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root/OpenMD/trunk/src/brains/MoleculeCreator.cpp

Comparing trunk/src/brains/MoleculeCreator.cpp (file contents):
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 6 | Line 6
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.
#	Line 37 | Line 28
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
46	–	* @time 13:44am
47		* @version 1.0
48		*/
49
#	Line 54 | Line 54
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
66	<	namespace oopse {
66	>	namespace OpenMD {
67
68		Molecule* MoleculeCreator::createMolecule(ForceField* ff,
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;
#	Line 95 | Line 100 | namespace oopse {
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
#	Line 106 | Line 111 | namespace oopse {
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
#	Line 116 | Line 121 | namespace oopse {
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
#	Line 126 | Line 131 | namespace oopse {
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		}
#	Line 138 | Line 144 | namespace oopse {
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
#	Line 169 | Line 176 | namespace oopse {
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 (std::size_t 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	+	bool printConstraintForce = false;
197	+
198	+	if (cStamp->havePrintConstraintForce()) {
199	+	printConstraintForce = cStamp->getPrintConstraintForce();
200	+	}
201	+
202	+	if (!cStamp->haveConstrainedDistance()) {
203	+	sprintf(painCave.errMsg,
204	+	"Constraint Error: A non-bond constraint was specified\n"
205	+	"\twithout providing a value for the constrainedDistance.\n");
206	+	painCave.isFatal = 1;
207	+	simError();
208	+	} else {
209	+	RealType distance = cStamp->getConstrainedDistance();
210	+	ConstraintElem* consElemA = new ConstraintElem(atomA);
211	+	ConstraintElem* consElemB = new ConstraintElem(atomB);
212	+	ConstraintPair* cPair = new ConstraintPair(consElemA, consElemB,
213	+	distance,
214	+	printConstraintForce);
215	+	mol->addConstraintPair(cPair);
216	+	}
217	+	}
218	+
219	+	// now create the constraint elements:
220	+
221		createConstraintElem(mol);
222
223	<	//the construction of this molecule is finished
223	>	// Does this molecule stamp define a total constrained charge value?
224	>	// If so, let the created molecule know about it.
225	>
226	>	if (molStamp->haveConstrainTotalCharge() ) {
227	>	mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
228	>	}
229	>
230	>	// The construction of this molecule is finished:
231		mol->complete();
232
233		return mol;
#	Line 198 | Line 249 | namespace oopse {
249		painCave.isFatal = 1;
250		simError();
251		}
252	<
252	>
253		//below code still have some kind of hard-coding smell
254		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");
255
210	–	painCave.isFatal = 1;
211	–	simError();
212	–	}
213	–
256		DirectionalAtom* dAtom;
257	<	dAtom = new DirectionalAtom(dAtomType);
257	>	dAtom = new DirectionalAtom(atomType);
258		atom = dAtom;
259		}
260		else{
#	Line 227 | Line 269 | namespace oopse {
269		RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
270		Molecule* mol,
271		RigidBodyStamp* rbStamp,
272	<	LocalIndexManager* localIndexMan) {
272	>	LocalIndexManager* localIndexMan){
273		Atom* atom;
274		int nAtoms;
275		Vector3d refCoor;
#	Line 251 | Line 293 | namespace oopse {
293		//set the local index of this rigid body, global index will be set later
294		rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
295
296	<	//the rule for naming rigidbody MoleculeName_RB_Integer
297	<	//The first part is the name of the molecule
298	<	//The second part is alway fixed as "RB"
299	<	//The third part is the index of the rigidbody defined in meta-data file
300	<	//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());
296	>	// The rule for naming a rigidbody is: MoleculeName_RB_Integer
297	>	// The first part is the name of the molecule
298	>	// The second part is always fixed as "RB"
299	>	// The third part is the index of the rigidbody defined in meta-data file
300	>	// For example, Butane_RB_0 is a valid rigid body name of butane molecule
