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

Comparing:
trunk/src/brains/MoleculeCreator.cpp (file contents), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/brains/MoleculeCreator.cpp (file contents), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 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"
56		#include "primitives/GhostBend.hpp"
57		#include "primitives/GhostTorsion.hpp"
58	<	#include "types/DirectionalAtomType.hpp"
58	>	#include "types/AtomType.hpp"
59		#include "types/FixedBondType.hpp"
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);
207	<
206	<	if (dAtomType == NULL) {
207	<	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
208	<
209	<	painCave.isFatal = 1;
210	<	simError();
211	<	}
212	<
213	<	DirectionalAtom* dAtom;
214	<	dAtom = new DirectionalAtom(dAtomType);
215	<	atom = dAtom;
205	>	DirectionalAtom* dAtom;
206	>	dAtom = new DirectionalAtom(atomType);
207	>	atom = dAtom;
208		}
209		else{
210	<	atom = new Atom(atomType);
210	>	atom = new Atom(atomType);
211		}
212
213		atom->setLocalIndex(localIndexMan->getNextAtomIndex());
214
215		return atom;
216	<	}
217	<
218	<	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
219	<	RigidBodyStamp* rbStamp,
220	<	LocalIndexManager* localIndexMan) {
216	>	}
217	>
218	>	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
219	>	Molecule* mol,
220	>	RigidBodyStamp* rbStamp,
221	>	LocalIndexManager* localIndexMan) {
222		Atom* atom;
223		int nAtoms;
224		Vector3d refCoor;
#	Line 234 | Line 227 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
227		RigidBody* rb = new RigidBody();
228		nAtoms = rbStamp->getNMembers();
229		for (int i = 0; i < nAtoms; ++i) {
230	<	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
231	<	//It is not the same as local index of atom which is the index of atom at DataStorage class
232	<	atom = mol->getAtomAt(rbStamp->getMember(i));
233	<	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
234	<	rb->addAtom(atom, atomStamp);
230	>	//rbStamp->getMember(i) return the local index of current atom
231	>	//inside the molecule.  It is not the same as local index of
232	>	//atom which is the index of atom at DataStorage class
233	>	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
234	>	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
235	>	rb->addAtom(atom, atomStamp);
236		}
237
238	<	//after all of the atoms are added, we need to calculate the reference coordinates
238	>	//after all of the atoms are added, we need to calculate the
239	>	//reference coordinates
240		rb->calcRefCoords();
241
242		//set the local index of this rigid body, global index will be set later
#	Line 253 | Line 248 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
248		//The third part is the index of the rigidbody defined in meta-data file
249		//For example, Butane_RB_0 is a valid rigid body name of butane molecule
250		/**@todo replace itoa by lexi_cast */
251	<	rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
252	<
251	>	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
252	>	rb->setType(mol->getType() + "_RB_" + s.c_str());
253	>
254		return rb;
255	<	}
255	>	}
256
257	<	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
257	>	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
258	>	BondStamp* stamp) {
259		BondType* bondType;
260		Atom* atomA;
261		Atom* atomB;
262	<
262	>
263		atomA = mol->getAtomAt(stamp->getA());
264		atomB = mol->getAtomAt(stamp->getB());
265	<
265	>
266		assert( atomA && atomB);
267
268		bondType = ff->getBondType(atomA->getType(), atomB->getType());
269
270		if (bondType == NULL) {
271	<	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
272	<	atomA->getType().c_str(),
273	<	atomB->getType().c_str());
274	<
275	<	painCave.isFatal = 1;
276	<	simError();
271	>	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
272	>	atomA->getType().c_str(),
273	>	atomB->getType().c_str());
274	>
275	>	painCave.isFatal = 1;
276	>	simError();
277		}
278		return new Bond(atomA, atomB, bondType);
279	<	}
279	>	}
280	>
281	>	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
282	>	BendStamp* stamp) {
283	>	Bend* bend = NULL;
284	>	std::vector<int> bendAtoms = stamp->getMembers();
