ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 2071 by gezelter, Sat Mar 7 21:41:51 2015 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 (std::size_t 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	+	bool printConstraintForce = false;
197	+
198	+	if (cStamp->havePrintConstraintForce()) {
199	+	printConstraintForce = cStamp->getPrintConstraintForce();
200	+	}
201	+
202	+	if (!cStamp->haveConstrainedDistance()) {
203	+	sprintf(painCave.errMsg,
204	+	"Constraint Error: A non-bond constraint was specified\n"
205	+	"\twithout providing a value for the constrainedDistance.\n");
206		painCave.isFatal = 1;
207	<	simError();
207	>	simError();
208	>	} else {
209	>	RealType distance = cStamp->getConstrainedDistance();
210	>	ConstraintElem* consElemA = new ConstraintElem(atomA);
211	>	ConstraintElem* consElemB = new ConstraintElem(atomB);
212	>	ConstraintPair* cPair = new ConstraintPair(consElemA, consElemB,
213	>	distance,
214	>	printConstraintForce);
215	>	mol->addConstraintPair(cPair);
216	>	}
217		}
218
219	<	//loop over the free atoms and then create one cutoff group for every single free atom
169	<	std::vector<Atom*>::iterator fai;
219	>	// now create the constraint elements:
220
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);
221		createConstraintElem(mol);
222
223	<	//the construction of this molecule is finished
224	<	mol->complete();
223	>	// Does this molecule stamp define a total constrained charge value?
224	>	// If so, let the created molecule know about it.
225
226	+	if (molStamp->haveConstrainTotalCharge() ) {
227	+	mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
228	+	}
229	+
230	+	// The construction of this molecule is finished:
231	+	mol->complete();
232	+
233		return mol;
234	<	}
234	>	}
235
236
237	<	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
238	<	LocalIndexManager* localIndexMan) {
237	>	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
238	>	AtomStamp* stamp,
239	>	LocalIndexManager* localIndexMan) {
240		AtomType * atomType;
241		Atom* atom;
242
243		atomType =  ff->getAtomType(stamp->getType());
244	<
244	>
245		if (atomType == NULL) {
246	<	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
247	<	stamp->getType());
246	>	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
247	>	stamp->getType().c_str());
248
249	<	painCave.isFatal = 1;
250	<	simError();
249	>	painCave.isFatal = 1;
250	>	simError();
251		}
252	<
252	>
253		//below code still have some kind of hard-coding smell
254		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");
255
256	<	painCave.isFatal = 1;
257	<	simError();
258	<	}
212	<
213	<	DirectionalAtom* dAtom;
214	<	dAtom = new DirectionalAtom(dAtomType);
215	<	atom = dAtom;
256	>	DirectionalAtom* dAtom;
257	>	dAtom = new DirectionalAtom(atomType);
258	>	atom = dAtom;
259		}
260		else{
261	<	atom = new Atom(atomType);
261	>	atom = new Atom(atomType);
262		}
263
264		atom->setLocalIndex(localIndexMan->getNextAtomIndex());
265
266		return atom;
267	<	}
268	<
269	<	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
270	<	RigidBodyStamp* rbStamp,
271	<	LocalIndexManager* localIndexMan) {
267	>	}
268	>
269	>	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
270	>	Molecule* mol,
271	>	RigidBodyStamp* rbStamp,
272	>	LocalIndexManager* localIndexMan){
273		Atom* atom;
274		int nAtoms;
275		Vector3d refCoor;
#	Line 234 | Line 278 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
278		RigidBody* rb = new RigidBody();
279		nAtoms = rbStamp->getNMembers();
280		for (int i = 0; i < nAtoms; ++i) {
281	<	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
282	<	//It is not the same as local index of atom which is the index of atom at DataStorage class
283	<	atom = mol->getAtomAt(rbStamp->getMember(i));
284	<	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
285	<	rb->addAtom(atom, atomStamp);
281	>	//rbStamp->getMember(i) return the local index of current atom
