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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1261 by chuckv, Wed Jun 18 17:03:30 2008 UTC vs.
Revision 1410 by chuckv, Wed Feb 24 15:22:03 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 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 1.7 2008-06-18 17:03:30 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_3;
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_3> points;  
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 +  // 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 <  // Copy the positon vector into a points vector for cgal.
109 <  for (int i = 0; i < pos.size(); ++i)
91 <    {
92 <      Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
93 <      points.push_back(pt);
94 <    }
108 >  boolT ismalloc = False;
109 >  /* Clean up memory from previous convex hull calculations*/
110    
111 <  // define object to hold convex hull
112 <  CGAL::Object ch_object_;
98 <  Polyhedron_3 polyhedron;
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 <  std::cerr << "Creating hull" << std::endl;
116 <  CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
117 <  std::cerr << "Done Creating hull" << std::endl;
118 <  std::vector<Point_3>::const_iterator p_it;
114 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
115 >    painCave.isFatal = 1;
116 >    simError();
117 >    
118 >  } //qh_new_qhull
119  
106 –  for (p_it = points.begin(); p_it != points.end(); p_it++)
107 –    {
108 –      std::cerr << (*p_it).x() << std::endl;
109 –    }
120  
121 <  /*
122 <  for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin();
123 <       ch_object_.vertices_end(); ++v){
124 <    std::cout<< v.point()<<std::endl;
125 <  }
126 <  */
117 < }
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 +  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 +  std::vector<double> coords;
134 +  std::vector<double> vels;
135 +  std::vector<int> indexMap;
136 +  std::vector<double> masses;
137  
138 < #else
139 < #ifdef HAVE_QHULL
140 < /* Old options Qt Qu Qg QG0 FA */
141 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
125 <                           //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
126 < {}
138 >  FORALLvertices{
139 >    localHullSites++;
140 >    
141 >    int idx = qh_pointid(vertex->point);
142  
143 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
144 < {
145 <  
146 <  
147 <  int numpoints = pos.size();
148 <  coordT* pt_array;
149 <  coordT* surfpt_array;
150 <  std::list<int> surface_atoms;
151 <  FILE *outdummy = NULL;
152 <  FILE *errdummy = NULL;
153 <  
154 <  pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
155 <  
156 <  
142 <  for (int i = 0; i < numpoints; i++) {
143 <    pt_array[dim_ * i] = pos[i][0];
144 <    pt_array[dim_ * i + 1] = pos[i][1];
145 <    pt_array[dim_ * i + 2] = pos[i][2];
143 >    indexMap.push_back(idx);
144 >
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 >    StuntDouble* sd = bodydoubles[idx];
150 >
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 >    masses.push_back(sd->getMass());
157    }
158 +
159 +  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
160 +                            1, MPI::INT);
161 +
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 <  
172 <  
173 <  
174 <  /*
152 <    qh_initflags(const_cast<char *>(options_.c_str()));
153 <    qh_init_B(pospoints, numpoints, dim_, ismalloc);
154 <    qh_qhull();
155 <    qh_check_output();
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 <    qh_produce_output();
177 <  */
178 <  boolT ismalloc = False;
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 <  if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
183 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
184 <    
164 <    vertexT *vertex, **vertexp;
165 <    facetT *facet;
166 <    setT *vertices;
167 <    unsigned int nf = qh num_facets;
168 <    
169 <    //Matrix idx(nf, dim);
170 <    /*
171 <      int j, i = 0, id = 0;
172 <      
173 <      int id2 = 0;
174 <      coordT *point,**pointp;
175 <      realT dist;
176 <      FORALLfacets {
177 <      j = 0;
178 <      
179 <      if (!facet->simplicial){
180 <      // should never happen with Qt
181 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
182 <      painCave.isFatal = 0;
183 <      simError();
184 <      }
185 <                        
186 <      vertices = qh_facet3vertex(facet);
187 <      FOREACHvertex_(vertices){
188 <      id = qh_pointid(vertex->point);
189 <      surface_atoms.push_back(id);
190 <      //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
191 <      }
192 <      qh_settempfree(&vertices);
193 <      
194 <      FOREACHpoint_(facet->coplanarset){
195 <      vertex= qh_nearvertex (facet, point, &dist);
196 <      //id= qh_pointid (vertex->point);
197 <      id2= qh_pointid (point);
198 <      surface_atoms.push_back(id2);
199 <      //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
200 <      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
201 <      //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
202 <                                        
