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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
Revision 1378 by gezelter, Wed Oct 21 15:48:12 2009 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 2008, 2009 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 1.8 2008-09-14 01:32:25 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.19 2009-10-21 15:48:12 gezelter Exp $
48   *
49   */
50  
51   /* Standard includes independent of library */
52 +
53   #include <iostream>
54   #include <fstream>
55   #include <list>
# Line 57 | Line 58
58   #include "math/ConvexHull.hpp"
59   #include "utils/simError.h"
60  
61 + #ifdef IS_MPI
62 + #include <mpi.h>
63 + #endif
64  
65   using namespace oopse;
66  
67 < /* CGAL version of convex hull first then QHULL */
68 < #ifdef HAVE_CGAL
69 < //#include <CGAL/Homogeneous.h>
70 < #include <CGAL/basic.h>
71 < //#include <CGAL/Simple_cartesian.h>
72 < #include <CGAL/Cartesian.h>
73 < #include <CGAL/Origin.h>
74 < #include <CGAL/Exact_predicates_exact_constructions_kernel.h>
75 < #include <CGAL/Convex_hull_traits_3.h>
76 < #include <CGAL/convex_hull_3.h>
77 < #include <CGAL/Polyhedron_traits_with_normals_3.h>
78 < #include <CGAL/Polyhedron_3.h>
75 < #include <CGAL/double.h>
76 < #include <CGAL/number_utils.h>
67 > #ifdef HAVE_QHULL
68 > extern "C"
69 > {
70 > #include <qhull/qhull.h>
71 > #include <qhull/mem.h>
72 > #include <qhull/qset.h>
73 > #include <qhull/geom.h>
74 > #include <qhull/merge.h>
75 > #include <qhull/poly.h>
76 > #include <qhull/io.h>
77 > #include <qhull/stat.h>
78 > }
79  
80 + /* Old options Qt Qu Qg QG0 FA */
81 + /* More old opts Qc Qi Pp*/
82  
83 < //#include <CGAL/Quotient.h>
84 < #include <CGAL/MP_Float.h>
81 < //#include <CGAL/Lazy_exact_nt.h>
83 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
84 > }
85  
86 <
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 < 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;
86 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
87  
88 +  int numpoints = bodydoubles.size();
89  
90 +  Triangles_.clear();
91 +  
92 +  vertexT *vertex, **vertexp;
93 +  facetT *facet;
94 +  setT *vertices;
95 +  int curlong, totlong;
96 +  
97 +  std::vector<double> ptArray(numpoints*dim_);
98  
99 < class Enriched_Point_3 : public K::Point_3{
100 < public:
101 <  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
102 <
103 <  bool isMyPoint() const{ return yupMyPoint; }
104 <  void myPoint(){ yupMyPoint = true; }
105 <  void setSD(StuntDouble* SD){mySD = SD;}
106 <  StuntDouble* getStuntDouble(){return mySD;}
107 < 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
99 >  // Copy the positon vector into a points vector for qhull.
100 >  std::vector<StuntDouble*>::iterator SD;
101 >  int i = 0;
102 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
103 >    Vector3d pos = (*SD)->getPos();      
104 >    ptArray[dim_ * i] = pos.x();
105 >    ptArray[dim_ * i + 1] = pos.y();
106 >    ptArray[dim_ * i + 2] = pos.z();
107 >    i++;
108    }
109 < };
109 >  
110 >  boolT ismalloc = False;
111 >  /* Clean up memory from previous convex hull calculations*/
112 >  
113 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
114 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
115  
116 < // coordinate-based hashing inefficient but can we do better if pts are copied?
