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root/OpenMD/trunk/src/math/ConvexHull.cpp
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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1261 by chuckv, Wed Jun 18 17:03:30 2008 UTC vs.
Revision 1376 by gezelter, Tue Oct 20 20:36:56 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 1.7 2008-06-18 17:03:30 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 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_3;
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_3> points;  
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 +  // 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    
111 <  // Copy the positon vector into a points vector for cgal.
112 <  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 <    }
111 >  boolT ismalloc = False;
112 >  /* Clean up memory from previous convex hull calculations*/
113    
114 <  // define object to hold convex hull
115 <  CGAL::Object ch_object_;
98 <  Polyhedron_3 polyhedron;
114 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
115 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
116  
117 <  // compute convex hull
118 <  std::cerr << "Creating hull" << std::endl;
119 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
120 <  std::cerr << "Done Creating hull" << std::endl;
121 <  std::vector<Point_3>::const_iterator p_it;
117 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
118 >    painCave.isFatal = 1;
119 >    simError();
120 >    
121 >  } //qh_new_qhull
122  
106 –  for (p_it = points.begin(); p_it != points.end(); p_it++)
107 –    {
108 –      std::cerr << (*p_it).x() << std::endl;
109 –    }
123  
124 <  /*
125 <  for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin();
126 <       ch_object_.vertices_end(); ++v){
127 <    std::cout<< v.point()<<std::endl;
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 >  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 >    StuntDouble* sd = bodydoubles[idx];
149 >
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 >    masses.push_back(sd->getMass());
156    }
116 –  */
117 – }
157  
158  
159  
160 < #else
161 < #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 < {}
160 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
161 >                            1, MPI::INT);
162  
163 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
164 < {
165 <  
166 <  
167 <  int numpoints = pos.size();
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];
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    }
147 –  
148 –  
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();
169  
170 <    qh_produce_output();
171 <  */
159 <  boolT ismalloc = False;
170 >  displacements[0] = 0;
171 >  vectorDisplacements[0] = 0;
172    
173 <  if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
174 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
175 <    
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 <                
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 +  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 +  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE,
184 +                             &globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0],
185 +                             MPI::DOUBLE);
186  
187 +  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
188 +                             &globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
189 +                             MPI::DOUBLE);
190  
191 +  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 +                             &globalMasses[0], &hullSitesOnProc[0], &displacements[0],
193 +                             MPI::DOUBLE);
194  
195 <  qh_getarea(qh facet_list);
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");
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;
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 –  */    
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 <        
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 <        
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 +    int ver = 0;
232  
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 +      Vector3d vel;
240 +      RealType mass;
241  
242 < RealType ConvexHull::getVolume()
243 < {
244 <  return volume_;
242 > #ifdef IS_MPI
243 >      vel = Vector3d(globalVels[dim_ * id],
244 >                     globalVels[dim_ * id + 1],
245 >                     globalVels[dim_ * id + 2]);
246 >      mass = globalMasses[id];
247 >
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 >    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);      
270 >
271 >  } //FORALLfacets
272 >  
273 >  qh_getarea(qh facet_list);
274 >  volume_ = qh totvol;
275 >  area_ = qh totarea;
276 >
277 > #ifdef IS_MPI
278 >  delete [] hullSitesOnProc;
279 >  delete [] coordsOnProc;
280 >  delete [] displacements;
281 >  delete [] vectorDisplacements;
282 > #endif
283 >  
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;    
289   }
290  
300 – void ConvexHull::geomviewHull(const std::string& geomFileName)
301 – {
291  
292 +
293 + void ConvexHull::printHull(const std::string& geomFileName) {
294    FILE *newGeomFile;
295    
296    //create new .md file based on old .md file
# Line 311 | Line 302 | void ConvexHull::geomviewHull(const std::string& geomF
302    fclose(newGeomFile);
303   }
304   #endif //QHULL
314 – #endif //CGAL
315 –
316 –
317 –

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