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

Comparing trunk/src/brains/MoleculeCreator.cpp (file contents):
Revision 403 by gezelter, Tue Mar 8 21:06:49 2005 UTC vs.
Revision 1979 by gezelter, Sat Apr 5 20:56:01 2014 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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
47	<	* @time 13:44am
48	<	* @version 1.0
48	<	*/
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/DirectionalAtomType.hpp"
57	>	#include "types/AtomType.hpp"
58		#include "types/FixedBondType.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61
62	<	namespace oopse {
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
63	–	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
64	–	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
65	–
66	–	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
67	–
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->getAtom(i);
77	<	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
78	<	mol->addAtom(atom);
76	>	currentAtomStamp = molStamp->getAtomStamp(i);
77	>	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
78	>	mol->addAtom(atom);
79		}
80
81		//create rigidbodies
#	Line 81 | Line 84 | Molecule* MoleculeCreator::createMolecule(ForceField*
84		int nRigidbodies = molStamp->getNRigidBodies();
85
86		for (int i = 0; i < nRigidbodies; ++i) {
87	<	currentRigidBodyStamp = molStamp->getRigidBody(i);
88	<	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
89	<	mol->addRigidBody(rb);
87	>	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
88	>	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
89	>	localIndexMan);
90	>	mol->addRigidBody(rb);
91		}
92	<
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->getBond(i);
100	<	bond = createBond(ff, mol, currentBondStamp);
101	<	mol->addBond(bond);
99	>	currentBondStamp = molStamp->getBondStamp(i);
100	>	bond = createBond(ff, mol, currentBondStamp, localIndexMan);
101	>	mol->addBond(bond);
102		}
103
104		//create bends
#	Line 102 | Line 106 | Molecule* MoleculeCreator::createMolecule(ForceField*
106		BendStamp* currentBendStamp;
107		int nBends = molStamp->getNBends();
108		for (int i = 0; i < nBends; ++i) {
109	<	currentBendStamp = molStamp->getBend(i);
110	<	bend = createBend(ff, mol, currentBendStamp);
111	<	mol->addBend(bend);
109	>	currentBendStamp = molStamp->getBendStamp(i);
110	>	bend = createBend(ff, mol, currentBendStamp, localIndexMan);
111	>	mol->addBend(bend);
112		}
113
114		//create torsions
#	Line 112 | Line 116 | Molecule* MoleculeCreator::createMolecule(ForceField*
116		TorsionStamp* currentTorsionStamp;
117		int nTorsions = molStamp->getNTorsions();
118		for (int i = 0; i < nTorsions; ++i) {
119	<	currentTorsionStamp = molStamp->getTorsion(i);
120	<	torsion = createTorsion(ff, mol, currentTorsionStamp);
121	<	mol->addTorsion(torsion);
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->getCutoffGroup(i);
143	<	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
144	<	mol->addCutoffGroup(cutoffGroup);
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::set<Atom*> allAtoms;
150	<	Molecule::AtomIterator ai;
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(ai); atom != NULL; atom = mol->nextAtom(ai)) {
155	<	allAtoms.insert(atom);
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;
141	–	std::set<Atom*> cutoffAtoms;
160
161	<	//add all of the atoms belong to cutoff groups into cutoffAtoms set
162	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
163	<
164	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
165	<	cutoffAtoms.insert(atom);
166	<	}
167	<
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	<	//find all free atoms (which do not belong to cutoff groups)
172	<	//performs the "difference" operation from set theory,  the output range contains a copy of every
173	<	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
174	<	//[cutoffAtoms.begin(), cutoffAtoms.end()).