117 < typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
116 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
117 >    painCave.isFatal = 1;
118 >    simError();
119 >    
120 >  } //qh_new_qhull
121  
138 – #ifdef IS_MPI
139 – struct {
140 –  double x,y,z;
141 – } surfacePt;
142 – #endif
122  
144 – ConvexHull::ConvexHull() : Hull(){
145 –  //If we are doing the mpi version, set up some vectors for data communication
123   #ifdef IS_MPI
124 +  //If we are doing the mpi version, set up some vectors for data communication
125 +  
126 +  int nproc = MPI::COMM_WORLD.Get_size();
127 +  int myrank = MPI::COMM_WORLD.Get_rank();
128 +  int localHullSites = 0;
129 +  int* hullSitesOnProc = new int[nproc];
130 +  int* coordsOnProc = new int[nproc];
131 +  int* displacements = new int[nproc];
132 +  int* vectorDisplacements = new int[nproc];
133  
134 +  std::vector<double> coords;
135 +  std::vector<double> vels;
136 +  std::vector<int> indexMap;
137 +  std::vector<double> masses;
138  
139 < nproc_ = MPI::COMM_WORLD.Get_size();
140 < myrank_ = MPI::COMM_WORLD.Get_rank();
141 < NstoProc_ = new int[nproc_];
142 < displs_   = new int[nproc_];
139 >  FORALLvertices{
140 >    localHullSites++;
141 >    
142 >    int idx = qh_pointid(vertex->point);
143  
144 < // Create a surface point type in MPI to send
155 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156 < surfacePtType.Commit();
157 <
144 >    indexMap.push_back(idx);
145  
146 < #endif
147 < }
146 >    coords.push_back(ptArray[dim_  * idx]);
147 >    coords.push_back(ptArray[dim_  * idx + 1]);
148 >    coords.push_back(ptArray[dim_  * idx + 2]);
149  
150 < 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;
150 >    StuntDouble* sd = bodydoubles[idx];
151  
152 <  // compute convex hull
153 <  
154 <  std::vector<Enriched_Point_3>::iterator testpt;
155 <  
189 <  
190 <
191 <  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 <
152 >    Vector3d vel = sd->getVel();
153 >    vels.push_back(vel.x());
154 >    vels.push_back(vel.y());
155 >    vels.push_back(vel.z());
156  
157 <
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];
157 >    masses.push_back(sd->getMass());
158    }
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);
159  
160 <  /* Build a displacements array */
161 <  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 < }
160 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
161 >                            1, MPI::INT);
162  
163 +  int globalHullSites = 0;
164 +  for (int iproc = 0; iproc < nproc; iproc++){
165 +    globalHullSites += hullSitesOnProc[iproc];
166 +    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
167 +  }
168  
169 <
170 <
366 <
367 <
368 <
369 < #else
370 < #ifdef HAVE_QHULL
371 < /* Old options Qt Qu Qg QG0 FA */
372 < ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt  Qci Tcv Pp") {
373 <  //If we are doing the mpi version, set up some vectors for data communication
374 < #ifdef IS_MPI
375 <
376 <
377 < nproc_ = MPI::COMM_WORLD.Get_size();
378 < myrank_ = MPI::COMM_WORLD.Get_rank();
379 < NstoProc_ = new int[nproc_];
380 < displs_   = new int[nproc_];
381 <
382 < // Create a surface point type in MPI to send
383 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
384 < surfacePtType.Commit();
385 <
386 <
387 < #endif
388 < }
389 <
390 <
391 <
392 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
393 < {
169 >  displacements[0] = 0;
170 >  vectorDisplacements[0] = 0;
171    
172 <  std::vector<int> surfaceIDs;
173 <  std::vector<int> surfaceIDsGlobal;
174 <  std::vector<int> localPtsMap;
175 <  int numpoints = bodydoubles.size();
172 >  for (int iproc = 1; iproc < nproc; iproc++){
173 >    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
174 >    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
175 >  }
176  
177 <  //coordT* pt_array;
178 <  coordT* surfpt_array;
179 <  vertexT *vertex, **vertexp;
403 <  facetT *facet;
404 <  setT *vertices;
405 <  int curlong,totlong;
406 <  int id;
407 <  
408 <  coordT *point,**pointp;
177 >  std::vector<double> globalCoords(dim_ * globalHullSites);
178 >  std::vector<double> globalVels(dim_ * globalHullSites);
179 >  std::vector<double> globalMasses(globalHullSites);
180  
181 <
411 <  FILE *outdummy = NULL;
412 <  FILE *errdummy = NULL;
181 >  int count = coordsOnProc[myrank];
182    
183 <  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
183 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
184 >                             &coordsOnProc[0], &vectorDisplacements[0],
185 >                             MPI::DOUBLE);
186  
187 <  double* ptArray = new double[numpoints * 3];
188 <  std::vector<bool> isSurfaceID(numpoints);
187 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
188 >                             &coordsOnProc[0], &vectorDisplacements[0],
189 >                             MPI::DOUBLE);
190  
191 <  // Copy the positon vector into a points vector for qhull.
