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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1188 by chuckv, Thu Nov 22 16:39:45 2007 UTC vs.
Revision 1304 by chuckv, Wed Oct 15 18:26:01 2008 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 2008 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 1.5 2007-11-22 16:39:45 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.10 2008-10-15 18:26:01 chuckv Exp $
48   *
49   */
50  
51 + /* Standard includes independent of library */
52   #include <iostream>
53   #include <fstream>
54   #include <list>
# Line 55 | Line 56
56   #include <iterator>
57   #include "math/ConvexHull.hpp"
58   #include "utils/simError.h"
59 +
60 +
61   using namespace oopse;
62  
63 < /* Old options Qt Qu Qg QG0 FA */
64 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
65 < //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
66 < {}
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  
65 – bool ConvexHull::genHull(std::vector<Vector3d> pos)
66 – {
78  
79 + //#include <CGAL/Quotient.h>
80 + #include <CGAL/MP_Float.h>
81 + //#include <CGAL/Lazy_exact_nt.h>
82  
69 –        int numpoints = pos.size();
70 –        coordT* pt_array;
71 –        coordT* surfpt_array;
72 –        std::list<int> surface_atoms;
73 –  FILE *outdummy = NULL;
74 –  FILE *errdummy = NULL;
83  
76 –        pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
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  
79 –        for (int i = 0; i < numpoints; i++) {
80 –                pt_array[dim_ * i] = pos[i][0];
81 –                pt_array[dim_ * i + 1] = pos[i][1];
82 –                pt_array[dim_ * i + 2] = pos[i][2];
83 –        }
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 <        /*
114 <                qh_initflags(const_cast<char *>(options_.c_str()));
115 <                qh_init_B(pospoints, numpoints, dim_, ismalloc);
116 <                qh_qhull();
117 <                qh_check_output();
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 <                qh_produce_output();
95 <        */
96 <        boolT ismalloc = False;
121 > };
122  
98 –        if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
99 –                          const_cast<char *>(options_.c_str()), NULL, stderr)) {
123  
101 –                vertexT *vertex, **vertexp;
102 –                facetT *facet;
103 –                setT *vertices;
104 –                unsigned int nf = qh num_facets;
124  
106 –                //Matrix idx(nf, dim);
107 – /*
108 –                int j, i = 0, id = 0;
109 –                        
110 –                        int id2 = 0;
111 –                        coordT *point,**pointp;
112 –                        realT dist;
113 –                        FORALLfacets {
114 –                            j = 0;
115 –                        
116 –                            if (!facet->simplicial){
117 –                            // should never happen with Qt
118 –                            sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
119 –                                    painCave.isFatal = 0;
120 –                                    simError();
121 –                            }
122 –                        
123 –                            vertices = qh_facet3vertex(facet);
124 –                            FOREACHvertex_(vertices){
125 –                                                id = qh_pointid(vertex->point);
126 –                                                surface_atoms.push_back(id);
127 –                                                //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
128 –                                        }
129 –                                        qh_settempfree(&vertices);
130 –                                        
131 –                            FOREACHpoint_(facet->coplanarset){
132 –                            vertex= qh_nearvertex (facet, point, &dist);
133 –                      //id= qh_pointid (vertex->point);
134 –                      id2= qh_pointid (point);
135 –                                        surface_atoms.push_back(id2);
136 –                                        //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
137 –                      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
