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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 1404 by chuckv, Fri Jan 15 20:46:49 2010 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 2008, 2009, 2010 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 >  pointT *intPoint;
94 >  
95 >  std::vector<double> ptArray(numpoints*dim_);
96  
97 <  std::vector<Point_3> points;
98 <  points.reserve(pos.size());
99 <  // Copy the positon vector into a points vector for cgal.
100 <  for (int i = 0; i < pos.size(); ++i)
101 <    {
102 <      Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
103 <      points.push_back(pt);
104 <    }
97 >  // Copy the positon vector into a points vector for qhull.
98 >  std::vector<StuntDouble*>::iterator SD;
99 >  int i = 0;
100 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
101 >    Vector3d pos = (*SD)->getPos();      
102 >    ptArray[dim_ * i] = pos.x();
103 >    ptArray[dim_ * i + 1] = pos.y();
104 >    ptArray[dim_ * i + 2] = pos.z();
105 >    i++;
106 >  }
107 >  
108 >  boolT ismalloc = False;
109 >  /* Clean up memory from previous convex hull calculations*/
110 >  
111 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
112 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
113  
114 <  // compute convex hull
115 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object);
116 <  // Make sure hull is a polyhedron
117 <  if ( CGAL::assign(ch_polyhedron, ch_object) )
118 <    {
79 <      return true;
80 <    }
81 <  else
82 <    {
83 <      return false;
84 <    }
85 < }
114 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
115 >    painCave.isFatal = 1;
116 >    simError();
117 >    
118 >  } //qh_new_qhull
119  
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));
120  
121 <  Triangulation T(L.begin(), L.end());
121 > #ifdef IS_MPI
122 >  //If we are doing the mpi version, set up some vectors for data communication
123 >  
124 >  int nproc = MPI::COMM_WORLD.Get_size();
125 >  int myrank = MPI::COMM_WORLD.Get_rank();
126 >  int localHullSites = 0;
127  
128 <  int n = T.number_of_vertices();
128 >  std::vector<int> hullSitesOnProc(nproc, 0);
129 >  std::vector<int> coordsOnProc(nproc, 0);
130 >  std::vector<int> displacements(nproc, 0);
131 >  std::vector<int> vectorDisplacements(nproc, 0);
132  
133 <  // insertion from a vector :
134 <  std::vector<Point> V(3);
135 <  V[0] = Point(0,0,1);
136 <  V[1] = Point(1,1,1);
103 <  V[2] = Point(2,2,2);
133 >  std::vector<double> coords;
134 >  std::vector<double> vels;
135 >  std::vector<int> indexMap;
136 >  std::vector<double> masses;
137  
138 <  n = n + T.insert(V.begin(), V.end());
138 >  FORALLvertices{
139 >    localHullSites++;
140 >    
141 >    int idx = qh_pointid(vertex->point);
142  
143 <  assert( n == 6 );       // 6 points have been inserted
108 <  assert( T.is_valid() ); // checking validity of T
143 >    indexMap.push_back(idx);
144  
145 <  double sum_v = 0;
146 <  for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it)
147 <    {
113 <      sum_v += T.tetrahedron(c_it).volume();
114 <    }
115 <  std::cout << "sum_v " << sum_v << std::endl;
116 < */
117 <        return 0.0;
118 < }
145 >    coords.push_back(ptArray[dim_  * idx]);
146 >    coords.push_back(ptArray[dim_  * idx + 1]);
147 >    coords.push_back(ptArray[dim_  * idx + 2]);
148  
149 < void ConvexHull::geomviewHull(const std::string& geomFileName)
121 < {
149 >    StuntDouble* sd = bodydoubles[idx];
150  
151 <  std::ofstream newGeomFile;
151 >    Vector3d vel = sd->getVel();
152 >    vels.push_back(vel.x());
153 >    vels.push_back(vel.y());
154 >    vels.push_back(vel.z());
155  
156 <  //create new .md file based on old .md file
157 <  newGeomFile.open(geomFileName.c_str());
156 >    masses.push_back(sd->getMass());
157 >  }
158  
159 <  // Write polyhedron in Object File Format (OFF).
