| 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 "utils/simError.h" |
| 60 |
|
#include "utils/StringUtils.hpp" |
| 65 |
|
MoleculeStamp *molStamp, |
| 66 |
|
int stampId, int globalIndex, |
| 67 |
|
LocalIndexManager* localIndexMan) { |
| 68 |
< |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
| 69 |
< |
|
| 68 |
> |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(), |
| 69 |
> |
molStamp->getRegion() ); |
| 70 |
> |
|
| 71 |
|
//create atoms |
| 72 |
|
Atom* atom; |
| 73 |
|
AtomStamp* currentAtomStamp; |
| 97 |
|
|
| 98 |
|
for (int i = 0; i < nBonds; ++i) { |
| 99 |
|
currentBondStamp = molStamp->getBondStamp(i); |
| 100 |
< |
bond = createBond(ff, mol, currentBondStamp); |
| 100 |
> |
bond = createBond(ff, mol, currentBondStamp, localIndexMan); |
| 101 |
|
mol->addBond(bond); |
| 102 |
|
} |
| 103 |
|
|
| 107 |
|
int nBends = molStamp->getNBends(); |
| 108 |
|
for (int i = 0; i < nBends; ++i) { |
| 109 |
|
currentBendStamp = molStamp->getBendStamp(i); |
| 110 |
< |
bend = createBend(ff, mol, currentBendStamp); |
| 110 |
> |
bend = createBend(ff, mol, currentBendStamp, localIndexMan); |
| 111 |
|
mol->addBend(bend); |
| 112 |
|
} |
| 113 |
|
|
| 117 |
|
int nTorsions = molStamp->getNTorsions(); |
| 118 |
|
for (int i = 0; i < nTorsions; ++i) { |
| 119 |
|
currentTorsionStamp = molStamp->getTorsionStamp(i); |
| 120 |
< |
torsion = createTorsion(ff, mol, currentTorsionStamp); |
| 120 |
> |
torsion = createTorsion(ff, mol, currentTorsionStamp, localIndexMan); |
| 121 |
|
mol->addTorsion(torsion); |
| 122 |
|
} |
| 123 |
|
|
| 127 |
|
int nInversions = molStamp->getNInversions(); |
| 128 |
|
for (int i = 0; i < nInversions; ++i) { |
| 129 |
|
currentInversionStamp = molStamp->getInversionStamp(i); |
| 130 |
< |
inversion = createInversion(ff, mol, currentInversionStamp); |
| 130 |
> |
inversion = createInversion(ff, mol, currentInversionStamp, |
| 131 |
> |
localIndexMan); |
| 132 |
|
if (inversion != NULL ) { |
| 133 |
|
mol->addInversion(inversion); |
| 134 |
|
} |
| 140 |
|
int nCutoffGroups = molStamp->getNCutoffGroups(); |
| 141 |
|
for (int i = 0; i < nCutoffGroups; ++i) { |
| 142 |
|
currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
| 143 |
< |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
| 143 |
> |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, |
| 144 |
> |
localIndexMan); |
| 145 |
|
mol->addCutoffGroup(cutoffGroup); |
| 146 |
|
} |
| 147 |
|
|
| 172 |
|
// every single free atom |
| 173 |
|
|
| 174 |
|
for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
| 175 |
< |
cutoffGroup = createCutoffGroup(mol, *fai); |
| 175 |
> |
cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan); |
| 176 |
|
mol->addCutoffGroup(cutoffGroup); |
| 177 |
|
} |
| 178 |
< |
//create constraints |
| 178 |
> |
|
| 179 |
> |
//create bonded constraintPairs: |
| 180 |
|
createConstraintPair(mol); |
| 181 |
+ |
|
| 182 |
+ |
//create non-bonded constraintPairs |
| 183 |
+ |
for (int i = 0; i < molStamp->getNConstraints(); ++i) { |
| 184 |
+ |
ConstraintStamp* cStamp = molStamp->getConstraintStamp(i); |
| 185 |
+ |
Atom* atomA; |
| 186 |
+ |
Atom* atomB; |
| 187 |
+ |
|
| 188 |
