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root/OpenMD/trunk/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.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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
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	–
70		//create atoms
71		Atom* atom;
72		AtomStamp* currentAtomStamp;
73		int nAtom = molStamp->getNAtoms();
74		for (int i = 0; i < nAtom; ++i) {
75	<	currentAtomStamp = molStamp->getAtom(i);
76	<	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
77	<	mol->addAtom(atom);
75	>	currentAtomStamp = molStamp->getAtomStamp(i);
76	>	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
77	>	mol->addAtom(atom);
78		}
79
80		//create rigidbodies
#	Line 81 | Line 83 | Molecule* MoleculeCreator::createMolecule(ForceField*
83		int nRigidbodies = molStamp->getNRigidBodies();
84
85		for (int i = 0; i < nRigidbodies; ++i) {
86	<	currentRigidBodyStamp = molStamp->getRigidBody(i);
87	<	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
88	<	mol->addRigidBody(rb);
86	>	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
87	>	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
88	>	localIndexMan);
89	>	mol->addRigidBody(rb);
90		}
91	<
91	>
92		//create bonds
93		Bond* bond;
94		BondStamp* currentBondStamp;
95		int nBonds = molStamp->getNBonds();
96
97		for (int i = 0; i < nBonds; ++i) {
98	<	currentBondStamp = molStamp->getBond(i);
99	<	bond = createBond(ff, mol, currentBondStamp);
100	<	mol->addBond(bond);
98	>	currentBondStamp = molStamp->getBondStamp(i);
99	>	bond = createBond(ff, mol, currentBondStamp);
100	>	mol->addBond(bond);
101		}
102
103		//create bends
#	Line 102 | Line 105 | Molecule* MoleculeCreator::createMolecule(ForceField*
105		BendStamp* currentBendStamp;
106		int nBends = molStamp->getNBends();
107		for (int i = 0; i < nBends; ++i) {
108	<	currentBendStamp = molStamp->getBend(i);
109	<	bend = createBend(ff, mol, currentBendStamp);
110	<	mol->addBend(bend);
108	>	currentBendStamp = molStamp->getBendStamp(i);
109	>	bend = createBend(ff, mol, currentBendStamp);
110	>	mol->addBend(bend);
111		}
112
113		//create torsions
#	Line 112 | Line 115 | Molecule* MoleculeCreator::createMolecule(ForceField*
115		TorsionStamp* currentTorsionStamp;
116		int nTorsions = molStamp->getNTorsions();
117		for (int i = 0; i < nTorsions; ++i) {
118	<	currentTorsionStamp = molStamp->getTorsion(i);
119	<	torsion = createTorsion(ff, mol, currentTorsionStamp);
120	<	mol->addTorsion(torsion);
118	>	currentTorsionStamp = molStamp->getTorsionStamp(i);
119	>	torsion = createTorsion(ff, mol, currentTorsionStamp);
120	>	mol->addTorsion(torsion);
121		}
122
123	+	//create inversions
124	+	Inversion* inversion;
125	+	InversionStamp* currentInversionStamp;
126	+	int nInversions = molStamp->getNInversions();
127	+	for (int i = 0; i < nInversions; ++i) {
128	+	currentInversionStamp = molStamp->getInversionStamp(i);
129	+	inversion = createInversion(ff, mol, currentInversionStamp);
130	+	if (inversion != NULL ) {
131	+	mol->addInversion(inversion);
132	+	}
133	+	}
134	+
135		//create cutoffGroups
136		CutoffGroup* cutoffGroup;
137		CutoffGroupStamp* currentCutoffGroupStamp;
138		int nCutoffGroups = molStamp->getNCutoffGroups();
139		for (int i = 0; i < nCutoffGroups; ++i) {
140	<	currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
141	<	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
142	<	mol->addCutoffGroup(cutoffGroup);
140	>	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
141	>	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan);
142	>	mol->addCutoffGroup(cutoffGroup);
143		}
144
145		//every free atom is a cutoff group
146	<	std::set<Atom*> allAtoms;
147	<	Molecule::AtomIterator ai;
146	>	std::vector<Atom*> freeAtoms;
147	>	std::vector<Atom*>::iterator ai;
148	>	std::vector<Atom*>::iterator fai;
149
150		//add all atoms into allAtoms set
151	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
152	<	allAtoms.insert(atom);
151	>	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
152	>	freeAtoms.push_back(atom);
153		}
154
155		Molecule::CutoffGroupIterator ci;
156		CutoffGroup* cg;
141	–	std::set<Atom*> cutoffAtoms;
157
158	<	//add all of the atoms belong to cutoff groups into cutoffAtoms set
159	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
160	<
161	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