301
302	+	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
303	+	rb->setType(mol->getType() + "_RB_" + s.c_str());
304		return rb;
305		}
306
307		Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
308	<	BondStamp* stamp) {
309	<	BondType* bondType;
308	>	BondStamp* stamp,
309	>	LocalIndexManager* localIndexMan) {
310	>	BondTypeParser btParser;
311	>	BondType* bondType = NULL;
312		Atom* atomA;
313		Atom* atomB;
314
#	Line 273 | Line 316 | namespace oopse {
316		atomB = mol->getAtomAt(stamp->getB());
317
318		assert( atomA && atomB);
276	–
277	–	bondType = ff->getBondType(atomA->getType(), atomB->getType());
319
320	<	if (bondType == NULL) {
321	<	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
322	<	atomA->getType().c_str(),
323	<	atomB->getType().c_str());
324	<
325	<	painCave.isFatal = 1;
326	<	simError();
320	>	if (stamp->hasOverride()) {
321	>
322	>	try {
323	>	bondType = btParser.parseTypeAndPars(stamp->getOverrideType(),
324	>	stamp->getOverridePars() );
325	>	}
326	>	catch( OpenMDException e) {
327	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
328	>	"for molecule %s\n",
329	>	e.what(), mol->getType().c_str() );
330	>	painCave.isFatal = 1;
331	>	simError();
332	>	}
333	>
334	>	} else {
335	>	bondType = ff->getBondType(atomA->getType(), atomB->getType());
336	>
337	>	if (bondType == NULL) {
338	>	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
339	>	atomA->getType().c_str(),
340	>	atomB->getType().c_str());
341	>
342	>	painCave.isFatal = 1;
343	>	simError();
344	>	}
345		}
346	<	return new Bond(atomA, atomB, bondType);
346	>
347	>	Bond* bond = new Bond(atomA, atomB, bondType);
348	>
349	>	//set the local index of this bond, the global index will be set later
350	>	bond->setLocalIndex(localIndexMan->getNextBondIndex());
351	>
352	>	// The rule for naming a bond is: MoleculeName_Bond_Integer
353	>	// The first part is the name of the molecule
354	>	// The second part is always fixed as "Bond"
355	>	// The third part is the index of the bond defined in meta-data file
356	>	// For example, Butane_bond_0 is a valid Bond name in a butane molecule
357	>
358	>	std::string s = OpenMD_itoa(mol->getNBonds(), 10);
359	>	bond->setName(mol->getType() + "_Bond_" + s.c_str());
360	>	return bond;
361		}
362
363		Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
364	<	BendStamp* stamp) {
365	<	Bend* bend = NULL;
366	<	std::vector<int> bendAtoms = stamp->getMembers();
364	>	BendStamp* stamp,
365	>	LocalIndexManager* localIndexMan) {
366	>	BendTypeParser btParser;
367	>	BendType* bendType = NULL;
368	>	Bend* bend = NULL;
369	>
370	>	std::vector<int> bendAtoms = stamp->getMembers();
371		if (bendAtoms.size() == 3) {
372		Atom* atomA = mol->getAtomAt(bendAtoms[0]);
373		Atom* atomB = mol->getAtomAt(bendAtoms[1]);
374		Atom* atomC = mol->getAtomAt(bendAtoms[2]);
375
376	<	assert( atomA && atomB && atomC);
377	<
378	<	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());
376	>	assert( atomA && atomB && atomC );
377	>
378	>	if (stamp->hasOverride()) {
379
380	<	painCave.isFatal = 1;
381	<	simError();
380	>	try {
381	>	bendType = btParser.parseTypeAndPars(stamp->getOverrideType(),
382	>	stamp->getOverridePars() );
383	>	}
384	>	catch( OpenMDException e) {
385	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
386	>	"for molecule %s\n",
387	>	e.what(), mol->getType().c_str() );
388	>	painCave.isFatal = 1;
389	>	simError();
390	>	}
391	>	} else {
392	>
393	>	bendType = ff->getBendType(atomA->getType().c_str(),
394	>	atomB->getType().c_str(),
395	>	atomC->getType().c_str());
396	>
397	>	if (bendType == NULL) {
398	>	sprintf(painCave.errMsg,
399	>	"Can not find Matching Bend Type for[%s, %s, %s]",
400	>	atomA->getType().c_str(),
401	>	atomB->getType().c_str(),
402	>	atomC->getType().c_str());
403	>
404	>	painCave.isFatal = 1;
405	>	simError();
406	>	}
407		}
408
409		bend = new Bend(atomA, atomB, atomC, bendType);
410	+
411		} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
412		int ghostIndex = stamp->getGhostVectorSource();
413	<	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
413	>	int normalIndex = ghostIndex != bendAtoms[0] ?
