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root/OpenMD/branches/development/src/brains/MoleculeCreator.cpp

Comparing:
trunk/src/brains/MoleculeCreator.cpp (file contents), Revision 292 by tim, Fri Feb 4 22:44:15 2005 UTC vs.
branches/development/src/brains/MoleculeCreator.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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, 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	<	/**
44	<	* @file MoleculeCreator.cpp
45	<	* @author tlin
46	<	* @date 11/04/2004
47	<	* @time 13:44am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file MoleculeCreator.cpp
45	>	* @author tlin
46	>	* @date 11/04/2004
47	>	* @time 13:44am
48	>	* @version 1.0
49	>	*/
50
51		#include <cassert>
52	+	#include <typeinfo>
53		#include <set>
54
55		#include "brains/MoleculeCreator.hpp"
#	Line 58 | Line 60
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62
63	<	namespace oopse {
64	<
65	<	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
66	<	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
67	<
68	<	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
63	>	namespace OpenMD {
64	>
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
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);
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);
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);
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->getCutoffGroup(i);
142	<	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
143	<	mol->addCutoffGroup(cutoffGroup);
141	>	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
142	>	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan);
143	>	mol->addCutoffGroup(cutoffGroup);
144		}
145
146		//every free atom is a cutoff group
147	<	std::set<Atom*> allAtoms;
148	<	Molecule::AtomIterator ai;
147	>	std::vector<Atom*> freeAtoms;
148	>	std::vector<Atom*>::iterator ai;
149	>	std::vector<Atom*>::iterator fai;
150
151		//add all atoms into allAtoms set
152	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
153	<	allAtoms.insert(atom);
152	>	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
153	>	freeAtoms.push_back(atom);
154		}
155
156		Molecule::CutoffGroupIterator ci;
157		CutoffGroup* cg;
141	–	std::set<Atom*> cutoffAtoms;
158
159	<	//add all of the atoms belong to cutoff groups into cutoffAtoms set
160	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
161	<
162	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
163	<	cutoffAtoms.insert(atom);
164	<	}
165	<
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),
165	>	freeAtoms.end());
166	>	}
167		}
168
169	<	//find all free atoms (which do not belong to cutoff groups)
170	<	//performs the "difference" operation from set theory,  the output range contains a copy of every
171	<	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
155	<	//[cutoffAtoms.begin(), cutoffAtoms.end()).
156	<	std::vector<Atom*> freeAtoms;
157	<	std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
158	<	std::back_inserter(freeAtoms));
159	<
160	<	if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
161	<	//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");
163	<
164	<	painCave.isFatal = 1;
165	<	simError();
166	<	}
167	<
168	<	//loop over the free atoms and then create one cutoff group for every single free atom
169	<	std::vector<Atom*>::iterator fai;
170	<
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);
174	<	mol->addCutoffGroup(cutoffGroup);
173	>	cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
174	>	mol->addCutoffGroup(cutoffGroup);
175		}
176		//create constraints
177		createConstraintPair(mol);
#	Line 178 | Line 179 | Molecule* MoleculeCreator::createMolecule(ForceField*
179
180		//the construction of this molecule is finished
181		mol->complete();
182	<
182	>
183		return mol;
184	<	}
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());
196	>	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
197	>	stamp->getType().c_str());
198
199	<	painCave.isFatal = 1;
200	<	simError();
199	>	painCave.isFatal = 1;
200	>	simError();
201		}
202
203		//below code still have some kind of hard-coding smell
204		if (atomType->isDirectional()){
205
206	<	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
206	>	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
207
208	<	if (dAtomType == NULL) {
209	<	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
208	>	if (dAtomType == NULL) {
209	>	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
210
211	<	painCave.isFatal = 1;
212	<	simError();
213	<	}
211	>	painCave.isFatal = 1;
212	>	simError();
213	>	}
214
215	<	DirectionalAtom* dAtom;
216	<	dAtom = new DirectionalAtom(dAtomType);
217	<	atom = dAtom;
215	>	DirectionalAtom* dAtom;
216	>	dAtom = new DirectionalAtom(dAtomType);
217	>	atom = dAtom;
218		}
219		else{
220	<	atom = new Atom(atomType);
220	>	atom = new Atom(atomType);
221		}
222
223		atom->setLocalIndex(localIndexMan->getNextAtomIndex());
224
225		return atom;
226	<	}
227	<
228	<	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
229	<	RigidBodyStamp* rbStamp,
230	<	LocalIndexManager* localIndexMan) {
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;
#	Line 234 | Line 237 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
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
242	<	atom = mol->getAtomAt(rbStamp->getMember(i));
243	<	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
244	<	rb->addAtom(atom, atomStamp);
