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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 1908 by gezelter, Fri Jul 19 21:25:45 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	>	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);
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);
178		createConstraintElem(mol);
179
180	+	// Does this molecule stamp define a total constrained charge value?
181	+	// If so, let the created molecule know about it.
182	+
183	+	if (molStamp->haveConstrainTotalCharge() ) {
184	+	mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
185	+	}
186	+
187		//the construction of this molecule is finished
188		mol->complete();
189	<
189	>
190		return mol;
191	<	}
191	>	}
192
193
194	<	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
195	<	LocalIndexManager* localIndexMan) {
194	>	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
195	>	AtomStamp* stamp,
196	>	LocalIndexManager* localIndexMan) {
197		AtomType * atomType;
198		Atom* atom;
199
200		atomType =  ff->getAtomType(stamp->getType());
201	<
201	>
202		if (atomType == NULL) {
203	<	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
204	<	stamp->getType());
203	>	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
204	>	stamp->getType().c_str());
205
206	<	painCave.isFatal = 1;
207	<	simError();
206	>	painCave.isFatal = 1;
207	>	simError();
208		}
209	<
209	>
210		//below code still have some kind of hard-coding smell
211		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");
212
213	<	painCave.isFatal = 1;
214	<	simError();
215	<	}
212	<
213	<	DirectionalAtom* dAtom;
214	<	dAtom = new DirectionalAtom(dAtomType);
215	<	atom = dAtom;
213	>	DirectionalAtom* dAtom;
214	>	dAtom = new DirectionalAtom(atomType);
215	>	atom = dAtom;
216		}
217		else{
218	<	atom = new Atom(atomType);
218	>	atom = new Atom(atomType);
219		}
220
221		atom->setLocalIndex(localIndexMan->getNextAtomIndex());
222
223		return atom;
224	<	}
225	<
226	<	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
227	<	RigidBodyStamp* rbStamp,
228	<	LocalIndexManager* localIndexMan) {
224	>	}
225	>
226	>	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
227	>	Molecule* mol,
228	>	RigidBodyStamp* rbStamp,
229	>	LocalIndexManager* localIndexMan) {
230		Atom* atom;
231		int nAtoms;
232		Vector3d refCoor;
#	Line 234 | Line 235 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
235		RigidBody* rb = new RigidBody();
236		nAtoms = rbStamp->getNMembers();
237		for (int i = 0; i < nAtoms; ++i) {
238	<	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
239	<	//It is not the same as local index of atom which is the index of atom at DataStorage class
240	<	atom = mol->getAtomAt(rbStamp->getMember(i));
241	<	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
242	<	rb->addAtom(atom, atomStamp);
238	>	//rbStamp->getMember(i) return the local index of current atom
239	>	//inside the molecule.  It is not the same as local index of
240	>	//atom which is the index of atom at DataStorage class
241	>	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
242	>	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
243	>	rb->addAtom(atom, atomStamp);
244		}
245
246	<	//after all of the atoms are added, we need to calculate the reference coordinates
246	>	//after all of the atoms are added, we need to calculate the
247	>	//reference coordinates
248		rb->calcRefCoords();
249
250		//set the local index of this rigid body, global index will be set later
#	Line 253 | Line 256 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
256		//The third part is the index of the rigidbody defined in meta-data file
257		//For example, Butane_RB_0 is a valid rigid body name of butane molecule
258		/**@todo replace itoa by lexi_cast */
259	<	std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
259	>	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
260		rb->setType(mol->getType() + "_RB_" + s.c_str());
261
262		return rb;
263	<	}
263	>	}
264
265	<	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
265	>	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
266	>	BondStamp* stamp) {
267		BondType* bondType;
268		Atom* atomA;
269		Atom* atomB;
270	<
270	>
271		atomA = mol->getAtomAt(stamp->getA());
272		atomB = mol->getAtomAt(stamp->getB());
273	<
273	>
274		assert( atomA && atomB);
275
