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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 2046 by gezelter, Tue Dec 2 22:11:04 2014 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	<	/**
44	<	* @file MoleculeCreator.cpp
45	<	* @author tlin
46	<	* @date 11/04/2004
47	<	* @time 13:44am
48	<	* @version 1.0
48	<	*/
43	>	/**
44	>	* @file MoleculeCreator.cpp
45	>	* @author tlin
46	>	* @date 11/04/2004
47	>	* @version 1.0
48	>	*/
49
50		#include <cassert>
51	+	#include <typeinfo>
52		#include <set>
53
54		#include "brains/MoleculeCreator.hpp"
55		#include "primitives/GhostBend.hpp"
56		#include "primitives/GhostTorsion.hpp"
57	<	#include "types/DirectionalAtomType.hpp"
57	>	#include "types/AtomType.hpp"
58		#include "types/FixedBondType.hpp"
59	+	#include "types/BondTypeParser.hpp"
60	+	#include "types/BendTypeParser.hpp"
61	+	#include "types/TorsionTypeParser.hpp"
62	+	#include "types/InversionTypeParser.hpp"
63		#include "utils/simError.h"
64		#include "utils/StringUtils.hpp"
65
66	<	namespace oopse {
66	>	namespace OpenMD {
67	>
68	>	Molecule* MoleculeCreator::createMolecule(ForceField* ff,
69	>	MoleculeStamp *molStamp,
70	>	int stampId, int globalIndex,
71	>	LocalIndexManager* localIndexMan) {
72	>	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(),
73	>	molStamp->getRegion() );
74
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	–
75		//create atoms
76		Atom* atom;
77		AtomStamp* currentAtomStamp;
78		int nAtom = molStamp->getNAtoms();
79		for (int i = 0; i < nAtom; ++i) {
80	<	currentAtomStamp = molStamp->getAtom(i);
81	<	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
82	<	mol->addAtom(atom);
80	>	currentAtomStamp = molStamp->getAtomStamp(i);
81	>	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
82	>	mol->addAtom(atom);
83		}
84
85		//create rigidbodies
#	Line 81 | Line 88 | Molecule* MoleculeCreator::createMolecule(ForceField*
88		int nRigidbodies = molStamp->getNRigidBodies();
89
90		for (int i = 0; i < nRigidbodies; ++i) {
91	<	currentRigidBodyStamp = molStamp->getRigidBody(i);
92	<	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
93	<	mol->addRigidBody(rb);
91	>	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
92	>	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
93	>	localIndexMan);
94	>	mol->addRigidBody(rb);
95		}
96	<
96	>
97		//create bonds
98		Bond* bond;
99		BondStamp* currentBondStamp;
100		int nBonds = molStamp->getNBonds();
101
102		for (int i = 0; i < nBonds; ++i) {
103	<	currentBondStamp = molStamp->getBond(i);
104	<	bond = createBond(ff, mol, currentBondStamp);
105	<	mol->addBond(bond);
103	>	currentBondStamp = molStamp->getBondStamp(i);
104	>	bond = createBond(ff, mol, currentBondStamp, localIndexMan);
105	>	mol->addBond(bond);
106		}
107
108		//create bends
#	Line 102 | Line 110 | Molecule* MoleculeCreator::createMolecule(ForceField*
110		BendStamp* currentBendStamp;
111		int nBends = molStamp->getNBends();
112		for (int i = 0; i < nBends; ++i) {
113	<	currentBendStamp = molStamp->getBend(i);
114	<	bend = createBend(ff, mol, currentBendStamp);
115	<	mol->addBend(bend);
113	>	currentBendStamp = molStamp->getBendStamp(i);
114	>	bend = createBend(ff, mol, currentBendStamp, localIndexMan);
115	>	mol->addBend(bend);
116		}
117
118		//create torsions
#	Line 112 | Line 120 | Molecule* MoleculeCreator::createMolecule(ForceField*
120		TorsionStamp* currentTorsionStamp;
121		int nTorsions = molStamp->getNTorsions();
122		for (int i = 0; i < nTorsions; ++i) {
123	<	currentTorsionStamp = molStamp->getTorsion(i);
124	<	torsion = createTorsion(ff, mol, currentTorsionStamp);
125	<	mol->addTorsion(torsion);
123	>	currentTorsionStamp = molStamp->getTorsionStamp(i);
124	>	torsion = createTorsion(ff, mol, currentTorsionStamp, localIndexMan);
125	>	mol->addTorsion(torsion);
126		}
127
128	+	//create inversions
129	+	Inversion* inversion;
130	+	InversionStamp* currentInversionStamp;
131	+	int nInversions = molStamp->getNInversions();
132	+	for (int i = 0; i < nInversions; ++i) {
133	+	currentInversionStamp = molStamp->getInversionStamp(i);
134	+	inversion = createInversion(ff, mol, currentInversionStamp,
135	+	localIndexMan);
136	+	if (inversion != NULL ) {
137	+	mol->addInversion(inversion);
138	+	}
139	+	}
140	+
141		//create cutoffGroups
