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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1308 by chuckv, Tue Oct 21 16:44:00 2008 UTC vs.
Revision 1374 by chuckv, Tue Oct 20 20:05:28 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 1.12 2008-10-21 16:44:00 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.16 2009-10-20 20:05:28 chuckv 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 + 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*3);
98 +  std::vector<bool> isSurfaceID(numpoints);
99  
100 < typedef CGAL::MP_Float RT;
101 < //typedef double RT;
102 < //typedef CGAL::Homogeneous<RT>                     K;
103 < typedef CGAL::Exact_predicates_exact_constructions_kernel K;
104 < typedef K::Vector_3                               Vector_3;
105 < //typedef CGAL::Convex_hull_traits_3<K>             Traits;
106 < typedef CGAL::Polyhedron_traits_with_normals_3<K> Traits;
107 < //typedef Traits::Polyhedron_3                      Polyhedron_3;
108 < typedef CGAL::Polyhedron_3<Traits>                     Polyhedron_3;
109 < typedef K::Point_3                                Point_3;
100 >  // Copy the positon vector into a points vector for qhull.
101 >  std::vector<StuntDouble*>::iterator SD;
102 >  int i = 0;
103 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
104 >    Vector3d pos = (*SD)->getPos();      
105 >    ptArray[dim_ * i] = pos.x();
106 >    ptArray[dim_ * i + 1] = pos.y();
107 >    ptArray[dim_ * i + 2] = pos.z();
108 >    i++;
109 >  }
110 >  
111 >  boolT ismalloc = False;
112 >  /* Clean up memory from previous convex hull calculations*/
113 >  
114 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
115 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
116  
117 +    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
118 +    painCave.isFatal = 1;
119 +    simError();
120 +    
121 +  } //qh_new_qhull
122  
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 –
123  
124 + #ifdef IS_MPI
125 +  //If we are doing the mpi version, set up some vectors for data communication
126 +  
127 +  int nproc = MPI::COMM_WORLD.Get_size();
128 +  int myrank = MPI::COMM_WORLD.Get_rank();
129 +  int localHullSites = 0;
130 +  int* hullSitesOnProc = new int[nproc];
131 +  int* coordsOnProc = new int[nproc];
132 +  int* displacements = new int[nproc];
133 +  int* vectorDisplacements = new int[nproc];
134  
135 < class Enriched_Point_3 : public K::Point_3{
136 < public:
137 <  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
135 >  std::vector<double> coords;
136 >  std::vector<double> vels;
137 >  std::vector<int> objectIDs;
138 >  std::vector<double> masses;
139  
140 <  bool isMyPoint() const{ return yupMyPoint; }
141 <  void myPoint(){ yupMyPoint = true; }
142 <  void setSD(StuntDouble* SD){mySD = SD;}
143 <  StuntDouble* getStuntDouble(){return mySD;}
144 < private:
145 <  bool yupMyPoint;
146 <  StuntDouble* mySD;
140 >  FORALLvertices{
141 >    localHullSites++;
142 >    
143 >    int idx = qh_pointid(vertex->point);
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 < };
148 >    StuntDouble* sd = bodydoubles[idx];
149  
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 +    masses.push_back(sd->getMass());
156 +  }
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; i < nproc; iproc++){
163 +    globalHullSites += hullSitesOnProc[iproc];
164 +    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
165 +  }
166  
167 <    // compare Point_3's... used in setting up the STL map from points to indices
168 < template <typename Pt3>
169 < struct Point_3_comp {
170 <  bool operator() (const Pt3 & p, const Pt3 & q) const {
171 <    return CGAL::lexicographically_xyz_smaller(p,q); // this is defined inline & hence we had to create fn object & not ptrfun
167 >  displacements[0] = 0;
168 >  vectorDisplacements[0] = 0;
169 >  
170 >  for (int iproc = 1; i < nproc; iproc++){
171 >    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
172 >    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
173    }
133 – };
174  
175 < // coordinate-based hashing inefficient but can we do better if pts are copied?