160 <  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 <    }
159 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
160 >                            1, MPI::INT);
161  
162 <  newGeomFile.close();
162 >  int globalHullSites = 0;
163 >  for (int iproc = 0; iproc < nproc; iproc++){
164 >    globalHullSites += hullSitesOnProc[iproc];
165 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
166 >  }
167  
168 +  displacements[0] = 0;
169 +  vectorDisplacements[0] = 0;
170 +  
171 +  for (int iproc = 1; iproc < nproc; iproc++){
172 +    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
173 +    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
174 +  }
175  
176 +  std::vector<double> globalCoords(dim_ * globalHullSites);
177 +  std::vector<double> globalVels(dim_ * globalHullSites);
178 +  std::vector<double> globalMasses(globalHullSites);
179 +
180 +  int count = coordsOnProc[myrank];
181 +  
182 +  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
183 +                             &coordsOnProc[0], &vectorDisplacements[0],
184 +                             MPI::DOUBLE);
185 +
186 +  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
187 +                             &coordsOnProc[0], &vectorDisplacements[0],
188 +                             MPI::DOUBLE);
189 +
190 +  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
191 +                             &globalMasses[0], &hullSitesOnProc[0],
192 +                             &displacements[0], MPI::DOUBLE);
193 +
194 +  // Free previous hull
195 +  qh_freeqhull(!qh_ALL);
196 +  qh_memfreeshort(&curlong, &totlong);
197 +  if (curlong || totlong)
198 +    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
199 +              << totlong << curlong << std::endl;
200 +  
201 +  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
202 +                   const_cast<char *>(options_.c_str()), NULL, stderr)){
203 +    
204 +    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
205 +    painCave.isFatal = 1;
206 +    simError();
207 +    
208 +  } //qh_new_qhull
209 +
210 + #endif
211 +  intPoint = qh interior_point;
212 +  RealType calcvol = 0.0;
213 +  FORALLfacets {  
214 +    Triangle face;
215 +    //Qhull sets the unit normal in facet->normal
216 +    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
217 +    face.setUnitNormal(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 +    int ver = 0;
233 +
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 +      int localID = id - displacements[myrank];
253 +
254 +      if (localID >= 0 && localID < hullSitesOnProc[myrank])
255 +        face.addVertexSD(bodydoubles[indexMap[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 +    face.addVertices(p[0], p[1], p[2]);
269 +    face.setFacetMass(faceMass);
270 +    face.setFacetVelocity(faceVel/3.0);
271 +    /*
272 +    RealType comparea = face.computeArea();
273 +    realT calcarea = qh_facetarea (facet);
274 +    Vector3d V3dCompNorm = -face.computeUnitNormal();
275 +    RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
276 +    RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
277 +    std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
278 +    calcvol +=  -dist*comparea/qh hull_dim;
279 +    */
280 +    Triangles_.push_back(face);
281 +    qh_settempfree(&vertices);      
282 +
283 +  } //FORALLfacets
284 +  
285 +  qh_getarea(qh facet_list);
286 +  volume_ = qh totvol;
287 +  area_ = qh totarea;
288 +  //  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
289 +  qh_freeqhull(!qh_ALL);
290 +  qh_memfreeshort(&curlong, &totlong);
291 +  if (curlong || totlong)
292 +    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
293 +              << totlong << curlong << std::endl;    
294   }
295 +
296 + void ConvexHull::printHull(const std::string& geomFileName) {
297 +
298 + #ifdef IS_MPI
299 +  if (worldRank == 0)  {
300 + #endif
301 +  FILE *newGeomFile;
302 +  
303 +  //create new .md file based on old .md file
304 +  newGeomFile = fopen(geomFileName.c_str(), "w");
305 +  qh_findgood_all(qh facet_list);
306 +  for (int i = 0; i < qh_PRINTEND; i++)
307 +    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
308 +  
309 +  fclose(newGeomFile);
310 + #ifdef IS_MPI
311 +  }
312 + #endif
313 + }
314 + #endif //QHULL

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