject; |
| 239 |
> |
StuntDouble* sd; |
| 240 |
|
RealType mass; |
| 241 |
|
Vector3d pos; |
| 242 |
|
Vector3d frc; |
| 273 |
|
} |
| 274 |
|
} |
| 275 |
|
|
| 276 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 277 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 276 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 277 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 278 |
|
|
| 279 |
|
if (freezeMolecule) |
| 280 |
< |
fdf += integrableObject->freeze(); |
| 280 |
> |
fdf += sd->freeze(); |
| 281 |
|
|
| 282 |
|
if (doLangevinForces) { |
| 283 |
< |
mass = integrableObject->getMass(); |
| 284 |
< |
if (integrableObject->isDirectional()){ |
| 283 |
> |
mass = sd->getMass(); |
| 284 |
> |
if (sd->isDirectional()){ |
| 285 |
|
|
| 286 |
|
// preliminaries for directional objects: |
| 287 |
|
|
| 288 |
< |
A = integrableObject->getA(); |
| 288 |
> |
A = sd->getA(); |
| 289 |
|
Atrans = A.transpose(); |
| 290 |
|
Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR(); |
| 291 |
|
|
| 296 |
|
genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_); |
| 297 |
|
Vector3d randomForceLab = Atrans * randomForceBody; |
| 298 |
|
Vector3d randomTorqueLab = Atrans * randomTorqueBody; |
| 299 |
< |
integrableObject->addFrc(randomForceLab); |
| 300 |
< |
integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab )); |
| 299 |
> |
sd->addFrc(randomForceLab); |
| 300 |
> |
sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab )); |
| 301 |
|
|
| 302 |
< |
Mat3x3d I = integrableObject->getI(); |
| 302 |
> |
Mat3x3d I = sd->getI(); |
| 303 |
|
Vector3d omegaBody; |
| 304 |
|
|
| 305 |
|
// What remains contains velocity explicitly, but the velocity required |
| 309 |
|
|
| 310 |
|
// this is the velocity at the half-step: |
| 311 |
|
|
| 312 |
< |
Vector3d vel =integrableObject->getVel(); |
| 313 |
< |
Vector3d angMom = integrableObject->getJ(); |
| 312 |
> |
Vector3d vel =sd->getVel(); |
| 313 |
> |
Vector3d angMom = sd->getJ(); |
| 314 |
|
|
| 315 |
|
//estimate velocity at full-step using everything but friction forces: |
| 316 |
|
|
| 317 |
< |
frc = integrableObject->getFrc(); |
| 317 |
> |
frc = sd->getFrc(); |
| 318 |
|
Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc; |
| 319 |
|
|
| 320 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 320 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 321 |
|
Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb; |
| 322 |
|
|
| 323 |
|
Vector3d omegaLab; |
| 336 |
|
|
| 337 |
|
for (int k = 0; k < maxIterNum_; k++) { |
| 338 |
|
|
| 339 |
< |
if (integrableObject->isLinear()) { |
| 340 |
< |
int linearAxis = integrableObject->linearAxis(); |
| 339 |
> |
if (sd->isLinear()) { |
| 340 |
> |
int linearAxis = sd->linearAxis(); |
| 341 |
|
int l = (linearAxis +1 )%3; |
| 342 |
|
int m = (linearAxis +2 )%3; |
| 343 |
|
omegaBody[l] = angMomStep[l] /I(l, l); |
| 376 |
|
break; // iteration ends here |
| 377 |
|
} |
| 378 |
|
|
| 379 |
< |
integrableObject->addFrc(frictionForceLab); |
| 380 |
< |
integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab)); |
| 379 |
> |
sd->addFrc(frictionForceLab); |
| 380 |
> |
sd->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab)); |
| 381 |
|
|
| 382 |
|
|
| 383 |
|
} else { |
| 386 |
|
Vector3d randomForce; |
| 387 |
|
Vector3d randomTorque; |
| 388 |
|
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
| 389 |
< |
integrableObject->addFrc(randomForce); |
| 389 |
> |
sd->addFrc(randomForce); |
| 390 |
|
|
| 391 |
|
// What remains contains velocity explicitly, but the velocity required |
| 392 |
|
// is at the full step: v(t + h), while we have initially the velocity |
| 395 |
|
|
| 396 |
|
// this is the velocity at the half-step: |
| 397 |
|
|
| 398 |
< |
Vector3d vel =integrableObject->getVel(); |
| 398 |
> |
Vector3d vel =sd->getVel(); |
| 399 |
|
|
| 400 |
|
//estimate velocity at full-step using everything but friction forces: |
| 401 |
|
|
| 402 |
< |
frc = integrableObject->getFrc(); |
| 402 |
> |
frc = sd->getFrc(); |
| 403 |
|
Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc; |
| 404 |
|
|
| 405 |
|
Vector3d frictionForce(0.0); |
| 425 |
|
break; // iteration ends here |
| 426 |
|
} |
| 427 |
|
|
| 428 |
< |
integrableObject->addFrc(frictionForce); |
| 428 |
> |
sd->addFrc(frictionForce); |
| 429 |
|
|
| 430 |
|
} |
| 431 |
|
} |
