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root/OpenMD/trunk/src/math/ConvexHull.cpp
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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1141 by chuckv, Wed May 30 18:47:04 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 1.3 2007-05-30 18:47:03 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>
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 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
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 < bool ConvexHull::genHull(std::vector<Vector3d> pos) {
81 <  FILE *outfile = stdout;
82 <  FILE *errfile = stderr;
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 > 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 <  int exitcode;
95 <  boolT ismalloc = False;
66 <  int curlong,totlong;
94 >  setT *vertices;
95 >  int curlong, totlong;
96    
97 <  int numpoints = pos.size();
98 <  
99 <  coordT points[numpoints][dim_];
100 <  
101 <  for (int i=0; i<numpoints; i++) {
102 <    points[i][0] = pos[i][0];
103 <    points[i][1] = pos[i][1];
104 <    points[i][2] = pos[i][2];          
97 >  std::vector<double> ptArray(numpoints*3);
98 >  std::vector<bool> isSurfaceID(numpoints);
99 >
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 <  qh_initflags (const_cast<char *>(options_.c_str()));
128 <  qh_init_B (points[0], numpoints, dim_, ismalloc);
129 <  qh_qhull();
130 <  qh_check_output();
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 >    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 >
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 >    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 +  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 +  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
188 +                             &globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
189 +                             MPI::DOUBLE);
190 +
191 +  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 +                             &globalMasses[0], &hullSitesOnProc[0], &displacements[0],
193 +                             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 +    int ver = 0;
232 +
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 +    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 +  } //FORALLfacets
272 +  
273    qh_getarea(qh facet_list);
274 <  volume_ = qh totvol;                                                  
275 <  area_ = qh totarea;                                          
274 >  volume_ = qh totvol;
275 >  area_ = qh totarea;
276 >
277 > #ifdef IS_MPI
278 >  delete [] hullSitesOnProc;
279 >  delete [] coordsOnProc;
280 >  delete [] displacements;
281 >  delete [] vectorDisplacements;
282 > #endif
283    
91 –  
92 –  
284    qh_freeqhull(!qh_ALL);
285 <  qh_memfreeshort (&curlong, &totlong);
285 >  qh_memfreeshort(&curlong, &totlong);
286    if (curlong || totlong)
287 <    fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
288 <             totlong, curlong);
98 <  
99 <  
100 <  return true;
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  
104 – RealType ConvexHull::getVolume() {
105 –  return volume_;
106 – }
292  
293 < void ConvexHull::geomviewHull(const std::string& geomFileName) {
293 > void ConvexHull::printHull(const std::string& geomFileName) {
294 >  FILE *newGeomFile;
295    
110 –  std::ofstream newGeomFile;
111 –  
296    //create new .md file based on old .md file
297 <  newGeomFile.open(geomFileName.c_str());
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 <  
116 <  newGeomFile.close();
302 >  fclose(newGeomFile);
303   }
304 + #endif //QHULL

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