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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1137 by chuckv, Tue May 29 22:50:14 2007 UTC vs.
Revision 1384 by gezelter, Thu Oct 22 19:43:10 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 1.2 2007-05-29 22:50:14 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.20 2009-10-22 19:43:10 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 < char options[] = "qhull Qt FA";
62 < int dim_ = 3;
61 > #ifdef IS_MPI
62 > #include <mpi.h>
63 > #endif
64  
65   using namespace oopse;
66  
67 < ConvexHull::ConvexHull(){}
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 + ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81 + }
82  
83 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
84 < {
85 <        FILE *outfile = stdout;
66 <        FILE *errfile = stderr;
67 <        facetT *facet;
68 <        int exitcode;
69 <        boolT ismalloc = False;
70 <        int curlong,totlong;
71 <        
72 <        int numpoints = pos.size();
73 <        
74 <        coordT points[numpoints][dim_];
75 <        
76 <        for (int i=0; i<numpoints; i++)
77 <        {
78 <     points[i][0] = pos[i][0];
79 <     points[i][1] = pos[i][1];
80 <     points[i][2] = pos[i][2];          
81 <        }
82 <  
83 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84 >
85 >  int numpoints = bodydoubles.size();
86  
87 +  Triangles_.clear();
88 +  
89 +  vertexT *vertex, **vertexp;
90 +  facetT *facet;
91 +  setT *vertices;
92 +  int curlong, totlong;
93 +  
94 +  std::vector<double> ptArray(numpoints*dim_);
95  
96 <        qh_initflags (options);
97 <    qh_init_B (points[0], numpoints, dim_, ismalloc);
98 <    qh_qhull();
99 <    qh_check_output();
100 <                                                        
101 <                                                        
102 <                                                        
103 <    qh_getarea(qh facet_list);
104 <    volume_ = qh totvol;                                                        
105 <        area_ = qh totarea;                                            
106 <                                                        
107 <                                                        
108 <                                                        
109 <    qh_freeqhull(!qh_ALL);
110 <        qh_memfreeshort (&curlong, &totlong);
111 <        if (curlong || totlong)
101 <                fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
102 <                                 totlong, curlong);
103 <        
96 >  // Copy the positon vector into a points vector for qhull.
97 >  std::vector<StuntDouble*>::iterator SD;
98 >  int i = 0;
99 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
100 >    Vector3d pos = (*SD)->getPos();      
101 >    ptArray[dim_ * i] = pos.x();
102 >    ptArray[dim_ * i + 1] = pos.y();
103 >    ptArray[dim_ * i + 2] = pos.z();
104 >    i++;
105 >  }
106 >  
107 >  boolT ismalloc = False;
108 >  /* Clean up memory from previous convex hull calculations*/
109 >  
110 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
111 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
112  
113 <        return true;
114 < }
113 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
114 >    painCave.isFatal = 1;
115 >    simError();
116 >    
117 >  } //qh_new_qhull
118  
119  
120 < RealType ConvexHull::getVolume()
121 < {
122 <        return volume_;
123 < }
120 > #ifdef IS_MPI
121 >  //If we are doing the mpi version, set up some vectors for data communication
122 >  
123 >  int nproc = MPI::COMM_WORLD.Get_size();
124 >  int myrank = MPI::COMM_WORLD.Get_rank();
125 >  int localHullSites = 0;
126  
127 < void ConvexHull::geomviewHull(const std::string& geomFileName)
128 < {
127 >  std::vector<int> hullSitesOnProc(nproc, 0);
128 >  std::vector<int> coordsOnProc(nproc, 0);
129 >  std::vector<int> displacements(nproc, 0);
130 >  std::vector<int> vectorDisplacements(nproc, 0);
131  
132 <  std::ofstream newGeomFile;
132 >  std::vector<double> coords;
133 >  std::vector<double> vels;
134 >  std::vector<int> indexMap;
135 >  std::vector<double> masses;
136  
137 <  //create new .md file based on old .md file
138 <  newGeomFile.open(geomFileName.c_str());
137 >  FORALLvertices{
138 >    localHullSites++;
139 >    
140 >    int idx = qh_pointid(vertex->point);
141  
142 +    indexMap.push_back(idx);
143  
144 <  newGeomFile.close();
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 +  }
157 +
158 +  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159 +                            1, MPI::INT);
160 +
161 +  int globalHullSites = 0;
162 +  for (int iproc = 0; iproc < nproc; iproc++){
163 +    globalHullSites += hullSitesOnProc[iproc];
164 +    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
165 +  }
166 +
167 +  displacements[0] = 0;
168 +  vectorDisplacements[0] = 0;
169 +  
170 +  for (int iproc = 1; iproc < nproc; iproc++){
171 +    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
172 +    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
173 +  }
174 +
175 +  std::vector<double> globalCoords(dim_ * globalHullSites);
176 +  std::vector<double> globalVels(dim_ * globalHullSites);
177 +  std::vector<double> globalMasses(globalHullSites);
178 +
179 +  int count = coordsOnProc[myrank];
180 +  
181 +  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
182 +                             &coordsOnProc[0], &vectorDisplacements[0],
183 +                             MPI::DOUBLE);
184 +
185 +  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
186 +                             &coordsOnProc[0], &vectorDisplacements[0],
187 +                             MPI::DOUBLE);
188 +
189 +  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
190 +                             &globalMasses[0], &hullSitesOnProc[0],
191 +                             &displacements[0], MPI::DOUBLE);
192 +
193 +  // Free previous hull
194 +  qh_freeqhull(!qh_ALL);
195 +  qh_memfreeshort(&curlong, &totlong);
196 +  if (curlong || totlong)
197 +    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
198 +              << totlong << curlong << std::endl;
199 +  
200 +  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
201 +                   const_cast<char *>(options_.c_str()), NULL, stderr)){
202 +    
203 +    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
204 +    painCave.isFatal = 1;
205 +    simError();
206 +    
207 +  } //qh_new_qhull
208 +
209 + #endif
210 +
211 +  FORALLfacets {  
212 +    Triangle face;
213 +
214 +    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
215 +    face.setNormal(V3dNormal);
216 +    
217 +    RealType faceArea = qh_facetarea(facet);
218 +    face.setArea(faceArea);
219 +    
220 +    vertices = qh_facet3vertex(facet);
221 +      
222 +    coordT *center = qh_getcenter(vertices);
223 +    Vector3d V3dCentroid(center[0], center[1], center[2]);
224 +    face.setCentroid(V3dCentroid);
225 +
226 +    Vector3d faceVel = V3Zero;
227 +    Vector3d p[3];
228 +    RealType faceMass = 0.0;
229 +
230 +    int ver = 0;
231 +
232 +    FOREACHvertex_(vertices){
233 +      int id = qh_pointid(vertex->point);
234 +      p[ver][0] = vertex->point[0];
235 +      p[ver][1] = vertex->point[1];
236 +      p[ver][2] = vertex->point[2];
237 +      
238 +      Vector3d vel;
239 +      RealType mass;
240 +
241 + #ifdef IS_MPI
242 +      vel = Vector3d(globalVels[dim_ * id],
243 +                     globalVels[dim_ * id + 1],
244 +                     globalVels[dim_ * id + 2]);
245 +      mass = globalMasses[id];
246 +
247 +      // localID will be between 0 and hullSitesOnProc[myrank] if we
248 +      // own this guy.
249 +
250 +      int localID = id - displacements[myrank];
251 +
252 +      if (localID >= 0 && localID < hullSitesOnProc[myrank])
253 +        face.addVertexSD(bodydoubles[indexMap[localID]]);
254 +      
255 + #else
256 +      vel = bodydoubles[id]->getVel();
257 +      mass = bodydoubles[id]->getMass();
258 +      face.addVertexSD(bodydoubles[id]);      
259 + #endif
260 +        
261 +      faceVel = faceVel + vel;
262 +      faceMass = faceMass + mass;
263 +      ver++;      
264 +    } //Foreachvertex
265 +
266 +    face.addVertices(p[0], p[1], p[2]);
267 +    face.setFacetMass(faceMass);
268 +    face.setFacetVelocity(faceVel/3.0);
269 +    Triangles_.push_back(face);
270 +    qh_settempfree(&vertices);      
271 +
272 +  } //FORALLfacets
273 +  
274 +  qh_getarea(qh facet_list);
275 +  volume_ = qh totvol;
276 +  area_ = qh totarea;
277 +
278 +  qh_freeqhull(!qh_ALL);
279 +  qh_memfreeshort(&curlong, &totlong);
280 +  if (curlong || totlong)
281 +    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
282 +              << totlong << curlong << std::endl;    
283   }
284 +
285 + void ConvexHull::printHull(const std::string& geomFileName) {
286 +
287 + #ifdef IS_MPI
288 +  if (worldRank == 0)  {
289 + #endif
290 +  FILE *newGeomFile;
291 +  
292 +  //create new .md file based on old .md file
293 +  newGeomFile = fopen(geomFileName.c_str(), "w");
294 +  qh_findgood_all(qh facet_list);
295 +  for (int i = 0; i < qh_PRINTEND; i++)
296 +    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
297 +  
298 +  fclose(newGeomFile);
299 + #ifdef IS_MPI
300 +  }
301 + #endif
302 + }
303 + #endif //QHULL

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