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());
    nObjects_.push_back(info_->getNGlobalMolecules());

    stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
    bonds_.resize(nObjects_[BOND]);
    bends_.resize(nObjects_[BEND]);
    torsions_.resize(nObjects_[TORSION]);
    inversions_.resize(nObjects_[INVERSION]);
    molecules_.resize(nObjects_[MOLECULE]);
    
    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)) {

      molecules_[mol->getGlobalIndex()] = mol;
      
      // 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:	2052
Committed:	Fri Jan 9 19:06:35 2015 UTC (10 years, 3 months ago) by gezelter
File size:	7548 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	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	gezelter	2052	nObjects_.push_back(info_->getNGlobalMolecules());
57	gezelter	1953
58			stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
59			bonds_.resize(nObjects_[BOND]);
60			bends_.resize(nObjects_[BEND]);
61			torsions_.resize(nObjects_[TORSION]);
62			inversions_.resize(nObjects_[INVERSION]);
63	gezelter	2052	molecules_.resize(nObjects_[MOLECULE]);
64	gezelter	1412
65			SimInfo::MoleculeIterator mi;
66	gezelter	1953	Molecule::IntegrableObjectIterator ioi;
67			Molecule::AtomIterator ai;
68			Molecule::RigidBodyIterator rbIter;
69			Molecule::BondIterator bondIter;
70			Molecule::BendIterator bendIter;
71			Molecule::TorsionIterator torsionIter;
72			Molecule::InversionIterator inversionIter;
73
74	gezelter	1412	Molecule* mol;
75	gezelter	1782	StuntDouble* sd;
76	gezelter	1412	Atom* atom;
77			RigidBody* rb;
78	gezelter	1953	Bond* bond;
79			Bend* bend;
80			Torsion* torsion;
81			Inversion* inversion;
82
83	gezelter	1412	for (mol = info_->beginMolecule(mi); mol != NULL;
84			mol = info_->nextMolecule(mi)) {
85	gezelter	2052
86			molecules_[mol->getGlobalIndex()] = mol;
87
88	gezelter	1412	// Hull is constructed from all known integrable objects.
89	gezelter	1782	for (sd = mol->beginIntegrableObject(ioi);
90			sd != NULL;
91			sd = mol->nextIntegrableObject(ioi)) {
92			localSites_.push_back(sd);
93	gezelter	1412	}
94
95			// selection can include atoms (which may be a subset of the IOs)
96			for(atom = mol->beginAtom(ai); atom != NULL;
97			atom = mol->nextAtom(ai)) {
98			stuntdoubles_[atom->getGlobalIndex()] = atom;
99			}
100
101			// and rigid bodies
102			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
103			rb = mol->nextRigidBody(rbIter)) {
104			stuntdoubles_[rb->getGlobalIndex()] = rb;
105			}
106	gezelter	1953
107			// These others are going to be inferred from the objects on the hull:
108			for (bond = mol->beginBond(bondIter); bond != NULL;
109			bond = mol->nextBond(bondIter)) {
110			bonds_[bond->getGlobalIndex()] = bond;
111			}
112			for (bend = mol->beginBend(bendIter); bend != NULL;
113			bend = mol->nextBend(bendIter)) {
114			bends_[bend->getGlobalIndex()] = bend;
115			}
116			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
117			torsion = mol->nextTorsion(torsionIter)) {
118			torsions_[torsion->getGlobalIndex()] = torsion;
119			}
120			for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
121			inversion = mol->nextInversion(inversionIter)) {
122			inversions_[inversion->getGlobalIndex()] = inversion;
123			}
124
125	chuckv	1438	}
126			#ifdef HAVE_QHULL
127			surfaceMesh_ = new ConvexHull();
128	chuckv	1439	#endif
129			}
130
131	gezelter	1879	HullFinder::~HullFinder() {
132			delete surfaceMesh_;
133			}
134
135	gezelter	1953	SelectionSet HullFinder::findHull() {
136			SelectionSet ssResult(nObjects_);
137	chuckv	1439	#ifdef HAVE_QHULL
138			surfaceMesh_->computeHull(localSites_);
139	chuckv	1438	#else
140			sprintf( painCave.errMsg,
141	gezelter	1782	"HullFinder : Hull calculation is not possible without libqhull.\n"
142			"\tPlease rebuild OpenMD with qhull enabled.");
143	gezelter	1879	painCave.severity = OPENMD_ERROR;
144			painCave.isFatal = 1;
145			simError();
146	chuckv	1438	#endif
147	chuckv	1439
148	gezelter	1412	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
149			// Loop over the mesh faces
150			std::vector<Triangle>::iterator face;
151			std::vector<StuntDouble*>::iterator vertex;
152
153	gezelter	1801	// This will work in parallel because the triangles returned by the mesh
154			// have a NULL stuntDouble if this processor doesn't own the
155
156	gezelter	1412	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
157			Triangle thisTriangle = *face;
158			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
159			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
160			if ((*vertex) != NULL) {
161	gezelter	1953	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
162	gezelter	1412	}
163			}
164			}
165	gezelter	1953	return ssResult;
166	gezelter	1412	}
167
168	gezelter	1953	SelectionSet HullFinder::findHull(int frame) {
169			SelectionSet ssResult(nObjects_);
170	gezelter	1816	#ifdef HAVE_QHULL
171			surfaceMesh_->computeHull(localSites_);
172			#else
173			sprintf( painCave.errMsg,
174			"HullFinder : Hull calculation is not possible without libqhull.\n"
175			"\tPlease rebuild OpenMD with qhull enabled.");
176			painCave.severity = OPENMD_ERROR;
177			painCave.isFatal = 1;
178			simError();
179			#endif
180
181			std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
182			// Loop over the mesh faces
183			std::vector<Triangle>::iterator face;
184			std::vector<StuntDouble*>::iterator vertex;
185
186			// This will work in parallel because the triangles returned by the mesh
187			// have a NULL stuntDouble if this processor doesn't own the
188
189			for (face = sMesh.begin(); face != sMesh.end(); ++face) {
190			Triangle thisTriangle = *face;
191			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
192			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
193			if ((*vertex) != NULL) {
194	gezelter	1953	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
195	gezelter	1816	}
196			}
197			}
198	gezelter	1903	surfaceArea_ = surfaceMesh_->getArea();
199	gezelter	1953	return ssResult;
200	gezelter	1816	}
201
202	gezelter	1412	}