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/* Copyright (c) 2008 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 1.11 2008-10-20 19:36:32 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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|
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|
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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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//#include <CGAL/Homogeneous.h> |
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#include <CGAL/basic.h> |
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//#include <CGAL/Simple_cartesian.h> |
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#include <CGAL/Cartesian.h> |
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#include <CGAL/Origin.h> |
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#include <CGAL/Exact_predicates_exact_constructions_kernel.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/Polyhedron_traits_with_normals_3.h> |
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#include <CGAL/Polyhedron_3.h> |
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#include <CGAL/double.h> |
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#include <CGAL/number_utils.h> |
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|
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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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|
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|
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typedef CGAL::MP_Float RT; |
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//typedef double RT; |
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//typedef CGAL::Homogeneous<RT> K; |
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typedef CGAL::Exact_predicates_exact_constructions_kernel K; |
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typedef K::Vector_3 Vector_3; |
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//typedef CGAL::Convex_hull_traits_3<K> Traits; |
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typedef CGAL::Polyhedron_traits_with_normals_3<K> Traits; |
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//typedef Traits::Polyhedron_3 Polyhedron_3; |
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typedef CGAL::Polyhedron_3<Traits> Polyhedron_3; |
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typedef K::Point_3 Point_3; |
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|
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|
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typedef Polyhedron_3::HalfedgeDS HalfedgeDS; |
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typedef Polyhedron_3::Facet_iterator Facet_iterator; |
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typedef Polyhedron_3::Halfedge_around_facet_circulator Halfedge_facet_circulator; |
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typedef Polyhedron_3::Halfedge_handle Halfedge_handle; |
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typedef Polyhedron_3::Facet_iterator Facet_iterator; |
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typedef Polyhedron_3::Plane_iterator Plane_iterator; |
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typedef Polyhedron_3::Vertex_iterator Vertex_iterator; |
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typedef Polyhedron_3::Vertex_handle Vertex_handle; |
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typedef Polyhedron_3::Point_iterator Point_iterator; |
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|
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|
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|
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class Enriched_Point_3 : public K::Point_3{ |
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public: |
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Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {} |
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|
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bool isMyPoint() const{ return yupMyPoint; } |
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void myPoint(){ yupMyPoint = true; } |
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void setSD(StuntDouble* SD){mySD = SD;} |
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StuntDouble* getStuntDouble(){return mySD;} |
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private: |
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bool yupMyPoint; |
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StuntDouble* mySD; |
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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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// compare Point_3's... used in setting up the STL map from points to indices |
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template <typename Pt3> |
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struct Point_3_comp { |
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bool operator() (const Pt3 & p, const Pt3 & q) const { |
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return CGAL::lexicographically_xyz_smaller(p,q); // this is defined inline & hence we had to create fn object & not ptrfun |
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} |
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}; |
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|
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// coordinate-based hashing inefficient but can we do better if pts are copied? |
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typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType; |
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|
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#ifdef IS_MPI |
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struct { |
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double x,y,z; |
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} surfacePt; |
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#endif |
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|
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ConvexHull::ConvexHull() : Hull(){ |
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//If we are doing the mpi version, set up some vectors for data communication |