175	<	std::vector<Atom*> freeAtoms;
176	<	std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
177	<	std::back_inserter(freeAtoms));
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
179	<	if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
180	<	//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
162	<	sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");
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();
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	<	//loop over the free atoms and then create one cutoff group for every single free atom
169	<	std::vector<Atom*>::iterator fai;
216	>	// now create the constraint elements:
217
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);
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	<
229	>
230		return mol;
231	<	}
231	>	}
232
233
234	<	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
235	<	LocalIndexManager* localIndexMan) {
234	>	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
235	>	AtomStamp* stamp,
236	>	LocalIndexManager* localIndexMan) {
237		AtomType * atomType;
238		Atom* atom;
239
240		atomType =  ff->getAtomType(stamp->getType());
241	<
241	>
242		if (atomType == NULL) {
243	<	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
244	<	stamp->getType());
243	>	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
244	>	stamp->getType().c_str());
245
246	<	painCave.isFatal = 1;
247	<	simError();
246	>	painCave.isFatal = 1;
247	>	simError();
248		}
249	<
249	>
250		//below code still have some kind of hard-coding smell
251		if (atomType->isDirectional()){
203	–
204	–	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
205	–
206	–	if (dAtomType == NULL) {
207	–	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
252
253	<	painCave.isFatal = 1;
254	<	simError();
255	<	}
212	<
213	<	DirectionalAtom* dAtom;
214	<	dAtom = new DirectionalAtom(dAtomType);
215	<	atom = dAtom;
253	>	DirectionalAtom* dAtom;
254	>	dAtom = new DirectionalAtom(atomType);
255	>	atom = dAtom;
256		}
257		else{
258	<	atom = new Atom(atomType);
258	>	atom = new Atom(atomType);
259		}
260
261		atom->setLocalIndex(localIndexMan->getNextAtomIndex());
262
263		return atom;
264	<	}
265	<
266	<	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
267	<	RigidBodyStamp* rbStamp,
268	<	LocalIndexManager* localIndexMan) {
264	>	}
265	>
266	>	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
267	>	Molecule* mol,
268	>	RigidBodyStamp* rbStamp,
269	>	LocalIndexManager* localIndexMan){
270		Atom* atom;
271		int nAtoms;
272		Vector3d refCoor;
#	Line 234 | Line 275 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
275		RigidBody* rb = new RigidBody();
276		nAtoms = rbStamp->getNMembers();
277		for (int i = 0; i < nAtoms; ++i) {
278	<	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
279	<	//It is not the same as local index of atom which is the index of atom at DataStorage class
280	<	atom = mol->getAtomAt(rbStamp->getMember(i));
281	<	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
282	<	rb->addAtom(atom, atomStamp);
278	>	//rbStamp->getMember(i) return the local index of current atom
279	>	//inside the molecule.  It is not the same as local index of
280	>	//atom which is the index of atom at DataStorage class
281	>	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
282	>	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
283	>	rb->addAtom(atom, atomStamp);
284		}
285
286	<	//after all of the atoms are added, we need to calculate the reference coordinates
286	>	//after all of the atoms are added, we need to calculate the
287	>	//reference coordinates
288		rb->calcRefCoords();
289
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
255	<	/**@todo replace itoa by lexi_cast */
256	<	std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
257	<	rb->setType(mol->getType() + "_RB_" + s.c_str());
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());
301		return rb;
302	<	}
302	>	}
303
304	<	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
304	>	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
305	>	BondStamp* stamp,
306	>	LocalIndexManager* localIndexMan) {
307		BondType* bondType;
308		Atom* atomA;
309		Atom* atomB;
310	<
310	>
