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/* |
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* GeometryBuilder.cpp |
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* nanorodBuilder |
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* |
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* Created by Charles Vardeman II on 4/4/05. |
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* Copyright 2005 University of Notre Dame. All rights reserved. |
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* |
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*/ |
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|
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include "GeometryBuilder.hpp" |
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|
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#include <CGAL/Simple_cartesian.h> |
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#include <CGAL/Polyhedron_incremental_builder_3.h> |
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#include <CGAL/Polyhedron_3.h> |
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#include <CGAL/Homogeneous.h> |
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#include <CGAL/Polyhedron_traits_with_normals_3.h> |
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#include <CGAL/Polyhedron_3.h> |
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#include <CGAL/Aff_transformation_3.h> |
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#include <CGAL/aff_transformation_tags.h> |
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#include <iostream> |
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#include <algorithm> |
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|
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using namespace oopse; |
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|
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//typedef CGAL::Homogeneous<int> Kernel; |
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typedef CGAL::Simple_cartesian<double> Kernel; |
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//typedef CGAL::Polyhedron_3<Kernel> Polyhedron; |
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|
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typedef Kernel::Point_3 Point_3; |
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typedef Kernel::Vector_3 Vector_3; |
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typedef CGAL::Polyhedron_traits_with_normals_3<Kernel> Traits; |
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//typedef CGAL::Polyhedron_3<Kernel> Polyhedron; |
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typedef CGAL::Polyhedron_3<Traits> Polyhedron; |
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typedef Polyhedron::HalfedgeDS HalfedgeDS; |
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typedef Polyhedron::Facet_iterator Facet_iterator; |
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typedef Polyhedron::Halfedge_around_facet_circulator Halfedge_facet_circulator; |
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typedef Polyhedron::Facet_iterator Facet_iterator; |
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typedef Polyhedron::Plane_iterator Plane_iterator; |
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typedef Polyhedron::Vertex_handle Vertex_handle; |
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|
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Polyhedron nanoRodPolyhedron; |
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|
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|
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|
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|
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|
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|
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|
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//typedef CGAL::Scaling Scaling; |
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//typedef Aff_transformation_3<Kernel> A;( const Scaling, |
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// Kernel::RT s=RT(20), |
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// Kernel::RT hw = RT(1)); |
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|
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// A modifier creating a triangle with the incremental builder. |
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template <class HDS> |
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class Build_nanorod : public CGAL::Modifier_base<HDS> { |
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public: |
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Vertex_handle end1; |
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Vertex_handle neight1; |
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Vertex_handle end2; |
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Vertex_handle neight2; |
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|
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Build_nanorod() {} |
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void operator()( HDS& hds) { |
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// Postcondition: `hds' is a valid polyhedral surface. |
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CGAL::Polyhedron_incremental_builder_3<HDS> B( hds, true); |
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B.begin_surface( 12, 15, 6); |
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typedef typename HDS::Vertex Vertex; |
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typedef typename Vertex::Point Point; |
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B.add_vertex( Point(-0.7887222926324, 0.4874571845315, -0.2562714077342)); |
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B.add_vertex( Point(-0.4874571845316, 0.4874571845315, 0.6709272557930)); |
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B.add_vertex( Point(-0.7887222926324, -0.4874571845315, -0.2562714077342)); //End vertex |
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end1 = B.add_vertex( Point( 0.0000000000000, 1.0000000000000, 0.0000000000000)); |
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B.add_vertex( Point(-0.4874571845315, -0.4874571845316, 0.6709272557930)); |
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neight1 = B.add_vertex( Point(-0.0000000000000, 0.4874571845316, -0.8293116961175)); |
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B.add_vertex( Point( 0.0000000000000, -0.4874571845316, -0.8293116961175)); |
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B.add_vertex( Point( 0.4874571845315, 0.4874571845316, 0.6709272557930)); |
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end2 = B.add_vertex( Point(-0.0000000000000, -1.0000000000000, 0.0000000000000)); //End Vertex |
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B.add_vertex( Point( 0.7887222926324, 0.4874571845315, -0.2562714077342)); |
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neight2 = B.add_vertex( Point( 0.4874571845316, -0.4874571845315, 0.6709272557930)); |
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B.add_vertex( Point( 0.7887222926324, -0.4874571845315, -0.2562714077342)); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 7); |
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B.add_vertex_to_facet( 9); |
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B.add_vertex_to_facet( 11); |
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B.add_vertex_to_facet( 10); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 8); |
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B.add_vertex_to_facet( 10); |
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B.add_vertex_to_facet( 11); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 3); |
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B.add_vertex_to_facet( 9); |
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B.add_vertex_to_facet( 7); |
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B.end_facet(); |
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B.begin_facet(); |
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B.add_vertex_to_facet( 9); |
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B.add_vertex_to_facet( 5); |
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B.add_vertex_to_facet( 6); |
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B.add_vertex_to_facet( 11); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 8); |
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B.add_vertex_to_facet( 11); |
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B.add_vertex_to_facet( 6); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 3); |
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B.add_vertex_to_facet( 5); |
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B.add_vertex_to_facet( 9); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 5); |
