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root/OpenMD/trunk/src/math/ConvexHull.cpp
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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1304 by chuckv, Wed Oct 15 18:26:01 2008 UTC vs.
Revision 1376 by gezelter, Tue Oct 20 20:36:56 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 1.10 2008-10-15 18:26:01 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.17 2009-10-20 20:36:56 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 + /* 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 <
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;
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 < class Enriched_Point_3 : public K::Point_3{
101 < public:
102 <  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
103 <
104 <  bool isMyPoint() const{ return yupMyPoint; }
105 <  void myPoint(){ yupMyPoint = true; }
106 <  void setSD(StuntDouble* SD){mySD = SD;}
107 <  StuntDouble* getStuntDouble(){return mySD;}
108 < 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
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 < };
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 < // coordinate-based hashing inefficient but can we do better if pts are copied?
118 < typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
117 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
118 >    painCave.isFatal = 1;
119 >    simError();
120 >    
121 >  } //qh_new_qhull
122  
138 – #ifdef IS_MPI
139 – struct {
140 –  double x,y,z;
141 – } surfacePt;
142 – #endif
123  
144 – ConvexHull::ConvexHull() : Hull(){
145 –  //If we are doing the mpi version, set up some vectors for data communication
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 +  std::vector<double> coords;
136 +  std::vector<double> vels;
137 +  std::vector<int> objectIDs;
138 +  std::vector<double> masses;
139  
140 < nproc_ = MPI::COMM_WORLD.Get_size();
141 < myrank_ = MPI::COMM_WORLD.Get_rank();
142 < NstoProc_ = new int[nproc_];
143 < displs_   = new int[nproc_];
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 < // Create a surface point type in MPI to send
155 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156 < surfacePtType.Commit();
157 <
148 >    StuntDouble* sd = bodydoubles[idx];
149  
150 < #endif
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 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
156 < {
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;
155 >    masses.push_back(sd->getMass());
156 >  }
157  
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;
158  
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 –
159  
160 <
161 <  Ns_ = polyhedron.size_of_vertices();
160 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
161 >                            1, MPI::INT);
162  
163 < #ifdef IS_MPI
164 <  /* Gather an array of the number of verticies on each processor */
165 <  
166 <
167 <  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];
163 >  int globalHullSites = 0;
164 >  for (int iproc = 0; iproc < nproc; iproc++){
165 >    std::cerr << "iproc = " << iproc << " sites = " << hullSitesOnProc[iproc] << "\n";
166 >    globalHullSites += hullSitesOnProc[iproc];
167 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
168    }
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);
169  
170 <  /* Build a displacements array */
171 <  for (int i = 1; i < nproc_; i++){
216 <    displs_[i] = displs_[i-1] + NstoProc_[i-1];
217 <  }
170 >  displacements[0] = 0;
171 >  vectorDisplacements[0] = 0;
172    
173 <  int noffset = displs_[myrank_];
174 <  /* gather the potential hull */
175 <  
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);
173 >  for (int iproc = 1; iproc < nproc; iproc++){
174 >    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
175 >    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
176    }
177  
178 <  MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType);
179 <  std::vector<surfacePt_>::iterator spt;
180 <  std::vector<Enriched_Point_3> gblpoints;
181 <
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 <
178 >  std::vector<double> globalCoords(dim_*globalHullSites);
179 >  std::vector<double> globalVels(dim_*globalHullSites);
180 >  std::vector<double> globalMasses(globalHullSites);
181 >  int count = coordsOnProc[myrank];
182    
183 <  /* Loop over all of the surface triangles and build data structures for atoms and normals*/
184 <  Facet_iterator j;
185 <  area_ = 0;
264 <  for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) {
265 <    Halfedge_handle h = j->halfedge();
183 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE,
184 >                             &globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0],
185 >                             MPI::DOUBLE);
186  
187 <    Point_3 r0=h->vertex()->point();
188 <    Point_3 r1=h->next()->vertex()->point();
189 <    Point_3 r2=h->next()->next()->vertex()->point();
187 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
188 >                             &globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
189 >                             MPI::DOUBLE);
190  
191 <    Point_3* pr0 = &r0;
192 <    Point_3* pr1 = &r1;
193 <    Point_3* pr2 = &r2;
191 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 >                             &globalMasses[0], &hullSitesOnProc[0], &displacements[0],
193 >                             MPI::DOUBLE);
194  
195 <    Enriched_Point_3* er0 = static_cast<Enriched_Point_3*>(pr0);
196 <    Enriched_Point_3* er1 = static_cast<Enriched_Point_3*>(pr1);
197 <    Enriched_Point_3* er2 = static_cast<Enriched_Point_3*>(pr2);
198 <
199 <    // StuntDouble* sd = er0->getStuntDouble();
200 <    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 <  }
195 >  // Free previous hull
