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, NULL);
    
    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:	1801
Committed:	Mon Oct 1 18:21:15 2012 UTC (12 years, 7 months ago) by gezelter
File size:	4508 byte(s)
Log Message:	Some parallel fixes for "select all" selection scripts. The distance finder selection, e.g. "select within(4.0, Au)", still needs work, however.
#	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, 24107 (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 OpenMD {
47	SelectionManager::SelectionManager(SimInfo* info) : info_(info){
48
49	int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
50
51	bsSelection_.resize(nStuntDoubles);
52	stuntdoubles_.resize(nStuntDoubles, NULL);
53
54	SimInfo::MoleculeIterator mi;
55	Molecule* mol;
56	Molecule::AtomIterator ai;
57	Atom* atom;
58	Molecule::RigidBodyIterator rbIter;
59	RigidBody* rb;
60
61	for (mol = info_->beginMolecule(mi); mol != NULL;
62	mol = info_->nextMolecule(mi)) {
63
64	for(atom = mol->beginAtom(ai); atom != NULL;
65	atom = mol->nextAtom(ai)) {
66	stuntdoubles_[atom->getGlobalIndex()] = atom;
67	}
68
69	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
70	rb = mol->nextRigidBody(rbIter)) {
71	stuntdoubles_[rb->getGlobalIndex()] = rb;
72	}
73	}
74	}
75
76	StuntDouble* SelectionManager::beginSelected(int& i) {
77	i = bsSelection_.firstOnBit();
78	return i == -1 ? NULL : stuntdoubles_[i];
79	}
80
81	StuntDouble* SelectionManager::nextSelected(int& i) {
82	i = bsSelection_.nextOnBit(i);
83	return i == -1 ? NULL : stuntdoubles_[i];
84	}
85
86	StuntDouble* SelectionManager::beginUnselected(int& i){
87	i = bsSelection_.firstOffBit();
88	return i == -1 ? NULL : stuntdoubles_[i];
89	}
90
91	StuntDouble* SelectionManager::nextUnSelected(int& i) {
92	i = bsSelection_.nextOffBit(i);
93	return i == -1 ? NULL : stuntdoubles_[i];
94	}
95
96	SelectionManager operator\| (const SelectionManager& sman1,
97	const SelectionManager& sman2) {
98	SelectionManager result(sman1);
99	result \|= sman2;
100	return result;
101	}
102
103	SelectionManager operator& (const SelectionManager& sman1,
104	const SelectionManager& sman2) {
105	SelectionManager result(sman1);
106	result &= sman2;
107	return result;
108	}
109
110	SelectionManager operator^ (const SelectionManager& sman1,
111	const SelectionManager& sman2) {
112	SelectionManager result(sman1);
113	result ^= sman2;
114	return result;
115	}
116
117	SelectionManager operator-(const SelectionManager& sman1,
118	const SelectionManager& sman2){
119	SelectionManager result(sman1);
120	result -= sman2;
121	return result;
122	}
123
124	}