| 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 |
|
|
| 43 |
|
/** |
| 44 |
|
* @file MoleculeCreator.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/04/2004 |
| 46 |
– |
* @time 13:44am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 54 |
|
#include "brains/MoleculeCreator.hpp" |
| 55 |
|
#include "primitives/GhostBend.hpp" |
| 56 |
|
#include "primitives/GhostTorsion.hpp" |
| 57 |
< |
#include "types/DirectionalAtomType.hpp" |
| 57 |
> |
#include "types/AtomType.hpp" |
| 58 |
|
#include "types/FixedBondType.hpp" |
| 59 |
+ |
#include "types/BondTypeParser.hpp" |
| 60 |
+ |
#include "types/BendTypeParser.hpp" |
| 61 |
+ |
#include "types/TorsionTypeParser.hpp" |
| 62 |
+ |
#include "types/InversionTypeParser.hpp" |
| 63 |
|
#include "utils/simError.h" |
| 64 |
|
#include "utils/StringUtils.hpp" |
| 65 |
|
|
| 69 |
|
MoleculeStamp *molStamp, |
| 70 |
|
int stampId, int globalIndex, |
| 71 |
|
LocalIndexManager* localIndexMan) { |
| 72 |
< |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
| 73 |
< |
|
| 72 |
> |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(), |
| 73 |
> |
molStamp->getRegion() ); |
| 74 |
> |
|
| 75 |
|
//create atoms |
| 76 |
|
Atom* atom; |
| 77 |
|
AtomStamp* currentAtomStamp; |
| 100 |
|
int nBonds = molStamp->getNBonds(); |
| 101 |
|
|
| 102 |
|
for (int i = 0; i < nBonds; ++i) { |
| 103 |
< |
currentBondStamp = molStamp->getBondStamp(i); |
| 104 |
< |
bond = createBond(ff, mol, currentBondStamp); |
| 103 |
> |
currentBondStamp = molStamp->getBondStamp(i); |
| 104 |
> |
bond = createBond(ff, mol, currentBondStamp, localIndexMan); |
| 105 |
|
mol->addBond(bond); |
| 106 |
|
} |
| 107 |
|
|
| 111 |
|
int nBends = molStamp->getNBends(); |
| 112 |
|
for (int i = 0; i < nBends; ++i) { |
| 113 |
|
currentBendStamp = molStamp->getBendStamp(i); |
| 114 |
< |
bend = createBend(ff, mol, currentBendStamp); |
| 114 |
> |
bend = createBend(ff, mol, currentBendStamp, localIndexMan); |
| 115 |
|
mol->addBend(bend); |
| 116 |
|
} |
| 117 |
|
|
| 121 |
|
int nTorsions = molStamp->getNTorsions(); |
| 122 |
|
for (int i = 0; i < nTorsions; ++i) { |
| 123 |
|
currentTorsionStamp = molStamp->getTorsionStamp(i); |
| 124 |
< |
torsion = createTorsion(ff, mol, currentTorsionStamp); |
| 124 |
> |
torsion = createTorsion(ff, mol, currentTorsionStamp, localIndexMan); |
| 125 |
|
mol->addTorsion(torsion); |
| 126 |
|
} |
| 127 |
|
|
| 131 |
|
int nInversions = molStamp->getNInversions(); |
| 132 |
|
for (int i = 0; i < nInversions; ++i) { |
| 133 |
|
currentInversionStamp = molStamp->getInversionStamp(i); |
| 134 |
< |
inversion = createInversion(ff, mol, currentInversionStamp); |
| 134 |
> |
inversion = createInversion(ff, mol, currentInversionStamp, |
| 135 |
> |
localIndexMan); |
| 136 |
|
if (inversion != NULL ) { |
| 137 |
|
mol->addInversion(inversion); |
| 138 |
|
} |
| 144 |
|
int nCutoffGroups = molStamp->getNCutoffGroups(); |
| 145 |
|
for (int i = 0; i < nCutoffGroups; ++i) { |
| 146 |
|
currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
| 147 |
< |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
| 147 |
> |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, |
| 148 |
> |
localIndexMan); |
| 149 |
|
mol->addCutoffGroup(cutoffGroup); |
| 150 |
|
} |
| 151 |
|
|
| 176 |
|
// every single free atom |
| 177 |
|
|
| 178 |
|
for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
| 179 |
< |
cutoffGroup = createCutoffGroup(mol, *fai); |
