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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 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
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	>	nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
49	>	nObjects_.push_back(info_->getNGlobalBonds());
50	>	nObjects_.push_back(info_->getNGlobalBends());
51	>	nObjects_.push_back(info_->getNGlobalTorsions());
52	>	nObjects_.push_back(info_->getNGlobalInversions());
53
54	<	int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
55	<
56	<	bsSelection_.resize(nStuntDoubles);
57	<	stuntdoubles_.resize(nStuntDoubles);
54	>	stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
55	>	bonds_.resize(nObjects_[BOND]);
56	>	bends_.resize(nObjects_[BEND]);
57	>	torsions_.resize(nObjects_[TORSION]);
58	>	inversions_.resize(nObjects_[INVERSION]);
59
60		SimInfo::MoleculeIterator mi;
54	–	Molecule* mol;
61		Molecule::AtomIterator ai;
56	–	Atom* atom;
62		Molecule::RigidBodyIterator rbIter;
63	<	RigidBody* rb;
63	>	Molecule::BondIterator bondIter;
64	>	Molecule::BendIterator bendIter;
65	>	Molecule::TorsionIterator torsionIter;
66	>	Molecule::InversionIterator inversionIter;
67
68	<
69	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
68	>	Molecule* mol;
69	>	Atom* atom;
70	>	RigidBody* rb;
71	>	Bond* bond;
72	>	Bend* bend;
73	>	Torsion* torsion;
74	>	Inversion* inversion;
75
76	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
77	<	stuntdoubles_[atom->getGlobalIndex()] = atom;
78	<	}
76	>	for (mol = info_->beginMolecule(mi); mol != NULL;
77	>	mol = info_->nextMolecule(mi)) {
78	>
79	>	for(atom = mol->beginAtom(ai); atom != NULL;
80	>	atom = mol->nextAtom(ai)) {
81	>	stuntdoubles_[atom->getGlobalIndex()] = atom;
82	>	}
83	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
84	>	rb = mol->nextRigidBody(rbIter)) {
85	>	stuntdoubles_[rb->getGlobalIndex()] = rb;
86	>	}
87	>	for (bond = mol->beginBond(bondIter); bond != NULL;
88	>	bond = mol->nextBond(bondIter)) {
89	>	bonds_[bond->getGlobalIndex()] = bond;
90	>	}
91	>	for (bend = mol->beginBend(bendIter); bend != NULL;
92	>	bend = mol->nextBend(bendIter)) {
93	>	bends_[bend->getGlobalIndex()] = bend;
94	>	}
95	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
96	>	torsion = mol->nextTorsion(torsionIter)) {
97	>	torsions_[torsion->getGlobalIndex()] = torsion;
98	>	}
99	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
100	>	inversion = mol->nextInversion(inversionIter)) {
101	>	inversions_[inversion->getGlobalIndex()] = inversion;
102	>	}
103	>	}
104	>	}
105
106	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
107	<	stuntdoubles_[rb->getGlobalIndex()] = rb;
108	<	}
109	<
71	<	}
72	<
73	<	}
106	>	StuntDouble* SelectionManager::beginSelected(int& i) {
107	>	i = ss_.bitsets_[STUNTDOUBLE].firstOnBit();
108	>	return i == -1 ? NULL : stuntdoubles_[i];
109	>	}
110
111	+	StuntDouble* SelectionManager::nextSelected(int& i) {
112	+	i = ss_.bitsets_[STUNTDOUBLE].nextOnBit(i);
113	+	return i == -1 ? NULL : stuntdoubles_[i];
114	+	}
115
116	<	StuntDouble* SelectionManager::beginSelected(int& i) {
117	<	i = bsSelection_.firstOnBit();
116	>	StuntDouble* SelectionManager::beginUnselected(int& i){
117	>	i = ss_.bitsets_[STUNTDOUBLE].firstOffBit();
118		return i == -1 ? NULL : stuntdoubles_[i];
119	<	}
80	<	StuntDouble* SelectionManager::nextSelected(int& i) {
81	<	i = bsSelection_.nextOnBit(i);
82	<	return i == -1 ? NULL : stuntdoubles_[i];
83	<	}
119	>	}
120
121	<	StuntDouble* SelectionManager::beginUnselected(int& i){
122	<	i = bsSelection_.firstOffBit();
121	>	StuntDouble* SelectionManager::nextUnSelected(int& i) {
122	>	i = ss_.bitsets_[STUNTDOUBLE].nextOffBit(i);
123		return i == -1 ? NULL : stuntdoubles_[i];
124	<	}
89	<	StuntDouble* SelectionManager::nextUnSelected(int& i) {
90	<	i = bsSelection_.nextOffBit(i);
91	<	return i == -1 ? NULL : stuntdoubles_[i];
