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/* Copyright (c) 2006 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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* ConvexHull.cpp |
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* |
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* Purpose: To calculate convexhull, hull volume libqhull. |
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* |
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* Created by Charles F. Vardeman II on 11 Dec 2006. |
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* @author Charles F. Vardeman II |
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* @version $Id: ConvexHull.cpp,v 1.6 2008-05-14 14:31:48 chuckv Exp $ |
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* |
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*/ |
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|
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/* Standard includes independent of library */ |
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#include <iostream> |
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#include <fstream> |
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#include <list> |
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#include <algorithm> |
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#include <iterator> |
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#include "math/ConvexHull.hpp" |
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#include "utils/simError.h" |
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using namespace oopse; |
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|
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/* CGAL version of convex hull first then QHULL */ |
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#ifdef HAVE_CGAL |
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|
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#include <CGAL/basic.h> |
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#include <CGAL/Simple_cartesian.h> |
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#include <CGAL/Convex_hull_traits_3.h> |
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#include <CGAL/convex_hull_3.h> |
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#include <CGAL/double.h> |
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|
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#include <CGAL/Quotient.h> |
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#include <CGAL/MP_Float.h> |
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#include <CGAL/Lazy_exact_nt.h> |
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|
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typedef double RT; |
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typedef CGAL::Simple_cartesian<RT> K; |
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typedef CGAL::Convex_hull_traits_3<K> Traits; |
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typedef Traits::Polyhedron_3 Polyhedron_3; |
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typedef K::Point_3 Point; |
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|
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|
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ConvexHull::ConvexHull(){} |
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|
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bool ConvexHull::genHull(std::vector<Vector3d> pos) |
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{ |
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|
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std::vector<Point> points; |
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|
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|
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// Copy the positon vector into a points vector for cgal. |
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for (int i = 0; i < pos.size(); ++i) |
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{ |
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Point pt(pos[i][0],pos[i][1],pos[i][2]); |
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points.push_back(pt); |
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} |
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|
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// define object to hold convex hull |
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Polyhedron_3 ch_object_; |
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// compute convex hull |
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CGAL::convex_hull_3(points.begin(), points.end(), ch_object_); |
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|
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for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin(); ch_object_.vertices_end(); ++v){ |
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std::cout<< v.point()<<std::endl; |
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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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#else |
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#ifdef HAVE_QHULL |
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/* Old options Qt Qu Qg QG0 FA */ |
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ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt Qci Tcv Pp") |
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//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i") |
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{} |
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|
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bool ConvexHull::genHull(std::vector<Vector3d> pos) |
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{ |
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|
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|
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int numpoints = pos.size(); |
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coordT* pt_array; |
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coordT* surfpt_array; |
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std::list<int> surface_atoms; |
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FILE *outdummy = NULL; |
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FILE *errdummy = NULL; |
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|
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pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_)); |
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|
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|
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for (int i = 0; i < numpoints; i++) { |
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pt_array[dim_ * i] = pos[i][0]; |
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pt_array[dim_ * i + 1] = pos[i][1]; |
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pt_array[dim_ * i + 2] = pos[i][2]; |
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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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qh_initflags(const_cast<char *>(options_.c_str())); |
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qh_init_B(pospoints, numpoints, dim_, ismalloc); |
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qh_qhull(); |
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qh_check_output(); |
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|
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qh_produce_output(); |
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*/ |
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boolT ismalloc = False; |
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|
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if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc, |
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const_cast<char *>(options_.c_str()), NULL, stderr)) { |
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|
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vertexT *vertex, **vertexp; |
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facetT *facet; |
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setT *vertices; |
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unsigned int nf = qh num_facets; |
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|
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//Matrix idx(nf, dim); |
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/* |
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int j, i = 0, id = 0; |
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|
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int id2 = 0; |
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coordT *point,**pointp; |
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realT dist; |
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FORALLfacets { |
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j = 0; |
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|
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if (!facet->simplicial){ |
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// should never happen with Qt |
