src/selection/IndexFinder.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/IndexFinder.hpp"
#include "primitives/Molecule.hpp"
namespace OpenMD {

  IndexFinder::IndexFinder(SimInfo* info) : info_(info){
    nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
    bitSets_.resize(info_->getNGlobalMolecules());
    init();
  }

  void IndexFinder::init() {

    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)) {
           
      OpenMDBitSet bs(nStuntDoubles_);
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        bs.setBitOn(atom->getGlobalIndex());
      }
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        bs.setBitOn(rb->getGlobalIndex());
      }
      bitSets_[mol->getGlobalIndex()] = bs;
    }
  }

  OpenMDBitSet IndexFinder::find(int molIndex){
    return bitSets_[molIndex];
  }

  OpenMDBitSet IndexFinder::find(int begMolIndex, int endMolIndex){
    OpenMDBitSet bs(nStuntDoubles_);
        
    for (int i = begMolIndex; i < endMolIndex; ++i) {
      bs |= bitSets_[i];
    }    
    return bs;
  }
}

Revision:	1803
Committed:	Wed Oct 3 14:20:07 2012 UTC (12 years, 6 months ago) by gezelter
File size:	3457 byte(s)
Log Message:	Merging trunk changes back to development branch
#	User	Rev	Content
1	tim	416	/*
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	416	* 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	416	* 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	416	*/
42			#include "selection/IndexFinder.hpp"
43			#include "primitives/Molecule.hpp"
44	gezelter	1390	namespace OpenMD {
45	tim	416
46	gezelter	507	IndexFinder::IndexFinder(SimInfo* info) : info_(info){
47	tim	416	nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
48			bitSets_.resize(info_->getNGlobalMolecules());
49			init();
50	gezelter	507	}
51	tim	416
52	gezelter	507	void IndexFinder::init() {
53	tim	416
54			SimInfo::MoleculeIterator mi;
55			Molecule* mol;
56			Molecule::AtomIterator ai;
57			Atom* atom;
58			Molecule::RigidBodyIterator rbIter;
59			RigidBody* rb;
60
61	gezelter	1803	for (mol = info_->beginMolecule(mi); mol != NULL;
62			mol = info_->nextMolecule(mi)) {
63	tim	416
64	gezelter	1390	OpenMDBitSet bs(nStuntDoubles_);
65	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
66			bs.setBitOn(atom->getGlobalIndex());
67			}
68	gezelter	1803	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
69			rb = mol->nextRigidBody(rbIter)) {
70	gezelter	507	bs.setBitOn(rb->getGlobalIndex());
71			}
72			bitSets_[mol->getGlobalIndex()] = bs;
73	gezelter	1803	}
74	gezelter	507	}
75	tim	416
76	gezelter	1390	OpenMDBitSet IndexFinder::find(int molIndex){
77	tim	416	return bitSets_[molIndex];
78	gezelter	507	}
79	tim	416
80	gezelter	1390	OpenMDBitSet IndexFinder::find(int begMolIndex, int endMolIndex){
81			OpenMDBitSet bs(nStuntDoubles_);
82	tim	416
83			for (int i = begMolIndex; i < endMolIndex; ++i) {
84	gezelter	507	bs \|= bitSets_[i];
85	gezelter	1803	}
86	tim	416	return bs;
87	gezelter	507	}
88	tim	416	}
89