applications/nanoRodBuilder/GeometryBuilder.cpp

/*
 *  GeometryBuilder.cpp
 *  nanorodBuilder
 *
 *  Created by Charles Vardeman II on 4/4/05.
 *  Copyright 2005 University of Notre Dame. All rights reserved.
 *
 */

/*
 * 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
                                                                                                                                                                                                                        *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
                                                                                                                                                                                                                        *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
                                                                                                                                                                                                                        *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#include "GeometryBuilder.hpp"

#include <CGAL/Simple_cartesian.h>
#include <CGAL/Polyhedron_incremental_builder_3.h>
#include <CGAL/Polyhedron_3.h>
#include <CGAL/Homogeneous.h>
#include <CGAL/Polyhedron_traits_with_normals_3.h>
#include <CGAL/Polyhedron_3.h>
#include <CGAL/Aff_transformation_3.h>
#include <CGAL/aff_transformation_tags.h>
#include <iostream>
#include <algorithm>

using namespace oopse;

//typedef CGAL::Homogeneous<int>              Kernel;
typedef CGAL::Simple_cartesian<double>     Kernel;
//typedef CGAL::Polyhedron_3<Kernel>         Polyhedron;

typedef Kernel::Point_3                    Point_3;
typedef Kernel::Vector_3                               Vector_3;
typedef CGAL::Polyhedron_traits_with_normals_3<Kernel> Traits;
//typedef CGAL::Polyhedron_3<Kernel>                     Polyhedron;
typedef CGAL::Polyhedron_3<Traits>                     Polyhedron;
typedef Polyhedron::HalfedgeDS             HalfedgeDS;
typedef Polyhedron::Facet_iterator                   Facet_iterator;
typedef Polyhedron::Halfedge_around_facet_circulator Halfedge_facet_circulator;
typedef Polyhedron::Facet_iterator Facet_iterator;
typedef Polyhedron::Plane_iterator Plane_iterator;
typedef Polyhedron::Vertex_handle Vertex_handle;

Polyhedron nanoRodPolyhedron;


//typedef CGAL::Scaling Scaling;
//typedef Aff_transformation_3<Kernel> A;( const Scaling,
//                                                                                                                              Kernel::RT s=RT(20),
//                                                                                                                              Kernel::RT hw = RT(1));

// A modifier creating a triangle with the incremental builder.
template <class HDS>
class Build_nanorod : public CGAL::Modifier_base<HDS> {
public:
  Vertex_handle end1;
  Vertex_handle neight1;
                Vertex_handle end2;
  Vertex_handle neight2;
  
  Build_nanorod() {}
  void operator()( HDS& hds) {
    // Postcondition: `hds' is a valid polyhedral surface.
    CGAL::Polyhedron_incremental_builder_3<HDS> B( hds, true);
    B.begin_surface( 12, 15, 6);
    typedef typename HDS::Vertex   Vertex;
    typedef typename Vertex::Point Point;
    
    
    B.add_vertex( Point(-0.7887222926324,    0.4874571845315, -0.2562714077342));
    B.add_vertex( Point(-0.4874571845316,    0.4874571845315,  0.6709272557930));
    B.add_vertex( Point(-0.7887222926324,   -0.4874571845315, -0.2562714077342)); //End vertex
    end1 = B.add_vertex( Point( 0.0000000000000,    1.0000000000000,  0.0000000000000));
    B.add_vertex( Point(-0.4874571845315,    -0.4874571845316,  0.6709272557930));
    neight1 = B.add_vertex( Point(-0.0000000000000,    0.4874571845316, -0.8293116961175));
    B.add_vertex( Point( 0.0000000000000,    -0.4874571845316, -0.8293116961175));
    B.add_vertex( Point( 0.4874571845315,    0.4874571845316,  0.6709272557930));
    end2 = B.add_vertex( Point(-0.0000000000000,    -1.0000000000000,  0.0000000000000)); //End Vertex
    B.add_vertex( Point( 0.7887222926324,    0.4874571845315, -0.2562714077342));
    neight2 = B.add_vertex( Point( 0.4874571845316,    -0.4874571845315,  0.6709272557930));
    B.add_vertex( Point( 0.7887222926324,    -0.4874571845315, -0.2562714077342));
    
    B.begin_facet();
    B.add_vertex_to_facet( 7);
    B.add_vertex_to_facet( 9);
    B.add_vertex_to_facet( 11);
    B.add_vertex_to_facet( 10);
    B.end_facet();
                                
