src/selection/HullFinder.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/HullFinder.hpp"
#include "primitives/Molecule.hpp"
#include "math/ConvexHull.hpp"

namespace OpenMD {

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

    nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
    stuntdoubles_.resize(nStuntDoubles_);
    
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    StuntDouble* sd;
    Molecule::IntegrableObjectIterator  ioi;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
        
      // Hull is constructed from all known integrable objects.
      for (sd = mol->beginIntegrableObject(ioi);
           sd != NULL;
           sd = mol->nextIntegrableObject(ioi)) {
        localSites_.push_back(sd);
      }
      
      // selection can include atoms (which may be a subset of the IOs)
      for(atom = mol->beginAtom(ai); atom != NULL; 
          atom = mol->nextAtom(ai)) {
        stuntdoubles_[atom->getGlobalIndex()] = atom;
      }
      
      // and rigid bodies
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        stuntdoubles_[rb->getGlobalIndex()] = rb;
      }
        
    }
#ifdef HAVE_QHULL
    surfaceMesh_ = new ConvexHull();
#endif
  }

  HullFinder::~HullFinder() {
    delete surfaceMesh_;
  }

  OpenMDBitSet HullFinder::findHull() {
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    OpenMDBitSet bsResult(nStuntDoubles_);
#ifdef HAVE_QHULL
    surfaceMesh_->computeHull(localSites_);
#else
    sprintf( painCave.errMsg,
             "HullFinder : Hull calculation is not possible without libqhull.\n"
             "\tPlease rebuild OpenMD with qhull enabled.");
    painCave.severity = OPENMD_ERROR;
    painCave.isFatal = 1;
    simError();
#endif
    
    std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
    int nTriangles = sMesh.size();
    // Loop over the mesh faces
    std::vector<Triangle>::iterator face;
    std::vector<StuntDouble*>::iterator vertex;

    // This will work in parallel because the triangles returned by the mesh
    // have a NULL stuntDouble if this processor doesn't own the 
    
    for (face = sMesh.begin(); face != sMesh.end(); ++face) {
      Triangle thisTriangle = *face;
      std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
        if ((*vertex) != NULL) {
          bsResult.setBitOn((*vertex)->getGlobalIndex());          
        }
      }
    }
    return bsResult;
  }

  OpenMDBitSet HullFinder::findHull(int frame) {
    Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
    OpenMDBitSet bsResult(nStuntDoubles_);
#ifdef HAVE_QHULL
    surfaceMesh_->computeHull(localSites_);
#else
    sprintf( painCave.errMsg,
             "HullFinder : Hull calculation is not possible without libqhull.\n"
             "\tPlease rebuild OpenMD with qhull enabled.");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
#endif
    
    std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
    int nTriangles = sMesh.size();
    // Loop over the mesh faces
    std::vector<Triangle>::iterator face;
    std::vector<StuntDouble*>::iterator vertex;

    // This will work in parallel because the triangles returned by the mesh
    // have a NULL stuntDouble if this processor doesn't own the 
    
    for (face = sMesh.begin(); face != sMesh.end(); ++face) {
      Triangle thisTriangle = *face;
      std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
        if ((*vertex) != NULL) {
          bsResult.setBitOn((*vertex)->getGlobalIndex());          
        }
      }
    }
    return bsResult;
  }

