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root/OpenMD/trunk/src/math/ConvexHull.cpp
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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1302 by chuckv, Tue Oct 7 17:12:48 2008 UTC vs.
Revision 1384 by gezelter, Thu Oct 22 19:43:10 2009 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2008 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 1.9 2008-10-07 17:12:48 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  
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 –
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;
106 –
107 –
108 –
109 – class Enriched_Point_3 : public K::Point_3{
110 – public:
111 –  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
112 –
113 –  bool isMyPoint() const{ return yupMyPoint; }
114 –  void myPoint(){ yupMyPoint = true; }
115 –  void setSD(StuntDouble* SD){mySD = SD;}
116 –  StuntDouble* getStuntDouble(){return mySD;}
117 – private:
118 –  bool yupMyPoint;
119 –  StuntDouble* mySD;
120 –
121 – };
122 –
123 –
124 –
125 –
126 –
127 –    // compare Point_3's... used in setting up the STL map from points to indices
128 – template <typename Pt3>
129 – struct Point_3_comp {
130 –  bool operator() (const Pt3 & p, const Pt3 & q) const {
131 –    return CGAL::lexicographically_xyz_smaller(p,q); // this is defined inline & hence we had to create fn object & not ptrfun
132 –  }
133 – };
134 –
135 – // coordinate-based hashing inefficient but can we do better if pts are copied?
136 – typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
137 –
61   #ifdef IS_MPI
62 < struct {
140 <  double x,y,z;
141 < } surfacePt;
62 > #include <mpi.h>
63   #endif
64  
65 < ConvexHull::ConvexHull() : Hull(){
145 <  //If we are doing the mpi version, set up some vectors for data communication
146 < #ifdef IS_MPI
65 > using namespace oopse;
66  
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 < 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
80 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81   }
82  
83 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
163 < {
83 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84  
85 <  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;
85 >  int numpoints = bodydoubles.size();
86  
87 <    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 <    }
87 >  Triangles_.clear();
88    
89 <  // define object to hold convex hull
90 <  CGAL::Object ch_object_;
91 <  Polyhedron_3 polyhedron;
89 >  vertexT *vertex, **vertexp;
90 >  facetT *facet;
91 >  setT *vertices;
92 >  int curlong, totlong;
93 >  
94 >  std::vector<double> ptArray(numpoints*dim_);
95  
96 <  // compute convex hull
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    
107 <  std::vector<Enriched_Point_3>::iterator testpt;
107 >  boolT ismalloc = False;
108 >  /* Clean up memory from previous convex hull calculations*/
109    
110 <  
111 <
191 <  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 <
110 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
111 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
112  
113 <
114 <  Ns_ = polyhedron.size_of_vertices();
113 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
114 >    painCave.isFatal = 1;
115 >    simError();
116 >    
117 >  } //qh_new_qhull
118  
119 +
120   #ifdef IS_MPI
121 <  /* Gather an array of the number of verticies on each processor */
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 <  surfacePtsGlobal_.clear();
128 <  surfacePtsLocal_.clear();
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 <  MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
132 >  std::vector<double> coords;
133 >  std::vector<double> vels;
134 >  std::vector<int> indexMap;
135 >  std::vector<double> masses;
136  
137 <  for (int i = 0; i < nproc_; i++){
138 <    Nsglobal_ += NstoProc_[i];
139 <  }
140 <  /*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);
137 >  FORALLvertices{
138 >    localHullSites++;
139 >    
140 >    int idx = qh_pointid(vertex->point);
141  
142 <  /* 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 <  }
142 >    indexMap.push_back(idx);
143  
144 <  MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType);
145 <  std::vector<surfacePt_>::iterator spt;
146 <  std::vector<Enriched_Point_3> gblpoints;
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 <  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);
148 >    StuntDouble* sd = bodydoubles[idx];
149  
150 <      mine++;
151 <    }
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 <  /* Compute the global hull */
156 <  polyhedron.clear();
254 <  CGAL::convex_hull_3(gblpoints.begin(), gblpoints.end(), polyhedron);
155 >    masses.push_back(sd->getMass());
156 >  }
157  
158 +  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159 +                            1, MPI::INT);
