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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1377 by gezelter, Wed Oct 21 02:49:43 2009 UTC vs.
Revision 1404 by chuckv, Fri Jan 15 20:46:49 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 1.18 2009-10-21 02:49:43 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*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 127 | 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;
130 –  int* hullSitesOnProc = new int[nproc];
131 –  int* coordsOnProc = new int[nproc];
132 –  int* displacements = new int[nproc];
133 –  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> objectIDs;
135 >  std::vector<int> indexMap;
136    std::vector<double> masses;
137  
138    FORALLvertices{
139      localHullSites++;
140      
141      int idx = qh_pointid(vertex->point);
142 +
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]);
# Line 155 | Line 156 | void ConvexHull::computeHull(std::vector<StuntDouble*>
156      masses.push_back(sd->getMass());
157    }
158  
158 –
159 –
159    MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
160                              1, MPI::INT);
161  
# 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 252 | Line 252 | void ConvexHull::computeHull(std::vector<StuntDouble*>
252        int localID = id - displacements[myrank];
253  
254        if (localID >= 0 && localID < hullSitesOnProc[myrank])
255 <        face.addVertexSD(bodydoubles[localID]);
255 >        face.addVertexSD(bodydoubles[indexMap[localID]]);
256        
257   #else
258        vel = bodydoubles[id]->getVel();
# Line 268 | Line 268 | void ConvexHull::computeHull(std::vector<StuntDouble*>
268      face.addVertices(p[0], p[1], p[2]);
269      face.setFacetMass(faceMass);
270      face.setFacetVelocity(faceVel/3.0);
271 +    /*
272 +    RealType comparea = face.computeArea();
273 +    realT calcarea = qh_facetarea (facet);
274 +    Vector3d V3dCompNorm = -face.computeUnitNormal();
275 +    RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
276 +    RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
277 +    std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
278 +    calcvol +=  -dist*comparea/qh hull_dim;
279 +    */
280      Triangles_.push_back(face);
281      qh_settempfree(&vertices);      
282  
# Line 276 | Line 285 | void ConvexHull::computeHull(std::vector<StuntDouble*>
285    qh_getarea(qh facet_list);
286    volume_ = qh totvol;
287    area_ = qh totarea;
288 <
280 < #ifdef IS_MPI
281 <  delete [] hullSitesOnProc;
282 <  delete [] coordsOnProc;
283 <  delete [] displacements;
284 <  delete [] vectorDisplacements;
285 < #endif
286 <  
288 >  //  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
289    qh_freeqhull(!qh_ALL);
290    qh_memfreeshort(&curlong, &totlong);
291    if (curlong || totlong)
# Line 292 | Line 294 | void ConvexHull::printHull(const std::string& geomFile
294   }
295  
296   void ConvexHull::printHull(const std::string& geomFileName) {
297 +
298 + #ifdef IS_MPI
299 +  if (worldRank == 0)  {
300 + #endif
301    FILE *newGeomFile;
302    
303    //create new .md file based on old .md file
# Line 301 | Line 307 | void ConvexHull::printHull(const std::string& geomFile
307      qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
308    
309    fclose(newGeomFile);
310 + #ifdef IS_MPI
311 +  }
312 + #endif
313   }
314   #endif //QHULL

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