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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1143 by chuckv, Wed May 30 19:51:07 2007 UTC vs.
Revision 1410 by chuckv, Wed Feb 24 15:22:03 2010 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 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 1.4 2007-05-30 19:51:07 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>
56 + #include <algorithm>
57 + #include <iterator>
58   #include "math/ConvexHull.hpp"
59 + #include "utils/simError.h"
60  
61 < using namespace oopse;
61 > #ifdef IS_MPI
62 > #include <mpi.h>
63 > #endif
64  
65 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
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 < bool ConvexHull::genHull(std::vector<Vector3d> pos) {
81 <  FILE *outfile = stdout;
82 <  FILE *errfile = stderr;
80 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81 > }
82 >
83 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84 >
85 >  int numpoints = bodydoubles.size();
86 >
87 >  Triangles_.clear();
88 >  
89 >  vertexT *vertex, **vertexp;
90    facetT *facet;
91 <  int exitcode;
92 <  boolT ismalloc = False;
93 <  int curlong,totlong;
91 >  setT *vertices;
92 >  int curlong, totlong;
93 >  pointT *intPoint;
94    
95 <  int numpoints = pos.size();
69 <
70 <  coordT* points;
71 <  points = (coordT*) malloc(sizeof(coordT) * (numpoints*dim_));
95 >  std::vector<double> ptArray(numpoints*dim_);
96  
97 <  for (int i=0; i<numpoints; i++) {
98 <    points[dim_ * i] = pos[i][0];
99 <    points[dim_ * i + 1] = pos[i][1];
100 <    points[dim_ * i + 2] = pos[i][2];          
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 +  boolT ismalloc = False;
109 +  /* Clean up memory from previous convex hull calculations*/
110    
111 <  qh_initflags (const_cast<char *>(options_.c_str()));
112 <  qh_init_B (points, numpoints, dim_, ismalloc);
113 <  qh_qhull();
114 <  qh_check_output();
111 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
112 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
113 >
114 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
115 >    painCave.isFatal = 1;
116 >    simError();
117 >    
118 >  } //qh_new_qhull
119 >
120 >
121 > #ifdef IS_MPI
122 >  //If we are doing the mpi version, set up some vectors for data communication
123    
124 +  int nproc = MPI::COMM_WORLD.Get_size();
125 +  int myrank = MPI::COMM_WORLD.Get_rank();
126 +  int localHullSites = 0;
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;
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]);
148 +
149 +    StuntDouble* sd = bodydoubles[idx];
150 +
151 +    Vector3d vel = sd->getVel();
152 +    vels.push_back(vel.x());
153 +    vels.push_back(vel.y());
154 +    vels.push_back(vel.z());
155 +
156 +    masses.push_back(sd->getMass());
157 +  }
158 +
159 +  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
160 +                            1, MPI::INT);
161 +
162 +  int globalHullSites = 0;
163 +  for (int iproc = 0; iproc < nproc; iproc++){
164 +    globalHullSites += hullSitesOnProc[iproc];
165 +    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
166 +  }
167 +
168 +  displacements[0] = 0;
169 +  vectorDisplacements[0] = 0;
170    
171 +  for (int iproc = 1; iproc < nproc; iproc++){
172 +    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
173 +    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
174 +  }
175 +
176 +  std::vector<double> globalCoords(dim_ * globalHullSites);
177 +  std::vector<double> globalVels(dim_ * globalHullSites);
178 +  std::vector<double> globalMasses(globalHullSites);
179 +
180 +  int count = coordsOnProc[myrank];
181    
182 <  qh_getarea(qh facet_list);
183 <  volume_ = qh totvol;                                                  
184 <  area_ = qh totarea;                                          
185 <  
186 <  
187 <  
182 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
183 >                             &coordsOnProc[0], &vectorDisplacements[0],
184 >                             MPI::DOUBLE);