282	>	//inside the molecule.  It is not the same as local index of
283	>	//atom which is the index of atom at DataStorage class
284	>	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
285	>	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
286	>	rb->addAtom(atom, atomStamp);
287		}
288
289	<	//after all of the atoms are added, we need to calculate the reference coordinates
289	>	//after all of the atoms are added, we need to calculate the
290	>	//reference coordinates
291		rb->calcRefCoords();
292
293		//set the local index of this rigid body, global index will be set later
294		rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
295
296	<	//the rule for naming rigidbody MoleculeName_RB_Integer
297	<	//The first part is the name of the molecule
298	<	//The second part is alway fixed as "RB"
299	<	//The third part is the index of the rigidbody defined in meta-data file
300	<	//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());
296	>	// The rule for naming a rigidbody is: MoleculeName_RB_Integer
297	>	// The first part is the name of the molecule
298	>	// The second part is always fixed as "RB"
299	>	// The third part is the index of the rigidbody defined in meta-data file
300	>	// For example, Butane_RB_0 is a valid rigid body name of butane molecule
301
302	+	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
303	+	rb->setType(mol->getType() + "_RB_" + s.c_str());
304		return rb;
305	<	}
305	>	}
306
307	<	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
308	<	BondType* bondType;
307	>	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
308	>	BondStamp* stamp,
309	>	LocalIndexManager* localIndexMan) {
310	>	BondTypeParser btParser;
311	>	BondType* bondType = NULL;
312		Atom* atomA;
313		Atom* atomB;
314	<
314	>
315		atomA = mol->getAtomAt(stamp->getA());
316		atomB = mol->getAtomAt(stamp->getB());
269	–
270	–	assert( atomA && atomB);
317
318	<	bondType = ff->getBondType(atomA->getType(), atomB->getType());
318	>	assert( atomA && atomB);
319
320	<	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());
320	>	if (stamp->hasOverride()) {
321
322	+	try {
323	+	bondType = btParser.parseTypeAndPars(stamp->getOverrideType(),
324	+	stamp->getOverridePars() );
325	+	}
326	+	catch( OpenMDException e) {
327	+	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
328	+	"for molecule %s\n",
329	+	e.what(), mol->getType().c_str() );
330		painCave.isFatal = 1;
331		simError();
332	<	}
282	<	return new Bond(atomA, atomB, bondType);
283	<	}
332	>	}
333
334	<	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
335	<	bool isGhostBend = false;
287	<	int ghostIndex;
334	>	} else {
335	>	bondType = ff->getBondType(atomA->getType(), atomB->getType());
336
337	<
338	<	//
339	<	if (stamp->haveExtras()){
340	<	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	<	}
337	>	if (bondType == NULL) {
338	>	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
339	>	atomA->getType().c_str(),
340	>	atomB->getType().c_str());
341
342	+	painCave.isFatal = 1;
343	+	simError();
344	+	}
345		}
346	+
347	+	Bond* bond = new Bond(atomA, atomB, bondType);
348
349	<	if (isGhostBend) {
349	>	//set the local index of this bond, the global index will be set later
350	>	bond->setLocalIndex(localIndexMan->getNextBondIndex());
351
352	<	int indexA = stamp->getA();
353	<	int indexB= stamp->getB();
352	>	// The rule for naming a bond is: MoleculeName_Bond_Integer
353	>	// The first part is the name of the molecule
354	>	// The second part is always fixed as "Bond"
355	>	// The third part is the index of the bond defined in meta-data file
356	>	// For example, Butane_bond_0 is a valid Bond name in a butane molecule
357
358	<	assert(indexA != indexB);
358	>	std::string s = OpenMD_itoa(mol->getNBonds(), 10);
359	>	bond->setName(mol->getType() + "_Bond_" + s.c_str());
360	>	return bond;
361	>	}
362	>
363	>	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
364	>	BendStamp* stamp,