| 179 |
> |
cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan); |
| 180 |
|
mol->addCutoffGroup(cutoffGroup); |
| 181 |
|
} |
| 182 |
< |
//create constraints |
| 182 |
> |
|
| 183 |
> |
//create bonded constraintPairs: |
| 184 |
|
createConstraintPair(mol); |
| 185 |
+ |
|
| 186 |
+ |
//create non-bonded constraintPairs |
| 187 |
+ |
for (int i = 0; i < molStamp->getNConstraints(); ++i) { |
| 188 |
+ |
ConstraintStamp* cStamp = molStamp->getConstraintStamp(i); |
| 189 |
+ |
Atom* atomA; |
| 190 |
+ |
Atom* atomB; |
| 191 |
+ |
|
| 192 |
+ |
atomA = mol->getAtomAt(cStamp->getA()); |
| 193 |
+ |
atomB = mol->getAtomAt(cStamp->getB()); |
| 194 |
+ |
assert( atomA && atomB ); |
| 195 |
+ |
|
| 196 |
+ |
RealType distance; |
| 197 |
+ |
bool printConstraintForce = false; |
| 198 |
+ |
|
| 199 |
+ |
if (!cStamp->haveConstrainedDistance()) { |
| 200 |
+ |
sprintf(painCave.errMsg, |
| 201 |
+ |
"Constraint Error: A non-bond constraint was specified\n" |
| 202 |
+ |
"\twithout providing a value for the constrainedDistance.\n"); |
| 203 |
+ |
painCave.isFatal = 1; |
| 204 |
+ |
simError(); |
| 205 |
+ |
} else { |
| 206 |
+ |
distance = cStamp->getConstrainedDistance(); |
| 207 |
+ |
} |
| 208 |
+ |
|
| 209 |
+ |
if (cStamp->havePrintConstraintForce()) { |
| 210 |
+ |
printConstraintForce = cStamp->getPrintConstraintForce(); |
| 211 |
+ |
} |
| 212 |
+ |
|
| 213 |
+ |
ConstraintElem* consElemA = new ConstraintElem(atomA); |
| 214 |
+ |
ConstraintElem* consElemB = new ConstraintElem(atomB); |
| 215 |
+ |
ConstraintPair* cPair = new ConstraintPair(consElemA, consElemB, distance, |
| 216 |
+ |
printConstraintForce); |
| 217 |
+ |
mol->addConstraintPair(cPair); |
| 218 |
+ |
} |
| 219 |
+ |
|
| 220 |
+ |
// now create the constraint elements: |
| 221 |
+ |
|
| 222 |
|
createConstraintElem(mol); |
| 223 |
|
|
| 224 |
+ |
// Does this molecule stamp define a total constrained charge value? |
| 225 |
+ |
// If so, let the created molecule know about it. |
| 226 |
+ |
|
| 227 |
+ |
if (molStamp->haveConstrainTotalCharge() ) { |
| 228 |
+ |
mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() ); |
| 229 |
+ |
} |
| 230 |
+ |
|
| 231 |
|
//the construction of this molecule is finished |
| 232 |
|
mol->complete(); |
| 233 |
|
|
| 250 |
|
painCave.isFatal = 1; |
| 251 |
|
simError(); |
| 252 |
|
} |
| 253 |
< |
|
| 253 |
> |
|
| 254 |
|
//below code still have some kind of hard-coding smell |
| 255 |
|
if (atomType->isDirectional()){ |
| 204 |
– |
|
| 205 |
– |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 206 |
– |
|
| 207 |
– |
if (dAtomType == NULL) { |
| 208 |
– |
sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType"); |
| 256 |
|
|
| 210 |
– |
painCave.isFatal = 1; |
| 211 |
– |
simError(); |
| 212 |
– |
} |
| 213 |
– |
|
| 257 |
|
DirectionalAtom* dAtom; |
| 258 |
< |
dAtom = new DirectionalAtom(dAtomType); |
| 258 |
> |
dAtom = new DirectionalAtom(atomType); |
| 259 |
|
atom = dAtom; |
| 260 |
|
} |
| 261 |
|
else{ |
| 270 |
|
RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, |
| 271 |
|
Molecule* mol, |
| 272 |
|
RigidBodyStamp* rbStamp, |
| 273 |
< |
LocalIndexManager* localIndexMan) { |
| 273 |
> |
LocalIndexManager* localIndexMan){ |
| 274 |
|
Atom* atom; |
| 275 |
|
int nAtoms; |
| 276 |
|
Vector3d refCoor; |
| 294 |
|
//set the local index of this rigid body, global index will be set later |
| 295 |
|
rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex()); |
