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) {

    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());

    stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
    bonds_.resize(nObjects_[BOND]);
    bends_.resize(nObjects_[BEND]);
    torsions_.resize(nObjects_[TORSION]);
    inversions_.resize(nObjects_[INVERSION]);
    
    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator ioi;
    Molecule::AtomIterator ai;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;
    Molecule::BendIterator bendIter;
    Molecule::TorsionIterator torsionIter;
    Molecule::InversionIterator inversionIter;
    
    Molecule* mol;
    StuntDouble* sd;
    Atom* atom;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;    

    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;
      }

      // These others are going to be inferred from the objects on the hull:
      for (bond = mol->beginBond(bondIter); bond != NULL; 
           bond = mol->nextBond(bondIter)) {
        bonds_[bond->getGlobalIndex()] = bond;
      }   
      for (bend = mol->beginBend(bendIter); bend != NULL; 
           bend = mol->nextBend(bendIter)) {
        bends_[bend->getGlobalIndex()] = bend;
      }   
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; 
           torsion = mol->nextTorsion(torsionIter)) {
        torsions_[torsion->getGlobalIndex()] = torsion;
      }   
      for (inversion = mol->beginInversion(inversionIter); inversion != NULL; 
           inversion = mol->nextInversion(inversionIter)) {
        inversions_[inversion->getGlobalIndex()] = inversion;
      }   

    }
#ifdef HAVE_QHULL
    surfaceMesh_ = new ConvexHull();
#endif
  }

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

  SelectionSet HullFinder::findHull() {
    SelectionSet ssResult(nObjects_);
#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) {
          ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
        }
      }
    }
    return ssResult;
  }

  SelectionSet HullFinder::findHull(int frame) {
    SelectionSet ssResult(nObjects_);
#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) {
          ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
        }
      }
    }
    surfaceArea_ = surfaceMesh_->getArea();
    return ssResult;
  }

