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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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> |
* @version $Id: ConvexHull.cpp,v 1.8 2008-09-14 01:32:25 chuckv Exp $ |
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* |
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*/ |
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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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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/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/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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< |
#include <CGAL/Quotient.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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> |
//#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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< |
ConvexHull::ConvexHull(){} |
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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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< |
bool ConvexHull::genHull(std::vector<Vector3d> pos) |
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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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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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// 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(); |
| 157 |
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|
| 158 |
> |
|
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> |
#endif |
| 160 |
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} |
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|
| 162 |
> |
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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std::vector<Point> points; |
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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) |
| 170 |
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std::vector<StuntDouble*>::iterator SD; |
| 171 |
> |
|
| 172 |
> |
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD) |
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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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> |
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 |
| 182 |
< |
Polyhedron_3 ch_object_; |
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> |
CGAL::Object ch_object_; |
| 183 |
> |
Polyhedron_3 polyhedron; |
| 184 |
> |
|
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// compute convex hull |
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CGAL::convex_hull_3(points.begin(), points.end(), ch_object_); |
| 186 |
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|
| 187 |
< |
for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin(); ch_object_.vertices_end(); ++v){ |
| 188 |
< |
std::cout<< v.point()<<std::endl; |
| 187 |
> |
std::vector<Enriched_Point_3>::iterator testpt; |
| 188 |
> |
|
| 189 |
> |
|
| 190 |
> |
|
| 191 |
> |
CGAL::convex_hull_3(points.begin(), points.end(), polyhedron); |
| 192 |
> |
|
| 193 |
> |
|
| 194 |
> |
|
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> |
Ns_ = polyhedron.size_of_vertices(); |
| 196 |
> |
|
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> |
#ifdef IS_MPI |
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> |
/* Gather an array of the number of verticies on each processor */ |
| 199 |
> |
|
| 200 |
> |
|
| 201 |
> |
surfacePtsGlobal_.clear(); |
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> |
surfacePtsLocal_.clear(); |
| 203 |
> |
|
| 204 |
> |
MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT); |
| 205 |
> |
|
| 206 |
> |
for (int i = 0; i < nproc_; i++){ |
| 207 |
> |
Nsglobal_ += NstoProc_[i]; |
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> |
} |
| 209 |
> |
/*Reminder ideally, we would like to reserve size for the vectors here*/ |
| 210 |
> |
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 */ |
| 215 |
> |
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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> |
|
| 219 |
> |
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){ |
| 224 |
> |
Point_3 mypoint = *hc; |
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> |
surfacePt_ mpiSurfacePt; |
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> |
mpiSurfacePt.x = CGAL::to_double(mypoint.x()); |
| 227 |
> |
mpiSurfacePt.y = CGAL::to_double(mypoint.y()); |
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> |
mpiSurfacePt.z = CGAL::to_double(mypoint.z()); |
| 229 |
> |
surfacePtsLocal_.push_back(mpiSurfacePt); |
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|
} |
| 231 |
+ |
|
| 232 |
+ |
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; |
| 235 |
+ |
|
| 236 |
+ |
int mine = 0; |
| 237 |
+ |
int pointidx = 0; |
| 238 |
+ |
for (spt = surfacePtsGlobal_.begin(); spt != surfacePtsGlobal_.end(); ++spt) |
| 239 |
+ |
{ |
| 240 |
+ |
surfacePt_ thispos = *spt; |
| 241 |
+ |
Enriched_Point_3 ept(thispos.x,thispos.y,thispos.z); |
| 242 |
+ |
if (mine >= noffset && mine < noffset + Ns_){ |
| 243 |
+ |
ept.myPoint(); |
| 244 |
+ |
ept.setSD(points[pointidx].getStuntDouble()); |
| 245 |
+ |
pointidx++; |
| 246 |
+ |
} |
| 247 |
+ |
gblpoints.push_back(ept); |
| 248 |
+ |
|
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+ |
mine++; |
| 250 |
+ |
} |
| 251 |
+ |
|
| 252 |
+ |
/* Compute the global hull */ |
| 253 |
+ |
polyhedron.clear(); |
| 254 |
+ |
CGAL::convex_hull_3(gblpoints.begin(), gblpoints.end(), polyhedron); |
| 255 |
+ |
|
| 256 |
+ |
|
| 257 |
+ |
#endif |
| 258 |
+ |
|
| 259 |
+ |
|
| 260 |
|
|
| 261 |
+ |
/* Loop over all of the surface triangles and build data structures for atoms and normals*/ |
| 262 |
+ |
Facet_iterator j; |
| 263 |
+ |
area_ = 0; |
| 264 |
+ |
for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) { |
| 265 |
+ |
Halfedge_handle h = j->halfedge(); |
| 266 |