| 296 |
|
|
| 297 |
< |
//the rule for naming rigidbody MoleculeName_RB_Integer |
| 298 |
< |
//The first part is the name of the molecule |
| 299 |
< |
//The second part is alway fixed as "RB" |
| 300 |
< |
//The third part is the index of the rigidbody defined in meta-data file |
| 301 |
< |
//For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 302 |
< |
/**@todo replace itoa by lexi_cast */ |
| 297 |
> |
// The rule for naming a rigidbody is: MoleculeName_RB_Integer |
| 298 |
> |
// The first part is the name of the molecule |
| 299 |
> |
// The second part is always fixed as "RB" |
| 300 |
> |
// The third part is the index of the rigidbody defined in meta-data file |
| 301 |
> |
// For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 302 |
> |
|
| 303 |
|
std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10); |
| 304 |
|
rb->setType(mol->getType() + "_RB_" + s.c_str()); |
| 262 |
– |
|
| 305 |
|
return rb; |
| 306 |
|
} |
| 307 |
|
|
| 308 |
|
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, |
| 309 |
< |
BondStamp* stamp) { |
| 310 |
< |
BondType* bondType; |
| 309 |
> |
BondStamp* stamp, |
| 310 |
> |
LocalIndexManager* localIndexMan) { |
| 311 |
> |
BondTypeParser btParser; |
| 312 |
> |
BondType* bondType = NULL; |
| 313 |
|
Atom* atomA; |
| 314 |
|
Atom* atomB; |
| 315 |
|
|
| 317 |
|
atomB = mol->getAtomAt(stamp->getB()); |
| 318 |
|
|
| 319 |
|
assert( atomA && atomB); |
| 276 |
– |
|
| 277 |
– |
bondType = ff->getBondType(atomA->getType(), atomB->getType()); |
| 320 |
|
|
| 321 |
< |
if (bondType == NULL) { |
| 322 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
| 323 |
< |
atomA->getType().c_str(), |
| 324 |
< |
atomB->getType().c_str()); |
| 325 |
< |
|
| 326 |
< |
painCave.isFatal = 1; |
| 327 |
< |
simError(); |
| 321 |
> |
if (stamp->hasOverride()) { |
| 322 |
> |
|
| 323 |
> |
try { |
| 324 |
> |
bondType = btParser.parseTypeAndPars(stamp->getOverrideType(), |
| 325 |
> |
stamp->getOverridePars() ); |
| 326 |
> |
} |
| 327 |
> |
catch( OpenMDException e) { |
| 328 |
> |
sprintf(painCave.errMsg, "MoleculeCreator Error: %s " |
| 329 |
> |
"for molecule %s\n", |
| 330 |
> |
e.what(), mol->getType().c_str() ); |
| 331 |
> |
painCave.isFatal = 1; |
| 332 |
> |
simError(); |
| 333 |
> |
} |
| 334 |
> |
|
| 335 |
> |
} else { |
| 336 |
> |
bondType = ff->getBondType(atomA->getType(), atomB->getType()); |
| 337 |
> |
|
| 338 |
> |
if (bondType == NULL) { |
| 339 |
> |
sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
| 340 |
> |
atomA->getType().c_str(), |
| 341 |
> |
atomB->getType().c_str()); |
| 342 |
> |
|
| 343 |
> |
painCave.isFatal = 1; |
| 344 |
> |
simError(); |
| 345 |
> |
} |
| 346 |
|
} |
| 347 |
< |
return new Bond(atomA, atomB, bondType); |
| 347 |
> |
|
| 348 |
> |
Bond* bond = new Bond(atomA, atomB, bondType); |
| 349 |
> |
|
| 350 |
> |
//set the local index of this bond, the global index will be set later |
| 351 |
> |
bond->setLocalIndex(localIndexMan->getNextBondIndex()); |
| 352 |
> |
|
| 353 |
> |
// The rule for naming a bond is: MoleculeName_Bond_Integer |
| 354 |
> |
// The first part is the name of the molecule |
| 355 |
> |
// The second part is always fixed as "Bond" |
| 356 |
> |
// The third part is the index of the bond defined in meta-data file |
| 357 |
> |
// For example, Butane_bond_0 is a valid Bond name in a butane molecule |
| 358 |
> |
|
| 359 |
> |
std::string s = OpenMD_itoa(mol->getNBonds(), 10); |
| 360 |
