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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1097 by chuckv, Thu Dec 14 19:32:32 2006 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 40 | Line 40
40   *
41   *  ConvexHull.cpp
42   *
43 < *  Purpose: To calculate convexhull, hull volume and radius
44 < *  using the CGAL library.
43 > *  Purpose: To calculate convexhull, hull volume libqhull.
44   *
45   *  Created by Charles F. Vardeman II on 11 Dec 2006.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: ConvexHull.cpp,v 1.1 2006-12-14 19:32:32 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.10 2008-10-15 18:26:01 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  
60  
61   using namespace oopse;
62  
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 + //#include <CGAL/Quotient.h>
80 + #include <CGAL/MP_Float.h>
81 + //#include <CGAL/Lazy_exact_nt.h>
82  
62 – bool ConvexHull::genHull(std::vector<Vector3d> pos)
63 – {
83  
65 –  std::vector<Point_3> points;
66 –  points.reserve(pos.size());
67 –  // Copy the positon vector into a points vector for cgal.
68 –  for (int i = 0; i < pos.size(); ++i)
69 –    {
70 –      Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
71 –      points.push_back(pt);
72 –    }
84  
85 <  // compute convex hull
86 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object);
87 <  // Make sure hull is a polyhedron
88 <  if ( CGAL::assign(ch_polyhedron, ch_object) )
89 <    {
90 <      return true;
91 <    }
92 <  else
93 <    {
94 <      return false;
84 <    }
85 < }
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  
87 – RealType ConvexHull::getVolume()
88 – {
89 –        /*
90 –  std::list<Point> L;
91 –  L.push_front(Point(0,0,0));
92 –  L.push_front(Point(1,0,0));
93 –  L.push_front(Point(0,1,0));
96  
97 <  Triangulation T(L.begin(), L.end());
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  
97 –  int n = T.number_of_vertices();
108  
109 <  // insertion from a vector :
110 <  std::vector<Point> V(3);
111 <  V[0] = Point(0,0,1);
102 <  V[1] = Point(1,1,1);
103 <  V[2] = Point(2,2,2);
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 <  n = n + T.insert(V.begin(), V.end());
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 <  assert( n == 6 );       // 6 points have been inserted
108 <  assert( T.is_valid() ); // checking validity of T
121 > };
122  
123 <  double sum_v = 0;
124 <  for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it)
125 <    {
126 <      sum_v += T.tetrahedron(c_it).volume();
127 <    }
128 <  std::cout << "sum_v " << sum_v << std::endl;
129 < */
130 <        return 0.0;
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());
# Line 146 | Line 356 | void ConvexHull::geomviewHull(const std::string& geomF
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) {
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 +  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 +
460 +  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
461 +
462 +
463 +  FORALLfacets {
464 +    
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 +    
473 +    vertices = qh_facet3vertex(facet);
474 +    FOREACHvertex_(vertices){
475 +      id = qh_pointid(vertex->point);
476 +
477 +      if( !isSurfaceID[id] ){
478 +        isSurfaceID[id] = true;
479 +      }
480 +    }      
481 +    qh_settempfree(&vertices);      
482 +      
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 +  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 +  if (myrank_ == 0){
560 +    for (i = 0; i < globalPts.size(); i++){
561 +      std::cout << globalPts[i] << std::endl;
562 +    }
563 +  }
564 +  */
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;
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 +      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 +
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 +
688 +
689 + void ConvexHull::printHull(const std::string& geomFileName)
690 + {
691 +
692 +  FILE *newGeomFile;
693 +  
694 +  //create new .md file based on old .md file
695 +  newGeomFile = fopen(geomFileName.c_str(), "w");
696 +  qh_findgood_all(qh facet_list);
697 +  for (int i = 0; i < qh_PRINTEND; i++)
698 +    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
699 +  
700 +  fclose(newGeomFile);
701 + }
702 + #endif //QHULL
703 + #endif //CGAL
704 +
705 +
706 +

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