+ |
atomA = mol->getAtomAt(cStamp->getA()); |
| 189 |
+ |
atomB = mol->getAtomAt(cStamp->getB()); |
| 190 |
+ |
assert( atomA && atomB ); |
| 191 |
+ |
|
| 192 |
+ |
RealType distance; |
| 193 |
+ |
bool printConstraintForce = false; |
| 194 |
+ |
|
| 195 |
+ |
if (!cStamp->haveConstrainedDistance()) { |
| 196 |
+ |
sprintf(painCave.errMsg, |
| 197 |
+ |
"Constraint Error: A non-bond constraint was specified\n" |
| 198 |
+ |
"\twithout providing a value for the constrainedDistance.\n"); |
| 199 |
+ |
painCave.isFatal = 1; |
| 200 |
+ |
simError(); |
| 201 |
+ |
} else { |
| 202 |
+ |
distance = cStamp->getConstrainedDistance(); |
| 203 |
+ |
} |
| 204 |
+ |
|
| 205 |
+ |
if (cStamp->havePrintConstraintForce()) { |
| 206 |
+ |
printConstraintForce = cStamp->getPrintConstraintForce(); |
| 207 |
+ |
} |
| 208 |
+ |
|
| 209 |
+ |
ConstraintElem* consElemA = new ConstraintElem(atomA); |
| 210 |
+ |
ConstraintElem* consElemB = new ConstraintElem(atomB); |
| 211 |
+ |
ConstraintPair* cPair = new ConstraintPair(consElemA, consElemB, distance, |
| 212 |
+ |
printConstraintForce); |
| 213 |
+ |
mol->addConstraintPair(cPair); |
| 214 |
+ |
} |
| 215 |
+ |
|
| 216 |
+ |
// now create the constraint elements: |
| 217 |
+ |
|
| 218 |
|
createConstraintElem(mol); |
| 219 |
|
|
| 220 |
+ |
// Does this molecule stamp define a total constrained charge value? |
| 221 |
+ |
// If so, let the created molecule know about it. |
| 222 |
+ |
|
| 223 |
+ |
if (molStamp->haveConstrainTotalCharge() ) { |
| 224 |
+ |
mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() ); |
| 225 |
+ |
} |
| 226 |
+ |
|
| 227 |
|
//the construction of this molecule is finished |
| 228 |
|
mol->complete(); |
| 229 |
|
|
| 246 |
|
painCave.isFatal = 1; |
| 247 |
|
simError(); |
| 248 |
|
} |
| 249 |
< |
|
| 249 |
> |
|
| 250 |
|
//below code still have some kind of hard-coding smell |
| 251 |
|
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"); |
| 252 |
|
|
| 210 |
– |
painCave.isFatal = 1; |
| 211 |
– |
simError(); |
| 212 |
– |
} |
| 213 |
– |
|
| 253 |
|
DirectionalAtom* dAtom; |
| 254 |
< |
dAtom = new DirectionalAtom(dAtomType); |
| 254 |
> |
dAtom = new DirectionalAtom(atomType); |
| 255 |
|
atom = dAtom; |
| 256 |
|
} |
| 257 |
|
else{ |
| 266 |
|
RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, |
| 267 |
|
Molecule* mol, |
| 268 |
|
RigidBodyStamp* rbStamp, |
| 269 |
< |
LocalIndexManager* localIndexMan) { |
| 269 |
> |
LocalIndexManager* localIndexMan){ |
| 270 |
|
Atom* atom; |
| 271 |
|
int nAtoms; |
| 272 |
|
Vector3d refCoor; |
| 290 |
|
//set the local index of this rigid body, global index will be set later |
| 291 |
|
rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex()); |
| 292 |
|
|
| 293 |
< |
//the rule for naming rigidbody MoleculeName_RB_Integer |
| 294 |
< |
//The first part is the name of the molecule |
| 295 |
< |
//The second part is alway fixed as "RB" |
| 296 |
< |
//The third part is the index of the rigidbody defined in meta-data file |
| 297 |
< |
//For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 298 |
< |
/**@todo replace itoa by lexi_cast */ |
| 293 |
> |
