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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 1384 by gezelter, Thu Oct 22 19:43:10 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 1.20 2009-10-22 19:43:10 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 + ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81 + }
82  
83 < //#include <CGAL/Quotient.h>
80 < #include <CGAL/MP_Float.h>
81 < //#include <CGAL/Lazy_exact_nt.h>
82 <
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 < 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;
83 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84  
85 +  int numpoints = bodydoubles.size();
86  
87 +  Triangles_.clear();
88 +  
89 +  vertexT *vertex, **vertexp;
90 +  facetT *facet;
91 +  setT *vertices;
92 +  int curlong, totlong;
93 +  
94 +  std::vector<double> ptArray(numpoints*dim_);
95  
96 < class Enriched_Point_3 : public K::Point_3{
97 < public:
98 <  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
99 <
100 <  bool isMyPoint() const{ return yupMyPoint; }
101 <  void myPoint(){ yupMyPoint = true; }
102 <  void setSD(StuntDouble* SD){mySD = SD;}
103 <  StuntDouble* getStuntDouble(){return mySD;}
104 < 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
96 >  // Copy the positon vector into a points vector for qhull.
97 >  std::vector<StuntDouble*>::iterator SD;
98 >  int i = 0;
99 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
100 >    Vector3d pos = (*SD)->getPos();      
101 >    ptArray[dim_ * i] = pos.x();
102 >    ptArray[dim_ * i + 1] = pos.y();
103 >    ptArray[dim_ * i + 2] = pos.z();
104 >    i++;
105    }
106 < };
106 >  
107 >  boolT ismalloc = False;
108 >  /* Clean up memory from previous convex hull calculations*/
109 >  
110 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
111 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
112  
113 < // coordinate-based hashing inefficient but can we do better if pts are copied?
114 < typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
113 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
114 >    painCave.isFatal = 1;
115 >    simError();
116 >    
117 >  } //qh_new_qhull
118  
138 – #ifdef IS_MPI
139 – struct {
140 –  double x,y,z;
141 – } surfacePt;
142 – #endif
119  
144 – ConvexHull::ConvexHull() : Hull(){
145 –  //If we are doing the mpi version, set up some vectors for data communication
120   #ifdef IS_MPI
121 +  //If we are doing the mpi version, set up some vectors for data communication
122 +  
123 +  int nproc = MPI::COMM_WORLD.Get_size();
124 +  int myrank = MPI::COMM_WORLD.Get_rank();
125 +  int localHullSites = 0;
126  
127 +  std::vector<int> hullSitesOnProc(nproc, 0);
128 +  std::vector<int> coordsOnProc(nproc, 0);
129 +  std::vector<int> displacements(nproc, 0);
130 +  std::vector<int> vectorDisplacements(nproc, 0);
131  
132 < nproc_ = MPI::COMM_WORLD.Get_size();
133 < myrank_ = MPI::COMM_WORLD.Get_rank();
134 < NstoProc_ = new int[nproc_];
135 < displs_   = new int[nproc_];
132 >  std::vector<double> coords;
133 >  std::vector<double> vels;
134 >  std::vector<int> indexMap;
135 >  std::vector<double> masses;
136  
137 < // Create a surface point type in MPI to send
138 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
139 < surfacePtType.Commit();
140 <
137 >  FORALLvertices{
138 >    localHullSites++;
139 >    
140 >    int idx = qh_pointid(vertex->point);
141  
142 < #endif
160 < }
142 >    indexMap.push_back(idx);
143  
144 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
145 < {
146 <
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;
144 >    coords.push_back(ptArray[dim_  * idx]);
145 >    coords.push_back(ptArray[dim_  * idx + 1]);
146 >    coords.push_back(ptArray[dim_  * idx + 2]);
147  
148 <    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;
148 >    StuntDouble* sd = bodydoubles[idx];
149  
150 <  // compute convex hull
151 <  
152 <  std::vector<Enriched_Point_3>::iterator testpt;
153 <  
189 <  
190 <
191 <  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 <
150 >    Vector3d vel = sd->getVel();
151 >    vels.push_back(vel.x());
152 >    vels.push_back(vel.y());
153 >    vels.push_back(vel.z());
154  
155 <
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];
155 >    masses.push_back(sd->getMass());
156    }
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 – }
157  
158 +  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159 +                            1, MPI::INT);
160  
161 +  int globalHullSites = 0;
162 +  for (int iproc = 0; iproc < nproc; iproc++){
163 +    globalHullSites += hullSitesOnProc[iproc];
164 +    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
165 +  }
166  
167 <
168 <
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 < {
167 >  displacements[0] = 0;
168 >  vectorDisplacements[0] = 0;
169    
170 <  std::vector<int> surfaceIDs;
171 <  std::vector<int> surfaceIDsGlobal;
172 <  std::vector<int> localPtsMap;
173 <  int numpoints = bodydoubles.size();
170 >  for (int iproc = 1; iproc < nproc; iproc++){
171 >    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
172 >    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
173 >  }
174  
175 <  //coordT* pt_array;
176 <  coordT* surfpt_array;
177 <  vertexT *vertex, **vertexp;
403 <  facetT *facet;
404 <  setT *vertices;
405 <  int curlong,totlong;
406 <  int id;
407 <  
408 <  coordT *point,**pointp;
175 >  std::vector<double> globalCoords(dim_ * globalHullSites);
176 >  std::vector<double> globalVels(dim_ * globalHullSites);
177 >  std::vector<double> globalMasses(globalHullSites);
178  
179 <
411 <  FILE *outdummy = NULL;
412 <  FILE *errdummy = NULL;
179 >  int count = coordsOnProc[myrank];
180    
181 <  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
181 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
182 >                             &coordsOnProc[0], &vectorDisplacements[0],
183 >                             MPI::DOUBLE);
184  
185 <  double* ptArray = new double[numpoints * 3];
186 <  std::vector<bool> isSurfaceID(numpoints);
185 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
186 >                             &coordsOnProc[0], &vectorDisplacements[0],
187 >                             MPI::DOUBLE);
188  
189 <  // Copy the positon vector into a points vector for qhull.