142		CutoffGroup* cutoffGroup;
143		CutoffGroupStamp* currentCutoffGroupStamp;
144		int nCutoffGroups = molStamp->getNCutoffGroups();
145		for (int i = 0; i < nCutoffGroups; ++i) {
146	<	currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
147	<	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
148	<	mol->addCutoffGroup(cutoffGroup);
146	>	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
147	>	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp,
148	>	localIndexMan);
149	>	mol->addCutoffGroup(cutoffGroup);
150		}
151
152		//every free atom is a cutoff group
153	<	std::set<Atom*> allAtoms;
154	<	Molecule::AtomIterator ai;
153	>	std::vector<Atom*> freeAtoms;
154	>	std::vector<Atom*>::iterator ai;
155	>	std::vector<Atom*>::iterator fai;
156
157		//add all atoms into allAtoms set
158	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
159	<	allAtoms.insert(atom);
158	>	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
159	>	freeAtoms.push_back(atom);
160		}
161
162		Molecule::CutoffGroupIterator ci;
163		CutoffGroup* cg;
141	–	std::set<Atom*> cutoffAtoms;
164
165	<	//add all of the atoms belong to cutoff groups into cutoffAtoms set
166	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
167	<
168	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
169	<	cutoffAtoms.insert(atom);
170	<	}
171	<
165	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
166	>	cg = mol->nextCutoffGroup(ci)) {
167	>
168	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
169	>	//erase the atoms belong to cutoff groups from freeAtoms vector
170	>	freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom),
171	>	freeAtoms.end());
172	>	}
173		}
174
175	<	//find all free atoms (which do not belong to cutoff groups)
176	<	//performs the "difference" operation from set theory,  the output range contains a copy of every
177	<	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
178	<	//[cutoffAtoms.begin(), cutoffAtoms.end()).
179	<	std::vector<Atom*> freeAtoms;
180	<	std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
181	<	std::back_inserter(freeAtoms));
175	>	// loop over the free atoms and then create one cutoff group for
176	>	// every single free atom
177	>
178	>	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
179	>	cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
180	>	mol->addCutoffGroup(cutoffGroup);
181	>	}
182
183	<	if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
184	<	//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");
183	>	//create bonded constraintPairs:
184	>	createConstraintPair(mol);
185
186	+	//create non-bonded constraintPairs
187	+	for (int i = 0; i < molStamp->getNConstraints(); ++i) {
188	+	ConstraintStamp* cStamp = molStamp->getConstraintStamp(i);
189	+	Atom* atomA;
190	+	Atom* atomB;
191	+
192	+	atomA = mol->getAtomAt(cStamp->getA());
193	+	atomB = mol->getAtomAt(cStamp->getB());
194	+	assert( atomA && atomB );
195	+
196	+	RealType distance;
197	+	bool printConstraintForce = false;
198	+
199	+	if (!cStamp->haveConstrainedDistance()) {
200	+	sprintf(painCave.errMsg,
201	+	"Constraint Error: A non-bond constraint was specified\n"
202	+	"\twithout providing a value for the constrainedDistance.\n");
203		painCave.isFatal = 1;
204	<	simError();
204	>	simError();
205	>	} else {
206	>	distance = cStamp->getConstrainedDistance();
207	>	}
208	>
209	>	if (cStamp->havePrintConstraintForce()) {
210	>	printConstraintForce = cStamp->getPrintConstraintForce();
211	>	}
212	>
213	>	ConstraintElem* consElemA = new ConstraintElem(atomA);
214	>	ConstraintElem* consElemB = new ConstraintElem(atomB);
215	>	ConstraintPair* cPair = new ConstraintPair(consElemA, consElemB, distance,
216	>	printConstraintForce);
217	>	mol->addConstraintPair(cPair);
218		}
219
220	<	//loop over the free atoms and then create one cutoff group for every single free atom
169	<	std::vector<Atom*>::iterator fai;
220	>	// now create the constraint elements:
221
171	–	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
172	–	cutoffGroup = createCutoffGroup(mol, *fai);
173	–	mol->addCutoffGroup(cutoffGroup);
174	–	}
175	–	//create constraints
176	–	createConstraintPair(mol);
222		createConstraintElem(mol);
223
224	+	// Does this molecule stamp define a total constrained charge value?
