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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1242 by chuckv, Wed May 14 14:31:48 2008 UTC vs.
Revision 1304 by chuckv, Wed Oct 15 18:26:01 2008 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved.
2   *
3   * The University of Notre Dame grants you ("Licensee") a
4   * non-exclusive, royalty free, license to use, modify and
# 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 1.6 2008-05-14 14:31:48 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.10 2008-10-15 18:26:01 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  
74 – typedef double RT;
75 – typedef CGAL::Simple_cartesian<RT>                K;
76 – typedef CGAL::Convex_hull_traits_3<K>             Traits;
77 – typedef Traits::Polyhedron_3                      Polyhedron_3;
78 – typedef K::Point_3                                Point;
83  
84  
85 < ConvexHull::ConvexHull(){}
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 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
96 >
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 >
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> 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 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
182 <  Polyhedron_3 ch_object_;
182 >  CGAL::Object ch_object_;
183 >  Polyhedron_3 polyhedron;
184 >
185    // compute convex hull
99 –  CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
186    
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 >
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 +  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 > /* More old opts Qc Qi Pp*/
373 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200) {
374 >  //If we are doing the mpi version, set up some vectors for data communication
375 > #ifdef IS_MPI
376  
377 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
377 >
378 > nproc_ = MPI::COMM_WORLD.Get_size();
379 > myrank_ = MPI::COMM_WORLD.Get_rank();
380 > NstoProc_ = new int[nproc_];
381 > displs_   = new int[nproc_];
382 >
383 > // Create a surface point type in MPI to send
384 > //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
385 > // surfacePtType.Commit();
386 >
387 >
388 > #endif
389 > }
390 >
391 >
392 >
393 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
394   {
395    
396 <  
397 <  int numpoints = pos.size();
398 <  coordT* pt_array;
396 >  std::vector<int> surfaceIDs;
397 >  std::vector<int> surfaceIDsGlobal;
398 >  std::vector<int> localPtsMap;
399 >  int numpoints = bodydoubles.size();
400 >
401 >  //coordT* pt_array;
402    coordT* surfpt_array;
403 <  std::list<int> surface_atoms;
403 >  vertexT *vertex, **vertexp;
404 >  facetT *facet;
405 >  setT *vertices;
406 >  int curlong,totlong;
407 >  int id;
408 >  
409 >  coordT *point,**pointp;
410 >
411 >
412    FILE *outdummy = NULL;
413    FILE *errdummy = NULL;
414    
415 <  pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
415 >  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
416 >
417 > //  double* ptArray = new double[numpoints * 3];
418 >  std::vector<double> ptArray(numpoints*3);
419 >  std::vector<bool> isSurfaceID(numpoints);
420 >
421 >  // Copy the positon vector into a points vector for qhull.
422 >  std::vector<StuntDouble*>::iterator SD;
423 >  int i = 0;
424 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
425 >    {
426 >      Vector3d pos = (*SD)->getPos();
427 >      
428 >      ptArray[dim_ * i] = pos.x();
429 >      ptArray[dim_ * i + 1] = pos.y();
430 >      ptArray[dim_ * i + 2] = pos.z();
431 >      i++;
432 >    }
433    
434 +
435    
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 –  }
436    
437    
438    
139 –  
140 –  /*
141 –    qh_initflags(const_cast<char *>(options_.c_str()));
142 –    qh_init_B(pospoints, numpoints, dim_, ismalloc);
143 –    qh_qhull();
144 –    qh_check_output();
145 –
146 –    qh_produce_output();
147 –  */
439    boolT ismalloc = False;
440 +  /* Clean up memory from previous convex hull calculations*/
441 +  Triangles_.clear();
442 +  surfaceSDs_.clear();
443 +  surfaceSDs_.reserve(Ns_);
444 +
445 +  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
446 +                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
447 +
448 +      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
449 +      painCave.isFatal = 0;
450 +      simError();
451 +      