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#ifdef IS_MPI |
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|
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|
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nproc_ = MPI::COMM_WORLD.Get_size(); |
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myrank_ = MPI::COMM_WORLD.Get_rank(); |
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NstoProc_ = new int[nproc_]; |
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displs_ = new int[nproc_]; |
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|
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// Create a surface point type in MPI to send |
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surfacePtType = MPI::DOUBLE.Create_contiguous(3); |
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surfacePtType.Commit(); |
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|
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|
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#endif |
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} |
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|
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void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) |
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{ |
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|
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std::vector<Enriched_Point_3> points; |
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ptMapType myMap; |
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Point_iterator hc; |
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|
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// Copy the positon vector into a points vector for cgal. |
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std::vector<StuntDouble*>::iterator SD; |
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|
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for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD) |
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{ |
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Vector3d pos = (*SD)->getPos(); |
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Enriched_Point_3* pt = new Enriched_Point_3(pos.x(),pos.y(),pos.z()); |
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pt->setSD(*SD); |
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points.push_back(*pt); |
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// myMap[pt]=(*SD); |
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} |
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|
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// define object to hold convex hull |
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CGAL::Object ch_object_; |
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Polyhedron_3 polyhedron; |
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|
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// compute convex hull |
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|
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std::vector<Enriched_Point_3>::iterator testpt; |
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|
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|
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|
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CGAL::convex_hull_3(points.begin(), points.end(), polyhedron); |
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|
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|
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|
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Ns_ = polyhedron.size_of_vertices(); |
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|
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#ifdef IS_MPI |
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/* Gather an array of the number of verticies on each processor */ |
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|
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|
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surfacePtsGlobal_.clear(); |
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surfacePtsLocal_.clear(); |
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|
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MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT); |
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|
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for (int i = 0; i < nproc_; i++){ |
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Nsglobal_ += NstoProc_[i]; |
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} |
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/*Reminder ideally, we would like to reserve size for the vectors here*/ |
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surfacePtsLocal_.reserve(Ns_); |
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surfacePtsGlobal_.resize(Nsglobal_); |
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// std::fill(surfacePtsGlobal_.begin(),surfacePtsGlobal_.end(),0); |
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|
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/* Build a displacements array */ |
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for (int i = 1; i < nproc_; i++){ |
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displs_[i] = displs_[i-1] + NstoProc_[i-1]; |
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} |
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|
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int noffset = displs_[myrank_]; |
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/* gather the potential hull */ |
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|
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|
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for (hc =polyhedron.points_begin();hc != polyhedron.points_end(); ++hc){ |
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Point_3 mypoint = *hc; |
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surfacePt_ mpiSurfacePt; |
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mpiSurfacePt.x = CGAL::to_double(mypoint.x()); |
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mpiSurfacePt.y = CGAL::to_double(mypoint.y()); |
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mpiSurfacePt.z = CGAL::to_double(mypoint.z()); |
