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/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved. |
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/* Copyright (c) 2008, 2009 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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* |
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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 1.3 2007-05-30 18:47:03 chuckv Exp $ |
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* @version $Id: ConvexHull.cpp,v 1.14 2009-10-12 20:11:29 chuckv Exp $ |
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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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ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") { |
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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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//#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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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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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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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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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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// 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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// 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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#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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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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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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vecdispls_ = new int[nproc_]; |
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displs_ = new int[nproc_]; |
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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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#endif |
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} |
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bool ConvexHull::genHull(std::vector<Vector3d> pos) { |
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FILE *outfile = stdout; |
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FILE *errfile = stderr; |
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facetT *facet; |
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int exitcode; |
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boolT ismalloc = False; |
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int curlong,totlong; |
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void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) |
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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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int numpoints = pos.size(); |
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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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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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coordT points[numpoints][dim_]; |
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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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// compute convex hull |
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for (int i=0; i<numpoints; i++) { |
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points[i][0] = pos[i][0]; |
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points[i][1] = pos[i][1]; |
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points[i][2] = pos[i][2]; |
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} |
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std::vector<Enriched_Point_3>::iterator testpt; |
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CGAL::convex_hull_3(points.begin(), points.end(), polyhedron); |
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Ns_ = polyhedron.size_of_vertices(); |
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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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qh_initflags (const_cast<char *>(options_.c_str())); |
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qh_init_B (points[0], numpoints, dim_, ismalloc); |
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qh_qhull(); |
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qh_check_output(); |
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surfacePtsGlobal_.clear(); |
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surfacePtsLocal_.clear(); |
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MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT); |
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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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/* Build a displacements array */ |
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for (int i = 1; i < nproc_; i++){ |
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vecdispls_[i] = vecdispls_[i-1] + NstoProc_[i-1]; |
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} |
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int noffset = vecdispls_[myrank_]; |
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/* gather the potential hull */ |
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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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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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MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,vecdispls_,surfacePtType); |
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std::vector<surfacePt_>::iterator spt; |
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std::vector<Enriched_Point_3> gblpoints; |
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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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mine++; |
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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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#endif |
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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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fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n", |
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totlong, curlong); |
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return true; |
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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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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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RealType ConvexHull::getVolume() { |
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return volume_; |
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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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void ConvexHull::geomviewHull(const std::string& geomFileName) { |
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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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// StuntDouble* sd = er0->getStuntDouble(); |
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std::cerr << "sd globalIndex = " << to_double(er0->x()) << "\n"; |
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Point_3 thisCentroid = CGAL::centroid(r0,r1,r2); |
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Vector_3 normal = CGAL::cross_product(r1-r0,r2-r0); |
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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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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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//create new .md file based on old .md file |
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newGeomFile.open(geomFileName.c_str()); |
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newGeomFile.open("testhull.off"); |