192 <  std::vector<StuntDouble*>::iterator SD;
193 <  int i = 0;
422 <  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
423 <    {
424 <      Vector3d pos = (*SD)->getPos();
425 <      
426 <      ptArray[dim_ * i] = pos.x();
427 <      ptArray[dim_ * i + 1] = pos.y();
428 <      ptArray[dim_ * i + 2] = pos.z();
429 <      i++;
430 <    }
431 <  
191 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 >                             &globalMasses[0], &hullSitesOnProc[0],
193 >                             &displacements[0], MPI::DOUBLE);
194  
433 –  
434 –  
435 –  
436 –  
437 –  boolT ismalloc = False;
438 –  Triangles_.clear();
439 –  surfaceSDs_.clear();
440 –  
441 –  if (qh_new_qhull(dim_, numpoints, ptArray, ismalloc,
442 –                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
443 –
444 –      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
445 –      painCave.isFatal = 0;
446 –      simError();
447 –      
448 –  } //qh_new_qhull
449 –
450 –
451 – #ifdef IS_MPI
452 –  std::vector<double> localPts;
453 –  int localPtArraySize;
454 –  
455 –  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
456 –
457 –  FORALLfacets {
458 –    
459 –    if (!facet->simplicial){
460 –      // should never happen with Qt
461 –      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
462 –      painCave.isFatal = 0;
463 –      simError();
464 –    }
465 –    
466 –    
467 –    vertices = qh_facet3vertex(facet);
468 –    FOREACHvertex_(vertices){
469 –      id = qh_pointid(vertex->point);
470 –
471 –      if( !isSurfaceID[id] ){
472 –        isSurfaceID[id] = true;
473 –      }
474 –    }      
475 –    qh_settempfree(&vertices);      
476 –      
477 –  } //FORALLfacets
478 –
479 –
480 –
481 –  /*
482 –  std::sort(surfaceIDs.begin(),surfaceIDs.end());
483 –  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
484 –  int localPtArraySize = surfaceIDs.size() * 3;
485 –  */
486 –
487 –  localPts.resize(localPtArraySize);
488 –  //  std::fill(localPts.begin(),globalPts.end(),0.0);
489 –
490 –
491 –  int idx = 0;
492 –  // Copy the surface points into an array.
493 –  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
494 –      list_iter != isSurfaceID.end(); list_iter++)
495 –    {
496 –      bool isIt = *list_iter;
497 –      if (isIt){
498 –        localPts.push_back(ptArray[dim_ * idx]);    
499 –        localPts.push_back(ptArray[dim_ * idx + 1]);
500 –        localPts.push_back(ptArray[dim_ * idx + 2]);
501 –        localPtsMap.push_back(idx);
502 –      } //Isit
503 –      idx++;
504 –    } //isSurfaceID
505 –  
506 –
507 –  localPtArraySize = localPts.size();
508 –  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
509 –
510 –  for (int i = 0; i < nproc_; i++){
511 –    Nsglobal_ += NstoProc_[i];
512 –  }
513 –
514 –  std::vector<double> globalPts;
515 –  globalPts.resize(Nsglobal_);
516 –  isSurfaceID.resize(int(Nsglobal_/3));
517 –  std::fill(globalPts.begin(),globalPts.end(),0.0);
518 –  /* Build a displacements array */
519 –  for (int i = 1; i < nproc_; i++){
520 –    displs_[i] = displs_[i-1] + NstoProc_[i-1];
521 –  }
522 –  
523 –  int noffset = displs_[myrank_];
524 –  /* gather the potential hull */
525 –  
526 –  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],NstoProc_,displs_,MPI::DOUBLE);
527 –
528 –
529 –
530 –
195    // Free previous hull
196    qh_freeqhull(!qh_ALL);
197    qh_memfreeshort(&curlong, &totlong);
198    if (curlong || totlong)
199      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
200                << totlong << curlong << std::endl;
201 <
202 <  if (qh_new_qhull(dim_, numpoints, &globalPts[0], ismalloc,
203 <                    const_cast<char *>(options_.c_str()), NULL, stderr)){
204 <
205 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
206 <      painCave.isFatal = 0;
207 <      simError();
208 <      
201 >  
202 >  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
203 >                   const_cast<char *>(options_.c_str()), NULL, stderr)){
204 >    
205 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
206 >    painCave.isFatal = 1;
207 >    simError();
208 >    
209    } //qh_new_qhull
210  
211   #endif
212  
213 +  FORALLfacets {  
214 +    Triangle face;
215  
216 <
217 <
552 <
553 <
554 <    unsigned int nf = qh num_facets;
216 >    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
217 >    face.setNormal(V3dNormal);
218      
219 <    /* Build Surface SD list first */
220 <