285	>	if (bendAtoms.size() == 3) {
286	>	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
287	>	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
288	>	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
289	>
290	>	assert( atomA && atomB && atomC);
291	>
292	>	BendType* bendType = ff->getBendType(atomA->getType().c_str(),
293	>	atomB->getType().c_str(),
294	>	atomC->getType().c_str());
295	>
296	>	if (bendType == NULL) {
297	>	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
298	>	atomA->getType().c_str(),
299	>	atomB->getType().c_str(),
300	>	atomC->getType().c_str());
301	>
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305	>
306	>	bend = new Bend(atomA, atomB, atomC, bendType);
307	>	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
308	>	int ghostIndex = stamp->getGhostVectorSource();
309	>	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
310	>	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
311	>	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
312	>	if (ghostAtom == NULL) {
313	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
314	>	painCave.isFatal = 1;
315	>	simError();
316	>	}
317	>
318	>	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
319
320	<	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
321	<	bool isGhostBend = false;
322	<	int ghostIndex;
320	>	if (bendType == NULL) {
321	>	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
322	>	normalAtom->getType().c_str(),
323	>	ghostAtom->getType().c_str(),
324	>	"GHOST");
325
326	+	painCave.isFatal = 1;
327	+	simError();
328	+	}
329	+
330	+	bend = new GhostBend(normalAtom, ghostAtom, bendType);
331	+
332	+	}
333
334	<	//
335	<	if (stamp->haveExtras()){
291	<	LinkedAssign* extras = stamp->getExtras();
292	<	LinkedAssign* currentExtra = extras;
334	>	return bend;
335	>	}
336
337	<	while (currentExtra != NULL){
338	<	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
296	<	switch (currentExtra->getType()){
297	<	case 0:
298	<	ghostIndex = currentExtra->getInt();
299	<	isGhostBend = true;
300	<	break;
337	>	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
338	>	TorsionStamp* stamp) {
339
340	<	default:
341	<	sprintf(painCave.errMsg,
342	<	"SimSetup Error: ghostVectorSource must be an int.\n");
343	<	painCave.isFatal = 1;
306	<	simError();
307	<	}
308	<	} else{
309	<	sprintf(painCave.errMsg,
310	<	"SimSetup Error: unhandled bend assignment:\n");
311	<	painCave.isFatal = 1;
312	<	simError();
313	<	}
314	<	currentExtra = currentExtra->getNext();
315	<	}
316	<
340	>	Torsion* torsion = NULL;
341	>	std::vector<int> torsionAtoms = stamp->getMembers();
342	>	if (torsionAtoms.size() < 3) {
343	>	return torsion;
344		}
345
346	<	if (isGhostBend) {
346	>	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
347	>	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
348	>	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
349
350	<	int indexA = stamp->getA();
351	<	int indexB= stamp->getB();
350	>	if (torsionAtoms.size() == 4) {
351	>	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
352
353	<	assert(indexA != indexB);
325	<
326	<	int normalIndex;
327	<	if (indexA == ghostIndex) {
328	<	normalIndex = indexB;
329	<	} else if (indexB == ghostIndex) {
330	<	normalIndex = indexA;
331	<	}
353	>	assert(atomA && atomB && atomC && atomD);
354
355	<	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
356	<	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
357	<	if (ghostAtom == NULL) {
358	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
362	<
363	<	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
364	<
343	<	if (bendType == NULL) {
344	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
345	<	normalAtom->getType().c_str(),
346	<	ghostAtom->getType().c_str(),
347	<	"GHOST");
348	<
349	<	painCave.isFatal = 1;
350	<	simError();
351	<	}
355	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
356	>	atomB->getType(),
357	>	atomC->getType(),
358	>	atomD->getType());
359	>	if (torsionType == NULL) {
360	>	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
361	>	atomA->getType().c_str(),
362	>	atomB->getType().c_str(),
363	>	atomC->getType().c_str(),
364	>	atomD->getType().c_str());
365