365	>	LocalIndexManager* localIndexMan) {
366	>	BendTypeParser btParser;
367	>	BendType* bendType = NULL;
368	>	Bend* bend = NULL;
369	>
370	>	std::vector<int> bendAtoms = stamp->getMembers();
371	>	if (bendAtoms.size() == 3) {
372	>	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
373	>	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
374	>	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
375	>
376	>	assert( atomA && atomB && atomC );
377
378	<	int normalIndex;
328	<	if (indexA == ghostIndex) {
329	<	normalIndex = indexB;
330	<	} else if (indexB == ghostIndex) {
331	<	normalIndex = indexA;
332	<	}
378	>	if (stamp->hasOverride()) {
379
380	<	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
381	<	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
382	<	if (ghostAtom == NULL) {
337	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
338	<	painCave.isFatal = 1;
339	<	simError();
380	>	try {
381	>	bendType = btParser.parseTypeAndPars(stamp->getOverrideType(),
382	>	stamp->getOverridePars() );
383		}
384	<
385	<	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
386	<
387	<	if (bendType == NULL) {
388	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
389	<	normalAtom->getType().c_str(),
347	<	ghostAtom->getType().c_str(),
348	<	"GHOST");
349	<
350	<	painCave.isFatal = 1;
351	<	simError();
384	>	catch( OpenMDException e) {
385	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
386	>	"for molecule %s\n",
387	>	e.what(), mol->getType().c_str() );
388	>	painCave.isFatal = 1;
389	>	simError();
390		}
391	<
392	<	return new GhostBend(normalAtom, ghostAtom, bendType);
393	<
394	<	} else {
395	<
396	<	Atom* atomA = mol->getAtomAt(stamp->getA());
397	<	Atom* atomB = mol->getAtomAt(stamp->getB());
398	<	Atom* atomC = mol->getAtomAt(stamp->getC());
399	<
400	<	assert( atomA && atomB && atomC);
401	<
402	<	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
403	<
404	<	if (bendType == NULL) {
405	<	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
406	<	atomA->getType().c_str(),
407	<	atomB->getType().c_str(),
408	<	atomC->getType().c_str());
391	>	} else {
392	>
393	>	bendType = ff->getBendType(atomA->getType().c_str(),
394	>	atomB->getType().c_str(),
395	>	atomC->getType().c_str());
396	>
397	>	if (bendType == NULL) {
398	>	sprintf(painCave.errMsg,
399	>	"Can not find Matching Bend Type for[%s, %s, %s]",
400	>	atomA->getType().c_str(),
401	>	atomB->getType().c_str(),
402	>	atomC->getType().c_str());
403	>
404	>	painCave.isFatal = 1;
405	>	simError();
406	>	}
407	>	}
408	>
409	>	bend = new Bend(atomA, atomB, atomC, bendType);
410	>
411	>	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
412	>	int ghostIndex = stamp->getGhostVectorSource();
413	>	int normalIndex = ghostIndex != bendAtoms[0] ?
414	>	bendAtoms[0] : bendAtoms[1];
415	>	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
416	>	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
417	>	if (ghostAtom == NULL) {
418	>	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
419	>	painCave.isFatal = 1;
420	>	simError();
421	>	}
422
423	<	painCave.isFatal = 1;
424	<	simError();
423	>	if (stamp->hasOverride()) {
424	>
425	>	try {
426	>	bendType = btParser.parseTypeAndPars(stamp->getOverrideType(),
427	>	stamp->getOverridePars() );
428		}
429	+	catch( OpenMDException e) {
430	+	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
431	+	"for molecule %s\n",
432	+	e.what(), mol->getType().c_str() );
433	+	painCave.isFatal = 1;
434	+	simError();
435	+	}
436	+	} else {
437	+
438	+	bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(),
439	+	"GHOST");
440	+
441	+	if (bendType == NULL) {
442	+	sprintf(painCave.errMsg,
443	+	"Can not find Matching Bend Type for[%s, %s, %s]",
444	+	normalAtom->getType().c_str(),
445	+	ghostAtom->getType().c_str(),
446	+	"GHOST");
447	+
448	+	painCave.isFatal = 1;
449	+	simError();
450	+	}
451	+	}
452	+
