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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1261 by chuckv, Wed Jun 18 17:03:30 2008 UTC vs.
Revision 1316 by chuckv, Fri Nov 14 15:44:34 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 1.7 2008-06-18 17:03:30 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.13 2008-11-14 15:44:34 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 > vecdispls_   = new int[nproc_];
153 > displs_ = new int[nproc_];
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 >    vecdispls_[i] = vecdispls_[i-1] + NstoProc_[i-1];
217 >  }
218 >  
219 >  int noffset = vecdispls_[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_,vecdispls_,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 > /* 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 < 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 > vecdispls_   = new int[nproc_];
382 > vecNstoProc_ = new int[nproc_];
383 > displs_ = new int[nproc_];
384 >
385 > // Create a surface point type in MPI to send
386 > //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
387 > // surfacePtType.Commit();
388 >
389 >
390 > #endif
391 > }
392 >
393 >
394 >
395 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
396   {
397    
398 <  
399 <  int numpoints = pos.size();
400 <  coordT* pt_array;
398 >  std::vector<int> surfaceIDs;
399 >  std::vector<int> surfaceIDsGlobal;
400 >  std::vector<int> localPtsMap;
401 >  int numpoints = bodydoubles.size();
402 >
403 >  //coordT* pt_array;
404    coordT* surfpt_array;
405 <  std::list<int> surface_atoms;
405 >  vertexT *vertex, **vertexp;
406 >  facetT *facet;
407 >  setT *vertices;
408 >  int curlong,totlong;
409 >  int id;
410 >  
411 >  coordT *point,**pointp;
412 >
413 >
414    FILE *outdummy = NULL;
415    FILE *errdummy = NULL;
416    
417 <  pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
417 >  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
418 >
419 > //  double* ptArray = new double[numpoints * 3];
420 >  std::vector<double> ptArray(numpoints*3);
421 >  std::vector<bool> isSurfaceID(numpoints);
422 >
423 >  // Copy the positon vector into a points vector for qhull.
424 >  std::vector<StuntDouble*>::iterator SD;
425 >  int i = 0;
426 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
427 >    {
428 >      Vector3d pos = (*SD)->getPos();
429 >      
430 >      ptArray[dim_ * i] = pos.x();
431 >      ptArray[dim_ * i + 1] = pos.y();
432 >      ptArray[dim_ * i + 2] = pos.z();
433 >      i++;
434 >    }
435    
436 +
437    
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 –  }
438    
439    
440    
441 +  boolT ismalloc = False;
442 +  /* Clean up memory from previous convex hull calculations*/
443    
444 <  /*
445 <    qh_initflags(const_cast<char *>(options_.c_str()));
446 <    qh_init_B(pospoints, numpoints, dim_, ismalloc);
154 <    qh_qhull();
155 <    qh_check_output();
444 >  Triangles_.clear();
445 >  surfaceSDs_.clear();
446 >  surfaceSDs_.reserve(Ns_);
447  
448 <    qh_produce_output();
449 <  */
450 <  boolT ismalloc = False;
448 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
449 >                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
450 >
451 >      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
452 >      painCave.isFatal = 1;
453 >      simError();
454 >      
455 >  } //qh_new_qhull
456 >
457 >
458 > #ifdef IS_MPI
459 >  std::vector<double> localPts;
460 >  std::vector<double> localVel;
461 >  std::vector<double> localMass;
462 >  int localPtArraySize;
463    
464 <  if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
465 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
464 >
465 >  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
466 >
467 >
468 >  FORALLfacets {
469      
470 <    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){
470 >    if (!facet->simplicial){
471        // should never happen with Qt
472        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
473 <      painCave.isFatal = 0;
473 >      painCave.isFatal = 1;
474        simError();
475 <      }
476 <                        
