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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1242 by chuckv, Wed May 14 14:31:48 2008 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 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 1.6 2008-05-14 14:31:48 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $
48   *
49   */
50  
51   /* Standard includes independent of library */
52 +
53   #include <iostream>
54   #include <fstream>
55   #include <list>
# Line 56 | Line 57
57   #include <iterator>
58   #include "math/ConvexHull.hpp"
59   #include "utils/simError.h"
59 – using namespace oopse;
60  
61 < /* CGAL version of convex hull first then QHULL */
62 < #ifdef HAVE_CGAL
61 > #ifdef IS_MPI
62 > #include <mpi.h>
63 > #endif
64  
65 < #include <CGAL/basic.h>
65 < #include <CGAL/Simple_cartesian.h>
66 < #include <CGAL/Convex_hull_traits_3.h>
67 < #include <CGAL/convex_hull_3.h>
68 < #include <CGAL/double.h>
65 > using namespace OpenMD;
66  
67 < #include <CGAL/Quotient.h>
68 < #include <CGAL/MP_Float.h>
69 < #include <CGAL/Lazy_exact_nt.h>
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 < typedef double RT;
81 < typedef CGAL::Simple_cartesian<RT>                K;
76 < typedef CGAL::Convex_hull_traits_3<K>             Traits;
77 < typedef Traits::Polyhedron_3                      Polyhedron_3;
78 < typedef K::Point_3                                Point;
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 < ConvexHull::ConvexHull(){}
82 <
83 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
84 < {
87 >  Triangles_.clear();
88    
89 <  std::vector<Point> points;    
89 >  vertexT *vertex, **vertexp;
90 >  facetT *facet;
91 >  setT *vertices;
92 >  int curlong, totlong;
93    
94 <  
95 <  // Copy the positon vector into a points vector for cgal.
96 <  for (int i = 0; i < pos.size(); ++i)
97 <    {
98 <      Point pt(pos[i][0],pos[i][1],pos[i][2]);
99 <      points.push_back(pt);
100 <    }
101 <  
102 <  // define object to hold convex hull
103 <  Polyhedron_3 ch_object_;
104 <  // compute convex hull
99 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
100 <  
101 <  for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin(); ch_object_.vertices_end(); ++v){
102 <    std::cout<< v.point()<<std::endl;
94 >  std::vector<double> ptArray(numpoints*dim_);
95 >
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 < }
110 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
111 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
112  
113 +    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
114 +    painCave.isFatal = 1;
115 +    simError();
116 +    
117 +  } //qh_new_qhull
118  
119  
120 < #else
121 < #ifdef HAVE_QHULL
112 < /* Old options Qt Qu Qg QG0 FA */
113 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
114 <                           //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
115 < {}
116 <
117 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
118 < {
120 > #ifdef IS_MPI
121 >  //If we are doing the mpi version, set up some vectors for data communication
122    
123 <  
124 <  int numpoints = pos.size();
125 <  coordT* pt_array;
126 <  coordT* surfpt_array;
127 <  std::list<int> surface_atoms;
128 <  FILE *outdummy = NULL;
129 <  FILE *errdummy = NULL;
130 <  
131 <  pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
132 <  
133 <  
134 <  for (int i = 0; i < numpoints; i++) {
135 <    pt_array[dim_ * i] = pos[i][0];
136 <    pt_array[dim_ * i + 1] = pos[i][1];
137 <    pt_array[dim_ * i + 2] = pos[i][2];
123 >  int nproc = MPI::COMM_WORLD.Get_size();
124 >  int myrank = MPI::COMM_WORLD.Get_rank();
125 >  int localHullSites = 0;
126 >
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 >  std::vector<double> coords;
133 >  std::vector<double> vels;
134 >  std::vector<int> indexMap;
135 >  std::vector<double> masses;
136 >
137 >  FORALLvertices{
138 >    localHullSites++;
139 >    
140 >    int idx = qh_pointid(vertex->point);
141 >
142 >    indexMap.push_back(idx);
143 >
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    }
136 –  
137 –  
138 –  
139 –  
140 –  /*
141 –    qh_initflags(const_cast<char *>(options_.c_str()));
142 –    qh_init_B(pospoints, numpoints, dim_, ismalloc);
143 –    qh_qhull();
144 –    qh_check_output();
157  
158 <    qh_produce_output();
159 <  */
160 <  boolT ismalloc = False;
158 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159 >                            1, MPI::INT);
160 >
