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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1316 by chuckv, Fri Nov 14 15:44:34 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 1.13 2008-11-14 15:44:34 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 < 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 <
132 >  std::vector<double> coords;
133 >  std::vector<double> vels;
134 >  std::vector<int> indexMap;
135 >  std::vector<double> masses;
136  
137 < #endif
138 < }
137 >  FORALLvertices{
138 >    localHullSites++;
139 >    
140 >    int idx = qh_pointid(vertex->point);
141  
142 < 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;
142 >    indexMap.push_back(idx);
143  
144 <    for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
145 <    {
146 <      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;
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 <  // compute convex hull
186 <  
187 <  std::vector<Enriched_Point_3>::iterator testpt;
188 <  
189 <  
190 <
191 <  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 <
148 >    StuntDouble* sd = bodydoubles[idx];
149  
150 <
151 <  Ns_ = polyhedron.size_of_vertices();
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 < #ifdef IS_MPI
156 <  /* Gather an array of the number of verticies on each processor */
199 <  
155 >    masses.push_back(sd->getMass());
156 >  }
157  
158 <  surfacePtsGlobal_.clear();
159 <  surfacePtsLocal_.clear();
158 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159 >                            1, MPI::INT);
160  
161 <  MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
162 <
163 <  for (int i = 0; i < nproc_; i++){
164 <    Nsglobal_ += NstoProc_[i];
161 >  int globalHullSites = 0;
162 >  for (int iproc = 0; iproc < nproc; iproc++){
163 >    globalHullSites += hullSitesOnProc[iproc];
164 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
165    }
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);
166  
167 <  /* Build a displacements array */
168 <  for (int i = 1; i < nproc_; i++){
216 <    vecdispls_[i] = vecdispls_[i-1] + NstoProc_[i-1];
217 <  }
167 >  displacements[0] = 0;
168 >  vectorDisplacements[0] = 0;
169    
170 <  int noffset = vecdispls_[myrank_];
171 <  /* gather the potential hull */
172 <  
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);
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 <  MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,vecdispls_,surfacePtType);
176 <  std::vector<surfacePt_>::iterator spt;
177 <  std::vector<Enriched_Point_3> gblpoints;
175 >  std::vector<double> globalCoords(dim_ * globalHullSites);
176 >  std::vector<double> globalVels(dim_ * globalHullSites);
177 >  std::vector<double> globalMasses(globalHullSites);
178  
179 <  int mine = 0;
180 <  int pointidx = 0;
181 <  for (spt = surfacePtsGlobal_.begin(); spt != surfacePtsGlobal_.end(); ++spt)
182 <    {    
183 <      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 < }
362 <
363 <
364 <
365 <
366 <
367 <
368 <
369 < #else
370 < #ifdef HAVE_QHULL
371 < /* Old options Qt Qu Qg QG0 FA */
372 < /* More old opts Qc Qi Pp*/
373 < ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
374 <  //If we are doing the mpi version, set up some vectors for data communication
375 < #ifdef IS_MPI
376 <
377 <
378 < nproc_ = MPI::COMM_WORLD.Get_size();
379 < myrank_ = MPI::COMM_WORLD.Get_rank();
380 < NstoProc_ = new int[nproc_];
381 < 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 <
179 >  int count = coordsOnProc[myrank];
180 >  
181 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
182 >                             &coordsOnProc[0], &vectorDisplacements[0],
183 >                             MPI::DOUBLE);
184  
185 +  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
186 +                             &coordsOnProc[0], &vectorDisplacements[0],
187 +                             MPI::DOUBLE);
188  
189 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
190 < {
191 <  
398 <  std::vector<int> surfaceIDs;
399 <  std::vector<int> surfaceIDsGlobal;
400 <  std::vector<int> localPtsMap;
401 <  int numpoints = bodydoubles.size();
189 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
190 >                             &globalMasses[0], &hullSitesOnProc[0],
191 >                             &displacements[0], MPI::DOUBLE);
192  
193 <  //coordT* pt_array;
194 <  coordT* surfpt_array;
195 <  vertexT *vertex, **vertexp;
196 <  facetT *facet;
197 <  setT *vertices;
198 <  int curlong,totlong;
409 <  int id;