453	+	bend = new GhostBend(normalAtom, ghostAtom, bendType);
454	+
455	+	}
456	+
457	+	//set the local index of this bend, the global index will be set later
458	+	bend->setLocalIndex(localIndexMan->getNextBendIndex());
459	+
460	+	// The rule for naming a bend is: MoleculeName_Bend_Integer
461	+	// The first part is the name of the molecule
462	+	// The second part is always fixed as "Bend"
463	+	// The third part is the index of the bend defined in meta-data file
464	+	// For example, Butane_Bend_0 is a valid Bend name in a butane molecule
465	+
466	+	std::string s = OpenMD_itoa(mol->getNBends(), 10);
467	+	bend->setName(mol->getType() + "_Bend_" + s.c_str());
468	+	return bend;
469	+	}
470
471	<	return new Bend(atomA, atomB, atomC, bendType);
471	>	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
472	>	TorsionStamp* stamp,
473	>	LocalIndexManager* localIndexMan) {
474	>
475	>	TorsionTypeParser ttParser;
476	>	TorsionType* torsionType = NULL;
477	>	Torsion* torsion = NULL;
478	>
479	>	std::vector<int> torsionAtoms = stamp->getMembers();
480	>	if (torsionAtoms.size() < 3) {
481	>	return torsion;
482		}
378	–	}
483
484	<	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
484	>	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
485	>	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
486	>	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
487
488	<	Atom* atomA = mol->getAtomAt(stamp->getA());
489	<	Atom* atomB = mol->getAtomAt(stamp->getB());
384	<	Atom* atomC = mol->getAtomAt(stamp->getC());
385	<	Torsion* torsion;
488	>	if (torsionAtoms.size() == 4) {
489	>	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
490
491	<	if (stamp->getD() != -1) {
388	<	Atom* atomD = mol->getAtomAt(stamp->getD());
491	>	assert(atomA && atomB && atomC && atomD );
492
493	<	assert(atomA && atomB && atomC && atomD);
493	>	if (stamp->hasOverride()) {
494
495	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
496	<	atomC->getType(), atomD->getType());
495	>	try {
496	>	torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(),
497	>	stamp->getOverridePars() );
498	>	}
499	>	catch( OpenMDException e) {
500	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
501	>	"for molecule %s\n",
502	>	e.what(), mol->getType().c_str() );
503	>	painCave.isFatal = 1;
504	>	simError();
505	>	}
506	>	} else {
507
508	+
509	+	torsionType = ff->getTorsionType(atomA->getType(),
510	+	atomB->getType(),
511	+	atomC->getType(),
512	+	atomD->getType());
513		if (torsionType == NULL) {
514	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
515	<	atomA->getType().c_str(),
516	<	atomB->getType().c_str(),
517	<	atomC->getType().c_str(),
518	<	atomD->getType().c_str());
519	<
520	<	painCave.isFatal = 1;
521	<	simError();
514	>	sprintf(painCave.errMsg,
515	>	"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();
523		}
524	+	}
525	+
526	+	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
527	+	} else {
528	+
529	+	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
530	+	if (dAtom == NULL) {
531	+	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
532	+	painCave.isFatal = 1;
533	+	simError();
534	+	}
535	+
536	+	if (stamp->hasOverride()) {
537
538	<	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
538	>	try {
539	>	torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(),
540	>	stamp->getOverridePars() );
541	>	}
542	>	catch( OpenMDException e) {
543	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
544	>	"for molecule %s\n",
545	>	e.what(), mol->getType().c_str() );
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549	>	} else {
550	>	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
551	>	atomC->getType(), "GHOST");
552	>
553	>	if (torsionType == NULL) {
554	>	sprintf(painCave.errMsg,
555	>	"Can not find Matching Torsion Type for[%s, %s, %s, %s]",
556	>	atomA->getType().c_str(),
557	>	atomB->getType().c_str(),
558	>	atomC->getType().c_str(),
559	>	"GHOST");
560	>