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surfacePtsLocal_.push_back(mpiSurfacePt); |
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} |
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|
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MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType); |
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std::vector<surfacePt_>::iterator spt; |
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std::vector<Enriched_Point_3> gblpoints; |
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|
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int mine = 0; |
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int pointidx = 0; |
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for (spt = surfacePtsGlobal_.begin(); spt != surfacePtsGlobal_.end(); ++spt) |
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{ |
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surfacePt_ thispos = *spt; |
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Enriched_Point_3 ept(thispos.x,thispos.y,thispos.z); |
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if (mine >= noffset && mine < noffset + Ns_){ |
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ept.myPoint(); |
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ept.setSD(points[pointidx].getStuntDouble()); |
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pointidx++; |
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} |
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gblpoints.push_back(ept); |
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|
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mine++; |
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} |
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|
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/* Compute the global hull */ |
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polyhedron.clear(); |
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CGAL::convex_hull_3(gblpoints.begin(), gblpoints.end(), polyhedron); |
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|
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|
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#endif |
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|
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|
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|
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/* Loop over all of the surface triangles and build data structures for atoms and normals*/ |
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Facet_iterator j; |
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area_ = 0; |
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for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) { |
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Halfedge_handle h = j->halfedge(); |
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|
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Point_3 r0=h->vertex()->point(); |
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Point_3 r1=h->next()->vertex()->point(); |
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Point_3 r2=h->next()->next()->vertex()->point(); |
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|
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Point_3* pr0 = &r0; |
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Point_3* pr1 = &r1; |
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Point_3* pr2 = &r2; |
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|
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Enriched_Point_3* er0 = static_cast<Enriched_Point_3*>(pr0); |
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Enriched_Point_3* er1 = static_cast<Enriched_Point_3*>(pr1); |
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Enriched_Point_3* er2 = static_cast<Enriched_Point_3*>(pr2); |
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|
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// StuntDouble* sd = er0->getStuntDouble(); |
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std::cerr << "sd globalIndex = " << to_double(er0->x()) << "\n"; |
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|
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Point_3 thisCentroid = CGAL::centroid(r0,r1,r2); |
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|
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Vector_3 normal = CGAL::cross_product(r1-r0,r2-r0); |
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|
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Triangle* face = new Triangle(); |
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Vector3d V3dNormal(CGAL::to_double(normal.x()),CGAL::to_double(normal.y()),CGAL::to_double(normal.z())); |
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Vector3d V3dCentroid(CGAL::to_double(thisCentroid.x()),CGAL::to_double(thisCentroid.y()),CGAL::to_double(thisCentroid.z())); |
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face->setNormal(V3dNormal); |
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face->setCentroid(V3dCentroid); |
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RealType faceArea = 0.5*V3dNormal.length(); |
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face->setArea(faceArea); |
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area_ += faceArea; |
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Triangles_.push_back(face); |
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// ptMapType::const_iterator locn=myMap.find(mypoint); |
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// int myIndex = locn->second; |
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|
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} |
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|
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std::cout << "Number of surface atoms is: " << Ns_ << std::endl; |
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|
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|
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|
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} |
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void ConvexHull::printHull(const std::string& geomFileName) |
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{ |
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/* |