311		atomA = mol->getAtomAt(stamp->getA());
312		atomB = mol->getAtomAt(stamp->getB());
313	<
313	>
314		assert( atomA && atomB);
315
316		bondType = ff->getBondType(atomA->getType(), atomB->getType());
317
318		if (bondType == NULL) {
319	<	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
320	<	atomA->getType().c_str(),
321	<	atomB->getType().c_str());
319	>	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
320	>	atomA->getType().c_str(),
321	>	atomB->getType().c_str());
322	>
323	>	painCave.isFatal = 1;
324	>	simError();
325	>	}
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,
344	+	LocalIndexManager* localIndexMan) {
345	+	Bend* bend = NULL;
346	+	std::vector<int> bendAtoms = stamp->getMembers();
347	+	if (bendAtoms.size() == 3) {
348	+	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
349	+	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
350	+	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
351	+
352	+	assert( atomA && atomB && atomC);
353	+
354	+	BendType* bendType = ff->getBendType(atomA->getType().c_str(),
355	+	atomB->getType().c_str(),
356	+	atomC->getType().c_str());
357	+
358	+	if (bendType == NULL) {
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());
364	+
365		painCave.isFatal = 1;
366		simError();
367	<	}
368	<	return new Bond(atomA, atomB, bondType);
369	<	}
367	>	}
368	>
369	>	bend = new Bend(atomA, atomB, atomC, bendType);
370	>	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
371	>	int ghostIndex = stamp->getGhostVectorSource();
372	>	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
373	>	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
374	>	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
375	>	if (ghostAtom == NULL) {
376	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
377	>	painCave.isFatal = 1;
378	>	simError();
379	>	}
380	>
381	>	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
382
383	<	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
384	<	bool isGhostBend = false;
385	<	int ghostIndex;
383	>	if (bendType == NULL) {
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");
389
390	<
391	<	//
392	<	if (stamp->haveExtras()){
393	<	LinkedAssign* extras = stamp->getExtras();
394	<	LinkedAssign* currentExtra = extras;
390	>	painCave.isFatal = 1;
391	>	simError();
392	>	}
393	>
394	>	bend = new GhostBend(normalAtom, ghostAtom, bendType);
395	>
396	>	}
397
398	<	while (currentExtra != NULL){
399	<	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
297	<	switch (currentExtra->getType()){
298	<	case 0:
299	<	ghostIndex = currentExtra->getInt();
300	<	isGhostBend = true;
301	<	break;
398	>	//set the local index of this bend, the global index will be set later
399	>	bend->setLocalIndex(localIndexMan->getNextBendIndex());
400
401	<	default:
402	<	sprintf(painCave.errMsg,
403	<	"SimSetup Error: ghostVectorSource must be an int.\n");
404	<	painCave.isFatal = 1;
405	<	simError();
308	<	}
309	<	} else{
310	<	sprintf(painCave.errMsg,
311	<	"SimSetup Error: unhandled bend assignment:\n");
312	<	painCave.isFatal = 1;
313	<	simError();
314	<	}
315	<	currentExtra = currentExtra->getNext();
316	<	}
317	<
318	<	}
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	<	if (isGhostBend) {
407	>	std::string s = OpenMD_itoa(mol->getNBends(), 10);
408	>	bend->setName(mol->getType() + "_Bend_" + s.c_str());
409	>	return bend;
410	>	}
411
412	<	int indexA = stamp->getA();
413	<	int indexB= stamp->getB();
412	>	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
413	>	TorsionStamp* stamp,
414	>	LocalIndexManager* localIndexMan) {
415
416	<	assert(indexA != indexB);
416	>	Torsion* torsion = NULL;
417	>	std::vector<int> torsionAtoms = stamp->getMembers();
418	>	if (torsionAtoms.size() < 3) {
419	>	return torsion;
420	>	}
421
422	<	int normalIndex;
423	<	if (indexA == ghostIndex) {
424	<	normalIndex = indexB;
330	<	} else if (indexB == ghostIndex) {
331	<	normalIndex = indexA;
332	<	}
333	<
334	<	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
335	<	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
336	<	if (ghostAtom == NULL) {
337	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
338	<	painCave.isFatal = 1;
339	<	simError();
340	<	}
341	<
