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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1188 by chuckv, Thu Nov 22 16:39:45 2007 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 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 1.5 2007-11-22 16:39:45 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 55 | Line 57
57   #include <iterator>
58   #include "math/ConvexHull.hpp"
59   #include "utils/simError.h"
58 – using namespace oopse;
60  
61 < /* Old options Qt Qu Qg QG0 FA */
62 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
63 < //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
63 < {}
61 > #ifdef IS_MPI
62 > #include <mpi.h>
63 > #endif
64  
65 < bool ConvexHull::genHull(std::vector<Vector3d> pos)
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 <        int numpoints = pos.size();
84 <        coordT* pt_array;
85 <        coordT* surfpt_array;
72 <        std::list<int> surface_atoms;
73 <  FILE *outdummy = NULL;
74 <  FILE *errdummy = NULL;
83 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84 >
85 >  int numpoints = bodydoubles.size();
86  
87 <        pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
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 +  // 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  
79 –        for (int i = 0; i < numpoints; i++) {
80 –                pt_array[dim_ * i] = pos[i][0];
81 –                pt_array[dim_ * i + 1] = pos[i][1];
82 –                pt_array[dim_ * i + 2] = pos[i][2];
83 –        }
122  
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 +  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 +  std::vector<double> coords;
136 +  std::vector<double> vels;
137 +  std::vector<int> indexMap;
138 +  std::vector<double> masses;
139  
140 <        /*
141 <                qh_initflags(const_cast<char *>(options_.c_str()));
142 <                qh_init_B(pospoints, numpoints, dim_, ismalloc);
143 <                qh_qhull();
92 <                qh_check_output();
140 >  FORALLvertices{
141 >    localHullSites++;
142 >    
143 >    int idx = qh_pointid(vertex->point);
144  
145 <                qh_produce_output();
95 <        */
96 <        boolT ismalloc = False;
145 >    indexMap.push_back(idx);
146  
147 <        if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
148 <                          const_cast<char *>(options_.c_str()), NULL, stderr)) {
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 <                vertexT *vertex, **vertexp;
102 <                facetT *facet;
103 <                setT *vertices;
104 <                unsigned int nf = qh num_facets;
151 >    StuntDouble* sd = bodydoubles[idx];
152  
153 <                //Matrix idx(nf, dim);
154 < /*
155 <                int j, i = 0, id = 0;
156 <                        
110 <                        int id2 = 0;
111 <                        coordT *point,**pointp;
112 <                        realT dist;
113 <                        FORALLfacets {
114 <                            j = 0;
115 <                        
116 <                            if (!facet->simplicial){
117 <                            // should never happen with Qt
118 <                            sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
119 <                                    painCave.isFatal = 0;
120 <                                    simError();
121 <                            }
122 <                        
123 <                            vertices = qh_facet3vertex(facet);
124 <                            FOREACHvertex_(vertices){
125 <                                                id = qh_pointid(vertex->point);
126 <                                                surface_atoms.push_back(id);
127 <                                                //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
128 <                                        }
129 <                                        qh_settempfree(&vertices);
130 <                                        
131 <                            FOREACHpoint_(facet->coplanarset){
132 <                            vertex= qh_nearvertex (facet, point, &dist);
133 <                      //id= qh_pointid (vertex->point);
134 <                      id2= qh_pointid (point);
135 <                                        surface_atoms.push_back(id2);
136 <                                        //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
137 <                      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
138 <                                        //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
139 <                                        
140 <                                }
141 <                                
142 <                        }
143 <                
144 < */
145 <                
146 <                
147 <        }
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 +    masses.push_back(sd->getMass());
159 +  }
160  
161 +  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
162 +                            1, MPI::INT);
163  
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 <        qh_getarea(qh facet_list);
171 <        volume_ = qh totvol;
172 <        area_ = qh totarea;
173 < //      FILE *newGeomFile;
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 <        /*
183 <                FORALLfacets {
184 <                    for (int k=0; k < qh hull_dim; k++)
185 <                      printf ("%6.2g ", facet->normal[k]);
186 <                    printf ("\n");
163 <                  }
164 <        */
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 <        int curlong,totlong;
189 < //      geomviewHull("junk.off");
190 <        qh_freeqhull(!qh_ALL);
169 <        qh_memfreeshort(&curlong, &totlong);
170 <        if (curlong || totlong)
171 <                std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
172 <                << totlong << curlong << std::endl;
173 <        free(pt_array);
174 < /*
175 <        int j = 0;
176 <        surface_atoms.sort();
177 <        surface_atoms.unique();
178 <        surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
179 <        for(std::list<int>::iterator list_iter = surface_atoms.begin();
180 <            list_iter != surface_atoms.end(); list_iter++)
181 <        {
182 <                int i = *list_iter;
183 <                        //surfpt_array[dim_ * j] = pos[i][0];
184 <                        //surfpt_array[dim_ * j + 1] = pos[i][1];
185 <                        //surfpt_array[dim_ * j + 2] = pos[i][2];
186 <                        std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
187 <                        j++;
188 <        }
189 < */      
190 <        
191 < /*      
192 <        std::string deloptions_ = "qhull d Qt";
193 <        facetT *facet, *neighbor;
194 <        ridgeT *ridge, **ridgep;
188 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
189 >                             &coordsOnProc[0], &vectorDisplacements[0],
190 >                             MPI::DOUBLE);
191  
192 <        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
193 <        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
192 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
193 >                             &globalMasses[0], &hullSitesOnProc[0],
194 >                             &displacements[0], MPI::DOUBLE);
195  
196 <                qh visit_id++;
197 <                FORALLfacets {
198 <                if (!facet->upperdelaunay) {
199 <                        facet->visitid= qh visit_id;
200 <                        qh_makeridges(facet);
201 <                        FOREACHridge_(facet->ridges) {
202 <                                neighbor= otherfacet_(ridge, facet);
203 <                                if (neighbor->visitid != qh visit_id) {
204 <                                                                                                                
205 <                                        FOREACHvertex_(ridge->vertices)
206 <                                                int id2 = qh_pointid (vertex->point);
207 <                                                std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
208 <                                }
209 <                        }
210 <                }
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 < }
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 <                qh_freeqhull(!qh_ALL);
249 <                qh_memfreeshort(&curlong, &totlong);
250 <                if (curlong || totlong)
251 <                        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
252 <                        << totlong << curlong << std::endl;
225 <                free(surfpt_array);
226 < */              
227 <        return true;
228 < }
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  
232 – RealType ConvexHull::getVolume()
233 – {
234 –        return volume_;
235 – }
259  
260 < void ConvexHull::geomviewHull(const std::string& geomFileName)
261 < {
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 <        FILE *newGeomFile;
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 <        //create new .md file based on old .md file
291 <        newGeomFile = fopen(geomFileName.c_str(), "w");
292 <        qh_findgood_all(qh facet_list);
293 <        for (int i = 0; i < qh_PRINTEND; i++)
294 <                qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
295 <
296 <        fclose(newGeomFile);
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 <
310 <
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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