561	>	painCave.isFatal = 1;
562	>	simError();
563	>	}
564	>	}
565	>
566	>	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
567		}
408	–	else {
568
569	<	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
570	<	if (dAtom == NULL) {
571	<	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
572	<	painCave.isFatal = 1;
573	<	simError();
574	<	}
569	>	//set the local index of this torsion, the global index will be set later
570	>	torsion->setLocalIndex(localIndexMan->getNextTorsionIndex());
571	>
572	>	// The rule for naming a torsion is: MoleculeName_Torsion_Integer
573	>	// The first part is the name of the molecule
574	>	// The second part is always fixed as "Torsion"
575	>	// The third part is the index of the torsion defined in meta-data file
576	>	// For example, Butane_Torsion_0 is a valid Torsion name in a
577	>	// butane molecule
578
579	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
580	<	atomC->getType(), "GHOST");
579	>	std::string s = OpenMD_itoa(mol->getNTorsions(), 10);
580	>	torsion->setName(mol->getType() + "_Torsion_" + s.c_str());
581	>	return torsion;
582	>	}
583
584	<	if (torsionType == NULL) {
585	<	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
586	<	atomA->getType().c_str(),
423	<	atomB->getType().c_str(),
424	<	atomC->getType().c_str(),
425	<	"GHOST");
584	>	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
585	>	InversionStamp* stamp,
586	>	LocalIndexManager* localIndexMan) {
587
588	<	painCave.isFatal = 1;
589	<	simError();
590	<	}
588	>	InversionTypeParser itParser;
589	>	InversionType* inversionType = NULL;
590	>	Inversion* inversion = NULL;
591	>
592	>	int center = stamp->getCenter();
593	>	std::vector<int> satellites = stamp->getSatellites();
594	>	if (satellites.size() != 3) {
595	>	return inversion;
596	>	}
597	>
598	>	Atom* atomA = mol->getAtomAt(center);
599	>	Atom* atomB = mol->getAtomAt(satellites[0]);
600	>	Atom* atomC = mol->getAtomAt(satellites[1]);
601	>	Atom* atomD = mol->getAtomAt(satellites[2]);
602	>
603	>	assert(atomA && atomB && atomC && atomD);
604	>
605	>	if (stamp->hasOverride()) {
606	>
607	>	try {
608	>	inversionType = itParser.parseTypeAndPars(stamp->getOverrideType(),
609	>	stamp->getOverridePars() );
610	>	}
611	>	catch( OpenMDException e) {
612	>	sprintf(painCave.errMsg, "MoleculeCreator Error: %s "
613	>	"for molecule %s\n",
614	>	e.what(), mol->getType().c_str() );
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	}
618	>	} else {
619	>
620	>	inversionType = ff->getInversionType(atomA->getType(),
621	>	atomB->getType(),
622	>	atomC->getType(),
623	>	atomD->getType());
624	>
625	>	if (inversionType == NULL) {
626	>	sprintf(painCave.errMsg,
627	>	"No Matching Inversion Type for[%s, %s, %s, %s]\n"
628	>	"\t(May not be a problem: not all inversions are parametrized)\n",
629	>	atomA->getType().c_str(),
630	>	atomB->getType().c_str(),
631	>	atomC->getType().c_str(),
632	>	atomD->getType().c_str());
633
634	<	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
634	>	painCave.isFatal = 0;
635	>	painCave.severity = OPENMD_INFO;
636	>	simError();
637	>	}
638		}
639	+	if (inversionType != NULL) {
640	+
641	+	inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
642	+
643	+	// set the local index of this inversion, the global index will
644	+	// be set later
645	+	inversion->setLocalIndex(localIndexMan->getNextInversionIndex());
646	+
647	+	// The rule for naming an inversion is: MoleculeName_Inversion_Integer
648	+	// The first part is the name of the molecule
649	+	// The second part is always fixed as "Inversion"
650	+	// The third part is the index of the inversion defined in meta-data file
651	+	// For example, Benzene_Inversion_0 is a valid Inversion name in a
652	+	// Benzene molecule
653
654	<	return torsion;
655	<	}
654	>	std::string s = OpenMD_itoa(mol->getNInversions(), 10);
655	>	inversion->setName(mol->getType() + "_Inversion_" + s.c_str());
656	>	return inversion;