225	+	// If so, let the created molecule know about it.
226	+
227	+	if (molStamp->haveConstrainTotalCharge() ) {
228	+	mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
229	+	}
230	+
231		//the construction of this molecule is finished
232		mol->complete();
233	<
233	>
234		return mol;
235	<	}
235	>	}
236
237
238	<	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
239	<	LocalIndexManager* localIndexMan) {
238	>	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
239	>	AtomStamp* stamp,
240	>	LocalIndexManager* localIndexMan) {
241		AtomType * atomType;
242		Atom* atom;
243
244		atomType =  ff->getAtomType(stamp->getType());
245	<
245	>
246		if (atomType == NULL) {
247	<	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
248	<	stamp->getType());
247	>	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
248	>	stamp->getType().c_str());
249
250	<	painCave.isFatal = 1;
251	<	simError();
250	>	painCave.isFatal = 1;
251	>	simError();
252		}
253	<
253	>
254		//below code still have some kind of hard-coding smell
255		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");
256
257	<	painCave.isFatal = 1;
258	<	simError();
259	<	}
212	<
213	<	DirectionalAtom* dAtom;
214	<	dAtom = new DirectionalAtom(dAtomType);
215	<	atom = dAtom;
257	>	DirectionalAtom* dAtom;
258	>	dAtom = new DirectionalAtom(atomType);
259	>	atom = dAtom;
260		}
261		else{
262	<	atom = new Atom(atomType);
262	>	atom = new Atom(atomType);
263		}
264
265		atom->setLocalIndex(localIndexMan->getNextAtomIndex());
266
267		return atom;
268	<	}
269	<
270	<	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
271	<	RigidBodyStamp* rbStamp,
272	<	LocalIndexManager* localIndexMan) {
268	>	}
269	>
270	>	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
271	>	Molecule* mol,
272	>	RigidBodyStamp* rbStamp,
273	>	LocalIndexManager* localIndexMan){
274		Atom* atom;
275		int nAtoms;
276		Vector3d refCoor;
#	Line 234 | Line 279 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
279		RigidBody* rb = new RigidBody();
280		nAtoms = rbStamp->getNMembers();
281		for (int i = 0; i < nAtoms; ++i) {
282	<	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
283	<	//It is not the same as local index of atom which is the index of atom at DataStorage class
284	<	atom = mol->getAtomAt(rbStamp->getMember(i));
285	<	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
286	<	rb->addAtom(atom, atomStamp);
282	>	//rbStamp->getMember(i) return the local index of current atom
283	>	//inside the molecule.  It is not the same as local index of
284	>	//atom which is the index of atom at DataStorage class
285	>	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
286	>	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
287	>	rb->addAtom(atom, atomStamp);
288		}
289
290	<	//after all of the atoms are added, we need to calculate the reference coordinates
290	>	//after all of the atoms are added, we need to calculate the
291	>	//reference coordinates
292		rb->calcRefCoords();
293
294		//set the local index of this rigid body, global index will be set later
295		rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
296
297	<	//the rule for naming rigidbody MoleculeName_RB_Integer
298	<	//The first part is the name of the molecule
299	<	//The second part is alway fixed as "RB"
300	<	//The third part is the index of the rigidbody defined in meta-data file
301	<	//For example, Butane_RB_0 is a valid rigid body name of butane molecule
255	<	/**@todo replace itoa by lexi_cast */
256	<	std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
257	<	rb->setType(mol->getType() + "_RB_" + s.c_str());
297	>	// The rule for naming a rigidbody is: MoleculeName_RB_Integer
298	>	// The first part is the name of the molecule
299	>	// The second part is always fixed as "RB"
300	>	// The third part is the index of the rigidbody defined in meta-data file
