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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 1411 by gezelter, Wed Feb 24 16:09:21 2010 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 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 >  /* Clean up memory from previous convex hull calculations */
109 >  boolT ismalloc = False;
110 >  
111 >  /* compute the hull for our local points (or all the points for single
112 >     processor versions) */
113 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
114 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
115 >    
116 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
117 >    painCave.isFatal = 1;
118 >    simError();
119 >    
120 >  } //qh_new_qhull
121  
74 –  // compute convex hull
75 –  CGAL::convex_hull_3(points.begin(), points.end(), ch_object);
76 –  // Make sure hull is a polyhedron
77 –  if ( CGAL::assign(ch_polyhedron, ch_object) )
78 –    {
79 –      return true;
80 –    }
81 –  else
82 –    {
83 –      return false;
84 –    }
85 – }
122  
123 < RealType ConvexHull::getVolume()
124 < {
125 <        /*
126 <  std::list<Point> L;
127 <  L.push_front(Point(0,0,0));
128 <  L.push_front(Point(1,0,0));
93 <  L.push_front(Point(0,1,0));
123 > #ifdef IS_MPI
124 >  //If we are doing the mpi version, set up some vectors for data communication
125 >  
126 >  int nproc = MPI::COMM_WORLD.Get_size();
127 >  int myrank = MPI::COMM_WORLD.Get_rank();
128 >  int localHullSites = 0;
129  
130 <  Triangulation T(L.begin(), L.end());
130 >  std::vector<int> hullSitesOnProc(nproc, 0);
131 >  std::vector<int> coordsOnProc(nproc, 0);
132 >  std::vector<int> displacements(nproc, 0);
133 >  std::vector<int> vectorDisplacements(nproc, 0);
134  
135 <  int n = T.number_of_vertices();
135 >  std::vector<double> coords;
136 >  std::vector<double> vels;
137 >  std::vector<int> indexMap;
138 >  std::vector<double> masses;
139  
140 <  // insertion from a vector :
141 <  std::vector<Point> V(3);
142 <  V[0] = Point(0,0,1);
143 <  V[1] = Point(1,1,1);
103 <  V[2] = Point(2,2,2);
140 >  FORALLvertices{
141 >    localHullSites++;
142 >    
143 >    int idx = qh_pointid(vertex->point);
144  
145 <  n = n + T.insert(V.begin(), V.end());
145 >    indexMap.push_back(idx);
146  
147 <  assert( n == 6 );       // 6 points have been inserted
148 <  assert( T.is_valid() ); // checking validity of T
147 >    coords.push_back(ptArray[dim_  * idx]);
148 >    coords.push_back(ptArray[dim_  * idx + 1]);
149 >    coords.push_back(ptArray[dim_  * idx + 2]);
150  
151 <  double sum_v = 0;
111 <  for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it)
112 <    {
113 <      sum_v += T.tetrahedron(c_it).volume();
114 <    }
115 <  std::cout << "sum_v " << sum_v << std::endl;
116 < */
117 <        return 0.0;
118 < }
151 >    StuntDouble* sd = bodydoubles[idx];
152  
153 < void ConvexHull::geomviewHull(const std::string& geomFileName)
154 < {
153 >    Vector3d vel = sd->getVel();
154 >    vels.push_back(vel.x());
155 >    vels.push_back(vel.y());
156 >    vels.push_back(vel.z());
157  
158 <  std::ofstream newGeomFile;
158 >    masses.push_back(sd->getMass());
159 >  }
160  
161 <  //create new .md file based on old .md file
162 <  newGeomFile.open(geomFileName.c_str());
161 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
162 >                            1, MPI::INT);
163  
164 <  // Write polyhedron in Object File Format (OFF).