162	<	cutoffAtoms.insert(atom);
163	<	}
164	<
158	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
159	>	cg = mol->nextCutoffGroup(ci)) {
160	>
161	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
162	>	//erase the atoms belong to cutoff groups from freeAtoms vector
163	>	freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom),
164	>	freeAtoms.end());
165	>	}
166		}
167
168	<	//find all free atoms (which do not belong to cutoff groups)
169	<	//performs the "difference" operation from set theory,  the output range contains a copy of every
170	<	//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	<
168	>	// loop over the free atoms and then create one cutoff group for
169	>	// every single free atom
170	>
171		for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
172	<	cutoffGroup = createCutoffGroup(mol, *fai);
173	<	mol->addCutoffGroup(cutoffGroup);
172	>	cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
173	>	mol->addCutoffGroup(cutoffGroup);
174		}
175		//create constraints
176		createConstraintPair(mol);
177		createConstraintElem(mol);
178
179	+	// Does this molecule stamp define a total constrained charge value?
180	+	// If so, let the created molecule know about it.
181	+
182	+	if (molStamp->haveConstrainTotalCharge() ) {
183	+	mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
184	+	}
185	+
186		//the construction of this molecule is finished
187		mol->complete();
188	<
188	>
189		return mol;
190	<	}
190	>	}
191
192
193	<	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
194	<	LocalIndexManager* localIndexMan) {
193	>	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
194	>	AtomStamp* stamp,
195	>	LocalIndexManager* localIndexMan) {
196		AtomType * atomType;
197		Atom* atom;
198
199		atomType =  ff->getAtomType(stamp->getType());
200	<
200	>
201		if (atomType == NULL) {
202	<	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
203	<	stamp->getType());
202	>	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
203	>	stamp->getType().c_str());
204
205	<	painCave.isFatal = 1;
206	<	simError();
205	>	painCave.isFatal = 1;
206	>	simError();
207		}
208	<
208	>
209		//below code still have some kind of hard-coding smell
210		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");
211
212	<	painCave.isFatal = 1;
213	<	simError();
214	<	}
212	<
213	<	DirectionalAtom* dAtom;
214	<	dAtom = new DirectionalAtom(dAtomType);
215	<	atom = dAtom;
212	>	DirectionalAtom* dAtom;
213	>	dAtom = new DirectionalAtom(atomType);
214	>	atom = dAtom;
215		}
216		else{
217	<	atom = new Atom(atomType);
217	>	atom = new Atom(atomType);
218		}
219
220		atom->setLocalIndex(localIndexMan->getNextAtomIndex());
221
222		return atom;
223	<	}
224	<
225	<	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
226	<	RigidBodyStamp* rbStamp,
227	<	LocalIndexManager* localIndexMan) {
223	>	}
224	>
225	>	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
226	>	Molecule* mol,
227	>	RigidBodyStamp* rbStamp,
228	>	LocalIndexManager* localIndexMan) {
229		Atom* atom;
230		int nAtoms;
231		Vector3d refCoor;
#	Line 234 | Line 234 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
234		RigidBody* rb = new RigidBody();
235		nAtoms = rbStamp->getNMembers();
236		for (int i = 0; i < nAtoms; ++i) {
237	<	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
238	<	//It is not the same as local index of atom which is the index of atom at DataStorage class
239	<	atom = mol->getAtomAt(rbStamp->getMember(i));
240	<	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
241	<	rb->addAtom(atom, atomStamp);
237	>	//rbStamp->getMember(i) return the local index of current atom
238	>	//inside the molecule.  It is not the same as local index of
239	>	//atom which is the index of atom at DataStorage class
240	>	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
241	>	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
242	>	rb->addAtom(atom, atomStamp);
243		}
244
245	<	//after all of the atoms are added, we need to calculate the reference coordinates
245	>	//after all of the atoms are added, we need to calculate the
246	>	//reference coordinates
247		rb->calcRefCoords();
248
249		//set the local index of this rigid body, global index will be set later
#	Line 253 | Line 255 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
255		//The third part is the index of the rigidbody defined in meta-data file