> |
bond->setName(mol->getType() + "_Bond_" + s.c_str()); |
| 361 |
> |
return bond; |
| 362 |
|
} |
| 363 |
|
|
| 364 |
|
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, |
| 365 |
< |
BendStamp* stamp) { |
| 366 |
< |
Bend* bend = NULL; |
| 367 |
< |
std::vector<int> bendAtoms = stamp->getMembers(); |
| 365 |
> |
BendStamp* stamp, |
| 366 |
> |
LocalIndexManager* localIndexMan) { |
| 367 |
> |
BendTypeParser btParser; |
| 368 |
> |
BendType* bendType = NULL; |
| 369 |
> |
Bend* bend = NULL; |
| 370 |
> |
|
| 371 |
> |
std::vector<int> bendAtoms = stamp->getMembers(); |
| 372 |
|
if (bendAtoms.size() == 3) { |
| 373 |
|
Atom* atomA = mol->getAtomAt(bendAtoms[0]); |
| 374 |
|
Atom* atomB = mol->getAtomAt(bendAtoms[1]); |
| 375 |
|
Atom* atomC = mol->getAtomAt(bendAtoms[2]); |
| 376 |
|
|
| 377 |
< |
assert( atomA && atomB && atomC); |
| 378 |
< |
|
| 379 |
< |
BendType* bendType = ff->getBendType(atomA->getType().c_str(), |
| 302 |
< |
atomB->getType().c_str(), |
| 303 |
< |
atomC->getType().c_str()); |
| 304 |
< |
|
| 305 |
< |
if (bendType == NULL) { |
| 306 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
| 307 |
< |
atomA->getType().c_str(), |
| 308 |
< |
atomB->getType().c_str(), |
| 309 |
< |
atomC->getType().c_str()); |
| 377 |
> |
assert( atomA && atomB && atomC ); |
| 378 |
> |
|
| 379 |
> |
if (stamp->hasOverride()) { |
| 380 |
|
|
| 381 |
< |
painCave.isFatal = 1; |
| 382 |
< |
simError(); |
| 381 |
> |
try { |
| 382 |
> |
bendType = btParser.parseTypeAndPars(stamp->getOverrideType(), |
| 383 |
> |
stamp->getOverridePars() ); |
| 384 |
> |
} |
| 385 |
> |
catch( OpenMDException e) { |
| 386 |
> |
sprintf(painCave.errMsg, "MoleculeCreator Error: %s " |
| 387 |
> |
"for molecule %s\n", |
| 388 |
> |
e.what(), mol->getType().c_str() ); |
| 389 |
> |
painCave.isFatal = 1; |
| 390 |
> |
simError(); |
| 391 |
> |
} |
| 392 |
> |
} else { |
| 393 |
> |
|
| 394 |
> |
bendType = ff->getBendType(atomA->getType().c_str(), |
| 395 |
> |
atomB->getType().c_str(), |
| 396 |
> |
atomC->getType().c_str()); |
| 397 |
> |
|
| 398 |
> |
if (bendType == NULL) { |
| 399 |
> |
sprintf(painCave.errMsg, |
| 400 |
> |
"Can not find Matching Bend Type for[%s, %s, %s]", |
| 401 |
> |
atomA->getType().c_str(), |
| 402 |
> |
atomB->getType().c_str(), |
| 403 |
> |
atomC->getType().c_str()); |
| 404 |
> |
|
| 405 |
> |
painCave.isFatal = 1; |
| 406 |
> |
simError(); |
| 407 |
> |
} |
| 408 |
|
} |
| 409 |
|
|
| 410 |
|
bend = new Bend(atomA, atomB, atomC, bendType); |
| 411 |
+ |
|
| 412 |
|
} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) { |
| 413 |
|
int ghostIndex = stamp->getGhostVectorSource(); |
| 414 |
< |
int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1]; |
| 414 |
> |
int normalIndex = ghostIndex != bendAtoms[0] ? |
| 415 |
> |
bendAtoms[0] : bendAtoms[1]; |
| 416 |
|
Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
| 417 |
|
DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex)); |
| 418 |
|
if (ghostAtom == NULL) { |
| 420 |
|
painCave.isFatal = 1; |
| 421 |
|
simError(); |
| 422 |
|
} |
| 326 |
– |
|
| 327 |
– |
BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
| 423 |
|
|
| 424 |
< |
if (bendType == NULL) { |
| 425 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
| 426 |
< |
normalAtom->getType().c_str(), |
| 427 |
< |
ghostAtom->getType().c_str(), |
| 428 |
< |
"GHOST"); |
| 429 |
< |
|
| 430 |
< |
painCave.isFatal = 1; |
| 431 |
< |
simError(); |
