| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
* publication of scientific results based in part on use of the |
| 11 |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
* the article in which the program was described (Matthew |
| 13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
* |
| 18 |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
/** |
| 43 |
* @file MoleculeCreator.cpp |
| 44 |
* @author tlin |
| 45 |
* @date 11/04/2004 |
| 46 |
* @time 13:44am |
| 47 |
* @version 1.0 |
| 48 |
*/ |
| 49 |
|
| 50 |
#include <cassert> |
| 51 |
#include <typeinfo> |
| 52 |
#include <set> |
| 53 |
|
| 54 |
#include "brains/MoleculeCreator.hpp" |
| 55 |
#include "primitives/GhostBend.hpp" |
| 56 |
#include "primitives/GhostTorsion.hpp" |
| 57 |
#include "types/DirectionalAtomType.hpp" |
| 58 |
#include "types/FixedBondType.hpp" |
| 59 |
#include "utils/simError.h" |
| 60 |
#include "utils/StringUtils.hpp" |
| 61 |
|
| 62 |
namespace oopse { |
| 63 |
|
| 64 |
Molecule* MoleculeCreator::createMolecule(ForceField* ff, |
| 65 |
MoleculeStamp *molStamp, |
| 66 |
int stampId, int globalIndex, |
| 67 |
LocalIndexManager* localIndexMan) { |
| 68 |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
| 69 |
|
| 70 |
//create atoms |
| 71 |
Atom* atom; |
| 72 |
AtomStamp* currentAtomStamp; |
| 73 |
int nAtom = molStamp->getNAtoms(); |
| 74 |
for (int i = 0; i < nAtom; ++i) { |
| 75 |
currentAtomStamp = molStamp->getAtomStamp(i); |
| 76 |
atom = createAtom(ff, mol, currentAtomStamp, localIndexMan); |
| 77 |
mol->addAtom(atom); |
| 78 |
} |
| 79 |
|
| 80 |
//create rigidbodies |
| 81 |
RigidBody* rb; |
| 82 |
RigidBodyStamp * currentRigidBodyStamp; |
| 83 |
int nRigidbodies = molStamp->getNRigidBodies(); |
| 84 |
|
| 85 |
for (int i = 0; i < nRigidbodies; ++i) { |
| 86 |
currentRigidBodyStamp = molStamp->getRigidBodyStamp(i); |
| 87 |
rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, |
| 88 |
localIndexMan); |
| 89 |
mol->addRigidBody(rb); |
| 90 |
} |
| 91 |
|
| 92 |
//create bonds |
| 93 |
Bond* bond; |
| 94 |
BondStamp* currentBondStamp; |
| 95 |
int nBonds = molStamp->getNBonds(); |
| 96 |
|
| 97 |
for (int i = 0; i < nBonds; ++i) { |
| 98 |
currentBondStamp = molStamp->getBondStamp(i); |
| 99 |
bond = createBond(ff, mol, currentBondStamp); |
| 100 |
mol->addBond(bond); |
| 101 |
} |
| 102 |
|
| 103 |
//create bends |
| 104 |
Bend* bend; |
| 105 |
BendStamp* currentBendStamp; |
| 106 |
int nBends = molStamp->getNBends(); |
| 107 |
for (int i = 0; i < nBends; ++i) { |
| 108 |
currentBendStamp = molStamp->getBendStamp(i); |
| 109 |
bend = createBend(ff, mol, currentBendStamp); |
| 110 |
mol->addBend(bend); |
| 111 |
} |
| 112 |
|
| 113 |
//create torsions |
| 114 |
Torsion* torsion; |
| 115 |
TorsionStamp* currentTorsionStamp; |
| 116 |
int nTorsions = molStamp->getNTorsions(); |
| 117 |
for (int i = 0; i < nTorsions; ++i) { |
| 118 |
currentTorsionStamp = molStamp->getTorsionStamp(i); |
| 119 |
torsion = createTorsion(ff, mol, currentTorsionStamp); |
| 120 |
mol->addTorsion(torsion); |
| 121 |
} |
| 122 |
|
| 123 |
//create inversions |
| 124 |
Inversion* inversion; |
| 125 |
InversionStamp* currentInversionStamp; |
| 126 |
int nInversions = molStamp->getNInversions(); |
| 127 |
for (int i = 0; i < nInversions; ++i) { |