176 < typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
175 >  std::vector<double> globalCoords(dim_*globalHullSites);
176 >  std::vector<double> globalVels(dim_*globalHullSites);
177 >  std::vector<double> globalMasses(globalHullSites);
178 >  int count = coordsOnProc[myrank];
179 >  
180 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE,
181 >                             &globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0],
182 >                             MPI::DOUBLE);
183  
184 < #ifdef IS_MPI
185 < struct {
186 <  double x,y,z;
141 < } surfacePt;
142 < #endif
184 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
185 >                             &globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
186 >                             MPI::DOUBLE);
187  
188 < ConvexHull::ConvexHull() : Hull(){
189 <  //If we are doing the mpi version, set up some vectors for data communication
190 < #ifdef IS_MPI
188 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
189 >                             &globalMasses[0], &hullSitesOnProc[0], &displacements[0],
190 >                             MPI::DOUBLE);
191  
192 <
193 < nproc_ = MPI::COMM_WORLD.Get_size();
194 < myrank_ = MPI::COMM_WORLD.Get_rank();
195 < NstoProc_ = new int[nproc_];
196 < displs_   = new int[nproc_];
197 <
154 < // Create a surface point type in MPI to send
155 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156 < surfacePtType.Commit();
157 <
158 <
159 < #endif
160 < }
161 <
162 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
163 < {
164 <
165 <  std::vector<Enriched_Point_3> points;
166 <  ptMapType myMap;
167 <  Point_iterator   hc;
192 >  // Free previous hull
193 >  qh_freeqhull(!qh_ALL);
194 >  qh_memfreeshort(&curlong, &totlong);
195 >  if (curlong || totlong)
196 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
197 >              << totlong << curlong << std::endl;
198    
199 <  // Copy the positon vector into a points vector for cgal.
200 <  std::vector<StuntDouble*>::iterator SD;
199 >  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
200 >                   const_cast<char *>(options_.c_str()), NULL, stderr)){
201 >    
202 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
203 >    painCave.isFatal = 1;
204 >    simError();
205 >    
206 >  } //qh_new_qhull
207  
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;
184 –
185 –  // 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 –
193 –
194 –
195 –  Ns_ = polyhedron.size_of_vertices();
196 –
197 – #ifdef IS_MPI
198 –  /* Gather an array of the number of verticies on each processor */
199 –  
200 –
201 –  surfacePtsGlobal_.clear();
202 –  surfacePtsLocal_.clear();
203 –
204 –  MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
205 –
206 –  for (int i = 0; i < nproc_; i++){
207 –    Nsglobal_ += NstoProc_[i];
208 –  }
209 –  /*Reminder ideally, we would like to reserve size for the vectors here*/
210 –  surfacePtsLocal_.reserve(Ns_);
211 –  surfacePtsGlobal_.resize(Nsglobal_);
212 –  //  std::fill(surfacePtsGlobal_.begin(),surfacePtsGlobal_.end(),0);
213 –
214 –  /* Build a displacements array */
215 –  for (int i = 1; i < nproc_; i++){
216 –    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 –
208   #endif
209  
210 +  FORALLfacets {  
211 +    Triangle face;
212  
213 <  
214 <  /* Loop over all of the surface triangles and build data structures for atoms and normals*/
215 <  Facet_iterator j;
216 <  area_ = 0;
217 <  for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) {
218 <    Halfedge_handle h = j->halfedge();
219 <
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 < displs_   = new int[nproc_];
382 <
383 < // Create a surface point type in MPI to send
384 < //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
385 < // surfacePtType.Commit();
386 <
387 <
388 < #endif
389 < }
390 <
391 <
392 <
393 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
394 < {
395 <  
396 <  std::vector<int> surfaceIDs;
397 <  std::vector<int> surfaceIDsGlobal;
398 <  std::vector<int> localPtsMap;
399 <  int numpoints = bodydoubles.size();
400 <
401 <  //coordT* pt_array;
402 <  coordT* surfpt_array;
403 <  vertexT *vertex, **vertexp;
404 <  facetT *facet;
405 <  setT *vertices;
406 <  int curlong,totlong;
407 <  int id;
408 <  
409 <  coordT *point,**pointp;
410 <
411 <
412 <  FILE *outdummy = NULL;
413 <  FILE *errdummy = NULL;
414 <  
415 <  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
416 <
417 < //  double* ptArray = new double[numpoints * 3];
418 <  std::vector<double> ptArray(numpoints*3);
419 <  std::vector<bool> isSurfaceID(numpoints);
420 <
421 <  // Copy the positon vector into a points vector for qhull.