301	>	// For example, Butane_RB_0 is a valid rigid body name of butane molecule
302
303	+	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
304	+	rb->setType(mol->getType() + "_RB_" + s.c_str());
305		return rb;
306	<	}
306	>	}
307
308	<	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
309	<	BondType* bondType;
308	>	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
309	>	BondStamp* stamp,
310	>	LocalIndexManager* localIndexMan) {
311	>	BondTypeParser btParser;
312	>	BondType* bondType = NULL;
313		Atom* atomA;
314		Atom* atomB;
315	<
315	>
316		atomA = mol->getAtomAt(stamp->getA());
317		atomB = mol->getAtomAt(stamp->getB());
269	–
270	–	assert( atomA && atomB);
318
319	<	bondType = ff->getBondType(atomA->getType(), atomB->getType());
319	>	assert( atomA && atomB);
320
321	<	if (bondType == NULL) {
275	<	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
276	<	atomA->getType().c_str(),
277	<	atomB->getType().c_str());
321	>	if (stamp->hasOverride()) {
322
323	+	try {
324	+	bondType = btParser.parseTypeAndPars(stamp->getOverrideType(),
325	+	stamp->getOverridePars() );
326	+	}
327	+	catch( OpenMDException e) {
328	+	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
329	+	"for molecule %s\n",
330	+	e.what(), mol->getType().c_str() );
331		painCave.isFatal = 1;
332		simError();
333	<	}
282	<	return new Bond(atomA, atomB, bondType);
283	<	}
333	>	}
334
335	<	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
336	<	bool isGhostBend = false;
287	<	int ghostIndex;
335	>	} else {
336	>	bondType = ff->getBondType(atomA->getType(), atomB->getType());
337
338	<
339	<	//
340	<	if (stamp->haveExtras()){
341	<	LinkedAssign* extras = stamp->getExtras();
293	<	LinkedAssign* currentExtra = extras;
294	<
295	<	while (currentExtra != NULL){
296	<	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
297	<	switch (currentExtra->getType()){
298	<	case 0:
299	<	ghostIndex = currentExtra->getInt();
300	<	isGhostBend = true;
301	<	break;
302	<
303	<	default:
304	<	sprintf(painCave.errMsg,
305	<	"SimSetup Error: ghostVectorSource must be an int.\n");
306	<	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	<	}
338	>	if (bondType == NULL) {
339	>	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
340	>	atomA->getType().c_str(),
341	>	atomB->getType().c_str());
342
343	+	painCave.isFatal = 1;
344	+	simError();
345	+	}
346		}
347	+
348	+	Bond* bond = new Bond(atomA, atomB, bondType);
349
350	<	if (isGhostBend) {
350	>	//set the local index of this bond, the global index will be set later
351	>	bond->setLocalIndex(localIndexMan->getNextBondIndex());
352
353	<	int indexA = stamp->getA();
354	<	int indexB= stamp->getB();
353	>	// The rule for naming a bond is: MoleculeName_Bond_Integer
354	>	// The first part is the name of the molecule
355	>	// The second part is always fixed as "Bond"
356	>	// The third part is the index of the bond defined in meta-data file
357	>	// For example, Butane_bond_0 is a valid Bond name in a butane molecule
358
359	<	assert(indexA != indexB);
359	>	std::string s = OpenMD_itoa(mol->getNBonds(), 10);
360	>	bond->setName(mol->getType() + "_Bond_" + s.c_str());
361	>	return bond;
362	>	}
363	>
364	>	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
365	>	BendStamp* stamp,
366	>	LocalIndexManager* localIndexMan) {
367	>	BendTypeParser btParser;
368	>	BendType* bendType = NULL;
369	>	Bend* bend = NULL;
370	>
371	>	std::vector<int> bendAtoms = stamp->getMembers();
372	>	if (bendAtoms.size() == 3) {
373	>	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
374	>	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
375	>	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
376	>
377	>	assert( atomA && atomB && atomC );
378
379	<	int normalIndex;
328	<	if (indexA == ghostIndex) {
329	<	normalIndex = indexB;
330	<	} else if (indexB == ghostIndex) {
331	<	normalIndex = indexA;
332	<	}
379	>	if (stamp->hasOverride()) {