| 128 |
currentInversionStamp = molStamp->getInversionStamp(i); |
| 129 |
inversion = createInversion(ff, mol, currentInversionStamp); |
| 130 |
if (inversion != NULL ) { |
| 131 |
mol->addInversion(inversion); |
| 132 |
} |
| 133 |
} |
| 134 |
|
| 135 |
//create cutoffGroups |
| 136 |
CutoffGroup* cutoffGroup; |
| 137 |
CutoffGroupStamp* currentCutoffGroupStamp; |
| 138 |
int nCutoffGroups = molStamp->getNCutoffGroups(); |
| 139 |
for (int i = 0; i < nCutoffGroups; ++i) { |
| 140 |
currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
| 141 |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
| 142 |
mol->addCutoffGroup(cutoffGroup); |
| 143 |
} |
| 144 |
|
| 145 |
//every free atom is a cutoff group |
| 146 |
std::vector<Atom*> freeAtoms; |
| 147 |
std::vector<Atom*>::iterator ai; |
| 148 |
std::vector<Atom*>::iterator fai; |
| 149 |
|
| 150 |
//add all atoms into allAtoms set |
| 151 |
for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) { |
| 152 |
freeAtoms.push_back(atom); |
| 153 |
} |
| 154 |
|
| 155 |
Molecule::CutoffGroupIterator ci; |
| 156 |
CutoffGroup* cg; |
| 157 |
|
| 158 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 159 |
cg = mol->nextCutoffGroup(ci)) { |
| 160 |
|
| 161 |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 162 |
//erase the atoms belong to cutoff groups from freeAtoms vector |
| 163 |
freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), |
| 164 |
freeAtoms.end()); |
| 165 |
} |
| 166 |
} |
| 167 |
|
| 168 |
// loop over the free atoms and then create one cutoff group for |
| 169 |
// every single free atom |
| 170 |
|
| 171 |
for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
| 172 |
cutoffGroup = createCutoffGroup(mol, *fai); |
| 173 |
mol->addCutoffGroup(cutoffGroup); |
| 174 |
} |
| 175 |
//create constraints |
| 176 |
createConstraintPair(mol); |
| 177 |
createConstraintElem(mol); |
| 178 |
|
| 179 |
//the construction of this molecule is finished |
| 180 |
mol->complete(); |
| 181 |
|
| 182 |
return mol; |
| 183 |
} |
| 184 |
|
| 185 |
|
| 186 |
Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, |
| 187 |
AtomStamp* stamp, |
| 188 |
LocalIndexManager* localIndexMan) { |
| 189 |
AtomType * atomType; |
| 190 |
Atom* atom; |
| 191 |
|
| 192 |
atomType = ff->getAtomType(stamp->getType()); |
| 193 |
|
| 194 |
if (atomType == NULL) { |
| 195 |
sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]", |
| 196 |
stamp->getType().c_str()); |
| 197 |
|
| 198 |
painCave.isFatal = 1; |
| 199 |
simError(); |
| 200 |
} |
| 201 |
|
| 202 |
//below code still have some kind of hard-coding smell |
| 203 |
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"); |
| 209 |
|
| 210 |
painCave.isFatal = 1; |
| 211 |
simError(); |
| 212 |
} |
| 213 |
|
| 214 |
DirectionalAtom* dAtom; |
| 215 |
dAtom = new DirectionalAtom(dAtomType); |
| 216 |
atom = dAtom; |
| 217 |
} |
| 218 |
else{ |
| 219 |
atom = new Atom(atomType); |
| 220 |
} |
| 221 |
|
| 222 |
atom->setLocalIndex(localIndexMan->getNextAtomIndex()); |
| 223 |
|
| 224 |
return atom; |
| 225 |
} |
| 226 |
|
| 227 |
RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, |
| 228 |
Molecule* mol, |
| 229 |
RigidBodyStamp* rbStamp, |
| 230 |
LocalIndexManager* localIndexMan) { |
| 231 |
Atom* atom; |
| 232 |
int nAtoms; |