422 <  std::vector<StuntDouble*>::iterator SD;
423 <  int i = 0;
424 <  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
425 <    {
426 <      Vector3d pos = (*SD)->getPos();
213 >    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
214 >    face.setNormal(V3dNormal);
215 >    
216 >    RealType faceArea = qh_facetarea(facet);
217 >    face.setArea(faceArea);
218 >    
219 >    vertices = qh_facet3vertex(facet);
220        
221 <      ptArray[dim_ * i] = pos.x();
222 <      ptArray[dim_ * i + 1] = pos.y();
223 <      ptArray[dim_ * i + 2] = pos.z();
431 <      i++;
432 <    }
433 <  
221 >    coordT *center = qh_getcenter(vertices);
222 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
223 >    face.setCentroid(V3dCentroid);
224  
225 <  
226 <  
227 <  
228 <  
439 <  boolT ismalloc = False;
440 <  /* Clean up memory from previous convex hull calculations*/
441 <  
442 <  Triangles_.clear();
443 <  surfaceSDs_.clear();
444 <  surfaceSDs_.reserve(Ns_);
225 >    Vector3d faceVel = V3Zero;
226 >    Vector3d p[3];
227 >    RealType faceMass = 0.0;
228 >    int ver = 0;
229  
230 <  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
231 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
232 <
233 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
234 <      painCave.isFatal = 1;
451 <      simError();
230 >    FOREACHvertex_(vertices){
231 >      int id = qh_pointid(vertex->point);
232 >      p[ver][0] = vertex->point[0];
233 >      p[ver][1] = vertex->point[1];
234 >      p[ver][2] = vertex->point[2];
235        
236 <  } //qh_new_qhull
236 >      Vector3d vel;
237 >      RealType mass;
238  
455 –
239   #ifdef IS_MPI
240 <  std::vector<double> localPts;
241 <  std::vector<double> localVel;
242 <  int localPtArraySize;
243 <  
461 <
462 <  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
463 <
240 >      vel = Vector3d(globalVels[dim_ * id],
241 >                     globalVels[dim_ * id + 1],
242 >                     globalVels[dim_ * id + 2]);
243 >      mass = globalMasses[id];
244  
245 <  FORALLfacets {
246 <    
247 <    if (!facet->simplicial){
248 <      // should never happen with Qt
249 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
250 <      painCave.isFatal = 1;
251 <      simError();
252 <    }
253 <    
254 <    
255 <    vertices = qh_facet3vertex(facet);
256 <    FOREACHvertex_(vertices){
257 <      id = qh_pointid(vertex->point);
245 >      // localID will be between 0 and hullSitesOnProc[myrank] if we own this guy.