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std::ofstream newGeomFile; |
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|
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//create new .md file based on old .md file |
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newGeomFile.open("testhull.off"); |
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|
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// Write polyhedron in Object File Format (OFF). |
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CGAL::set_ascii_mode( std::cout); |
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newGeomFile << "OFF" << std::endl << polyhedron.size_of_vertices() << ' ' |
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<< polyhedron.size_of_facets() << " 0" << std::endl; |
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std::copy( polyhedron.points_begin(), polyhedron.points_end(), |
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std::ostream_iterator<Point_3>( newGeomFile, "\n")); |
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for ( Facet_iterator i = polyhedron.facets_begin(); i != polyhedron.facets_end(); ++i) { |
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Halfedge_facet_circulator j = i->facet_begin(); |
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// Facets in polyhedral surfaces are at least triangles. |
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CGAL_assertion( CGAL::circulator_size(j) >= 3); |
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newGeomFile << CGAL::circulator_size(j) << ' '; |
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do { |
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newGeomFile << ' ' << std::distance(polyhedron.vertices_begin(), j->vertex()); |
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} while ( ++j != i->facet_begin()); |
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newGeomFile << std::endl; |
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} |
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|
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newGeomFile.close(); |
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*/ |
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/* |
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std::ofstream newGeomFile; |
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|
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//create new .md file based on old .md file |
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newGeomFile.open(geomFileName.c_str()); |
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|
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// Write polyhedron in Object File Format (OFF). |
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CGAL::set_ascii_mode( std::cout); |
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newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' ' |
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<< ch_polyhedron.size_of_facets() << " 0" << std::endl; |
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std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(), |
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std::ostream_iterator<Point_3>( newGeomFile, "\n")); |
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for ( Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i) |
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{ |
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Halfedge_facet_circulator j = i->facet_begin(); |
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// Facets in polyhedral surfaces are at least triangles. |
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CGAL_assertion( CGAL::circulator_size(j) >= 3); |
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newGeomFile << CGAL::circulator_size(j) << ' '; |
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do |
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{ |
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newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex()); |
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} |
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while ( ++j != i->facet_begin()); |
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newGeomFile << std::endl; |
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} |
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|
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newGeomFile.close(); |
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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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#else |
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#ifdef HAVE_QHULL |
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/* Old options Qt Qu Qg QG0 FA */ |
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/* More old opts Qc Qi Pp*/ |
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ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) { |
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//If we are doing the mpi version, set up some vectors for data communication |
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#ifdef IS_MPI |
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|
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|
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nproc_ = MPI::COMM_WORLD.Get_size(); |
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myrank_ = MPI::COMM_WORLD.Get_rank(); |
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NstoProc_ = new int[nproc_]; |
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displs_ = new int[nproc_]; |
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|
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// Create a surface point type in MPI to send |
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//surfacePtType = MPI::DOUBLE.Create_contiguous(3); |
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// surfacePtType.Commit(); |
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|
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|
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#endif |
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} |
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|
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|
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|
