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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1374 by chuckv, Tue Oct 20 20:05:28 2009 UTC vs.
Revision 1411 by gezelter, Wed Feb 24 16:09:21 2010 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2008, 2009 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 1.16 2009-10-20 20:05:28 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $
48   *
49   */
50  
# Line 62 | Line 62
62   #include <mpi.h>
63   #endif
64  
65 < using namespace oopse;
65 > using namespace OpenMD;
66  
67   #ifdef HAVE_QHULL
68   extern "C"
# Line 77 | Line 77 | extern "C"
77   #include <qhull/stat.h>
78   }
79  
80 – /* Old options Qt Qu Qg QG0 FA */
81 – /* More old opts Qc Qi Pp*/
82 –
80   ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81   }
82  
# Line 93 | Line 90 | void ConvexHull::computeHull(std::vector<StuntDouble*>
90    facetT *facet;
91    setT *vertices;
92    int curlong, totlong;
93 +  pointT *intPoint;
94    
95 <  std::vector<double> ptArray(numpoints*3);
98 <  std::vector<bool> isSurfaceID(numpoints);
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;
# Line 108 | Line 105 | void ConvexHull::computeHull(std::vector<StuntDouble*>
105      i++;
106    }
107    
108 +  /* Clean up memory from previous convex hull calculations */
109    boolT ismalloc = False;
112 –  /* Clean up memory from previous convex hull calculations*/
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 <
115 >    
116      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
117      painCave.isFatal = 1;
118      simError();
# Line 127 | Line 126 | void ConvexHull::computeHull(std::vector<StuntDouble*>
126    int nproc = MPI::COMM_WORLD.Get_size();
127    int myrank = MPI::COMM_WORLD.Get_rank();
128    int localHullSites = 0;
130 –  int* hullSitesOnProc = new int[nproc];
131 –  int* coordsOnProc = new int[nproc];
132 –  int* displacements = new int[nproc];
133 –  int* vectorDisplacements = new int[nproc];
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> objectIDs;
137 >  std::vector<int> indexMap;
138    std::vector<double> masses;
139  
140    FORALLvertices{
141      localHullSites++;
142      
143      int idx = qh_pointid(vertex->point);
144 +
145 +    indexMap.push_back(idx);
146 +
147      coords.push_back(ptArray[dim_  * idx]);
148      coords.push_back(ptArray[dim_  * idx + 1]);
149      coords.push_back(ptArray[dim_  * idx + 2]);
# Line 159 | Line 162 | void ConvexHull::computeHull(std::vector<StuntDouble*>
162                              1, MPI::INT);
163  
164    int globalHullSites = 0;
165 <  for (int iproc = 0; i < nproc; iproc++){
165 >  for (int iproc = 0; iproc < nproc; iproc++){
166      globalHullSites += hullSitesOnProc[iproc];
167      coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
168    }
# Line 167 | Line 170 | void ConvexHull::computeHull(std::vector<StuntDouble*>
170    displacements[0] = 0;
171    vectorDisplacements[0] = 0;
172    
173 <  for (int iproc = 1; i < nproc; iproc++){
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);
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,
185 <                             &globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0],
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,
189 <                             &globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
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], &displacements[0],
194 <                             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 <    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
201 <              << totlong << curlong << std::endl;
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)){
# Line 206 | Line 214 | void ConvexHull::computeHull(std::vector<StuntDouble*>
214    } //qh_new_qhull
215  
216   #endif
217 <
217 >  intPoint = qh interior_point;
218 >  RealType calcvol = 0.0;
219    FORALLfacets {  
220      Triangle face;
221 <
221 >    //Qhull sets the unit normal in facet->normal
222      Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
223 <    face.setNormal(V3dNormal);
223 >    face.setUnitNormal(V3dNormal);
224      
225      RealType faceArea = qh_facetarea(facet);
226      face.setArea(faceArea);
# Line 225 | Line 234 | void ConvexHull::computeHull(std::vector<StuntDouble*>
234      Vector3d faceVel = V3Zero;
235      Vector3d p[3];
236      RealType faceMass = 0.0;
237 +
238      int ver = 0;
239  
240      FOREACHvertex_(vertices){
# Line 232 | Line 242 | void ConvexHull::computeHull(std::vector<StuntDouble*>
242        p[ver][0] = vertex->point[0];
243        p[ver][1] = vertex->point[1];
244        p[ver][2] = vertex->point[2];
235 –      
245        Vector3d vel;
246        RealType mass;
247  
# Line 242 | Line 251 | void ConvexHull::computeHull(std::vector<StuntDouble*>
251                       globalVels[dim_ * id + 2]);
252        mass = globalMasses[id];
253  
254 <      // localID will be between 0 and hullSitesOnProc[myrank] if we own this guy.
254 >      // localID will be between 0 and hullSitesOnProc[myrank] if we
255 >      // own this guy.
256 >
257        int localID = id - displacements[myrank];
258 <      if (id >= 0 && id < hullSitesOnProc[myrank])
259 <        face.addVertexSD(bodydoubles[localID]);
260 <      else
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
256 <        
269 > #endif  
270        faceVel = faceVel + vel;
271        faceMass = faceMass + mass;
272        ver++;      
# Line 262 | Line 275 | void ConvexHull::computeHull(std::vector<StuntDouble*>
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  
# Line 270 | Line 292 | void ConvexHull::computeHull(std::vector<StuntDouble*>
292    qh_getarea(qh facet_list);
293    volume_ = qh totvol;
294    area_ = qh totarea;
295 <
274 < #ifdef IS_MPI
275 <  delete [] hullSitesOnProc;
276 <  delete [] coordsOnProc;
277 <  delete [] displacements;
278 <  delete [] vectorDisplacements;
279 < #endif
280 <  
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 <    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
300 <              << totlong << curlong << std::endl;    
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  
288 –
289 –
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
# Line 297 | Line 318 | void ConvexHull::printHull(const std::string& geomFile
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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