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
#	Line 253 | Line 258 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
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	<	char buffer [33];
262	<	sprintf(buffer, "%d", mol->getNRigidBodies());
258	<	//rb->setType(mol->getType() + "_RB_" + toString<int>(mol->getNRigidBodies()));
259	<	rb->setType(mol->getType() + "_RB_" + buffer);
261	>	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
262	>	rb->setType(mol->getType() + "_RB_" + s.c_str());
263
264		return rb;
265	<	}
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());
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();
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		return new Bond(atomA, atomB, bondType);
289	<	}
289	>	}
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	>
300	>	assert( atomA && atomB && atomC);
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	>
312	>	painCave.isFatal = 1;
313	>	simError();
314	>	}
315	>
316	>	bend = new Bend(atomA, atomB, atomC, bendType);
317	>	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
318	>	int ghostIndex = stamp->getGhostVectorSource();
319	>	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
320	>	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
321	>	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
322	>	if (ghostAtom == NULL) {
323	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>
328	>	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
329
330	<	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
331	<	bool isGhostBend = false;
332	<	int ghostIndex;
330	>	if (bendType == NULL) {
331	>	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
332	>	normalAtom->getType().c_str(),
333	>	ghostAtom->getType().c_str(),
334	>	"GHOST");
335
336	+	painCave.isFatal = 1;
337	+	simError();
338	+	}
339	+
340	+	bend = new GhostBend(normalAtom, ghostAtom, bendType);
341	+
342	+	}
343
344	<	//
345	<	if (stamp->haveExtras()){
294	<	LinkedAssign* extras = stamp->getExtras();
295	<	LinkedAssign* currentExtra = extras;
344	>	return bend;
345	>	}
346
347	<	while (currentExtra != NULL){
348	<	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
299	<	switch (currentExtra->getType()){
300	<	case 0:
301	<	ghostIndex = currentExtra->getInt();
302	<	isGhostBend = true;
303	<	break;
347	>	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
348	>	TorsionStamp* stamp) {
349
350	<	default:
351	<	sprintf(painCave.errMsg,
352	<	"SimSetup Error: ghostVectorSource must be an int.\n");
353	<	painCave.isFatal = 1;
309	<	simError();
310	<	}
311	<	} else{
312	<	sprintf(painCave.errMsg,
313	<	"SimSetup Error: unhandled bend assignment:\n");
314	<	painCave.isFatal = 1;
315	<	simError();
316	<	}
317	<	currentExtra = currentExtra->getNext();
318	<	}
319	<
350	>	Torsion* torsion = NULL;
351	>	std::vector<int> torsionAtoms = stamp->getMembers();
352	>	if (torsionAtoms.size() < 3) {
353	>	return torsion;
354		}
355
356	<	if (isGhostBend) {
356	>	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
357	>	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
358	>	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
359
360	<	int indexA = stamp->getA();
361	<	int indexB= stamp->getB();
360	>	if (torsionAtoms.size() == 4) {
361	>	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
362
363	<	assert(indexA != indexB);
328	<
329	<	int normalIndex;
330	<	if (indexA == ghostIndex) {
331	<	normalIndex = indexB;
332	<	} else if (indexB == ghostIndex) {
333	<	normalIndex = indexA;
334	<	}
363	>	assert(atomA && atomB && atomC && atomD);
364
365	<	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
366	<	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
367	<	if (ghostAtom == NULL) {
368	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
369	<	painCave.isFatal = 1;
370	<	simError();
371	<	}
372	<
373	<	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
374	<
346	<	if (bendType == NULL) {
347	<	sprintf(painCave.errMsg, "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	<	}
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
376	<	return new GhostBend(normalAtom, ghostAtom, bendType);
377	<
378	<	} else {
379	<
380	<	Atom* atomA = mol->getAtomAt(stamp->getA());
381	<	Atom* atomB = mol->getAtomAt(stamp->getB());
382	<	Atom* atomC = mol->getAtomAt(stamp->getC());
383	<
384	<	assert( atomA && atomB && atomC);
376	>	painCave.isFatal = 1;
377	>	simError();
378	>	}
379	>
380	>	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
381	>	}
382	>	else {
383	>
384	>	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
385	>	if (dAtom == NULL) {
386	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
387	>	painCave.isFatal = 1;
388	>	simError();
389	>	}
390	>
391	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
392	>	atomC->getType(), "GHOST");
393	>
394	>	if (torsionType == NULL) {
395	>	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
396	>	atomA->getType().c_str(),
397	>	atomB->getType().c_str(),
398	>	atomC->getType().c_str(),
399	>	"GHOST");
400
401	<	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
402	<
403	<	if (bendType == NULL) {
404	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
405	<	atomA->getType().c_str(),
371	<	atomB->getType().c_str(),
372	<	atomC->getType().c_str());
373	<
374	<	painCave.isFatal = 1;
375	<	simError();
376	<	}
377	<
378	<	return new Bend(atomA, atomB, atomC, bendType);
401	>	painCave.isFatal = 1;
402	>	simError();
403	>	}
404	>