| 424 |
> |
if (stamp->hasOverride()) { |
| 425 |
> |
|
| 426 |
> |
try { |
| 427 |
> |
bendType = btParser.parseTypeAndPars(stamp->getOverrideType(), |
| 428 |
> |
stamp->getOverridePars() ); |
| 429 |
> |
} |
| 430 |
> |
catch( OpenMDException e) { |
| 431 |
> |
sprintf(painCave.errMsg, "MoleculeCreator Error: %s " |
| 432 |
> |
"for molecule %s\n", |
| 433 |
> |
e.what(), mol->getType().c_str() ); |
| 434 |
> |
painCave.isFatal = 1; |
| 435 |
> |
simError(); |
| 436 |
> |
} |
| 437 |
> |
} else { |
| 438 |
> |
|
| 439 |
> |
bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), |
| 440 |
> |
"GHOST"); |
| 441 |
> |
|
| 442 |
> |
if (bendType == NULL) { |
| 443 |
> |
sprintf(painCave.errMsg, |
| 444 |
> |
"Can not find Matching Bend Type for[%s, %s, %s]", |
| 445 |
> |
normalAtom->getType().c_str(), |
| 446 |
> |
ghostAtom->getType().c_str(), |
| 447 |
> |
"GHOST"); |
| 448 |
> |
|
| 449 |
> |
painCave.isFatal = 1; |
| 450 |
> |
simError(); |
| 451 |
> |
} |
| 452 |
|
} |
| 453 |
|
|
| 454 |
|
bend = new GhostBend(normalAtom, ghostAtom, bendType); |
| 455 |
|
|
| 456 |
|
} |
| 457 |
|
|
| 458 |
+ |
//set the local index of this bend, the global index will be set later |
| 459 |
+ |
bend->setLocalIndex(localIndexMan->getNextBendIndex()); |
| 460 |
+ |
|
| 461 |
+ |
// The rule for naming a bend is: MoleculeName_Bend_Integer |
| 462 |
+ |
// The first part is the name of the molecule |
| 463 |
+ |
// The second part is always fixed as "Bend" |
| 464 |
+ |
// The third part is the index of the bend defined in meta-data file |
| 465 |
+ |
// For example, Butane_Bend_0 is a valid Bend name in a butane molecule |
| 466 |
+ |
|
| 467 |
+ |
std::string s = OpenMD_itoa(mol->getNBends(), 10); |
| 468 |
+ |
bend->setName(mol->getType() + "_Bend_" + s.c_str()); |
| 469 |
|
return bend; |
| 470 |
|
} |
| 471 |
|
|
| 472 |
|
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, |
| 473 |
< |
TorsionStamp* stamp) { |
| 473 |
> |
TorsionStamp* stamp, |
| 474 |
> |
LocalIndexManager* localIndexMan) { |
| 475 |
|
|
| 476 |
+ |
TorsionTypeParser ttParser; |
| 477 |
+ |
TorsionType* torsionType = NULL; |
| 478 |
|
Torsion* torsion = NULL; |
| 479 |
+ |
|
| 480 |
|
std::vector<int> torsionAtoms = stamp->getMembers(); |
| 481 |
|
if (torsionAtoms.size() < 3) { |
| 482 |
|
return torsion; |
| 489 |
|
if (torsionAtoms.size() == 4) { |
| 490 |
|
Atom* atomD = mol->getAtomAt(torsionAtoms[3]); |
| 491 |
|
|
| 492 |
< |
assert(atomA && atomB && atomC && atomD); |
| 492 |
> |
assert(atomA && atomB && atomC && atomD ); |
| 493 |
> |
|
| 494 |
> |
if (stamp->hasOverride()) { |
| 495 |
|
|
| 496 |
< |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), |
| 497 |
< |
atomB->getType(), |
| 498 |
< |
atomC->getType(), |
| 499 |
< |
atomD->getType()); |
| 500 |
< |
if (torsionType == NULL) { |
| 501 |
< |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 502 |
< |
atomA->getType().c_str(), |
| 503 |
< |
atomB->getType().c_str(), |
| 504 |
< |
atomC->getType().c_str(), |
| 505 |
< |
atomD->getType().c_str()); |
| 496 |
> |
try { |
| 497 |
> |
torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(), |
| 498 |
> |
stamp->getOverridePars() ); |
| 499 |
> |
} |
| 500 |
> |
catch( OpenMDException e) { |
| 501 |
> |
sprintf(painCave.errMsg, "MoleculeCreator Error: %s " |
| 502 |
> |
"for molecule %s\n", |
| 503 |
> |
e.what(), mol->getType().c_str() ); |
| 504 |
> |
painCave.isFatal = 1; |
| 505 |
> |