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void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) |
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{ |
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|
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std::vector<int> surfaceIDs; |
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std::vector<int> surfaceIDsGlobal; |
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std::vector<int> localPtsMap; |
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int numpoints = bodydoubles.size(); |
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|
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//coordT* pt_array; |
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coordT* surfpt_array; |
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vertexT *vertex, **vertexp; |
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facetT *facet; |
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setT *vertices; |
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int curlong,totlong; |
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int id; |
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|
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coordT *point,**pointp; |
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|
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|
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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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// double* ptArray = new double[numpoints * 3]; |
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std::vector<double> ptArray(numpoints*3); |
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std::vector<bool> isSurfaceID(numpoints); |
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|
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// Copy the positon vector into a points vector for qhull. |
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std::vector<StuntDouble*>::iterator SD; |
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int i = 0; |
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for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD) |
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{ |
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Vector3d pos = (*SD)->getPos(); |
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|
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ptArray[dim_ * i] = pos.x(); |
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ptArray[dim_ * i + 1] = pos.y(); |
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ptArray[dim_ * i + 2] = pos.z(); |
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i++; |
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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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boolT ismalloc = False; |
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/* Clean up memory from previous convex hull calculations*/ |
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Triangles_.clear(); |
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surfaceSDs_.clear(); |
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surfaceSDs_.reserve(Ns_); |
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|
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if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc, |
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const_cast<char *>(options_.c_str()), NULL, stderr)) { |
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|
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sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull"); |
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painCave.isFatal = 1; |
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simError(); |
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|
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} //qh_new_qhull |
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|
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|
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#ifdef IS_MPI |
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std::vector<double> localPts; |
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std::vector<double> localVel; |
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int localPtArraySize; |
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|
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|
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std::fill(isSurfaceID.begin(),isSurfaceID.end(),false); |
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|
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|
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FORALLfacets { |
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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 = 1; |
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simError(); |
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} |
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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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|
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if( !isSurfaceID[id] ){ |
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isSurfaceID[id] = true; |
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} |
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} |
| 482 |
qh_settempfree(&vertices); |
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|
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} //FORALLfacets |
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|
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|
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|
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/* |
| 489 |
std::sort(surfaceIDs.begin(),surfaceIDs.end()); |
| 490 |
surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end()); |
| 491 |
int localPtArraySize = surfaceIDs.size() * 3; |
| 492 |
*/ |
| 493 |
|
| 494 |
//localPts.resize(localPtArraySize); |
| 495 |
//std::fill(localPts.begin(),localPts.end(),0.0); |
| 496 |
|
| 497 |
|
| 498 |
int idx = 0; |
| 499 |
int nIsIts = 0; |
| 500 |
/* |
| 501 |
// Copy the surface points into an array. |
| 502 |
for(std::vector<bool>::iterator list_iter = isSurfaceID.begin(); |
| 503 |
list_iter != isSurfaceID.end(); list_iter++) |