452 +  } //qh_new_qhull
453 +
454 +
455 + #ifdef IS_MPI
456 +  std::vector<double> localPts;
457 +  int localPtArraySize;
458    
459 <  if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
460 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
459 >
460 >  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
461 >
462 >
463 >  FORALLfacets {
464      
465 <    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){
465 >    if (!facet->simplicial){
466        // should never happen with Qt
467        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
468        painCave.isFatal = 0;
469        simError();
470 <      }
471 <                        
472 <      vertices = qh_facet3vertex(facet);
473 <      FOREACHvertex_(vertices){
470 >    }
471 >    
472 >    
473 >    vertices = qh_facet3vertex(facet);
474 >    FOREACHvertex_(vertices){
475        id = qh_pointid(vertex->point);
476 <      surface_atoms.push_back(id);
477 <      //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
476 >
477 >      if( !isSurfaceID[id] ){
478 >        isSurfaceID[id] = true;
479        }
480 <      qh_settempfree(&vertices);
480 >    }      
481 >    qh_settempfree(&vertices);      
482        
483 <      FOREACHpoint_(facet->coplanarset){
484 <      vertex= qh_nearvertex (facet, point, &dist);
485 <      //id= qh_pointid (vertex->point);
486 <      id2= qh_pointid (point);
487 <      surface_atoms.push_back(id2);
488 <      //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
489 <      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
490 <      //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
491 <                                        
492 <      }
493 <      
494 <      }
495 <                
496 < */
497 <                
498 <                
483 >  } //FORALLfacets
484 >
485 >
486 >
487 >  /*
488 >  std::sort(surfaceIDs.begin(),surfaceIDs.end());
489 >  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
490 >  int localPtArraySize = surfaceIDs.size() * 3;
491 >  */
492 >
493 >  //localPts.resize(localPtArraySize);
494 >  //std::fill(localPts.begin(),localPts.end(),0.0);
495 >
496 >
497 >  int idx = 0;
498 >  int nIsIts = 0;
499 > /*
500 >  // Copy the surface points into an array.
501 >  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
502 >      list_iter != isSurfaceID.end(); list_iter++)
503 >    {
504 >      bool isIt = *list_iter;
505 >      if (isIt){
506 >        localPts.push_back(ptArray[dim_ * idx]);    
507 >        localPts.push_back(ptArray[dim_ * idx + 1]);
508 >        localPts.push_back(ptArray[dim_ * idx + 2]);
509 >        localPtsMap.push_back(idx);
510 >        nIsIts++;
511 >      } //Isit
512 >      idx++;
513 >    } //isSurfaceID
514 >  */
515 >  FORALLvertices {
516 >    idx = qh_pointid(vertex->point);
517 >    localPts.push_back(ptArray[dim_ * idx]);    
518 >    localPts.push_back(ptArray[dim_ * idx + 1]);
519 >    localPts.push_back(ptArray[dim_ * idx + 2]);
520 >    localPtsMap.push_back(idx);
521    }
522  
523  
524 +  localPtArraySize = localPts.size();
525  
526 +
527 +  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
528  
529 <  qh_getarea(qh facet_list);
530 <  volume_ = qh totvol;
531 <  area_ = qh totarea;
532 <  //    FILE *newGeomFile;
529 >  Nsglobal_=0;
530 >  for (int i = 0; i < nproc_; i++){
531 >    Nsglobal_ += NstoProc_[i];
532 >  }
533    
534 +
535 +  int nglobalPts = int(Nsglobal_/3);
536 +
537 +
538 +  std::vector<double> globalPts;
539 +  globalPts.resize(Nsglobal_);
540 +
541 +  isSurfaceID.resize(nglobalPts);
542 +
543 +
544 +  std::fill(globalPts.begin(),globalPts.end(),0.0);
545 +
546 +  displs_[0] = 0;
547 +  /* Build a displacements array */
548 +  for (int i = 1; i < nproc_; i++){
549 +    displs_[i] = displs_[i-1] + NstoProc_[i-1];
550 +  }
551    
552 +  
553 +  int noffset = displs_[myrank_];
554 +  /* gather the potential hull */
555 +  
556 +  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
557 +
558    /*
559 <    FORALLfacets {
560 <    for (int k=0; k < qh hull_dim; k++)
561 <    printf ("%6.2g ", facet->normal[k]);
214 <    printf ("\n");
559 >  if (myrank_ == 0){
560 >    for (i = 0; i < globalPts.size(); i++){
561 >      std::cout << globalPts[i] << std::endl;
562      }
563 +  }
564    */
565 <  
218 <  int curlong,totlong;
219 <  //    geomviewHull("junk.off");
565 >  // Free previous hull
566    qh_freeqhull(!qh_ALL);