simError(); |
| 506 |
> |
} |
| 507 |
> |
} else { |
| 508 |
> |
|
| 509 |
|
|
| 510 |
< |
painCave.isFatal = 1; |
| 511 |
< |
simError(); |
| 510 |
> |
torsionType = ff->getTorsionType(atomA->getType(), |
| 511 |
> |
atomB->getType(), |
| 512 |
> |
atomC->getType(), |
| 513 |
> |
atomD->getType()); |
| 514 |
> |
if (torsionType == NULL) { |
| 515 |
> |
sprintf(painCave.errMsg, |
| 516 |
> |
"Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 517 |
> |
atomA->getType().c_str(), |
| 518 |
> |
atomB->getType().c_str(), |
| 519 |
> |
atomC->getType().c_str(), |
| 520 |
> |
atomD->getType().c_str()); |
| 521 |
> |
|
| 522 |
> |
painCave.isFatal = 1; |
| 523 |
> |
simError(); |
| 524 |
> |
} |
| 525 |
|
} |
| 526 |
|
|
| 527 |
|
torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType); |
| 528 |
< |
} |
| 381 |
< |
else { |
| 528 |
> |
} else { |
| 529 |
|
|
| 530 |
|
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource())); |
| 531 |
|
if (dAtom == NULL) { |
| 533 |
|
painCave.isFatal = 1; |
| 534 |
|
simError(); |
| 535 |
|
} |
| 536 |
< |
|
| 537 |
< |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
| 391 |
< |
atomC->getType(), "GHOST"); |
| 392 |
< |
|
| 393 |
< |
if (torsionType == NULL) { |
| 394 |
< |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 395 |
< |
atomA->getType().c_str(), |
| 396 |
< |
atomB->getType().c_str(), |
| 397 |
< |
atomC->getType().c_str(), |
| 398 |
< |
"GHOST"); |
| 536 |
> |
|
| 537 |
> |
if (stamp->hasOverride()) { |
| 538 |
|
|
| 539 |
< |
painCave.isFatal = 1; |
| 540 |
< |
simError(); |
| 541 |
< |
} |
| 539 |
> |
try { |
| 540 |
> |
torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(), |
| 541 |
> |
stamp->getOverridePars() ); |
| 542 |
> |
} |
| 543 |
> |
catch( OpenMDException e) { |
| 544 |
> |
sprintf(painCave.errMsg, "MoleculeCreator Error: %s " |
| 545 |
> |
"for molecule %s\n", |
| 546 |
> |
e.what(), mol->getType().c_str() ); |
| 547 |
> |
painCave.isFatal = 1; |
| 548 |
> |
simError(); |
| 549 |
> |
} |
| 550 |
> |
} else { |
| 551 |
> |
torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
| 552 |
> |
atomC->getType(), "GHOST"); |
| 553 |
|
|
| 554 |
+ |
if (torsionType == NULL) { |
| 555 |
+ |
sprintf(painCave.errMsg, |
| 556 |
+ |
"Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 557 |
+ |
atomA->getType().c_str(), |
| 558 |
+ |
atomB->getType().c_str(), |
| 559 |
+ |
atomC->getType().c_str(), |
| 560 |
+ |
"GHOST"); |
| 561 |
+ |
|
| 562 |
+ |
painCave.isFatal = 1; |
| 563 |
+ |
simError(); |
| 564 |
+ |
} |
| 565 |
+ |
} |
| 566 |
+ |
|
| 567 |
|
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
| 568 |
|
} |
| 569 |
+ |
|
| 570 |
+ |
//set the local index of this torsion, the global index will be set later |
| 571 |
+ |
torsion->setLocalIndex(localIndexMan->getNextTorsionIndex()); |
| 572 |
|
|
| 573 |
+ |
// The rule for naming a torsion is: MoleculeName_Torsion_Integer |
| 574 |
+ |
// The first part is the name of the molecule |
| 575 |
+ |
// The second part is always fixed as "Torsion" |
| 576 |
+ |
// The third part is the index of the torsion defined in meta-data file |
| 577 |
+ |
// For example, Butane_Torsion_0 is a valid Torsion name in a |
| 578 |
+ |
// butane molecule |
| 579 |
+ |
|
| 580 |
+ |
std::string s = OpenMD_itoa(mol->getNTorsions(), 10); |
| 581 |
+ |
torsion->setName(mol->getType() + "_Torsion_" + s.c_str()); |
| 582 |
|
return torsion; |
| 583 |
|
} |
| 584 |
|
|
| 585 |
|
Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, |
| 586 |
< |
InversionStamp* stamp) { |
| 587 |
< |
|
| 586 |
> |
InversionStamp* stamp, |
| 587 |
> |
LocalIndexManager* localIndexMan) { |
| 588 |
> |
|
| 589 |
> |
InversionTypeParser itParser; |
| 590 |
> |
InversionType* inversionType = NULL; |
| 591 |
|
Inversion* inversion = NULL; |
| 592 |
+ |
|
| 593 |
|
int center = stamp->getCenter(); |
| 594 |
|
std::vector<int> satellites = stamp->getSatellites(); |
| 595 |
|
if (satellites.size() != 3) { |
| 602 |
|
Atom* atomD = mol->getAtomAt(satellites[2]); |
| 603 |
|
|
| 604 |
|
assert(atomA && atomB && atomC && atomD); |
| 426 |
– |
|
| 427 |
– |
InversionType* inversionType = ff->getInversionType(atomA->getType(), |
| 428 |
– |
atomB->getType(), |
| 429 |
– |
atomC->getType(), |
| 430 |
– |
atomD->getType()); |
| 605 |
|
|
| 606 |
< |
if (inversionType == NULL) { |
| 433 |
< |
sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n" |
| 434 |
< |
"\t(May not be a problem: not all inversions are parametrized)\n", |
| 435 |
< |
atomA->getType().c_str(), |
| 436 |
< |
atomB->getType().c_str(), |
| 437 |
< |
atomC->getType().c_str(), |
| 438 |
< |
atomD->getType().c_str()); |
| 606 |
> |
if (stamp->hasOverride()) { |
| 607 |
|
|
| 608 |
< |
painCave.isFatal = 0; |
| 609 |
< |
painCave.severity = OPENMD_INFO; |
| 610 |
< |
simError(); |
| 611 |
< |
return NULL; |
| 608 |
> |
try { |
| 609 |
> |
inversionType = itParser.parseTypeAndPars(stamp->getOverrideType(), |
| 610 |
> |
stamp->getOverridePars() ); |
| 611 |
> |
} |
| 612 |
> |
catch( OpenMDException e) { |
| 613 |
> |
sprintf(painCave.errMsg, "MoleculeCreator Error: %s " |
| 614 |
> |
"for molecule %s\n", |
| 615 |
> |
e.what(), mol->getType().c_str() ); |
| 616 |
> |
painCave.isFatal = 1; |
| 617 |
> |
simError(); |
| 618 |
> |
} |
| 619 |
|
} else { |
| 620 |
|
|
| 621 |
+ |
inversionType = ff->getInversionType(atomA->getType(), |
| 622 |
+ |
atomB->getType(), |
| 623 |
+ |
atomC->getType(), |
| 624 |
+ |
atomD->getType()); |
| 625 |
+ |
|
| 626 |
+ |
if (inversionType == NULL) { |
| 627 |
+ |
sprintf(painCave.errMsg, |
| 628 |
+ |
"No Matching Inversion Type for[%s, %s, %s, %s]\n" |
| 629 |
+ |
"\t(May not be a problem: not all inversions are parametrized)\n", |
| 630 |
+ |
atomA->getType().c_str(), |
| 631 |
+ |
atomB->getType().c_str(), |
| 632 |
+ |
atomC->getType().c_str(), |
| 633 |
+ |
atomD->getType().c_str()); |
| 634 |
+ |
|
| 635 |
+ |
painCave.isFatal = 0; |
| 636 |
+ |
painCave.severity = OPENMD_INFO; |
| 637 |
+ |
simError(); |
| 638 |
+ |
} |
| 639 |
+ |
} |
| 640 |
+ |
if (inversionType != NULL) { |
| 641 |
+ |
|
| 642 |
|
inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType); |
| 643 |
+ |
|
| 644 |
+ |
// set the local index of this inversion, the global index will |
| 645 |
+ |
// be set later |
| 646 |
+ |
inversion->setLocalIndex(localIndexMan->getNextInversionIndex()); |
| 647 |
+ |
|
| 648 |
+ |
// The rule for naming an inversion is: MoleculeName_Inversion_Integer |
| 649 |
+ |
// The first part is the name of the molecule |
| 650 |
+ |
// The second part is always fixed as "Inversion" |
| 651 |
+ |
// The third part is the index of the inversion defined in meta-data file |
| 652 |
+ |
// For example, Benzene_Inversion_0 is a valid Inversion name in a |
| 653 |
+ |
// Benzene molecule |
| 654 |
+ |
|
| 655 |
+ |
std::string s = OpenMD_itoa(mol->getNInversions(), 10); |
| 656 |
+ |