380
381	<	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
382	<	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
383	<	if (ghostAtom == NULL) {
337	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
338	<	painCave.isFatal = 1;
339	<	simError();
381	>	try {
382	>	bendType = btParser.parseTypeAndPars(stamp->getOverrideType(),
383	>	stamp->getOverridePars() );
384		}
385	<
386	<	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
387	<
388	<	if (bendType == NULL) {
389	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
390	<	normalAtom->getType().c_str(),
347	<	ghostAtom->getType().c_str(),
348	<	"GHOST");
349	<
350	<	painCave.isFatal = 1;
351	<	simError();
385	>	catch( OpenMDException e) {
386	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
387	>	"for molecule %s\n",
388	>	e.what(), mol->getType().c_str() );
389	>	painCave.isFatal = 1;
390	>	simError();
391		}
392	+	} else {
393
394	<	return new GhostBend(normalAtom, ghostAtom, bendType);
395	<
396	<	} else {
397	<
398	<	Atom* atomA = mol->getAtomAt(stamp->getA());
399	<	Atom* atomB = mol->getAtomAt(stamp->getB());
400	<	Atom* atomC = mol->getAtomAt(stamp->getC());
401	<
402	<	assert( atomA && atomB && atomC);
403	<
404	<	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
405	<
406	<	if (bendType == NULL) {
407	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
408	<	atomA->getType().c_str(),
409	<	atomB->getType().c_str(),
410	<	atomC->getType().c_str());
394	>	bendType = ff->getBendType(atomA->getType().c_str(),
395	>	atomB->getType().c_str(),
396	>	atomC->getType().c_str());
397	>
398	>	if (bendType == NULL) {
399	>	sprintf(painCave.errMsg,
400	>	"Can not find Matching Bend Type for[%s, %s, %s]",
401	>	atomA->getType().c_str(),
402	>	atomB->getType().c_str(),
403	>	atomC->getType().c_str());
404	>
405	>	painCave.isFatal = 1;
406	>	simError();
407	>	}
408	>	}
409	>
410	>	bend = new Bend(atomA, atomB, atomC, bendType);
411	>
412	>	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
413	>	int ghostIndex = stamp->getGhostVectorSource();
414	>	int normalIndex = ghostIndex != bendAtoms[0] ?
415	>	bendAtoms[0] : bendAtoms[1];
416	>	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
417	>	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
418	>	if (ghostAtom == NULL) {
419	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
420	>	painCave.isFatal = 1;
421	>	simError();
422	>	}
423
424	<	painCave.isFatal = 1;
425	<	simError();
424	>	if (stamp->hasOverride()) {
425	>
426	>	try {
427	>	bendType = btParser.parseTypeAndPars(stamp->getOverrideType(),
428	>	stamp->getOverridePars() );
429		}
430	+	catch( OpenMDException e) {
431	+	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
432	+	"for molecule %s\n",
433	+	e.what(), mol->getType().c_str() );
434	+	painCave.isFatal = 1;
435	+	simError();
436	+	}
437	+	} else {
438	+
439	+	bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(),
440	+	"GHOST");
441	+
442	+	if (bendType == NULL) {
443	+	sprintf(painCave.errMsg,
444	+	"Can not find Matching Bend Type for[%s, %s, %s]",
445	+	normalAtom->getType().c_str(),
446	+	ghostAtom->getType().c_str(),
447	+	"GHOST");
448	+
449	+	painCave.isFatal = 1;
450	+	simError();
451	+	}
452	+	}
453	+
454	+	bend = new GhostBend(normalAtom, ghostAtom, bendType);
455	+
456	+	}
457	+
458	+	//set the local index of this bend, the global index will be set later
459	+	bend->setLocalIndex(localIndexMan->getNextBendIndex());
460	+
461	+	// The rule for naming a bend is: MoleculeName_Bend_Integer
462	+	// The first part is the name of the molecule
463	+	// The second part is always fixed as "Bend"
464	+	// The third part is the index of the bend defined in meta-data file
465	+	// For example, Butane_Bend_0 is a valid Bend name in a butane molecule
466	+
467	+	std::string s = OpenMD_itoa(mol->getNBends(), 10);
468	+	bend->setName(mol->getType() + "_Bend_" + s.c_str());