+ |
|
| 267 |
+ |
Point_3 r0=h->vertex()->point(); |
| 268 |
+ |
Point_3 r1=h->next()->vertex()->point(); |
| 269 |
+ |
Point_3 r2=h->next()->next()->vertex()->point(); |
| 270 |
+ |
|
| 271 |
+ |
Point_3* pr0 = &r0; |
| 272 |
+ |
Point_3* pr1 = &r1; |
| 273 |
+ |
Point_3* pr2 = &r2; |
| 274 |
+ |
|
| 275 |
+ |
Enriched_Point_3* er0 = static_cast<Enriched_Point_3*>(pr0); |
| 276 |
+ |
Enriched_Point_3* er1 = static_cast<Enriched_Point_3*>(pr1); |
| 277 |
+ |
Enriched_Point_3* er2 = static_cast<Enriched_Point_3*>(pr2); |
| 278 |
+ |
|
| 279 |
+ |
// StuntDouble* sd = er0->getStuntDouble(); |
| 280 |
+ |
std::cerr << "sd globalIndex = " << to_double(er0->x()) << "\n"; |
| 281 |
+ |
|
| 282 |
+ |
Point_3 thisCentroid = CGAL::centroid(r0,r1,r2); |
| 283 |
+ |
|
| 284 |
+ |
Vector_3 normal = CGAL::cross_product(r1-r0,r2-r0); |
| 285 |
+ |
|
| 286 |
+ |
Triangle* face = new Triangle(); |
| 287 |
+ |
Vector3d V3dNormal(CGAL::to_double(normal.x()),CGAL::to_double(normal.y()),CGAL::to_double(normal.z())); |
| 288 |
+ |
Vector3d V3dCentroid(CGAL::to_double(thisCentroid.x()),CGAL::to_double(thisCentroid.y()),CGAL::to_double(thisCentroid.z())); |
| 289 |
+ |
face->setNormal(V3dNormal); |
| 290 |
+ |
face->setCentroid(V3dCentroid); |
| 291 |
+ |
RealType faceArea = 0.5*V3dNormal.length(); |
| 292 |
+ |
face->setArea(faceArea); |
| 293 |
+ |
area_ += faceArea; |
| 294 |
+ |
Triangles_.push_back(face); |
| 295 |
+ |
// ptMapType::const_iterator locn=myMap.find(mypoint); |
| 296 |
+ |
// int myIndex = locn->second; |
| 297 |
+ |
|
| 298 |
+ |
} |
| 299 |
|
|
| 300 |
+ |
std::cout << "Number of surface atoms is: " << Ns_ << std::endl; |
| 301 |
+ |
|
| 302 |
+ |
|
| 303 |
+ |
|
| 304 |
|
} |
| 305 |
+ |
void ConvexHull::printHull(const std::string& geomFileName) |
| 306 |
+ |
{ |
| 307 |
+ |
/* |
| 308 |
+ |
std::ofstream newGeomFile; |
| 309 |
+ |
|
| 310 |
+ |
//create new .md file based on old .md file |
| 311 |
+ |
newGeomFile.open("testhull.off"); |
| 312 |
+ |
|
| 313 |
+ |
// Write polyhedron in Object File Format (OFF). |
| 314 |
+ |
CGAL::set_ascii_mode( std::cout); |
| 315 |
+ |
newGeomFile << "OFF" << std::endl << polyhedron.size_of_vertices() << ' ' |
| 316 |
+ |
<< polyhedron.size_of_facets() << " 0" << std::endl; |
| 317 |
+ |
std::copy( polyhedron.points_begin(), polyhedron.points_end(), |
| 318 |
+ |
std::ostream_iterator<Point_3>( newGeomFile, "\n")); |
| 319 |
+ |
for ( Facet_iterator i = polyhedron.facets_begin(); i != polyhedron.facets_end(); ++i) { |
| 320 |
+ |
Halfedge_facet_circulator j = i->facet_begin(); |
| 321 |
+ |
// Facets in polyhedral surfaces are at least triangles. |
| 322 |
+ |
CGAL_assertion( CGAL::circulator_size(j) >= 3); |
| 323 |
+ |
newGeomFile << CGAL::circulator_size(j) << ' '; |
| 324 |
+ |
do { |
| 325 |
+ |
newGeomFile << ' ' << std::distance(polyhedron.vertices_begin(), j->vertex()); |
| 326 |
+ |
} while ( ++j != i->facet_begin()); |
| 327 |
+ |
newGeomFile << std::endl; |
| 328 |
+ |
} |
| 329 |
+ |
|
| 330 |
+ |
newGeomFile.close(); |
| 331 |
+ |
*/ |
| 332 |
+ |
/* |
| 333 |