203 <      }
204 <      
205 <      }
206 <                
207 < */
208 <                
209 <                
210 <  }
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 <
215 <  qh_getarea(qh facet_list);
216 <  volume_ = qh totvol;
217 <  area_ = qh totarea;
218 <  //    FILE *newGeomFile;
219 <  
220 <  
221 <  /*
222 <    FORALLfacets {
223 <    for (int k=0; k < qh hull_dim; k++)
224 <    printf ("%6.2g ", facet->normal[k]);
225 <    printf ("\n");
226 <    }
227 <  */
228 <  
229 <  int curlong,totlong;
230 <  //    geomviewHull("junk.off");
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;
236 –  free(pt_array);
237 –  /*
238 –    int j = 0;
239 –    surface_atoms.sort();
240 –    surface_atoms.unique();
241 –    surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
242 –    for(std::list<int>::iterator list_iter = surface_atoms.begin();
243 –    list_iter != surface_atoms.end(); list_iter++)
244 –    {
245 –    int i = *list_iter;
246 –    //surfpt_array[dim_ * j] = pos[i][0];
247 –    //surfpt_array[dim_ * j + 1] = pos[i][1];
248 –    //surfpt_array[dim_ * j + 2] = pos[i][2];
249 –    std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
250 –    j++;
251 –    }
252 –  */    
200    
201 <  /*    
202 <        std::string deloptions_ = "qhull d Qt";
203 <        facetT *facet, *neighbor;
204 <        ridgeT *ridge, **ridgep;
205 <        
206 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
207 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
208 <        
262 <        qh visit_id++;
263 <        FORALLfacets {
264 <        if (!facet->upperdelaunay) {
265 <        facet->visitid= qh visit_id;
266 <        qh_makeridges(facet);
267 <        FOREACHridge_(facet->ridges) {
268 <        neighbor= otherfacet_(ridge, facet);
269 <        if (neighbor->visitid != qh visit_id) {
270 <        
271 <        FOREACHvertex_(ridge->vertices)
272 <        int id2 = qh_pointid (vertex->point);
273 <        std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
274 <        }
275 <        }
276 <        }
277 <        
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 <        
229 <        }
228 >    Vector3d faceVel = V3Zero;
229 >    Vector3d p[3];
230 >    RealType faceMass = 0.0;
231  
232 <        qh_freeqhull(!qh_ALL);
284 <        qh_memfreeshort(&curlong, &totlong);
285 <        if (curlong || totlong)
286 <        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
287 <        << totlong << curlong << std::endl;
288 <        free(surfpt_array);
289 <  */            
290 <  return true;
291 < }
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 +      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 < RealType ConvexHull::getVolume()
249 < {
250 <  return volume_;
248 >      // localID will be between 0 and hullSitesOnProc[myrank] if we
249 >      // own this guy.
250 >
251 >      int localID = id - displacements[myrank];
252 >
253 >
254 >      if (localID >= 0 && localID < hullSitesOnProc[myrank]){
255 >        face.addVertexSD(bodydoubles[indexMap[localID]]);
256 >      }else{
257 >        face.addVertexSD(NULL);
258 >      }
259 > #else
260 >      vel = bodydoubles[id]->getVel();
261 >      mass = bodydoubles[id]->getMass();
262 >      face.addVertexSD(bodydoubles[id]);      
263 >
264 >
265 > #endif
266 >        
267 >      faceVel = faceVel + vel;
268 >      faceMass = faceMass + mass;
269 >      ver++;      
270 >    } //Foreachvertex
271 >
272 >    face.addVertices(p[0], p[1], p[2]);
273 >    face.setFacetMass(faceMass);
274 >    face.setFacetVelocity(faceVel/3.0);
275 >    /*
276 >    RealType comparea = face.computeArea();
277 >    realT calcarea = qh_facetarea (facet);
278 >    Vector3d V3dCompNorm = -face.computeUnitNormal();
279 >    RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
280 >    RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
281 >    std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
282 >    calcvol +=  -dist*comparea/qh hull_dim;
283 >    */
284 >    Triangles_.push_back(face);
285 >    qh_settempfree(&vertices);      
286 >
287 >  } //FORALLfacets
288 >  
289 >  qh_getarea(qh facet_list);
290 >  volume_ = qh totvol;
291 >  area_ = qh totarea;
292 >  //  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
293 >  qh_freeqhull(!qh_ALL);
294 >  qh_memfreeshort(&curlong, &totlong);
295 >  if (curlong || totlong)
296 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
297 >              << totlong << curlong << std::endl;    
298   }
299  
300 < void ConvexHull::geomviewHull(const std::string& geomFileName)
301 < {
300 > void ConvexHull::printHull(const std::string& geomFileName) {
301  
302 + #ifdef IS_MPI
303 +  if (worldRank == 0)  {
304 + #endif
305    FILE *newGeomFile;
306    
307    //create new .md file based on old .md file
# Line 309 | Line 311 | void ConvexHull::geomviewHull(const std::string& geomF
311      qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
312    
313    fclose(newGeomFile);
314 + #ifdef IS_MPI
315 +  }
316 + #endif
317   }
318   #endif //QHULL
314 – #endif //CGAL
315 –
316 –
317 –

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