92	<	}
124	>	}
125
126	+	Bond* SelectionManager::beginSelectedBond(int& i) {
127	+	i = ss_.bitsets_[BOND].firstOnBit();
128	+	return i == -1 ? NULL : bonds_[i];
129	+	}
130
131	<	SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) {
131	>	Bond* SelectionManager::nextSelectedBond(int& i) {
132	>	i = ss_.bitsets_[BOND].nextOnBit(i);
133	>	return i == -1 ? NULL : bonds_[i];
134	>	}
135	>
136	>	Bond* SelectionManager::beginUnselectedBond(int& i){
137	>	i = ss_.bitsets_[BOND].firstOffBit();
138	>	return i == -1 ? NULL : bonds_[i];
139	>	}
140	>
141	>	Bond* SelectionManager::nextUnSelectedBond(int& i) {
142	>	i = ss_.bitsets_[BOND].nextOffBit(i);
143	>	return i == -1 ? NULL : bonds_[i];
144	>	}
145	>
146	>	Bend* SelectionManager::beginSelectedBend(int& i) {
147	>	i = ss_.bitsets_[BEND].firstOnBit();
148	>	return i == -1 ? NULL : bends_[i];
149	>	}
150	>
151	>	Bend* SelectionManager::nextSelectedBend(int& i) {
152	>	i = ss_.bitsets_[BEND].nextOnBit(i);
153	>	return i == -1 ? NULL : bends_[i];
154	>	}
155	>
156	>	Bend* SelectionManager::beginUnselectedBend(int& i){
157	>	i = ss_.bitsets_[BEND].firstOffBit();
158	>	return i == -1 ? NULL : bends_[i];
159	>	}
160	>
161	>	Bend* SelectionManager::nextUnSelectedBend(int& i) {
162	>	i = ss_.bitsets_[BEND].nextOffBit(i);
163	>	return i == -1 ? NULL : bends_[i];
164	>	}
165	>
166	>	Torsion* SelectionManager::beginSelectedTorsion(int& i) {
167	>	i = ss_.bitsets_[TORSION].firstOnBit();
168	>	return i == -1 ? NULL : torsions_[i];
169	>	}
170	>
171	>	Torsion* SelectionManager::nextSelectedTorsion(int& i) {
172	>	i = ss_.bitsets_[TORSION].nextOnBit(i);
173	>	return i == -1 ? NULL : torsions_[i];
174	>	}
175	>
176	>	Torsion* SelectionManager::beginUnselectedTorsion(int& i){
177	>	i = ss_.bitsets_[TORSION].firstOffBit();
178	>	return i == -1 ? NULL : torsions_[i];
179	>	}
180	>
181	>	Torsion* SelectionManager::nextUnSelectedTorsion(int& i) {
182	>	i = ss_.bitsets_[TORSION].nextOffBit(i);
183	>	return i == -1 ? NULL : torsions_[i];
184	>	}
185	>
186	>	Inversion* SelectionManager::beginSelectedInversion(int& i) {
187	>	i = ss_.bitsets_[INVERSION].firstOnBit();
188	>	return i == -1 ? NULL : inversions_[i];
189	>	}
190	>
191	>	Inversion* SelectionManager::nextSelectedInversion(int& i) {
192	>	i = ss_.bitsets_[INVERSION].nextOnBit(i);
193	>	return i == -1 ? NULL : inversions_[i];
194	>	}
195	>
196	>	Inversion* SelectionManager::beginUnselectedInversion(int& i){
197	>	i = ss_.bitsets_[INVERSION].firstOffBit();
198	>	return i == -1 ? NULL : inversions_[i];
199	>	}
200	>
201	>	Inversion* SelectionManager::nextUnSelectedInversion(int& i) {
202	>	i = ss_.bitsets_[INVERSION].nextOffBit(i);
203	>	return i == -1 ? NULL : inversions_[i];
204	>	}
205	>
206	>	SelectionManager operator| (const SelectionManager& sman1,
207	>	const SelectionManager& sman2) {
208		SelectionManager result(sman1);
209		result |= sman2;
210		return result;
211	<	}
212	<	SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
211	>	}
212	>
213	>	SelectionManager operator& (const SelectionManager& sman1,
214	>	const SelectionManager& sman2) {
215		SelectionManager result(sman1);
216		result &= sman2;
217		return result;
218	+	}
219
220	<	}
221	<	SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
220	>	SelectionManager operator^ (const SelectionManager& sman1,
221	>	const SelectionManager& sman2) {
222		SelectionManager result(sman1);
223		result ^= sman2;
224		return result;
225	+	}
226
227	<	}
228	<	SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
227	>	SelectionManager operator-(const SelectionManager& sman1,
228	>	const SelectionManager& sman2){
229		SelectionManager result(sman1);
230		result -= sman2;
231		return result;
232	+	}
233
234		}
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 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 0 | Line 1
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