+ |
std::ofstream newGeomFile; |
| 334 |
|
|
| 335 |
+ |
//create new .md file based on old .md file |
| 336 |
+ |
newGeomFile.open(geomFileName.c_str()); |
| 337 |
|
|
| 338 |
+ |
// Write polyhedron in Object File Format (OFF). |
| 339 |
+ |
CGAL::set_ascii_mode( std::cout); |
| 340 |
+ |
newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' ' |
| 341 |
+ |
<< ch_polyhedron.size_of_facets() << " 0" << std::endl; |
| 342 |
+ |
std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(), |
| 343 |
+ |
std::ostream_iterator<Point_3>( newGeomFile, "\n")); |
| 344 |
+ |
for ( Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i) |
| 345 |
+ |
{ |
| 346 |
+ |
Halfedge_facet_circulator j = i->facet_begin(); |
| 347 |
+ |
// Facets in polyhedral surfaces are at least triangles. |
| 348 |
+ |
CGAL_assertion( CGAL::circulator_size(j) >= 3); |
| 349 |
+ |
newGeomFile << CGAL::circulator_size(j) << ' '; |
| 350 |
+ |
do |
| 351 |
+ |
{ |
| 352 |
+ |
newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex()); |
| 353 |
+ |
} |
| 354 |
+ |
while ( ++j != i->facet_begin()); |
| 355 |
+ |
newGeomFile << std::endl; |
| 356 |
+ |
} |
| 357 |
|
|
| 358 |
+ |
newGeomFile.close(); |
| 359 |
+ |
*/ |
| 360 |
+ |
|
| 361 |
+ |
} |
| 362 |
+ |
|
| 363 |
+ |
|
| 364 |
+ |
|
| 365 |
+ |
|
| 366 |
+ |
|
| 367 |
+ |
|
| 368 |
+ |
|
| 369 |
|
#else |
| 370 |
|
#ifdef HAVE_QHULL |
| 371 |
|
/* Old options Qt Qu Qg QG0 FA */ |
| 372 |
< |
ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt Qci Tcv Pp") |
| 373 |
< |
//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i") |
| 374 |
< |
{} |
| 372 |
> |
ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Qci Tcv Pp") { |
| 373 |
> |
//If we are doing the mpi version, set up some vectors for data communication |
| 374 |
> |
#ifdef IS_MPI |
| 375 |
|
|
| 376 |
< |
bool ConvexHull::genHull(std::vector<Vector3d> pos) |
| 376 |
> |
|
| 377 |
> |
nproc_ = MPI::COMM_WORLD.Get_size(); |
| 378 |
> |
myrank_ = MPI::COMM_WORLD.Get_rank(); |
| 379 |
> |
NstoProc_ = new int[nproc_]; |
| 380 |
> |
displs_ = new int[nproc_]; |
| 381 |
> |
|
| 382 |
> |
// Create a surface point type in MPI to send |
| 383 |
> |
surfacePtType = MPI::DOUBLE.Create_contiguous(3); |
| 384 |
> |
surfacePtType.Commit(); |
| 385 |
> |
|
| 386 |
> |
|
| 387 |
> |
#endif |
| 388 |
> |
} |
| 389 |
> |
|
| 390 |
> |
|
| 391 |
> |
|
| 392 |
> |
void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) |
| 393 |
|
{ |
| 394 |
|
|
| 395 |
< |
|
| 396 |
< |
int numpoints = pos.size(); |
| 397 |
< |
coordT* pt_array; |
| 395 |
> |
std::vector<int> surfaceIDs; |
| 396 |
> |
std::vector<int> surfaceIDsGlobal; |
| 397 |
> |
std::vector<int> localPtsMap; |
| 398 |
> |
int numpoints = bodydoubles.size(); |
| 399 |
> |
|
| 400 |
> |
//coordT* pt_array; |
| 401 |
|
coordT* surfpt_array; |
| 402 |
< |
std::list<int> surface_atoms; |
| 402 |
> |
vertexT *vertex, **vertexp; |
| 403 |
> |
facetT *facet; |
| 404 |
> |
setT *vertices; |
| 405 |
> |
int curlong,totlong; |
| 406 |
> |
int id; |
| 407 |
> |
|
| 408 |
> |
