ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/brains/MoleculeCreator.cpp
Revision: 1953
Committed: Thu Dec 5 18:19:26 2013 UTC (11 years, 4 months ago) by gezelter
File size: 20806 byte(s)
Log Message:
Rewrote much of selection module, added a bond correlation function

File Contents

# Content
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. Redistributions of source code must retain the above copyright
10 * notice, this list of conditions and the following disclaimer.
11 *
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.
16 *
17 * This software is provided "AS IS," without a warranty of any
18 * kind. All express or implied conditions, representations and
19 * warranties, including any implied warranty of merchantability,
20 * fitness for a particular purpose or non-infringement, are hereby
21 * excluded. The University of Notre Dame and its licensors shall not
22 * be liable for any damages suffered by licensee as a result of
23 * using, modifying or distributing the software or its
24 * derivatives. In no event will the University of Notre Dame or its
25 * licensors be liable for any lost revenue, profit or data, or for
26 * direct, indirect, special, consequential, incidental or punitive
27 * damages, however caused and regardless of the theory of liability,
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, 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
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/AtomType.hpp"
58 #include "types/FixedBondType.hpp"
59 #include "utils/simError.h"
60 #include "utils/StringUtils.hpp"
61
62 namespace OpenMD {
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 molStamp->getRegion() );
70
71 //create atoms
72 Atom* atom;
73 AtomStamp* currentAtomStamp;
74 int nAtom = molStamp->getNAtoms();
75 for (int i = 0; i < nAtom; ++i) {
76 currentAtomStamp = molStamp->getAtomStamp(i);
77 atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
78 mol->addAtom(atom);
79 }
80
81 //create rigidbodies
82 RigidBody* rb;
83 RigidBodyStamp * currentRigidBodyStamp;
84 int nRigidbodies = molStamp->getNRigidBodies();
85
86 for (int i = 0; i < nRigidbodies; ++i) {
87 currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
88 rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
89 localIndexMan);
90 mol->addRigidBody(rb);
91 }
92
93 //create bonds
94 Bond* bond;
95 BondStamp* currentBondStamp;
96 int nBonds = molStamp->getNBonds();
97
98 for (int i = 0; i < nBonds; ++i) {
99 currentBondStamp = molStamp->getBondStamp(i);
100 bond = createBond(ff, mol, currentBondStamp, localIndexMan);
101 mol->addBond(bond);
102 }
103
104 //create bends
105 Bend* bend;
106 BendStamp* currentBendStamp;
107 int nBends = molStamp->getNBends();
108 for (int i = 0; i < nBends; ++i) {
109 currentBendStamp = molStamp->getBendStamp(i);
110 bend = createBend(ff, mol, currentBendStamp, localIndexMan);
111 mol->addBend(bend);
112 }
113
114 //create torsions
115 Torsion* torsion;
116 TorsionStamp* currentTorsionStamp;
117 int nTorsions = molStamp->getNTorsions();
118 for (int i = 0; i < nTorsions; ++i) {
119 currentTorsionStamp = molStamp->getTorsionStamp(i);
120 torsion = createTorsion(ff, mol, currentTorsionStamp, localIndexMan);
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 localIndexMan);
132 if (inversion != NULL ) {
133 mol->addInversion(inversion);
134 }
135 }
136
137 //create cutoffGroups
138 CutoffGroup* cutoffGroup;
139 CutoffGroupStamp* currentCutoffGroupStamp;
140 int nCutoffGroups = molStamp->getNCutoffGroups();
141 for (int i = 0; i < nCutoffGroups; ++i) {
142 currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
143 cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp,
144 localIndexMan);
145 mol->addCutoffGroup(cutoffGroup);
146 }
147
148 //every free atom is a cutoff group
149 std::vector<Atom*> freeAtoms;
150 std::vector<Atom*>::iterator ai;
151 std::vector<Atom*>::iterator fai;
152
153 //add all atoms into allAtoms set
154 for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
155 freeAtoms.push_back(atom);
156 }
157
158 Molecule::CutoffGroupIterator ci;
159 CutoffGroup* cg;
160
161 for (cg = mol->beginCutoffGroup(ci); cg != NULL;
162 cg = mol->nextCutoffGroup(ci)) {
163
164 for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
165 //erase the atoms belong to cutoff groups from freeAtoms vector
166 freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom),
167 freeAtoms.end());
168 }
169 }
170
171 // loop over the free atoms and then create one cutoff group for
172 // every single free atom
173
174 for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
175 cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
176 mol->addCutoffGroup(cutoffGroup);
177 }
178 //create constraints
179 createConstraintPair(mol);
180 createConstraintElem(mol);
181
182 // Does this molecule stamp define a total constrained charge value?