// The rule for naming a rigidbody is: MoleculeName_RB_Integer |
| 294 |
> |
// The first part is the name of the molecule |
| 295 |
> |
// The second part is always fixed as "RB" |
| 296 |
> |
// The third part is the index of the rigidbody defined in meta-data file |
| 297 |
> |
// For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 298 |
> |
|
| 299 |
|
std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10); |
| 300 |
|
rb->setType(mol->getType() + "_RB_" + s.c_str()); |
| 262 |
– |
|
| 301 |
|
return rb; |
| 302 |
|
} |
| 303 |
|
|
| 304 |
|
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, |
| 305 |
< |
BondStamp* stamp) { |
| 305 |
> |
BondStamp* stamp, |
| 306 |
> |
LocalIndexManager* localIndexMan) { |
| 307 |
|
BondType* bondType; |
| 308 |
|
Atom* atomA; |
| 309 |
|
Atom* atomB; |
| 323 |
|
painCave.isFatal = 1; |
| 324 |
|
simError(); |
| 325 |
|
} |
| 326 |
< |
return new Bond(atomA, atomB, bondType); |
| 326 |
> |
Bond* bond = new Bond(atomA, atomB, bondType); |
| 327 |
> |
|
| 328 |
> |
//set the local index of this bond, the global index will be set later |
| 329 |
> |
bond->setLocalIndex(localIndexMan->getNextBondIndex()); |
| 330 |
> |
|
| 331 |
> |
// The rule for naming a bond is: MoleculeName_Bond_Integer |
| 332 |
> |
// The first part is the name of the molecule |
| 333 |
> |
// The second part is always fixed as "Bond" |
| 334 |
> |
// The third part is the index of the bond defined in meta-data file |
| 335 |
> |
// For example, Butane_bond_0 is a valid Bond name in a butane molecule |
| 336 |
> |
|
| 337 |
> |
std::string s = OpenMD_itoa(mol->getNBonds(), 10); |
| 338 |
> |
bond->setName(mol->getType() + "_Bond_" + s.c_str()); |
| 339 |
> |
return bond; |
| 340 |
|
} |
| 341 |
|
|
| 342 |
|
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, |
| 343 |
< |
BendStamp* stamp) { |
| 343 |
> |
BendStamp* stamp, |
| 344 |
> |
LocalIndexManager* localIndexMan) { |
| 345 |
|
Bend* bend = NULL; |
| 346 |
|
std::vector<int> bendAtoms = stamp->getMembers(); |
| 347 |
|
if (bendAtoms.size() == 3) { |
| 356 |
|
atomC->getType().c_str()); |
| 357 |
|
|
| 358 |
|
if (bendType == NULL) { |
| 359 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
| 359 |
> |
sprintf(painCave.errMsg, |
| 360 |
> |
"Can not find Matching Bend Type for[%s, %s, %s]", |
| 361 |
|
atomA->getType().c_str(), |
| 362 |
|
atomB->getType().c_str(), |
| 363 |
|
atomC->getType().c_str()); |
| 381 |
|
BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
| 382 |
|
|
| 383 |
|
if (bendType == NULL) { |
| 384 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
| 384 |
> |
sprintf(painCave.errMsg, |
| 385 |
> |
"Can not find Matching Bend Type for[%s, %s, %s]", |
| 386 |
|
normalAtom->getType().c_str(), |
| 387 |
|
ghostAtom->getType().c_str(), |
| 388 |
|
"GHOST"); |
| 394 |
|
bend = new GhostBend(normalAtom, ghostAtom, bendType); |
| 395 |
|
|
| 396 |
|
} |
| 397 |
< |
|
| 397 |
> |
|
| 398 |
> |
//set the local index of this bend, the global index will be set later |
| 399 |
> |
bend->setLocalIndex(localIndexMan->getNextBendIndex()); |
| 400 |
> |
|
| 401 |
> |
// The rule for naming a bend is: MoleculeName_Bend_Integer |
| 402 |
