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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1242 by chuckv, Wed May 14 14:31:48 2008 UTC vs.
Revision 1378 by gezelter, Wed Oct 21 15:48:12 2009 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 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 1.6 2008-05-14 14:31:48 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 56 | Line 57
57   #include <iterator>
58   #include "math/ConvexHull.hpp"
59   #include "utils/simError.h"
59 – using namespace oopse;
60  
61 < /* CGAL version of convex hull first then QHULL */
62 < #ifdef HAVE_CGAL
61 > #ifdef IS_MPI
62 > #include <mpi.h>
63 > #endif
64  
65 < #include <CGAL/basic.h>
65 < #include <CGAL/Simple_cartesian.h>
66 < #include <CGAL/Convex_hull_traits_3.h>
67 < #include <CGAL/convex_hull_3.h>
68 < #include <CGAL/double.h>
65 > using namespace oopse;
66  
67 < #include <CGAL/Quotient.h>
68 < #include <CGAL/MP_Float.h>
69 < #include <CGAL/Lazy_exact_nt.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 < typedef double RT;
81 < typedef CGAL::Simple_cartesian<RT>                K;
76 < typedef CGAL::Convex_hull_traits_3<K>             Traits;
77 < typedef Traits::Polyhedron_3                      Polyhedron_3;
78 < typedef K::Point_3                                Point;
80 > /* Old options Qt Qu Qg QG0 FA */
81 > /* More old opts Qc Qi Pp*/
82  
83 + ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
84 + }
85  
86 < ConvexHull::ConvexHull(){}
86 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
87 >
88 >  int numpoints = bodydoubles.size();
89  
90 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
84 < {
90 >  Triangles_.clear();
91    
92 <  std::vector<Point> points;    
92 >  vertexT *vertex, **vertexp;
93 >  facetT *facet;
94 >  setT *vertices;
95 >  int curlong, totlong;
96    
97 <  
98 <  // Copy the positon vector into a points vector for cgal.
99 <  for (int i = 0; i < pos.size(); ++i)
100 <    {
101 <      Point pt(pos[i][0],pos[i][1],pos[i][2]);
102 <      points.push_back(pt);
103 <    }
104 <  
105 <  // define object to hold convex hull
106 <  Polyhedron_3 ch_object_;
107 <  // compute convex hull
99 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
100 <  
101 <  for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin(); ch_object_.vertices_end(); ++v){
102 <    std::cout<< v.point()<<std::endl;
97 >  std::vector<double> ptArray(numpoints*dim_);
98 >
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 < }
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  
122  
123 < #else
124 < #ifdef HAVE_QHULL
112 < /* Old options Qt Qu Qg QG0 FA */
113 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
114 <                           //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
115 < {}
116 <
117 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
118 < {
123 > #ifdef IS_MPI
124 >  //If we are doing the mpi version, set up some vectors for data communication
125    
126 <  
127 <  int numpoints = pos.size();
128 <  coordT* pt_array;
129 <  coordT* surfpt_array;
130 <  std::list<int> surface_atoms;
131 <  FILE *outdummy = NULL;
132 <  FILE *errdummy = NULL;
127 <  
128 <  pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
129 <  
130 <  
131 <  for (int i = 0; i < numpoints; i++) {
132 <    pt_array[dim_ * i] = pos[i][0];
133 <    pt_array[dim_ * i + 1] = pos[i][1];
134 <    pt_array[dim_ * i + 2] = pos[i][2];
135 <  }
136 <  
137 <  
138 <  
139 <  
140 <  /*
141 <    qh_initflags(const_cast<char *>(options_.c_str()));
142 <    qh_init_B(pospoints, numpoints, dim_, ismalloc);
143 <    qh_qhull();
144 <    qh_check_output();
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 <    qh_produce_output();
135 <  */
136 <  boolT ismalloc = False;
137 <  
138 <  if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
139 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
134 >  std::vector<double> coords;
135 >  std::vector<double> vels;
136 >  std::vector<int> indexMap;
137 >  std::vector<double> masses;
138 >
139 >  FORALLvertices{
140 >    localHullSites++;
141      
142 <    vertexT *vertex, **vertexp;
154 <    facetT *facet;
155 <    setT *vertices;
156 <    unsigned int nf = qh num_facets;
157 <    
158 <    //Matrix idx(nf, dim);
159 <    /*
160 <      int j, i = 0, id = 0;
161 <      
162 <      int id2 = 0;
163 <      coordT *point,**pointp;
164 <      realT dist;
165 <      FORALLfacets {
166 <      j = 0;
167 <      
168 <      if (!facet->simplicial){
169 <      // should never happen with Qt
170 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
171 <      painCave.isFatal = 0;
172 <      simError();
173 <      }
174 <                        
175 <      vertices = qh_facet3vertex(facet);
176 <      FOREACHvertex_(vertices){
177 <      id = qh_pointid(vertex->point);
178 <      surface_atoms.push_back(id);
179 <      //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
180 <      }
181 <      qh_settempfree(&vertices);
182 <      
183 <      FOREACHpoint_(facet->coplanarset){
184 <      vertex= qh_nearvertex (facet, point, &dist);
185 <      //id= qh_pointid (vertex->point);
186 <      id2= qh_pointid (point);
187 <      surface_atoms.push_back(id2);
188 <      //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