185 >
186 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
187 >                             &coordsOnProc[0], &vectorDisplacements[0],
188 >                             MPI::DOUBLE);
189 >
190 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
191 >                             &globalMasses[0], &hullSitesOnProc[0],
192 >                             &displacements[0], MPI::DOUBLE);
193 >
194 >  // Free previous hull
195    qh_freeqhull(!qh_ALL);
196 <  qh_memfreeshort (&curlong, &totlong);
196 >  qh_memfreeshort(&curlong, &totlong);
197    if (curlong || totlong)
198 <    fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
199 <             totlong, curlong);
198 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
199 >              << totlong << curlong << std::endl;
200    
201 <  
202 <  return true;
203 < }
201 >  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
202 >                   const_cast<char *>(options_.c_str()), NULL, stderr)){
203 >    
204 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
205 >    painCave.isFatal = 1;
206 >    simError();
207 >    
208 >  } //qh_new_qhull
209  
210 + #endif
211 +  intPoint = qh interior_point;
212 +  RealType calcvol = 0.0;
213 +  FORALLfacets {  
214 +    Triangle face;
215 +    //Qhull sets the unit normal in facet->normal
216 +    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
217 +    face.setUnitNormal(V3dNormal);
218 +    
219 +    RealType faceArea = qh_facetarea(facet);
220 +    face.setArea(faceArea);
221 +    
222 +    vertices = qh_facet3vertex(facet);
223 +      
224 +    coordT *center = qh_getcenter(vertices);
225 +    Vector3d V3dCentroid(center[0], center[1], center[2]);
226 +    face.setCentroid(V3dCentroid);
227  
228 < RealType ConvexHull::getVolume() {
229 <  return volume_;
228 >    Vector3d faceVel = V3Zero;
229 >    Vector3d p[3];
230 >    RealType faceMass = 0.0;
231 >
232 >    int ver = 0;
233 >
234 >    FOREACHvertex_(vertices){
235 >      int id = qh_pointid(vertex->point);
236 >      p[ver][0] = vertex->point[0];
237 >      p[ver][1] = vertex->point[1];
238 >      p[ver][2] = vertex->point[2];
239 >      Vector3d vel;
240 >      RealType mass;
241 >
242 > #ifdef IS_MPI
243 >      vel = Vector3d(globalVels[dim_ * id],
244 >                     globalVels[dim_ * id + 1],
245 >                     globalVels[dim_ * id + 2]);
246 >      mass = globalMasses[id];
247 >
248 >      // localID will be between 0 and hullSitesOnProc[myrank] if we
249 >      // own this guy.
250 >
251 >      int localID = id - displacements[myrank];
252 >
253 >
254 >      if (localID >= 0 && localID < hullSitesOnProc[myrank]){
255 >        face.addVertexSD(bodydoubles[indexMap[localID]]);
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;
268 >      faceMass = faceMass + mass;
269 >      ver++;      
270 >    } //Foreachvertex
271 >
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 >
287 >  } //FORALLfacets
288 >  
289 >  qh_getarea(qh facet_list);
290 >  volume_ = qh totvol;
291 >  area_ = qh totarea;
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)
296 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
297 >              << totlong << curlong << std::endl;    
298   }
299  
300 < void ConvexHull::geomviewHull(const std::string& geomFileName) {
300 > void ConvexHull::printHull(const std::string& geomFileName) {
301 >
302 > #ifdef IS_MPI
303 >  if (worldRank == 0)  {
304 > #endif
305 >  FILE *newGeomFile;
306    
110 –  std::ofstream newGeomFile;
111 –  
307    //create new .md file based on old .md file
308 <  newGeomFile.open(geomFileName.c_str());
308 >  newGeomFile = fopen(geomFileName.c_str(), "w");
309 >  qh_findgood_all(qh facet_list);
310 >  for (int i = 0; i < qh_PRINTEND; i++)
311 >    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
312    
313 <  
314 <  newGeomFile.close();
313 >  fclose(newGeomFile);
314 > #ifdef IS_MPI
315 >  }
316 > #endif
317   }
318 + #endif //QHULL

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