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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1292 by chuckv, Wed Jun 18 17:03:30 2008 UTC vs.
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC

# Line 44 | Line 44
44   *
45   *  Created by Charles F. Vardeman II on 11 Dec 2006.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: ConvexHull.cpp,v 1.7 2008-06-18 17:03:30 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.8 2008-09-14 01:32:25 chuckv Exp $
48   *
49   */
50  
# Line 56 | Line 56
56   #include <iterator>
57   #include "math/ConvexHull.hpp"
58   #include "utils/simError.h"
59 +
60 +
61   using namespace oopse;
62  
63   /* CGAL version of convex hull first then QHULL */
64   #ifdef HAVE_CGAL
65 <
65 > //#include <CGAL/Homogeneous.h>
66   #include <CGAL/basic.h>
67 < #include <CGAL/Simple_cartesian.h>
67 > //#include <CGAL/Simple_cartesian.h>
68 > #include <CGAL/Cartesian.h>
69 > #include <CGAL/Origin.h>
70 > #include <CGAL/Exact_predicates_exact_constructions_kernel.h>
71   #include <CGAL/Convex_hull_traits_3.h>
72   #include <CGAL/convex_hull_3.h>
73 + #include <CGAL/Polyhedron_traits_with_normals_3.h>
74 + #include <CGAL/Polyhedron_3.h>
75   #include <CGAL/double.h>
76 + #include <CGAL/number_utils.h>
77  
78 < #include <CGAL/Quotient.h>
78 >
79 > //#include <CGAL/Quotient.h>
80   #include <CGAL/MP_Float.h>
81 < #include <CGAL/Lazy_exact_nt.h>
81 > //#include <CGAL/Lazy_exact_nt.h>
82  
83 < typedef double RT;
84 < typedef CGAL::Simple_cartesian<RT>                K;
85 < typedef CGAL::Convex_hull_traits_3<K>             Traits;
86 < typedef Traits::Polyhedron_3                      Polyhedron_3;
83 >
84 >
85 > typedef CGAL::MP_Float RT;
86 > //typedef double RT;
87 > //typedef CGAL::Homogeneous<RT>                     K;
88 > typedef CGAL::Exact_predicates_exact_constructions_kernel K;
89 > typedef K::Vector_3                               Vector_3;
90 > //typedef CGAL::Convex_hull_traits_3<K>             Traits;
91 > typedef CGAL::Polyhedron_traits_with_normals_3<K> Traits;
92 > //typedef Traits::Polyhedron_3                      Polyhedron_3;
93 > typedef CGAL::Polyhedron_3<Traits>                     Polyhedron_3;
94   typedef K::Point_3                                Point_3;
95  
96  
97 < ConvexHull::ConvexHull(){}
97 > typedef Polyhedron_3::HalfedgeDS             HalfedgeDS;
98 > typedef Polyhedron_3::Facet_iterator                   Facet_iterator;
99 > typedef Polyhedron_3::Halfedge_around_facet_circulator Halfedge_facet_circulator;
100 > typedef Polyhedron_3::Halfedge_handle Halfedge_handle;
101 > typedef Polyhedron_3::Facet_iterator Facet_iterator;
102 > typedef Polyhedron_3::Plane_iterator Plane_iterator;
103 > typedef Polyhedron_3::Vertex_iterator Vertex_iterator;
104 > typedef Polyhedron_3::Vertex_handle Vertex_handle;
105 > typedef Polyhedron_3::Point_iterator Point_iterator;
106 >
107  
108 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
108 >
109 > class Enriched_Point_3 : public K::Point_3{
110 > public:
111 >  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
112 >
113 >  bool isMyPoint() const{ return yupMyPoint; }
114 >  void myPoint(){ yupMyPoint = true; }
115 >  void setSD(StuntDouble* SD){mySD = SD;}
116 >  StuntDouble* getStuntDouble(){return mySD;}
117 > private:
118 >  bool yupMyPoint;
119 >  StuntDouble* mySD;
120 >
121 > };
122 >
123 >
124 >
125 >
126 >
127 >    // compare Point_3's... used in setting up the STL map from points to indices
128 > template <typename Pt3>
129 > struct Point_3_comp {
130 >  bool operator() (const Pt3 & p, const Pt3 & q) const {
131 >    return CGAL::lexicographically_xyz_smaller(p,q); // this is defined inline & hence we had to create fn object & not ptrfun
132 >  }
133 > };
134 >
135 > // coordinate-based hashing inefficient but can we do better if pts are copied?
