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

Comparing trunk/src/selection/SelectionManager.cpp (file contents):
Revision 353 by tim, Wed Feb 16 19:36:30 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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
43		#include "selection/SelectionManager.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "brains/SimInfo.hpp"
46	<	namespace oopse {
47	<	SelectionManager::SelectionManager(SimInfo* info) : info_(info){
46	>	namespace OpenMD {
47	>	SelectionManager::SelectionManager(SimInfo* info) : info_(info){
48
49		int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
50
51		bsSelection_.resize(nStuntDoubles);
52	<	stuntdoubles_.resize(nStuntDoubles);
52	>	stuntdoubles_.resize(nStuntDoubles, NULL);
53
54		SimInfo::MoleculeIterator mi;
55		Molecule* mol;
#	Line 56 | Line 57 | SelectionManager::SelectionManager(SimInfo* info) : in
57		Atom* atom;
58		Molecule::RigidBodyIterator rbIter;
59		RigidBody* rb;
59	–
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	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
65	<	stuntdoubles_[atom->getGlobalIndex()] = atom;
66	<	}
64	>	for(atom = mol->beginAtom(ai); atom != NULL;
65	>	atom = mol->nextAtom(ai)) {
66	>	stuntdoubles_[atom->getGlobalIndex()] = atom;
67	>	}
68	>
69	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
70	>	rb = mol->nextRigidBody(rbIter)) {
71	>	stuntdoubles_[rb->getGlobalIndex()] = rb;
72	>	}
73	>	}
74	>	}
75
76	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
68	<	stuntdoubles_[rb->getGlobalIndex()] = rb;
69	<	}
70	<
71	<	}
72	<
73	<	}
74	<
75	<
76	<	StuntDouble* SelectionManager::beginSelected(int& i) {
76	>	StuntDouble* SelectionManager::beginSelected(int& i) {
77		i = bsSelection_.firstOnBit();
78		return i == -1 ? NULL : stuntdoubles_[i];
79	<	}
80	<	StuntDouble* SelectionManager::nextSelected(int& i) {
79	>	}
80	>
81	>	StuntDouble* SelectionManager::nextSelected(int& i) {
82		i = bsSelection_.nextOnBit(i);
83		return i == -1 ? NULL : stuntdoubles_[i];
84	<	}
84	>	}
85
86	<	StuntDouble* SelectionManager::beginUnselected(int& i){
86	>	StuntDouble* SelectionManager::beginUnselected(int& i){
87		i = bsSelection_.firstOffBit();
88		return i == -1 ? NULL : stuntdoubles_[i];
89	<	}
90	<	StuntDouble* SelectionManager::nextUnSelected(int& i) {
89	>	}
90	>
91	>	StuntDouble* SelectionManager::nextUnSelected(int& i) {
92		i = bsSelection_.nextOffBit(i);
93		return i == -1 ? NULL : stuntdoubles_[i];
94	<	}
94	>	}
95
96	<
97	<	SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) {
96	>	SelectionManager operator| (const SelectionManager& sman1,
97	>	const SelectionManager& sman2) {
98		SelectionManager result(sman1);
99		result |= sman2;
100		return result;
101	<	}
102	<	SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
101	>	}
102	>
103	>	SelectionManager operator& (const SelectionManager& sman1,
104	>	const SelectionManager& sman2) {
105		SelectionManager result(sman1);
106		result &= sman2;
107		return result;
108	+	}
109
110	<	}
111	<	SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
110	>	SelectionManager operator^ (const SelectionManager& sman1,
111	>	const SelectionManager& sman2) {
112		SelectionManager result(sman1);
113		result ^= sman2;
114		return result;
115	+	}
116
117	<	}
118	<	SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
117	>	SelectionManager operator-(const SelectionManager& sman1,
118	>	const SelectionManager& sman2){
119		SelectionManager result(sman1);
120		result -= sman2;
121		return result;
122	+	}
123
124		}
118	–
119	–	}

Comparing trunk/src/selection/SelectionManager.cpp (property svn:keywords):
Revision 353 by tim, Wed Feb 16 19:36:30 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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