276		bondType = ff->getBondType(atomA->getType(), atomB->getType());
277
278		if (bondType == NULL) {
279	<	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
280	<	atomA->getType().c_str(),
281	<	atomB->getType().c_str());
282	<
283	<	painCave.isFatal = 1;
284	<	simError();
279	>	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
280	>	atomA->getType().c_str(),
281	>	atomB->getType().c_str());
282	>
283	>	painCave.isFatal = 1;
284	>	simError();
285		}
286		return new Bond(atomA, atomB, bondType);
287	<	}
287	>	}
288	>
289	>	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
290	>	BendStamp* stamp) {
291	>	Bend* bend = NULL;
292	>	std::vector<int> bendAtoms = stamp->getMembers();
293	>	if (bendAtoms.size() == 3) {
294	>	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
295	>	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
296	>	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
297	>
298	>	assert( atomA && atomB && atomC);
299	>
300	>	BendType* bendType = ff->getBendType(atomA->getType().c_str(),
301	>	atomB->getType().c_str(),
302	>	atomC->getType().c_str());
303	>
304	>	if (bendType == NULL) {
305	>	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
306	>	atomA->getType().c_str(),
307	>	atomB->getType().c_str(),
308	>	atomC->getType().c_str());
309	>
310	>	painCave.isFatal = 1;
311	>	simError();
312	>	}
313	>
314	>	bend = new Bend(atomA, atomB, atomC, bendType);
315	>	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
316	>	int ghostIndex = stamp->getGhostVectorSource();
317	>	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
318	>	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
319	>	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
320	>	if (ghostAtom == NULL) {
321	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
322	>	painCave.isFatal = 1;
323	>	simError();
324	>	}
325	>
326	>	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
327
328	<	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
329	<	bool isGhostBend = false;
330	<	int ghostIndex;
328	>	if (bendType == NULL) {
329	>	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
330	>	normalAtom->getType().c_str(),
331	>	ghostAtom->getType().c_str(),
332	>	"GHOST");
333
334	+	painCave.isFatal = 1;
335	+	simError();
336	+	}
337	+
338	+	bend = new GhostBend(normalAtom, ghostAtom, bendType);
339	+
340	+	}
341
342	<	//
343	<	if (stamp->haveExtras()){
292	<	LinkedAssign* extras = stamp->getExtras();
293	<	LinkedAssign* currentExtra = extras;
342	>	return bend;
343	>	}
344
345	<	while (currentExtra != NULL){
346	<	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
297	<	switch (currentExtra->getType()){
298	<	case 0:
299	<	ghostIndex = currentExtra->getInt();
300	<	isGhostBend = true;
301	<	break;
345	>	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
346	>	TorsionStamp* stamp) {
347
348	<	default:
349	<	sprintf(painCave.errMsg,
350	<	"SimSetup Error: ghostVectorSource must be an int.\n");
351	<	painCave.isFatal = 1;
307	<	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	<
348	>	Torsion* torsion = NULL;
349	>	std::vector<int> torsionAtoms = stamp->getMembers();
350	>	if (torsionAtoms.size() < 3) {
351	>	return torsion;
352		}
353
354	<	if (isGhostBend) {
354	>	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
355	>	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
356	>	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
357
358	<	int indexA = stamp->getA();
359	<	int indexB= stamp->getB();
358	>	if (torsionAtoms.size() == 4) {
359	>	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
360
361	<	assert(indexA != indexB);
326	<
327	<	int normalIndex;
328	<	if (indexA == ghostIndex) {
329	<	normalIndex = indexB;
330	<	} else if (indexB == ghostIndex) {
331	<	normalIndex = indexA;
332	<	}
361	>	assert(atomA && atomB && atomC && atomD);
362
363	<	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
364	<	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
365	<	if (ghostAtom == NULL) {
366	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
367	<	painCave.isFatal = 1;
368	<	simError();
369	<	}
370	<
371	<	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
372	<
344	<	if (bendType == NULL) {
345	<	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");
349	<
350	<	painCave.isFatal = 1;
351	<	simError();
352	<	}