136 > typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
137 >
138 > #ifdef IS_MPI
139 > struct {
140 >  double x,y,z;
141 > } surfacePt;
142 > #endif
143 >
144 > ConvexHull::ConvexHull() : Hull(){
145 >  //If we are doing the mpi version, set up some vectors for data communication
146 > #ifdef IS_MPI
147 >
148 >
149 > nproc_ = MPI::COMM_WORLD.Get_size();
150 > myrank_ = MPI::COMM_WORLD.Get_rank();
151 > NstoProc_ = new int[nproc_];
152 > displs_   = new int[nproc_];
153 >
154 > // Create a surface point type in MPI to send
155 > surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156 > surfacePtType.Commit();
157 >
158 >
159 > #endif
160 > }
161 >
162 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
163   {
164 +
165 +  std::vector<Enriched_Point_3> points;
166 +  ptMapType myMap;
167 +  Point_iterator   hc;
168    
86 –  std::vector<Point_3> points;  
87 –  
88 –  
169    // Copy the positon vector into a points vector for cgal.
170 <  for (int i = 0; i < pos.size(); ++i)
170 >  std::vector<StuntDouble*>::iterator SD;
171 >
172 >    for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
173      {
174 <      Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
175 <      points.push_back(pt);
174 >      Vector3d pos = (*SD)->getPos();
175 >      Enriched_Point_3* pt = new Enriched_Point_3(pos.x(),pos.y(),pos.z());
176 >      pt->setSD(*SD);    
177 >      points.push_back(*pt);
178 >      // myMap[pt]=(*SD);
179      }
180    
181    // define object to hold convex hull
# Line 98 | Line 183 | bool ConvexHull::genHull(std::vector<Vector3d> pos)
183    Polyhedron_3 polyhedron;
184  
185    // compute convex hull
186 <  std::cerr << "Creating hull" << std::endl;
187 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
188 <  std::cerr << "Done Creating hull" << std::endl;
189 <  std::vector<Point_3>::const_iterator p_it;
186 >  
187 >  std::vector<Enriched_Point_3>::iterator testpt;
188 >  
189 >  
190 >
191 >  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 >
193  
194 <  for (p_it = points.begin(); p_it != points.end(); p_it++)
195 <    {
196 <      std::cerr << (*p_it).x() << std::endl;
194 >
195 >  Ns_ = polyhedron.size_of_vertices();
196 >
197 > #ifdef IS_MPI
198 >  /* Gather an array of the number of verticies on each processor */
199 >  
200 >
201 >  surfacePtsGlobal_.clear();
202 >  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];
208 >  }
209 >  /*Reminder ideally, we would like to reserve size for the vectors here*/
210 >  surfacePtsLocal_.reserve(Ns_);
211 >  surfacePtsGlobal_.resize(Nsglobal_);
212 >  //  std::fill(surfacePtsGlobal_.begin(),surfacePtsGlobal_.end(),0);
213 >
214 >  /* Build a displacements array */
215 >  for (int i = 1; i < nproc_; i++){
216 >    displs_[i] = displs_[i-1] + NstoProc_[i-1];
217 >  }
218 >  
219 >  int noffset = displs_[myrank_];
220 >  /* gather the potential hull */
221 >  
222 >  
223 >  for (hc =polyhedron.points_begin();hc != polyhedron.points_end(); ++hc){
224 >    Point_3 mypoint = *hc;
225 >    surfacePt_ mpiSurfacePt;
226 >    mpiSurfacePt.x = CGAL::to_double(mypoint.x());
227 >    mpiSurfacePt.y = CGAL::to_double(mypoint.y());
228 >    mpiSurfacePt.z = CGAL::to_double(mypoint.z());
229 >    surfacePtsLocal_.push_back(mpiSurfacePt);
230 >  }
231 >
232 >  MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType);
233 >  std::vector<surfacePt_>::iterator spt;
234 >  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 >