256		//For example, Butane_RB_0 is a valid rigid body name of butane molecule
257		/**@todo replace itoa by lexi_cast */
258	<	rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
259	<
258	>	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
259	>	rb->setType(mol->getType() + "_RB_" + s.c_str());
260	>
261		return rb;
262	<	}
262	>	}
263
264	<	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
264	>	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
265	>	BondStamp* stamp) {
266		BondType* bondType;
267		Atom* atomA;
268		Atom* atomB;
269	<
269	>
270		atomA = mol->getAtomAt(stamp->getA());
271		atomB = mol->getAtomAt(stamp->getB());
272	<
272	>
273		assert( atomA && atomB);
274
275		bondType = ff->getBondType(atomA->getType(), atomB->getType());
276
277		if (bondType == NULL) {
278	<	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
279	<	atomA->getType().c_str(),
280	<	atomB->getType().c_str());
281	<
282	<	painCave.isFatal = 1;
283	<	simError();
278	>	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
279	>	atomA->getType().c_str(),
280	>	atomB->getType().c_str());
281	>
282	>	painCave.isFatal = 1;
283	>	simError();
284		}
285		return new Bond(atomA, atomB, bondType);
286	<	}
286	>	}
287	>
288	>	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
289	>	BendStamp* stamp) {
290	>	Bend* bend = NULL;
291	>	std::vector<int> bendAtoms = stamp->getMembers();
292	>	if (bendAtoms.size() == 3) {
293	>	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
294	>	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
295	>	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
296	>
297	>	assert( atomA && atomB && atomC);
298	>
299	>	BendType* bendType = ff->getBendType(atomA->getType().c_str(),
300	>	atomB->getType().c_str(),
301	>	atomC->getType().c_str());
302	>
303	>	if (bendType == NULL) {
304	>	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
305	>	atomA->getType().c_str(),
306	>	atomB->getType().c_str(),
307	>	atomC->getType().c_str());
308	>
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>
313	>	bend = new Bend(atomA, atomB, atomC, bendType);
314	>	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
315	>	int ghostIndex = stamp->getGhostVectorSource();
316	>	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
317	>	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
318	>	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
319	>	if (ghostAtom == NULL) {
320	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
321	>	painCave.isFatal = 1;
322	>	simError();
323	>	}
324	>
325	>	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
326
327	<	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
328	<	bool isGhostBend = false;
329	<	int ghostIndex;
327	>	if (bendType == NULL) {
328	>	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
329	>	normalAtom->getType().c_str(),
330	>	ghostAtom->getType().c_str(),
331	>	"GHOST");
332
333	+	painCave.isFatal = 1;
334	+	simError();
335	+	}
336	+
337	+	bend = new GhostBend(normalAtom, ghostAtom, bendType);
338	+
339	+	}
340
341	<	//
342	<	if (stamp->haveExtras()){
291	<	LinkedAssign* extras = stamp->getExtras();
292	<	LinkedAssign* currentExtra = extras;
341	>	return bend;
342	>	}
343
344	<	while (currentExtra != NULL){
345	<	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
296	<	switch (currentExtra->getType()){
297	<	case 0:
298	<	ghostIndex = currentExtra->getInt();
299	<	isGhostBend = true;
300	<	break;
344	>	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
345	>	TorsionStamp* stamp) {
346
347	<	default:
348	<	sprintf(painCave.errMsg,
349	<	"SimSetup Error: ghostVectorSource must be an int.\n");
350	<	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	<
347	>	Torsion* torsion = NULL;
348	>	std::vector<int> torsionAtoms = stamp->getMembers();
349	>	if (torsionAtoms.size() < 3) {
350	>	return torsion;
351		}
352
353	<	if (isGhostBend) {
353	>	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
354	>	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
355	>	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
356
357	<	int indexA = stamp->getA();
358	<	int indexB= stamp->getB();
357	>	if (torsionAtoms.size() == 4) {
358	>	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
359
360	<	assert(indexA != indexB);
325	<
326	<	int normalIndex;