    B.begin_facet();
    B.add_vertex_to_facet( 8);
    B.add_vertex_to_facet( 10);
    B.add_vertex_to_facet( 11);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 3);
    B.add_vertex_to_facet( 9);
    B.add_vertex_to_facet( 7);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 9);
    B.add_vertex_to_facet( 5);
    B.add_vertex_to_facet( 6);
    B.add_vertex_to_facet( 11);
    B.end_facet();
                                
    B.begin_facet();
    B.add_vertex_to_facet( 8);
    B.add_vertex_to_facet( 11);
    B.add_vertex_to_facet( 6);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 3);
    B.add_vertex_to_facet( 5);
    B.add_vertex_to_facet( 9);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 5);
    B.add_vertex_to_facet( 0);
    B.add_vertex_to_facet( 2);
    B.add_vertex_to_facet( 6);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 8);
    B.add_vertex_to_facet( 6);
    B.add_vertex_to_facet( 2);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 3);
    B.add_vertex_to_facet( 0);
    B.add_vertex_to_facet( 5);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 0);
    B.add_vertex_to_facet( 1);
    B.add_vertex_to_facet( 4);
    B.add_vertex_to_facet( 2);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 8);
    B.add_vertex_to_facet( 2);
    B.add_vertex_to_facet( 4);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 3);
    B.add_vertex_to_facet( 1);
    B.add_vertex_to_facet( 0);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 1);
    B.add_vertex_to_facet( 7);
    B.add_vertex_to_facet( 10);
    B.add_vertex_to_facet( 4);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 8);
    B.add_vertex_to_facet( 4);
    B.add_vertex_to_facet( 10);
    B.end_facet();
    
    B.begin_facet();
    B.add_vertex_to_facet( 3);
    B.add_vertex_to_facet( 7);
    B.add_vertex_to_facet( 1);
    B.end_facet();
    
                                
    B.end_surface();
  }
};


struct Normal_vector {
  template <class Facet>
  typename Facet::Plane_3 operator()( Facet& f) {
    typename Facet::Halfedge_handle h = f.halfedge();
    // Facet::Plane_3 is the normal vector type. We assume the
    // CGAL Kernel here and use its global functions.
    return CGAL::cross_product( 
                               h->next()->vertex()->point() - h->vertex()->point(),
                               h->next()->next()->vertex()->point() - h->next()->vertex()->point());
  }
};


bool GeometryBuilder::isInsidePolyhedron(double x, double y, double z) {
        
        Point_3 point(x,y,z);
  Plane_iterator i;
  Facet_iterator j;
  for ( i =nanoRodPolyhedron.planes_begin(), j = nanoRodPolyhedron.facets_begin(); i != nanoRodPolyhedron.planes_end() && j !=nanoRodPolyhedron.facets_end(); ++i, ++j) {
    Halfedge_facet_circulator k = j->facet_begin();
    
    Vector_3 newVector = point - k->vertex()->point();
    Vector_3 normal = *i;               
    double dot_product = newVector.x() * normal.x() + newVector.y() * normal.y() + newVector.z() * normal.z();
    
    if (dot_product < 0) {
      return false;     
    }
  }
  
  return true;
}


GeometryBuilder::GeometryBuilder(double length,double width) {
// Create the geometry for nanorod
  Build_nanorod<HalfedgeDS> nanorod;
  
  nanoRodPolyhedron.delegate( nanorod);
   
        double y1 = nanorod.end1->point().y() - nanorod.neight1->point().y();
        double y2 = nanorod.end2->point().y() - nanorod.neight2->point().y();
        
        CGAL::Aff_transformation_3<Kernel> aff_tranformation( width,
                                                                                                                                                                                                                                0.0,
                                                                                                                                                                                                                                0.0,
                                                                                                                                                                                                                                0.0,
                                                                                                                                                                                                                                0.0,
                                                                                                                                                                                                                                length,
                                                                                                                                                                                                                                0.0,
                                                                                                                                                                                                                                0.0,
                                                                                                                                                                                                                                0.0,
                                                                                                                                                                                                                                0.0,
                                                                                                                                                                                                                                width,
                                                                                                                                                                                                                                0.0);   
        std::transform( nanoRodPolyhedron.points_begin(), nanoRodPolyhedron.points_end(), nanoRodPolyhedron.points_begin(), aff_tranformation);
        
