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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1097 by chuckv, Thu Dec 14 19:32:32 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 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
5   * redistribute this software in source and binary code form, provided
6   * that the following conditions are met:
7   *
8 < * 1. Acknowledgement of the program authors must be made in any
9 < *    publication of scientific results based in part on use of the
10 < *    program.  An acceptable form of acknowledgement is citation of
11 < *    the article in which the program was described (Matthew
12 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14 < *    Parallel Simulation Engine for Molecular Dynamics,"
15 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
16 < *
17 < * 2. Redistributions of source code must retain the above copyright
8 > * 1. Redistributions of source code must retain the above copyright
9   *    notice, this list of conditions and the following disclaimer.
10   *
11 < * 3. Redistributions in binary form must reproduce the above copyright
11 > * 2. Redistributions in binary form must reproduce the above copyright
12   *    notice, this list of conditions and the following disclaimer in the
13   *    documentation and/or other materials provided with the
14   *    distribution.
# Line 37 | Line 28
28   * University of Notre Dame has been advised of the possibility of
29   * such damages.
30   *
31 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
32 + * research, please cite the appropriate papers when you publish your
33 + * work.  Good starting points are:
34 + *                                                                      
35 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
36 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
37 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 + * [4]  Vardeman & Gezelter, in progress (2009).                        
39   *
40 + *
41   *  ConvexHull.cpp
42   *
43 < *  Purpose: To calculate convexhull, hull volume and radius
44 < *  using the CGAL library.
43 > *  Purpose: To calculate convexhull, hull volume libqhull.
44   *
45   *  Created by Charles F. Vardeman II on 11 Dec 2006.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: ConvexHull.cpp,v 1.1 2006-12-14 19:32:32 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 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 + #ifdef IS_MPI
62 + #include <mpi.h>
63 + #endif
64  
65 < using namespace oopse;
65 > using namespace OpenMD;
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 + ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81 + }
82  
83 + void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84 +
85 +  int numpoints = bodydoubles.size();
86  
87 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
88 < {
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 <  std::vector<Point_3> points;
97 <  points.reserve(pos.size());
98 <  // Copy the positon vector into a points vector for cgal.
99 <  for (int i = 0; i < pos.size(); ++i)
100 <    {
101 <      Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
102 <      points.push_back(pt);
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 <  // compute convex hull
114 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object);
115 <  // Make sure hull is a polyhedron
116 <  if ( CGAL::assign(ch_polyhedron, ch_object) )
117 <    {
79 <      return true;
80 <    }
81 <  else
82 <    {
83 <      return false;
84 <    }
85 < }
113 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
114 >    painCave.isFatal = 1;
115 >    simError();
116 >    
117 >  } //qh_new_qhull
118  
87 – RealType ConvexHull::getVolume()
88 – {
89 –        /*
90 –  std::list<Point> L;
91 –  L.push_front(Point(0,0,0));
92 –  L.push_front(Point(1,0,0));
93 –  L.push_front(Point(0,1,0));
119  
120 <  Triangulation T(L.begin(), L.end());
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 <  int n = T.number_of_vertices();
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 <  // insertion from a vector :
133 <  std::vector<Point> V(3);
134 <  V[0] = Point(0,0,1);
135 <  V[1] = Point(1,1,1);
103 <  V[2] = Point(2,2,2);
132 >  std::vector<double> coords;
133 >  std::vector<double> vels;
134 >  std::vector<int> indexMap;
135 >  std::vector<double> masses;
136  
137 <  n = n + T.insert(V.begin(), V.end());
137 >  FORALLvertices{
138 >    localHullSites++;
139 >    
140 >    int idx = qh_pointid(vertex->point);
141  
142 <  assert( n == 6 );       // 6 points have been inserted
108 <  assert( T.is_valid() ); // checking validity of T
142 >    indexMap.push_back(idx);
143  
144 <  double sum_v = 0;
145 <  for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it)
146 <    {
113 <      sum_v += T.tetrahedron(c_it).volume();
114 <    }
115 <  std::cout << "sum_v " << sum_v << std::endl;
116 < */
117 <        return 0.0;
118 < }
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 < void ConvexHull::geomviewHull(const std::string& geomFileName)
121 < {
148 >    StuntDouble* sd = bodydoubles[idx];
149  
150 <  std::ofstream newGeomFile;
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 <  //create new .md file based on old .md file
156 <  newGeomFile.open(geomFileName.c_str());
155 >    masses.push_back(sd->getMass());
156 >  }
157  
158 <  // Write polyhedron in Object File Format (OFF).
159 <  CGAL::set_ascii_mode( std::cout);
130 <  newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
131 <  << ch_polyhedron.size_of_facets() << " 0" << std::endl;
132 <  std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
133 <             std::ostream_iterator<Point_3>( newGeomFile, "\n"));
134 <  for (  Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
135 <    {
136 <      Halfedge_facet_circulator j = i->facet_begin();
137 <      // Facets in polyhedral surfaces are at least triangles.
138 <      CGAL_assertion( CGAL::circulator_size(j) >= 3);
139 <      newGeomFile << CGAL::circulator_size(j) << ' ';
140 <      do
141 <        {
142 <          newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
143 <        }
144 <      while ( ++j != i->facet_begin());
145 <      newGeomFile << std::endl;
146 <    }
158 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159 >                            1, MPI::INT);
160  
161 <  newGeomFile.close();
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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