414	>	bendAtoms[0] : bendAtoms[1];
415		Atom* normalAtom = mol->getAtomAt(normalIndex) ;
416		DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
417		if (ghostAtom == NULL) {
#	Line 323 | Line 419 | namespace oopse {
419		painCave.isFatal = 1;
420		simError();
421		}
326	–
327	–	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
422
423	<	if (bendType == NULL) {
424	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
425	<	normalAtom->getType().c_str(),
426	<	ghostAtom->getType().c_str(),
427	<	"GHOST");
428	<
429	<	painCave.isFatal = 1;
430	<	simError();
423	>	if (stamp->hasOverride()) {
424	>
425	>	try {
426	>	bendType = btParser.parseTypeAndPars(stamp->getOverrideType(),
427	>	stamp->getOverridePars() );
428	>	}
429	>	catch( OpenMDException e) {
430	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
431	>	"for molecule %s\n",
432	>	e.what(), mol->getType().c_str() );
433	>	painCave.isFatal = 1;
434	>	simError();
435	>	}
436	>	} else {
437	>
438	>	bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(),
439	>	"GHOST");
440	>
441	>	if (bendType == NULL) {
442	>	sprintf(painCave.errMsg,
443	>	"Can not find Matching Bend Type for[%s, %s, %s]",
444	>	normalAtom->getType().c_str(),
445	>	ghostAtom->getType().c_str(),
446	>	"GHOST");
447	>
448	>	painCave.isFatal = 1;
449	>	simError();
450	>	}
451		}
452
453		bend = new GhostBend(normalAtom, ghostAtom, bendType);
454
455		}
456
457	+	//set the local index of this bend, the global index will be set later
458	+	bend->setLocalIndex(localIndexMan->getNextBendIndex());
459	+
460	+	// The rule for naming a bend is: MoleculeName_Bend_Integer
461	+	// The first part is the name of the molecule
462	+	// The second part is always fixed as "Bend"
463	+	// The third part is the index of the bend defined in meta-data file
464	+	// For example, Butane_Bend_0 is a valid Bend name in a butane molecule
465	+
466	+	std::string s = OpenMD_itoa(mol->getNBends(), 10);
467	+	bend->setName(mol->getType() + "_Bend_" + s.c_str());
468		return bend;
469		}
470
471		Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
472	<	TorsionStamp* stamp) {
472	>	TorsionStamp* stamp,
473	>	LocalIndexManager* localIndexMan) {
474
475	+	TorsionTypeParser ttParser;
476	+	TorsionType* torsionType = NULL;
477		Torsion* torsion = NULL;
478	+
479		std::vector<int> torsionAtoms = stamp->getMembers();
480		if (torsionAtoms.size() < 3) {
481		return torsion;
#	Line 359 | Line 488 | namespace oopse {
488		if (torsionAtoms.size() == 4) {
489		Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
490
491	<	assert(atomA && atomB && atomC && atomD);
491	>	assert(atomA && atomB && atomC && atomD );
492	>
493	>	if (stamp->hasOverride()) {
494
495	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
496	<	atomB->getType(),
497	<	atomC->getType(),
498	<	atomD->getType());
499	<	if (torsionType == NULL) {
500	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
501	<	atomA->getType().c_str(),
502	<	atomB->getType().c_str(),
503	<	atomC->getType().c_str(),
504	<	atomD->getType().c_str());
495	>	try {
496	>	torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(),
497	>	stamp->getOverridePars() );
498	>	}
499	>	catch( OpenMDException e) {
500	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
501	>	"for molecule %s\n",
502	>	e.what(), mol->getType().c_str() );
503	>	painCave.isFatal = 1;
504	>	simError();
505	>	}
506	>	} else {
507	>
508
509	<	painCave.isFatal = 1;
510	<	simError();
509	>	torsionType = ff->getTorsionType(atomA->getType(),
510	>	atomB->getType(),
511	>	atomC->getType(),
512	>	atomD->getType());
513	>	if (torsionType == NULL) {
514	>	sprintf(painCave.errMsg,
515	>	"Can not find Matching Torsion Type for[%s, %s, %s, %s]",
516	>	atomA->getType().c_str(),
517	>	atomB->getType().c_str(),