160  
161 < #endif
162 <
163 <
164 <  
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 <
161 >  int globalHullSites = 0;
162 >  for (int iproc = 0; iproc < nproc; iproc++){
163 >    globalHullSites += hullSitesOnProc[iproc];
164 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
165    }
299 –  
300 –  std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
301 –  
166  
167 <
168 < }
305 < void ConvexHull::printHull(const std::string& geomFileName)
306 < {
307 <  /*
308 <  std::ofstream newGeomFile;
167 >  displacements[0] = 0;
168 >  vectorDisplacements[0] = 0;
169    
170 <  //create new .md file based on old .md file
171 <  newGeomFile.open("testhull.off");
172 <  
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;
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    }
329 –  
330 –  newGeomFile.close();
331 –  */
332 – /*
333 –  std::ofstream newGeomFile;
174  
175 <  //create new .md file based on old .md file
176 <  newGeomFile.open(geomFileName.c_str());
177 <
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 <
175 >  std::vector<double> globalCoords(dim_ * globalHullSites);
176 >  std::vector<double> globalVels(dim_ * globalHullSites);
177 >  std::vector<double> globalMasses(globalHullSites);
178  
179 <
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"), Ns_(200) {
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 < {
179 >  int count = coordsOnProc[myrank];
180    
181 <  std::vector<int> surfaceIDs;
182 <  std::vector<int> surfaceIDsGlobal;
183 <  std::vector<int> localPtsMap;
398 <  int numpoints = bodydoubles.size();
181 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
182 >                             &coordsOnProc[0], &vectorDisplacements[0],
183 >                             MPI::DOUBLE);
184  
185 <  //coordT* pt_array;
186 <  coordT* surfpt_array;
187 <  vertexT *vertex, **vertexp;
403 <  facetT *facet;
404 <  setT *vertices;
405 <  int curlong,totlong;
406 <  int id;
407 <  
408 <  coordT *point,**pointp;
185 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
186 >                             &coordsOnProc[0], &vectorDisplacements[0],
187 >                             MPI::DOUBLE);
188  
189 +  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
190 +                             &globalMasses[0], &hullSitesOnProc[0],
191 +                             &displacements[0], MPI::DOUBLE);
192  
411 –  FILE *outdummy = NULL;
412 –  FILE *errdummy = NULL;
413 –  
414 –  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
415 –
416 – //  double* ptArray = new double[numpoints * 3];
417 –  std::vector<double> ptArray(numpoints*3);
418 –  std::vector<bool> isSurfaceID(numpoints);
419 –
420 –  // Copy the positon vector into a points vector for qhull.
421 –  std::vector<StuntDouble*>::iterator SD;
422 –  int i = 0;
423 –  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
424 –    {
425 –      Vector3d pos = (*SD)->getPos();
426 –      
427 –      ptArray[dim_ * i] = pos.x();
428 –      ptArray[dim_ * i + 1] = pos.y();
429 –      ptArray[dim_ * i + 2] = pos.z();
430 –      i++;
431 –    }
432 –  
433 –
434 –  
435 –  
436 –  
437 –  
438 –  boolT ismalloc = False;
439 –  /* Clean up memory from previous convex hull calculations*/
440 –  Triangles_.clear();
441 –  surfaceSDs_.clear();
442 –  surfaceSDs_.reserve(Ns_);
443 –
444 –  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
445 –                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
446 –
447 –      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
448 –      painCave.isFatal = 0;
449 –      simError();
450 –      
451 –  } //qh_new_qhull
452 –
453 –
454 – #ifdef IS_MPI
455 –  std::vector<double> localPts;
456 –  int localPtArraySize;
457 –  
458 –
459 –  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
460 –
461 –
462 –  FORALLfacets {
463 –    
464 –    if (!facet->simplicial){
465 –      // should never happen with Qt
466 –      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
467 –      painCave.isFatal = 0;
468 –      simError();
469 –    }
470 –    
471 –    
472 –    vertices = qh_facet3vertex(facet);
473 –    FOREACHvertex_(vertices){
474 –      id = qh_pointid(vertex->point);
475 –
476 –      if( !isSurfaceID[id] ){
477 –        isSurfaceID[id] = true;
478 –      }
479 –    }      
480 –    qh_settempfree(&vertices);      
481 –      
482 –  } //FORALLfacets
483 –
484 –
485 –
486 –  /*
487 –  std::sort(surfaceIDs.begin(),surfaceIDs.end());
488 –  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
489 –  int localPtArraySize = surfaceIDs.size() * 3;
490 –  */
491 –
492 –  //localPts.resize(localPtArraySize);
493 –  //std::fill(localPts.begin(),localPts.end(),0.0);
494 –
495 –
496 –  int idx = 0;
497 –  int nIsIts = 0;
498 – /*
499 –  // Copy the surface points into an array.