inversion->setName(mol->getType() + "_Inversion_" + s.c_str()); |
| 657 |
|
return inversion; |
| 658 |
+ |
} else { |
| 659 |
+ |
return NULL; |
| 660 |
|
} |
| 661 |
|
} |
| 662 |
|
|
| 663 |
|
|
| 664 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
| 664 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, |
| 665 |
> |
CutoffGroupStamp* stamp, |
| 666 |
> |
LocalIndexManager* localIndexMan) { |
| 667 |
|
int nAtoms; |
| 668 |
|
CutoffGroup* cg; |
| 669 |
|
Atom* atom; |
| 675 |
|
assert(atom); |
| 676 |
|
cg->addAtom(atom); |
| 677 |
|
} |
| 678 |
< |
|
| 678 |
> |
|
| 679 |
> |
//set the local index of this cutoffGroup, global index will be set later |
| 680 |
> |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 681 |
> |
|
| 682 |
|
return cg; |
| 683 |
|
} |
| 684 |
< |
|
| 685 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
| 684 |
> |
|
| 685 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom, |
| 686 |
> |
LocalIndexManager* localIndexMan) { |
| 687 |
|
CutoffGroup* cg; |
| 688 |
|
cg = new CutoffGroup(); |
| 689 |
|
cg->addAtom(atom); |
| 690 |
+ |
|
| 691 |
+ |
//set the local index of this cutoffGroup, global index will be set later |
| 692 |
+ |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 693 |
+ |
|
| 694 |
|
return cg; |
| 695 |
|
} |
| 696 |
|
|
| 699 |
|
//add bond constraints |
| 700 |
|
Molecule::BondIterator bi; |
| 701 |
|
Bond* bond; |
| 702 |
+ |
ConstraintPair* cPair; |
| 703 |
+ |
|
| 704 |
|
for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) { |
| 705 |
|
|
| 706 |
|
BondType* bt = bond->getBondType(); |
| 707 |
|
|
| 484 |
– |
//class Parent1 {}; |
| 485 |
– |
//class Child1 : public Parent {}; |
| 486 |
– |
//class Child2 : public Parent {}; |
| 487 |
– |
//Child1* ch1 = new Child1(); |
| 488 |
– |
//Child2* ch2 = dynamic_cast<Child2*>(ch1); |
| 489 |
– |
//the dynamic_cast is succeed in above line. A compiler bug? |
| 490 |
– |
|
| 708 |
|
if (typeid(FixedBondType) == typeid(*bt)) { |
| 709 |
|
FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt); |
| 710 |
|
|
| 711 |
|
ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA()); |
| 712 |
|
ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB()); |
| 713 |
< |
ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength()); |
| 714 |
< |
mol->addConstraintPair(consPair); |
| 713 |
> |
cPair = new ConstraintPair(consElemA, consElemB, |
| 714 |
> |
fbt->getEquilibriumBondLength(), false); |
| 715 |
> |
mol->addConstraintPair(cPair); |
| 716 |
|
} |
| 717 |
|
} |
| 718 |
|
|
| 724 |
|
ConstraintPair* consPair; |
| 725 |
|
Molecule::ConstraintPairIterator cpi; |
| 726 |
|
std::set<StuntDouble*> sdSet; |
| 727 |
< |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) { |
| 727 |
> |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; |
| 728 |
> |
consPair = mol->nextConstraintPair(cpi)) { |
| 729 |
|
|
| 730 |
|
StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble(); |
| 731 |
|
if (sdSet.find(sdA) == sdSet.end()){ |
| 732 |
|
sdSet.insert(sdA); |
| 733 |
|
mol->addConstraintElem(new ConstraintElem(sdA)); |
| 734 |
|
} |
| 735 |
< |
|
| 735 |
> |
|
| 736 |
|
StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble(); |
| 737 |
|
if (sdSet.find(sdB) == sdSet.end()){ |
| 738 |
|
sdSet.insert(sdB); |
| 739 |
|
mol->addConstraintElem(new ConstraintElem(sdB)); |
| 740 |
< |
} |
| 522 |
< |
|
| 740 |
> |
} |
| 741 |
|
} |
| 524 |
– |
|
| 742 |
|
} |
| 526 |
– |
|
| 743 |
|
} |