342	<	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
422	>	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
423	>	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
424	>	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
425
426	<	if (bendType == NULL) {
427	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
346	<	normalAtom->getType().c_str(),
347	<	ghostAtom->getType().c_str(),
348	<	"GHOST");
426	>	if (torsionAtoms.size() == 4) {
427	>	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
428
429	<	painCave.isFatal = 1;
351	<	simError();
352	<	}
429	>	assert(atomA && atomB && atomC && atomD);
430
431	<	return new GhostBend(normalAtom, ghostAtom, bendType);
432	<
433	<	} else {
434	<
435	<	Atom* atomA = mol->getAtomAt(stamp->getA());
436	<	Atom* atomB = mol->getAtomAt(stamp->getB());
437	<	Atom* atomC = mol->getAtomAt(stamp->getC());
438	<
439	<	assert( atomA && atomB && atomC);
431	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
432	>	atomB->getType(),
433	>	atomC->getType(),
434	>	atomD->getType());
435	>	if (torsionType == NULL) {
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(),
441	>	atomD->getType().c_str());
442
443	<	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
443	>	painCave.isFatal = 1;
444	>	simError();
445	>	}
446	>
447	>	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
448	>	}
449	>	else {
450	>
451	>	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
452	>	if (dAtom == NULL) {
453	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
454	>	painCave.isFatal = 1;
455	>	simError();
456	>	}
457	>
458	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
459	>	atomC->getType(), "GHOST");
460	>
461	>	if (torsionType == NULL) {
462	>	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
463	>	atomA->getType().c_str(),
464	>	atomB->getType().c_str(),
465	>	atomC->getType().c_str(),
466	>	"GHOST");
467	>
468	>	painCave.isFatal = 1;
469	>	simError();
470	>	}
471	>
472	>	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
473	>	}
474
475	<	if (bendType == NULL) {
476	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
477	<	atomA->getType().c_str(),
478	<	atomB->getType().c_str(),
479	<	atomC->getType().c_str());
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	<	painCave.isFatal = 1;
486	<	simError();
487	<	}
485	>	std::string s = OpenMD_itoa(mol->getNTorsions(), 10);
486	>	torsion->setName(mol->getType() + "_Torsion_" + s.c_str());
487	>	return torsion;
488	>	}
489
490	<	return new Bend(atomA, atomB, atomC, bendType);
490	>	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
491	>	InversionStamp* stamp,
492	>	LocalIndexManager* localIndexMan) {
493	>
494	>	Inversion* inversion = NULL;
495	>	int center = stamp->getCenter();
496	>	std::vector<int> satellites = stamp->getSatellites();
497	>	if (satellites.size() != 3) {
498	>	return inversion;
499		}
378	–	}
500
501	<	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
501	>	Atom* atomA = mol->getAtomAt(center);
502	>	Atom* atomB = mol->getAtomAt(satellites[0]);
503	>	Atom* atomC = mol->getAtomAt(satellites[1]);
504	>	Atom* atomD = mol->getAtomAt(satellites[2]);
505	>
506	>	assert(atomA && atomB && atomC && atomD);
507	>
508	>	InversionType* inversionType = ff->getInversionType(atomA->getType(),
509	>	atomB->getType(),
510	>	atomC->getType(),
511	>	atomD->getType());
512
513	<	Atom* atomA = mol->getAtomAt(stamp->getA());
514	<	Atom* atomB = mol->getAtomAt(stamp->getB());
515	<	Atom* atomC = mol->getAtomAt(stamp->getC());
516	<	Torsion* torsion;
513	>	if (inversionType == NULL) {
514	>	sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
515	>	"\t(May not be a problem: not all inversions are parametrized)\n",
516	>	atomA->getType().c_str(),
517	>	atomB->getType().c_str(),
518	>	atomC->getType().c_str(),
519	>	atomD->getType().c_str());
520	>
521	>	painCave.isFatal = 0;
522	>	painCave.severity = OPENMD_INFO;
523	>	simError();
524	>	return NULL;
525	>	} else {
526	>
527	>	inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
528
529	<	if (stamp->getD() != -1) {
530	<	Atom* atomD = mol->getAtomAt(stamp->getD());
529	>	// set the local index of this inversion, the global index will
530	>	// be set later