469	+	return bend;
470	+	}
471
472	<	return new Bend(atomA, atomB, atomC, bendType);
472	>	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
473	>	TorsionStamp* stamp,
474	>	LocalIndexManager* localIndexMan) {
475	>
476	>	TorsionTypeParser ttParser;
477	>	TorsionType* torsionType = NULL;
478	>	Torsion* torsion = NULL;
479	>
480	>	std::vector<int> torsionAtoms = stamp->getMembers();
481	>	if (torsionAtoms.size() < 3) {
482	>	return torsion;
483		}
378	–	}
484
485	<	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
485	>	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
486	>	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
487	>	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
488
489	<	Atom* atomA = mol->getAtomAt(stamp->getA());
490	<	Atom* atomB = mol->getAtomAt(stamp->getB());
384	<	Atom* atomC = mol->getAtomAt(stamp->getC());
385	<	Torsion* torsion;
489	>	if (torsionAtoms.size() == 4) {
490	>	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
491
492	<	if (stamp->getD() != -1) {
388	<	Atom* atomD = mol->getAtomAt(stamp->getD());
492	>	assert(atomA && atomB && atomC && atomD );
493
494	<	assert(atomA && atomB && atomC && atomD);
494	>	if (stamp->hasOverride()) {
495
496	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
497	<	atomC->getType(), atomD->getType());
496	>	try {
497	>	torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(),
498	>	stamp->getOverridePars() );
499	>	}
500	>	catch( OpenMDException e) {
501	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
502	>	"for molecule %s\n",
503	>	e.what(), mol->getType().c_str() );
504	>	painCave.isFatal = 1;
505	>	simError();
506	>	}
507	>	} else {
508
509	+
510	+	torsionType = ff->getTorsionType(atomA->getType(),
511	+	atomB->getType(),
512	+	atomC->getType(),
513	+	atomD->getType());
514		if (torsionType == NULL) {
515	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
516	<	atomA->getType().c_str(),
517	<	atomB->getType().c_str(),
518	<	atomC->getType().c_str(),
519	<	atomD->getType().c_str());
520	<
521	<	painCave.isFatal = 1;
522	<	simError();
515	>	sprintf(painCave.errMsg,
516	>	"Can not find Matching Torsion Type for[%s, %s, %s, %s]",
517	>	atomA->getType().c_str(),
518	>	atomB->getType().c_str(),
519	>	atomC->getType().c_str(),
520	>	atomD->getType().c_str());
521	>
522	>	painCave.isFatal = 1;
523	>	simError();
524		}
525	+	}
526	+
527	+	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
528	+	} else {
529	+
530	+	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
531	+	if (dAtom == NULL) {
532	+	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
533	+	painCave.isFatal = 1;
534	+	simError();
535	+	}
536	+
537	+	if (stamp->hasOverride()) {
538
539	<	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
539	>	try {
540	>	torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(),
541	>	stamp->getOverridePars() );
542	>	}
543	>	catch( OpenMDException e) {
544	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
545	>	"for molecule %s\n",
546	>	e.what(), mol->getType().c_str() );
547	>	painCave.isFatal = 1;
548	>	simError();
549	>	}
550	>	} else {
551	>	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
552	>	atomC->getType(), "GHOST");
553	>
554	>	if (torsionType == NULL) {
555	>	sprintf(painCave.errMsg,
556	>	"Can not find Matching Torsion Type for[%s, %s, %s, %s]",
557	>	atomA->getType().c_str(),
558	>	atomB->getType().c_str(),
559	>	atomC->getType().c_str(),
560	>	"GHOST");
561	>
562	>	painCave.isFatal = 1;
563	>	simError();
564	>	}
565	>	}
566	>
567	>	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
568		}
408	–	else {
569
570	<	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
571	<	if (dAtom == NULL) {
572	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
573	<	painCave.isFatal = 1;
574	<	simError();
575	<	}
570	>	//set the local index of this torsion, the global index will be set later