567    qh_memfreeshort(&curlong, &totlong);
568    if (curlong || totlong)
569      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
570                << totlong << curlong << std::endl;
225 –  free(pt_array);
226 –  /*
227 –    int j = 0;
228 –    surface_atoms.sort();
229 –    surface_atoms.unique();
230 –    surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
231 –    for(std::list<int>::iterator list_iter = surface_atoms.begin();
232 –    list_iter != surface_atoms.end(); list_iter++)
233 –    {
234 –    int i = *list_iter;
235 –    //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++;
240 –    }
241 –  */    
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 –        
571  
572 +  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
573 +                    const_cast<char *>(options_.c_str()), NULL, stderr)){
574  
575 +      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
576 +      painCave.isFatal = 1;
577 +      simError();
578 +      
579 +  } //qh_new_qhull
580 +
581 + #endif
582 +
583 +
584 +
585 +
586 +
587 +
588 +    unsigned int nf = qh num_facets;
589 +    
590 +    /* Build Surface SD list first */
591 +
592 +    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
593 +
594 +    FORALLfacets {
595 +      
596 +      if (!facet->simplicial){
597 +      // should never happen with Qt
598 +        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
599 +        painCave.isFatal = 1;
600 +        simError();
601 +      } //simplicical
602 +      
603 +      Triangle* face = new Triangle();
604 +      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
605 +      face->setNormal(V3dNormal);
606 +
607 +      
608 +
609 +      RealType faceArea = 0.5*V3dNormal.length();
610 +      face->setArea(faceArea);
611 +
612 +
613 +      vertices = qh_facet3vertex(facet);
614 +      
615 +      coordT *center = qh_getcenter(vertices);
616 +      Vector3d V3dCentroid(center[0], center[1], center[2]);
617 +      face->setCentroid(V3dCentroid);
618 +
619 +      FOREACHvertex_(vertices){
620 +        id = qh_pointid(vertex->point);
621 +        int localindex = id;
622 + #ifdef IS_MPI
623          
624 +        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
625 +          localindex = localPtsMap[id-noffset/3];
626 + #endif
627 +          face->addVertex(bodydoubles[localindex]);
628 +          if( !isSurfaceID[id] ){
629 +            isSurfaceID[id] = true;
630 + #ifdef IS_MPI      
631 +            
632 + #endif
633 +            
634 +            surfaceSDs_.push_back(bodydoubles[localindex]);
635 +            
636 +          } //IF isSurfaceID
637 +
638 + #ifdef IS_MPI
639 +        
640 +        }else{
641 +          face->addVertex(NULL);
642 +          }
643 + #endif
644 +      } //Foreachvertex
645 +      /*
646 +      if (!SETempty_(facet->coplanarset)){
647 +        FOREACHpoint_(facet->coplanarset){
648 +          id = qh_pointid(point);
649 +          surfaceSDs_.push_back(bodydoubles[id]);
650          }
651 +      }
652  
653 <        qh_freeqhull(!qh_ALL);
654 <        qh_memfreeshort(&curlong, &totlong);
655 <        if (curlong || totlong)
656 <        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 < }
653 >      Triangles_.push_back(face);
654 >      qh_settempfree(&vertices);      
655 >      */
656 >    } //FORALLfacets
657  
658 +    /*
659 +    std::cout << surfaceSDs_.size() << std::endl;
660 +    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
661 +      Vector3d thisatom = (*SD)->getPos();
662 +      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
663 +    }
664 +    */
665  
666  
667 < RealType ConvexHull::getVolume()
668 < {
669 <  return volume_;
667 >
668 >    Ns_ = surfaceSDs_.size();
669 >    
670 >    
671 >    qh_getarea(qh facet_list);
672 >    volume_ = qh totvol;
673 >    area_ = qh totarea;
674 >    
675 >    
676 >    
677 >    qh_freeqhull(!qh_ALL);
678 >    qh_memfreeshort(&curlong, &totlong);
679 >    if (curlong || totlong)
680 >      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
681 >                << totlong << curlong << std::endl;
682 >    
683 >    
684 >    
685   }
686  
687 < void ConvexHull::geomviewHull(const std::string& geomFileName)
687 >
688 >
689 > void ConvexHull::printHull(const std::string& geomFileName)
690   {
691  
692    FILE *newGeomFile;

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