518	>	atomC->getType().c_str(),
519	>	atomD->getType().c_str());
520	>
521	>	painCave.isFatal = 1;
522	>	simError();
523	>	}
524		}
525
526		torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
527	<	}
381	<	else {
527	>	} else {
528
529		DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
530		if (dAtom == NULL) {
#	Line 386 | Line 532 | namespace oopse {
532		painCave.isFatal = 1;
533		simError();
534		}
535	<
536	<	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");
535	>
536	>	if (stamp->hasOverride()) {
537
538	<	painCave.isFatal = 1;
539	<	simError();
540	<	}
538	>	try {
539	>	torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(),
540	>	stamp->getOverridePars() );
541	>	}
542	>	catch( OpenMDException e) {
543	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
544	>	"for molecule %s\n",
545	>	e.what(), mol->getType().c_str() );
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549	>	} else {
550	>	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
551	>	atomC->getType(), "GHOST");
552
553	+	if (torsionType == NULL) {
554	+	sprintf(painCave.errMsg,
555	+	"Can not find Matching Torsion Type for[%s, %s, %s, %s]",
556	+	atomA->getType().c_str(),
557	+	atomB->getType().c_str(),
558	+	atomC->getType().c_str(),
559	+	"GHOST");
560	+
561	+	painCave.isFatal = 1;
562	+	simError();
563	+	}
564	+	}
565	+
566		torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
567		}
568	+
569	+	//set the local index of this torsion, the global index will be set later
570	+	torsion->setLocalIndex(localIndexMan->getNextTorsionIndex());
571
572	+	// The rule for naming a torsion is: MoleculeName_Torsion_Integer
573	+	// The first part is the name of the molecule
574	+	// The second part is always fixed as "Torsion"
575	+	// The third part is the index of the torsion defined in meta-data file
576	+	// For example, Butane_Torsion_0 is a valid Torsion name in a
577	+	// butane molecule
578	+
579	+	std::string s = OpenMD_itoa(mol->getNTorsions(), 10);
580	+	torsion->setName(mol->getType() + "_Torsion_" + s.c_str());
581		return torsion;
582		}
583
584		Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
585	<	InversionStamp* stamp) {
586	<
585	>	InversionStamp* stamp,
586	>	LocalIndexManager* localIndexMan) {
587	>
588	>	InversionTypeParser itParser;
589	>	InversionType* inversionType = NULL;
590		Inversion* inversion = NULL;
591	+
592		int center = stamp->getCenter();
593		std::vector<int> satellites = stamp->getSatellites();
594		if (satellites.size() != 3) {
#	Line 423 | Line 601 | namespace oopse {
601		Atom* atomD = mol->getAtomAt(satellites[2]);
602
603		assert(atomA && atomB && atomC && atomD);
426	–
427	–	InversionType* inversionType = ff->getInversionType(atomA->getType(),
428	–	atomB->getType(),
429	–	atomC->getType(),
430	–	atomD->getType());
604
605	<	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());
605	>	if (stamp->hasOverride()) {
606
607	<	painCave.isFatal = 0;
608	<	painCave.severity = OOPSE_INFO;
609	<	simError();
610	<	return NULL;
607	>	try {
608	>	inversionType = itParser.parseTypeAndPars(stamp->getOverrideType(),
609	>	stamp->getOverridePars() );
610	>	}
611	>	catch( OpenMDException e) {
612	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
613	>	"for molecule %s\n",
614	>	e.what(), mol->getType().c_str() );
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	}
618		} else {
619
620	+	inversionType = ff->getInversionType(atomA->getType(),
621	+	atomB->getType(),
622	+	atomC->getType(),
623	+	atomD->getType());
624	+
625	+	if (inversionType == NULL) {
626	+	sprintf(painCave.errMsg,
627	+	"No Matching Inversion Type for[%s, %s, %s, %s]\n"
628	+	"\t(May not be a problem: not all inversions are parametrized)\n",
629	+	atomA->getType().c_str(),
