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root/OpenMD/trunk/src/math/ConvexHull.cpp
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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1143 by chuckv, Wed May 30 19:51:07 2007 UTC vs.
Revision 1261 by chuckv, Wed Jun 18 17:03:30 2008 UTC

# 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 1.4 2007-05-30 19:51:07 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.7 2008-06-18 17:03:30 chuckv Exp $
48   *
49   */
50  
51 + /* Standard includes independent of library */
52   #include <iostream>
53   #include <fstream>
54 + #include <list>
55 + #include <algorithm>
56 + #include <iterator>
57   #include "math/ConvexHull.hpp"
58 <
58 > #include "utils/simError.h"
59   using namespace oopse;
60  
61 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
61 > /* CGAL version of convex hull first then QHULL */
62 > #ifdef HAVE_CGAL
63 >
64 > #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>
69 >
70 > #include <CGAL/Quotient.h>
71 > #include <CGAL/MP_Float.h>
72 > #include <CGAL/Lazy_exact_nt.h>
73 >
74 > typedef double RT;
75 > 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_3;
79 >
80 >
81 > ConvexHull::ConvexHull(){}
82 >
83 > bool ConvexHull::genHull(std::vector<Vector3d> pos)
84 > {
85 >  
86 >  std::vector<Point_3> points;  
87 >  
88 >  
89 >  // Copy the positon vector into a points vector for cgal.
90 >  for (int i = 0; i < pos.size(); ++i)
91 >    {
92 >      Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
93 >      points.push_back(pt);
94 >    }
95 >  
96 >  // define object to hold convex hull
97 >  CGAL::Object ch_object_;
98 >  Polyhedron_3 polyhedron;
99 >
100 >  // compute convex hull
101 >  std::cerr << "Creating hull" << std::endl;
102 >  CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
103 >  std::cerr << "Done Creating hull" << std::endl;
104 >  std::vector<Point_3>::const_iterator p_it;
105 >
106 >  for (p_it = points.begin(); p_it != points.end(); p_it++)
107 >    {
108 >      std::cerr << (*p_it).x() << std::endl;
109 >    }
110 >
111 >  /*
112 >  for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin();
113 >       ch_object_.vertices_end(); ++v){
114 >    std::cout<< v.point()<<std::endl;
115 >  }
116 >  */
117   }
118  
119 < bool ConvexHull::genHull(std::vector<Vector3d> pos) {
120 <  FILE *outfile = stdout;
121 <  FILE *errfile = stderr;
122 <  facetT *facet;
123 <  int exitcode;
124 <  boolT ismalloc = False;
125 <  int curlong,totlong;
119 >
120 >
121 > #else
122 > #ifdef HAVE_QHULL
123 > /* Old options Qt Qu Qg QG0 FA */
124 > ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
125 >                           //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
126 > {}
127 >
128 > bool ConvexHull::genHull(std::vector<Vector3d> pos)
129 > {
130    
131 +  
132    int numpoints = pos.size();
133 <
134 <  coordT* points;
135 <  points = (coordT*) malloc(sizeof(coordT) * (numpoints*dim_));
136 <
137 <  for (int i=0; i<numpoints; i++) {
138 <    points[dim_ * i] = pos[i][0];
139 <    points[dim_ * i + 1] = pos[i][1];
140 <    points[dim_ * i + 2] = pos[i][2];          
133 >  coordT* pt_array;
134 >  coordT* surfpt_array;
135 >  std::list<int> surface_atoms;
136 >  FILE *outdummy = NULL;
137 >  FILE *errdummy = NULL;
138 >  
139 >  pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
140 >  
141 >  
142 >  for (int i = 0; i < numpoints; i++) {
143 >    pt_array[dim_ * i] = pos[i][0];
144 >    pt_array[dim_ * i + 1] = pos[i][1];
145 >    pt_array[dim_ * i + 2] = pos[i][2];
146    }
147    
148    
80 –  qh_initflags (const_cast<char *>(options_.c_str()));
81 –  qh_init_B (points, numpoints, dim_, ismalloc);
82 –  qh_qhull();
83 –  qh_check_output();
149    
150    
151 +  /*
152 +    qh_initflags(const_cast<char *>(options_.c_str()));
153 +    qh_init_B(pospoints, numpoints, dim_, ismalloc);
154 +    qh_qhull();
155 +    qh_check_output();
156 +
157 +    qh_produce_output();
158 +  */
159 +  boolT ismalloc = False;
160    
161 +  if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
162 +                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
163 +    
164 +    vertexT *vertex, **vertexp;
165 +    facetT *facet;
166 +    setT *vertices;
167 +    unsigned int nf = qh num_facets;
168 +    
169 +    //Matrix idx(nf, dim);
170 +    /*
171 +      int j, i = 0, id = 0;
172 +      
173 +      int id2 = 0;
174 +      coordT *point,**pointp;
175 +      realT dist;
176 +      FORALLfacets {
177 +      j = 0;
178 +      
179 +      if (!facet->simplicial){
180 +      // should never happen with Qt
181 +      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
