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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1137 by chuckv, Tue May 29 22:50:14 2007 UTC vs.
Revision 1308 by chuckv, Tue Oct 21 16:44:00 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 1.2 2007-05-29 22:50:14 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.12 2008-10-21 16:44:00 chuckv Exp $
48   *
49   */
50  
51 < #include "math/ConvexHull.hpp"
51 > /* Standard includes independent of library */
52   #include <iostream>
53   #include <fstream>
54 + #include <list>
55 + #include <algorithm>
56 + #include <iterator>
57 + #include "math/ConvexHull.hpp"
58 + #include "utils/simError.h"
59  
55 – char options[] = "qhull Qt FA";
56 – int dim_ = 3;
60  
61   using namespace oopse;
62  
63 < ConvexHull::ConvexHull(){}
63 > /* CGAL version of convex hull first then QHULL */
64 > #ifdef HAVE_CGAL
65 > //#include <CGAL/Homogeneous.h>
66 > #include <CGAL/basic.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  
79 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
80 < {
81 <        FILE *outfile = stdout;
66 <        FILE *errfile = stderr;
67 <        facetT *facet;
68 <        int exitcode;
69 <        boolT ismalloc = False;
70 <        int curlong,totlong;
71 <        
72 <        int numpoints = pos.size();
73 <        
74 <        coordT points[numpoints][dim_];
75 <        
76 <        for (int i=0; i<numpoints; i++)
77 <        {
78 <     points[i][0] = pos[i][0];
79 <     points[i][1] = pos[i][1];
80 <     points[i][2] = pos[i][2];          
81 <        }
82 <  
79 > //#include <CGAL/Quotient.h>
80 > #include <CGAL/MP_Float.h>
81 > //#include <CGAL/Lazy_exact_nt.h>
82  
83  
85 –        qh_initflags (options);
86 –    qh_init_B (points[0], numpoints, dim_, ismalloc);
87 –    qh_qhull();
88 –    qh_check_output();
89 –                                                        
90 –                                                        
91 –                                                        
92 –    qh_getarea(qh facet_list);
93 –    volume_ = qh totvol;                                                        
94 –        area_ = qh totarea;                                            
95 –                                                        
96 –                                                        
97 –                                                        
98 –    qh_freeqhull(!qh_ALL);
99 –        qh_memfreeshort (&curlong, &totlong);
100 –        if (curlong || totlong)
101 –                fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
102 –                                 totlong, curlong);
103 –        
84  
85 <        return true;
86 < }
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 < RealType ConvexHull::getVolume()
98 < {
99 <        return volume_;
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::geomviewHull(const std::string& geomFileName)
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 +  
169 +  // Copy the positon vector into a points vector for cgal.
170 +  std::vector<StuntDouble*>::iterator SD;
171  
172 +    for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
173 +    {
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 +  CGAL::Object ch_object_;
183 +  Polyhedron_3 polyhedron;
184 +
185 +  // compute convex hull
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 +
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 + /* More old opts Qc Qi Pp*/
373 + ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
374 +  //If we are doing the mpi version, set up some vectors for data communication
375 + #ifdef IS_MPI
376 +
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 +  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 +  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_));
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 +  
436 +  
437 +  
438 +  
439 +  boolT ismalloc = False;
440 +  /* Clean up memory from previous convex hull calculations*/
441 +  
442 +  Triangles_.clear();
443 +  surfaceSDs_.clear();
444 +  surfaceSDs_.reserve(Ns_);
445 +
446 +  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
447 +                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
448 +
449 +      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
450 +      painCave.isFatal = 1;
451 +      simError();
452 +      
453 +  } //qh_new_qhull
454 +
455 +
456 + #ifdef IS_MPI
457 +  std::vector<double> localPts;
458 +  std::vector<double> localVel;
459 +  int localPtArraySize;
460 +  
461 +
462 +  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
463 +
464 +
465 +  FORALLfacets {
466 +    
467 +    if (!facet->simplicial){
468 +      // should never happen with Qt
469 +      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
470 +      painCave.isFatal = 1;
471 +      simError();
472 +    }
473 +    
474 +    
475 +    vertices = qh_facet3vertex(facet);
476 +    FOREACHvertex_(vertices){
477 +      id = qh_pointid(vertex->point);
478 +
479 +      if( !isSurfaceID[id] ){
480 +        isSurfaceID[id] = true;
481 +      }
482 +    }      
483 +    qh_settempfree(&vertices);      
484 +      
485 +  } //FORALLfacets
486 +
487 +
488 +
489 +  /*
490 +  std::sort(surfaceIDs.begin(),surfaceIDs.end());
491 +  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
492 +  int localPtArraySize = surfaceIDs.size() * 3;
493 +  */
494 +
495 +  //localPts.resize(localPtArraySize);
496 +  //std::fill(localPts.begin(),localPts.end(),0.0);
497 +
498 +
499 +  int idx = 0;
500 +  int nIsIts = 0;
501 + /*
502 +  // Copy the surface points into an array.