| 233 |
Vector3d refCoor; |
| 234 |
AtomStamp* atomStamp; |
| 235 |
|
| 236 |
RigidBody* rb = new RigidBody(); |
| 237 |
nAtoms = rbStamp->getNMembers(); |
| 238 |
for (int i = 0; i < nAtoms; ++i) { |
| 239 |
//rbStamp->getMember(i) return the local index of current atom |
| 240 |
//inside the molecule. It is not the same as local index of |
| 241 |
//atom which is the index of atom at DataStorage class |
| 242 |
atom = mol->getAtomAt(rbStamp->getMemberAt(i)); |
| 243 |
atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i)); |
| 244 |
rb->addAtom(atom, atomStamp); |
| 245 |
} |
| 246 |
|
| 247 |
//after all of the atoms are added, we need to calculate the |
| 248 |
//reference coordinates |
| 249 |
rb->calcRefCoords(); |
| 250 |
|
| 251 |
//set the local index of this rigid body, global index will be set later |
| 252 |
rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex()); |
| 253 |
|
| 254 |
//the rule for naming rigidbody MoleculeName_RB_Integer |
| 255 |
//The first part is the name of the molecule |
| 256 |
//The second part is alway fixed as "RB" |
| 257 |
//The third part is the index of the rigidbody defined in meta-data file |
| 258 |
//For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 259 |
/**@todo replace itoa by lexi_cast */ |
| 260 |
std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10); |
| 261 |
rb->setType(mol->getType() + "_RB_" + s.c_str()); |
| 262 |
|
| 263 |
return rb; |
| 264 |
} |
| 265 |
|
| 266 |
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, |
| 267 |
BondStamp* stamp) { |
| 268 |
BondType* bondType; |
| 269 |
Atom* atomA; |
| 270 |
Atom* atomB; |
| 271 |
|
| 272 |
atomA = mol->getAtomAt(stamp->getA()); |
| 273 |
atomB = mol->getAtomAt(stamp->getB()); |
| 274 |
|
| 275 |
assert( atomA && atomB); |
| 276 |
|
| 277 |
bondType = ff->getBondType(atomA->getType(), atomB->getType()); |
| 278 |
|
| 279 |
if (bondType == NULL) { |
| 280 |
sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
| 281 |
atomA->getType().c_str(), |
| 282 |
atomB->getType().c_str()); |
| 283 |
|
| 284 |
painCave.isFatal = 1; |
| 285 |
simError(); |
| 286 |
} |
| 287 |
return new Bond(atomA, atomB, bondType); |
| 288 |
} |
| 289 |
|
| 290 |
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, |
| 291 |
BendStamp* stamp) { |
| 292 |
Bend* bend = NULL; |
| 293 |
std::vector<int> bendAtoms = stamp->getMembers(); |
| 294 |
if (bendAtoms.size() == 3) { |
| 295 |
Atom* atomA = mol->getAtomAt(bendAtoms[0]); |
| 296 |
Atom* atomB = mol->getAtomAt(bendAtoms[1]); |
| 297 |
Atom* atomC = mol->getAtomAt(bendAtoms[2]); |
| 298 |
|
| 299 |
assert( atomA && atomB && atomC); |
| 300 |
|
| 301 |
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()); |
| 310 |
|
| 311 |
painCave.isFatal = 1; |
| 312 |
simError(); |
| 313 |
} |
| 314 |
|
| 315 |
bend = new Bend(atomA, atomB, atomC, bendType); |
| 316 |
} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) { |
| 317 |
int ghostIndex = stamp->getGhostVectorSource(); |
| 318 |
int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1]; |
| 319 |
Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
| 320 |
DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex)); |
| 321 |
if (ghostAtom == NULL) { |
| 322 |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
| 323 |
