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root/OpenMD/branches/development/src/brains/MoleculeCreator.cpp

Comparing:
trunk/src/brains/MoleculeCreator.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/MoleculeCreator.cpp (file contents), Revision 1718 by gezelter, Thu May 24 01:29:59 2012 UTC

#	Line 36 | Line 36
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, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
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		/**
#	Line 54 | Line 55
55		#include "brains/MoleculeCreator.hpp"
56		#include "primitives/GhostBend.hpp"
57		#include "primitives/GhostTorsion.hpp"
58	<	#include "types/DirectionalAtomType.hpp"
58	>	#include "types/AtomType.hpp"
59		#include "types/FixedBondType.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
#	Line 66 | Line 67 | namespace OpenMD {
67		int stampId, int globalIndex,
68		LocalIndexManager* localIndexMan) {
69		Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
70	<
70	>
71		//create atoms
72		Atom* atom;
73		AtomStamp* currentAtomStamp;
#	Line 138 | Line 139 | namespace OpenMD {
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 169 | Line 170 | namespace OpenMD {
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
#	Line 201 | Line 209 | namespace OpenMD {
209
210		//below code still have some kind of hard-coding smell
211		if (atomType->isDirectional()){
212	<
213	<	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
206	<
207	<	if (dAtomType == NULL) {
208	<	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
209	<
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
213	<
214	<	DirectionalAtom* dAtom;
215	<	dAtom = new DirectionalAtom(dAtomType);
212	>	DirectionalAtom* dAtom;
213	>	dAtom = new DirectionalAtom(atomType);
214		atom = dAtom;
215		}
216		else{
#	Line 449 | Line 447 | namespace OpenMD {
447		}
448
449
450	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
450	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
451	>	CutoffGroupStamp* stamp,
452	>	LocalIndexManager* localIndexMan) {
453		int nAtoms;
454		CutoffGroup* cg;
455		Atom* atom;
#	Line 461 | Line 461 | namespace OpenMD {
461		assert(atom);
462		cg->addAtom(atom);
463		}
464	<
464	>
465	>	//set the local index of this cutoffGroup, global index will be set later
466	>	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
467	>
468		return cg;
469		}
470	<
471	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
470	>
471	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
472	>	LocalIndexManager* localIndexMan) {
473		CutoffGroup* cg;
474		cg  = new CutoffGroup();
475		cg->addAtom(atom);
476	+
477	+	//set the local index of this cutoffGroup, global index will be set later
478	+	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
479	+
480		return cg;
481		}
482

Comparing:
trunk/src/brains/MoleculeCreator.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/MoleculeCreator.cpp (property svn:keywords), Revision 1718 by gezelter, Thu May 24 01:29:59 2012 UTC

#	Line 0 | Line 1
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