503 +  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
504 +      list_iter != isSurfaceID.end(); list_iter++)
505 +    {
506 +      bool isIt = *list_iter;
507 +      if (isIt){
508 +        localPts.push_back(ptArray[dim_ * idx]);    
509 +        localPts.push_back(ptArray[dim_ * idx + 1]);
510 +        localPts.push_back(ptArray[dim_ * idx + 2]);
511 +        localPtsMap.push_back(idx);
512 +        nIsIts++;
513 +      } //Isit
514 +      idx++;
515 +    } //isSurfaceID
516 +  */
517 +  FORALLvertices {
518 +    idx = qh_pointid(vertex->point);
519 +    localPts.push_back(ptArray[dim_ * idx]);    
520 +    localPts.push_back(ptArray[dim_ * idx + 1]);
521 +    localPts.push_back(ptArray[dim_ * idx + 2]);
522 +
523 +    Vector3d vel = bodydoubles[idx]->getVel();
524 +    localVel.push_back(vel.x());
525 +    localVel.push_back(vel.y());
526 +    localVel.push_back(vel.z());
527 +
528 +    localPtsMap.push_back(idx);
529 +  }
530 +
531 +
532 +  localPtArraySize = localPts.size();
533 +
534 +
535 +  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
536 +
537 +  Nsglobal_=0;
538 +  for (int i = 0; i < nproc_; i++){
539 +    Nsglobal_ += NstoProc_[i];
540 +  }
541 +  
542 +
543 +  int nglobalPts = int(Nsglobal_/3);
544 +
545 +
546 +  std::vector<double> globalPts(Nsglobal_);
547 +  std::vector<double> globalVel(Nsglobal_);
548 +
549 +  isSurfaceID.resize(nglobalPts);
550 +
551 +
552 +  std::fill(globalPts.begin(),globalPts.end(),0.0);
553 +
554 +  displs_[0] = 0;
555 +  /* Build a displacements array */
556 +  for (int i = 1; i < nproc_; i++){
557 +    displs_[i] = displs_[i-1] + NstoProc_[i-1];
558 +  }
559 +  
560 +  
561 +  int noffset = displs_[myrank_];
562 +  /* gather the potential hull */
563 +  
564 +  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
565 +  MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize,MPI::DOUBLE,&globalVel[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
566 +
567 +  /*
568 +  if (myrank_ == 0){
569 +    for (i = 0; i < globalPts.size(); i++){
570 +      std::cout << globalPts[i] << std::endl;
571 +    }
572 +  }
573 +  */
574 +  // Free previous hull
575 +  qh_freeqhull(!qh_ALL);
576 +  qh_memfreeshort(&curlong, &totlong);
577 +  if (curlong || totlong)
578 +    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
579 +              << totlong << curlong << std::endl;
580 +
581 +  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
582 +                    const_cast<char *>(options_.c_str()), NULL, stderr)){
583 +
584 +      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
585 +      painCave.isFatal = 1;
586 +      simError();
587 +      
588 +  } //qh_new_qhull
589 +
590 + #endif
591 +
592 +
593 +
594 +
595 +
596 +
597 +    unsigned int nf = qh num_facets;
598 +    
599 +    /* Build Surface SD list first */
600 +
601 +    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
602 +
603 +    FORALLfacets {
604 +      
605 +      if (!facet->simplicial){
606 +      // should never happen with Qt
607 +        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
608 +        painCave.isFatal = 1;
609 +        simError();
610 +      } //simplicical
611 +      
