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root/OpenMD/trunk/src/math/ConvexHull.cpp
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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 1374 by chuckv, Tue Oct 20 20:05:28 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 1.16 2009-10-20 20:05:28 chuckv 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  
158 <                vertexT *vertex, **vertexp;
159 <                facetT *facet;
103 <                setT *vertices;
104 <                unsigned int nf = qh num_facets;
158 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159 >                            1, MPI::INT);
160  
161 <                //Matrix idx(nf, dim);
162 < /*
163 <                int j, i = 0, id = 0;
164 <                        
165 <                        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 <        }
161 >  int globalHullSites = 0;
162 >  for (int iproc = 0; i < 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; i < 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 +  int count = coordsOnProc[myrank];
179 +  
180 +  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE,
181 +                             &globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0],
182 +                             MPI::DOUBLE);
183  
184 +  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
185 +                             &globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
186 +                             MPI::DOUBLE);
187  
188 <        qh_getarea(qh facet_list);
189 <        volume_ = qh totvol;
190 <        area_ = qh totarea;
191 < //      FILE *newGeomFile;
188 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
189 >                             &globalMasses[0], &hullSitesOnProc[0], &displacements[0],
190 >                             MPI::DOUBLE);
191 >
192 >  // Free previous hull
193 >  qh_freeqhull(!qh_ALL);
194 >  qh_memfreeshort(&curlong, &totlong);
195 >  if (curlong || totlong)
196 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
197 >              << totlong << curlong << std::endl;
198 >  
199 >  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
200 >                   const_cast<char *>(options_.c_str()), NULL, stderr)){
201 >    
202 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
203 >    painCave.isFatal = 1;
204 >    simError();
205 >    
206 >  } //qh_new_qhull
207  
208 + #endif
209  
210 <        /*
211 <                FORALLfacets {
160 <                    for (int k=0; k < qh hull_dim; k++)
161 <                      printf ("%6.2g ", facet->normal[k]);
162 <                    printf ("\n");
163 <                  }
164 <        */
210 >  FORALLfacets {  
211 >    Triangle face;
212  
213 <        int curlong,totlong;
214 < //      geomviewHull("junk.off");
215 <        qh_freeqhull(!qh_ALL);
216 <        qh_memfreeshort(&curlong, &totlong);
217 <        if (curlong || totlong)
218 <                std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
219 <                << totlong << curlong << std::endl;
220 <        free(pt_array);
221 < /*
222 <        int j = 0;
223 <        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;
213 >    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
214 >    face.setNormal(V3dNormal);
215 >    
216 >    RealType faceArea = qh_facetarea(facet);
217 >    face.setArea(faceArea);
218 >    
219 >    vertices = qh_facet3vertex(facet);
220 >      
221 >    coordT *center = qh_getcenter(vertices);
222 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
223 >    face.setCentroid(V3dCentroid);
224  
225 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
226 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
225 >    Vector3d faceVel = V3Zero;
226 >    Vector3d p[3];
227 >    RealType faceMass = 0.0;
228 >    int ver = 0;
229  
230 <                qh visit_id++;
231 <                FORALLfacets {
232 <                if (!facet->upperdelaunay) {
233 <                        facet->visitid= qh visit_id;
234 <                        qh_makeridges(facet);
235 <                        FOREACHridge_(facet->ridges) {
236 <                                neighbor= otherfacet_(ridge, facet);
237 <                                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 <                }
230 >    FOREACHvertex_(vertices){
231 >      int id = qh_pointid(vertex->point);
232 >      p[ver][0] = vertex->point[0];
233 >      p[ver][1] = vertex->point[1];
234 >      p[ver][2] = vertex->point[2];
235 >      
236 >      Vector3d vel;
237 >      RealType mass;
238  
239 + #ifdef IS_MPI
240 +      vel = Vector3d(globalVels[dim_ * id],
241 +                     globalVels[dim_ * id + 1],
242 +                     globalVels[dim_ * id + 2]);
243 +      mass = globalMasses[id];
244  
245 +      // localID will be between 0 and hullSitesOnProc[myrank] if we own this guy.
246 +      int localID = id - displacements[myrank];
247 +      if (id >= 0 && id < hullSitesOnProc[myrank])
248 +        face.addVertexSD(bodydoubles[localID]);
249 +      else
250 +        face.addVertexSD(NULL);
251 + #else
252 +      vel = bodydoubles[id]->getVel();
253 +      mass = bodydoubles[id]->getMass();
254 +      face.addVertexSD(bodydoubles[id]);      
255 + #endif
256 +        
257 +      faceVel = faceVel + vel;
258 +      faceMass = faceMass + mass;
259 +      ver++;      
260 +    } //Foreachvertex
261  
262 +    face.addVertices(p[0], p[1], p[2]);
263 +    face.setFacetMass(faceMass);
264 +    face.setFacetVelocity(faceVel/3.0);
265 +    Triangles_.push_back(face);
266 +    qh_settempfree(&vertices);      
267  
268 < }
268 >  } //FORALLfacets
269 >  
270 >  qh_getarea(qh facet_list);
271 >  volume_ = qh totvol;
272 >  area_ = qh totarea;
273  
274 <                qh_freeqhull(!qh_ALL);
275 <                qh_memfreeshort(&curlong, &totlong);
276 <                if (curlong || totlong)
277 <                        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
278 <                        << totlong << curlong << std::endl;
279 <                free(surfpt_array);
280 < */              
281 <        return true;
274 > #ifdef IS_MPI
275 >  delete [] hullSitesOnProc;
276 >  delete [] coordsOnProc;
277 >  delete [] displacements;
278 >  delete [] vectorDisplacements;
279 > #endif
280 >  
281 >  qh_freeqhull(!qh_ALL);
282 >  qh_memfreeshort(&curlong, &totlong);
283 >  if (curlong || totlong)
284 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
285 >              << totlong << curlong << std::endl;    
286   }
287  
288  
289  
290 < RealType ConvexHull::getVolume()
291 < {
292 <        return volume_;
290 > void ConvexHull::printHull(const std::string& geomFileName) {
291 >  FILE *newGeomFile;
292 >  
293 >  //create new .md file based on old .md file
294 >  newGeomFile = fopen(geomFileName.c_str(), "w");
295 >  qh_findgood_all(qh facet_list);
296 >  for (int i = 0; i < qh_PRINTEND; i++)
297 >    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
298 >  
299 >  fclose(newGeomFile);
300   }
301 <
237 < void ConvexHull::geomviewHull(const std::string& geomFileName)
238 < {
239 <
240 <        FILE *newGeomFile;
241 <
242 <        //create new .md file based on old .md file
243 <        newGeomFile = fopen(geomFileName.c_str(), "w");
244 <        qh_findgood_all(qh facet_list);
245 <        for (int i = 0; i < qh_PRINTEND; i++)
246 <                qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
247 <
248 <        fclose(newGeomFile);
249 < }
250 <
251 <
252 <
253 <
301 > #endif //QHULL

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