500 –  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
501 –      list_iter != isSurfaceID.end(); list_iter++)
502 –    {
503 –      bool isIt = *list_iter;
504 –      if (isIt){
505 –        localPts.push_back(ptArray[dim_ * idx]);    
506 –        localPts.push_back(ptArray[dim_ * idx + 1]);
507 –        localPts.push_back(ptArray[dim_ * idx + 2]);
508 –        localPtsMap.push_back(idx);
509 –        nIsIts++;
510 –      } //Isit
511 –      idx++;
512 –    } //isSurfaceID
513 –  */
514 –  FORALLvertices {
515 –    idx = qh_pointid(vertex->point);
516 –    localPts.push_back(ptArray[dim_ * idx]);    
517 –    localPts.push_back(ptArray[dim_ * idx + 1]);
518 –    localPts.push_back(ptArray[dim_ * idx + 2]);
519 –    localPtsMap.push_back(idx);
520 –  }
521 –
522 –
523 –  localPtArraySize = localPts.size();
524 –
525 –
526 –  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
527 –
528 –  Nsglobal_=0;
529 –  for (int i = 0; i < nproc_; i++){
530 –    Nsglobal_ += NstoProc_[i];
531 –  }
532 –  
533 –
534 –  int nglobalPts = int(Nsglobal_/3);
535 –
536 –
537 –  std::vector<double> globalPts;
538 –  globalPts.resize(Nsglobal_);
539 –
540 –  isSurfaceID.resize(nglobalPts);
541 –
542 –
543 –  std::fill(globalPts.begin(),globalPts.end(),0.0);
544 –
545 –  displs_[0] = 0;
546 –  /* Build a displacements array */
547 –  for (int i = 1; i < nproc_; i++){
548 –    displs_[i] = displs_[i-1] + NstoProc_[i-1];
549 –  }
550 –  
551 –  
552 –  int noffset = displs_[myrank_];
553 –  /* gather the potential hull */
554 –  
555 –  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
556 –
557 –  /*
558 –  if (myrank_ == 0){
559 –    for (i = 0; i < globalPts.size(); i++){
560 –      std::cout << globalPts[i] << std::endl;
561 –    }
562 –  }
563 –  */
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_, nglobalPts, &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 = 1;
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 +    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
215 +    face.setNormal(V3dNormal);
216 +    
217 +    RealType faceArea = qh_facetarea(facet);
218 +    face.setArea(faceArea);
219 +    
220 +    vertices = qh_facet3vertex(facet);
221 +      
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 +    int ver = 0;
231  
232 <
233 <    unsigned int nf = qh num_facets;
234 <    
235 <    /* Build Surface SD list first */
236 <
591 <    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
592 <
593 <    FORALLfacets {
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 <      if (!facet->simplicial){
239 <      // 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 = new Triangle();
603 <      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
604 <      face->setNormal(V3dNormal);
605 <      //face->setCentroid(V3dCentroid);
606 <      RealType faceArea = 0.5*V3dNormal.length();
607 <      //face->setArea(faceArea);
238 >      Vector3d vel;
239 >      RealType mass;
240  
609 –
610 –      vertices = qh_facet3vertex(facet);
611 –      FOREACHvertex_(vertices){
612 –        id = qh_pointid(vertex->point);
613 –        int localindex = id;
241   #ifdef IS_MPI
242 <        
243 <        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
244 <          localindex = localPtsMap[id-noffset/3];
245 < #endif
619 <          face->addVertex(bodydoubles[localindex]);
620 <          if( !isSurfaceID[id] ){
621 <            isSurfaceID[id] = true;
622 < #ifdef IS_MPI      
623 <            
624 < #endif
625 <            
626 <            surfaceSDs_.push_back(bodydoubles[localindex]);
627 <            
628 <          } //IF isSurfaceID
242 >      vel = Vector3d(globalVels[dim_ * id],
243 >                     globalVels[dim_ * id + 1],
244 >                     globalVels[dim_ * id + 2]);
245 >      mass = globalMasses[id];
246  
247 < #ifdef IS_MPI
248 <        
632 <        }else{
633 <          face->addVertex(NULL);
634 <          }
635 < #endif
636 <      } //Foreachvertex
247 >      // localID will be between 0 and hullSitesOnProc[myrank] if we
248 >      // own this guy.
249  
250 <      Triangles_.push_back(face);
251 <      qh_settempfree(&vertices);      
250 >      int localID = id - displacements[myrank];
251 >
252 >      if (localID >= 0 && localID < hullSitesOnProc[myrank])
253 >        face.addVertexSD(bodydoubles[indexMap[localID]]);
254        
255 <    } //FORALLfacets
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 <                        
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 <  Ns_ = surfaceSDs_.size();
273 <
647 <
272 >  } //FORALLfacets
273 >  
274    qh_getarea(qh facet_list);
275    volume_ = qh totvol;
276    area_ = qh totarea;
277  
652 –  
653 –
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;
659 <  
660 <
661 <  
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 < {
668 <
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 675 | 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
680 – #endif //CGAL
681 –
682 –
683 –

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