}
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 5 months ago) by gezelter
File size:	7403 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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	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	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	gezelter	1953	nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
52			nObjects_.push_back(info_->getNGlobalBonds());
53			nObjects_.push_back(info_->getNGlobalBends());
54			nObjects_.push_back(info_->getNGlobalTorsions());
55			nObjects_.push_back(info_->getNGlobalInversions());
56
57			stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
58			bonds_.resize(nObjects_[BOND]);
59			bends_.resize(nObjects_[BEND]);
60			torsions_.resize(nObjects_[TORSION]);
61			inversions_.resize(nObjects_[INVERSION]);
62	gezelter	1412
63			SimInfo::MoleculeIterator mi;
64	gezelter	1953	Molecule::IntegrableObjectIterator ioi;
65			Molecule::AtomIterator ai;
66			Molecule::RigidBodyIterator rbIter;
67			Molecule::BondIterator bondIter;
68			Molecule::BendIterator bendIter;
69			Molecule::TorsionIterator torsionIter;
70			Molecule::InversionIterator inversionIter;
71
72	gezelter	1412	Molecule* mol;
73	gezelter	1782	StuntDouble* sd;
74	gezelter	1412	Atom* atom;
75			RigidBody* rb;
76	gezelter	1953	Bond* bond;
77			Bend* bend;
78			Torsion* torsion;
79			Inversion* inversion;
80
81	gezelter	1412	for (mol = info_->beginMolecule(mi); mol != NULL;
82			mol = info_->nextMolecule(mi)) {
83
84			// Hull is constructed from all known integrable objects.
85	gezelter	1782	for (sd = mol->beginIntegrableObject(ioi);
86			sd != NULL;
87			sd = mol->nextIntegrableObject(ioi)) {
88			localSites_.push_back(sd);
89	gezelter	1412	}
90
91			// selection can include atoms (which may be a subset of the IOs)
92			for(atom = mol->beginAtom(ai); atom != NULL;
93			atom = mol->nextAtom(ai)) {
94			stuntdoubles_[atom->getGlobalIndex()] = atom;
95			}
96
97			// and rigid bodies
98			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
99			rb = mol->nextRigidBody(rbIter)) {
100			stuntdoubles_[rb->getGlobalIndex()] = rb;
101			}
102	gezelter	1953
103			// These others are going to be inferred from the objects on the hull:
104			for (bond = mol->beginBond(bondIter); bond != NULL;
105			bond = mol->nextBond(bondIter)) {
106			bonds_[bond->getGlobalIndex()] = bond;
107			}
108			for (bend = mol->beginBend(bendIter); bend != NULL;
109			bend = mol->nextBend(bendIter)) {
110			bends_[bend->getGlobalIndex()] = bend;
111			}
112			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
113			torsion = mol->nextTorsion(torsionIter)) {
114			torsions_[torsion->getGlobalIndex()] = torsion;
115			}
116			for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
117			inversion = mol->nextInversion(inversionIter)) {
118			inversions_[inversion->getGlobalIndex()] = inversion;
119			}
120
121	chuckv	1438	}
122			#ifdef HAVE_QHULL
123			surfaceMesh_ = new ConvexHull();
124	chuckv	1439	#endif
125			}
126
127	gezelter	1879	HullFinder::~HullFinder() {
128			delete surfaceMesh_;
129			}
130
131	gezelter	1953	SelectionSet HullFinder::findHull() {
132			SelectionSet ssResult(nObjects_);
133	chuckv	1439	#ifdef HAVE_QHULL
134			surfaceMesh_->computeHull(localSites_);
135	chuckv	1438	#else
136			sprintf( painCave.errMsg,
137	gezelter	1782	"HullFinder : Hull calculation is not possible without libqhull.\n"
138			"\tPlease rebuild OpenMD with qhull enabled.");
139	gezelter	1879	painCave.severity = OPENMD_ERROR;
140			painCave.isFatal = 1;
141			simError();
142	chuckv	1438	#endif
143	chuckv	1439
144	gezelter	1412	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
145			// Loop over the mesh faces
146			std::vector<Triangle>::iterator face;
147			std::vector<StuntDouble*>::iterator vertex;
148
149	gezelter	1801	// This will work in parallel because the triangles returned by the mesh
150			// have a NULL stuntDouble if this processor doesn't own the
151
152	gezelter	1412	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
153			Triangle thisTriangle = *face;
154			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
155			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
156			if ((*vertex) != NULL) {
157	gezelter	1953	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
158	gezelter	1412	}
159			}
160			}
161	gezelter	1953	return ssResult;
162	gezelter	1412	}
163
164	gezelter	1953	SelectionSet HullFinder::findHull(int frame) {
165			SelectionSet ssResult(nObjects_);
166	gezelter	1816	#ifdef HAVE_QHULL
167			surfaceMesh_->computeHull(localSites_);
168			#else
169			sprintf( painCave.errMsg,
170			"HullFinder : Hull calculation is not possible without libqhull.\n"
171			"\tPlease rebuild OpenMD with qhull enabled.");
172			painCave.severity = OPENMD_ERROR;
173			painCave.isFatal = 1;
174			simError();
175			#endif
176
177			std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
178			// Loop over the mesh faces
179			std::vector<Triangle>::iterator face;
180			std::vector<StuntDouble*>::iterator vertex;
181
182			// This will work in parallel because the triangles returned by the mesh
183			// have a NULL stuntDouble if this processor doesn't own the
184
185			for (face = sMesh.begin(); face != sMesh.end(); ++face) {
186			Triangle thisTriangle = *face;
187			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
188			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
189			if ((*vertex) != NULL) {
190	gezelter	1953	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
191	gezelter	1816	}
192			}
193			}
194	gezelter	1903	surfaceArea_ = surfaceMesh_->getArea();
195	gezelter	1953	return ssResult;
196	gezelter	1816	}
197
198	gezelter	1412	}