189 <      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
190 <      //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
191 <                                        
192 <      }
193 <      
194 <      }
195 <                
196 < */
197 <                
198 <                
199 <  }
142 >    int idx = qh_pointid(vertex->point);
143  
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 <  qh_getarea(qh facet_list);
153 <  volume_ = qh totvol;
154 <  area_ = qh totarea;
155 <  //    FILE *newGeomFile;
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 >    masses.push_back(sd->getMass());
158 >  }
159 >
160 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
161 >                            1, MPI::INT);
162 >
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 >  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 +  int count = coordsOnProc[myrank];
182    
183 <  /*
184 <    FORALLfacets {
185 <    for (int k=0; k < qh hull_dim; k++)
186 <    printf ("%6.2g ", facet->normal[k]);
187 <    printf ("\n");
188 <    }
189 <  */
190 <  
191 <  int curlong,totlong;
192 <  //    geomviewHull("junk.off");
183 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
184 >                             &coordsOnProc[0], &vectorDisplacements[0],
185 >                             MPI::DOUBLE);
186 >
187 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
188 >                             &coordsOnProc[0], &vectorDisplacements[0],
189 >                             MPI::DOUBLE);
190 >
191 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 >                             &globalMasses[0], &hullSitesOnProc[0],
193 >                             &displacements[0], MPI::DOUBLE);
194 >
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;
225 –  free(pt_array);
226 –  /*
227 –    int j = 0;
228 –    surface_atoms.sort();
229 –    surface_atoms.unique();
230 –    surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
231 –    for(std::list<int>::iterator list_iter = surface_atoms.begin();
232 –    list_iter != surface_atoms.end(); list_iter++)
233 –    {
234 –    int i = *list_iter;
235 –    //surfpt_array[dim_ * j] = pos[i][0];
236 –    //surfpt_array[dim_ * j + 1] = pos[i][1];
237 –    //surfpt_array[dim_ * j + 2] = pos[i][2];
238 –    std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
239 –    j++;
240 –    }
241 –  */    
201    
202 <  /*    
203 <        std::string deloptions_ = "qhull d Qt";
204 <        facetT *facet, *neighbor;
205 <        ridgeT *ridge, **ridgep;
206 <        
207 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
208 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
209 <        
251 <        qh visit_id++;
252 <        FORALLfacets {
253 <        if (!facet->upperdelaunay) {
254 <        facet->visitid= qh visit_id;
255 <        qh_makeridges(facet);
256 <        FOREACHridge_(facet->ridges) {
257 <        neighbor= otherfacet_(ridge, facet);
258 <        if (neighbor->visitid != qh visit_id) {
259 <        
260 <        FOREACHvertex_(ridge->vertices)
261 <        int id2 = qh_pointid (vertex->point);
262 <        std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
263 <        }
264 <        }
265 <        }
266 <        
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 + #endif
212  
213 <        
214 <        }
213 >  FORALLfacets {  
214 >    Triangle face;
215  
216 <        qh_freeqhull(!qh_ALL);
217 <        qh_memfreeshort(&curlong, &totlong);
218 <        if (curlong || totlong)
219 <        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
220 <        << totlong << curlong << std::endl;
221 <        free(surfpt_array);
222 <  */            
223 <  return true;
224 < }
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 +    Vector3d faceVel = V3Zero;
229 +    Vector3d p[3];
230 +    RealType faceMass = 0.0;
231  
232 +    int ver = 0;
233  
234 < RealType ConvexHull::getVolume()
235 < {
236 <  return volume_;
237 < }
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 < void ConvexHull::geomviewHull(const std::string& geomFileName)
244 < {
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 +      // localID will be between 0 and hullSitesOnProc[myrank] if we
250 +      // own this guy.
251 +
252 +      int localID = id - displacements[myrank];
253 +
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 +    face.addVertices(p[0], p[1], p[2]);
269 +    face.setFacetMass(faceMass);
270 +    face.setFacetVelocity(faceVel/3.0);
271 +    Triangles_.push_back(face);
272 +    qh_settempfree(&vertices);      
273 +
274 +  } //FORALLfacets
275 +  
276 +  qh_getarea(qh facet_list);
277 +  volume_ = qh totvol;
278 +  area_ = qh totarea;
279 +
280 + #ifdef IS_MPI
281 +  delete [] hullSitesOnProc;
282 +  delete [] coordsOnProc;
283 +  delete [] displacements;
284 +  delete [] vectorDisplacements;
285 + #endif
286 +  
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;    
292 + }
293 +
294 + void ConvexHull::printHull(const std::string& geomFileName) {
295    FILE *newGeomFile;
296    
297    //create new .md file based on old .md file
# Line 300 | Line 303 | void ConvexHull::geomviewHull(const std::string& geomF
303    fclose(newGeomFile);
304   }
305   #endif //QHULL
303 – #endif //CGAL
304 –
305 –
306 –

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