477 <      vertices = qh_facet3vertex(facet);
478 <      FOREACHvertex_(vertices){
475 >    }
476 >    
477 >    
478 >    vertices = qh_facet3vertex(facet);
479 >    FOREACHvertex_(vertices){
480        id = qh_pointid(vertex->point);
481 <      surface_atoms.push_back(id);
482 <      //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
481 >
482 >      if( !isSurfaceID[id] ){
483 >        isSurfaceID[id] = true;
484        }
485 <      qh_settempfree(&vertices);
485 >    }      
486 >    qh_settempfree(&vertices);      
487        
488 <      FOREACHpoint_(facet->coplanarset){
489 <      vertex= qh_nearvertex (facet, point, &dist);
490 <      //id= qh_pointid (vertex->point);
491 <      id2= qh_pointid (point);
492 <      surface_atoms.push_back(id2);
493 <      //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
494 <      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
495 <      //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
496 <                                        
497 <      }
498 <      
499 <      }
500 <                
501 < */
502 <                
503 <                
488 >  } //FORALLfacets
489 >
490 >
491 >
492 >
493 >  int idx = 0;
494 >  int nIsIts = 0;
495 >  FORALLvertices {
496 >    idx = qh_pointid(vertex->point);
497 >    localPts.push_back(ptArray[dim_ * idx]);    
498 >    localPts.push_back(ptArray[dim_ * idx + 1]);
499 >    localPts.push_back(ptArray[dim_ * idx + 2]);
500 >
501 >    Vector3d vel = bodydoubles[idx]->getVel();
502 >    localVel.push_back(vel.x());
503 >    localVel.push_back(vel.y());
504 >    localVel.push_back(vel.z());
505 >
506 >    RealType bdmass = bodydoubles[idx]->getMass();
507 >    localMass.push_back(bdmass);
508 >
509 >    localPtsMap.push_back(idx);
510 >
511 >
512    }
513  
514  
515  
516 +  localPtArraySize = int(localPts.size()/3.0);
517  
518 <  qh_getarea(qh facet_list);
519 <  volume_ = qh totvol;
217 <  area_ = qh totarea;
218 <  //    FILE *newGeomFile;
518 >
519 >  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
520    
521 +  Nsglobal_=0;
522 +  for (int i = 0; i < nproc_; i++){
523 +    Nsglobal_ += NstoProc_[i];
524 +    vecNstoProc_[i] = NstoProc_[i]*3;
525 +  }
526    
527 +
528 +  int nglobalPts = Nsglobal_*3;
529 +
530 +
531 +  std::vector<double> globalPts(nglobalPts);
532 +  std::vector<double> globalVel(nglobalPts);
533 +  std::vector<double> globalMass(Nsglobal_);
534 +
535 +  isSurfaceID.resize(nglobalPts);
536 +
537 +
538 +  std::fill(globalPts.begin(),globalPts.end(),0.0);
539 +
540 +  vecdispls_[0] = 0;
541 +  /* Build a displacements array */
542 +  for (int i = 1; i < nproc_; i++){
543 +    vecdispls_[i] = vecdispls_[i-1] + vecNstoProc_[i-1];
544 +  }
545 +  
546 +  displs_[0] = 0;
547 +  for (int i = 1; i < nproc_; i++){
548 +    displs_[i] = displs_[i-1] + NstoProc_[i-1];
549 +  }
550 +  
551 +  int noffset = vecdispls_[myrank_];
552 +  /* gather the potential hull */
553 +  
554 +  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
555 +  MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize,MPI::DOUBLE,&globalVel[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
556 +  MPI::COMM_WORLD.Allgatherv(&localMass[0],localPtArraySize,MPI::DOUBLE,&globalMass[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
557    /*
558 <    FORALLfacets {
559 <    for (int k=0; k < qh hull_dim; k++)
560 <    printf ("%6.2g ", facet->normal[k]);
225 <    printf ("\n");
558 >  if (myrank_ == 0){
559 >    for (i = 0; i < globalPts.size(); i++){
560 >      std::cout << globalPts[i] << std::endl;
561      }
562 +  }
563    */
564 <  
229 <  int curlong,totlong;
230 <  //    geomviewHull("junk.off");
564 >  // Free previous hull
565    qh_freeqhull(!qh_ALL);
566    qh_memfreeshort(&curlong, &totlong);
567    if (curlong || totlong)
568      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
569                << totlong << curlong << std::endl;
236 –  free(pt_array);
237 –  /*
238 –    int j = 0;
239 –    surface_atoms.sort();
240 –    surface_atoms.unique();
241 –    surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
