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:
#	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	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	nObjects_.push_back(info_->getNGlobalMolecules());
57
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	molecules_.resize(nObjects_[MOLECULE]);
64
65	SimInfo::MoleculeIterator mi;
66	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	Molecule* mol;
75	StuntDouble* sd;
76	Atom* atom;
77	RigidBody* rb;
78	Bond* bond;
79	Bend* bend;
80	Torsion* torsion;
81	Inversion* inversion;
82
83	for (mol = info_->beginMolecule(mi); mol != NULL;
84	mol = info_->nextMolecule(mi)) {
85
86	molecules_[mol->getGlobalIndex()] = mol;
87
88	// Hull is constructed from all known integrable objects.
89	for (sd = mol->beginIntegrableObject(ioi);
90	sd != NULL;
91	sd = mol->nextIntegrableObject(ioi)) {
92	localSites_.push_back(sd);
93	}
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
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	}
126	#ifdef HAVE_QHULL
127	surfaceMesh_ = new ConvexHull();
128	#endif
129	}
130
131	HullFinder::~HullFinder() {
132	delete surfaceMesh_;
133	}
134
135	SelectionSet HullFinder::findHull() {
136	SelectionSet ssResult(nObjects_);
137	#ifdef HAVE_QHULL
138	surfaceMesh_->computeHull(localSites_);
139	#else
140	sprintf( painCave.errMsg,
141	"HullFinder : Hull calculation is not possible without libqhull.\n"
142	"\tPlease rebuild OpenMD with qhull enabled.");
143	painCave.severity = OPENMD_ERROR;
144	painCave.isFatal = 1;
145	simError();
146	#endif
147
148	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	// 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	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	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
162	}
163	}
164	}
165	return ssResult;
166	}
167
168	SelectionSet HullFinder::findHull(int frame) {
169	SelectionSet ssResult(nObjects_);
170	#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	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
195	}
196	}
197	}
198	surfaceArea_ = surfaceMesh_->getArea();
199	return ssResult;
200	}
201
202	}