405	>	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
406		}
407	<	}
407	>
408	>	return torsion;
409	>	}
410
411	<	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
412	<
413	<	Atom* atomA = mol->getAtomAt(stamp->getA());
414	<	Atom* atomB = mol->getAtomAt(stamp->getB());
415	<	Atom* atomC = mol->getAtomAt(stamp->getC());
416	<	Torsion* torsion;
417	<
418	<	if (stamp->getD() != -1) {
390	<	Atom* atomD = mol->getAtomAt(stamp->getD());
391	<
392	<	assert(atomA && atomB && atomC && atomD);
393	<
394	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
395	<	atomC->getType(), atomD->getType());
396	<
397	<	if (torsionType == NULL) {
398	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
399	<	atomA->getType().c_str(),
400	<	atomB->getType().c_str(),
401	<	atomC->getType().c_str(),
402	<	atomD->getType().c_str());
403	<
404	<	painCave.isFatal = 1;
405	<	simError();
406	<	}
407	<
408	<	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
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		}
410	–	else {
420
421	<	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
422	<	if (dAtom == NULL) {
423	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
424	<	painCave.isFatal = 1;
425	<	simError();
426	<	}
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	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
434	<	atomC->getType(), "GHOST");
435	<
436	<	if (torsionType == NULL) {
437	<	sprintf(painCave.errMsg, "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	<	"GHOST");
442	<
443	<	painCave.isFatal = 1;
444	<	simError();
445	<	}
446	<
447	<	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
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	<	return torsion;
454	<	}
455	<
439	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
453	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
454	>	CutoffGroupStamp* stamp,
455	>	LocalIndexManager* localIndexMan) {
456		int nAtoms;
457		CutoffGroup* cg;
458		Atom* atom;
#	Line 444 | Line 460 | CutoffGroup* MoleculeCreator::createCutoffGroup(Molecu
460
461		nAtoms = stamp->getNMembers();
462		for (int i =0; i < nAtoms; ++i) {
463	<	atom = mol->getAtomAt(stamp->getMember(i));
464	<	assert(atom);
465	<	cg->addAtom(atom);
463	>	atom = mol->getAtomAt(stamp->getMemberAt(i));
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) {
472	>	}
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	<	}
484	>	}
485
486	<	void MoleculeCreator::createConstraintPair(Molecule* mol) {
486	>	void MoleculeCreator::createConstraintPair(Molecule* mol) {
487
488		//add bond constraints
489		Molecule::BondIterator bi;
490		Bond* bond;
491		for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
492
493	<	BondType* bt = bond->getBondType();
493	>	BondType* bt = bond->getBondType();
494
495	<	//class Parent1 {};
496	<	//class Child1 : public Parent {};
497	<	//class Child2 : public Parent {};
498	<	//Child1* ch1 = new Child1();
499	<	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
500	<	//the dynamic_cast is succeed in above line. A compiler bug?
495	>	//class Parent1 {};
496	>	//class Child1 : public Parent {};
497	>	//class Child2 : public Parent {};
498	>	//Child1* ch1 = new Child1();
499	>	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
500	>	//the dynamic_cast is succeed in above line. A compiler bug?
501
502	<	if (typeid(FixedBondType) == typeid(*bt)) {
503	<	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
502	>	if (typeid(FixedBondType) == typeid(*bt)) {
503	>	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
504
505	<	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
506	<	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
507	<	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
508	<	mol->addConstraintPair(consPair);
509	<	}
505	>	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
506	>	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
507	>	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
508	>	mol->addConstraintPair(consPair);
509	>	}
510		}
511
512		//rigidbody -- rigidbody constraint is not support yet
513	<	}
513	>	}
514
515	<	void MoleculeCreator::createConstraintElem(Molecule* mol) {
515	>	void MoleculeCreator::createConstraintElem(Molecule* mol) {
516
517		ConstraintPair* consPair;
518		Molecule::ConstraintPairIterator cpi;
519		std::set<StuntDouble*> sdSet;
520		for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
521
522	<	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
523	<	if (sdSet.find(sdA) == sdSet.end()){
524	<	sdSet.insert(sdA);
525	<	mol->addConstraintElem(new ConstraintElem(sdA));
526	<	}
522	>	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
523	>	if (sdSet.find(sdA) == sdSet.end()){
524	>	sdSet.insert(sdA);
525	>	mol->addConstraintElem(new ConstraintElem(sdA));
526	>	}
527
528	<	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
529	<	if (sdSet.find(sdB) == sdSet.end()){
530	<	sdSet.insert(sdB);
531	<	mol->addConstraintElem(new ConstraintElem(sdB));
532	<	}
528	>	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
529	>	if (sdSet.find(sdB) == sdSet.end()){
530	>	sdSet.insert(sdB);
531	>	mol->addConstraintElem(new ConstraintElem(sdB));
532	>	}
533
534		}
535
536	<	}
536	>	}
537
538		}

Comparing:
trunk/src/brains/MoleculeCreator.cpp (property svn:keywords), Revision 292 by tim, Fri Feb 4 22:44:15 2005 UTC vs.
branches/development/src/brains/MoleculeCreator.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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