183 // If so, let the created molecule know about it.
184
185 if (molStamp->haveConstrainTotalCharge() ) {
186 mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
187 }
188
189 //the construction of this molecule is finished
190 mol->complete();
191
192 return mol;
193 }
194
195
196 Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
197 AtomStamp* stamp,
198 LocalIndexManager* localIndexMan) {
199 AtomType * atomType;
200 Atom* atom;
201
202 atomType = ff->getAtomType(stamp->getType());
203
204 if (atomType == NULL) {
205 sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
206 stamp->getType().c_str());
207
208 painCave.isFatal = 1;
209 simError();
210 }
211
212 //below code still have some kind of hard-coding smell
213 if (atomType->isDirectional()){
214
215 DirectionalAtom* dAtom;
216 dAtom = new DirectionalAtom(atomType);
217 atom = dAtom;
218 }
219 else{
220 atom = new Atom(atomType);
221 }
222
223 atom->setLocalIndex(localIndexMan->getNextAtomIndex());
224
225 return atom;
226 }
227
228 RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
229 Molecule* mol,
230 RigidBodyStamp* rbStamp,
231 LocalIndexManager* localIndexMan){
232 Atom* atom;
233 int nAtoms;
234 Vector3d refCoor;
235 AtomStamp* atomStamp;
236
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
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
249 //reference coordinates
250 rb->calcRefCoords();
251
252 //set the local index of this rigid body, global index will be set later
253 rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
254
255 // The rule for naming a rigidbody is: MoleculeName_RB_Integer
256 // The first part is the name of the molecule
257 // The second part is always fixed as "RB"
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
261 std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
262 rb->setType(mol->getType() + "_RB_" + s.c_str());
263 return rb;
264 }
265
266 Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
267 BondStamp* stamp,
268 LocalIndexManager* localIndexMan) {
269 BondType* bondType;
270 Atom* atomA;
271 Atom* atomB;
272
273 atomA = mol->getAtomAt(stamp->getA());
274 atomB = mol->getAtomAt(stamp->getB());
275
276 assert( atomA && atomB);
277
278 bondType = ff->getBondType(atomA->getType(), atomB->getType());
279
280 if (bondType == NULL) {
281 sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
282 atomA->getType().c_str(),
283 atomB->getType().c_str());
284
285 painCave.isFatal = 1;
286 simError();
287 }
288 Bond* bond = new Bond(atomA, atomB, bondType);
289
290 //set the local index of this bond, the global index will be set later
291 bond->setLocalIndex(localIndexMan->getNextBondIndex());
292
293 // The rule for naming a bond is: MoleculeName_Bond_Integer
294 // The first part is the name of the molecule
295 // The second part is always fixed as "Bond"
296 // The third part is the index of the bond defined in meta-data file
297 // For example, Butane_bond_0 is a valid Bond name in a butane molecule
298
299 std::string s = OpenMD_itoa(mol->getNBonds(), 10);
300 bond->setName(mol->getType() + "_Bond_" + s.c_str());
301 return bond;
302 }
303
304 Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
305 BendStamp* stamp,
306 LocalIndexManager* localIndexMan) {
307 Bend* bend = NULL;
308 std::vector<int> bendAtoms = stamp->getMembers();
309 if (bendAtoms.size() == 3) {
310 Atom* atomA = mol->getAtomAt(bendAtoms[0]);
311 Atom* atomB = mol->getAtomAt(bendAtoms[1]);
312 Atom* atomC = mol->getAtomAt(bendAtoms[2]);
313
314 assert( atomA && atomB && atomC);
315
316 BendType* bendType = ff->getBendType(atomA->getType().c_str(),
317 atomB->getType().c_str(),
318 atomC->getType().c_str());
319
320 if (bendType == NULL) {
321 sprintf(painCave.errMsg,
322 "Can not find Matching Bend Type for[%s, %s, %s]",
323 atomA->getType().c_str(),
324 atomB->getType().c_str(),
325 atomC->getType().c_str());
326
327 painCave.isFatal = 1;
328 simError();
329 }
330
