src/selection/DistanceFinder.cpp

/*
 * Copyright (c) 2005, 2010 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/DistanceFinder.hpp"
#include "primitives/Molecule.hpp"
namespace OpenMD {

  DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {

    nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
    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;
      }
    }
  }

  OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
    StuntDouble * center;
    Vector3d centerPos;
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    OpenMDBitSet bsResult(nStuntDoubles_);
    assert(bsResult.size() == bs.size());
   
    for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
      if (stuntdoubles_[j]->isRigidBody()) {
        RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
        rb->updateAtoms();
      }
    }
   
    // This will fail in parallel because i might not be on this processor.

    for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
      center = stuntdoubles_[i];
      centerPos = center->getPos();
      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
        Vector3d r =centerPos - stuntdoubles_[j]->getPos();
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.setBitOn(j);
        }
      }
    }

    return bsResult;
  }

}
Revision:	1801
Committed:	Mon Oct 1 18:21:15 2012 UTC (12 years, 7 months ago) by gezelter
File size:	4038 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.
#	User	Rev	Content
1	tim	295	/*
2	chuckv	1434	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3	tim	295	*
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	295	* 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	295	* 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	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	295	*/
42
43			#include "selection/DistanceFinder.hpp"
44			#include "primitives/Molecule.hpp"
45	gezelter	1390	namespace OpenMD {
46	tim	295
47	gezelter	507	DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
48	tim	295
49			nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
50			stuntdoubles_.resize(nStuntDoubles_);
51
52			SimInfo::MoleculeIterator mi;
53			Molecule* mol;
54			Molecule::AtomIterator ai;
55			Atom* atom;
56			Molecule::RigidBodyIterator rbIter;
57			RigidBody* rb;
58
59
60	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
61			mol = info_->nextMolecule(mi)) {
62	tim	295
63	gezelter	1801	for(atom = mol->beginAtom(ai); atom != NULL;
64			atom = mol->nextAtom(ai)) {
65	gezelter	507	stuntdoubles_[atom->getGlobalIndex()] = atom;
66			}
67	tim	295
68	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
69			rb = mol->nextRigidBody(rbIter)) {
70	gezelter	507	stuntdoubles_[rb->getGlobalIndex()] = rb;
71			}
72	gezelter	1801	}
73	gezelter	507	}
74	tim	295
75	gezelter	1390	OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
76	tim	295	StuntDouble * center;
77			Vector3d centerPos;
78			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
79	gezelter	1390	OpenMDBitSet bsResult(nStuntDoubles_);
80	tim	295	assert(bsResult.size() == bs.size());
81	chuckv	1434
82	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
83	chuckv	1434	if (stuntdoubles_[j]->isRigidBody()) {
84			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
85			rb->updateAtoms();
86			}
87			}
88
89	gezelter	1801	// This will fail in parallel because i might not be on this processor.
90
91	tim	358	for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
92	gezelter	507	center = stuntdoubles_[i];
93			centerPos = center->getPos();
94	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
95	gezelter	507	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
96			currSnapshot->wrapVector(r);
97			if (r.length() <= distance) {
98			bsResult.setBitOn(j);
99			}
100			}
101	tim	295	}
102
103			return bsResult;
104	gezelter	507	}
105	tim	295
106			}