src/selection/SelectionManager.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "selection/SelectionManager.hpp"
#include "brains/SimInfo.hpp"
namespace OpenMD {
  SelectionManager::SelectionManager(SimInfo* info) : info_(info){
    nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
    nObjects_.push_back(info_->getNGlobalBonds());
    nObjects_.push_back(info_->getNGlobalBends());
    nObjects_.push_back(info_->getNGlobalTorsions());
    nObjects_.push_back(info_->getNGlobalInversions());
    nObjects_.push_back(info_->getNGlobalMolecules());

    stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
    bonds_.resize(nObjects_[BOND]);
    bends_.resize(nObjects_[BEND]);
    torsions_.resize(nObjects_[TORSION]);
    inversions_.resize(nObjects_[INVERSION]);
    molecules_.resize(nObjects_[MOLECULE]);
    
    SimInfo::MoleculeIterator mi;
    Molecule::AtomIterator ai;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;
    Molecule::BendIterator bendIter;
    Molecule::TorsionIterator torsionIter;
    Molecule::InversionIterator inversionIter;

    Molecule* mol;
    Atom* atom;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;    
        
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      molecules_[mol->getGlobalIndex()] = mol;
      
      for(atom = mol->beginAtom(ai); atom != NULL; 
          atom = mol->nextAtom(ai)) {
        stuntdoubles_[atom->getGlobalIndex()] = atom;
      }  
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        stuntdoubles_[rb->getGlobalIndex()] = rb;
      }   
      for (bond = mol->beginBond(bondIter); bond != NULL; 
           bond = mol->nextBond(bondIter)) {
        bonds_[bond->getGlobalIndex()] = bond;
      }   
      for (bend = mol->beginBend(bendIter); bend != NULL; 
           bend = mol->nextBend(bendIter)) {
        bends_[bend->getGlobalIndex()] = bend;
      }   
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; 
           torsion = mol->nextTorsion(torsionIter)) {
        torsions_[torsion->getGlobalIndex()] = torsion;
      }   
      for (inversion = mol->beginInversion(inversionIter); inversion != NULL; 
           inversion = mol->nextInversion(inversionIter)) {
        inversions_[inversion->getGlobalIndex()] = inversion;
      }   
    }
  }

  StuntDouble* SelectionManager::beginSelected(int& i) {
    i = ss_.bitsets_[STUNTDOUBLE].firstOnBit();
    return i == -1 ? NULL : stuntdoubles_[i];
  }

  StuntDouble* SelectionManager::nextSelected(int& i) {
    i = ss_.bitsets_[STUNTDOUBLE].nextOnBit(i);
    return i == -1 ? NULL : stuntdoubles_[i];
  }

  StuntDouble* SelectionManager::beginUnselected(int& i){
    i = ss_.bitsets_[STUNTDOUBLE].firstOffBit();
    return i == -1 ? NULL : stuntdoubles_[i];
  }

  StuntDouble* SelectionManager::nextUnSelected(int& i) {
    i = ss_.bitsets_[STUNTDOUBLE].nextOffBit(i);
    return i == -1 ? NULL : stuntdoubles_[i];
  }

  Bond* SelectionManager::beginSelectedBond(int& i) {
    i = ss_.bitsets_[BOND].firstOnBit();
    return i == -1 ? NULL : bonds_[i];
  }

  Bond* SelectionManager::nextSelectedBond(int& i) {
    i = ss_.bitsets_[BOND].nextOnBit(i);
    return i == -1 ? NULL : bonds_[i];
  }

  Bond* SelectionManager::beginUnselectedBond(int& i){
    i = ss_.bitsets_[BOND].firstOffBit();
    return i == -1 ? NULL : bonds_[i];
  }

  Bond* SelectionManager::nextUnSelectedBond(int& i) {
    i = ss_.bitsets_[BOND].nextOffBit(i);
    return i == -1 ? NULL : bonds_[i];
  }

  Bend* SelectionManager::beginSelectedBend(int& i) {
    i = ss_.bitsets_[BEND].firstOnBit();
    return i == -1 ? NULL : bends_[i];
  }

  Bend* SelectionManager::nextSelectedBend(int& i) {
    i = ss_.bitsets_[BEND].nextOnBit(i);
    return i == -1 ? NULL : bends_[i];
  }

  Bend* SelectionManager::beginUnselectedBend(int& i){
    i = ss_.bitsets_[BEND].firstOffBit();
    return i == -1 ? NULL : bends_[i];
  }

  Bend* SelectionManager::nextUnSelectedBend(int& i) {
    i = ss_.bitsets_[BEND].nextOffBit(i);
    return i == -1 ? NULL : bends_[i];
  }

  Torsion* SelectionManager::beginSelectedTorsion(int& i) {
    i = ss_.bitsets_[TORSION].firstOnBit();
    return i == -1 ? NULL : torsions_[i];
  }

