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root/OpenMD/trunk/src/math/ConvexHull.cpp
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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1097 by chuckv, Thu Dec 14 19:32:32 2006 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 40 | Line 40
40   *
41   *  ConvexHull.cpp
42   *
43 < *  Purpose: To calculate convexhull, hull volume and radius
44 < *  using the CGAL library.
43 > *  Purpose: To calculate convexhull, hull volume libqhull.
44   *
45   *  Created by Charles F. Vardeman II on 11 Dec 2006.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: ConvexHull.cpp,v 1.1 2006-12-14 19:32:32 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.19 2009-10-21 15:48:12 gezelter Exp $
48   *
49   */
50  
51 < #include "math/ConvexHull.hpp"
51 > /* Standard includes independent of library */
52 >
53   #include <iostream>
54   #include <fstream>
55 + #include <list>
56 + #include <algorithm>
57 + #include <iterator>
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 + #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 + ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
84 + }
85  
86 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
87 < {
86 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
87 >
88 >  int numpoints = bodydoubles.size();
89  
90 <  std::vector<Point_3> points;
91 <  points.reserve(pos.size());
92 <  // Copy the positon vector into a points vector for cgal.
93 <  for (int i = 0; i < pos.size(); ++i)
94 <    {
95 <      Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
96 <      points.push_back(pt);
97 <    }
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 <  // compute convex hull
100 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object);
101 <  // Make sure hull is a polyhedron
102 <  if ( CGAL::assign(ch_polyhedron, ch_object) )
103 <    {
104 <      return true;
105 <    }
106 <  else
107 <    {
108 <      return false;
109 <    }
110 < }
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 < RealType ConvexHull::getVolume()
117 < {
118 <        /*
119 <  std::list<Point> L;
120 <  L.push_front(Point(0,0,0));
92 <  L.push_front(Point(1,0,0));
93 <  L.push_front(Point(0,1,0));
116 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
117 >    painCave.isFatal = 1;
118 >    simError();
119 >    
120 >  } //qh_new_qhull
121  
95 –  Triangulation T(L.begin(), L.end());
122  
123 <  int n = T.number_of_vertices();
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 <  // insertion from a vector :
135 <  std::vector<Point> V(3);
136 <  V[0] = Point(0,0,1);
137 <  V[1] = Point(1,1,1);
103 <  V[2] = Point(2,2,2);
134 >  std::vector<double> coords;
135 >  std::vector<double> vels;
136 >  std::vector<int> indexMap;
137 >  std::vector<double> masses;
138  
139 <  n = n + T.insert(V.begin(), V.end());
139 >  FORALLvertices{
140 >    localHullSites++;
141 >    
142 >    int idx = qh_pointid(vertex->point);
143  
144 <  assert( n == 6 );       // 6 points have been inserted
108 <  assert( T.is_valid() ); // checking validity of T
144 >    indexMap.push_back(idx);
145  
146 <  double sum_v = 0;
147 <  for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it)
148 <    {
113 <      sum_v += T.tetrahedron(c_it).volume();
114 <    }
115 <  std::cout << "sum_v " << sum_v << std::endl;
116 < */
117 <        return 0.0;
118 < }
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 < void ConvexHull::geomviewHull(const std::string& geomFileName)
121 < {
150 >    StuntDouble* sd = bodydoubles[idx];
151  
152 <  std::ofstream 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 <  //create new .md file based on old .md file
158 <  newGeomFile.open(geomFileName.c_str());
157 >    masses.push_back(sd->getMass());
158 >  }
159  
160 <  // Write polyhedron in Object File Format (OFF).
161 <  CGAL::set_ascii_mode( std::cout);
130 <  newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
131 <  << ch_polyhedron.size_of_facets() << " 0" << std::endl;
132 <  std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
133 <             std::ostream_iterator<Point_3>( newGeomFile, "\n"));
134 <  for (  Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
135 <    {
136 <      Halfedge_facet_circulator j = i->facet_begin();
137 <      // Facets in polyhedral surfaces are at least triangles.
138 <      CGAL_assertion( CGAL::circulator_size(j) >= 3);
139 <      newGeomFile << CGAL::circulator_size(j) << ' ';
140 <      do
141 <        {
142 <          newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
143 <        }
144 <      while ( ++j != i->facet_begin());
145 <      newGeomFile << std::endl;
146 <    }
160 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
161 >                            1, MPI::INT);
162  
163 <  newGeomFile.close();
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 +  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;
201 +  
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 +  FORALLfacets {  
214 +    Triangle face;
215 +
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 +    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 + #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
298 +  newGeomFile = fopen(geomFileName.c_str(), "w");
299 +  qh_findgood_all(qh facet_list);
300 +  for (int i = 0; i < qh_PRINTEND; i++)
301 +    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
302 +  
303 +  fclose(newGeomFile);
304 + }
305 + #endif //QHULL

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