363	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
364	>	atomB->getType(),
365	>	atomC->getType(),
366	>	atomD->getType());
367	>	if (torsionType == NULL) {
368	>	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
369	>	atomA->getType().c_str(),
370	>	atomB->getType().c_str(),
371	>	atomC->getType().c_str(),
372	>	atomD->getType().c_str());
373
374	<	return new GhostBend(normalAtom, ghostAtom, bendType);
375	<
376	<	} else {
377	<
378	<	Atom* atomA = mol->getAtomAt(stamp->getA());
379	<	Atom* atomB = mol->getAtomAt(stamp->getB());
380	<	Atom* atomC = mol->getAtomAt(stamp->getC());
381	<
382	<	assert( atomA && atomB && atomC);
374	>	painCave.isFatal = 1;
375	>	simError();
376	>	}
377	>
378	>	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
379	>	}
380	>	else {
381	>
382	>	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
383	>	if (dAtom == NULL) {
384	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
385	>	painCave.isFatal = 1;
386	>	simError();
387	>	}
388	>
389	>	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
390	>	atomC->getType(), "GHOST");
391	>
392	>	if (torsionType == NULL) {
393	>	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
394	>	atomA->getType().c_str(),
395	>	atomB->getType().c_str(),
396	>	atomC->getType().c_str(),
397	>	"GHOST");
398
399	<	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
400	<
401	<	if (bendType == NULL) {
402	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
403	<	atomA->getType().c_str(),
369	<	atomB->getType().c_str(),
370	<	atomC->getType().c_str());
371	<
372	<	painCave.isFatal = 1;
373	<	simError();
374	<	}
375	<
376	<	return new Bend(atomA, atomB, atomC, bendType);
399	>	painCave.isFatal = 1;
400	>	simError();
401	>	}
402	>
403	>	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
404		}
405	<	}
405	>
406	>	return torsion;
407	>	}
408
409	<	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
410	<
411	<	Atom* atomA = mol->getAtomAt(stamp->getA());
412	<	Atom* atomB = mol->getAtomAt(stamp->getB());
413	<	Atom* atomC = mol->getAtomAt(stamp->getC());
414	<	Torsion* torsion;
415	<
416	<	if (stamp->getD() != -1) {
388	<	Atom* atomD = mol->getAtomAt(stamp->getD());
389	<
390	<	assert(atomA && atomB && atomC && atomD);
391	<
392	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
393	<	atomC->getType(), atomD->getType());
394	<
395	<	if (torsionType == NULL) {
396	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
397	<	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);
409	>	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
410	>	InversionStamp* stamp) {
411	>
412	>	Inversion* inversion = NULL;
413	>	int center = stamp->getCenter();
414	>	std::vector<int> satellites = stamp->getSatellites();
415	>	if (satellites.size() != 3) {
416	>	return inversion;
417		}
408	–	else {
418
419	<	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
420	<	if (dAtom == NULL) {
421	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
422	<	painCave.isFatal = 1;
423	<	simError();
424	<	}
419	>	Atom* atomA = mol->getAtomAt(center);
420	>	Atom* atomB = mol->getAtomAt(satellites[0]);
421	>	Atom* atomC = mol->getAtomAt(satellites[1]);
422	>	Atom* atomD = mol->getAtomAt(satellites[2]);
423	>
424	>	assert(atomA && atomB && atomC && atomD);
425	>
426	>	InversionType* inversionType = ff->getInversionType(atomA->getType(),
427	>	atomB->getType(),
428	>	atomC->getType(),
429	>	atomD->getType());
430
431	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
432	<	atomC->getType(), "GHOST");
433	<
434	<	if (torsionType == NULL) {
435	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
436	<	atomA->getType().c_str(),
437	<	atomB->getType().c_str(),
438	<	atomC->getType().c_str(),
439	<	"GHOST");
440	<
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<
445	<	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
431	>	if (inversionType == NULL) {
432	>	sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
433	>	"\t(May not be a problem: not all inversions are parametrized)\n",
434	>	atomA->getType().c_str(),
435	>	atomB->getType().c_str(),
436	>	atomC->getType().c_str(),
437	>	atomD->getType().c_str());
438	>
439	>	painCave.isFatal = 0;
440	>	painCave.severity = OPENMD_INFO;
441	>	simError();
442	>	return NULL;
443	>	} else {
444	>
445	>	inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