249 >      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 <  for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin();
309 <       ch_object_.vertices_end(); ++v){
310 <    std::cout<< v.point()<<std::endl;
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    
142 –  for (int i = 0; i < numpoints; i++) {
143 –    pt_array[dim_ * i] = pos[i][0];
144 –    pt_array[dim_ * i + 1] = pos[i][1];
145 –    pt_array[dim_ * i + 2] = pos[i][2];
146 –  }
434    
435    
436    
437 +  boolT ismalloc = False;
438 +  Triangles_.clear();
439 +  surfaceSDs_.clear();
440    
441 <  /*
442 <    qh_initflags(const_cast<char *>(options_.c_str()));
153 <    qh_init_B(pospoints, numpoints, dim_, ismalloc);
154 <    qh_qhull();
155 <    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;
165 <    facetT *facet;
166 <    setT *vertices;
167 <    unsigned int nf = qh num_facets;
168 <    
169 <    //Matrix idx(nf, dim);
170 <    /*
171 <      int j, i = 0, id = 0;
172 <      
173 <      int id2 = 0;
174 <      coordT *point,**pointp;
175 <      realT dist;
176 <      FORALLfacets {
177 <      j = 0;
178 <      
179 <      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){
195 <      vertex= qh_nearvertex (facet, point, &dist);
196 <      //id= qh_pointid (vertex->point);
197 <      id2= qh_pointid (point);
198 <      surface_atoms.push_back(id2);
199 <      //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
200 <      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
201 <      //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
202 <                                        
203 <      }
204 <      
205 <      }
206 <                
207 < */
208 <                
209 <                
210 <  }
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 {
223 <    for (int k=0; k < qh hull_dim; k++)
224 <    printf ("%6.2g ", facet->normal[k]);
225 <    printf ("\n");
226 <    }
227 <  */
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];
247 <    //surfpt_array[dim_ * j + 1] = pos[i][1];
248 <    //surfpt_array[dim_ * j + 2] = pos[i][2];
249 <    std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
250 <    j++;
603 >    surfaceSDs_.push_back(bodydoubles[i]);
604      }
605 <  */    
253 <  
254 <  /*    
255 <        std::string deloptions_ = "qhull d Qt";
256 <        facetT *facet, *neighbor;
257 <        ridgeT *ridge, **ridgep;
258 <        
259 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
260 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
261 <        
262 <        qh visit_id++;
263 <        FORALLfacets {
264 <        if (!facet->upperdelaunay) {
265 <        facet->visitid= qh visit_id;
266 <        qh_makeridges(facet);
267 <        FOREACHridge_(facet->ridges) {
268 <        neighbor= otherfacet_(ridge, facet);
269 <        if (neighbor->visitid != qh visit_id) {
270 <        
271 <        FOREACHvertex_(ridge->vertices)
272 <        int id2 = qh_pointid (vertex->point);
273 <        std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
274 <        }
275 <        }
276 <        }
277 <        
605 >    */
606  
607  
280 –        
281 –        }
608  
283 –        qh_freeqhull(!qh_ALL);
284 –        qh_memfreeshort(&curlong, &totlong);
285 –        if (curlong || totlong)
286 –        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
287 –        << totlong << curlong << std::endl;
288 –        free(surfpt_array);
289 –  */            
290 –  return true;
291 – }
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;

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