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, 234107 (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){
    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());

    selectionSets_.resize(info_->getNGlobalMolecules());
    init();
  }

  void IndexFinder::init() {

    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)) {
           
      SelectionSet ss(nObjects_);
      ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());

      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
      }
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
      }
      for (bond = mol->beginBond(bondIter); bond != NULL; 
           bond = mol->nextBond(bondIter)) {
        ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
      }   
      for (bend = mol->beginBend(bendIter); bend != NULL; 
           bend = mol->nextBend(bendIter)) {
        ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
      }   
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; 
           torsion = mol->nextTorsion(torsionIter)) {
        ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
      }   
      for (inversion = mol->beginInversion(inversionIter); inversion != NULL; 
           inversion = mol->nextInversion(inversionIter)) {
        ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
      }   

      selectionSets_[mol->getGlobalIndex()] = ss;
    }
  }

  SelectionSet IndexFinder::find(int molIndex){
    return selectionSets_[molIndex];
  }

  SelectionSet IndexFinder::find(int begMolIndex, int endMolIndex){
    SelectionSet ss(nObjects_);
        
    for (int i = begMolIndex; i < endMolIndex; ++i) {
      ss |= selectionSets_[i];
    }    
    return ss;
  }
}

Revision:	2052
Committed:	Fri Jan 9 19:06:35 2015 UTC (10 years, 9 months ago) by gezelter
File size:	4877 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	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	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	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	gezelter	1953	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	gezelter	2052	nObjects_.push_back(info_->getNGlobalMolecules());
53	gezelter	1953
54			selectionSets_.resize(info_->getNGlobalMolecules());
55	tim	416	init();
56	gezelter	507	}
57	tim	416
58	gezelter	507	void IndexFinder::init() {
59	tim	416
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	416	Molecule* mol;
69			Atom* atom;
70			RigidBody* rb;
71	gezelter	1953	Bond* bond;
72			Bend* bend;
73			Torsion* torsion;
74			Inversion* inversion;
75	tim	416
76	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
77			mol = info_->nextMolecule(mi)) {
78	tim	416
79	gezelter	1953	SelectionSet ss(nObjects_);
80	gezelter	2052	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
81	gezelter	1953
82	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
83	gezelter	1953	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
84	gezelter	507	}
85	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
86			rb = mol->nextRigidBody(rbIter)) {
87	gezelter	1953	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
88	gezelter	507	}
89	gezelter	1953	for (bond = mol->beginBond(bondIter); bond != NULL;
90			bond = mol->nextBond(bondIter)) {
91			ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
92			}
93			for (bend = mol->beginBend(bendIter); bend != NULL;
94			bend = mol->nextBend(bendIter)) {
95			ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
96			}
97			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
98			torsion = mol->nextTorsion(torsionIter)) {
99			ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
100			}
101			for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
102			inversion = mol->nextInversion(inversionIter)) {
103			ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
104			}
105
106			selectionSets_[mol->getGlobalIndex()] = ss;
107	gezelter	1801	}
108	gezelter	507	}
109	tim	416
110	gezelter	1953	SelectionSet IndexFinder::find(int molIndex){
111			return selectionSets_[molIndex];
112	gezelter	507	}
113	tim	416
114	gezelter	1953	SelectionSet IndexFinder::find(int begMolIndex, int endMolIndex){
115			SelectionSet ss(nObjects_);
116	tim	416
117			for (int i = begMolIndex; i < endMolIndex; ++i) {
118	gezelter	1953	ss \|= selectionSets_[i];
119	gezelter	1801	}
120	gezelter	1953	return ss;
121	gezelter	507	}
122	tim	416	}
123