  Torsion* SelectionManager::nextSelectedTorsion(int& i) {
    i = ss_.bitsets_[TORSION].nextOnBit(i);
    return i == -1 ? NULL : torsions_[i];
  }

  Torsion* SelectionManager::beginUnselectedTorsion(int& i){
    i = ss_.bitsets_[TORSION].firstOffBit();
    return i == -1 ? NULL : torsions_[i];
  }

  Torsion* SelectionManager::nextUnSelectedTorsion(int& i) {
    i = ss_.bitsets_[TORSION].nextOffBit(i);
    return i == -1 ? NULL : torsions_[i];
  }

  Inversion* SelectionManager::beginSelectedInversion(int& i) {
    i = ss_.bitsets_[INVERSION].firstOnBit();
    return i == -1 ? NULL : inversions_[i];
  }

  Inversion* SelectionManager::nextSelectedInversion(int& i) {
    i = ss_.bitsets_[INVERSION].nextOnBit(i);
    return i == -1 ? NULL : inversions_[i];
  }

  Inversion* SelectionManager::beginUnselectedInversion(int& i){
    i = ss_.bitsets_[INVERSION].firstOffBit();
    return i == -1 ? NULL : inversions_[i];
  }

  Inversion* SelectionManager::nextUnSelectedInversion(int& i) {
    i = ss_.bitsets_[INVERSION].nextOffBit(i);
    return i == -1 ? NULL : inversions_[i];
  }
  
  Molecule* SelectionManager::beginSelectedMolecule(int& i) {
    i = ss_.bitsets_[MOLECULE].firstOnBit();
    return i == -1 ? NULL : molecules_[i];
  }

  Molecule* SelectionManager::nextSelectedMolecule(int& i) {
    i = ss_.bitsets_[MOLECULE].nextOnBit(i);
    return i == -1 ? NULL : molecules_[i];
  }

  Molecule* SelectionManager::beginUnselectedMolecule(int& i){
    i = ss_.bitsets_[MOLECULE].firstOffBit();
    return i == -1 ? NULL : molecules_[i];
  }

  Molecule* SelectionManager::nextUnSelectedMolecule(int& i) {
    i = ss_.bitsets_[MOLECULE].nextOffBit(i);
    return i == -1 ? NULL : molecules_[i];
  }

  SelectionManager operator| (const SelectionManager& sman1, 
                              const SelectionManager& sman2) {
    SelectionManager result(sman1);
    result |= sman2;
    return result;
  }

  SelectionManager operator& (const SelectionManager& sman1, 
                              const SelectionManager& sman2) {
    SelectionManager result(sman1);
    result &= sman2;
    return result;
  }

  SelectionManager operator^ (const SelectionManager& sman1, 
                              const SelectionManager& sman2) {
    SelectionManager result(sman1);
    result ^= sman2;
    return result;
  }

  SelectionManager operator-(const SelectionManager& sman1, 
                             const SelectionManager& sman2){
    SelectionManager result(sman1);
    result -= sman2;
    return result;
  }

}
Revision:	2052
Committed:	Fri Jan 9 19:06:35 2015 UTC (10 years, 3 months ago) by gezelter
File size:	8940 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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 "brains/SimInfo.hpp"
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	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;
62	Molecule::AtomIterator ai;
63	Molecule::RigidBodyIterator rbIter;
64	Molecule::BondIterator bondIter;
65	Molecule::BendIterator bendIter;
66	Molecule::TorsionIterator torsionIter;
67	Molecule::InversionIterator inversionIter;
68
69	Molecule* mol;
70	Atom* atom;
71	RigidBody* rb;
72	Bond* bond;
73	Bend* bend;
74	Torsion* torsion;
75	Inversion* inversion;
76
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	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::beginUnselected(int& i){
119	i = ss_.bitsets_[STUNTDOUBLE].firstOffBit();
120	return i == -1 ? NULL : stuntdoubles_[i];
121	}
122
123	StuntDouble* SelectionManager::nextUnSelected(int& i) {
124	i = ss_.bitsets_[STUNTDOUBLE].nextOffBit(i);
125	return i == -1 ? NULL : stuntdoubles_[i];
126	}
127
128	Bond* SelectionManager::beginSelectedBond(int& i) {
129	i = ss_.bitsets_[BOND].firstOnBit();
130	return i == -1 ? NULL : bonds_[i];
131	}
132
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
235	SelectionManager operator& (const SelectionManager& sman1,
236	const SelectionManager& sman2) {
237	SelectionManager result(sman1);
238	result &= sman2;
239	return result;
240	}
241
242	SelectionManager operator^ (const SelectionManager& sman1,
243	const SelectionManager& sman2) {
244	SelectionManager result(sman1);
245	result ^= sman2;
246	return result;
247	}
248
249	SelectionManager operator-(const SelectionManager& sman1,
250	const SelectionManager& sman2){
251	SelectionManager result(sman1);
252	result -= sman2;
253	return result;
254	}
255
256	}