246 >      int localID = id - displacements[myrank];
247 >      if (id >= 0 && id < hullSitesOnProc[myrank])
248 >        face.addVertexSD(bodydoubles[localID]);
249 >      else
250 >        face.addVertexSD(NULL);
251 > #else
252 >      vel = bodydoubles[id]->getVel();
253 >      mass = bodydoubles[id]->getMass();
254 >      face.addVertexSD(bodydoubles[id]);      
255 > #endif
256 >        
257 >      faceVel = faceVel + vel;
258 >      faceMass = faceMass + mass;
259 >      ver++;      
260 >    } //Foreachvertex
261  
262 <      if( !isSurfaceID[id] ){
263 <        isSurfaceID[id] = true;
264 <      }
265 <    }      
262 >    face.addVertices(p[0], p[1], p[2]);
263 >    face.setFacetMass(faceMass);
264 >    face.setFacetVelocity(faceVel/3.0);
265 >    Triangles_.push_back(face);
266      qh_settempfree(&vertices);      
484 –      
485 –  } //FORALLfacets
267  
268 <
488 <
489 <  /*
490 <  std::sort(surfaceIDs.begin(),surfaceIDs.end());
491 <  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
492 <  int localPtArraySize = surfaceIDs.size() * 3;
493 <  */
494 <
495 <  //localPts.resize(localPtArraySize);
496 <  //std::fill(localPts.begin(),localPts.end(),0.0);
497 <
498 <
499 <  int idx = 0;
500 <  int nIsIts = 0;
501 < /*
502 <  // Copy the surface points into an array.
503 <  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
504 <      list_iter != isSurfaceID.end(); list_iter++)
505 <    {
506 <      bool isIt = *list_iter;
507 <      if (isIt){
508 <        localPts.push_back(ptArray[dim_ * idx]);    
509 <        localPts.push_back(ptArray[dim_ * idx + 1]);
510 <        localPts.push_back(ptArray[dim_ * idx + 2]);
511 <        localPtsMap.push_back(idx);
512 <        nIsIts++;
513 <      } //Isit
514 <      idx++;
515 <    } //isSurfaceID
516 <  */
517 <  FORALLvertices {
518 <    idx = qh_pointid(vertex->point);
519 <    localPts.push_back(ptArray[dim_ * idx]);    
520 <    localPts.push_back(ptArray[dim_ * idx + 1]);
521 <    localPts.push_back(ptArray[dim_ * idx + 2]);
522 <
523 <    Vector3d vel = bodydoubles[idx]->getVel();
524 <    localVel.push_back(vel.x());
525 <    localVel.push_back(vel.y());
526 <    localVel.push_back(vel.z());
527 <
528 <    localPtsMap.push_back(idx);
529 <  }
530 <
531 <
532 <  localPtArraySize = localPts.size();
533 <
534 <
535 <  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
536 <
537 <  Nsglobal_=0;
538 <  for (int i = 0; i < nproc_; i++){
539 <    Nsglobal_ += NstoProc_[i];
540 <  }
268 >  } //FORALLfacets
269    
270 <
271 <  int nglobalPts = int(Nsglobal_/3);
272 <
270 >  qh_getarea(qh facet_list);
271 >  volume_ = qh totvol;
272 >  area_ = qh totarea;
273  
274 <  std::vector<double> globalPts(Nsglobal_);
275 <  std::vector<double> globalVel(Nsglobal_);
276 <
277 <  isSurfaceID.resize(nglobalPts);
278 <
279 <
552 <  std::fill(globalPts.begin(),globalPts.end(),0.0);
553 <
554 <  displs_[0] = 0;
555 <  /* Build a displacements array */
556 <  for (int i = 1; i < nproc_; i++){
557 <    displs_[i] = displs_[i-1] + NstoProc_[i-1];
558 <  }
274 > #ifdef IS_MPI
275 >  delete [] hullSitesOnProc;
276 >  delete [] coordsOnProc;
277 >  delete [] displacements;
278 >  delete [] vectorDisplacements;
279 > #endif
280    
560 –  
561 –  int noffset = displs_[myrank_];
562 –  /* gather the potential hull */
563 –  
564 –  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
565 –  MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize,MPI::DOUBLE,&globalVel[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
566 –
567 –  /*
568 –  if (myrank_ == 0){
569 –    for (i = 0; i < globalPts.size(); i++){
570 –      std::cout << globalPts[i] << std::endl;
571 –    }
572 –  }
573 –  */
574 –  // Free previous hull
281    qh_freeqhull(!qh_ALL);
282    qh_memfreeshort(&curlong, &totlong);