366	<	return new GhostBend(normalAtom, ghostAtom, bendType);
367	<
368	<	} else {
369	<
370	<	Atom* atomA = mol->getAtomAt(stamp->getA());
371	<	Atom* atomB = mol->getAtomAt(stamp->getB());
372	<	Atom* atomC = mol->getAtomAt(stamp->getC());
373	<
374	<	assert( atomA && atomB && atomC);
366	>	painCave.isFatal = 1;
367	>	simError();
368	>	}
369	>
370	>	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
371	>	}
372	>	else {
373	>
374	>	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
375	>	if (dAtom == NULL) {
376	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
377	>	painCave.isFatal = 1;
378	>	simError();
379	>	}
380	>
381	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
382	>	atomC->getType(), "GHOST");
383	>
384	>	if (torsionType == NULL) {
385	>	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
386	>	atomA->getType().c_str(),
387	>	atomB->getType().c_str(),
388	>	atomC->getType().c_str(),
389	>	"GHOST");
390
391	<	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
392	<
393	<	if (bendType == NULL) {
394	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
395	<	atomA->getType().c_str(),
368	<	atomB->getType().c_str(),
369	<	atomC->getType().c_str());
370	<
371	<	painCave.isFatal = 1;
372	<	simError();
373	<	}
374	<
375	<	return new Bend(atomA, atomB, atomC, bendType);
391	>	painCave.isFatal = 1;
392	>	simError();
393	>	}
394	>
395	>	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
396		}
397	<	}
397	>
398	>	return torsion;
399	>	}
400
401	<	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
402	<
403	<	Atom* atomA = mol->getAtomAt(stamp->getA());
404	<	Atom* atomB = mol->getAtomAt(stamp->getB());
405	<	Atom* atomC = mol->getAtomAt(stamp->getC());
406	<	Torsion* torsion;
407	<
408	<	if (stamp->getD() != -1) {
387	<	Atom* atomD = mol->getAtomAt(stamp->getD());
388	<
389	<	assert(atomA && atomB && atomC && atomD);
390	<
391	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
392	<	atomC->getType(), atomD->getType());
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	<	atomD->getType().c_str());
400	<
401	<	painCave.isFatal = 1;
402	<	simError();
403	<	}
404	<
405	<	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
401	>	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
402	>	InversionStamp* stamp) {
403	>
404	>	Inversion* inversion = NULL;
405	>	int center = stamp->getCenter();
406	>	std::vector<int> satellites = stamp->getSatellites();
407	>	if (satellites.size() != 3) {
408	>	return inversion;
409		}
407	–	else {
410
411	<	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
412	<	if (dAtom == NULL) {
413	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
414	<	painCave.isFatal = 1;
415	<	simError();
416	<	}
411	>	Atom* atomA = mol->getAtomAt(center);
412	>	Atom* atomB = mol->getAtomAt(satellites[0]);
413	>	Atom* atomC = mol->getAtomAt(satellites[1]);
414	>	Atom* atomD = mol->getAtomAt(satellites[2]);
415	>
416	>	assert(atomA && atomB && atomC && atomD);
417	>
418	>	InversionType* inversionType = ff->getInversionType(atomA->getType(),
419	>	atomB->getType(),
420	>	atomC->getType(),
421	>	atomD->getType());
422
423	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
424	<	atomC->getType(), "GHOST");
425	<
426	<	if (torsionType == NULL) {
427	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
428	<	atomA->getType().c_str(),
429	<	atomB->getType().c_str(),
430	<	atomC->getType().c_str(),
431	<	"GHOST");
432	<
433	<	painCave.isFatal = 1;
434	<	simError();
435	<	}
436	<
437	<	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
423	>	if (inversionType == NULL) {
424	>	sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
425	>	"\t(May not be a problem: not all inversions are parametrized)\n",
426	>	atomA->getType().c_str(),
427	>	atomB->getType().c_str(),
428	>	atomC->getType().c_str(),
429	>	atomD->getType().c_str());
430	>
431	>	painCave.isFatal = 0;
432	>	painCave.severity = OPENMD_INFO;
433	>	simError();
434	>	return NULL;
435	>	} else {
436	>
437	>	inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
438	>	return inversion;
439		}
440	+	}
441	+
442
443	<	return torsion;
444	<	}
445	<
436	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
443	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
