| 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 |
|
#include <fstream> |
| 43 |
|
#include <iostream> |
| 47 |
|
#include "hydrodynamics/Sphere.hpp" |
| 48 |
|
#include "hydrodynamics/Ellipsoid.hpp" |
| 49 |
|
#include "utils/ElementsTable.hpp" |
| 50 |
+ |
#include "types/LennardJonesAdapter.hpp" |
| 51 |
+ |
#include "types/GayBerneAdapter.hpp" |
| 52 |
|
|
| 53 |
|
namespace OpenMD { |
| 54 |
|
|
| 55 |
< |
LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) { |
| 55 |
> |
LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), |
| 56 |
> |
maxIterNum_(4), |
| 57 |
> |
forceTolerance_(1e-6) { |
| 58 |
|
simParams = info->getSimParams(); |
| 59 |
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veloMunge = new Velocitizer(info); |
| 60 |
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|
| 97 |
|
std::map<std::string, HydroProp*> hydroPropMap; |
| 98 |
|
|
| 99 |
|
Molecule* mol; |
| 100 |
< |
StuntDouble* integrableObject; |
| 100 |
> |
StuntDouble* sd; |
| 101 |
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SimInfo::MoleculeIterator i; |
| 102 |
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Molecule::IntegrableObjectIterator j; |
| 103 |
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bool needHydroPropFile = false; |
| 104 |
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|
| 105 |
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for (mol = info->beginMolecule(i); mol != NULL; |
| 106 |
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mol = info->nextMolecule(i)) { |
| 107 |
< |
for (integrableObject = mol->beginIntegrableObject(j); |
| 108 |
< |
integrableObject != NULL; |
| 109 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 107 |
> |
|
| 108 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 109 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 110 |
|
|
| 111 |
< |
if (integrableObject->isRigidBody()) { |
| 112 |
< |
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 111 |
> |
if (sd->isRigidBody()) { |
| 112 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 113 |
|
if (rb->getNumAtoms() > 1) needHydroPropFile = true; |
| 114 |
|
} |
| 115 |
|
|
| 132 |
|
|
| 133 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
| 134 |
|
mol = info->nextMolecule(i)) { |
| 130 |
– |
for (integrableObject = mol->beginIntegrableObject(j); |
| 131 |
– |
integrableObject != NULL; |
| 132 |
– |
integrableObject = mol->nextIntegrableObject(j)) { |
| 135 |
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|
| 136 |
< |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 136 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 137 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 138 |
> |
|
| 139 |
> |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType()); |
| 140 |
|
if (iter != hydroPropMap.end()) { |
| 141 |
|
hydroProps_.push_back(iter->second); |
| 142 |
|
} else { |
| 143 |
|
sprintf( painCave.errMsg, |
| 144 |
< |
"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str()); |
| 144 |
> |
"Can not find resistance tensor for atom [%s]\n", sd->getType().c_str()); |
| 145 |
|
painCave.severity = OPENMD_ERROR; |
| 146 |
|
painCave.isFatal = 1; |
| 147 |
|
simError(); |
| 153 |
|
std::map<std::string, HydroProp*> hydroPropMap; |
| 154 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
| 155 |
|
mol = info->nextMolecule(i)) { |
| 156 |
< |
for (integrableObject = mol->beginIntegrableObject(j); |
| 157 |
< |
integrableObject != NULL; |
| 158 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 156 |
> |
|
| 157 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 158 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 159 |
> |
|
| 160 |
|
Shape* currShape = NULL; |
| 161 |
|
|
| 162 |
< |
if (integrableObject->isAtom()){ |
| 163 |
< |
Atom* atom = static_cast<Atom*>(integrableObject); |
| 162 |
> |
if (sd->isAtom()){ |
| 163 |
> |
Atom* atom = static_cast<Atom*>(sd); |
| 164 |
|
AtomType* atomType = atom->getAtomType(); |