coordT *point,**pointp; |
| 409 |
> |
|
| 410 |
> |
|
| 411 |
|
FILE *outdummy = NULL; |
| 412 |
|
FILE *errdummy = NULL; |
| 413 |
|
|
| 414 |
< |
pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_)); |
| 414 |
> |
//pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_)); |
| 415 |
> |
|
| 416 |
> |
double* ptArray = new double[numpoints * 3]; |
| 417 |
> |
std::vector<bool> isSurfaceID(numpoints); |
| 418 |
> |
|
| 419 |
> |
// Copy the positon vector into a points vector for qhull. |
| 420 |
> |
std::vector<StuntDouble*>::iterator SD; |
| 421 |
> |
int i = 0; |
| 422 |
> |
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD) |
| 423 |
> |
{ |
| 424 |
> |
Vector3d pos = (*SD)->getPos(); |
| 425 |
> |
|
| 426 |
> |
ptArray[dim_ * i] = pos.x(); |
| 427 |
> |
ptArray[dim_ * i + 1] = pos.y(); |
| 428 |
> |
ptArray[dim_ * i + 2] = pos.z(); |
| 429 |
> |
i++; |
| 430 |
> |
} |
| 431 |
|
|
| 432 |
+ |
|
| 433 |
|
|
| 131 |
– |
for (int i = 0; i < numpoints; i++) { |
| 132 |
– |
pt_array[dim_ * i] = pos[i][0]; |
| 133 |
– |
pt_array[dim_ * i + 1] = pos[i][1]; |
| 134 |
– |
pt_array[dim_ * i + 2] = pos[i][2]; |
| 135 |
– |
} |
| 434 |
|
|
| 435 |
|
|
| 436 |
|
|
| 437 |
+ |
boolT ismalloc = False; |
| 438 |
+ |
Triangles_.clear(); |
| 439 |
+ |
surfaceSDs_.clear(); |
| 440 |
|
|
| 441 |
< |
/* |
| 442 |
< |
qh_initflags(const_cast<char *>(options_.c_str())); |
| 142 |
< |
qh_init_B(pospoints, numpoints, dim_, ismalloc); |
| 143 |
< |
qh_qhull(); |
| 144 |
< |
qh_check_output(); |
| 441 |
> |
if (qh_new_qhull(dim_, numpoints, ptArray, ismalloc, |
| 442 |
> |
const_cast<char *>(options_.c_str()), NULL, stderr)) { |
| 443 |
|
|
| 444 |
< |
qh_produce_output(); |
| 445 |
< |
*/ |
| 446 |
< |
boolT ismalloc = False; |
| 444 |
> |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull"); |
| 445 |
> |
painCave.isFatal = 0; |
| 446 |
> |
simError(); |
| 447 |
> |
|
| 448 |
> |
} //qh_new_qhull |
| 449 |
> |
|
| 450 |
> |
|
| 451 |
> |
#ifdef IS_MPI |
| 452 |
> |
std::vector<double> localPts; |
| 453 |
> |
int localPtArraySize; |
| 454 |
|
|
| 455 |
< |
if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc, |
| 456 |
< |
const_cast<char *>(options_.c_str()), NULL, stderr)) { |
| 455 |
> |
std::fill(isSurfaceID.begin(),isSurfaceID.end(),false); |
| 456 |
> |
|
| 457 |
> |
FORALLfacets { |
| 458 |
|
|
| 459 |
< |
vertexT *vertex, **vertexp; |
| 154 |
< |
facetT *facet; |
| 155 |
< |
setT *vertices; |
| 156 |
< |
unsigned int nf = qh num_facets; |
| 157 |
< |
|
| 158 |
< |
//Matrix idx(nf, dim); |
| 159 |
< |
/* |
| 160 |
< |
int j, i = 0, id = 0; |
| 161 |
< |
|
| 162 |
< |
int id2 = 0; |
| 163 |
< |
coordT *point,**pointp; |
| 164 |
< |
realT dist; |
| 165 |
< |
FORALLfacets { |
| 166 |
< |
j = 0; |
| 167 |
< |
|
| 168 |
< |
if (!facet->simplicial){ |
| 459 |
> |
if (!facet->simplicial){ |
| 460 |
|
// should never happen with Qt |
| 461 |
|
sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected"); |
| 462 |
|
painCave.isFatal = 0; |
| 463 |
|
simError(); |
| 464 |
< |
} |
| 465 |
< |
|
| 466 |
< |