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sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected"); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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vertices = qh_facet3vertex(facet); |
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FOREACHvertex_(vertices){ |
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id = qh_pointid(vertex->point); |
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surface_atoms.push_back(id); |
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//std::cout << "Ag " << pos[id][0] << " " << pos[id][1] << " " << pos[id][2]<< std::endl; |
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} |
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qh_settempfree(&vertices); |
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|
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FOREACHpoint_(facet->coplanarset){ |
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vertex= qh_nearvertex (facet, point, &dist); |
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//id= qh_pointid (vertex->point); |
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id2= qh_pointid (point); |
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surface_atoms.push_back(id2); |
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//std::cout << "Ag " << pos[id2][0] << " " << pos[id2][1] << " " << pos[id2][2]<< std::endl; |
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//printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist); |
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//std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id; |
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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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|
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} |
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|
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|
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|
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|
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qh_getarea(qh facet_list); |
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volume_ = qh totvol; |
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area_ = qh totarea; |
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// FILE *newGeomFile; |
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|
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|
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/* |
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FORALLfacets { |
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for (int k=0; k < qh hull_dim; k++) |
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printf ("%6.2g ", facet->normal[k]); |
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printf ("\n"); |
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} |
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*/ |
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|
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int curlong,totlong; |
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// geomviewHull("junk.off"); |
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qh_freeqhull(!qh_ALL); |
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qh_memfreeshort(&curlong, &totlong); |
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if (curlong || totlong) |
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std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
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<< totlong << curlong << std::endl; |
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free(pt_array); |
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/* |
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int j = 0; |
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surface_atoms.sort(); |
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surface_atoms.unique(); |
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surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_)); |
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for(std::list<int>::iterator list_iter = surface_atoms.begin(); |
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list_iter != surface_atoms.end(); list_iter++) |
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{ |
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int i = *list_iter; |
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//surfpt_array[dim_ * j] = pos[i][0]; |
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//surfpt_array[dim_ * j + 1] = pos[i][1]; |
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//surfpt_array[dim_ * j + 2] = pos[i][2]; |
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std::cout << "Ag " << pos[i][0] << " " << pos[i][1] << " "<< pos[i][2] << std::endl; |
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j++; |
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} |
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*/ |
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|
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/* |
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std::string deloptions_ = "qhull d Qt"; |
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facetT *facet, *neighbor; |
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ridgeT *ridge, **ridgep; |
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|
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if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc, |
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const_cast<char *>(deloptions_.c_str()), NULL, stderr)) { |
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|
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qh visit_id++; |
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FORALLfacets { |
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if (!facet->upperdelaunay) { |
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facet->visitid= qh visit_id; |
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qh_makeridges(facet); |
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FOREACHridge_(facet->ridges) { |
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neighbor= otherfacet_(ridge, facet); |
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if (neighbor->visitid != qh visit_id) { |
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|
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FOREACHvertex_(ridge->vertices) |
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int id2 = qh_pointid (vertex->point); |
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std::cout << "Ag " << pos[id2][0] << " " << pos[id2][1] << " " << pos[id2][2]<< std::endl; |
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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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} |
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|
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qh_freeqhull(!qh_ALL); |
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qh_memfreeshort(&curlong, &totlong); |
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if (curlong || totlong) |
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std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
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<< totlong << curlong << std::endl; |
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free(surfpt_array); |
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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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|
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RealType ConvexHull::getVolume() |
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{ |
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return volume_; |
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} |
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|
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void ConvexHull::geomviewHull(const std::string& geomFileName) |
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{ |
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|
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FILE *newGeomFile; |
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|
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//create new .md file based on old .md file |
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newGeomFile = fopen(geomFileName.c_str(), "w"); |
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qh_findgood_all(qh facet_list); |
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for (int i = 0; i < qh_PRINTEND; i++) |
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qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
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|
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fclose(newGeomFile); |
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} |
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#endif //QHULL |
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#endif //CGAL |
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|
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|
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|
