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

Comparing trunk/src/selection/IndexFinder.cpp (file contents):
Revision 416 by tim, Wed Mar 9 18:48:14 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 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		#include "selection/IndexFinder.hpp"
43		#include "primitives/Molecule.hpp"
44	<	namespace oopse {
44	>	namespace OpenMD {
45
46	+	IndexFinder::IndexFinder(SimInfo* info) : info_(info){
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
53	<
47	<	IndexFinder::IndexFinder(SimInfo* info) : info_(info){
48	<	nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
49	<	bitSets_.resize(info_->getNGlobalMolecules());
53	>	selectionSets_.resize(info_->getNGlobalMolecules());
54		init();
55	<	}
55	>	}
56
57	+	void IndexFinder::init() {
58
54	–	void IndexFinder::init() {
55	–
59		SimInfo::MoleculeIterator mi;
57	–	Molecule* mol;
60		Molecule::AtomIterator ai;
59	–	Atom* atom;
61		Molecule::RigidBodyIterator rbIter;
62	+	Molecule::BondIterator bondIter;
63	+	Molecule::BendIterator bendIter;
64	+	Molecule::TorsionIterator torsionIter;
65	+	Molecule::InversionIterator inversionIter;
66	+
67	+	Molecule* mol;
68	+	Atom* atom;
69		RigidBody* rb;
70	+	Bond* bond;
71	+	Bend* bend;
72	+	Torsion* torsion;
73	+	Inversion* inversion;
74
75	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
75	>	for (mol = info_->beginMolecule(mi); mol != NULL;
76	>	mol = info_->nextMolecule(mi)) {
77
78	<	BitSet bs(nStuntDoubles_);
66	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
67	<	bs.setBitOn(atom->getGlobalIndex());
68	<	}
78	>	SelectionSet ss(nObjects_);
79
80	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
81	<	bs.setBitOn(rb->getGlobalIndex());
82	<	}
80	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
81	>	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
82	>	}
83	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
84	>	rb = mol->nextRigidBody(rbIter)) {
85	>	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
86	>	}
87	>	for (bond = mol->beginBond(bondIter); bond != NULL;
88	>	bond = mol->nextBond(bondIter)) {
89	>	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
90	>	}
91	>	for (bend = mol->beginBend(bendIter); bend != NULL;
92	>	bend = mol->nextBend(bendIter)) {
93	>	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
94	>	}
95	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
96	>	torsion = mol->nextTorsion(torsionIter)) {
97	>	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
98	>	}
99	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
100	>	inversion = mol->nextInversion(inversionIter)) {
101	>	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
102	>	}
103
104	<	bitSets_[mol->getGlobalIndex()] = bs;
105	<	}
104	>	selectionSets_[mol->getGlobalIndex()] = ss;
105	>	}
106	>	}
107
108	<	}
108	>	SelectionSet IndexFinder::find(int molIndex){
109	>	return selectionSets_[molIndex];
110	>	}
111
112	<	BitSet IndexFinder::find(int molIndex){
113	<	return bitSets_[molIndex];
81	<	}
82	<
83	<	BitSet IndexFinder::find(int begMolIndex, int endMolIndex){
84	<	BitSet bs(nStuntDoubles_);
112	>	SelectionSet IndexFinder::find(int begMolIndex, int endMolIndex){
113	>	SelectionSet ss(nObjects_);
114
115		for (int i = begMolIndex; i < endMolIndex; ++i) {
116	<	bs |= bitSets_[i];
117	<	}
118	<
119	<	return bs;
116	>	ss |= selectionSets_[i];
117	>	}
118	>	return ss;
119	>	}
120		}
121
93	–
94	–	}
95	–

Comparing trunk/src/selection/IndexFinder.cpp (property svn:keywords):
Revision 416 by tim, Wed Mar 9 18:48:14 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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