painCave.isFatal = 1; |
| 324 |
simError(); |
| 325 |
} |
| 326 |
|
| 327 |
BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
| 328 |
|
| 329 |
if (bendType == NULL) { |
| 330 |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
| 331 |
normalAtom->getType().c_str(), |
| 332 |
ghostAtom->getType().c_str(), |
| 333 |
"GHOST"); |
| 334 |
|
| 335 |
painCave.isFatal = 1; |
| 336 |
simError(); |
| 337 |
} |
| 338 |
|
| 339 |
bend = new GhostBend(normalAtom, ghostAtom, bendType); |
| 340 |
|
| 341 |
} |
| 342 |
|
| 343 |
return bend; |
| 344 |
} |
| 345 |
|
| 346 |
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, |
| 347 |
TorsionStamp* stamp) { |
| 348 |
|
| 349 |
Torsion* torsion = NULL; |
| 350 |
std::vector<int> torsionAtoms = stamp->getMembers(); |
| 351 |
if (torsionAtoms.size() < 3) { |
| 352 |
return torsion; |
| 353 |
} |
| 354 |
|
| 355 |
Atom* atomA = mol->getAtomAt(torsionAtoms[0]); |
| 356 |
Atom* atomB = mol->getAtomAt(torsionAtoms[1]); |
| 357 |
Atom* atomC = mol->getAtomAt(torsionAtoms[2]); |
| 358 |
|
| 359 |
if (torsionAtoms.size() == 4) { |
| 360 |
Atom* atomD = mol->getAtomAt(torsionAtoms[3]); |
| 361 |
|
| 362 |
assert(atomA && atomB && atomC && atomD); |
| 363 |
|
| 364 |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), |
| 365 |
atomB->getType(), |
| 366 |
atomC->getType(), |
| 367 |
atomD->getType()); |
| 368 |
|
| 369 |
if (torsionType == NULL) { |
| 370 |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 371 |
atomA->getType().c_str(), |
| 372 |
atomB->getType().c_str(), |
| 373 |
atomC->getType().c_str(), |
| 374 |
atomD->getType().c_str()); |
| 375 |
|
| 376 |
painCave.isFatal = 1; |
| 377 |
simError(); |
| 378 |
} |
| 379 |
|
| 380 |
torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType); |
| 381 |
} |
| 382 |
else { |
| 383 |
|
| 384 |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource())); |
| 385 |
if (dAtom == NULL) { |
| 386 |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
| 387 |
painCave.isFatal = 1; |
| 388 |
simError(); |
| 389 |
} |
| 390 |
|
| 391 |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
| 392 |
atomC->getType(), "GHOST"); |
| 393 |
|
| 394 |
if (torsionType == NULL) { |
| 395 |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 396 |
atomA->getType().c_str(), |
| 397 |
atomB->getType().c_str(), |
| 398 |
atomC->getType().c_str(), |
| 399 |
"GHOST"); |
| 400 |
|
| 401 |
painCave.isFatal = 1; |
| 402 |
simError(); |
| 403 |
} |
| 404 |
|
| 405 |
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
| 406 |
} |
| 407 |
|
| 408 |
return torsion; |
| 409 |
} |
| 410 |
|
| 411 |
Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, |
| 412 |
InversionStamp* stamp) { |
| 413 |
|
| 414 |
Inversion* inversion = NULL; |
| 415 |
int center = stamp->getCenter(); |
| 416 |
std::vector<int> satellites = stamp->getSatellites(); |
| 417 |
if (satellites.size() != 3) { |
| 418 |
return inversion; |
| 419 |
} |
| 420 |
|
| 421 |
Atom* atomA = mol->getAtomAt(center); |
| 422 |
Atom* atomB = mol->getAtomAt(satellites[0]); |
| 423 |
Atom* atomC = mol->getAtomAt(satellites[1]); |
| 424 |
Atom* atomD = mol->getAtomAt(satellites[2]); |
| 425 |
|
| 426 |
assert(atomA && atomB && atomC && atomD); |
| 427 |
|
| 428 |
InversionType* inversionType = ff->getInversionType(atomA->getType(), |