> |
// The first part is the name of the molecule |
| 403 |
> |
// The second part is always fixed as "Bend" |
| 404 |
> |
// The third part is the index of the bend defined in meta-data file |
| 405 |
> |
// For example, Butane_Bend_0 is a valid Bend name in a butane molecule |
| 406 |
> |
|
| 407 |
> |
std::string s = OpenMD_itoa(mol->getNBends(), 10); |
| 408 |
> |
bend->setName(mol->getType() + "_Bend_" + s.c_str()); |
| 409 |
|
return bend; |
| 410 |
|
} |
| 411 |
|
|
| 412 |
|
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, |
| 413 |
< |
TorsionStamp* stamp) { |
| 413 |
> |
TorsionStamp* stamp, |
| 414 |
> |
LocalIndexManager* localIndexMan) { |
| 415 |
|
|
| 416 |
|
Torsion* torsion = NULL; |
| 417 |
|
std::vector<int> torsionAtoms = stamp->getMembers(); |
| 433 |
|
atomC->getType(), |
| 434 |
|
atomD->getType()); |
| 435 |
|
if (torsionType == NULL) { |
| 436 |
< |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 436 |
> |
sprintf(painCave.errMsg, |
| 437 |
> |
"Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 438 |
|
atomA->getType().c_str(), |
| 439 |
|
atomB->getType().c_str(), |
| 440 |
|
atomC->getType().c_str(), |
| 471 |
|
|
| 472 |
|
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
| 473 |
|
} |
| 474 |
+ |
|
| 475 |
+ |
//set the local index of this torsion, the global index will be set later |
| 476 |
+ |
torsion->setLocalIndex(localIndexMan->getNextTorsionIndex()); |
| 477 |
|
|
| 478 |
+ |
// The rule for naming a torsion is: MoleculeName_Torsion_Integer |
| 479 |
+ |
// The first part is the name of the molecule |
| 480 |
+ |
// The second part is always fixed as "Torsion" |
| 481 |
+ |
// The third part is the index of the torsion defined in meta-data file |
| 482 |
+ |
// For example, Butane_Torsion_0 is a valid Torsion name in a |
| 483 |
+ |
// butane molecule |
| 484 |
+ |
|
| 485 |
+ |
std::string s = OpenMD_itoa(mol->getNTorsions(), 10); |
| 486 |
+ |
torsion->setName(mol->getType() + "_Torsion_" + s.c_str()); |
| 487 |
|
return torsion; |
| 488 |
|
} |
| 489 |
|
|
| 490 |
|
Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, |
| 491 |
< |
InversionStamp* stamp) { |
| 491 |
> |
InversionStamp* stamp, |
| 492 |
> |
LocalIndexManager* localIndexMan) { |
| 493 |
|
|
| 494 |
|
Inversion* inversion = NULL; |
| 495 |
|
int center = stamp->getCenter(); |
| 525 |
|
} else { |
| 526 |
|
|
| 527 |
|
inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType); |
| 528 |
+ |
|
| 529 |
+ |
// set the local index of this inversion, the global index will |
| 530 |
+ |
// be set later |
| 531 |
+ |
inversion->setLocalIndex(localIndexMan->getNextInversionIndex()); |
| 532 |
+ |
|
| 533 |
+ |
// The rule for naming an inversion is: MoleculeName_Inversion_Integer |
| 534 |
+ |
// The first part is the name of the molecule |
| 535 |
+ |
// The second part is always fixed as "Inversion" |
| 536 |
+ |
// The third part is the index of the inversion defined in meta-data file |
| 537 |
+ |
// For example, Benzene_Inversion_0 is a valid Inversion name in a |
| 538 |
+ |
// Benzene molecule |
| 539 |
+ |
|
| 540 |
+ |
std::string s = OpenMD_itoa(mol->getNInversions(), 10); |
| 541 |
