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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 2052 by gezelter, Fri Jan 9 19:06:35 2015 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"
43	–	#include "primitives/Molecule.hpp"
44		#include "brains/SimInfo.hpp"
45	<	namespace oopse {
46	<	SelectionManager::SelectionManager(SimInfo* info) : info_(info){
45	>	namespace OpenMD {
46	>	SelectionManager::SelectionManager(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	>	nObjects_.push_back(info_->getNGlobalMolecules());
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	>	molecules_.resize(nObjects_[MOLECULE]);
60
61		SimInfo::MoleculeIterator mi;
54	–	Molecule* mol;
62		Molecule::AtomIterator ai;
56	–	Atom* atom;
63		Molecule::RigidBodyIterator rbIter;
64	<	RigidBody* rb;
64	>	Molecule::BondIterator bondIter;
65	>	Molecule::BendIterator bendIter;
66	>	Molecule::TorsionIterator torsionIter;
67	>	Molecule::InversionIterator inversionIter;
68
69	<
70	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
69	>	Molecule* mol;
70	>	Atom* atom;
71	>	RigidBody* rb;
72	>	Bond* bond;
73	>	Bend* bend;
74	>	Torsion* torsion;
75	>	Inversion* inversion;
76
77	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
78	<	stuntdoubles_[atom->getGlobalIndex()] = atom;
79	<	}
77	>	for (mol = info_->beginMolecule(mi); mol != NULL;
78	>	mol = info_->nextMolecule(mi)) {
79	>	molecules_[mol->getGlobalIndex()] = mol;
80	>
81	>	for(atom = mol->beginAtom(ai); atom != NULL;
82	>	atom = mol->nextAtom(ai)) {
83	>	stuntdoubles_[atom->getGlobalIndex()] = atom;
84	>	}
85	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
86	>	rb = mol->nextRigidBody(rbIter)) {
87	>	stuntdoubles_[rb->getGlobalIndex()] = rb;
88	>	}
89	>	for (bond = mol->beginBond(bondIter); bond != NULL;
90	>	bond = mol->nextBond(bondIter)) {
91	>	bonds_[bond->getGlobalIndex()] = bond;
92	>	}
93	>	for (bend = mol->beginBend(bendIter); bend != NULL;
94	>	bend = mol->nextBend(bendIter)) {
95	>	bends_[bend->getGlobalIndex()] = bend;
96	>	}
97	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
98	>	torsion = mol->nextTorsion(torsionIter)) {
99	>	torsions_[torsion->getGlobalIndex()] = torsion;
100	>	}
101	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
102	>	inversion = mol->nextInversion(inversionIter)) {
103	>	inversions_[inversion->getGlobalIndex()] = inversion;
104	>	}
105	>	}
106	>	}
107
108	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
109	<	stuntdoubles_[rb->getGlobalIndex()] = rb;
110	<	}
111	<
71	<	}
72	<
73	<	}
108	>	StuntDouble* SelectionManager::beginSelected(int& i) {
109	>	i = ss_.bitsets_[STUNTDOUBLE].firstOnBit();
110	>	return i == -1 ? NULL : stuntdoubles_[i];
111	>	}
112
113	+	StuntDouble* SelectionManager::nextSelected(int& i) {
114	+	i = ss_.bitsets_[STUNTDOUBLE].nextOnBit(i);
115	+	return i == -1 ? NULL : stuntdoubles_[i];
116	+	}
117
118	<	StuntDouble* SelectionManager::beginSelected(int& i) {
119	<	i = bsSelection_.firstOnBit();
118	>	StuntDouble* SelectionManager::beginUnselected(int& i){
119	>	i = ss_.bitsets_[STUNTDOUBLE].firstOffBit();
120		return i == -1 ? NULL : stuntdoubles_[i];
121	<	}
80	<	StuntDouble* SelectionManager::nextSelected(int& i) {
81	<	i = bsSelection_.nextOnBit(i);
82	<	return i == -1 ? NULL : stuntdoubles_[i];
83	<	}
121	>	}
122
123	<	StuntDouble* SelectionManager::beginUnselected(int& i){
124	<	i = bsSelection_.firstOffBit();
123	>	StuntDouble* SelectionManager::nextUnSelected(int& i) {
124	>	i = ss_.bitsets_[STUNTDOUBLE].nextOffBit(i);
125		return i == -1 ? NULL : stuntdoubles_[i];
126	<	}
89	<	StuntDouble* SelectionManager::nextUnSelected(int& i) {
90	<	i = bsSelection_.nextOffBit(i);
91	<	return i == -1 ? NULL : stuntdoubles_[i];
92	<	}
126	>	}
127
128	+	Bond* SelectionManager::beginSelectedBond(int& i) {
129	+	i = ss_.bitsets_[BOND].firstOnBit();
130	+	return i == -1 ? NULL : bonds_[i];
131	+	}
132
133	<	SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) {
133	>	Bond* SelectionManager::nextSelectedBond(int& i) {
134	>	i = ss_.bitsets_[BOND].nextOnBit(i);
135	>	return i == -1 ? NULL : bonds_[i];
136	>	}
137	>
138	>	Bond* SelectionManager::beginUnselectedBond(int& i){