446	>	return inversion;
447		}
448	+	}
449	+
450
451	<	return torsion;
452	<	}
453	<
437	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
451	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
452	>	CutoffGroupStamp* stamp,
453	>	LocalIndexManager* localIndexMan) {
454		int nAtoms;
455		CutoffGroup* cg;
456		Atom* atom;
#	Line 442 | Line 458 | CutoffGroup* MoleculeCreator::createCutoffGroup(Molecu
458
459		nAtoms = stamp->getNMembers();
460		for (int i =0; i < nAtoms; ++i) {
461	<	atom = mol->getAtomAt(stamp->getMember(i));
462	<	assert(atom);
463	<	cg->addAtom(atom);
461	>	atom = mol->getAtomAt(stamp->getMemberAt(i));
462	>	assert(atom);
463	>	cg->addAtom(atom);
464		}
465	<
465	>
466	>	//set the local index of this cutoffGroup, global index will be set later
467	>	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
468	>
469		return cg;
470	<	}
471	<
472	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
470	>	}
471	>
472	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
473	>	LocalIndexManager* localIndexMan) {
474		CutoffGroup* cg;
475		cg  = new CutoffGroup();
476		cg->addAtom(atom);
477	+
478	+	//set the local index of this cutoffGroup, global index will be set later
479	+	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
480	+
481		return cg;
482	<	}
482	>	}
483
484	<	void MoleculeCreator::createConstraintPair(Molecule* mol) {
484	>	void MoleculeCreator::createConstraintPair(Molecule* mol) {
485
486		//add bond constraints
487		Molecule::BondIterator bi;
488		Bond* bond;
489		for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
490
491	<	BondType* bt = bond->getBondType();
491	>	BondType* bt = bond->getBondType();
492
493	<	//class Parent1 {};
494	<	//class Child1 : public Parent {};
495	<	//class Child2 : public Parent {};
496	<	//Child1* ch1 = new Child1();
497	<	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
498	<	//the dynamic_cast is succeed in above line. A compiler bug?
493	>	//class Parent1 {};
494	>	//class Child1 : public Parent {};
495	>	//class Child2 : public Parent {};
496	>	//Child1* ch1 = new Child1();
497	>	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
498	>	//the dynamic_cast is succeed in above line. A compiler bug?
499
500	<	if (typeid(FixedBondType) == typeid(*bt)) {
501	<	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
500	>	if (typeid(FixedBondType) == typeid(*bt)) {
501	>	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
502
503	<	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
504	<	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
505	<	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
506	<	mol->addConstraintPair(consPair);
507	<	}
503	>	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
504	>	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
505	>	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
506	>	mol->addConstraintPair(consPair);
507	>	}
508		}
509
510		//rigidbody -- rigidbody constraint is not support yet
511	<	}
511	>	}
512
513	<	void MoleculeCreator::createConstraintElem(Molecule* mol) {
513	>	void MoleculeCreator::createConstraintElem(Molecule* mol) {
514
515		ConstraintPair* consPair;
516		Molecule::ConstraintPairIterator cpi;
517		std::set<StuntDouble*> sdSet;
518		for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
519
520	<	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
521	<	if (sdSet.find(sdA) == sdSet.end()){
522	<	sdSet.insert(sdA);
523	<	mol->addConstraintElem(new ConstraintElem(sdA));
524	<	}
520	>	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
521	>	if (sdSet.find(sdA) == sdSet.end()){
522	>	sdSet.insert(sdA);
523	>	mol->addConstraintElem(new ConstraintElem(sdA));
524	>	}
525
526	<	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
527	<	if (sdSet.find(sdB) == sdSet.end()){
528	<	sdSet.insert(sdB);
529	<	mol->addConstraintElem(new ConstraintElem(sdB));
530	<	}
526	>	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
527	>	if (sdSet.find(sdB) == sdSet.end()){
528	>	sdSet.insert(sdB);
529	>	mol->addConstraintElem(new ConstraintElem(sdB));
530	>	}
531
532		}
533
534	<	}
534	>	}
535
536		}

Comparing trunk/src/brains/MoleculeCreator.cpp (property svn:keywords):
Revision 403 by gezelter, Tue Mar 8 21:06:49 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

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