| 165 |
< |
if (atomType->isGayBerne()) { |
| 166 |
< |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 167 |
< |
GenericData* data = dAtomType->getPropertyByName("GayBerne"); |
| 168 |
< |
if (data != NULL) { |
| 169 |
< |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 164 |
< |
|
| 165 |
< |
if (gayBerneData != NULL) { |
| 166 |
< |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
| 167 |
< |
currShape = new Ellipsoid(V3Zero, |
| 168 |
< |
gayBerneParam.GB_l / 2.0, |
| 169 |
< |
gayBerneParam.GB_d / 2.0, |
| 170 |
< |
Mat3x3d::identity()); |
| 171 |
< |
} else { |
| 172 |
< |
sprintf( painCave.errMsg, |
| 173 |
< |
"Can not cast GenericData to GayBerneParam\n"); |
| 174 |
< |
painCave.severity = OPENMD_ERROR; |
| 175 |
< |
painCave.isFatal = 1; |
| 176 |
< |
simError(); |
| 177 |
< |
} |
| 178 |
< |
} else { |
| 179 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); |
| 180 |
< |
painCave.severity = OPENMD_ERROR; |
| 181 |
< |
painCave.isFatal = 1; |
| 182 |
< |
simError(); |
| 183 |
< |
} |
| 165 |
> |
GayBerneAdapter gba = GayBerneAdapter(atomType); |
| 166 |
> |
if (gba.isGayBerne()) { |
| 167 |
> |
currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0, |
| 168 |
> |
gba.getD() / 2.0, |
| 169 |
> |
Mat3x3d::identity()); |
| 170 |
|
} else { |
| 171 |
< |
if (atomType->isLennardJones()){ |
| 172 |
< |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 173 |
< |
if (data != NULL) { |
| 188 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 189 |
< |
if (ljData != NULL) { |
| 190 |
< |
LJParam ljParam = ljData->getData(); |
| 191 |
< |
currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); |
| 192 |
< |
} else { |
| 193 |
< |
sprintf( painCave.errMsg, |
| 194 |
< |
"Can not cast GenericData to LJParam\n"); |
| 195 |
< |
painCave.severity = OPENMD_ERROR; |
| 196 |
< |
painCave.isFatal = 1; |
| 197 |
< |
simError(); |
| 198 |
< |
} |
| 199 |
< |
} |
| 171 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
| 172 |
> |
if (lja.isLennardJones()){ |
| 173 |
> |
currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0); |
| 174 |
|
} else { |
| 175 |
|
int aNum = etab.GetAtomicNum((atom->getType()).c_str()); |
| 176 |
|
if (aNum != 0) { |
| 202 |
|
|
| 203 |
|
|
| 204 |
|
HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp()); |
| 205 |
< |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 205 |
> |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType()); |
| 206 |
|
if (iter != hydroPropMap.end()) |
| 207 |
|
hydroProps_.push_back(iter->second); |
| 208 |
|
else { |
| 209 |
|
currHydroProp->complete(); |
| 210 |
< |
hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp)); |
| 210 |
> |
hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(sd->getType(), currHydroProp)); |
| 211 |
|
hydroProps_.push_back(currHydroProp); |
| 212 |
|
} |
| 213 |
+ |
delete currShape; |
| 214 |
|
} |
| 215 |
|
} |
| 216 |
|
} |
| 234 |
|
return props; |
| 235 |
|
} |
| 236 |
|
|
| 237 |
< |
void LDForceManager::postCalculation(bool needStress){ |
| 237 |
> |
void LDForceManager::postCalculation(){ |
| 238 |
|
SimInfo::MoleculeIterator i; |
| 239 |
|
Molecule::IntegrableObjectIterator j; |
| 240 |
|
Molecule* mol; |
| 241 |
< |
StuntDouble* integrableObject; |
| 241 |
> |
StuntDouble* sd; |
| 242 |
|
RealType mass; |
| 243 |
|
Vector3d pos; |
| 244 |
|
Vector3d frc; |
| 275 |
|
} |
| 276 |
|
} |
| 277 |
|
|
| 278 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 279 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 278 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 279 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 280 |
|
|
| 281 |
|
if (freezeMolecule) |
| 282 |
< |
fdf += integrableObject->freeze(); |
| 282 |
> |
fdf += sd->freeze(); |
| 283 |
|
|
| 284 |
|
if (doLangevinForces) { |
| 285 |
< |
mass = integrableObject->getMass(); |
| 286 |
< |
if (integrableObject->isDirectional()){ |
| 285 |
> |
mass = sd->getMass(); |