612 +      Triangle face;
613 +      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
614 +      face.setNormal(V3dNormal);
615 +
616 +      
617 +
618 +      RealType faceArea = 0.5*V3dNormal.length();
619 +      face.setArea(faceArea);
620 +
621 +
622 +      vertices = qh_facet3vertex(facet);
623 +      
624 +      coordT *center = qh_getcenter(vertices);
625 +      Vector3d V3dCentroid(center[0], center[1], center[2]);
626 +      face.setCentroid(V3dCentroid);
627 +      Vector3d faceVel = V3Zero;
628 +      FOREACHvertex_(vertices){
629 +        id = qh_pointid(vertex->point);
630 +        int localindex = id;
631 + #ifdef IS_MPI
632 +        Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
633 +        faceVel = faceVel + velVector;
634 +        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
635 +          localindex = localPtsMap[id-noffset/3];
636 + #else
637 +          faceVel = faceVel + bodydoubles[localindex]->getVel();
638 + #endif
639 +          face.addVertex(bodydoubles[localindex]);
640 +          if( !isSurfaceID[id] ){
641 +            isSurfaceID[id] = true;
642 + #ifdef IS_MPI      
643 +            
644 + #endif
645 +            
646 +            surfaceSDs_.push_back(bodydoubles[localindex]);
647 +            
648 +          } //IF isSurfaceID
649 +
650 + #ifdef IS_MPI
651 +        
652 +        }else{
653 +          face.addVertex(NULL);
654 +          }
655 + #endif
656 +      } //Foreachvertex
657 +      /*
658 +      if (!SETempty_(facet->coplanarset)){
659 +        FOREACHpoint_(facet->coplanarset){
660 +          id = qh_pointid(point);
661 +          surfaceSDs_.push_back(bodydoubles[id]);
662 +        }
663 +      }
664 +      */
665 +      face.setFacetVelocity(faceVel/3.0);
666 +      Triangles_.push_back(face);
667 +      qh_settempfree(&vertices);      
668 +
669 +    } //FORALLfacets
670 +
671 +    /*
672 +    std::cout << surfaceSDs_.size() << std::endl;
673 +    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
674 +      Vector3d thisatom = (*SD)->getPos();
675 +      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
676 +    }
677 +    */
678 +
679 +
680 +
681 +    Ns_ = surfaceSDs_.size();
682 +    nTriangles_ = Triangles_.size();
683 +    
684 +    qh_getarea(qh facet_list);
685 +    volume_ = qh totvol;
686 +    area_ = qh totarea;
687 +    
688 +    
689 +    
690 +    qh_freeqhull(!qh_ALL);
691 +    qh_memfreeshort(&curlong, &totlong);
692 +    if (curlong || totlong)
693 +      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
694 +                << totlong << curlong << std::endl;
695 +    
696 +    
697 +    
698 + }
699 +
700 +
701 +
702 + void ConvexHull::printHull(const std::string& geomFileName)
703 + {
704 +
705 +  FILE *newGeomFile;
706 +  
707 +  //create new .md file based on old .md file
708 +  newGeomFile = fopen(geomFileName.c_str(), "w");
709 +  qh_findgood_all(qh facet_list);
710 +  for (int i = 0; i < qh_PRINTEND; i++)
711 +    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
712 +  
713 +  fclose(newGeomFile);
714 + }
715 + #endif //QHULL
716 + #endif //CGAL
717 +
718 +
719 +

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