571	>	torsion->setLocalIndex(localIndexMan->getNextTorsionIndex());
572	>
573	>	// The rule for naming a torsion is: MoleculeName_Torsion_Integer
574	>	// The first part is the name of the molecule
575	>	// The second part is always fixed as "Torsion"
576	>	// The third part is the index of the torsion defined in meta-data file
577	>	// For example, Butane_Torsion_0 is a valid Torsion name in a
578	>	// butane molecule
579
580	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
581	<	atomC->getType(), "GHOST");
580	>	std::string s = OpenMD_itoa(mol->getNTorsions(), 10);
581	>	torsion->setName(mol->getType() + "_Torsion_" + s.c_str());
582	>	return torsion;
583	>	}
584
585	<	if (torsionType == NULL) {
586	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
587	<	atomA->getType().c_str(),
423	<	atomB->getType().c_str(),
424	<	atomC->getType().c_str(),
425	<	"GHOST");
585	>	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
586	>	InversionStamp* stamp,
587	>	LocalIndexManager* localIndexMan) {
588
589	<	painCave.isFatal = 1;
590	<	simError();
591	<	}
589	>	InversionTypeParser itParser;
590	>	InversionType* inversionType = NULL;
591	>	Inversion* inversion = NULL;
592	>
593	>	int center = stamp->getCenter();
594	>	std::vector<int> satellites = stamp->getSatellites();
595	>	if (satellites.size() != 3) {
596	>	return inversion;
597	>	}
598	>
599	>	Atom* atomA = mol->getAtomAt(center);
600	>	Atom* atomB = mol->getAtomAt(satellites[0]);
601	>	Atom* atomC = mol->getAtomAt(satellites[1]);
602	>	Atom* atomD = mol->getAtomAt(satellites[2]);
603	>
604	>	assert(atomA && atomB && atomC && atomD);
605	>
606	>	if (stamp->hasOverride()) {
607	>
608	>	try {
609	>	inversionType = itParser.parseTypeAndPars(stamp->getOverrideType(),
610	>	stamp->getOverridePars() );
611	>	}
612	>	catch( OpenMDException e) {
613	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
614	>	"for molecule %s\n",
615	>	e.what(), mol->getType().c_str() );
616	>	painCave.isFatal = 1;
617	>	simError();
618	>	}
619	>	} else {
620	>
621	>	inversionType = ff->getInversionType(atomA->getType(),
622	>	atomB->getType(),
623	>	atomC->getType(),
624	>	atomD->getType());
625	>
626	>	if (inversionType == NULL) {
627	>	sprintf(painCave.errMsg,
628	>	"No Matching Inversion Type for[%s, %s, %s, %s]\n"
629	>	"\t(May not be a problem: not all inversions are parametrized)\n",
630	>	atomA->getType().c_str(),
631	>	atomB->getType().c_str(),
632	>	atomC->getType().c_str(),
633	>	atomD->getType().c_str());
634
635	<	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
635	>	painCave.isFatal = 0;
636	>	painCave.severity = OPENMD_INFO;
637	>	simError();
638	>	}
639		}
640	+	if (inversionType != NULL) {
641	+
642	+	inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
643	+
644	+	// set the local index of this inversion, the global index will
645	+	// be set later
646	+	inversion->setLocalIndex(localIndexMan->getNextInversionIndex());
647	+
648	+	// The rule for naming an inversion is: MoleculeName_Inversion_Integer
649	+	// The first part is the name of the molecule
650	+	// The second part is always fixed as "Inversion"
651	+	// The third part is the index of the inversion defined in meta-data file
652	+	// For example, Benzene_Inversion_0 is a valid Inversion name in a
653	+	// Benzene molecule
654
655	<	return torsion;
656	<	}
655	>	std::string s = OpenMD_itoa(mol->getNInversions(), 10);
656	>	inversion->setName(mol->getType() + "_Inversion_" + s.c_str());
657	>	return inversion;
658	>	} else {
659	>	return NULL;
660	>	}
661	>	}
662	>
663
664	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
664	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
665	>	CutoffGroupStamp* stamp,
666	>	LocalIndexManager* localIndexMan) {
667		int nAtoms;
668		CutoffGroup* cg;
669		Atom* atom;
#	Line 442 | Line 671 | CutoffGroup* MoleculeCreator::createCutoffGroup(Molecu
671