138 –                                        //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
139 –                                        
140 –                                }
141 –                                
142 –                        }
143 –                
144 – */
145 –                
146 –                
147 –        }
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  
138 <        qh_getarea(qh facet_list);
139 <        volume_ = qh totvol;
140 <        area_ = qh totarea;
141 < //      FILE *newGeomFile;
138 > #ifdef IS_MPI
139 > struct {
140 >  double x,y,z;
141 > } surfacePt;
142 > #endif
143  
144 + ConvexHull::ConvexHull() : Hull(){
145 +  //If we are doing the mpi version, set up some vectors for data communication
146 + #ifdef IS_MPI
147  
158 –        /*
159 –                FORALLfacets {
160 –                    for (int k=0; k < qh hull_dim; k++)
161 –                      printf ("%6.2g ", facet->normal[k]);
162 –                    printf ("\n");
163 –                  }
164 –        */
148  
149 <        int curlong,totlong;
150 < //      geomviewHull("junk.off");
151 <        qh_freeqhull(!qh_ALL);
152 <        qh_memfreeshort(&curlong, &totlong);
170 <        if (curlong || totlong)
171 <                std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
172 <                << totlong << curlong << std::endl;
173 <        free(pt_array);
174 < /*
175 <        int j = 0;
176 <        surface_atoms.sort();
177 <        surface_atoms.unique();
178 <        surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
179 <        for(std::list<int>::iterator list_iter = surface_atoms.begin();
180 <            list_iter != surface_atoms.end(); list_iter++)
181 <        {
182 <                int i = *list_iter;
183 <                        //surfpt_array[dim_ * j] = pos[i][0];
184 <                        //surfpt_array[dim_ * j + 1] = pos[i][1];
185 <                        //surfpt_array[dim_ * j + 2] = pos[i][2];
186 <                        std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
187 <                        j++;
188 <        }
189 < */      
190 <        
191 < /*      
192 <        std::string deloptions_ = "qhull d Qt";
193 <        facetT *facet, *neighbor;
194 <        ridgeT *ridge, **ridgep;
149 > 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 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
155 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
154 > // Create a surface point type in MPI to send
155 > surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156 > surfacePtType.Commit();
157 >
158  
159 <                qh visit_id++;
160 <                FORALLfacets {
161 <                if (!facet->upperdelaunay) {
162 <                        facet->visitid= qh visit_id;
163 <                        qh_makeridges(facet);
164 <                        FOREACHridge_(facet->ridges) {
165 <                                neighbor= otherfacet_(ridge, facet);
166 <                                if (neighbor->visitid != qh visit_id) {
167 <                                                                                                                
168 <                                        FOREACHvertex_(ridge->vertices)
169 <                                                int id2 = qh_pointid (vertex->point);
170 <                                                std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
171 <                                }
172 <                        }
173 <                }
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;
168 >  
169 >  // Copy the positon vector into a points vector for cgal.
170 >  std::vector<StuntDouble*>::iterator SD;
171 >
172 >    for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
173 >    {
174 >      Vector3d pos = (*SD)->getPos();
175 >      Enriched_Point_3* pt = new Enriched_Point_3(pos.x(),pos.y(),pos.z());
176 >      pt->setSD(*SD);    
177 >      points.push_back(*pt);
178 >      // myMap[pt]=(*SD);
179 >    }
180 >  
181 >  // define object to hold convex hull
182 >  CGAL::Object ch_object_;
183 >  Polyhedron_3 polyhedron;
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 >
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  
218 – }
