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 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

#	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
46	–	* @time 13:44am
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, MoleculeStamp *molStamp,
65	<	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
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
66	–	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
67	–
71		//create atoms
72		Atom* atom;
73		AtomStamp* currentAtomStamp;
#	Line 82 | Line 85 | namespace oopse {
85
86		for (int i = 0; i < nRigidbodies; ++i) {
87		currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
88	<	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
88	>	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
89	>	localIndexMan);
90		mol->addRigidBody(rb);
91		}
92	<
92	>
93		//create bonds
94		Bond* bond;
95		BondStamp* currentBondStamp;
#	Line 117 | Line 121 | namespace oopse {
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->getCutoffGroupStamp(i);
142	<	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
142	>	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan);
143		mol->addCutoffGroup(cutoffGroup);
144		}
145
#	Line 140 | Line 156 | namespace oopse {
156		Molecule::CutoffGroupIterator ci;
157		CutoffGroup* cg;
158
159	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
160	<
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), freeAtoms.end());
165	<	}
166	<
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	<	//loop over the free atoms and then create one cutoff group for every single free atom
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);
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		}
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().c_str());
#	Line 180 | Line 206 | namespace oopse {
206		painCave.isFatal = 1;
207		simError();
208		}
209	<
209	>
210		//below code still have some kind of hard-coding smell
211		if (atomType->isDirectional()){
186	–
187	–	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
188	–
189	–	if (dAtomType == NULL) {
190	–	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
212
192	–	painCave.isFatal = 1;
193	–	simError();
194	–	}
195	–
213		DirectionalAtom* dAtom;
214	<	dAtom = new DirectionalAtom(dAtomType);
214	>	dAtom = new DirectionalAtom(atomType);
215		atom = dAtom;
216		}
217		else{
#	Line 205 | Line 222 | namespace oopse {
222
223		return atom;
224		}
225	<
226	<	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
225	>
226	>	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
227	>	Molecule* mol,
228		RigidBodyStamp* rbStamp,
229		LocalIndexManager* localIndexMan) {
230		Atom* atom;
#	Line 217 | Line 235 | namespace oopse {
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
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 236 | Line 256 | namespace oopse {
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		}
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());
#	Line 258 | Line 279 | namespace oopse {
279		sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
280		atomA->getType().c_str(),
281		atomB->getType().c_str());
282	<
282	>
283		painCave.isFatal = 1;
284		simError();
285		}
286		return new Bond(atomA, atomB, bondType);
287		}
288	<
289	<	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
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	<
297	>
298		assert( atomA && atomB && atomC);
299	<
300	<	BendType* bendType = ff->getBendType(atomA->getType().c_str(), atomB->getType().c_str(), atomC->getType().c_str());
301	<
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	<
309	>
310		painCave.isFatal = 1;
311		simError();
312		}
313	<
313	>
314		bend = new Bend(atomA, atomB, atomC, bendType);
315		} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
316		int ghostIndex = stamp->getGhostVectorSource();
#	Line 310 | Line 334 | namespace oopse {
334		painCave.isFatal = 1;
335		simError();
336		}
337	<
337	>
338		bend = new GhostBend(normalAtom, ghostAtom, bendType);
339	<
339	>
340		}
341
342		return bend;
343		}
344
345	<	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
345	>	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
346	>	TorsionStamp* stamp) {
347
348		Torsion* torsion = NULL;
349		std::vector<int> torsionAtoms = stamp->getMembers();
#	Line 335 | Line 360 | namespace oopse {
360
361		assert(atomA && atomB && atomC && atomD);
362
363	<	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
364	<	atomC->getType(), atomD->getType());
365	<
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	<
373	>
374		painCave.isFatal = 1;
375		simError();
376		}
377	<
377	>
378		torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
379		}
380		else {
381	<
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	<
388	>
389		TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
390		atomC->getType(), "GHOST");
391	<
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	<
398	>
399		painCave.isFatal = 1;
400		simError();
401		}
402	<
402	>
403		torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
404		}
405	<
405	>
406		return torsion;
407		}
408
409	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
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	>	}
418	>
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	>	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	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
452	>	CutoffGroupStamp* stamp,
453	>	LocalIndexManager* localIndexMan) {
454		int nAtoms;
455		CutoffGroup* cg;
456		Atom* atom;
#	Line 392 | Line 462 | namespace oopse {
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) {
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		}
483

Comparing trunk/src/brains/MoleculeCreator.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

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

Diff Legend

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