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 "primitives/Molecule.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());

    stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
    bonds_.resize(nObjects_[BOND]);
    bends_.resize(nObjects_[BEND]);
    torsions_.resize(nObjects_[TORSION]);
    inversions_.resize(nObjects_[INVERSION]);
    
    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)) {
      
      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];
  }

  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:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 4 months ago) by gezelter
File size:	8204 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	User	Rev	Content
1	tim	317	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	317	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	317	* 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	gezelter	1390	*
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	gezelter	1801	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	317	*/
42
43			#include "selection/SelectionManager.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "brains/SimInfo.hpp"
46	gezelter	1390	namespace OpenMD {
47	gezelter	507	SelectionManager::SelectionManager(SimInfo* info) : info_(info){
48	gezelter	1953	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	tim	317
54	gezelter	1953	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	tim	317
60			SimInfo::MoleculeIterator mi;
61	gezelter	1953	Molecule::AtomIterator ai;
62			Molecule::RigidBodyIterator rbIter;
63			Molecule::BondIterator bondIter;
64			Molecule::BendIterator bendIter;
65			Molecule::TorsionIterator torsionIter;
66			Molecule::InversionIterator inversionIter;
67
68	tim	317	Molecule* mol;
69			Atom* atom;
70			RigidBody* rb;
71	gezelter	1953	Bond* bond;
72			Bend* bend;
73			Torsion* torsion;
74			Inversion* inversion;
75
76	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
77			mol = info_->nextMolecule(mi)) {
78	gezelter	1953
79	gezelter	1801	for(atom = mol->beginAtom(ai); atom != NULL;
80			atom = mol->nextAtom(ai)) {
81	gezelter	507	stuntdoubles_[atom->getGlobalIndex()] = atom;
82	gezelter	1953	}
83	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
84			rb = mol->nextRigidBody(rbIter)) {
85	gezelter	507	stuntdoubles_[rb->getGlobalIndex()] = rb;
86	gezelter	1801	}
87	gezelter	1953	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	gezelter	1801	}
104	gezelter	507	}
105	tim	317
106	gezelter	507	StuntDouble* SelectionManager::beginSelected(int& i) {
107	gezelter	1953	i = ss_.bitsets_[STUNTDOUBLE].firstOnBit();
108	tim	317	return i == -1 ? NULL : stuntdoubles_[i];
109	gezelter	507	}
110	gezelter	1801
111	gezelter	507	StuntDouble* SelectionManager::nextSelected(int& i) {
112	gezelter	1953	i = ss_.bitsets_[STUNTDOUBLE].nextOnBit(i);
113	tim	317	return i == -1 ? NULL : stuntdoubles_[i];
114	gezelter	507	}
115	tim	317
116	gezelter	507	StuntDouble* SelectionManager::beginUnselected(int& i){
117	gezelter	1953	i = ss_.bitsets_[STUNTDOUBLE].firstOffBit();
118	tim	317	return i == -1 ? NULL : stuntdoubles_[i];
119	gezelter	507	}
120	gezelter	1801
121	gezelter	507	StuntDouble* SelectionManager::nextUnSelected(int& i) {
122	gezelter	1953	i = ss_.bitsets_[STUNTDOUBLE].nextOffBit(i);
123	tim	317	return i == -1 ? NULL : stuntdoubles_[i];
124	gezelter	507	}
125	tim	317
126	gezelter	1953	Bond* SelectionManager::beginSelectedBond(int& i) {
127			i = ss_.bitsets_[BOND].firstOnBit();
128			return i == -1 ? NULL : bonds_[i];
129			}
130
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	gezelter	1801	SelectionManager operator\| (const SelectionManager& sman1,
207			const SelectionManager& sman2) {
208	tim	353	SelectionManager result(sman1);
209			result \|= sman2;
210			return result;
211	gezelter	507	}
212	gezelter	1801
213			SelectionManager operator& (const SelectionManager& sman1,
214			const SelectionManager& sman2) {
215	tim	353	SelectionManager result(sman1);
216			result &= sman2;
217			return result;
218	gezelter	1801	}
219	tim	353
220	gezelter	1801	SelectionManager operator^ (const SelectionManager& sman1,
221			const SelectionManager& sman2) {
222	tim	353	SelectionManager result(sman1);
223			result ^= sman2;
224			return result;
225	gezelter	1801	}
226	tim	353
227	gezelter	1801	SelectionManager operator-(const SelectionManager& sman1,
228			const SelectionManager& sman2){
229	tim	353	SelectionManager result(sman1);
230			result -= sman2;
231			return result;
232	gezelter	507	}
233	tim	353
234			}