242 –    for(std::list<int>::iterator list_iter = surface_atoms.begin();
243 –    list_iter != surface_atoms.end(); list_iter++)
244 –    {
245 –    int i = *list_iter;
246 –    //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++;
251 –    }
252 –  */    
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 –        
570  
571 +  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
572 +                    const_cast<char *>(options_.c_str()), NULL, stderr)){
573  
574 +      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
575 +      painCave.isFatal = 1;
576 +      simError();
577 +      
578 +  } //qh_new_qhull
579 +
580 + #endif
581 +
582 +
583 +
584 +
585 +
586 +
587 +    unsigned int nf = qh num_facets;
588 +    
589 +    /* Build Surface SD list first */
590 +
591 +    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
592 +
593 +    FORALLfacets {
594 +      
595 +      if (!facet->simplicial){
596 +      // should never happen with Qt
597 +        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
598 +        painCave.isFatal = 1;
599 +        simError();
600 +      } //simplicical
601 +      
602 +      Triangle face;
603 +      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
604 +      face.setNormal(V3dNormal);
605 +
606 +      
607 +
608 +      //RealType faceArea = 0.5*V3dNormal.length();
609 +      RealType faceArea = qh_facetarea(facet);
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 +      Vector3d faceVel = V3Zero;
619 +      Vector3d p[3];
620 +      RealType faceMass = 0.0;
621 +      int ver = 0;
622 +      FOREACHvertex_(vertices){
623 +        id = qh_pointid(vertex->point);
624 +        p[ver][0] = vertex->point[0];
625 +        p[ver][1] = vertex->point[1];
626 +        p[ver][2] = vertex->point[2];
627 +        int localindex = id;
628 + #ifdef IS_MPI
629 +        Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
630          
631 +        faceVel = faceVel + velVector;
632 +        faceMass = faceMass + globalMass[id];
633 +        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
634 +          localindex = localPtsMap[id-noffset/3];
635 + #else
636 +          faceVel = faceVel + bodydoubles[localindex]->getVel();
637 +          faceMass = faceMass + bodydoubles[localindex]->getMass();
638 + #endif
639 +          face.addVertexSD(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.addVertexSD(NULL);
654 +          }
655 + #endif
656 +        ver++;
657 +      } //Foreachvertex
658 +      /*
659 +      if (!SETempty_(facet->coplanarset)){
660 +        FOREACHpoint_(facet->coplanarset){
661 +          id = qh_pointid(point);
662 +          surfaceSDs_.push_back(bodydoubles[id]);
663          }
664 +      }
665 +      */
666 +      face.addVertices(p[0],p[1],p[2]);
667 +      face.setFacetMass(faceMass);
668 +      face.setFacetVelocity(faceVel/3.0);
669 +      Triangles_.push_back(face);
670 +      qh_settempfree(&vertices);      
671  
672 <        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 < }
672 >    } //FORALLfacets
673  
674 +    /*
675 +    std::cout << surfaceSDs_.size() << std::endl;
676 +    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
677 +      Vector3d thisatom = (*SD)->getPos();
678 +      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
679 +    }
680 +    */
681  
682  
683 < RealType ConvexHull::getVolume()
684 < {
685 <  return volume_;
683 >
684 >    Ns_ = surfaceSDs_.size();
685 >    nTriangles_ = Triangles_.size();
686 >    
687 >    qh_getarea(qh facet_list);
688 >    volume_ = qh totvol;
689 >    area_ = qh totarea;
690 >    
691 >    
692 >    
693 >    qh_freeqhull(!qh_ALL);
694 >    qh_memfreeshort(&curlong, &totlong);
695 >    if (curlong || totlong)
696 >      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
697 >                << totlong << curlong << std::endl;
698 >    
699 >    
700 >    
701   }
702  
703 < void ConvexHull::geomviewHull(const std::string& geomFileName)
703 >
704 >
705 > void ConvexHull::printHull(const std::string& geomFileName)
706   {
707  
708    FILE *newGeomFile;

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