444	>	CutoffGroupStamp* stamp,
445	>	LocalIndexManager* localIndexMan) {
446		int nAtoms;
447		CutoffGroup* cg;
448		Atom* atom;
#	Line 441 | Line 450 | CutoffGroup* MoleculeCreator::createCutoffGroup(Molecu
450
451		nAtoms = stamp->getNMembers();
452		for (int i =0; i < nAtoms; ++i) {
453	<	atom = mol->getAtomAt(stamp->getMember(i));
454	<	assert(atom);
455	<	cg->addAtom(atom);
453	>	atom = mol->getAtomAt(stamp->getMemberAt(i));
454	>	assert(atom);
455	>	cg->addAtom(atom);
456		}
457	<
457	>
458	>	//set the local index of this cutoffGroup, global index will be set later
459	>	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
460	>
461		return cg;
462	<	}
463	<
464	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
462	>	}
463	>
464	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
465	>	LocalIndexManager* localIndexMan) {
466		CutoffGroup* cg;
467		cg  = new CutoffGroup();
468		cg->addAtom(atom);
469	+
470	+	//set the local index of this cutoffGroup, global index will be set later
471	+	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
472	+
473		return cg;
474	<	}
474	>	}
475
476	<	void MoleculeCreator::createConstraintPair(Molecule* mol) {
476	>	void MoleculeCreator::createConstraintPair(Molecule* mol) {
477
478		//add bond constraints
479		Molecule::BondIterator bi;
480		Bond* bond;
481		for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
482
483	<	BondType* bt = bond->getBondType();
483	>	BondType* bt = bond->getBondType();
484
485	<	//class Parent1 {};
486	<	//class Child1 : public Parent {};
487	<	//class Child2 : public Parent {};
488	<	//Child1* ch1 = new Child1();
489	<	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
490	<	//the dynamic_cast is succeed in above line. A compiler bug?
485	>	//class Parent1 {};
486	>	//class Child1 : public Parent {};
487	>	//class Child2 : public Parent {};
488	>	//Child1* ch1 = new Child1();
489	>	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
490	>	//the dynamic_cast is succeed in above line. A compiler bug?
491
492	<	if (typeid(FixedBondType) == typeid(*bt)) {
493	<	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
492	>	if (typeid(FixedBondType) == typeid(*bt)) {
493	>	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
494
495	<	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
496	<	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
497	<	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
498	<	mol->addConstraintPair(consPair);
499	<	}
495	>	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
496	>	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
497	>	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
498	>	mol->addConstraintPair(consPair);
499	>	}
500		}
501
502		//rigidbody -- rigidbody constraint is not support yet
503	<	}
503	>	}
504
505	<	void MoleculeCreator::createConstraintElem(Molecule* mol) {
505	>	void MoleculeCreator::createConstraintElem(Molecule* mol) {
506
507		ConstraintPair* consPair;
508		Molecule::ConstraintPairIterator cpi;
509		std::set<StuntDouble*> sdSet;
510		for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
511
512	<	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
513	<	if (sdSet.find(sdA) == sdSet.end()){
514	<	sdSet.insert(sdA);
515	<	mol->addConstraintElem(new ConstraintElem(sdA));
516	<	}
512	>	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
513	>	if (sdSet.find(sdA) == sdSet.end()){
514	>	sdSet.insert(sdA);
515	>	mol->addConstraintElem(new ConstraintElem(sdA));
516	>	}
517
518	<	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
519	<	if (sdSet.find(sdB) == sdSet.end()){
520	<	sdSet.insert(sdB);
521	<	mol->addConstraintElem(new ConstraintElem(sdB));
522	<	}
518	>	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
519	>	if (sdSet.find(sdB) == sdSet.end()){
520	>	sdSet.insert(sdB);
521	>	mol->addConstraintElem(new ConstraintElem(sdB));
522	>	}
523
524		}
525
526	<	}
526	>	}
527
528		}

Comparing:
trunk/src/brains/MoleculeCreator.cpp (property svn:keywords), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/brains/MoleculeCreator.cpp (property svn:keywords), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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