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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1188 by chuckv, Thu Nov 22 16:39:45 2007 UTC vs.
Revision 1377 by gezelter, Wed Oct 21 02:49:43 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 1.5 2007-11-22 16:39:45 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.18 2009-10-21 02:49:43 gezelter Exp $
48   *
49   */
50  
51 + /* Standard includes independent of library */
52 +
53   #include <iostream>
54   #include <fstream>
55   #include <list>
# Line 55 | Line 57
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 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
62 < //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
63 < {}
81 > /* More old opts Qc Qi Pp*/
82  
83 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
84 < {
83 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
84 > }
85  
86 + void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
87 +
88 +  int numpoints = bodydoubles.size();
89  
90 <        int numpoints = pos.size();
91 <        coordT* pt_array;
92 <        coordT* surfpt_array;
93 <        std::list<int> surface_atoms;
94 <  FILE *outdummy = NULL;
95 <  FILE *errdummy = NULL;
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*3);
98 >  std::vector<bool> isSurfaceID(numpoints);
99  
100 <        pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
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 >  boolT ismalloc = False;
112 >  /* Clean up memory from previous convex hull calculations*/
113 >  
114 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
115 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
116  
117 +    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
118 +    painCave.isFatal = 1;
119 +    simError();
120 +    
121 +  } //qh_new_qhull
122  
79 –        for (int i = 0; i < numpoints; i++) {
80 –                pt_array[dim_ * i] = pos[i][0];
81 –                pt_array[dim_ * i + 1] = pos[i][1];
82 –                pt_array[dim_ * i + 2] = pos[i][2];
83 –        }
123  
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 <        /*
89 <                qh_initflags(const_cast<char *>(options_.c_str()));
90 <                qh_init_B(pospoints, numpoints, dim_, ismalloc);
91 <                qh_qhull();
92 <                qh_check_output();
148 >    StuntDouble* sd = bodydoubles[idx];
149  
150 <                qh_produce_output();
151 <        */
152 <        boolT ismalloc = False;
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 <        if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
156 <                          const_cast<char *>(options_.c_str()), NULL, stderr)) {
155 >    masses.push_back(sd->getMass());
156 >  }
157  
101 –                vertexT *vertex, **vertexp;
102 –                facetT *facet;
103 –                setT *vertices;
104 –                unsigned int nf = qh num_facets;
158  
106 –                //Matrix idx(nf, dim);
107 – /*
108 –                int j, i = 0, id = 0;
109 –                        
110 –                        int id2 = 0;
111 –                        coordT *point,**pointp;
112 –                        realT dist;
113 –                        FORALLfacets {
114 –                            j = 0;
115 –                        
116 –                            if (!facet->simplicial){
117 –                            // should never happen with Qt
118 –                            sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
119 –                                    painCave.isFatal = 0;
120 –                                    simError();
121 –                            }
122 –                        
123 –                            vertices = qh_facet3vertex(facet);
124 –                            FOREACHvertex_(vertices){
125 –                                                id = qh_pointid(vertex->point);
126 –                                                surface_atoms.push_back(id);
127 –                                                //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
128 –                                        }
129 –                                        qh_settempfree(&vertices);
130 –                                        
131 –                            FOREACHpoint_(facet->coplanarset){
132 –                            vertex= qh_nearvertex (facet, point, &dist);
133 –                      //id= qh_pointid (vertex->point);
134 –                      id2= qh_pointid (point);
135 –                                        surface_atoms.push_back(id2);
136 –                                        //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
137 –                      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
138 –                                        //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
139 –                                        
140 –                                }
141 –                                
142 –                        }
143 –                
144 – */
145 –                
146 –                
147 –        }
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 <        qh_getarea(qh facet_list);
178 <        volume_ = qh totvol;
179 <        area_ = qh totarea;
155 < //      FILE *newGeomFile;
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 <        /*
188 <                FORALLfacets {
189 <                    for (int k=0; k < qh hull_dim; k++)
161 <                      printf ("%6.2g ", facet->normal[k]);
162 <                    printf ("\n");
163 <                  }
164 <        */
187 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
188 >                             &coordsOnProc[0], &vectorDisplacements[0],
189 >                             MPI::DOUBLE);
190  
191 <        int curlong,totlong;
192 < //      geomviewHull("junk.off");
193 <        qh_freeqhull(!qh_ALL);
169 <        qh_memfreeshort(&curlong, &totlong);
170 <        if (curlong || totlong)
171 <                std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
172 <                << totlong << curlong << std::endl;
173 <        free(pt_array);
174 < /*
175 <        int j = 0;
176 <        surface_atoms.sort();
177 <        surface_atoms.unique();
178 <        surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
179 <        for(std::list<int>::iterator list_iter = surface_atoms.begin();
180 <            list_iter != surface_atoms.end(); list_iter++)
181 <        {
182 <                int i = *list_iter;
183 <                        //surfpt_array[dim_ * j] = pos[i][0];
184 <                        //surfpt_array[dim_ * j + 1] = pos[i][1];
185 <                        //surfpt_array[dim_ * j + 2] = pos[i][2];
186 <                        std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
187 <                        j++;
188 <        }
189 < */      
190 <        
191 < /*      
192 <        std::string deloptions_ = "qhull d Qt";
193 <        facetT *facet, *neighbor;
194 <        ridgeT *ridge, **ridgep;
191 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 >                             &globalMasses[0], &hullSitesOnProc[0],
193 >                             &displacements[0], MPI::DOUBLE);
194  
195 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
196 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
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 <                qh visit_id++;
200 <                FORALLfacets {
201 <                if (!facet->upperdelaunay) {
202 <                        facet->visitid= qh visit_id;
203 <                        qh_makeridges(facet);
204 <                        FOREACHridge_(facet->ridges) {
205 <                                neighbor= otherfacet_(ridge, facet);
206 <                                if (neighbor->visitid != qh visit_id) {
207 <                                                                                                                
208 <                                        FOREACHvertex_(ridge->vertices)
209 <                                                int id2 = qh_pointid (vertex->point);
210 <                                                std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
211 <                                }
212 <                        }
213 <                }
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 < }
232 >    int ver = 0;
233  
234 <                qh_freeqhull(!qh_ALL);
235 <                qh_memfreeshort(&curlong, &totlong);
236 <                if (curlong || totlong)
237 <                        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
238 <                        << totlong << curlong << std::endl;
239 <                free(surfpt_array);
240 < */              
241 <        return true;
228 < }
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 < RealType ConvexHull::getVolume()
233 < {
234 <        return volume_;
235 < }
252 >      int localID = id - displacements[myrank];
253  
254 < void ConvexHull::geomviewHull(const std::string& geomFileName)
255 < {
254 >      if (localID >= 0 && localID < hullSitesOnProc[myrank])
255 >        face.addVertexSD(bodydoubles[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 <        FILE *newGeomFile;
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 <        //create new .md file based on old .md file
275 <        newGeomFile = fopen(geomFileName.c_str(), "w");
276 <        qh_findgood_all(qh facet_list);
277 <        for (int i = 0; i < qh_PRINTEND; i++)
278 <                qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
274 >  } //FORALLfacets
275 >  
276 >  qh_getarea(qh facet_list);
277 >  volume_ = qh totvol;
278 >  area_ = qh totarea;
279  
280 <        fclose(newGeomFile);
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 <
295 <
296 <
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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