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() {
    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();
    // 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) {
    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();
    // 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());          
        }
      }
    }
    surfaceArea_ = surfaceMesh_->getArea();
    return bsResult;
  }

}
Revision:	1903
Committed:	Tue Jul 16 18:58:08 2013 UTC (11 years, 9 months ago) by gezelter
File size:	5960 byte(s)
Log Message:	Test to see if we can eliminate a bug in MPI runs involving RNEMD.
#	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, 234107 (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/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	StuntDouble* sd;
57	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	for (sd = mol->beginIntegrableObject(ioi);
68	sd != NULL;
69	sd = mol->nextIntegrableObject(ioi)) {
70	localSites_.push_back(sd);
71	}
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	}
86	#ifdef HAVE_QHULL
87	surfaceMesh_ = new ConvexHull();
88	#endif
89	}
90
91	HullFinder::~HullFinder() {
92	delete surfaceMesh_;
93	}
94
95	OpenMDBitSet HullFinder::findHull() {
96	OpenMDBitSet bsResult(nStuntDoubles_);
97	#ifdef HAVE_QHULL
98	surfaceMesh_->computeHull(localSites_);
99	#else
100	sprintf( painCave.errMsg,
101	"HullFinder : Hull calculation is not possible without libqhull.\n"
102	"\tPlease rebuild OpenMD with qhull enabled.");
103	painCave.severity = OPENMD_ERROR;
104	painCave.isFatal = 1;
105	simError();
106	#endif
107
108	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
109	// Loop over the mesh faces
110	std::vector<Triangle>::iterator face;
111	std::vector<StuntDouble*>::iterator vertex;
112
113	// This will work in parallel because the triangles returned by the mesh
114	// have a NULL stuntDouble if this processor doesn't own the
115
116	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
117	Triangle thisTriangle = *face;
118	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
119	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
120	if ((*vertex) != NULL) {
121	bsResult.setBitOn((*vertex)->getGlobalIndex());
122	}
123	}
124	}
125	return bsResult;
126	}
127
128	OpenMDBitSet HullFinder::findHull(int frame) {
129	OpenMDBitSet bsResult(nStuntDoubles_);
130	#ifdef HAVE_QHULL
131	surfaceMesh_->computeHull(localSites_);
132	#else
133	sprintf( painCave.errMsg,
134	"HullFinder : Hull calculation is not possible without libqhull.\n"
135	"\tPlease rebuild OpenMD with qhull enabled.");
136	painCave.severity = OPENMD_ERROR;
137	painCave.isFatal = 1;
138	simError();
139	#endif
140
141	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
142	// Loop over the mesh faces
143	std::vector<Triangle>::iterator face;
144	std::vector<StuntDouble*>::iterator vertex;
145
146	// This will work in parallel because the triangles returned by the mesh
147	// have a NULL stuntDouble if this processor doesn't own the
148
149	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
150	Triangle thisTriangle = *face;
151	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
152	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
153	if ((*vertex) != NULL) {
154	bsResult.setBitOn((*vertex)->getGlobalIndex());
155	}
156	}
157	}
158	surfaceArea_ = surfaceMesh_->getArea();
159	return bsResult;
160	}
161
162	}