331 bend = new Bend(atomA, atomB, atomC, bendType);
332 } else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
333 int ghostIndex = stamp->getGhostVectorSource();
334 int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
335 Atom* normalAtom = mol->getAtomAt(normalIndex) ;
336 DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
337 if (ghostAtom == NULL) {
338 sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
339 painCave.isFatal = 1;
340 simError();
341 }
342
343 BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
344
345 if (bendType == NULL) {
346 sprintf(painCave.errMsg,
347 "Can not find Matching Bend Type for[%s, %s, %s]",
348 normalAtom->getType().c_str(),
349 ghostAtom->getType().c_str(),
350 "GHOST");
351
352 painCave.isFatal = 1;
353 simError();
354 }
355
356 bend = new GhostBend(normalAtom, ghostAtom, bendType);
357
358 }
359
360 //set the local index of this bend, the global index will be set later
361 bend->setLocalIndex(localIndexMan->getNextBendIndex());
362
363 // The rule for naming a bend is: MoleculeName_Bend_Integer
364 // The first part is the name of the molecule
365 // The second part is always fixed as "Bend"
366 // The third part is the index of the bend defined in meta-data file
367 // For example, Butane_Bend_0 is a valid Bend name in a butane molecule
368
369 std::string s = OpenMD_itoa(mol->getNBends(), 10);
370 bend->setName(mol->getType() + "_Bend_" + s.c_str());
371 return bend;
372 }
373
374 Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
375 TorsionStamp* stamp,
376 LocalIndexManager* localIndexMan) {
377
378 Torsion* torsion = NULL;
379 std::vector<int> torsionAtoms = stamp->getMembers();
380 if (torsionAtoms.size() < 3) {
381 return torsion;
382 }
383
384 Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
385 Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
386 Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
387
388 if (torsionAtoms.size() == 4) {
389 Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
390
391 assert(atomA && atomB && atomC && atomD);
392
393 TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
394 atomB->getType(),
395 atomC->getType(),
396 atomD->getType());
397 if (torsionType == NULL) {
398 sprintf(painCave.errMsg,
399 "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
400 atomA->getType().c_str(),
401 atomB->getType().c_str(),
402 atomC->getType().c_str(),
403 atomD->getType().c_str());
404
405 painCave.isFatal = 1;
406 simError();
407 }
408
409 torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
410 }
411 else {
412
413 DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
414 if (dAtom == NULL) {
415 sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
416 painCave.isFatal = 1;
417 simError();
418 }
419
420 TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
421 atomC->getType(), "GHOST");
422
423 if (torsionType == NULL) {
424 sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
425 atomA->getType().c_str(),
426 atomB->getType().c_str(),
427 atomC->getType().c_str(),
428 "GHOST");
429
430 painCave.isFatal = 1;
431 simError();
432 }
433
434 torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
435 }
436
437 //set the local index of this torsion, the global index will be set later
438 torsion->setLocalIndex(localIndexMan->getNextTorsionIndex());
439
440 // The rule for naming a torsion is: MoleculeName_Torsion_Integer
441 // The first part is the name of the molecule
442 // The second part is always fixed as "Torsion"
443 // The third part is the index of the torsion defined in meta-data file
444 // For example, Butane_Torsion_0 is a valid Torsion name in a
445 // butane molecule
446
447 std::string s = OpenMD_itoa(mol->getNTorsions(), 10);
448 torsion->setName(mol->getType() + "_Torsion_" + s.c_str());
449 return torsion;
450 }
451
452 Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
453 InversionStamp* stamp,
454 LocalIndexManager* localIndexMan) {
455
456 Inversion* inversion = NULL;
