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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 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 5 | Line 5
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 126 | Line 123 | void ConvexHull::computeHull(std::vector<StuntDouble*>
123    int nproc = MPI::COMM_WORLD.Get_size();
124    int myrank = MPI::COMM_WORLD.Get_rank();
125    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];
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;
# Line 277 | Line 275 | void ConvexHull::computeHull(std::vector<StuntDouble*>
275    volume_ = qh totvol;
276    area_ = qh totarea;
277  
280 – #ifdef IS_MPI
281 –  delete [] hullSitesOnProc;
282 –  delete [] coordsOnProc;
283 –  delete [] displacements;
284 –  delete [] vectorDisplacements;
285 – #endif
286 –  
278    qh_freeqhull(!qh_ALL);
279    qh_memfreeshort(&curlong, &totlong);
280    if (curlong || totlong)
# Line 292 | Line 283 | void ConvexHull::printHull(const std::string& geomFile
283   }
284  
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 301 | Line 296 | void ConvexHull::printHull(const std::string& geomFile
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

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