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 <  if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
171 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
172 <    
153 <    vertexT *vertex, **vertexp;
154 <    facetT *facet;
155 <    setT *vertices;
156 <    unsigned int nf = qh num_facets;
157 <    
158 <    //Matrix idx(nf, dim);
159 <    /*
160 <      int j, i = 0, id = 0;
161 <      
162 <      int id2 = 0;
163 <      coordT *point,**pointp;
164 <      realT dist;
165 <      FORALLfacets {
166 <      j = 0;
167 <      
168 <      if (!facet->simplicial){
169 <      // should never happen with Qt
170 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
171 <      painCave.isFatal = 0;
172 <      simError();
173 <      }
174 <                        
175 <      vertices = qh_facet3vertex(facet);
176 <      FOREACHvertex_(vertices){
177 <      id = qh_pointid(vertex->point);
178 <      surface_atoms.push_back(id);
179 <      //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
180 <      }
181 <      qh_settempfree(&vertices);
182 <      
183 <      FOREACHpoint_(facet->coplanarset){
184 <      vertex= qh_nearvertex (facet, point, &dist);
185 <      //id= qh_pointid (vertex->point);
186 <      id2= qh_pointid (point);
187 <      surface_atoms.push_back(id2);
188 <      //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
189 <      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
190 <      //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
191 <                                        
192 <      }
193 <      
194 <      }
195 <                
196 < */
197 <                
198 <                
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 <  qh_getarea(qh facet_list);
190 <  volume_ = qh totvol;
191 <  area_ = qh totarea;
192 <  //    FILE *newGeomFile;
193 <  
209 <  
210 <  /*
211 <    FORALLfacets {
212 <    for (int k=0; k < qh hull_dim; k++)
213 <    printf ("%6.2g ", facet->normal[k]);
214 <    printf ("\n");
215 <    }
216 <  */
217 <  
218 <  int curlong,totlong;
219 <  //    geomviewHull("junk.off");
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;
225 –  free(pt_array);
226 –  /*
227 –    int j = 0;
228 –    surface_atoms.sort();
229 –    surface_atoms.unique();
230 –    surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
231 –    for(std::list<int>::iterator list_iter = surface_atoms.begin();
232 –    list_iter != surface_atoms.end(); list_iter++)
233 –    {
234 –    int i = *list_iter;
235 –    //surfpt_array[dim_ * j] = pos[i][0];
236 –    //surfpt_array[dim_ * j + 1] = pos[i][1];
237 –    //surfpt_array[dim_ * j + 2] = pos[i][2];
238 –    std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
239 –    j++;
240 –    }
241 –  */    
199    
200 <  /*    
201 <        std::string deloptions_ = "qhull d Qt";
202 <        facetT *facet, *neighbor;
203 <        ridgeT *ridge, **ridgep;
204 <        
205 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
206 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
207 <        
251 <        qh visit_id++;
252 <        FORALLfacets {
253 <        if (!facet->upperdelaunay) {
254 <        facet->visitid= qh visit_id;
255 <        qh_makeridges(facet);
256 <        FOREACHridge_(facet->ridges) {
257 <        neighbor= otherfacet_(ridge, facet);
258 <        if (neighbor->visitid != qh visit_id) {
259 <        
260 <        FOREACHvertex_(ridge->vertices)
261 <        int id2 = qh_pointid (vertex->point);
262 <        std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
263 <        }
264 <        }
265 <        }
266 <        
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 <        
212 <        }
211 >  FORALLfacets {  
212 >    Triangle face;
213  
214 <        qh_freeqhull(!qh_ALL);
215 <        qh_memfreeshort(&curlong, &totlong);
216 <        if (curlong || totlong)
217 <        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
218 <        << totlong << curlong << std::endl;
219 <        free(surfpt_array);
220 <  */            
221 <  return true;
222 < }
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 < RealType ConvexHull::getVolume()
233 < {
234 <  return volume_;
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::geomviewHull(const std::string& geomFileName)
290 < {
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
# Line 298 | Line 296 | void ConvexHull::geomviewHull(const std::string& geomF
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
303 – #endif //CGAL
304 –
305 –
306 –

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