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root/OpenMD/trunk/src/selection/IndexFinder.cpp

Comparing trunk/src/selection/IndexFinder.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 35 | Line 35
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, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
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		#include "selection/IndexFinder.hpp"
43		#include "primitives/Molecule.hpp"
44		namespace OpenMD {
45
45	–
46	–
46		IndexFinder::IndexFinder(SimInfo* info) : info_(info){
47		nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
48		bitSets_.resize(info_->getNGlobalMolecules());
49		init();
50		}
51
53	–
52		void IndexFinder::init() {
53
54		SimInfo::MoleculeIterator mi;
#	Line 60 | Line 58 | namespace OpenMD {
58		Molecule::RigidBodyIterator rbIter;
59		RigidBody* rb;
60
61	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
61	>	for (mol = info_->beginMolecule(mi); mol != NULL;
62	>	mol = info_->nextMolecule(mi)) {
63
64		OpenMDBitSet bs(nStuntDoubles_);
65		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
66		bs.setBitOn(atom->getGlobalIndex());
67		}
68	<
69	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
68	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
69	>	rb = mol->nextRigidBody(rbIter)) {
70		bs.setBitOn(rb->getGlobalIndex());
71		}
73	–
72		bitSets_[mol->getGlobalIndex()] = bs;
73	<	}
76	<
73	>	}
74		}
75
76		OpenMDBitSet IndexFinder::find(int molIndex){
#	Line 85 | Line 82 | namespace OpenMD {
82
83		for (int i = begMolIndex; i < endMolIndex; ++i) {
84		bs |= bitSets_[i];
85	<	}
89	<
85	>	}
86		return bs;
87		}
92	–
93	–
88		}
89

Comparing trunk/src/selection/IndexFinder.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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

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