| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 49 |
|
*/ |
| 50 |
|
|
| 51 |
|
#include <cassert> |
| 52 |
+ |
#include <typeinfo> |
| 53 |
|
#include <set> |
| 54 |
|
|
| 55 |
|
#include "brains/MoleculeCreator.hpp" |
| 60 |
|
#include "utils/simError.h" |
| 61 |
|
#include "utils/StringUtils.hpp" |
| 62 |
|
|
| 63 |
< |
namespace oopse { |
| 63 |
> |
namespace OpenMD { |
| 64 |
|
|
| 65 |
< |
Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, |
| 66 |
< |
int stampId, int globalIndex, LocalIndexManager* localIndexMan) { |
| 67 |
< |
|
| 65 |
> |
Molecule* MoleculeCreator::createMolecule(ForceField* ff, |
| 66 |
> |
MoleculeStamp *molStamp, |
| 67 |
> |
int stampId, int globalIndex, |
| 68 |
> |
LocalIndexManager* localIndexMan) { |
| 69 |
|
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
| 70 |
|
|
| 71 |
|
//create atoms |
| 85 |
|
|
| 86 |
|
for (int i = 0; i < nRigidbodies; ++i) { |
| 87 |
|
currentRigidBodyStamp = molStamp->getRigidBodyStamp(i); |
| 88 |
< |
rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan); |
| 88 |
> |
rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, |
| 89 |
> |
localIndexMan); |
| 90 |
|
mol->addRigidBody(rb); |
| 91 |
|
} |
| 92 |
< |
|
| 92 |
> |
|
| 93 |
|
//create bonds |
| 94 |
|
Bond* bond; |
| 95 |
|
BondStamp* currentBondStamp; |
| 121 |
|
mol->addTorsion(torsion); |
| 122 |
|
} |
| 123 |
|
|
| 124 |
+ |
//create inversions |
| 125 |
+ |
Inversion* inversion; |
| 126 |
+ |
InversionStamp* currentInversionStamp; |
| 127 |
+ |
int nInversions = molStamp->getNInversions(); |
| 128 |
+ |
for (int i = 0; i < nInversions; ++i) { |
| 129 |
+ |
currentInversionStamp = molStamp->getInversionStamp(i); |
| 130 |
+ |
inversion = createInversion(ff, mol, currentInversionStamp); |
| 131 |
+ |
if (inversion != NULL ) { |
| 132 |
+ |
mol->addInversion(inversion); |
| 133 |
+ |
} |
| 134 |
+ |
} |
| 135 |
+ |
|
| 136 |
|
//create cutoffGroups |
| 137 |
|
CutoffGroup* cutoffGroup; |
| 138 |
|
CutoffGroupStamp* currentCutoffGroupStamp; |
| 139 |
|
int nCutoffGroups = molStamp->getNCutoffGroups(); |
| 140 |
|
for (int i = 0; i < nCutoffGroups; ++i) { |
| 141 |
|
currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
| 142 |
< |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
| 142 |
> |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan); |
| 143 |
|
mol->addCutoffGroup(cutoffGroup); |
| 144 |
|
} |
| 145 |
|
|
| 156 |
|
Molecule::CutoffGroupIterator ci; |
| 157 |
|
CutoffGroup* cg; |
| 158 |
|
|
| 159 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 160 |
< |
|
| 159 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 160 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 161 |
> |
|
| 162 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 163 |
< |
//erase the atoms belong to cutoff groups from freeAtoms vector |
| 164 |
< |
freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), freeAtoms.end()); |
| 165 |
< |
} |
| 166 |
< |
|
| 163 |
> |
//erase the atoms belong to cutoff groups from freeAtoms vector |
| 164 |
> |
freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), |
| 165 |
> |
freeAtoms.end()); |
| 166 |
> |
} |
| 167 |
|
} |
| 168 |
|
|
| 169 |
< |
//loop over the free atoms and then create one cutoff group for every single free atom |
| 169 |
> |
// loop over the free atoms and then create one cutoff group for |
| 170 |
> |
// every single free atom |
| 171 |
|
|
| 172 |
|
for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
| 173 |
< |
cutoffGroup = createCutoffGroup(mol, *fai); |
| 173 |
> |
cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan); |
| 174 |
|
mol->addCutoffGroup(cutoffGroup); |
| 175 |
|
} |
| 176 |
|
//create constraints |
| 179 |
|
|
| 180 |
|
//the construction of this molecule is finished |
| 181 |
|
mol->complete(); |
| 182 |
< |
|
| 182 |
> |
|
| 183 |
|
return mol; |
| 184 |
|
} |
| 185 |
|