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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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newGeomFile.close(); |
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*/ |
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/* |
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std::ofstream newGeomFile; |
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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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// 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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newGeomFile.close(); |
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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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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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vecdispls_ = new int[nproc_]; |
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vecNstoProc_ = new int[nproc_]; |
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displs_ = new int[nproc_]; |
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|
| 384 |
+ |
// Create a surface point type in MPI to send |
| 385 |
+ |
//surfacePtType = MPI::DOUBLE.Create_contiguous(3); |
| 386 |
+ |
// surfacePtType.Commit(); |
| 387 |
+ |
|
| 388 |
+ |
|
| 389 |
+ |
#endif |
| 390 |
+ |
} |
| 391 |
+ |
|
| 392 |
+ |
|
| 393 |
+ |
|
| 394 |
+ |
void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) |
| 395 |
+ |
{ |
| 396 |
+ |
|
| 397 |
+ |
std::vector<int> surfaceIDs; |
| 398 |
+ |
std::vector<int> surfaceIDsGlobal; |
| 399 |
+ |
std::vector<int> localPtsMap; |
| 400 |
+ |
int numpoints = bodydoubles.size(); |
| 401 |
+ |
|
| 402 |
+ |
//coordT* pt_array; |
| 403 |
+ |
coordT* surfpt_array; |
| 404 |
+ |
vertexT *vertex, **vertexp; |
| 405 |
+ |
facetT *facet; |
| 406 |
+ |
setT *vertices; |
| 407 |
+ |
int curlong,totlong; |
| 408 |
+ |
int id; |
| 409 |
+ |
|
| 410 |
+ |
coordT *point,**pointp; |
| 411 |
+ |
|
| 412 |
+ |
|
| 413 |
+ |
FILE *outdummy = NULL; |
| 414 |
+ |
FILE *errdummy = NULL; |
| 415 |
+ |
|
| 416 |
+ |
//pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_)); |
| 417 |
+ |
|
| 418 |
+ |
// double* ptArray = new double[numpoints * 3]; |
| 419 |
+ |
std::vector<double> ptArray(numpoints*3); |
| 420 |
+ |
std::vector<bool> isSurfaceID(numpoints); |
| 421 |
+ |
|
| 422 |
+ |
// Copy the positon vector into a points vector for qhull. |
| 423 |
+ |
std::vector<StuntDouble*>::iterator SD; |
| 424 |
+ |
int i = 0; |
| 425 |
+ |
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD) |
| 426 |
+ |
{ |
| 427 |
+ |
Vector3d pos = (*SD)->getPos(); |
| 428 |
+ |
|
| 429 |
+ |
ptArray[dim_ * i] = pos.x(); |
| 430 |
+ |
ptArray[dim_ * i + 1] = pos.y(); |
| 431 |
+ |
ptArray[dim_ * i + 2] = pos.z(); |
| 432 |
+ |
i++; |
| 433 |
+ |
} |
| 434 |
+ |
|
| 435 |
+ |
|
| 436 |
+ |
|
| 437 |
+ |
|
| 438 |
+ |
|
| 439 |
+ |
|
| 440 |
+ |
boolT ismalloc = False; |
| 441 |
+ |
/* Clean up memory from previous convex hull calculations*/ |
| 442 |
+ |
|
| 443 |
+ |
Triangles_.clear(); |
| 444 |
+ |
surfaceSDs_.clear(); |
| 445 |
+ |
surfaceSDs_.reserve(Ns_); |
| 446 |
+ |
|
| 447 |
+ |
if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc, |
| 448 |
+ |
const_cast<char *>(options_.c_str()), NULL, stderr)) { |
| 449 |
+ |
|
| 450 |
+ |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull"); |
| 451 |
+ |
painCave.isFatal = 1; |
| 452 |
+ |
simError(); |
| 453 |
+ |
|
| 454 |
+ |
} //qh_new_qhull |
| 455 |
+ |
|
| 456 |
+ |
|
| 457 |
+ |
#ifdef IS_MPI |
| 458 |
+ |
std::vector<double> localPts; |
| 459 |
+ |
std::vector<double> localVel; |
| 460 |
+ |
std::vector<double> localMass; |
| 461 |
+ |
int localPtArraySize; |
| 462 |
+ |
|
| 463 |
+ |
|
| 464 |
+ |
std::fill(isSurfaceID.begin(),isSurfaceID.end(),false); |
| 465 |
+ |
|
| 466 |
+ |
|
| 467 |
+ |
FORALLfacets { |
| 468 |
+ |
|
| 469 |
+ |
if (!facet->simplicial){ |
| 470 |
+ |
// should never happen with Qt |
| 471 |
+ |
sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected"); |
| 472 |
+ |
painCave.isFatal = 1; |
| 473 |
+ |
simError(); |
| 474 |
+ |
} |
| 475 |
+ |
|
| 476 |
+ |
|
| 477 |
+ |
vertices = qh_facet3vertex(facet); |
| 478 |
+ |
FOREACHvertex_(vertices){ |