364  
220 –                qh_freeqhull(!qh_ALL);
221 –                qh_memfreeshort(&curlong, &totlong);
222 –                if (curlong || totlong)
223 –                        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
224 –                        << totlong << curlong << std::endl;
225 –                free(surfpt_array);
226 – */              
227 –        return true;
228 – }
365  
366  
367  
368 < RealType ConvexHull::getVolume()
369 < {
370 <        return volume_;
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) {
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 < void ConvexHull::geomviewHull(const std::string& geomFileName)
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 <        FILE *newGeomFile;
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  
242 –        //create new .md file based on old .md file
243 –        newGeomFile = fopen(geomFileName.c_str(), "w");
244 –        qh_findgood_all(qh facet_list);
245 –        for (int i = 0; i < qh_PRINTEND; i++)
246 –                qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
411  
412 <        fclose(newGeomFile);
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();
427 >      
428 >      ptArray[dim_ * i] = pos.x();
429 >      ptArray[dim_ * i + 1] = pos.y();
430 >      ptArray[dim_ * i + 2] = pos.z();
431 >      i++;
432 >    }
433 >  
434 >
435 >  
436 >  
437 >  
438 >  
439 >  boolT ismalloc = False;
440 >  /* Clean up memory from previous convex hull calculations*/
441 >  Triangles_.clear();
442 >  surfaceSDs_.clear();
443 >  surfaceSDs_.reserve(Ns_);
444 >
445 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
446 >                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
447 >
448 >      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
449 >      painCave.isFatal = 0;
450 >      simError();
451 >      
452 >  } //qh_new_qhull
453 >
454 >
455 > #ifdef IS_MPI
456 >  std::vector<double> localPts;
457 >  int localPtArraySize;
458 >  
459 >
460 >  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
461 >
462 >
463 >  FORALLfacets {
464 >    
465 >    if (!facet->simplicial){
466 >      // should never happen with Qt
467 >      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
468 >      painCave.isFatal = 0;
469 >      simError();
470 >    }
471 >    
472 >    
473 >    vertices = qh_facet3vertex(facet);
474 >    FOREACHvertex_(vertices){
475 >      id = qh_pointid(vertex->point);
476 >
477 >      if( !isSurfaceID[id] ){
478 >        isSurfaceID[id] = true;
479 >      }
480 >    }      
481 >    qh_settempfree(&vertices);      
482 >      
483 >  } //FORALLfacets
484 >
485 >
486 >
487 >  /*
488 >  std::sort(surfaceIDs.begin(),surfaceIDs.end());
489 >  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
490 >  int localPtArraySize = surfaceIDs.size() * 3;
491 >  */
492 >
493 >  //localPts.resize(localPtArraySize);
494 >  //std::fill(localPts.begin(),localPts.end(),0.0);
495 >
496 >
497 >  int idx = 0;
498 >  int nIsIts = 0;
499 > /*
500 >  // Copy the surface points into an array.
501 >  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
502 >      list_iter != isSurfaceID.end(); list_iter++)
503 >    {
504 >      bool isIt = *list_iter;
505 >      if (isIt){
506 >        localPts.push_back(ptArray[dim_ * idx]);    
507 >        localPts.push_back(ptArray[dim_ * idx + 1]);
508 >        localPts.push_back(ptArray[dim_ * idx + 2]);
509 >        localPtsMap.push_back(idx);
510 >        nIsIts++;
511 >      } //Isit
512 >      idx++;
513 >    } //isSurfaceID
514 >  */
515 >  FORALLvertices {
516 >    idx = qh_pointid(vertex->point);
517 >    localPts.push_back(ptArray[dim_ * idx]);    
518 >    localPts.push_back(ptArray[dim_ * idx + 1]);
519 >    localPts.push_back(ptArray[dim_ * idx + 2]);
520 >    localPtsMap.push_back(idx);
521 >  }
522 >
523 >
524 >  localPtArraySize = localPts.size();
525 >
526 >
527 >  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
528 >
529 >  Nsglobal_=0;
530 >  for (int i = 0; i < nproc_; i++){
531 >    Nsglobal_ += NstoProc_[i];
532 >  }
533 >  
534 >
535 >  int nglobalPts = int(Nsglobal_/3);
536 >
537 >
538 >  std::vector<double> globalPts;
539 >  globalPts.resize(Nsglobal_);
540 >
541 >  isSurfaceID.resize(nglobalPts);
542 >
543 >