657	>	} else {
658	>	return NULL;
659	>	}
660	>	}
661	>
662
663	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
663	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
664	>	CutoffGroupStamp* stamp,
665	>	LocalIndexManager* localIndexMan) {
666		int nAtoms;
667		CutoffGroup* cg;
668		Atom* atom;
#	Line 442 | Line 670 | CutoffGroup* MoleculeCreator::createCutoffGroup(Molecu
670
671		nAtoms = stamp->getNMembers();
672		for (int i =0; i < nAtoms; ++i) {
673	<	atom = mol->getAtomAt(stamp->getMember(i));
674	<	assert(atom);
675	<	cg->addAtom(atom);
673	>	atom = mol->getAtomAt(stamp->getMemberAt(i));
674	>	assert(atom);
675	>	cg->addAtom(atom);
676		}
677	<
677	>
678	>	//set the local index of this cutoffGroup, global index will be set later
679	>	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
680	>
681		return cg;
682	<	}
683	<
684	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
682	>	}
683	>
684	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
685	>	LocalIndexManager* localIndexMan) {
686		CutoffGroup* cg;
687		cg  = new CutoffGroup();
688		cg->addAtom(atom);
689	+
690	+	//set the local index of this cutoffGroup, global index will be set later
691	+	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
692	+
693		return cg;
694	<	}
694	>	}
695
696	<	void MoleculeCreator::createConstraintPair(Molecule* mol) {
696	>	void MoleculeCreator::createConstraintPair(Molecule* mol) {
697
698		//add bond constraints
699		Molecule::BondIterator bi;
700		Bond* bond;
701	+	ConstraintPair* cPair;
702	+
703		for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
704
705	<	BondType* bt = bond->getBondType();
705	>	BondType* bt = bond->getBondType();
706
707	<	//class Parent1 {};
708	<	//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?
707	>	if (typeid(FixedBondType) == typeid(*bt)) {
708	>	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
709
710	<	if (typeid(FixedBondType) == typeid(*bt)) {
711	<	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
712	<
713	<	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
714	<	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
715	<	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
482	<	mol->addConstraintPair(consPair);
483	<	}
710	>	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
711	>	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
712	>	cPair = new ConstraintPair(consElemA, consElemB,
713	>	fbt->getEquilibriumBondLength(), false);
714	>	mol->addConstraintPair(cPair);
715	>	}
716		}
717
718		//rigidbody -- rigidbody constraint is not support yet
719	<	}
719	>	}
720
721	<	void MoleculeCreator::createConstraintElem(Molecule* mol) {
721	>	void MoleculeCreator::createConstraintElem(Molecule* mol) {
722
723		ConstraintPair* consPair;
724		Molecule::ConstraintPairIterator cpi;
725		std::set<StuntDouble*> sdSet;
726	<	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
726	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
727	>	consPair = mol->nextConstraintPair(cpi)) {
728
729	<	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
730	<	if (sdSet.find(sdA) == sdSet.end()){
731	<	sdSet.insert(sdA);
732	<	mol->addConstraintElem(new ConstraintElem(sdA));
733	<	}
734	<
735	<	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
736	<	if (sdSet.find(sdB) == sdSet.end()){
737	<	sdSet.insert(sdB);
738	<	mol->addConstraintElem(new ConstraintElem(sdB));
739	<	}
507	<
729	>	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
730	>	if (sdSet.find(sdA) == sdSet.end()){
731	>	sdSet.insert(sdA);
732	>	mol->addConstraintElem(new ConstraintElem(sdA));
733	>	}
734	>
735	>	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
736	>	if (sdSet.find(sdB) == sdSet.end()){
737	>	sdSet.insert(sdB);
738	>	mol->addConstraintElem(new ConstraintElem(sdB));
739	>	}
740		}
741	<
741	>	}
742		}
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 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines