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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 1378 by gezelter, Wed Oct 21 15:48:12 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 1.19 2009-10-21 15:48:12 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 + 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*dim_);
98  
99 < typedef CGAL::MP_Float RT;
100 < //typedef double RT;
101 < //typedef CGAL::Homogeneous<RT>                     K;
102 < typedef CGAL::Exact_predicates_exact_constructions_kernel K;
103 < typedef K::Vector_3                               Vector_3;
104 < //typedef CGAL::Convex_hull_traits_3<K>             Traits;
105 < typedef CGAL::Polyhedron_traits_with_normals_3<K> Traits;
106 < //typedef Traits::Polyhedron_3                      Polyhedron_3;
107 < typedef CGAL::Polyhedron_3<Traits>                     Polyhedron_3;
108 < typedef K::Point_3                                Point_3;
99 >  // Copy the positon vector into a points vector for qhull.
100 >  std::vector<StuntDouble*>::iterator SD;
101 >  int i = 0;
102 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
103 >    Vector3d pos = (*SD)->getPos();      
104 >    ptArray[dim_ * i] = pos.x();
105 >    ptArray[dim_ * i + 1] = pos.y();
106 >    ptArray[dim_ * i + 2] = pos.z();
107 >    i++;
108 >  }
109 >  
110 >  boolT ismalloc = False;
111 >  /* Clean up memory from previous convex hull calculations*/
112 >  
113 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
114 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
115  
116 +    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
117 +    painCave.isFatal = 1;
118 +    simError();
119 +    
120 +  } //qh_new_qhull
121  
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 –
122  
123 + #ifdef IS_MPI
124 +  //If we are doing the mpi version, set up some vectors for data communication
125 +  
126 +  int nproc = MPI::COMM_WORLD.Get_size();
127 +  int myrank = MPI::COMM_WORLD.Get_rank();
128 +  int localHullSites = 0;
129 +  int* hullSitesOnProc = new int[nproc];
130 +  int* coordsOnProc = new int[nproc];
131 +  int* displacements = new int[nproc];
132 +  int* vectorDisplacements = new int[nproc];
133  
134 < class Enriched_Point_3 : public K::Point_3{
135 < public:
136 <  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
134 >  std::vector<double> coords;
135 >  std::vector<double> vels;
136 >  std::vector<int> indexMap;
137 >  std::vector<double> masses;
138  
139 <  bool isMyPoint() const{ return yupMyPoint; }
140 <  void myPoint(){ yupMyPoint = true; }
141 <  void setSD(StuntDouble* SD){mySD = SD;}
142 <  StuntDouble* getStuntDouble(){return mySD;}
117 < private:
118 <  bool yupMyPoint;
119 <  StuntDouble* mySD;
139 >  FORALLvertices{
140 >    localHullSites++;
141 >    
142 >    int idx = qh_pointid(vertex->point);
143  
144 < };
144 >    indexMap.push_back(idx);
145  
146 +    coords.push_back(ptArray[dim_  * idx]);
147 +    coords.push_back(ptArray[dim_  * idx + 1]);
148 +    coords.push_back(ptArray[dim_  * idx + 2]);
149  
150 +    StuntDouble* sd = bodydoubles[idx];
151  
152 +    Vector3d vel = sd->getVel();
153 +    vels.push_back(vel.x());
154 +    vels.push_back(vel.y());
155 +    vels.push_back(vel.z());
156  
157 <
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
157 >    masses.push_back(sd->getMass());
158    }
133 – };
159  
160 < // coordinate-based hashing inefficient but can we do better if pts are copied?
161 < typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
160 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
161 >                            1, MPI::INT);
162  
163 < #ifdef IS_MPI
164 < struct {
165 <  double x,y,z;
166 < } surfacePt;
167 < #endif
163 >  int globalHullSites = 0;
164 >  for (int iproc = 0; iproc < nproc; iproc++){
165 >    globalHullSites += hullSitesOnProc[iproc];
166 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
167 >  }
168  
169 < ConvexHull::ConvexHull() : Hull(){
170 <  //If we are doing the mpi version, set up some vectors for data communication
171 < #ifdef IS_MPI
169 >  displacements[0] = 0;
170 >  vectorDisplacements[0] = 0;
171 >  
172 >  for (int iproc = 1; iproc < nproc; iproc++){
173 >    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
174 >    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
175 >  }
176  
177 +  std::vector<double> globalCoords(dim_ * globalHullSites);
178 +  std::vector<double> globalVels(dim_ * globalHullSites);
179 +  std::vector<double> globalMasses(globalHullSites);
180  
181 < nproc_ = MPI::COMM_WORLD.Get_size();
182 < myrank_ = MPI::COMM_WORLD.Get_rank();
183 < NstoProc_ = new int[nproc_];
184 < displs_   = new int[nproc_];
181 >  int count = coordsOnProc[myrank];
182 >  
183 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
184 >                             &coordsOnProc[0], &vectorDisplacements[0],
185 >                             MPI::DOUBLE);
186  
187 < // Create a surface point type in MPI to send
188 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
189 < surfacePtType.Commit();
157 <
187 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
188 >                             &coordsOnProc[0], &vectorDisplacements[0],
189 >                             MPI::DOUBLE);
190  
191 < #endif
192 < }
191 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 >                             &globalMasses[0], &hullSitesOnProc[0],
193 >                             &displacements[0], MPI::DOUBLE);
194  
195 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
196 < {
197 <
198 <  std::vector<Enriched_Point_3> points;
199 <  ptMapType myMap;
200 <  Point_iterator   hc;
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 <  // Copy the positon vector into a points vector for cgal.
203 <  std::vector<StuntDouble*>::iterator SD;
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  
211 <    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;
211 > #endif
212  
213 <  // compute convex hull
214 <  
187 <  std::vector<Enriched_Point_3>::iterator testpt;
188 <  
189 <  
190 <
191 <  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 <
213 >  FORALLfacets {  
214 >    Triangle face;
215  
216 <
217 <  Ns_ = polyhedron.size_of_vertices();
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 >    coordT *center = qh_getcenter(vertices);
225 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
226 >    face.setCentroid(V3dCentroid);
227  
228 < #ifdef IS_MPI
229 <  /* Gather an array of the number of verticies on each processor */
230 <  
228 >    Vector3d faceVel = V3Zero;
229 >    Vector3d p[3];
230 >    RealType faceMass = 0.0;
231  
232 <  surfacePtsGlobal_.clear();
202 <  surfacePtsLocal_.clear();
232 >    int ver = 0;
233  
234 <  MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
234 >    FOREACHvertex_(vertices){
235 >      int id = qh_pointid(vertex->point);
236 >      p[ver][0] = vertex->point[0];
237 >      p[ver][1] = vertex->point[1];
238 >      p[ver][2] = vertex->point[2];
239 >      
240 >      Vector3d vel;
241 >      RealType mass;
242  
243 <  for (int i = 0; i < nproc_; i++){
244 <    Nsglobal_ += NstoProc_[i];
245 <  }
246 <  /*Reminder ideally, we would like to reserve size for the vectors here*/
247 <  surfacePtsLocal_.reserve(Ns_);
211 <  surfacePtsGlobal_.resize(Nsglobal_);
212 <  //  std::fill(surfacePtsGlobal_.begin(),surfacePtsGlobal_.end(),0);
243 > #ifdef IS_MPI
244 >      vel = Vector3d(globalVels[dim_ * id],
245 >                     globalVels[dim_ * id + 1],
246 >                     globalVels[dim_ * id + 2]);
247 >      mass = globalMasses[id];
248  
249 <  /* Build a displacements array */
250 <  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 <  }
249 >      // localID will be between 0 and hullSitesOnProc[myrank] if we
250 >      // own this guy.
251  
252 <  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;
252 >      int localID = id - displacements[myrank];
253  
254 <  int mine = 0;
255 <  int pointidx = 0;
256 <  for (spt = surfacePtsGlobal_.begin(); spt != surfacePtsGlobal_.end(); ++spt)
257 <    {    
258 <      surfacePt_ thispos = *spt;
259 <      Enriched_Point_3 ept(thispos.x,thispos.y,thispos.z);
260 <      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 <
254 >      if (localID >= 0 && localID < hullSitesOnProc[myrank])
255 >        face.addVertexSD(bodydoubles[indexMap[localID]]);
256 >      
257 > #else
258 >      vel = bodydoubles[id]->getVel();
259 >      mass = bodydoubles[id]->getMass();
260 >      face.addVertexSD(bodydoubles[id]);      
261   #endif
262 +        
263 +      faceVel = faceVel + vel;
264 +      faceMass = faceMass + mass;
265 +      ver++;      
266 +    } //Foreachvertex
267  
268 <
269 <  
270 <  /* 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;
268 >    face.addVertices(p[0], p[1], p[2]);
269 >    face.setFacetMass(faceMass);
270 >    face.setFacetVelocity(faceVel/3.0);
271      Triangles_.push_back(face);
272 <    //    ptMapType::const_iterator locn=myMap.find(mypoint);
296 <    //    int myIndex = locn->second;
272 >    qh_settempfree(&vertices);      
273  
274 <  }
274 >  } //FORALLfacets
275    
276 <  std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
277 <  
276 >  qh_getarea(qh facet_list);
277 >  volume_ = qh totvol;
278 >  area_ = qh totarea;
279  
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) {
374 –  //If we are doing the mpi version, set up some vectors for data communication
280   #ifdef IS_MPI
281 <
282 <
283 < nproc_ = MPI::COMM_WORLD.Get_size();
284 < 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 <
281 >  delete [] hullSitesOnProc;
282 >  delete [] coordsOnProc;
283 >  delete [] displacements;
284 >  delete [] vectorDisplacements;
285   #endif
389 – }
390 –
391 –
392 –
393 – void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
394 – {
286    
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();
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
287    qh_freeqhull(!qh_ALL);
288    qh_memfreeshort(&curlong, &totlong);
289    if (curlong || totlong)
290      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
291 <              << 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 <    
291 >              << totlong << curlong << std::endl;    
292   }
293  
294 <
688 <
689 < void ConvexHull::printHull(const std::string& geomFileName)
690 < {
691 <
294 > void ConvexHull::printHull(const std::string& geomFileName) {
295    FILE *newGeomFile;
296    
297    //create new .md file based on old .md file
# Line 700 | Line 303 | void ConvexHull::printHull(const std::string& geomFile
303    fclose(newGeomFile);
304   }
305   #endif //QHULL
703 – #endif //CGAL
704 –
705 –
706 –

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