457 int center = stamp->getCenter();
458 std::vector<int> satellites = stamp->getSatellites();
459 if (satellites.size() != 3) {
460 return inversion;
461 }
462
463 Atom* atomA = mol->getAtomAt(center);
464 Atom* atomB = mol->getAtomAt(satellites[0]);
465 Atom* atomC = mol->getAtomAt(satellites[1]);
466 Atom* atomD = mol->getAtomAt(satellites[2]);
467
468 assert(atomA && atomB && atomC && atomD);
469
470 InversionType* inversionType = ff->getInversionType(atomA->getType(),
471 atomB->getType(),
472 atomC->getType(),
473 atomD->getType());
474
475 if (inversionType == NULL) {
476 sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
477 "\t(May not be a problem: not all inversions are parametrized)\n",
478 atomA->getType().c_str(),
479 atomB->getType().c_str(),
480 atomC->getType().c_str(),
481 atomD->getType().c_str());
482
483 painCave.isFatal = 0;
484 painCave.severity = OPENMD_INFO;
485 simError();
486 return NULL;
487 } else {
488
489 inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
490
491 // set the local index of this inversion, the global index will
492 // be set later
493 inversion->setLocalIndex(localIndexMan->getNextInversionIndex());
494
495 // The rule for naming an inversion is: MoleculeName_Inversion_Integer
496 // The first part is the name of the molecule
497 // The second part is always fixed as "Inversion"
498 // The third part is the index of the inversion defined in meta-data file
499 // For example, Benzene_Inversion_0 is a valid Inversion name in a
500 // Benzene molecule
501
502 std::string s = OpenMD_itoa(mol->getNInversions(), 10);
503 inversion->setName(mol->getType() + "_Inversion_" + s.c_str());
504 return inversion;
505 }
506 }
507
508
509 CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
510 CutoffGroupStamp* stamp,
511 LocalIndexManager* localIndexMan) {
512 int nAtoms;
513 CutoffGroup* cg;
514 Atom* atom;
515 cg = new CutoffGroup();
516
517 nAtoms = stamp->getNMembers();
518 for (int i =0; i < nAtoms; ++i) {
519 atom = mol->getAtomAt(stamp->getMemberAt(i));
520 assert(atom);
521 cg->addAtom(atom);
522 }
523
524 //set the local index of this cutoffGroup, global index will be set later
525 cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
526
527 return cg;
528 }
529
530 CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
531 LocalIndexManager* localIndexMan) {
532 CutoffGroup* cg;
533 cg = new CutoffGroup();
534 cg->addAtom(atom);
535
536 //set the local index of this cutoffGroup, global index will be set later
537 cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
538
539 return cg;
540 }
541
542 void MoleculeCreator::createConstraintPair(Molecule* mol) {
543
544 //add bond constraints
545 Molecule::BondIterator bi;
546 Bond* bond;
547 for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
548
549 BondType* bt = bond->getBondType();
550
551 if (typeid(FixedBondType) == typeid(*bt)) {
552 FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
553
554 ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
555 ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
556 ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
557 mol->addConstraintPair(consPair);
558 }
559 }
560
561 //rigidbody -- rigidbody constraint is not support yet
562 }
563
564 void MoleculeCreator::createConstraintElem(Molecule* mol) {
565
566 ConstraintPair* consPair;
567 Molecule::ConstraintPairIterator cpi;
568 std::set<StuntDouble*> sdSet;
569 for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
570
571 StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
572 if (sdSet.find(sdA) == sdSet.end()){
573 sdSet.insert(sdA);
574 mol->addConstraintElem(new ConstraintElem(sdA));
575 }
576
577 StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
578 if (sdSet.find(sdB) == sdSet.end()){
579 sdSet.insert(sdB);
580 mol->addConstraintElem(new ConstraintElem(sdB));
581 }
582
583 }
584
585 }
586
587 }

Properties

Name Value
svn:executable *
svn:keywords Author Id Revision Date