}
Revision:	1867
Committed:	Mon Apr 29 17:53:48 2013 UTC (12 years ago) by gezelter
File size:	6144 byte(s)
Log Message:	Attempt to fix memory leak in Multiple hull calls
#	User	Rev	Content
1	gezelter	1412	/*
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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	1412	*/
42
43			#include "selection/HullFinder.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "math/ConvexHull.hpp"
46
47			namespace OpenMD {
48
49			HullFinder::HullFinder(SimInfo* info) : info_(info) {
50
51			nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
52			stuntdoubles_.resize(nStuntDoubles_);
53
54			SimInfo::MoleculeIterator mi;
55			Molecule* mol;
56	gezelter	1769	StuntDouble* sd;
57	gezelter	1412	Molecule::IntegrableObjectIterator ioi;
58			Molecule::AtomIterator ai;
59			Atom* atom;
60			Molecule::RigidBodyIterator rbIter;
61			RigidBody* rb;
62
63			for (mol = info_->beginMolecule(mi); mol != NULL;
64			mol = info_->nextMolecule(mi)) {
65
66			// Hull is constructed from all known integrable objects.
67	gezelter	1769	for (sd = mol->beginIntegrableObject(ioi);
68			sd != NULL;
69			sd = mol->nextIntegrableObject(ioi)) {
70			localSites_.push_back(sd);
71	gezelter	1412	}
72
73			// selection can include atoms (which may be a subset of the IOs)
74			for(atom = mol->beginAtom(ai); atom != NULL;
75			atom = mol->nextAtom(ai)) {
76			stuntdoubles_[atom->getGlobalIndex()] = atom;
77			}
78
79			// and rigid bodies
80			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
81			rb = mol->nextRigidBody(rbIter)) {
82			stuntdoubles_[rb->getGlobalIndex()] = rb;
83			}
84
85	chuckv	1438	}
86			#ifdef HAVE_QHULL
87			surfaceMesh_ = new ConvexHull();
88	chuckv	1439	#endif
89			}
90
91	gezelter	1867	HullFinder::~HullFinder() {
92			delete surfaceMesh_;
93			}
94
95	chuckv	1439	OpenMDBitSet HullFinder::findHull() {
96			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
97			OpenMDBitSet bsResult(nStuntDoubles_);
98			#ifdef HAVE_QHULL
99			surfaceMesh_->computeHull(localSites_);
100	chuckv	1438	#else
101			sprintf( painCave.errMsg,
102	gezelter	1618	"HullFinder : Hull calculation is not possible without libqhull.\n"
103			"\tPlease rebuild OpenMD with qhull enabled.");
104	gezelter	1866	painCave.severity = OPENMD_ERROR;
105			painCave.isFatal = 1;
106			simError();
107	chuckv	1438	#endif
108	chuckv	1439
109	gezelter	1412	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
110			int nTriangles = sMesh.size();
111			// Loop over the mesh faces
112			std::vector<Triangle>::iterator face;
113			std::vector<StuntDouble*>::iterator vertex;
114
115	gezelter	1803	// This will work in parallel because the triangles returned by the mesh
116			// have a NULL stuntDouble if this processor doesn't own the
117
118	gezelter	1412	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
119			Triangle thisTriangle = *face;
120			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
121			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
122			if ((*vertex) != NULL) {
123			bsResult.setBitOn((*vertex)->getGlobalIndex());
124			}
125			}
126			}
127			return bsResult;
128			}
129
130	gezelter	1831	OpenMDBitSet HullFinder::findHull(int frame) {
131			Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
132			OpenMDBitSet bsResult(nStuntDoubles_);
133			#ifdef HAVE_QHULL
134			surfaceMesh_->computeHull(localSites_);
135			#else
136			sprintf( painCave.errMsg,
137			"HullFinder : Hull calculation is not possible without libqhull.\n"
138			"\tPlease rebuild OpenMD with qhull enabled.");
139			painCave.severity = OPENMD_ERROR;
140			painCave.isFatal = 1;
141			simError();
142			#endif
143
144			std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
145			int nTriangles = sMesh.size();
146			// Loop over the mesh faces
147			std::vector<Triangle>::iterator face;
148			std::vector<StuntDouble*>::iterator vertex;
149
150			// This will work in parallel because the triangles returned by the mesh
151			// have a NULL stuntDouble if this processor doesn't own the
152
153			for (face = sMesh.begin(); face != sMesh.end(); ++face) {
154			Triangle thisTriangle = *face;
155			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
156			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
157			if ((*vertex) != NULL) {
158			bsResult.setBitOn((*vertex)->getGlobalIndex());
159			}
160			}
161			}
162			return bsResult;
163			}
164
165	gezelter	1412	}