531	>	inversion->setLocalIndex(localIndexMan->getNextInversionIndex());
532
533	<	assert(atomA && atomB && atomC && atomD);
534	<
535	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
536	<	atomC->getType(), atomD->getType());
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	<	if (torsionType == NULL) {
541	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
542	<	atomA->getType().c_str(),
398	<	atomB->getType().c_str(),
399	<	atomC->getType().c_str(),
400	<	atomD->getType().c_str());
401	<
402	<	painCave.isFatal = 1;
403	<	simError();
404	<	}
405	<
406	<	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
540	>	std::string s = OpenMD_itoa(mol->getNInversions(), 10);
541	>	inversion->setName(mol->getType() + "_Inversion_" + s.c_str());
542	>	return inversion;
543		}
544	<	else {
544	>	}
545	>
546
547	<	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
548	<	if (dAtom == NULL) {
549	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
413	<	painCave.isFatal = 1;
414	<	simError();
415	<	}
416	<
417	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
418	<	atomC->getType(), "GHOST");
419	<
420	<	if (torsionType == NULL) {
421	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
422	<	atomA->getType().c_str(),
423	<	atomB->getType().c_str(),
424	<	atomC->getType().c_str(),
425	<	"GHOST");
426	<
427	<	painCave.isFatal = 1;
428	<	simError();
429	<	}
430	<
431	<	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
432	<	}
433	<
434	<	return torsion;
435	<	}
436	<
437	<	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;
#	Line 442 | Line 554 | CutoffGroup* MoleculeCreator::createCutoffGroup(Molecu
554
555		nAtoms = stamp->getNMembers();
556		for (int i =0; i < nAtoms; ++i) {
557	<	atom = mol->getAtomAt(stamp->getMember(i));
558	<	assert(atom);
559	<	cg->addAtom(atom);
557	>	atom = mol->getAtomAt(stamp->getMemberAt(i));
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) {
566	>	}
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	<	}
578	>	}
579
580	<	void MoleculeCreator::createConstraintPair(Molecule* mol) {
580	>	void MoleculeCreator::createConstraintPair(Molecule* mol) {
581
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();
589	>	BondType* bt = bond->getBondType();
590
591	<	//class Parent1 {};
592	<	//class Child1 : public Parent {};
471	<	//class Child2 : public Parent {};
472	<	//Child1* ch1 = new Child1();
473	<	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
474	<	//the dynamic_cast is succeed in above line. A compiler bug?
591	>	if (typeid(FixedBondType) == typeid(*bt)) {
592	>	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
593
594	<	if (typeid(FixedBondType) == typeid(*bt)) {
595	<	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
596	<
597	<	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
598	<	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
599	<	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
482	<	mol->addConstraintPair(consPair);
483	<	}
594	>	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
595	>	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
596	>	cPair = new ConstraintPair(consElemA, consElemB,
597	>	fbt->getEquilibriumBondLength(), false);
598	>	mol->addConstraintPair(cPair);
599	>	}
600		}
601
602		//rigidbody -- rigidbody constraint is not support yet
603	<	}
603	>	}
604
605	<	void MoleculeCreator::createConstraintElem(Molecule* mol) {
605	>	void MoleculeCreator::createConstraintElem(Molecule* mol) {
606
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	<
619	<	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
620	<	if (sdSet.find(sdB) == sdSet.end()){
621	<	sdSet.insert(sdB);
622	<	mol->addConstraintElem(new ConstraintElem(sdB));
623	<	}
507	<
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	>
619	>	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
620	>	if (sdSet.find(sdB) == sdSet.end()){
621	>	sdSet.insert(sdB);
622	>	mol->addConstraintElem(new ConstraintElem(sdB));
623	>	}
624		}
625	<
625	>	}
626		}
511	–
512	–	}

Comparing trunk/src/brains/MoleculeCreator.cpp (property svn:keywords):
Revision 403 by gezelter, Tue Mar 8 21:06:49 2005 UTC vs.
Revision 1979 by gezelter, Sat Apr 5 20:56:01 2014 UTC

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