+ |
inversion->setName(mol->getType() + "_Inversion_" + s.c_str()); |
| 542 |
|
return inversion; |
| 543 |
|
} |
| 544 |
|
} |
| 545 |
|
|
| 546 |
|
|
| 547 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
| 547 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, |
| 548 |
> |
CutoffGroupStamp* stamp, |
| 549 |
> |
LocalIndexManager* localIndexMan) { |
| 550 |
|
int nAtoms; |
| 551 |
|
CutoffGroup* cg; |
| 552 |
|
Atom* atom; |
| 558 |
|
assert(atom); |
| 559 |
|
cg->addAtom(atom); |
| 560 |
|
} |
| 561 |
< |
|
| 561 |
> |
|
| 562 |
> |
//set the local index of this cutoffGroup, global index will be set later |
| 563 |
> |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 564 |
> |
|
| 565 |
|
return cg; |
| 566 |
|
} |
| 567 |
< |
|
| 568 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
| 567 |
> |
|
| 568 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom, |
| 569 |
> |
LocalIndexManager* localIndexMan) { |
| 570 |
|
CutoffGroup* cg; |
| 571 |
|
cg = new CutoffGroup(); |
| 572 |
|
cg->addAtom(atom); |
| 573 |
+ |
|
| 574 |
+ |
//set the local index of this cutoffGroup, global index will be set later |
| 575 |
+ |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 576 |
+ |
|
| 577 |
|
return cg; |
| 578 |
|
} |
| 579 |
|
|
| 582 |
|
//add bond constraints |
| 583 |
|
Molecule::BondIterator bi; |
| 584 |
|
Bond* bond; |
| 585 |
+ |
ConstraintPair* cPair; |
| 586 |
+ |
|
| 587 |
|
for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) { |
| 588 |
|
|
| 589 |
|
BondType* bt = bond->getBondType(); |
| 590 |
|
|
| 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 |
– |
|
| 591 |
|
if (typeid(FixedBondType) == typeid(*bt)) { |
| 592 |
|
FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt); |
| 593 |
|
|
| 594 |
|
ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA()); |
| 595 |
|
ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB()); |
| 596 |
< |
ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength()); |
| 597 |
< |
mol->addConstraintPair(consPair); |
| 596 |
> |
cPair = new ConstraintPair(consElemA, consElemB, |
| 597 |
> |
fbt->getEquilibriumBondLength(), false); |
| 598 |
> |
mol->addConstraintPair(cPair); |
| 599 |
|
} |
| 600 |
|
} |
| 601 |
|
|
| 607 |
|
ConstraintPair* consPair; |
| 608 |
|
Molecule::ConstraintPairIterator cpi; |
| 609 |
|
std::set<StuntDouble*> sdSet; |
| 610 |
< |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) { |
| 610 |
> |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; |
| 611 |
> |
consPair = mol->nextConstraintPair(cpi)) { |
| 612 |
|
|
| 613 |
|
StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble(); |
| 614 |
|
if (sdSet.find(sdA) == sdSet.end()){ |
| 615 |
|
sdSet.insert(sdA); |
| 616 |
|
mol->addConstraintElem(new ConstraintElem(sdA)); |
| 617 |
|
} |
| 618 |
< |
|
| 618 |
> |
|
| 619 |
|
StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble(); |
| 620 |
|
if (sdSet.find(sdB) == sdSet.end()){ |
| 621 |
|
sdSet.insert(sdB); |
| 622 |
|
mol->addConstraintElem(new ConstraintElem(sdB)); |
| 623 |
< |
} |
| 522 |
< |
|
| 623 |
> |
} |
| 624 |
|
} |
| 524 |
– |
|
| 625 |
|
} |
| 526 |
– |
|
| 626 |
|
} |