165 <  CGAL::set_ascii_mode( std::cout);
166 <  newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
167 <  << ch_polyhedron.size_of_facets() << " 0" << std::endl;
168 <  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 <    }
164 >  int globalHullSites = 0;
165 >  for (int iproc = 0; iproc < nproc; iproc++){
166 >    globalHullSites += hullSitesOnProc[iproc];
167 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
168 >  }
169  
170 <  newGeomFile.close();
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  
182 +  int count = coordsOnProc[myrank];
183 +  
184 +  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
185 +                             &coordsOnProc[0], &vectorDisplacements[0],
186 +                             MPI::DOUBLE);
187 +
188 +  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
189 +                             &coordsOnProc[0], &vectorDisplacements[0],
190 +                             MPI::DOUBLE);
191 +
192 +  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
193 +                             &globalMasses[0], &hullSitesOnProc[0],
194 +                             &displacements[0], MPI::DOUBLE);
195 +
196 +  // Free previous hull
197 +  qh_freeqhull(!qh_ALL);
198 +  qh_memfreeshort(&curlong, &totlong);
199 +  if (curlong || totlong) {
200 +    sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
201 +            "\tdid not free %d bytes of long memory (%d pieces)",
202 +            totlong, curlong);
203 +    painCave.isFatal = 1;
204 +    simError();
205 +  }
206 +  
207 +  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
208 +                   const_cast<char *>(options_.c_str()), NULL, stderr)){
209 +    
210 +    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
211 +    painCave.isFatal = 1;
212 +    simError();
213 +    
214 +  } //qh_new_qhull
215 +
216 + #endif
217 +  intPoint = qh interior_point;
218 +  RealType calcvol = 0.0;
219 +  FORALLfacets {  
220 +    Triangle face;
221 +    //Qhull sets the unit normal in facet->normal
222 +    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
223 +    face.setUnitNormal(V3dNormal);
224 +    
225 +    RealType faceArea = qh_facetarea(facet);
226 +    face.setArea(faceArea);
227 +    
228 +    vertices = qh_facet3vertex(facet);
229 +      
230 +    coordT *center = qh_getcenter(vertices);
231 +    Vector3d V3dCentroid(center[0], center[1], center[2]);
232 +    face.setCentroid(V3dCentroid);
233 +
234 +    Vector3d faceVel = V3Zero;
235 +    Vector3d p[3];
236 +    RealType faceMass = 0.0;
237 +
238 +    int ver = 0;
239 +
240 +    FOREACHvertex_(vertices){
241 +      int id = qh_pointid(vertex->point);
242 +      p[ver][0] = vertex->point[0];
243 +      p[ver][1] = vertex->point[1];
244 +      p[ver][2] = vertex->point[2];
245 +      Vector3d vel;
246 +      RealType mass;
247 +
248 + #ifdef IS_MPI
249 +      vel = Vector3d(globalVels[dim_ * id],
250 +                     globalVels[dim_ * id + 1],
251 +                     globalVels[dim_ * id + 2]);
252 +      mass = globalMasses[id];
253 +
254 +      // localID will be between 0 and hullSitesOnProc[myrank] if we
255 +      // own this guy.
256 +
257 +      int localID = id - displacements[myrank];
258 +
259 +
260 +      if (localID >= 0 && localID < hullSitesOnProc[myrank]){
261 +        face.addVertexSD(bodydoubles[indexMap[localID]]);
262 +      }else{
263 +        face.addVertexSD(NULL);
264 +      }
265 + #else
266 +      vel = bodydoubles[id]->getVel();
267 +      mass = bodydoubles[id]->getMass();
268 +      face.addVertexSD(bodydoubles[id]);      
269 + #endif  
270 +      faceVel = faceVel + vel;
271 +      faceMass = faceMass + mass;
272 +      ver++;      
273 +    } //Foreachvertex
274 +
275 +    face.addVertices(p[0], p[1], p[2]);
276 +    face.setFacetMass(faceMass);
277 +    face.setFacetVelocity(faceVel/3.0);
278 +    /*
279 +    RealType comparea = face.computeArea();
280 +    realT calcarea = qh_facetarea (facet);
281 +    Vector3d V3dCompNorm = -face.computeUnitNormal();
282 +    RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
283 +    RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
284 +    std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
285 +    calcvol +=  -dist*comparea/qh hull_dim;
286 +    */
287 +    Triangles_.push_back(face);
288 +    qh_settempfree(&vertices);      
289 +
290 +  } //FORALLfacets
291 +  
292 +  qh_getarea(qh facet_list);
293 +  volume_ = qh totvol;
294 +  area_ = qh totarea;
295 +  //  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
296 +  qh_freeqhull(!qh_ALL);
297 +  qh_memfreeshort(&curlong, &totlong);
298 +  if (curlong || totlong) {
299 +    sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
300 +            "\tdid not free %d bytes of long memory (%d pieces)",
301 +            totlong, curlong);
302 +    painCave.isFatal = 1;
303 +    simError();
304 +  }
305   }
306 +
307 + void ConvexHull::printHull(const std::string& geomFileName) {
308 +
309 + #ifdef IS_MPI
310 +  if (worldRank == 0)  {
311 + #endif
312 +  FILE *newGeomFile;
313 +  
314 +  //create new .md file based on old .md file
315 +  newGeomFile = fopen(geomFileName.c_str(), "w");
316 +  qh_findgood_all(qh facet_list);
317 +  for (int i = 0; i < qh_PRINTEND; i++)
318 +    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
319 +  
320 +  fclose(newGeomFile);
321 + #ifdef IS_MPI
322 +  }
323 + #endif
324 + }
325 + #endif //QHULL

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