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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 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 1.5 2007-11-22 16:39:45 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 55 | Line 57
57   #include <iterator>
58   #include "math/ConvexHull.hpp"
59   #include "utils/simError.h"
58 – using namespace oopse;
60  
61 < /* Old options Qt Qu Qg QG0 FA */
62 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
63 < //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
63 < {}
61 > #ifdef IS_MPI
62 > #include <mpi.h>
63 > #endif
64  
65 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
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 <        int numpoints = pos.size();
84 <        coordT* pt_array;
71 <        coordT* surfpt_array;
72 <        std::list<int> surface_atoms;
73 <  FILE *outdummy = NULL;
74 <  FILE *errdummy = NULL;
83 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
84 > }
85  
86 <        pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
86 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
87 >
88 >  int numpoints = bodydoubles.size();
89  
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 <        for (int i = 0; i < numpoints; i++) {
101 <                pt_array[dim_ * i] = pos[i][0];
102 <                pt_array[dim_ * i + 1] = pos[i][1];
103 <                pt_array[dim_ * i + 2] = pos[i][2];
104 <        }
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  
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 <        /*
136 <                qh_initflags(const_cast<char *>(options_.c_str()));
137 <                qh_init_B(pospoints, numpoints, dim_, ismalloc);
138 <                qh_qhull();
92 <                qh_check_output();
135 >  std::vector<double> coords;
136 >  std::vector<double> vels;
137 >  std::vector<int> objectIDs;
138 >  std::vector<double> masses;
139  
140 <                qh_produce_output();
141 <        */
142 <        boolT ismalloc = False;
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 <        if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
99 <                          const_cast<char *>(options_.c_str()), NULL, stderr)) {
148 >    StuntDouble* sd = bodydoubles[idx];
149  
150 <                vertexT *vertex, **vertexp;
151 <                facetT *facet;
152 <                setT *vertices;
153 <                unsigned int nf = qh num_facets;
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 <                //Matrix idx(nf, dim);
156 < /*
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 <        }
155 >    masses.push_back(sd->getMass());
156 >  }
157  
158  
159  
160 +  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
161 +                            1, MPI::INT);
162  
163 <        qh_getarea(qh facet_list);
164 <        volume_ = qh totvol;
165 <        area_ = qh totarea;
166 < //      FILE *newGeomFile;
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 >  }
169  
170 +  displacements[0] = 0;
171 +  vectorDisplacements[0] = 0;
172 +  
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 <        /*
179 <                FORALLfacets {
180 <                    for (int k=0; k < qh hull_dim; k++)
181 <                      printf ("%6.2g ", facet->normal[k]);
182 <                    printf ("\n");
183 <                  }
184 <        */
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 <        int curlong,totlong;
188 < //      geomviewHull("junk.off");
189 <        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;
187 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
188 >                             &globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
189 >                             MPI::DOUBLE);
190  
191 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
192 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
191 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 >                             &globalMasses[0], &hullSitesOnProc[0], &displacements[0],
193 >                             MPI::DOUBLE);
194  
195 <                qh visit_id++;
196 <                FORALLfacets {
197 <                if (!facet->upperdelaunay) {
198 <                        facet->visitid= qh visit_id;
199 <                        qh_makeridges(facet);
200 <                        FOREACHridge_(facet->ridges) {
201 <                                neighbor= otherfacet_(ridge, facet);
202 <                                if (neighbor->visitid != qh visit_id) {
203 <                                                                                                                
204 <                                        FOREACHvertex_(ridge->vertices)
205 <                                                int id2 = qh_pointid (vertex->point);
206 <                                                std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
207 <                                }
208 <                        }
209 <                }
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 < }
228 >    Vector3d faceVel = V3Zero;
229 >    Vector3d p[3];
230 >    RealType faceMass = 0.0;
231 >    int ver = 0;
232  
233 <                qh_freeqhull(!qh_ALL);
234 <                qh_memfreeshort(&curlong, &totlong);
235 <                if (curlong || totlong)
236 <                        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
237 <                        << totlong << curlong << std::endl;
238 <                free(surfpt_array);
239 < */              
240 <        return true;
228 < }
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 + #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 < RealType ConvexHull::getVolume()
266 < {
267 <        return volume_;
268 < }
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 < void ConvexHull::geomviewHull(const std::string& geomFileName)
272 < {
271 >  } //FORALLfacets
272 >  
273 >  qh_getarea(qh facet_list);
274 >  volume_ = qh totvol;
275 >  area_ = qh totarea;
276  
277 <        FILE *newGeomFile;
278 <
279 <        //create new .md file based on old .md file
280 <        newGeomFile = fopen(geomFileName.c_str(), "w");
281 <        qh_findgood_all(qh facet_list);
282 <        for (int i = 0; i < qh_PRINTEND; i++)
283 <                qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
284 <
285 <        fclose(newGeomFile);
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  
291  
292  
293 <
293 > void ConvexHull::printHull(const std::string& geomFileName) {
294 >  FILE *newGeomFile;
295 >  
296 >  //create new .md file based on old .md file
297 >  newGeomFile = fopen(geomFileName.c_str(), "w");
298 >  qh_findgood_all(qh facet_list);
299 >  for (int i = 0; i < qh_PRINTEND; i++)
300 >    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
301 >  
302 >  fclose(newGeomFile);
303 > }
304 > #endif //QHULL

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