672		nAtoms = stamp->getNMembers();
673		for (int i =0; i < nAtoms; ++i) {
674	<	atom = mol->getAtomAt(stamp->getMember(i));
675	<	assert(atom);
676	<	cg->addAtom(atom);
674	>	atom = mol->getAtomAt(stamp->getMemberAt(i));
675	>	assert(atom);
676	>	cg->addAtom(atom);
677		}
678	<
678	>
679	>	//set the local index of this cutoffGroup, global index will be set later
680	>	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
681	>
682		return cg;
683	<	}
684	<
685	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
683	>	}
684	>
685	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
686	>	LocalIndexManager* localIndexMan) {
687		CutoffGroup* cg;
688		cg  = new CutoffGroup();
689		cg->addAtom(atom);
690	+
691	+	//set the local index of this cutoffGroup, global index will be set later
692	+	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
693	+
694		return cg;
695	<	}
695	>	}
696
697	<	void MoleculeCreator::createConstraintPair(Molecule* mol) {
697	>	void MoleculeCreator::createConstraintPair(Molecule* mol) {
698
699		//add bond constraints
700		Molecule::BondIterator bi;
701		Bond* bond;
702	+	ConstraintPair* cPair;
703	+
704		for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
705
706	<	BondType* bt = bond->getBondType();
706	>	BondType* bt = bond->getBondType();
707
708	<	//class Parent1 {};
709	<	//class Child1 : public Parent {};
471	<	//class Child2 : public Parent {};
472	<	//Child1* ch1 = new Child1();
473	<	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
474	<	//the dynamic_cast is succeed in above line. A compiler bug?
708	>	if (typeid(FixedBondType) == typeid(*bt)) {
709	>	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
710
711	<	if (typeid(FixedBondType) == typeid(*bt)) {
712	<	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
713	<
714	<	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
715	<	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
716	<	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
482	<	mol->addConstraintPair(consPair);
483	<	}
711	>	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
712	>	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
713	>	cPair = new ConstraintPair(consElemA, consElemB,
714	>	fbt->getEquilibriumBondLength(), false);
715	>	mol->addConstraintPair(cPair);
716	>	}
717		}
718
719		//rigidbody -- rigidbody constraint is not support yet
720	<	}
720	>	}
721
722	<	void MoleculeCreator::createConstraintElem(Molecule* mol) {
722	>	void MoleculeCreator::createConstraintElem(Molecule* mol) {
723
724		ConstraintPair* consPair;
725		Molecule::ConstraintPairIterator cpi;
726		std::set<StuntDouble*> sdSet;
727	<	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
727	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
728	>	consPair = mol->nextConstraintPair(cpi)) {
729
730	<	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
731	<	if (sdSet.find(sdA) == sdSet.end()){
732	<	sdSet.insert(sdA);
733	<	mol->addConstraintElem(new ConstraintElem(sdA));
734	<	}
735	<
736	<	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
737	<	if (sdSet.find(sdB) == sdSet.end()){
738	<	sdSet.insert(sdB);
739	<	mol->addConstraintElem(new ConstraintElem(sdB));
740	<	}
507	<
730	>	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
731	>	if (sdSet.find(sdA) == sdSet.end()){
732	>	sdSet.insert(sdA);
733	>	mol->addConstraintElem(new ConstraintElem(sdA));
734	>	}
735	>
736	>	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
737	>	if (sdSet.find(sdB) == sdSet.end()){
738	>	sdSet.insert(sdB);
739	>	mol->addConstraintElem(new ConstraintElem(sdB));
740	>	}
741		}
742	<
742	>	}
743		}
511	–
512	–	}

Comparing trunk/src/brains/MoleculeCreator.cpp (property svn:keywords):
Revision 403 by gezelter, Tue Mar 8 21:06:49 2005 UTC vs.
Revision 2046 by gezelter, Tue Dec 2 22:11:04 2014 UTC

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