vertices = qh_facet3vertex(facet); |
| 467 |
< |
FOREACHvertex_(vertices){ |
| 464 |
> |
} |
| 465 |
> |
|
| 466 |
> |
|
| 467 |
> |
vertices = qh_facet3vertex(facet); |
| 468 |
> |
FOREACHvertex_(vertices){ |
| 469 |
|
id = qh_pointid(vertex->point); |
| 470 |
< |
surface_atoms.push_back(id); |
| 471 |
< |
//std::cout << "Ag " << pos[id][0] << " " << pos[id][1] << " " << pos[id][2]<< std::endl; |
| 470 |
> |
|
| 471 |
> |
if( !isSurfaceID[id] ){ |
| 472 |
> |
isSurfaceID[id] = true; |
| 473 |
|
} |
| 474 |
< |
qh_settempfree(&vertices); |
| 474 |
> |
} |
| 475 |
> |
qh_settempfree(&vertices); |
| 476 |
|
|
| 477 |
< |
FOREACHpoint_(facet->coplanarset){ |
| 184 |
< |
vertex= qh_nearvertex (facet, point, &dist); |
| 185 |
< |
//id= qh_pointid (vertex->point); |
| 186 |
< |
id2= qh_pointid (point); |
| 187 |
< |
surface_atoms.push_back(id2); |
| 188 |
< |
//std::cout << "Ag " << pos[id2][0] << " " << pos[id2][1] << " " << pos[id2][2]<< std::endl; |
| 189 |
< |
//printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist); |
| 190 |
< |
//std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id; |
| 191 |
< |
|
| 192 |
< |
} |
| 193 |
< |
|
| 194 |
< |
} |
| 195 |
< |
|
| 196 |
< |
*/ |
| 197 |
< |
|
| 198 |
< |
|
| 199 |
< |
} |
| 477 |
> |
} //FORALLfacets |
| 478 |
|
|
| 479 |
+ |
|
| 480 |
|
|
| 481 |
+ |
/* |
| 482 |
+ |
std::sort(surfaceIDs.begin(),surfaceIDs.end()); |
| 483 |
+ |
surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end()); |
| 484 |
+ |
int localPtArraySize = surfaceIDs.size() * 3; |
| 485 |
+ |
*/ |
| 486 |
|
|
| 487 |
+ |
localPts.resize(localPtArraySize); |
| 488 |
+ |
// std::fill(localPts.begin(),globalPts.end(),0.0); |
| 489 |
|
|
| 490 |
< |
qh_getarea(qh facet_list); |
| 491 |
< |
volume_ = qh totvol; |
| 492 |
< |
area_ = qh totarea; |
| 493 |
< |
// FILE *newGeomFile; |
| 490 |
> |
|
| 491 |
> |
int idx = 0; |
| 492 |
> |
// Copy the surface points into an array. |
| 493 |
> |
for(std::vector<bool>::iterator list_iter = isSurfaceID.begin(); |
| 494 |
> |
list_iter != isSurfaceID.end(); list_iter++) |
| 495 |
> |
{ |
| 496 |
> |
bool isIt = *list_iter; |
| 497 |
> |
if (isIt){ |
| 498 |
> |
localPts.push_back(ptArray[dim_ * idx]); |
| 499 |
> |
localPts.push_back(ptArray[dim_ * idx + 1]); |
| 500 |
> |
localPts.push_back(ptArray[dim_ * idx + 2]); |
| 501 |
> |
localPtsMap.push_back(idx); |
| 502 |
> |
} //Isit |
| 503 |
> |
idx++; |
| 504 |
> |
} //isSurfaceID |
| 505 |
|
|
| 506 |
+ |
|
| 507 |
+ |
localPtArraySize = localPts.size(); |
| 508 |
+ |
MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT); |
| 509 |
+ |
|
| 510 |
+ |
for (int i = 0; i < nproc_; i++){ |
| 511 |
+ |
Nsglobal_ += NstoProc_[i]; |
| 512 |
+ |
} |
| 513 |
+ |
|
| 514 |
+ |
std::vector<double> globalPts; |
| 515 |
+ |
globalPts.resize(Nsglobal_); |
| 516 |
+ |
isSurfaceID.resize(int(Nsglobal_/3)); |
| 517 |
+ |
std::fill(globalPts.begin(),globalPts.end(),0.0); |
| 518 |
+ |
/* Build a displacements array */ |
| 519 |
+ |
for (int i = 1; i < nproc_; i++){ |
| 520 |
+ |
displs_[i] = displs_[i-1] + NstoProc_[i-1]; |