221 <    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
222 <
560 <    FORALLfacets {
219 >    RealType faceArea = qh_facetarea(facet);
220 >    face.setArea(faceArea);
221 >    
222 >    vertices = qh_facet3vertex(facet);
223        
224 <      if (!facet->simplicial){
225 <      // should never happen with Qt
226 <        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
565 <        painCave.isFatal = 0;
566 <        simError();
567 <      } //simplicical
568 <      
569 <      Triangle* face = new Triangle();
570 <      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
571 <      face->setNormal(V3dNormal);
572 <      //face->setCentroid(V3dCentroid);
573 <      RealType faceArea = 0.5*V3dNormal.length();
574 <      face->setArea(faceArea);
224 >    coordT *center = qh_getcenter(vertices);
225 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
226 >    face.setCentroid(V3dCentroid);
227  
228 +    Vector3d faceVel = V3Zero;
229 +    Vector3d p[3];
230 +    RealType faceMass = 0.0;
231  
232 <      vertices = qh_facet3vertex(facet);
578 <      FOREACHvertex_(vertices){
579 <        id = qh_pointid(vertex->point);
580 <        face->addVertex(bodydoubles[id]);
581 <        if( !isSurfaceID[id] ){
582 <          isSurfaceID[id] = true;
583 <          surfaceSDs_.push_back(bodydoubles[id]);
584 <        } //IF isSurfaceID
585 <      } //Foreachvertex
232 >    int ver = 0;
233  
234 <
235 <      Triangles_.push_back(face);
236 <      qh_settempfree(&vertices);      
234 >    FOREACHvertex_(vertices){
235 >      int id = qh_pointid(vertex->point);
236 >      p[ver][0] = vertex->point[0];
237 >      p[ver][1] = vertex->point[1];
238 >      p[ver][2] = vertex->point[2];
239        
240 <    } //FORALLfacets
241 <                
240 >      Vector3d vel;
241 >      RealType mass;
242  
243 <                
244 <                
245 <    /*
246 <  std::sort(surfaceIDs.begin(),surfaceIDs.end());
247 <  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
599 <  for(std::vector<int>::iterator list_iter = surfaceIDs.begin();
600 <      list_iter != surfaceIDs.end(); list_iter++)
601 <    {
602 <    int i = *list_iter;
603 <    surfaceSDs_.push_back(bodydoubles[i]);
604 <    }
605 <    */
243 > #ifdef IS_MPI
244 >      vel = Vector3d(globalVels[dim_ * id],
245 >                     globalVels[dim_ * id + 1],
246 >                     globalVels[dim_ * id + 2]);
247 >      mass = globalMasses[id];
248  
249 +      // localID will be between 0 and hullSitesOnProc[myrank] if we
250 +      // own this guy.
251  
252 +      int localID = id - displacements[myrank];
253  
254 +      if (localID >= 0 && localID < hullSitesOnProc[myrank])
255 +        face.addVertexSD(bodydoubles[indexMap[localID]]);
256 +      
257 + #else
258 +      vel = bodydoubles[id]->getVel();
259 +      mass = bodydoubles[id]->getMass();
260 +      face.addVertexSD(bodydoubles[id]);      
261 + #endif
262 +        
263 +      faceVel = faceVel + vel;
264 +      faceMass = faceMass + mass;
265 +      ver++;      
266 +    } //Foreachvertex
267  
268 +    face.addVertices(p[0], p[1], p[2]);
269 +    face.setFacetMass(faceMass);
270 +    face.setFacetVelocity(faceVel/3.0);
271 +    Triangles_.push_back(face);
272 +    qh_settempfree(&vertices);      
273  
274 <
275 <  Ns_ = surfaceSDs_.size();
613 <
614 <
274 >  } //FORALLfacets
275 >  
276    qh_getarea(qh facet_list);
277    volume_ = qh totvol;
278    area_ = qh totarea;
279  
280 + #ifdef IS_MPI
281 +  delete [] hullSitesOnProc;
282 +  delete [] coordsOnProc;
283 +  delete [] displacements;
284 +  delete [] vectorDisplacements;
285 + #endif
286    
620 –
287    qh_freeqhull(!qh_ALL);
288    qh_memfreeshort(&curlong, &totlong);
289    if (curlong || totlong)
290      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
291 <              << totlong << curlong << std::endl;
626 <  
627 <  
628 <  // free(pt_array);
629 <  
291 >              << totlong << curlong << std::endl;    
292   }
293  
294 <
633 <
634 < void ConvexHull::printHull(const std::string& geomFileName)
635 < {
636 <
294 > void ConvexHull::printHull(const std::string& geomFileName) {
295    FILE *newGeomFile;
296    
297    //create new .md file based on old .md file
# Line 645 | Line 303 | void ConvexHull::printHull(const std::string& geomFile
303    fclose(newGeomFile);
304   }
305   #endif //QHULL
648 – #endif //CGAL
649 –
650 –
651 –

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