283    if (curlong || totlong)
284      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
285 <              << totlong << curlong << std::endl;
580 <
581 <  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
582 <                    const_cast<char *>(options_.c_str()), NULL, stderr)){
583 <
584 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
585 <      painCave.isFatal = 1;
586 <      simError();
587 <      
588 <  } //qh_new_qhull
589 <
590 < #endif
591 <
592 <
593 <
594 <
595 <
596 <
597 <    unsigned int nf = qh num_facets;
598 <    
599 <    /* Build Surface SD list first */
600 <
601 <    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
602 <
603 <    FORALLfacets {
604 <      
605 <      if (!facet->simplicial){
606 <      // should never happen with Qt
607 <        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
608 <        painCave.isFatal = 1;
609 <        simError();
610 <      } //simplicical
611 <      
612 <      Triangle face;
613 <      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
614 <      face.setNormal(V3dNormal);
615 <
616 <      
617 <
618 <      RealType faceArea = 0.5*V3dNormal.length();
619 <      face.setArea(faceArea);
620 <
621 <
622 <      vertices = qh_facet3vertex(facet);
623 <      
624 <      coordT *center = qh_getcenter(vertices);
625 <      Vector3d V3dCentroid(center[0], center[1], center[2]);
626 <      face.setCentroid(V3dCentroid);
627 <      Vector3d faceVel = V3Zero;
628 <      FOREACHvertex_(vertices){
629 <        id = qh_pointid(vertex->point);
630 <        int localindex = id;
631 < #ifdef IS_MPI
632 <        Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
633 <        faceVel = faceVel + velVector;
634 <        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
635 <          localindex = localPtsMap[id-noffset/3];
636 < #else
637 <          faceVel = faceVel + bodydoubles[localindex]->getVel();
638 < #endif
639 <          face.addVertex(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.addVertex(NULL);
654 <          }
655 < #endif
656 <      } //Foreachvertex
657 <      /*
658 <      if (!SETempty_(facet->coplanarset)){
659 <        FOREACHpoint_(facet->coplanarset){
660 <          id = qh_pointid(point);
661 <          surfaceSDs_.push_back(bodydoubles[id]);
662 <        }
663 <      }
664 <      */
665 <      face.setFacetVelocity(faceVel/3.0);
666 <      Triangles_.push_back(face);
667 <      qh_settempfree(&vertices);      
668 <
669 <    } //FORALLfacets
670 <
671 <    /*
672 <    std::cout << surfaceSDs_.size() << std::endl;
673 <    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
674 <      Vector3d thisatom = (*SD)->getPos();
675 <      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
676 <    }
677 <    */
678 <
679 <
680 <
681 <    Ns_ = surfaceSDs_.size();
682 <    nTriangles_ = Triangles_.size();
683 <    
684 <    qh_getarea(qh facet_list);
685 <    volume_ = qh totvol;
686 <    area_ = qh totarea;
687 <    
688 <    
689 <    
690 <    qh_freeqhull(!qh_ALL);
691 <    qh_memfreeshort(&curlong, &totlong);
692 <    if (curlong || totlong)
693 <      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
694 <                << totlong << curlong << std::endl;
695 <    
696 <    
697 <    
285 >              << totlong << curlong << std::endl;    
286   }
287  
288  
289  
290 < void ConvexHull::printHull(const std::string& geomFileName)
703 < {
704 <
290 > void ConvexHull::printHull(const std::string& geomFileName) {
291    FILE *newGeomFile;
292    
293    //create new .md file based on old .md file
# Line 713 | Line 299 | void ConvexHull::printHull(const std::string& geomFile
299    fclose(newGeomFile);
300   }
301   #endif //QHULL
716 – #endif //CGAL
717 –
718 –
719 –

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