196 >  qh_freeqhull(!qh_ALL);
197 >  qh_memfreeshort(&curlong, &totlong);
198 >  if (curlong || totlong)
199 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
200 >              << totlong << curlong << std::endl;
201    
202 <  std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
203 <  
204 <
205 <
206 < }
207 < void ConvexHull::printHull(const std::string& geomFileName)
208 < {
209 <  /*
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 <
202 >  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
203 >                   const_cast<char *>(options_.c_str()), NULL, stderr)){
204 >    
205 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
206 >    painCave.isFatal = 1;
207 >    simError();
208 >    
209 >  } //qh_new_qhull
210  
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) {
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 –
211   #endif
389 – }
212  
213 +  FORALLfacets {  
214 +    Triangle face;
215  
216 <
217 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
218 < {
219 <  
220 <  std::vector<int> surfaceIDs;
221 <  std::vector<int> surfaceIDsGlobal;
222 <  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();
216 >    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
217 >    face.setNormal(V3dNormal);
218 >    
219 >    RealType faceArea = qh_facetarea(facet);
220 >    face.setArea(faceArea);
221 >    
222 >    vertices = qh_facet3vertex(facet);
223        
224 <      ptArray[dim_ * i] = pos.x();
225 <      ptArray[dim_ * i + 1] = pos.y();
226 <      ptArray[dim_ * i + 2] = pos.z();
431 <      i++;
432 <    }
433 <  
224 >    coordT *center = qh_getcenter(vertices);
225 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
226 >    face.setCentroid(V3dCentroid);
227  
228 <  
229 <  
230 <  
231 <  
439 <  boolT ismalloc = False;
440 <  /* Clean up memory from previous convex hull calculations*/
441 <  Triangles_.clear();
442 <  surfaceSDs_.clear();
443 <  surfaceSDs_.reserve(Ns_);
228 >    Vector3d faceVel = V3Zero;
229 >    Vector3d p[3];
230 >    RealType faceMass = 0.0;
231 >    int ver = 0;
232  
233 <  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
234 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
235 <
236 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
237 <      painCave.isFatal = 0;
450 <      simError();
233 >    FOREACHvertex_(vertices){
234 >      int id = qh_pointid(vertex->point);
235 >      p[ver][0] = vertex->point[0];
236 >      p[ver][1] = vertex->point[1];
237 >      p[ver][2] = vertex->point[2];
238        
239 <  } //qh_new_qhull
239 >      Vector3d vel;
240 >      RealType mass;
241  
454 –
242   #ifdef IS_MPI
243 <  std::vector<double> localPts;
244 <  int localPtArraySize;
245 <  
246 <
460 <  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
461 <
243 >      vel = Vector3d(globalVels[dim_ * id],
244 >                     globalVels[dim_ * id + 1],
245 >                     globalVels[dim_ * id + 2]);
246 >      mass = globalMasses[id];
247  
248 <  FORALLfacets {
249 <    
250 <    if (!facet->simplicial){
251 <      // should never happen with Qt
252 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
253 <      painCave.isFatal = 0;
254 <      simError();
255 <    }
256 <    
257 <    
258 <    vertices = qh_facet3vertex(facet);
259 <    FOREACHvertex_(vertices){
260 <      id = qh_pointid(vertex->point);
248 >      // localID will be between 0 and hullSitesOnProc[myrank] if we own this guy.
249 >      int localID = id - displacements[myrank];
250 >      if (id >= 0 && id < hullSitesOnProc[myrank])
251 >        face.addVertexSD(bodydoubles[localID]);
252 >      else
253 >        face.addVertexSD(NULL);
254 > #else
255 >      vel = bodydoubles[id]->getVel();
256 >      mass = bodydoubles[id]->getMass();
257 >      face.addVertexSD(bodydoubles[id]);      
258 > #endif
259 >        
260 >      faceVel = faceVel + vel;
261 >      faceMass = faceMass + mass;
262 >      ver++;      
263 >    } //Foreachvertex
264  
265 <      if( !isSurfaceID[id] ){
266 <        isSurfaceID[id] = true;
267 <      }
268 <    }      
265 >    face.addVertices(p[0], p[1], p[2]);
266 >    face.setFacetMass(faceMass);
267 >    face.setFacetVelocity(faceVel/3.0);
268 >    Triangles_.push_back(face);
269      qh_settempfree(&vertices);      
482 –      
483 –  } //FORALLfacets
270  
271 <
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 <  }
271 >  } //FORALLfacets
272    
273 <
274 <  int nglobalPts = int(Nsglobal_/3);
275 <
273 >  qh_getarea(qh facet_list);
274 >  volume_ = qh totvol;
275 >  area_ = qh totarea;
276  
277 <  std::vector<double> globalPts;
278 <  globalPts.resize(Nsglobal_);
279 <
280 <  isSurfaceID.resize(nglobalPts);
281 <
282 <
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 <  }
277 > #ifdef IS_MPI
278 >  delete [] hullSitesOnProc;
279 >  delete [] coordsOnProc;
280 >  delete [] displacements;
281 >  delete [] vectorDisplacements;
282 > #endif
283    
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
284    qh_freeqhull(!qh_ALL);
285    qh_memfreeshort(&curlong, &totlong);
286    if (curlong || totlong)
287      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
288 <              << 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 <    
288 >              << totlong << curlong << std::endl;    
289   }
290  
291  
292  
293 < void ConvexHull::printHull(const std::string& geomFileName)
690 < {
691 <
293 > void ConvexHull::printHull(const std::string& geomFileName) {
294    FILE *newGeomFile;
295    
296    //create new .md file based on old .md file
# Line 700 | Line 302 | void ConvexHull::printHull(const std::string& geomFile
302    fclose(newGeomFile);
303   }
304   #endif //QHULL
703 – #endif //CGAL
704 –
705 –
706 –

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