327	<	if (indexA == ghostIndex) {
328	<	normalIndex = indexB;
329	<	} else if (indexB == ghostIndex) {
330	<	normalIndex = indexA;
331	<	}
360	>	assert(atomA && atomB && atomC && atomD);
361
362	<	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
363	<	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
364	<	if (ghostAtom == NULL) {
365	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
366	<	painCave.isFatal = 1;
367	<	simError();
368	<	}
369	<
370	<	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
371	<
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	<	}
362	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
363	>	atomB->getType(),
364	>	atomC->getType(),
365	>	atomD->getType());
366	>	if (torsionType == NULL) {
367	>	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
368	>	atomA->getType().c_str(),
369	>	atomB->getType().c_str(),
370	>	atomC->getType().c_str(),
371	>	atomD->getType().c_str());
372
373	<	return new GhostBend(normalAtom, ghostAtom, bendType);
374	<
375	<	} else {
376	<
377	<	Atom* atomA = mol->getAtomAt(stamp->getA());
378	<	Atom* atomB = mol->getAtomAt(stamp->getB());
379	<	Atom* atomC = mol->getAtomAt(stamp->getC());
380	<
381	<	assert( atomA && atomB && atomC);
373	>	painCave.isFatal = 1;
374	>	simError();
375	>	}
376	>
377	>	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
378	>	}
379	>	else {
380	>
381	>	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
382	>	if (dAtom == NULL) {
383	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
384	>	painCave.isFatal = 1;
385	>	simError();
386	>	}
387	>
388	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
389	>	atomC->getType(), "GHOST");
390	>
391	>	if (torsionType == NULL) {
392	>	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
393	>	atomA->getType().c_str(),
394	>	atomB->getType().c_str(),
395	>	atomC->getType().c_str(),
396	>	"GHOST");
397
398	<	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
399	<
400	<	if (bendType == NULL) {
401	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
402	<	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);
398	>	painCave.isFatal = 1;
399	>	simError();
400	>	}
401	>
402	>	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
403		}
404	<	}
404	>
405	>	return torsion;
406	>	}
407
408	<	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
409	<
410	<	Atom* atomA = mol->getAtomAt(stamp->getA());
411	<	Atom* atomB = mol->getAtomAt(stamp->getB());
412	<	Atom* atomC = mol->getAtomAt(stamp->getC());
413	<	Torsion* torsion;
414	<
415	<	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);
408	>	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
409	>	InversionStamp* stamp) {
410	>
411	>	Inversion* inversion = NULL;
412	>	int center = stamp->getCenter();
413	>	std::vector<int> satellites = stamp->getSatellites();
414	>	if (satellites.size() != 3) {
415	>	return inversion;
416		}
407	–	else {
417
418	<	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
419	<	if (dAtom == NULL) {
420	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
421	<	painCave.isFatal = 1;
422	<	simError();
423	<	}
418	>	Atom* atomA = mol->getAtomAt(center);
419	>	Atom* atomB = mol->getAtomAt(satellites[0]);
420	>	Atom* atomC = mol->getAtomAt(satellites[1]);
421	>	Atom* atomD = mol->getAtomAt(satellites[2]);
422	>
423	>	assert(atomA && atomB && atomC && atomD);
424	>
425	>	InversionType* inversionType = ff->getInversionType(atomA->getType(),
426	>	atomB->getType(),
427	>	atomC->getType(),
428	>	atomD->getType());
429
430	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
431	<	atomC->getType(), "GHOST");
432	<
433	<	if (torsionType == NULL) {
434	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
435	<	atomA->getType().c_str(),
436	<	atomB->getType().c_str(),
437	<	atomC->getType().c_str(),
438	<	"GHOST");
439	<
440	<	painCave.isFatal = 1;
441	<	simError();
442	<	}
443	<
444	<	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
430	>	if (inversionType == NULL) {
431	>	sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
432	>	"\t(May not be a problem: not all inversions are parametrized)\n",
433	>	atomA->getType().c_str(),
434	>	atomB->getType().c_str(),
435	>	atomC->getType().c_str(),
436	>	atomD->getType().c_str());
437	>
438	>	painCave.isFatal = 0;
439	>	painCave.severity = OPENMD_INFO;
440	>	simError();
441	>	return NULL;
442	>	} else {
443	>
