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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 1665 by gezelter, Tue Nov 22 20:38:56 2011 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 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
#	Line 449 | Line 450 | namespace OpenMD {
450		}
451
452
453	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
453	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
454	>	CutoffGroupStamp* stamp,
455	>	LocalIndexManager* localIndexMan) {
456		int nAtoms;
457		CutoffGroup* cg;
458		Atom* atom;
#	Line 461 | Line 464 | namespace OpenMD {
464		assert(atom);
465		cg->addAtom(atom);
466		}
467	<
467	>
468	>	//set the local index of this cutoffGroup, global index will be set later
469	>	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
470	>
471		return cg;
472		}
473	<
474	<	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
473	>
474	>	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
475	>	LocalIndexManager* localIndexMan) {
476		CutoffGroup* cg;
477		cg  = new CutoffGroup();
478		cg->addAtom(atom);
479	+
480	+	//set the local index of this cutoffGroup, global index will be set later
481	+	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
482	+
483		return cg;
484		}
485

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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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