182 +      painCave.isFatal = 0;
183 +      simError();
184 +      }
185 +                        
186 +      vertices = qh_facet3vertex(facet);
187 +      FOREACHvertex_(vertices){
188 +      id = qh_pointid(vertex->point);
189 +      surface_atoms.push_back(id);
190 +      //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
191 +      }
192 +      qh_settempfree(&vertices);
193 +      
194 +      FOREACHpoint_(facet->coplanarset){
195 +      vertex= qh_nearvertex (facet, point, &dist);
196 +      //id= qh_pointid (vertex->point);
197 +      id2= qh_pointid (point);
198 +      surface_atoms.push_back(id2);
199 +      //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
200 +      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
201 +      //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
202 +                                        
203 +      }
204 +      
205 +      }
206 +                
207 + */
208 +                
209 +                
210 +  }
211 +
212 +
213 +
214 +
215    qh_getarea(qh facet_list);
216 <  volume_ = qh totvol;                                                  
217 <  area_ = qh totarea;                                          
216 >  volume_ = qh totvol;
217 >  area_ = qh totarea;
218 >  //    FILE *newGeomFile;
219    
220    
221 +  /*
222 +    FORALLfacets {
223 +    for (int k=0; k < qh hull_dim; k++)
224 +    printf ("%6.2g ", facet->normal[k]);
225 +    printf ("\n");
226 +    }
227 +  */
228    
229 +  int curlong,totlong;
230 +  //    geomviewHull("junk.off");
231    qh_freeqhull(!qh_ALL);
232 <  qh_memfreeshort (&curlong, &totlong);
232 >  qh_memfreeshort(&curlong, &totlong);
233    if (curlong || totlong)
234 <    fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
235 <             totlong, curlong);
234 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
235 >              << totlong << curlong << std::endl;
236 >  free(pt_array);
237 >  /*
238 >    int j = 0;
239 >    surface_atoms.sort();
240 >    surface_atoms.unique();
241 >    surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
242 >    for(std::list<int>::iterator list_iter = surface_atoms.begin();
243 >    list_iter != surface_atoms.end(); list_iter++)
244 >    {
245 >    int i = *list_iter;
246 >    //surfpt_array[dim_ * j] = pos[i][0];
247 >    //surfpt_array[dim_ * j + 1] = pos[i][1];
248 >    //surfpt_array[dim_ * j + 2] = pos[i][2];
249 >    std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
250 >    j++;
251 >    }
252 >  */    
253    
254 <  
254 >  /*    
255 >        std::string deloptions_ = "qhull d Qt";
256 >        facetT *facet, *neighbor;
257 >        ridgeT *ridge, **ridgep;
258 >        
259 >        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
260 >        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
261 >        
262 >        qh visit_id++;
263 >        FORALLfacets {
264 >        if (!facet->upperdelaunay) {
265 >        facet->visitid= qh visit_id;
266 >        qh_makeridges(facet);
267 >        FOREACHridge_(facet->ridges) {
268 >        neighbor= otherfacet_(ridge, facet);
269 >        if (neighbor->visitid != qh visit_id) {
270 >        
271 >        FOREACHvertex_(ridge->vertices)
272 >        int id2 = qh_pointid (vertex->point);
273 >        std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
274 >        }
275 >        }
276 >        }
277 >        
278 >
279 >
280 >        
281 >        }
282 >
283 >        qh_freeqhull(!qh_ALL);
284 >        qh_memfreeshort(&curlong, &totlong);
285 >        if (curlong || totlong)
286 >        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
287 >        << totlong << curlong << std::endl;
288 >        free(surfpt_array);
289 >  */            
290    return true;
291   }
292  
293  
294 < RealType ConvexHull::getVolume() {
294 >
295 > RealType ConvexHull::getVolume()
296 > {
297    return volume_;
298   }
299  
300 < void ConvexHull::geomviewHull(const std::string& geomFileName) {
300 > void ConvexHull::geomviewHull(const std::string& geomFileName)
301 > {
302 >
303 >  FILE *newGeomFile;
304    
110 –  std::ofstream newGeomFile;
111 –  
305    //create new .md file based on old .md file
306 <  newGeomFile.open(geomFileName.c_str());
306 >  newGeomFile = fopen(geomFileName.c_str(), "w");
307 >  qh_findgood_all(qh facet_list);
308 >  for (int i = 0; i < qh_PRINTEND; i++)
309 >    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
310    
311 <  
116 <  newGeomFile.close();
311 >  fclose(newGeomFile);
312   }
313 + #endif //QHULL
314 + #endif //CGAL
315 +
316 +
317 +

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