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, 24107 (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){

    int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();

    bsSelection_.resize(nStuntDoubles);
    stuntdoubles_.resize(nStuntDoubles);
    
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;

    
    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;
      }
        
    }    
    
  }


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

  StuntDouble* SelectionManager::beginUnselected(int& i){
    i = bsSelection_.firstOffBit();
    return i == -1 ? NULL : stuntdoubles_[i];
  }
  StuntDouble* SelectionManager::nextUnSelected(int& i) {
    i = bsSelection_.nextOffBit(i);
    return i == -1 ? NULL : stuntdoubles_[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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	4389 byte(s)
Log Message:	updated copyright notices
#	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			* [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, 24107 (2008).
39	gezelter	1665	* [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	tim	317
49			int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
50
51			bsSelection_.resize(nStuntDoubles);
52			stuntdoubles_.resize(nStuntDoubles);
53
54			SimInfo::MoleculeIterator mi;
55			Molecule* mol;
56			Molecule::AtomIterator ai;
57			Atom* atom;
58			Molecule::RigidBodyIterator rbIter;
59			RigidBody* rb;
60
61
62			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
63
64	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
65			stuntdoubles_[atom->getGlobalIndex()] = atom;
66			}
67	tim	317
68	gezelter	507	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
69			stuntdoubles_[rb->getGlobalIndex()] = rb;
70			}
71	tim	317
72			}
73
74	gezelter	507	}
75	tim	317
76
77	gezelter	507	StuntDouble* SelectionManager::beginSelected(int& i) {
78	tim	317	i = bsSelection_.firstOnBit();
79			return i == -1 ? NULL : stuntdoubles_[i];
80	gezelter	507	}
81			StuntDouble* SelectionManager::nextSelected(int& i) {
82	tim	317	i = bsSelection_.nextOnBit(i);
83			return i == -1 ? NULL : stuntdoubles_[i];
84	gezelter	507	}
85	tim	317
86	gezelter	507	StuntDouble* SelectionManager::beginUnselected(int& i){
87	tim	317	i = bsSelection_.firstOffBit();
88			return i == -1 ? NULL : stuntdoubles_[i];
89	gezelter	507	}
90			StuntDouble* SelectionManager::nextUnSelected(int& i) {
91	tim	317	i = bsSelection_.nextOffBit(i);
92			return i == -1 ? NULL : stuntdoubles_[i];
93	gezelter	507	}
94	tim	317
95	tim	353
96	gezelter	507	SelectionManager operator\| (const SelectionManager& sman1, const SelectionManager& sman2) {
97	tim	353	SelectionManager result(sman1);
98			result \|= sman2;
99			return result;
100	gezelter	507	}
101			SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
102	tim	353	SelectionManager result(sman1);
103			result &= sman2;
104			return result;
105
106	gezelter	507	}
107			SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
108	tim	353	SelectionManager result(sman1);
109			result ^= sman2;
110			return result;
111
112	gezelter	507	}
113			SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
114	tim	353	SelectionManager result(sman1);
115			result -= sman2;
116			return result;
117
118	gezelter	507	}
119	tim	353
120			}