| 479 |
+ |
id = qh_pointid(vertex->point); |
| 480 |
+ |
|
| 481 |
+ |
if( !isSurfaceID[id] ){ |
| 482 |
+ |
isSurfaceID[id] = true; |
| 483 |
+ |
} |
| 484 |
+ |
} |
| 485 |
+ |
qh_settempfree(&vertices); |
| 486 |
+ |
|
| 487 |
+ |
} //FORALLfacets |
| 488 |
+ |
|
| 489 |
+ |
|
| 490 |
+ |
|
| 491 |
+ |
|
| 492 |
+ |
int idx = 0; |
| 493 |
+ |
int nIsIts = 0; |
| 494 |
+ |
FORALLvertices { |
| 495 |
+ |
idx = qh_pointid(vertex->point); |
| 496 |
+ |
localPts.push_back(ptArray[dim_ * idx]); |
| 497 |
+ |
localPts.push_back(ptArray[dim_ * idx + 1]); |
| 498 |
+ |
localPts.push_back(ptArray[dim_ * idx + 2]); |
| 499 |
+ |
|
| 500 |
+ |
Vector3d vel = bodydoubles[idx]->getVel(); |
| 501 |
+ |
localVel.push_back(vel.x()); |
| 502 |
+ |
localVel.push_back(vel.y()); |
| 503 |
+ |
localVel.push_back(vel.z()); |
| 504 |
+ |
|
| 505 |
+ |
|
| 506 |
+ |
RealType bdmass = bodydoubles[idx]->getMass(); |
| 507 |
+ |
localMass.push_back(bdmass); |
| 508 |
+ |
|
| 509 |
+ |
localPtsMap.push_back(idx); |
| 510 |
+ |
|
| 511 |
+ |
} |
| 512 |
+ |
|
| 513 |
+ |
|
| 514 |
+ |
localPtArraySize = int(localPts.size()/3.0); |
| 515 |
+ |
|
| 516 |
+ |
MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT); |
| 517 |
+ |
|
| 518 |
+ |
Nsglobal_=0; |
| 519 |
+ |
for (int i = 0; i < nproc_; i++){ |
| 520 |
+ |
Nsglobal_ += NstoProc_[i]; |
| 521 |
+ |
vecNstoProc_[i] = NstoProc_[i]*3; |
| 522 |
+ |
} |
| 523 |
+ |
|
| 524 |
+ |
|
| 525 |
+ |
int nglobalPts = Nsglobal_*3; |
| 526 |
+ |
|
| 527 |
+ |
|
| 528 |
+ |
std::vector<double> globalPts(nglobalPts); |
| 529 |
+ |
std::vector<double> globalVel(nglobalPts); |
| 530 |
+ |
std::vector<double> globalMass(Nsglobal_); |
| 531 |
+ |
|
| 532 |
+ |
|
| 533 |
+ |
|
| 534 |
+ |
isSurfaceID.resize(nglobalPts); |
| 535 |
+ |
|
| 536 |
+ |
|
| 537 |
+ |
std::fill(globalPts.begin(),globalPts.end(),0.0); |
| 538 |
+ |
|
| 539 |
+ |
vecdispls_[0] = 0; |
| 540 |
+ |
/* Build a displacements array */ |
| 541 |
+ |
for (int i = 1; i < nproc_; i++){ |
| 542 |
+ |
vecdispls_[i] = vecdispls_[i-1] + vecNstoProc_[i-1]; |
| 543 |
+ |
} |
| 544 |
+ |
|
| 545 |
+ |
displs_[0] = 0; |
| 546 |
+ |
for (int i = 1; i < nproc_; i++){ |
| 547 |
+ |
displs_[i] = displs_[i-1] + NstoProc_[i-1]; |
| 548 |
+ |
} |
| 549 |
+ |
|
| 550 |
+ |
int noffset = vecdispls_[myrank_]; |
| 551 |
+ |
/* gather the potential hull */ |
| 552 |
+ |
|
| 553 |
+ |
MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize*3,MPI::DOUBLE,&globalPts[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE); |
| 554 |
+ |
MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize*3,MPI::DOUBLE,&globalVel[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE); |
| 555 |
+ |
MPI::COMM_WORLD.Allgatherv(&localMass[0],localPtArraySize,MPI::DOUBLE,&globalMass[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE); |
| 556 |
+ |
|
| 557 |
+ |
/* |
| 558 |
+ |
int tmpidx = 0; |
| 559 |
+ |
|
| 560 |
+ |
if (myrank_ == 0){ |
| 561 |
+ |
for (i = 0; i < nglobalPts-3; i++){ |
| 562 |
+ |
std::cout << "Au " << globalPts[tmpidx] << " " << globalPts[tmpidx+1] << " " << globalPts[tmpidx +2] << std::endl; |
| 563 |
+ |
tmpidx = tmpidx + 3; |
| 564 |
+ |
} |
| 565 |
+ |
} |
| 566 |
+ |
*/ |
| 567 |
+ |
|
| 568 |
+ |
// Free previous hull |
| 569 |
+ |
qh_freeqhull(!qh_ALL); |
| 570 |
+ |
qh_memfreeshort(&curlong, &totlong); |
| 571 |
+ |
if (curlong || totlong) |
| 572 |
+ |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 573 |
+ |
<< totlong << curlong << std::endl; |
| 574 |
+ |
|
| 575 |
+ |
if (qh_new_qhull(dim_, Nsglobal_, &globalPts[0], ismalloc, |
| 576 |
+ |
const_cast<char *>(options_.c_str()), NULL, stderr)){ |
| 577 |
+ |
|
| 578 |
+ |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull"); |
| 579 |
+ |
painCave.isFatal = 1; |
| 580 |
+ |
simError(); |
| 581 |
+ |
|
| 582 |
+ |
} //qh_new_qhull |
| 583 |
+ |
|
| 584 |
+ |
#endif |
| 585 |
+ |
|
| 586 |
+ |
|
| 587 |
+ |
|
| 588 |
+ |
|
| 589 |
+ |
|
| 590 |
+ |
|
| 591 |
+ |
unsigned int nf = qh num_facets; |
| 592 |
+ |
|
| 593 |
+ |
/* Build Surface SD list first */ |
| 594 |
+ |
|
| 595 |
+ |
std::fill(isSurfaceID.begin(),isSurfaceID.end(),false); |
| 596 |
+ |
|
| 597 |
+ |
FORALLfacets { |
| 598 |
+ |
|
| 599 |
+ |
if (!facet->simplicial){ |
| 600 |
+ |
// should never happen with Qt |
| 601 |
+ |
sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected"); |
| 602 |
+ |
painCave.isFatal = 1; |
| 603 |
+ |
simError(); |
| 604 |
+ |
} //simplicical |
| 605 |
+ |
|
| 606 |
+ |
Triangle face; |
| 607 |
+ |
Vector3d V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]); |
| 608 |
+ |
face.setNormal(V3dNormal); |
| 609 |
+ |
|
| 610 |
+ |
|
| 611 |
+ |
|
| 612 |
+ |
//RealType faceArea = 0.5*V3dNormal.length(); |
| 613 |
+ |
RealType faceArea = qh_facetarea(facet); |
| 614 |
+ |
face.setArea(faceArea); |
| 615 |
+ |
|
| 616 |
+ |
|
| 617 |
+ |
vertices = qh_facet3vertex(facet); |
| 618 |
+ |
|
| 619 |
+ |
coordT *center = qh_getcenter(vertices); |
| 620 |
+ |
Vector3d V3dCentroid(center[0], center[1], center[2]); |
| 621 |
+ |
face.setCentroid(V3dCentroid); |
| 622 |
+ |
Vector3d faceVel = V3Zero; |
| 623 |
+ |
Vector3d p[3]; |
| 624 |
+ |
RealType faceMass = 0.0; |
| 625 |
+ |
int ver = 0; |
| 626 |
+ |
FOREACHvertex_(vertices){ |
| 627 |
+ |
id = qh_pointid(vertex->point); |
| 628 |
+ |
p[ver][0] = vertex->point[0]; |
| 629 |
+ |
p[ver][1] = vertex->point[1]; |
| 630 |
+ |
p[ver][2] = vertex->point[2]; |
| 631 |
+ |
int localindex = id; |
| 632 |
+ |
#ifdef IS_MPI |
| 633 |
+ |
Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]); |
| 634 |
+ |
|
| 635 |
+ |
faceVel = faceVel + velVector; |
| 636 |
+ |
faceMass = faceMass + globalMass[id]; |
| 637 |
+ |
if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){ |
| 638 |
+ |
localindex = localPtsMap[id-noffset/3]; |
| 639 |
+ |
#else |
| 640 |
+ |
faceVel = faceVel + bodydoubles[localindex]->getVel(); |
| 641 |
+ |
faceMass = faceMass + bodydoubles[localindex]->getMass(); |
| 642 |
+ |
#endif |
| 643 |
+ |
face.addVertexSD(bodydoubles[localindex]); |
| 644 |
+ |
if( !isSurfaceID[id] ){ |
| 645 |
+ |
isSurfaceID[id] = true; |
| 646 |
+ |
#ifdef IS_MPI |
| 647 |
+ |
|
| 648 |
+ |
#endif |
| 649 |
+ |
|
| 650 |
+ |
surfaceSDs_.push_back(bodydoubles[localindex]); |
| 651 |
+ |
|
| 652 |
+ |
} //IF isSurfaceID |
| 653 |
+ |
|
| 654 |
+ |
#ifdef IS_MPI |
| 655 |
+ |
|
| 656 |
+ |
}else{ |
| 657 |
+ |
face.addVertexSD(NULL); |
| 658 |
+ |
} |
| 659 |
+ |
#endif |
| 660 |
+ |
ver++; |
| 661 |
+ |
} //Foreachvertex |
| 662 |
+ |
/* |
| 663 |
+ |
if (!SETempty_(facet->coplanarset)){ |
| 664 |
+ |
FOREACHpoint_(facet->coplanarset){ |
| 665 |
+ |
id = qh_pointid(point); |
| 666 |
+ |
surfaceSDs_.push_back(bodydoubles[id]); |
| 667 |
+ |
} |
| 668 |
+ |
} |
| 669 |
+ |
*/ |
| 670 |
+ |
face.addVertices(p[0],p[1],p[2]); |
| 671 |
+ |
face.setFacetMass(faceMass); |
| 672 |
+ |
face.setFacetVelocity(faceVel/3.0); |
| 673 |
+ |
Triangles_.push_back(face); |
| 674 |
+ |
qh_settempfree(&vertices); |
| 675 |
+ |
|
| 676 |
+ |
} //FORALLfacets |
| 677 |
+ |
|
| 678 |
+ |
/* |
| 679 |
+ |
std::cout << surfaceSDs_.size() << std::endl; |
| 680 |
+ |
for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){ |
| 681 |
+ |
Vector3d thisatom = (*SD)->getPos(); |
| 682 |
+ |
std::cout << "Au " << thisatom.x() << " " << thisatom.y() << " " << thisatom.z() << std::endl; |
| 683 |
+ |
} |
| 684 |
+ |
*/ |
| 685 |
+ |
|
| 686 |
+ |
|
| 687 |
+ |
|
| 688 |
+ |
Ns_ = surfaceSDs_.size(); |
| 689 |
+ |
nTriangles_ = Triangles_.size(); |
| 690 |
+ |
|
| 691 |
+ |
qh_getarea(qh facet_list); |
| 692 |
+ |
volume_ = qh totvol; |
| 693 |
+ |
area_ = qh totarea; |
| 694 |
+ |
|
| 695 |
+ |
|
| 696 |
+ |
|
| 697 |
+ |
qh_freeqhull(!qh_ALL); |
| 698 |
+ |
qh_memfreeshort(&curlong, &totlong); |
| 699 |
+ |
if (curlong || totlong) |
| 700 |
+ |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 701 |
+ |
<< totlong << curlong << std::endl; |
| 702 |
+ |
|
| 703 |
+ |
|
| 704 |
+ |
|
| 705 |
+ |
} |
| 706 |
+ |
|
| 707 |
+ |
|
| 708 |
+ |
|
| 709 |
+ |
void ConvexHull::printHull(const std::string& geomFileName) |
| 710 |
+ |
{ |
| 711 |
+ |
|
| 712 |
+ |
FILE *newGeomFile; |
| 713 |
+ |
|
| 714 |
+ |
//create new .md file based on old .md file |
| 715 |
+ |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 716 |
+ |
qh_findgood_all(qh facet_list); |
| 717 |
+ |
for (int i = 0; i < qh_PRINTEND; i++) |
| 718 |
+ |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 719 |
+ |
|
| 720 |
+ |
fclose(newGeomFile); |
| 721 |
+ |
} |
| 722 |
+ |
#endif //QHULL |
| 723 |
+ |
#endif //CGAL |
| 724 |
+ |
|
| 725 |
+ |
|
| 726 |
+ |
|