444	>	inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
445	>	return inversion;
446		}
447	+	}
448	+
449
450	<	return torsion;
451	<	}
452	<
436	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
450	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
451	>	CutoffGroupStamp* stamp,
452	>	LocalIndexManager* localIndexMan) {
453		int nAtoms;
454		CutoffGroup* cg;
455		Atom* atom;
#	Line 441 | Line 457 | CutoffGroup* MoleculeCreator::createCutoffGroup(Molecu
457
458		nAtoms = stamp->getNMembers();
459		for (int i =0; i < nAtoms; ++i) {
460	<	atom = mol->getAtomAt(stamp->getMember(i));
461	<	assert(atom);
462	<	cg->addAtom(atom);
460	>	atom = mol->getAtomAt(stamp->getMemberAt(i));
461	>	assert(atom);
462	>	cg->addAtom(atom);
463		}
464	<
464	>
465	>	//set the local index of this cutoffGroup, global index will be set later
466	>	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
467	>
468		return cg;
469	<	}
470	<
471	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
469	>	}
470	>
471	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
472	>	LocalIndexManager* localIndexMan) {
473		CutoffGroup* cg;
474		cg  = new CutoffGroup();
475		cg->addAtom(atom);
476	+
477	+	//set the local index of this cutoffGroup, global index will be set later
478	+	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
479	+
480		return cg;
481	<	}
481	>	}
482
483	<	void MoleculeCreator::createConstraintPair(Molecule* mol) {
483	>	void MoleculeCreator::createConstraintPair(Molecule* mol) {
484
485		//add bond constraints
486		Molecule::BondIterator bi;
487		Bond* bond;
488		for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
489
490	<	BondType* bt = bond->getBondType();
490	>	BondType* bt = bond->getBondType();
491
492	<	//class Parent1 {};
493	<	//class Child1 : public Parent {};
494	<	//class Child2 : public Parent {};
495	<	//Child1* ch1 = new Child1();
496	<	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
497	<	//the dynamic_cast is succeed in above line. A compiler bug?
492	>	//class Parent1 {};
493	>	//class Child1 : public Parent {};
494	>	//class Child2 : public Parent {};
495	>	//Child1* ch1 = new Child1();
496	>	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
497	>	//the dynamic_cast is succeed in above line. A compiler bug?
498
499	<	if (typeid(FixedBondType) == typeid(*bt)) {
500	<	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
499	>	if (typeid(FixedBondType) == typeid(*bt)) {
500	>	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
501
502	<	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
503	<	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
504	<	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
505	<	mol->addConstraintPair(consPair);
506	<	}
502	>	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
503	>	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
504	>	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
505	>	mol->addConstraintPair(consPair);
506	>	}
507		}
508
509		//rigidbody -- rigidbody constraint is not support yet
510	<	}
510	>	}
511
512	<	void MoleculeCreator::createConstraintElem(Molecule* mol) {
512	>	void MoleculeCreator::createConstraintElem(Molecule* mol) {
513
514		ConstraintPair* consPair;
515		Molecule::ConstraintPairIterator cpi;
516		std::set<StuntDouble*> sdSet;
517		for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
518
519	<	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
520	<	if (sdSet.find(sdA) == sdSet.end()){
521	<	sdSet.insert(sdA);
522	<	mol->addConstraintElem(new ConstraintElem(sdA));
523	<	}
519	>	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
520	>	if (sdSet.find(sdA) == sdSet.end()){
521	>	sdSet.insert(sdA);
522	>	mol->addConstraintElem(new ConstraintElem(sdA));
523	>	}
524
525	<	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
526	<	if (sdSet.find(sdB) == sdSet.end()){
527	<	sdSet.insert(sdB);
528	<	mol->addConstraintElem(new ConstraintElem(sdB));
529	<	}
525	>	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
526	>	if (sdSet.find(sdB) == sdSet.end()){
527	>	sdSet.insert(sdB);
528	>	mol->addConstraintElem(new ConstraintElem(sdB));
529	>	}
530
531		}
532
533	<	}
533	>	}
534
535		}

Comparing trunk/src/brains/MoleculeCreator.cpp (property svn:keywords):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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