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B.add_vertex_to_facet( 0); |
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B.add_vertex_to_facet( 2); |
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B.add_vertex_to_facet( 6); |
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B.end_facet(); |
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B.begin_facet(); |
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B.add_vertex_to_facet( 8); |
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B.add_vertex_to_facet( 6); |
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B.add_vertex_to_facet( 2); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 3); |
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B.add_vertex_to_facet( 0); |
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B.add_vertex_to_facet( 5); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 0); |
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B.add_vertex_to_facet( 1); |
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B.add_vertex_to_facet( 4); |
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B.add_vertex_to_facet( 2); |
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B.end_facet(); |
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B.begin_facet(); |
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B.add_vertex_to_facet( 8); |
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B.add_vertex_to_facet( 2); |
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B.add_vertex_to_facet( 4); |
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B.end_facet(); |
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B.begin_facet(); |
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B.add_vertex_to_facet( 3); |
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B.add_vertex_to_facet( 1); |
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B.add_vertex_to_facet( 0); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 1); |
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B.add_vertex_to_facet( 7); |
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B.add_vertex_to_facet( 10); |
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B.add_vertex_to_facet( 4); |
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B.end_facet(); |
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B.begin_facet(); |
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B.add_vertex_to_facet( 8); |
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B.add_vertex_to_facet( 4); |
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B.add_vertex_to_facet( 10); |
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B.end_facet(); |
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|
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B.begin_facet(); |
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B.add_vertex_to_facet( 3); |
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B.add_vertex_to_facet( 7); |
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B.add_vertex_to_facet( 1); |
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B.end_facet(); |
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|
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B.end_surface(); |
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} |
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}; |
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|
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struct Normal_vector { |
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template <class Facet> |
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typename Facet::Plane_3 operator()( Facet& f) { |
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typename Facet::Halfedge_handle h = f.halfedge(); |
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// Facet::Plane_3 is the normal vector type. We assume the |
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// CGAL Kernel here and use its global functions. |
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return CGAL::cross_product( |
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h->next()->vertex()->point() - h->vertex()->point(), |
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h->next()->next()->vertex()->point() - h->next()->vertex()->point()); |
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} |
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}; |
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|
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|
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bool GeometryBuilder::isInsidePolyhedron(double x, double y, double z) { |
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|
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Point_3 point(x,y,z); |
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Plane_iterator i; |
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Facet_iterator j; |
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for ( i =nanoRodPolyhedron.planes_begin(), j = nanoRodPolyhedron.facets_begin(); i != nanoRodPolyhedron.planes_end() && j !=nanoRodPolyhedron.facets_end(); ++i, ++j) { |
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Halfedge_facet_circulator k = j->facet_begin(); |
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|
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Vector_3 newVector = point - k->vertex()->point(); |
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Vector_3 normal = *i; |
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double dot_product = newVector.x() * normal.x() + newVector.y() * normal.y() + newVector.z() * normal.z(); |
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|
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if (dot_product < 0) { |
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return false; |
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} |
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} |
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return true; |
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} |
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|
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|
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GeometryBuilder::GeometryBuilder(double length,double width) { |
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// Create the geometry for nanorod |
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Build_nanorod<HalfedgeDS> nanorod; |
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nanoRodPolyhedron.delegate( nanorod); |
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|
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double y1 = nanorod.end1->point().y() - nanorod.neight1->point().y(); |
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double y2 = nanorod.end2->point().y() - nanorod.neight2->point().y(); |
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|
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CGAL::Aff_transformation_3<Kernel> aff_tranformation( width, |
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0.0, |
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0.0, |
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0.0, |
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0.0, |
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length, |
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0.0, |
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0.0, |
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0.0, |
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0.0, |
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width, |
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0.0); |
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std::transform( nanoRodPolyhedron.points_begin(), nanoRodPolyhedron.points_end(), nanoRodPolyhedron.points_begin(), aff_tranformation); |
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Point_3 point1(nanorod.end1->point().x(), y1 + nanorod.neight1->point().y(), nanorod.end1->point().z()); |
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Point_3 point2(nanorod.end2->point().x(), y2+ nanorod.neight2->point().y(), nanorod.end2->point().z()); |
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nanorod.end1->point() = point1; |
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nanorod.end2->point() = point2; |
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|
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// Construct normal vector for each face. |
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std::transform( nanoRodPolyhedron.facets_begin(), nanoRodPolyhedron.facets_end(), nanoRodPolyhedron.planes_begin(), |
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Normal_vector()); |
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|
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} |
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|