| 521 |
+ |
} |
| 522 |
|
|
| 523 |
< |
/* |
| 524 |
< |
FORALLfacets { |
| 212 |
< |
for (int k=0; k < qh hull_dim; k++) |
| 213 |
< |
printf ("%6.2g ", facet->normal[k]); |
| 214 |
< |
printf ("\n"); |
| 215 |
< |
} |
| 216 |
< |
*/ |
| 523 |
> |
int noffset = displs_[myrank_]; |
| 524 |
> |
/* gather the potential hull */ |
| 525 |
|
|
| 526 |
< |
int curlong,totlong; |
| 527 |
< |
// geomviewHull("junk.off"); |
| 526 |
> |
MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],NstoProc_,displs_,MPI::DOUBLE); |
| 527 |
> |
|
| 528 |
> |
|
| 529 |
> |
|
| 530 |
> |
|
| 531 |
> |
// Free previous hull |
| 532 |
|
qh_freeqhull(!qh_ALL); |
| 533 |
|
qh_memfreeshort(&curlong, &totlong); |
| 534 |
|
if (curlong || totlong) |
| 535 |
|
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 536 |
|
<< totlong << curlong << std::endl; |
| 537 |
< |
free(pt_array); |
| 538 |
< |
/* |
| 539 |
< |
int j = 0; |
| 540 |
< |
surface_atoms.sort(); |
| 541 |
< |
surface_atoms.unique(); |
| 542 |
< |
surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_)); |
| 543 |
< |
for(std::list<int>::iterator list_iter = surface_atoms.begin(); |
| 544 |
< |
list_iter != surface_atoms.end(); list_iter++) |
| 537 |
> |
|
| 538 |
> |
if (qh_new_qhull(dim_, numpoints, &globalPts[0], ismalloc, |
| 539 |
> |
const_cast<char *>(options_.c_str()), NULL, stderr)){ |
| 540 |
> |
|
| 541 |
> |
sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull"); |
| 542 |
> |
painCave.isFatal = 0; |
| 543 |
> |
simError(); |
| 544 |
> |
|
| 545 |
> |
} //qh_new_qhull |
| 546 |
> |
|
| 547 |
> |
#endif |
| 548 |
> |
|
| 549 |
> |
|
| 550 |
> |
|
| 551 |
> |
|
| 552 |
> |
|
| 553 |
> |
|
| 554 |
> |
unsigned int nf = qh num_facets; |
| 555 |
> |
|
| 556 |
> |
/* Build Surface SD list first */ |
| 557 |
> |
|
| 558 |
> |
std::fill(isSurfaceID.begin(),isSurfaceID.end(),false); |
| 559 |
> |
|
| 560 |
> |
FORALLfacets { |
| 561 |
> |
|
| 562 |
> |
if (!facet->simplicial){ |
| 563 |
> |
// should never happen with Qt |
| 564 |
> |
sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected"); |
| 565 |
> |
painCave.isFatal = 0; |
| 566 |
> |
simError(); |
| 567 |
> |
} //simplicical |
| 568 |
> |
|
| 569 |
> |
Triangle* face = new Triangle(); |
| 570 |
> |
Vector3d V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]); |
| 571 |
> |
face->setNormal(V3dNormal); |
| 572 |
> |
//face->setCentroid(V3dCentroid); |
| 573 |
> |
RealType faceArea = 0.5*V3dNormal.length(); |
| 574 |
> |
face->setArea(faceArea); |
| 575 |
> |
|
| 576 |
> |
|
| 577 |
> |
vertices = qh_facet3vertex(facet); |
| 578 |
> |
FOREACHvertex_(vertices){ |
| 579 |
> |
id = qh_pointid(vertex->point); |
| 580 |
> |
face->addVertex(bodydoubles[id]); |
| 581 |
> |
if( !isSurfaceID[id] ){ |
| 582 |
> |
isSurfaceID[id] = true; |
| 583 |
> |
surfaceSDs_.push_back(bodydoubles[id]); |
| 584 |
> |
} //IF isSurfaceID |
| 585 |
> |
} //Foreachvertex |
| 586 |
> |
|
| 587 |
> |
|
| 588 |
> |
Triangles_.push_back(face); |
| 589 |
> |
qh_settempfree(&vertices); |
| 590 |
> |
|
| 591 |
> |