        Point_3 point1(nanorod.end1->point().x(), y1 + nanorod.neight1->point().y(), nanorod.end1->point().z());
        Point_3 point2(nanorod.end2->point().x(), y2+ nanorod.neight2->point().y(), nanorod.end2->point().z());
        nanorod.end1->point() = point1;
        nanorod.end2->point() = point2;
        
        // Construct normal vector for each face.
        std::transform( nanoRodPolyhedron.facets_begin(), nanoRodPolyhedron.facets_end(), nanoRodPolyhedron.planes_begin(),
                                                                        Normal_vector());
        
  
}

Revision:	2164
Committed:	Mon Apr 11 21:37:30 2005 UTC (19 years, 2 months ago) by chuckv
File size:	10133 byte(s)
Log Message:	Importing nanoRodBuilder application (may not work yet). ((Doesn't work yet.)) (((May never work....)))
#	User	Rev	Content
1	chuckv	2164	/*
2			* GeometryBuilder.cpp
3			* nanorodBuilder
4			*
5			* Created by Charles Vardeman II on 4/4/05.
6			* Copyright 2005 University of Notre Dame. All rights reserved.
7			*
8			*/
9
10			/*
11			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
12			*
13			* The University of Notre Dame grants you ("Licensee") a
14			* non-exclusive, royalty free, license to use, modify and
15			* redistribute this software in source and binary code form, provided
16			* that the following conditions are met:
17			*
18			* 1. Acknowledgement of the program authors must be made in any
19			* publication of scientific results based in part on use of the
20			* program. An acceptable form of acknowledgement is citation of
21			* the article in which the program was described (Matthew
22			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
23			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
24			* Parallel Simulation Engine for Molecular Dynamics,"
25			* J. Comput. Chem. 26, pp. 252-271 (2005))
26			*
27			* 2. Redistributions of source code must retain the above copyright
28			* notice, this list of conditions and the following disclaimer.
29			*
30			* 3. Redistributions in binary form must reproduce the above copyright
31			* notice, this list of conditions and the following disclaimer in the
32			* documentation and/or other materials provided with the
33			* distribution.
34			*
35			* This software is provided "AS IS," without a warranty of any
36			* kind. All express or implied conditions, representations and
37			* warranties, including any implied warranty of merchantability,
38			* fitness for a particular purpose or non-infringement, are hereby
39			* excluded. The University of Notre Dame and its licensors shall not
40			* be liable for any damages suffered by licensee as a result of
41			* using, modifying or distributing the software or its
42			* derivatives. In no event will the University of Notre Dame or its
43			* licensors be liable for any lost revenue, profit or data, or for
44			* direct, indirect, special, consequential, incidental or punitive
45			* damages, however caused and regardless of the theory of liability,
46			* arising out of the use of or inability to use software, even if the
47			* University of Notre Dame has been advised of the possibility of
48			* such damages.
49			*/
50
51			#include "GeometryBuilder.hpp"
52
53			#include <CGAL/Simple_cartesian.h>
54			#include <CGAL/Polyhedron_incremental_builder_3.h>
55			#include <CGAL/Polyhedron_3.h>
56			#include <CGAL/Homogeneous.h>
57			#include <CGAL/Polyhedron_traits_with_normals_3.h>
58			#include <CGAL/Polyhedron_3.h>
59			#include <CGAL/Aff_transformation_3.h>
60			#include <CGAL/aff_transformation_tags.h>
61			#include <iostream>
62			#include <algorithm>
63
64			using namespace oopse;
65
66			//typedef CGAL::Homogeneous<int> Kernel;