| 286 |
> |
if (sd->isDirectional()){ |
| 287 |
|
|
| 288 |
|
// preliminaries for directional objects: |
| 289 |
|
|
| 290 |
< |
A = integrableObject->getA(); |
| 290 |
> |
A = sd->getA(); |
| 291 |
|
Atrans = A.transpose(); |
| 292 |
|
Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR(); |
| 293 |
|
|
| 298 |
|
genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_); |
| 299 |
|
Vector3d randomForceLab = Atrans * randomForceBody; |
| 300 |
|
Vector3d randomTorqueLab = Atrans * randomTorqueBody; |
| 301 |
< |
integrableObject->addFrc(randomForceLab); |
| 302 |
< |
integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab )); |
| 301 |
> |
sd->addFrc(randomForceLab); |
| 302 |
> |
sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab )); |
| 303 |
|
|
| 304 |
< |
Mat3x3d I = integrableObject->getI(); |
| 304 |
> |
Mat3x3d I = sd->getI(); |
| 305 |
|
Vector3d omegaBody; |
| 306 |
|
|
| 307 |
|
// What remains contains velocity explicitly, but the velocity required |
| 311 |
|
|
| 312 |
|
// this is the velocity at the half-step: |
| 313 |
|
|
| 314 |
< |
Vector3d vel =integrableObject->getVel(); |
| 315 |
< |
Vector3d angMom = integrableObject->getJ(); |
| 314 |
> |
Vector3d vel =sd->getVel(); |
| 315 |
> |
Vector3d angMom = sd->getJ(); |
| 316 |
|
|
| 317 |
|
//estimate velocity at full-step using everything but friction forces: |
| 318 |
|
|
| 319 |
< |
frc = integrableObject->getFrc(); |
| 319 |
> |
frc = sd->getFrc(); |
| 320 |
|
Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc; |
| 321 |
|
|
| 322 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 322 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 323 |
|
Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb; |
| 324 |
|
|
| 325 |
|
Vector3d omegaLab; |
| 338 |
|
|
| 339 |
|
for (int k = 0; k < maxIterNum_; k++) { |
| 340 |
|
|
| 341 |
< |
if (integrableObject->isLinear()) { |
| 342 |
< |
int linearAxis = integrableObject->linearAxis(); |
| 341 |
> |
if (sd->isLinear()) { |
| 342 |
> |
int linearAxis = sd->linearAxis(); |
| 343 |
|
int l = (linearAxis +1 )%3; |
| 344 |
|
int m = (linearAxis +2 )%3; |
| 345 |
|
omegaBody[l] = angMomStep[l] /I(l, l); |
| 378 |
|
break; // iteration ends here |
| 379 |
|
} |
| 380 |
|
|
| 381 |
< |
integrableObject->addFrc(frictionForceLab); |
| 382 |
< |
integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab)); |
| 381 |
> |
sd->addFrc(frictionForceLab); |
| 382 |
> |
sd->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab)); |
| 383 |
|
|
| 384 |
|
|
| 385 |
|
} else { |
| 388 |
|
Vector3d randomForce; |
| 389 |
|
Vector3d randomTorque; |
| 390 |
|
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
| 391 |
< |
integrableObject->addFrc(randomForce); |
| 391 |
> |
sd->addFrc(randomForce); |
| 392 |
|
|
| 393 |
|
// What remains contains velocity explicitly, but the velocity required |
| 394 |
|
// is at the full step: v(t + h), while we have initially the velocity |
| 397 |
|
|
| 398 |
|
// this is the velocity at the half-step: |
| 399 |
|
|
| 400 |
< |
Vector3d vel =integrableObject->getVel(); |
| 400 |
> |
Vector3d vel =sd->getVel(); |
| 401 |
|
|
| 402 |
|
//estimate velocity at full-step using everything but friction forces: |
| 403 |
|
|
| 404 |
< |
frc = integrableObject->getFrc(); |
| 404 |
> |
frc = sd->getFrc(); |
| 405 |
|
Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc; |
| 406 |
|
|
| 407 |
|
Vector3d frictionForce(0.0); |
| 427 |
|
break; // iteration ends here |
| 428 |
|
} |
| 429 |
|
|
| 430 |
< |
integrableObject->addFrc(frictionForce); |
| 430 |
> |
sd->addFrc(frictionForce); |
| 431 |
|
|
| 432 |
|
} |
| 433 |
|
} |
| 443 |
|
if(!simParams->getUsePeriodicBoundaryConditions()) |
| 444 |
|
veloMunge->removeAngularDrift(); |
| 445 |
|
|
| 446 |
< |
ForceManager::postCalculation(needStress); |
| 446 |
> |
ForceManager::postCalculation(); |
| 447 |
|
} |
| 448 |
|
|
| 449 |
|
void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
