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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1378 by gezelter, Wed Oct 21 15:48:12 2009 UTC vs.
Revision 1410 by chuckv, Wed Feb 24 15:22:03 2010 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2008, 2009 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 1.19 2009-10-21 15:48:12 gezelter 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*dim_);
96  
# Line 126 | Line 124 | void ConvexHull::computeHull(std::vector<StuntDouble*>
124    int nproc = MPI::COMM_WORLD.Get_size();
125    int myrank = MPI::COMM_WORLD.Get_rank();
126    int localHullSites = 0;
129 –  int* hullSitesOnProc = new int[nproc];
130 –  int* coordsOnProc = new int[nproc];
131 –  int* displacements = new int[nproc];
132 –  int* vectorDisplacements = new int[nproc];
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;
# Line 209 | Line 208 | void ConvexHull::computeHull(std::vector<StuntDouble*>
208    } //qh_new_qhull
209  
210   #endif
211 <
211 >  intPoint = qh interior_point;
212 >  RealType calcvol = 0.0;
213    FORALLfacets {  
214      Triangle face;
215 <
215 >    //Qhull sets the unit normal in facet->normal
216      Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
217 <    face.setNormal(V3dNormal);
217 >    face.setUnitNormal(V3dNormal);
218      
219      RealType faceArea = qh_facetarea(facet);
220      face.setArea(faceArea);
# Line 236 | Line 236 | void ConvexHull::computeHull(std::vector<StuntDouble*>
236        p[ver][0] = vertex->point[0];
237        p[ver][1] = vertex->point[1];
238        p[ver][2] = vertex->point[2];
239 –      
239        Vector3d vel;
240        RealType mass;
241  
# Line 251 | Line 250 | void ConvexHull::computeHull(std::vector<StuntDouble*>
250  
251        int localID = id - displacements[myrank];
252  
253 <      if (localID >= 0 && localID < hullSitesOnProc[myrank])
253 >
254 >      if (localID >= 0 && localID < hullSitesOnProc[myrank]){
255          face.addVertexSD(bodydoubles[indexMap[localID]]);
256 <      
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;
# Line 268 | Line 272 | void ConvexHull::computeHull(std::vector<StuntDouble*>
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  
# Line 276 | Line 289 | void ConvexHull::computeHull(std::vector<StuntDouble*>
289    qh_getarea(qh facet_list);
290    volume_ = qh totvol;
291    area_ = qh totarea;
292 <
280 < #ifdef IS_MPI
281 <  delete [] hullSitesOnProc;
282 <  delete [] coordsOnProc;
283 <  delete [] displacements;
284 <  delete [] vectorDisplacements;
285 < #endif
286 <  
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)
# Line 292 | Line 298 | void ConvexHull::printHull(const std::string& geomFile
298   }
299  
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 301 | Line 311 | void ConvexHull::printHull(const std::string& geomFile
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

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