67			typedef CGAL::Simple_cartesian<double> Kernel;
68			//typedef CGAL::Polyhedron_3<Kernel> Polyhedron;
69
70			typedef Kernel::Point_3 Point_3;
71			typedef Kernel::Vector_3 Vector_3;
72			typedef CGAL::Polyhedron_traits_with_normals_3<Kernel> Traits;
73			//typedef CGAL::Polyhedron_3<Kernel> Polyhedron;
74			typedef CGAL::Polyhedron_3<Traits> Polyhedron;
75			typedef Polyhedron::HalfedgeDS HalfedgeDS;
76			typedef Polyhedron::Facet_iterator Facet_iterator;
77			typedef Polyhedron::Halfedge_around_facet_circulator Halfedge_facet_circulator;
78			typedef Polyhedron::Facet_iterator Facet_iterator;
79			typedef Polyhedron::Plane_iterator Plane_iterator;
80			typedef Polyhedron::Vertex_handle Vertex_handle;
81
82			Polyhedron nanoRodPolyhedron;
83
84
85
86
87
88
89
90			//typedef CGAL::Scaling Scaling;
91			//typedef Aff_transformation_3<Kernel> A;( const Scaling,
92			// Kernel::RT s=RT(20),
93			// Kernel::RT hw = RT(1));
94
95			// A modifier creating a triangle with the incremental builder.
96			template <class HDS>
97			class Build_nanorod : public CGAL::Modifier_base<HDS> {
98			public:
99			Vertex_handle end1;
100			Vertex_handle neight1;
101			Vertex_handle end2;
102			Vertex_handle neight2;
103
104			Build_nanorod() {}
105			void operator()( HDS& hds) {
106			// Postcondition: `hds' is a valid polyhedral surface.
107			CGAL::Polyhedron_incremental_builder_3<HDS> B( hds, true);
108			B.begin_surface( 12, 15, 6);
109			typedef typename HDS::Vertex Vertex;
110			typedef typename Vertex::Point Point;
111
112
113
114
115
116			B.add_vertex( Point(-0.7887222926324, 0.4874571845315, -0.2562714077342));
117			B.add_vertex( Point(-0.4874571845316, 0.4874571845315, 0.6709272557930));
118			B.add_vertex( Point(-0.7887222926324, -0.4874571845315, -0.2562714077342)); //End vertex
119			end1 = B.add_vertex( Point( 0.0000000000000, 1.0000000000000, 0.0000000000000));
120			B.add_vertex( Point(-0.4874571845315, -0.4874571845316, 0.6709272557930));
121			neight1 = B.add_vertex( Point(-0.0000000000000, 0.4874571845316, -0.8293116961175));
122			B.add_vertex( Point( 0.0000000000000, -0.4874571845316, -0.8293116961175));
123			B.add_vertex( Point( 0.4874571845315, 0.4874571845316, 0.6709272557930));
124			end2 = B.add_vertex( Point(-0.0000000000000, -1.0000000000000, 0.0000000000000)); //End Vertex
125			B.add_vertex( Point( 0.7887222926324, 0.4874571845315, -0.2562714077342));
126			neight2 = B.add_vertex( Point( 0.4874571845316, -0.4874571845315, 0.6709272557930));
127			B.add_vertex( Point( 0.7887222926324, -0.4874571845315, -0.2562714077342));
128
129			B.begin_facet();
130			B.add_vertex_to_facet( 7);
131			B.add_vertex_to_facet( 9);
132			B.add_vertex_to_facet( 11);
133			B.add_vertex_to_facet( 10);
134			B.end_facet();
135
136			B.begin_facet();
137			B.add_vertex_to_facet( 8);
138			B.add_vertex_to_facet( 10);
139			B.add_vertex_to_facet( 11);
140			B.end_facet();
141
142			B.begin_facet();
143			B.add_vertex_to_facet( 3);
144			B.add_vertex_to_facet( 9);
145			B.add_vertex_to_facet( 7);
146			B.end_facet();
147
148			B.begin_facet();
149			B.add_vertex_to_facet( 9);
150			B.add_vertex_to_facet( 5);
151			B.add_vertex_to_facet( 6);
152			B.add_vertex_to_facet( 11);
153			B.end_facet();
154
155			B.begin_facet();
156			B.add_vertex_to_facet( 8);
157			B.add_vertex_to_facet( 11);
158			B.add_vertex_to_facet( 6);
159			B.end_facet();
160
161			B.begin_facet();
162			B.add_vertex_to_facet( 3);
163			B.add_vertex_to_facet( 5);
164			B.add_vertex_to_facet( 9);
165			B.end_facet();
166
167			B.begin_facet();
168			B.add_vertex_to_facet( 5);
169			B.add_vertex_to_facet( 0);
170			B.add_vertex_to_facet( 2);
171			B.add_vertex_to_facet( 6);