| 504 |
{ |
| 505 |
bool isIt = *list_iter; |
| 506 |
if (isIt){ |
| 507 |
localPts.push_back(ptArray[dim_ * idx]); |
| 508 |
localPts.push_back(ptArray[dim_ * idx + 1]); |
| 509 |
localPts.push_back(ptArray[dim_ * idx + 2]); |
| 510 |
localPtsMap.push_back(idx); |
| 511 |
nIsIts++; |
| 512 |
} //Isit |
| 513 |
idx++; |
| 514 |
} //isSurfaceID |
| 515 |
*/ |
| 516 |
FORALLvertices { |
| 517 |
idx = qh_pointid(vertex->point); |
| 518 |
localPts.push_back(ptArray[dim_ * idx]); |
| 519 |
localPts.push_back(ptArray[dim_ * idx + 1]); |
| 520 |
localPts.push_back(ptArray[dim_ * idx + 2]); |
| 521 |
|
| 522 |
Vector3d vel = bodydoubles[idx]->getVel(); |
| 523 |
localVel.push_back(vel.x()); |
| 524 |
localVel.push_back(vel.y()); |
| 525 |
localVel.push_back(vel.z()); |
| 526 |
|
| 527 |
localPtsMap.push_back(idx); |
| 528 |
} |
| 529 |
|
| 530 |
|
| 531 |
localPtArraySize = localPts.size(); |
| 532 |
|
| 533 |
|
| 534 |
MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT); |
| 535 |
|
| 536 |
Nsglobal_=0; |
| 537 |
for (int i = 0; i < nproc_; i++){ |
| 538 |
Nsglobal_ += NstoProc_[i]; |
| 539 |
} |
| 540 |
|
| 541 |
|
| 542 |
int nglobalPts = int(Nsglobal_/3); |
| 543 |
|
| 544 |
|
| 545 |
std::vector<double> globalPts(Nsglobal_); |
| 546 |
std::vector<double> globalVel(Nsglobal_); |
| 547 |
|
| 548 |
isSurfaceID.resize(nglobalPts); |
| 549 |
|
| 550 |
|
| 551 |
std::fill(globalPts.begin(),globalPts.end(),0.0); |
| 552 |
|
| 553 |
displs_[0] = 0; |
| 554 |
/* Build a displacements array */ |
| 555 |
for (int i = 1; i < nproc_; i++){ |
| 556 |
displs_[i] = displs_[i-1] + NstoProc_[i-1]; |
| 557 |
} |
| 558 |
|
| 559 |
|
| 560 |
int noffset = displs_[myrank_]; |
| 561 |
/* gather the potential hull */ |
| 562 |
|
| 563 |
MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE); |
| 564 |
MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize,MPI::DOUBLE,&globalVel[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE); |
| 565 |
|
| 566 |
/* |
| 567 |
if (myrank_ == 0){ |
| 568 |
for (i = 0; i < globalPts.size(); i++){ |
| 569 |
std::cout << globalPts[i] << std::endl; |
| 570 |
} |
| 571 |
} |
| 572 |
*/ |
| 573 |
// Free previous hull |
| 574 |
qh_freeqhull(!qh_ALL); |
| 575 |
qh_memfreeshort(&curlong, &totlong); |
| 576 |
if (curlong || totlong) |
| 577 |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 578 |
<< totlong << curlong << std::endl; |
| 579 |
|
| 580 |
if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc, |
| 581 |
const_cast<char *>(options_.c_str()), NULL, stderr)){ |
| 582 |
|
| 583 |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull"); |
| 584 |
painCave.isFatal = 1; |
| 585 |
simError(); |
| 586 |
|
| 587 |
} //qh_new_qhull |
| 588 |
|
| 589 |
#endif |
| 590 |
|
| 591 |
|
| 592 |
|
| 593 |
|
| 594 |
|
| 595 |
|
| 596 |
unsigned int nf = qh num_facets; |
| 597 |
|
| 598 |
/* Build Surface SD list first */ |
| 599 |
|
| 600 |
std::fill(isSurfaceID.begin(),isSurfaceID.end(),false); |
| 601 |
|
| 602 |
FORALLfacets { |
| 603 |
|
| 604 |
if (!facet->simplicial){ |
| 605 |
// should never happen with Qt |
| 606 |
sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected"); |
| 607 |
painCave.isFatal = 1; |
| 608 |
simError(); |
| 609 |
} //simplicical |
| 610 |
|
| 611 |
Triangle* face = new Triangle(); |
| 612 |
Vector3d V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]); |
| 613 |
face->setNormal(V3dNormal); |
| 614 |
|
| 615 |
|
| 616 |
|
| 617 |
RealType faceArea = 0.5*V3dNormal.length(); |
| 618 |
face->setArea(faceArea); |
| 619 |
|
| 620 |
|
| 621 |
vertices = qh_facet3vertex(facet); |
| 622 |
|
| 623 |
coordT *center = qh_getcenter(vertices); |
| 624 |
Vector3d V3dCentroid(center[0], center[1], center[2]); |
| 625 |
face->setCentroid(V3dCentroid); |
| 626 |
Vector3d faceVel = V3Zero; |
| 627 |
FOREACHvertex_(vertices){ |
| 628 |
id = qh_pointid(vertex->point); |
| 629 |
int localindex = id; |
| 630 |
#ifdef IS_MPI |
| 631 |
Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]); |
| 632 |
faceVel = faceVel + velVector; |
| 633 |
if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){ |
| 634 |
localindex = localPtsMap[id-noffset/3]; |
| 635 |
#else |
| 636 |
faceVel = faceVel + bodydoubles[localindex]->getVel(); |
| 637 |
#endif |
| 638 |
face->addVertex(bodydoubles[localindex]); |
| 639 |
if( !isSurfaceID[id] ){ |
| 640 |
isSurfaceID[id] = true; |
| 641 |
#ifdef IS_MPI |
| 642 |
|
| 643 |
#endif |
| 644 |
|
| 645 |
surfaceSDs_.push_back(bodydoubles[localindex]); |
| 646 |
|
| 647 |
} //IF isSurfaceID |
| 648 |
|
| 649 |
#ifdef IS_MPI |
| 650 |
|
| 651 |
}else{ |
| 652 |
face->addVertex(NULL); |
| 653 |
} |
| 654 |
#endif |
| 655 |
} //Foreachvertex |
| 656 |
/* |
| 657 |
if (!SETempty_(facet->coplanarset)){ |
| 658 |
FOREACHpoint_(facet->coplanarset){ |
| 659 |
id = qh_pointid(point); |
| 660 |
surfaceSDs_.push_back(bodydoubles[id]); |
| 661 |
} |
| 662 |
} |
| 663 |
*/ |
| 664 |
face->setFacetVelocity(faceVel/3.0); |
| 665 |
Triangles_.push_back(face); |
| 666 |
qh_settempfree(&vertices); |
| 667 |
|
| 668 |
} //FORALLfacets |
| 669 |
|
| 670 |
/* |
| 671 |
std::cout << surfaceSDs_.size() << std::endl; |
| 672 |
for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){ |
| 673 |
Vector3d thisatom = (*SD)->getPos(); |
| 674 |
std::cout << "Au " << thisatom.x() << " " << thisatom.y() << " " << thisatom.z() << std::endl; |
| 675 |
} |
| 676 |
*/ |
| 677 |
|
| 678 |
|
| 679 |
|
| 680 |
Ns_ = surfaceSDs_.size(); |
| 681 |
nTriangles_ = Triangles_.size(); |
| 682 |
|
| 683 |
qh_getarea(qh facet_list); |
| 684 |
volume_ = qh totvol; |
| 685 |
area_ = qh totarea; |
| 686 |
|
| 687 |
|
| 688 |
|
| 689 |
qh_freeqhull(!qh_ALL); |
| 690 |
qh_memfreeshort(&curlong, &totlong); |
| 691 |
if (curlong || totlong) |
| 692 |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 693 |
<< totlong << curlong << std::endl; |
| 694 |
|
| 695 |
|
| 696 |
|
| 697 |
} |
| 698 |
|
| 699 |
|
| 700 |
|
| 701 |
void ConvexHull::printHull(const std::string& geomFileName) |
| 702 |
{ |
| 703 |
|
| 704 |
FILE *newGeomFile; |
| 705 |
|
| 706 |
//create new .md file based on old .md file |
| 707 |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 708 |
qh_findgood_all(qh facet_list); |
| 709 |
for (int i = 0; i < qh_PRINTEND; i++) |
| 710 |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 711 |
|
| 712 |
fclose(newGeomFile); |
| 713 |
} |
| 714 |
#endif //QHULL |
| 715 |
#endif //CGAL |
| 716 |
|
| 717 |
|
| 718 |
|