|
| 186 |
|
|
| 187 |
< |
Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, |
| 188 |
< |
LocalIndexManager* localIndexMan) { |
| 187 |
> |
Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, |
| 188 |
> |
AtomStamp* stamp, |
| 189 |
> |
LocalIndexManager* localIndexMan) { |
| 190 |
|
AtomType * atomType; |
| 191 |
|
Atom* atom; |
| 192 |
|
|
| 193 |
|
atomType = ff->getAtomType(stamp->getType()); |
| 194 |
< |
|
| 194 |
> |
|
| 195 |
|
if (atomType == NULL) { |
| 196 |
|
sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]", |
| 197 |
|
stamp->getType().c_str()); |
| 224 |
|
|
| 225 |
|
return atom; |
| 226 |
|
} |
| 227 |
< |
|
| 228 |
< |
RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol, |
| 227 |
> |
|
| 228 |
> |
RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, |
| 229 |
> |
Molecule* mol, |
| 230 |
|
RigidBodyStamp* rbStamp, |
| 231 |
|
LocalIndexManager* localIndexMan) { |
| 232 |
|
Atom* atom; |
| 237 |
|
RigidBody* rb = new RigidBody(); |
| 238 |
|
nAtoms = rbStamp->getNMembers(); |
| 239 |
|
for (int i = 0; i < nAtoms; ++i) { |
| 240 |
< |
//rbStamp->getMember(i) return the local index of current atom inside the molecule. |
| 241 |
< |
//It is not the same as local index of atom which is the index of atom at DataStorage class |
| 240 |
> |
//rbStamp->getMember(i) return the local index of current atom |
| 241 |
> |
//inside the molecule. It is not the same as local index of |
| 242 |
> |
//atom which is the index of atom at DataStorage class |
| 243 |
|
atom = mol->getAtomAt(rbStamp->getMemberAt(i)); |
| 244 |
|
atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i)); |
| 245 |
|
rb->addAtom(atom, atomStamp); |
| 246 |
|
} |
| 247 |
|
|
| 248 |
< |
//after all of the atoms are added, we need to calculate the reference coordinates |
| 248 |
> |
//after all of the atoms are added, we need to calculate the |
| 249 |
> |
//reference coordinates |
| 250 |
|
rb->calcRefCoords(); |
| 251 |
|
|
| 252 |
|
//set the local index of this rigid body, global index will be set later |
| 258 |
|
//The third part is the index of the rigidbody defined in meta-data file |
| 259 |
|
//For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 260 |
|
/**@todo replace itoa by lexi_cast */ |
| 261 |
< |
std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10); |
| 261 |
> |
std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10); |
| 262 |
|
rb->setType(mol->getType() + "_RB_" + s.c_str()); |
| 263 |
|
|
| 264 |
|
return rb; |
| 265 |
|
} |
| 266 |
|
|
| 267 |
< |
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) { |
| 267 |
> |
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, |
| 268 |
> |
BondStamp* stamp) { |
| 269 |
|
BondType* bondType; |
| 270 |
|
Atom* atomA; |
| 271 |
|
Atom* atomB; |
| 272 |
< |
|
| 272 |
> |
|
| 273 |
|
atomA = mol->getAtomAt(stamp->getA()); |
| 274 |
|
atomB = mol->getAtomAt(stamp->getB()); |
| 275 |
< |
|
| 275 |
> |
|
| 276 |
|
assert( atomA && atomB); |
| 277 |
|
|
| 278 |
|
bondType = ff->getBondType(atomA->getType(), atomB->getType()); |
| 281 |
|
sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
| 282 |
|
atomA->getType().c_str(), |
| 283 |
|
atomB->getType().c_str()); |
| 284 |
< |
|
| 284 |
> |
|
| 285 |
|
painCave.isFatal = 1; |
| 286 |
|
simError(); |
| 287 |
|
} |
| 288 |
|
return new Bond(atomA, atomB, bondType); |
| 289 |
|
} |
| 290 |
< |
|
| 291 |
< |
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) { |
| 290 |
> |
|
| 291 |
> |
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, |
| 292 |
> |
BendStamp* stamp) { |
| 293 |
|
Bend* bend = NULL; |
| 294 |
|
std::vector<int> bendAtoms = stamp->getMembers(); |
| 295 |
|
if (bendAtoms.size() == 3) { |
| 296 |
|
Atom* atomA = mol->getAtomAt(bendAtoms[0]); |
| 297 |
|
Atom* atomB = mol->getAtomAt(bendAtoms[1]); |
| 298 |
|
Atom* atomC = mol->getAtomAt(bendAtoms[2]); |
| 299 |
< |
|