172			B.end_facet();
173
174			B.begin_facet();
175			B.add_vertex_to_facet( 8);
176			B.add_vertex_to_facet( 6);
177			B.add_vertex_to_facet( 2);
178			B.end_facet();
179
180			B.begin_facet();
181			B.add_vertex_to_facet( 3);
182			B.add_vertex_to_facet( 0);
183			B.add_vertex_to_facet( 5);
184			B.end_facet();
185
186			B.begin_facet();
187			B.add_vertex_to_facet( 0);
188			B.add_vertex_to_facet( 1);
189			B.add_vertex_to_facet( 4);
190			B.add_vertex_to_facet( 2);
191			B.end_facet();
192
193			B.begin_facet();
194			B.add_vertex_to_facet( 8);
195			B.add_vertex_to_facet( 2);
196			B.add_vertex_to_facet( 4);
197			B.end_facet();
198
199			B.begin_facet();
200			B.add_vertex_to_facet( 3);
201			B.add_vertex_to_facet( 1);
202			B.add_vertex_to_facet( 0);
203			B.end_facet();
204
205			B.begin_facet();
206			B.add_vertex_to_facet( 1);
207			B.add_vertex_to_facet( 7);
208			B.add_vertex_to_facet( 10);
209			B.add_vertex_to_facet( 4);
210			B.end_facet();
211
212			B.begin_facet();
213			B.add_vertex_to_facet( 8);
214			B.add_vertex_to_facet( 4);
215			B.add_vertex_to_facet( 10);
216			B.end_facet();
217
218			B.begin_facet();
219			B.add_vertex_to_facet( 3);
220			B.add_vertex_to_facet( 7);
221			B.add_vertex_to_facet( 1);
222			B.end_facet();
223
224
225			B.end_surface();
226			}
227			};
228
229
230
231			struct Normal_vector {
232			template <class Facet>
233			typename Facet::Plane_3 operator()( Facet& f) {
234			typename Facet::Halfedge_handle h = f.halfedge();
235			// Facet::Plane_3 is the normal vector type. We assume the
236			// CGAL Kernel here and use its global functions.
237			return CGAL::cross_product(
238			h->next()->vertex()->point() - h->vertex()->point(),
239			h->next()->next()->vertex()->point() - h->next()->vertex()->point());
240			}
241			};
242
243
244			bool GeometryBuilder::isInsidePolyhedron(double x, double y, double z) {
245
246			Point_3 point(x,y,z);
247			Plane_iterator i;
248			Facet_iterator j;
249			for ( i =nanoRodPolyhedron.planes_begin(), j = nanoRodPolyhedron.facets_begin(); i != nanoRodPolyhedron.planes_end() && j !=nanoRodPolyhedron.facets_end(); ++i, ++j) {
250			Halfedge_facet_circulator k = j->facet_begin();
251
252			Vector_3 newVector = point - k->vertex()->point();
253			Vector_3 normal = *i;
254			double dot_product = newVector.x() * normal.x() + newVector.y() * normal.y() + newVector.z() * normal.z();
255
256			if (dot_product < 0) {
257			return false;
258			}
259			}
260
261			return true;
262			}
263
264
265			GeometryBuilder::GeometryBuilder(double length,double width) {
266			// Create the geometry for nanorod
267			Build_nanorod<HalfedgeDS> nanorod;
268
269			nanoRodPolyhedron.delegate( nanorod);
270
271			double y1 = nanorod.end1->point().y() - nanorod.neight1->point().y();
272			double y2 = nanorod.end2->point().y() - nanorod.neight2->point().y();
273
274			CGAL::Aff_transformation_3<Kernel> aff_tranformation( width,
275			0.0,
276			0.0,
277			0.0,
278			0.0,
279			length,
280			0.0,
281			0.0,
282			0.0,
283			0.0,
284			width,
285			0.0);
286			std::transform( nanoRodPolyhedron.points_begin(), nanoRodPolyhedron.points_end(), nanoRodPolyhedron.points_begin(), aff_tranformation);
287
288			Point_3 point1(nanorod.end1->point().x(), y1 + nanorod.neight1->point().y(), nanorod.end1->point().z());
289			Point_3 point2(nanorod.end2->point().x(), y2+ nanorod.neight2->point().y(), nanorod.end2->point().z());
290			nanorod.end1->point() = point1;
291			nanorod.end2->point() = point2;
292
293			// Construct normal vector for each face.
294			std::transform( nanoRodPolyhedron.facets_begin(), nanoRodPolyhedron.facets_end(), nanoRodPolyhedron.planes_begin(),
295			Normal_vector());
296
297
298
299			}
300