630	+	atomB->getType().c_str(),
631	+	atomC->getType().c_str(),
632	+	atomD->getType().c_str());
633	+
634	+	painCave.isFatal = 0;
635	+	painCave.severity = OPENMD_INFO;
636	+	simError();
637	+	}
638	+	}
639	+	if (inversionType != NULL) {
640	+
641		inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
642	+
643	+	// set the local index of this inversion, the global index will
644	+	// be set later
645	+	inversion->setLocalIndex(localIndexMan->getNextInversionIndex());
646	+
647	+	// The rule for naming an inversion is: MoleculeName_Inversion_Integer
648	+	// The first part is the name of the molecule
649	+	// The second part is always fixed as "Inversion"
650	+	// The third part is the index of the inversion defined in meta-data file
651	+	// For example, Benzene_Inversion_0 is a valid Inversion name in a
652	+	// Benzene molecule
653	+
654	+	std::string s = OpenMD_itoa(mol->getNInversions(), 10);
655	+	inversion->setName(mol->getType() + "_Inversion_" + s.c_str());
656		return inversion;
657	+	} else {
658	+	return NULL;
659		}
660		}
661
662
663	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
663	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
664	>	CutoffGroupStamp* stamp,
665	>	LocalIndexManager* localIndexMan) {
666		int nAtoms;
667		CutoffGroup* cg;
668		Atom* atom;
#	Line 461 | Line 674 | namespace oopse {
674		assert(atom);
675		cg->addAtom(atom);
676		}
677	<
677	>
678	>	//set the local index of this cutoffGroup, global index will be set later
679	>	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
680	>
681		return cg;
682		}
683	<
684	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
683	>
684	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
685	>	LocalIndexManager* localIndexMan) {
686		CutoffGroup* cg;
687		cg  = new CutoffGroup();
688		cg->addAtom(atom);
689	+
690	+	//set the local index of this cutoffGroup, global index will be set later
691	+	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
692	+
693		return cg;
694		}
695
#	Line 477 | Line 698 | namespace oopse {
698		//add bond constraints
699		Molecule::BondIterator bi;
700		Bond* bond;
701	+	ConstraintPair* cPair;
702	+
703		for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
704
705		BondType* bt = bond->getBondType();
706
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	–
707		if (typeid(FixedBondType) == typeid(*bt)) {
708		FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
709
710		ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
711		ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
712	<	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
713	<	mol->addConstraintPair(consPair);
712	>	cPair = new ConstraintPair(consElemA, consElemB,
713	>	fbt->getEquilibriumBondLength(), false);
714	>	mol->addConstraintPair(cPair);
715		}
716		}
717
#	Line 506 | Line 723 | namespace oopse {
723		ConstraintPair* consPair;
724		Molecule::ConstraintPairIterator cpi;
725		std::set<StuntDouble*> sdSet;
726	<	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
726	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
727	>	consPair = mol->nextConstraintPair(cpi)) {
728
729		StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
730		if (sdSet.find(sdA) == sdSet.end()){
731		sdSet.insert(sdA);
732		mol->addConstraintElem(new ConstraintElem(sdA));
733		}
734	<
734	>
735		StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
736		if (sdSet.find(sdB) == sdSet.end()){
737		sdSet.insert(sdB);
738		mol->addConstraintElem(new ConstraintElem(sdB));
739	<	}
522	<
739	>	}
740		}
524	–
741		}
526	–
742		}

Comparing trunk/src/brains/MoleculeCreator.cpp (property svn:keywords):
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 0 | Line 1
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