139	>	i = ss_.bitsets_[BOND].firstOffBit();
140	>	return i == -1 ? NULL : bonds_[i];
141	>	}
142	>
143	>	Bond* SelectionManager::nextUnSelectedBond(int& i) {
144	>	i = ss_.bitsets_[BOND].nextOffBit(i);
145	>	return i == -1 ? NULL : bonds_[i];
146	>	}
147	>
148	>	Bend* SelectionManager::beginSelectedBend(int& i) {
149	>	i = ss_.bitsets_[BEND].firstOnBit();
150	>	return i == -1 ? NULL : bends_[i];
151	>	}
152	>
153	>	Bend* SelectionManager::nextSelectedBend(int& i) {
154	>	i = ss_.bitsets_[BEND].nextOnBit(i);
155	>	return i == -1 ? NULL : bends_[i];
156	>	}
157	>
158	>	Bend* SelectionManager::beginUnselectedBend(int& i){
159	>	i = ss_.bitsets_[BEND].firstOffBit();
160	>	return i == -1 ? NULL : bends_[i];
161	>	}
162	>
163	>	Bend* SelectionManager::nextUnSelectedBend(int& i) {
164	>	i = ss_.bitsets_[BEND].nextOffBit(i);
165	>	return i == -1 ? NULL : bends_[i];
166	>	}
167	>
168	>	Torsion* SelectionManager::beginSelectedTorsion(int& i) {
169	>	i = ss_.bitsets_[TORSION].firstOnBit();
170	>	return i == -1 ? NULL : torsions_[i];
171	>	}
172	>
173	>	Torsion* SelectionManager::nextSelectedTorsion(int& i) {
174	>	i = ss_.bitsets_[TORSION].nextOnBit(i);
175	>	return i == -1 ? NULL : torsions_[i];
176	>	}
177	>
178	>	Torsion* SelectionManager::beginUnselectedTorsion(int& i){
179	>	i = ss_.bitsets_[TORSION].firstOffBit();
180	>	return i == -1 ? NULL : torsions_[i];
181	>	}
182	>
183	>	Torsion* SelectionManager::nextUnSelectedTorsion(int& i) {
184	>	i = ss_.bitsets_[TORSION].nextOffBit(i);
185	>	return i == -1 ? NULL : torsions_[i];
186	>	}
187	>
188	>	Inversion* SelectionManager::beginSelectedInversion(int& i) {
189	>	i = ss_.bitsets_[INVERSION].firstOnBit();
190	>	return i == -1 ? NULL : inversions_[i];
191	>	}
192	>
193	>	Inversion* SelectionManager::nextSelectedInversion(int& i) {
194	>	i = ss_.bitsets_[INVERSION].nextOnBit(i);
195	>	return i == -1 ? NULL : inversions_[i];
196	>	}
197	>
198	>	Inversion* SelectionManager::beginUnselectedInversion(int& i){
199	>	i = ss_.bitsets_[INVERSION].firstOffBit();
200	>	return i == -1 ? NULL : inversions_[i];
201	>	}
202	>
203	>	Inversion* SelectionManager::nextUnSelectedInversion(int& i) {
204	>	i = ss_.bitsets_[INVERSION].nextOffBit(i);
205	>	return i == -1 ? NULL : inversions_[i];
206	>	}
207	>
208	>	Molecule* SelectionManager::beginSelectedMolecule(int& i) {
209	>	i = ss_.bitsets_[MOLECULE].firstOnBit();
210	>	return i == -1 ? NULL : molecules_[i];
211	>	}
212	>
213	>	Molecule* SelectionManager::nextSelectedMolecule(int& i) {
214	>	i = ss_.bitsets_[MOLECULE].nextOnBit(i);
215	>	return i == -1 ? NULL : molecules_[i];
216	>	}
217	>
218	>	Molecule* SelectionManager::beginUnselectedMolecule(int& i){
219	>	i = ss_.bitsets_[MOLECULE].firstOffBit();
220	>	return i == -1 ? NULL : molecules_[i];
221	>	}
222	>
223	>	Molecule* SelectionManager::nextUnSelectedMolecule(int& i) {
224	>	i = ss_.bitsets_[MOLECULE].nextOffBit(i);
225	>	return i == -1 ? NULL : molecules_[i];
226	>	}
227	>
228	>	SelectionManager operator| (const SelectionManager& sman1,
229	>	const SelectionManager& sman2) {
230		SelectionManager result(sman1);
231		result |= sman2;
232		return result;
233	<	}
234	<	SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
233	>	}
234	>
235	>	SelectionManager operator& (const SelectionManager& sman1,
236	>	const SelectionManager& sman2) {
237		SelectionManager result(sman1);
238		result &= sman2;
239		return result;
240	+	}
241
242	<	}
243	<	SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
242	>	SelectionManager operator^ (const SelectionManager& sman1,
243	>	const SelectionManager& sman2) {
244		SelectionManager result(sman1);
245		result ^= sman2;
246		return result;
247	+	}
248
249	<	}
250	<	SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
249	>	SelectionManager operator-(const SelectionManager& sman1,
250	>	const SelectionManager& sman2){
251		SelectionManager result(sman1);
252		result -= sman2;
253		return result;
254	+	}
255
256		}
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 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

#	Line 0 | Line 1
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