| 299 |
> |
|
| 300 |
|
assert( atomA && atomB && atomC); |
| 301 |
< |
|
| 302 |
< |
BendType* bendType = ff->getBendType(atomA->getType().c_str(), atomB->getType().c_str(), atomC->getType().c_str()); |
| 303 |
< |
|
| 301 |
> |
|
| 302 |
> |
BendType* bendType = ff->getBendType(atomA->getType().c_str(), |
| 303 |
> |
atomB->getType().c_str(), |
| 304 |
> |
atomC->getType().c_str()); |
| 305 |
> |
|
| 306 |
|
if (bendType == NULL) { |
| 307 |
|
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
| 308 |
|
atomA->getType().c_str(), |
| 309 |
|
atomB->getType().c_str(), |
| 310 |
|
atomC->getType().c_str()); |
| 311 |
< |
|
| 311 |
> |
|
| 312 |
|
painCave.isFatal = 1; |
| 313 |
|
simError(); |
| 314 |
|
} |
| 315 |
< |
|
| 315 |
> |
|
| 316 |
|
bend = new Bend(atomA, atomB, atomC, bendType); |
| 317 |
|
} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) { |
| 318 |
|
int ghostIndex = stamp->getGhostVectorSource(); |
| 336 |
|
painCave.isFatal = 1; |
| 337 |
|
simError(); |
| 338 |
|
} |
| 339 |
< |
|
| 339 |
> |
|
| 340 |
|
bend = new GhostBend(normalAtom, ghostAtom, bendType); |
| 341 |
< |
|
| 341 |
> |
|
| 342 |
|
} |
| 343 |
|
|
| 344 |
|
return bend; |
| 345 |
|
} |
| 346 |
|
|
| 347 |
< |
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) { |
| 347 |
> |
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, |
| 348 |
> |
TorsionStamp* stamp) { |
| 349 |
|
|
| 350 |
|
Torsion* torsion = NULL; |
| 351 |
|
std::vector<int> torsionAtoms = stamp->getMembers(); |
| 362 |
|
|
| 363 |
|
assert(atomA && atomB && atomC && atomD); |
| 364 |
|
|
| 365 |
< |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
| 366 |
< |
atomC->getType(), atomD->getType()); |
| 367 |
< |
|
| 365 |
> |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), |
| 366 |
> |
atomB->getType(), |
| 367 |
> |
atomC->getType(), |
| 368 |
> |
atomD->getType()); |
| 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 |
< |
|
| 375 |
> |
|
| 376 |
|
painCave.isFatal = 1; |
| 377 |
|
simError(); |
| 378 |
|
} |
| 379 |
< |
|
| 379 |
> |
|
| 380 |
|
torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType); |
| 381 |
|
} |
| 382 |
|
else { |
| 383 |
< |
|
| 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 |
< |
|
| 390 |
> |
|
| 391 |
|
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
| 392 |
|
atomC->getType(), "GHOST"); |
| 393 |
< |
|
| 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 |
< |
|
| 400 |
> |
|
| 401 |
|
painCave.isFatal = 1; |
| 402 |
|
simError(); |
| 403 |
|
} |
| 404 |
< |
|
| 404 |
> |
|
| 405 |
|
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
| 406 |
|
} |
| 407 |
< |
|
| 407 |
> |
|
| 408 |
|
return torsion; |
| 409 |
|
} |
| 410 |
|
|
| 411 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
| 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 = OPENMD_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, |
| 454 |
> |
CutoffGroupStamp* stamp, |
| 455 |
> |
LocalIndexManager* localIndexMan) { |
| 456 |
|
int nAtoms; |
| 457 |
|
CutoffGroup* cg; |
| 458 |
|
Atom* atom; |
| 464 |
|
assert(atom); |
| 465 |
|
cg->addAtom(atom); |
| 466 |
|
} |
| 467 |
< |
|
| 467 |
> |
|
| 468 |
> |
//set the local index of this cutoffGroup, global index will be set later |
| 469 |
> |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 470 |
> |
|
| 471 |
|
return cg; |
| 472 |
|
} |
| 473 |
< |
|
| 474 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
| 473 |
> |
|
| 474 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom, |
| 475 |
> |
LocalIndexManager* localIndexMan) { |
| 476 |
|
CutoffGroup* cg; |
| 477 |
|
cg = new CutoffGroup(); |
| 478 |
|
cg->addAtom(atom); |
| 479 |
+ |
|
| 480 |
+ |
//set the local index of this cutoffGroup, global index will be set later |
| 481 |
+ |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 482 |
+ |
|
| 483 |
|
return cg; |
| 484 |
|
} |
| 485 |
|
|