| 429 |
atomB->getType(), |
| 430 |
atomC->getType(), |
| 431 |
atomD->getType()); |
| 432 |
|
| 433 |
if (inversionType == NULL) { |
| 434 |
sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n" |
| 435 |
"\t(May not be a problem: not all inversions are parametrized)\n", |
| 436 |
atomA->getType().c_str(), |
| 437 |
atomB->getType().c_str(), |
| 438 |
atomC->getType().c_str(), |
| 439 |
atomD->getType().c_str()); |
| 440 |
|
| 441 |
painCave.isFatal = 0; |
| 442 |
painCave.severity = OOPSE_INFO; |
| 443 |
simError(); |
| 444 |
return NULL; |
| 445 |
} else { |
| 446 |
|
| 447 |
inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType); |
| 448 |
return inversion; |
| 449 |
} |
| 450 |
} |
| 451 |
|
| 452 |
|
| 453 |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
| 454 |
int nAtoms; |
| 455 |
CutoffGroup* cg; |
| 456 |
Atom* atom; |
| 457 |
cg = new CutoffGroup(); |
| 458 |
|
| 459 |
nAtoms = stamp->getNMembers(); |
| 460 |
for (int i =0; i < nAtoms; ++i) { |
| 461 |
atom = mol->getAtomAt(stamp->getMemberAt(i)); |
| 462 |
assert(atom); |
| 463 |
cg->addAtom(atom); |
| 464 |
} |
| 465 |
|
| 466 |
return cg; |
| 467 |
} |
| 468 |
|
| 469 |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
| 470 |
CutoffGroup* cg; |
| 471 |
cg = new CutoffGroup(); |
| 472 |
cg->addAtom(atom); |
| 473 |
return cg; |
| 474 |
} |
| 475 |
|
| 476 |
void MoleculeCreator::createConstraintPair(Molecule* mol) { |
| 477 |
|
| 478 |
//add bond constraints |
| 479 |
Molecule::BondIterator bi; |
| 480 |
Bond* bond; |
| 481 |
for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) { |
| 482 |
|
| 483 |
BondType* bt = bond->getBondType(); |
| 484 |
|
| 485 |
//class Parent1 {}; |
| 486 |
//class Child1 : public Parent {}; |
| 487 |
//class Child2 : public Parent {}; |
| 488 |
//Child1* ch1 = new Child1(); |
| 489 |
//Child2* ch2 = dynamic_cast<Child2*>(ch1); |
| 490 |
//the dynamic_cast is succeed in above line. A compiler bug? |
| 491 |
|
| 492 |
if (typeid(FixedBondType) == typeid(*bt)) { |
| 493 |
FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt); |
| 494 |
|
| 495 |
ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA()); |
| 496 |
ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB()); |
| 497 |
ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength()); |
| 498 |
mol->addConstraintPair(consPair); |
| 499 |
} |
| 500 |
} |
| 501 |
|
| 502 |
//rigidbody -- rigidbody constraint is not support yet |
| 503 |
} |
| 504 |
|
| 505 |
void MoleculeCreator::createConstraintElem(Molecule* mol) { |
| 506 |
|
| 507 |
ConstraintPair* consPair; |
| 508 |
Molecule::ConstraintPairIterator cpi; |
| 509 |
std::set<StuntDouble*> sdSet; |
| 510 |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) { |
| 511 |
|
| 512 |
StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble(); |
| 513 |
if (sdSet.find(sdA) == sdSet.end()){ |
| 514 |
sdSet.insert(sdA); |
| 515 |
mol->addConstraintElem(new ConstraintElem(sdA)); |
| 516 |
} |
| 517 |
|
| 518 |
StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble(); |
| 519 |
if (sdSet.find(sdB) == sdSet.end()){ |
| 520 |
sdSet.insert(sdB); |
| 521 |
mol->addConstraintElem(new ConstraintElem(sdB)); |
| 522 |
} |
| 523 |
|
| 524 |
} |
| 525 |
|
| 526 |
} |
| 527 |
|
| 528 |
} |