190 <  std::vector<StuntDouble*>::iterator SD;
191 <  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 <  
189 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
190 >                             &globalMasses[0], &hullSitesOnProc[0],
191 >                             &displacements[0], MPI::DOUBLE);
192  
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 –
193    // Free previous hull
194    qh_freeqhull(!qh_ALL);
195    qh_memfreeshort(&curlong, &totlong);
196    if (curlong || totlong)
197      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
198                << totlong << curlong << std::endl;
199 <
200 <  if (qh_new_qhull(dim_, numpoints, &globalPts[0], ismalloc,
201 <                    const_cast<char *>(options_.c_str()), NULL, stderr)){
202 <
203 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
204 <      painCave.isFatal = 0;
205 <      simError();
206 <      
199 >  
200 >  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
201 >                   const_cast<char *>(options_.c_str()), NULL, stderr)){
202 >    
203 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
204 >    painCave.isFatal = 1;
205 >    simError();
206 >    
207    } //qh_new_qhull
208  
209   #endif
210  
211 +  FORALLfacets {  
212 +    Triangle face;
213  
214 <
215 <
552 <
553 <
554 <    unsigned int nf = qh num_facets;
214 >    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
215 >    face.setNormal(V3dNormal);
216      
217 <    /* Build Surface SD list first */
218 <
219 <    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
220 <
560 <    FORALLfacets {
217 >    RealType faceArea = qh_facetarea(facet);
218 >    face.setArea(faceArea);
219 >    
220 >    vertices = qh_facet3vertex(facet);
221        
222 <      if (!facet->simplicial){
223 <      // should never happen with Qt
224 <        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);
222 >    coordT *center = qh_getcenter(vertices);
223 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
224 >    face.setCentroid(V3dCentroid);
225  
226 +    Vector3d faceVel = V3Zero;
227 +    Vector3d p[3];
228 +    RealType faceMass = 0.0;
229  
230 <      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
230 >    int ver = 0;
231  
232 <
233 <      Triangles_.push_back(face);
234 <      qh_settempfree(&vertices);      
232 >    FOREACHvertex_(vertices){
233 >      int id = qh_pointid(vertex->point);
234 >      p[ver][0] = vertex->point[0];
235 >      p[ver][1] = vertex->point[1];
236 >      p[ver][2] = vertex->point[2];
237        
238 <    } //FORALLfacets
239 <                
238 >      Vector3d vel;
239 >      RealType mass;
240  
241 <                
242 <                
243 <    /*
244 <  std::sort(surfaceIDs.begin(),surfaceIDs.end());
245 <  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 <    */
241 > #ifdef IS_MPI
242 >      vel = Vector3d(globalVels[dim_ * id],
243 >                     globalVels[dim_ * id + 1],
244 >                     globalVels[dim_ * id + 2]);
245 >      mass = globalMasses[id];
246  
247 +      // localID will be between 0 and hullSitesOnProc[myrank] if we
248 +      // own this guy.
249  
250 +      int localID = id - displacements[myrank];
251  
252 +      if (localID >= 0 && localID < hullSitesOnProc[myrank])
253 +        face.addVertexSD(bodydoubles[indexMap[localID]]);
254 +      
255 + #else
256 +      vel = bodydoubles[id]->getVel();
257 +      mass = bodydoubles[id]->getMass();
258 +      face.addVertexSD(bodydoubles[id]);      
259 + #endif
260 +        
261 +      faceVel = faceVel + vel;
262 +      faceMass = faceMass + mass;
263 +      ver++;      
264 +    } //Foreachvertex
265  
266 +    face.addVertices(p[0], p[1], p[2]);
267 +    face.setFacetMass(faceMass);
268 +    face.setFacetVelocity(faceVel/3.0);
269 +    Triangles_.push_back(face);
270 +    qh_settempfree(&vertices);      
271  
272 <
273 <  Ns_ = surfaceSDs_.size();
613 <
614 <
272 >  } //FORALLfacets
273 >  
274    qh_getarea(qh facet_list);
275    volume_ = qh totvol;
276    area_ = qh totarea;
277  
619 –  
620 –
278    qh_freeqhull(!qh_ALL);
279    qh_memfreeshort(&curlong, &totlong);
280    if (curlong || totlong)
281      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
282 <              << totlong << curlong << std::endl;
626 <  
627 <  
628 <  // free(pt_array);
629 <  
282 >              << totlong << curlong << std::endl;    
283   }
284  
285 + void ConvexHull::printHull(const std::string& geomFileName) {
286  
287 <
288 < void ConvexHull::printHull(const std::string& geomFileName)
289 < {
636 <
287 > #ifdef IS_MPI
288 >  if (worldRank == 0)  {
289 > #endif
290    FILE *newGeomFile;
291    
292    //create new .md file based on old .md file
# Line 643 | Line 296 | void ConvexHull::printHull(const std::string& geomFile
296      qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
297    
298    fclose(newGeomFile);
299 + #ifdef IS_MPI
300 +  }
301 + #endif
302   }
303   #endif //QHULL
648 – #endif //CGAL
649 –
650 –
651 –

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