544 >  std::fill(globalPts.begin(),globalPts.end(),0.0);
545 >
546 >  displs_[0] = 0;
547 >  /* Build a displacements array */
548 >  for (int i = 1; i < nproc_; i++){
549 >    displs_[i] = displs_[i-1] + NstoProc_[i-1];
550 >  }
551 >  
552 >  
553 >  int noffset = displs_[myrank_];
554 >  /* gather the potential hull */
555 >  
556 >  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
557 >
558 >  /*
559 >  if (myrank_ == 0){
560 >    for (i = 0; i < globalPts.size(); i++){
561 >      std::cout << globalPts[i] << std::endl;
562 >    }
563 >  }
564 >  */
565 >  // Free previous hull
566 >  qh_freeqhull(!qh_ALL);
567 >  qh_memfreeshort(&curlong, &totlong);
568 >  if (curlong || totlong)
569 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
570 >              << totlong << curlong << std::endl;
571 >
572 >  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
573 >                    const_cast<char *>(options_.c_str()), NULL, stderr)){
574 >
575 >      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
576 >      painCave.isFatal = 1;
577 >      simError();
578 >      
579 >  } //qh_new_qhull
580 >
581 > #endif
582 >
583 >
584 >
585 >
586 >
587 >
588 >    unsigned int nf = qh num_facets;
589 >    
590 >    /* Build Surface SD list first */
591 >
592 >    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
593 >
594 >    FORALLfacets {
595 >      
596 >      if (!facet->simplicial){
597 >      // should never happen with Qt
598 >        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
599 >        painCave.isFatal = 1;
600 >        simError();
601 >      } //simplicical
602 >      
603 >      Triangle* face = new Triangle();
604 >      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
605 >      face->setNormal(V3dNormal);
606 >
607 >      
608 >
609 >      RealType faceArea = 0.5*V3dNormal.length();
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 >
619 >      FOREACHvertex_(vertices){
620 >        id = qh_pointid(vertex->point);
621 >        int localindex = id;
622 > #ifdef IS_MPI
623 >        
624 >        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
625 >          localindex = localPtsMap[id-noffset/3];
626 > #endif
627 >          face->addVertex(bodydoubles[localindex]);
628 >          if( !isSurfaceID[id] ){
629 >            isSurfaceID[id] = true;
630 > #ifdef IS_MPI      
631 >            
632 > #endif
633 >            
634 >            surfaceSDs_.push_back(bodydoubles[localindex]);
635 >            
636 >          } //IF isSurfaceID
637 >
638 > #ifdef IS_MPI
639 >        
640 >        }else{
641 >          face->addVertex(NULL);
642 >          }
643 > #endif
644 >      } //Foreachvertex
645 >      /*
646 >      if (!SETempty_(facet->coplanarset)){
647 >        FOREACHpoint_(facet->coplanarset){
648 >          id = qh_pointid(point);
649 >          surfaceSDs_.push_back(bodydoubles[id]);
650 >        }
651 >      }
652 >
653 >      Triangles_.push_back(face);
654 >      qh_settempfree(&vertices);      
655 >      */
656 >    } //FORALLfacets
657 >
658 >    /*
659 >    std::cout << surfaceSDs_.size() << std::endl;
660 >    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
661 >      Vector3d thisatom = (*SD)->getPos();
662 >      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
663 >    }
664 >    */
665 >
666 >
667 >
668 >    Ns_ = surfaceSDs_.size();
669 >    
670 >    
671 >    qh_getarea(qh facet_list);
672 >    volume_ = qh totvol;
673 >    area_ = qh totarea;
674 >    
675 >    
676 >    
677 >    qh_freeqhull(!qh_ALL);
678 >    qh_memfreeshort(&curlong, &totlong);
679 >    if (curlong || totlong)
680 >      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
681 >                << totlong << curlong << std::endl;
682 >    
683 >    
684 >    
685   }
686  
687  
688  
689 + void ConvexHull::printHull(const std::string& geomFileName)
690 + {
691  
692 +  FILE *newGeomFile;
693 +  
694 +  //create new .md file based on old .md file
695 +  newGeomFile = fopen(geomFileName.c_str(), "w");
696 +  qh_findgood_all(qh facet_list);
697 +  for (int i = 0; i < qh_PRINTEND; i++)
698 +    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
699 +  
700 +  fclose(newGeomFile);
701 + }
702 + #endif //QHULL
703 + #endif //CGAL
704 +
705 +
706 +

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