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 <  coordT *point,**pointp;
201 <
202 <
203 <  FILE *outdummy = NULL;
204 <  FILE *errdummy = NULL;
205 <  
206 <  //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 <  
438 <  
439 <  
440 <  
441 <  boolT ismalloc = False;
442 <  /* Clean up memory from previous convex hull calculations*/
443 <  
444 <  Triangles_.clear();
445 <  surfaceSDs_.clear();
446 <  surfaceSDs_.reserve(Ns_);
447 <
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 <      
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 < #ifdef IS_MPI
212 <  std::vector<double> localPts;
460 <  std::vector<double> localVel;
461 <  std::vector<double> localMass;
462 <  int localPtArraySize;
463 <  
464 <
465 <  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
466 <
211 >  FORALLfacets {  
212 >    Triangle face;
213  
214 <  FORALLfacets {
214 >    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
215 >    face.setNormal(V3dNormal);
216      
217 <    if (!facet->simplicial){
218 <      // should never happen with Qt
472 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
473 <      painCave.isFatal = 1;
474 <      simError();
475 <    }
217 >    RealType faceArea = qh_facetarea(facet);
218 >    face.setArea(faceArea);
219      
477 –    
220      vertices = qh_facet3vertex(facet);
479 –    FOREACHvertex_(vertices){
480 –      id = qh_pointid(vertex->point);
481 –
482 –      if( !isSurfaceID[id] ){
483 –        isSurfaceID[id] = true;
484 –      }
485 –    }      
486 –    qh_settempfree(&vertices);      
221        
222 <  } //FORALLfacets
222 >    coordT *center = qh_getcenter(vertices);
223 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
224 >    face.setCentroid(V3dCentroid);
225  
226 <
226 >    Vector3d faceVel = V3Zero;
227 >    Vector3d p[3];
228 >    RealType faceMass = 0.0;
229  
230 +    int ver = 0;
231  
232 <  int idx = 0;
233 <  int nIsIts = 0;
234 <  FORALLvertices {
235 <    idx = qh_pointid(vertex->point);
236 <    localPts.push_back(ptArray[dim_ * idx]);    
237 <    localPts.push_back(ptArray[dim_ * idx + 1]);
238 <    localPts.push_back(ptArray[dim_ * idx + 2]);
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 >      Vector3d vel;
239 >      RealType mass;
240  
241 <    Vector3d vel = bodydoubles[idx]->getVel();
242 <    localVel.push_back(vel.x());
243 <    localVel.push_back(vel.y());
244 <    localVel.push_back(vel.z());
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 <    RealType bdmass = bodydoubles[idx]->getMass();
248 <    localMass.push_back(bdmass);
247 >      // localID will be between 0 and hullSitesOnProc[myrank] if we
248 >      // own this guy.
249  
250 <    localPtsMap.push_back(idx);
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 <  }
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 <
515 <
516 <  localPtArraySize = int(localPts.size()/3.0);
517 <
518 <
519 <  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
272 >  } //FORALLfacets
273    
274 <  Nsglobal_=0;
275 <  for (int i = 0; i < nproc_; i++){
276 <    Nsglobal_ += NstoProc_[i];
524 <    vecNstoProc_[i] = NstoProc_[i]*3;
525 <  }
526 <  
527 <
528 <  int nglobalPts = Nsglobal_*3;
529 <
274 >  qh_getarea(qh facet_list);
275 >  volume_ = qh totvol;
276 >  area_ = qh totarea;
277  
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 –  if (myrank_ == 0){
559 –    for (i = 0; i < globalPts.size(); i++){
560 –      std::cout << globalPts[i] << std::endl;
561 –    }
562 –  }
563 –  */
564 –  // Free previous hull
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;
282 >              << totlong << curlong << std::endl;    
283 > }
284  
285 <  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
572 <                    const_cast<char *>(options_.c_str()), NULL, stderr)){
285 > void ConvexHull::printHull(const std::string& geomFileName) {
286  
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;
287   #ifdef IS_MPI
288 <        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();
288 >  if (worldRank == 0)  {
289   #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 –    } //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 –
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 –
704 –
705 – void ConvexHull::printHull(const std::string& geomFileName)
706 – {
707 –
290    FILE *newGeomFile;
291    
292    //create new .md file based on old .md file
# Line 714 | 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
719 – #endif //CGAL
720 –
721 –
722 –

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