} //FORALLfacets |
| 592 |
> |
|
| 593 |
> |
|
| 594 |
> |
|
| 595 |
> |
|
| 596 |
> |
/* |
| 597 |
> |
std::sort(surfaceIDs.begin(),surfaceIDs.end()); |
| 598 |
> |
surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end()); |
| 599 |
> |
for(std::vector<int>::iterator list_iter = surfaceIDs.begin(); |
| 600 |
> |
list_iter != surfaceIDs.end(); list_iter++) |
| 601 |
|
{ |
| 602 |
|
int i = *list_iter; |
| 603 |
< |
//surfpt_array[dim_ * j] = pos[i][0]; |
| 236 |
< |
//surfpt_array[dim_ * j + 1] = pos[i][1]; |
| 237 |
< |
//surfpt_array[dim_ * j + 2] = pos[i][2]; |
| 238 |
< |
std::cout << "Ag " << pos[i][0] << " " << pos[i][1] << " "<< pos[i][2] << std::endl; |
| 239 |
< |
j++; |
| 603 |
> |
surfaceSDs_.push_back(bodydoubles[i]); |
| 604 |
|
} |
| 605 |
< |
*/ |
| 242 |
< |
|
| 243 |
< |
/* |
| 244 |
< |
std::string deloptions_ = "qhull d Qt"; |
| 245 |
< |
facetT *facet, *neighbor; |
| 246 |
< |
ridgeT *ridge, **ridgep; |
| 247 |
< |
|
| 248 |
< |
if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc, |
| 249 |
< |
const_cast<char *>(deloptions_.c_str()), NULL, stderr)) { |
| 250 |
< |
|
| 251 |
< |
qh visit_id++; |
| 252 |
< |
FORALLfacets { |
| 253 |
< |
if (!facet->upperdelaunay) { |
| 254 |
< |
facet->visitid= qh visit_id; |
| 255 |
< |
qh_makeridges(facet); |
| 256 |
< |
FOREACHridge_(facet->ridges) { |
| 257 |
< |
neighbor= otherfacet_(ridge, facet); |
| 258 |
< |
if (neighbor->visitid != qh visit_id) { |
| 259 |
< |
|
| 260 |
< |
FOREACHvertex_(ridge->vertices) |
| 261 |
< |
int id2 = qh_pointid (vertex->point); |
| 262 |
< |
std::cout << "Ag " << pos[id2][0] << " " << pos[id2][1] << " " << pos[id2][2]<< std::endl; |
| 263 |
< |
} |
| 264 |
< |
} |
| 265 |
< |
} |
| 266 |
< |
|
| 605 |
> |
*/ |
| 606 |
|
|
| 607 |
|
|
| 269 |
– |
|
| 270 |
– |
} |
| 608 |
|
|
| 272 |
– |
qh_freeqhull(!qh_ALL); |
| 273 |
– |
qh_memfreeshort(&curlong, &totlong); |
| 274 |
– |
if (curlong || totlong) |
| 275 |
– |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 276 |
– |
<< totlong << curlong << std::endl; |
| 277 |
– |
free(surfpt_array); |
| 278 |
– |
*/ |
| 279 |
– |
return true; |
| 280 |
– |
} |
| 609 |
|
|
| 610 |
|
|
| 611 |
|
|
| 612 |
< |
RealType ConvexHull::getVolume() |
| 613 |
< |
{ |
| 614 |
< |
return volume_; |
| 612 |
> |
Ns_ = surfaceSDs_.size(); |
| 613 |
> |
|
| 614 |
> |
|
| 615 |
> |
qh_getarea(qh facet_list); |
| 616 |
> |
volume_ = qh totvol; |
| 617 |
> |
area_ = qh totarea; |
| 618 |
> |
|
| 619 |
> |
|
| 620 |
> |
|
| 621 |
> |
qh_freeqhull(!qh_ALL); |
| 622 |
> |
qh_memfreeshort(&curlong, &totlong); |
| 623 |
> |
if (curlong || totlong) |
| 624 |
> |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 625 |
> |
<< totlong << curlong << std::endl; |
| 626 |
> |
|
| 627 |
> |
|
| 628 |
> |
// free(pt_array); |
| 629 |
> |
|
| 630 |
|
} |
| 631 |
|
|
| 632 |
< |
void ConvexHull::geomviewHull(const std::string& geomFileName) |
| 632 |
> |
|
| 633 |
> |
|
| 634 |
> |
void ConvexHull::printHull(const std::string& geomFileName) |
| 635 |
|
{ |
| 636 |
|
|
| 637 |
|
FILE *newGeomFile; |
