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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 2052 by gezelter, Fri Jan 9 19:06:35 2015 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());
47	>	nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
48	>	nObjects_.push_back(info_->getNGlobalBonds());
49	>	nObjects_.push_back(info_->getNGlobalBends());
50	>	nObjects_.push_back(info_->getNGlobalTorsions());
51	>	nObjects_.push_back(info_->getNGlobalInversions());
52	>	nObjects_.push_back(info_->getNGlobalMolecules());
53	>
54	>	selectionSets_.resize(info_->getNGlobalMolecules());
55		init();
56		}
57
53	–
58		void IndexFinder::init() {
59
60		SimInfo::MoleculeIterator mi;
57	–	Molecule* mol;
61		Molecule::AtomIterator ai;
59	–	Atom* atom;
62		Molecule::RigidBodyIterator rbIter;
63	+	Molecule::BondIterator bondIter;
64	+	Molecule::BendIterator bendIter;
65	+	Molecule::TorsionIterator torsionIter;
66	+	Molecule::InversionIterator inversionIter;
67	+
68	+	Molecule* mol;
69	+	Atom* atom;
70		RigidBody* rb;
71	+	Bond* bond;
72	+	Bend* bend;
73	+	Torsion* torsion;
74	+	Inversion* inversion;
75
76	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
76	>	for (mol = info_->beginMolecule(mi); mol != NULL;
77	>	mol = info_->nextMolecule(mi)) {
78
79	<	OpenMDBitSet bs(nStuntDoubles_);
79	>	SelectionSet ss(nObjects_);
80	>	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
81	>
82		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
83	<	bs.setBitOn(atom->getGlobalIndex());
83	>	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
84		}
85	<
86	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
87	<	bs.setBitOn(rb->getGlobalIndex());
85	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
86	>	rb = mol->nextRigidBody(rbIter)) {
87	>	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
88		}
89	+	for (bond = mol->beginBond(bondIter); bond != NULL;
90	+	bond = mol->nextBond(bondIter)) {
91	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
92	+	}
93	+	for (bend = mol->beginBend(bendIter); bend != NULL;
94	+	bend = mol->nextBend(bendIter)) {
95	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
96	+	}
97	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
98	+	torsion = mol->nextTorsion(torsionIter)) {
99	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
100	+	}
101	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
102	+	inversion = mol->nextInversion(inversionIter)) {
103	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
104	+	}
105
106	<	bitSets_[mol->getGlobalIndex()] = bs;
107	<	}
76	<
106	>	selectionSets_[mol->getGlobalIndex()] = ss;
107	>	}
108		}
109
110	<	OpenMDBitSet IndexFinder::find(int molIndex){
111	<	return bitSets_[molIndex];
110	>	SelectionSet IndexFinder::find(int molIndex){
111	>	return selectionSets_[molIndex];
112		}
113
114	<	OpenMDBitSet IndexFinder::find(int begMolIndex, int endMolIndex){
115	<	OpenMDBitSet bs(nStuntDoubles_);
114	>	SelectionSet IndexFinder::find(int begMolIndex, int endMolIndex){
115	>	SelectionSet ss(nObjects_);
116
117		for (int i = begMolIndex; i < endMolIndex; ++i) {
118	<	bs |= bitSets_[i];
119	<	}
120	<
90	<	return bs;
118	>	ss |= selectionSets_[i];
119	>	}
120	>	return ss;
121		}
92	–
93	–
122		}
123

Comparing trunk/src/selection/IndexFinder.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

#	Line 0 | Line 1
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