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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1316 by chuckv, Fri Nov 14 15:44:34 2008 UTC vs.
Revision 1377 by gezelter, Wed Oct 21 02:49:43 2009 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 2008, 2009 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
# Line 44 | Line 44
44   *
45   *  Created by Charles F. Vardeman II on 11 Dec 2006.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: ConvexHull.cpp,v 1.13 2008-11-14 15:44:34 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.18 2009-10-21 02:49:43 gezelter Exp $
48   *
49   */
50  
51   /* Standard includes independent of library */
52 +
53   #include <iostream>
54   #include <fstream>
55   #include <list>
# Line 57 | Line 58
58   #include "math/ConvexHull.hpp"
59   #include "utils/simError.h"
60  
60 –
61 – using namespace oopse;
62 –
63 – /* CGAL version of convex hull first then QHULL */
64 – #ifdef HAVE_CGAL
65 – //#include <CGAL/Homogeneous.h>
66 – #include <CGAL/basic.h>
67 – //#include <CGAL/Simple_cartesian.h>
68 – #include <CGAL/Cartesian.h>
69 – #include <CGAL/Origin.h>
70 – #include <CGAL/Exact_predicates_exact_constructions_kernel.h>
71 – #include <CGAL/Convex_hull_traits_3.h>
72 – #include <CGAL/convex_hull_3.h>
73 – #include <CGAL/Polyhedron_traits_with_normals_3.h>
74 – #include <CGAL/Polyhedron_3.h>
75 – #include <CGAL/double.h>
76 – #include <CGAL/number_utils.h>
77 –
78 –
79 – //#include <CGAL/Quotient.h>
80 – #include <CGAL/MP_Float.h>
81 – //#include <CGAL/Lazy_exact_nt.h>
82 –
83 –
84 –
85 – typedef CGAL::MP_Float RT;
86 – //typedef double RT;
87 – //typedef CGAL::Homogeneous<RT>                     K;
88 – typedef CGAL::Exact_predicates_exact_constructions_kernel K;
89 – typedef K::Vector_3                               Vector_3;
90 – //typedef CGAL::Convex_hull_traits_3<K>             Traits;
91 – typedef CGAL::Polyhedron_traits_with_normals_3<K> Traits;
92 – //typedef Traits::Polyhedron_3                      Polyhedron_3;
93 – typedef CGAL::Polyhedron_3<Traits>                     Polyhedron_3;
94 – typedef K::Point_3                                Point_3;
95 –
96 –
97 – typedef Polyhedron_3::HalfedgeDS             HalfedgeDS;
98 – typedef Polyhedron_3::Facet_iterator                   Facet_iterator;
99 – typedef Polyhedron_3::Halfedge_around_facet_circulator Halfedge_facet_circulator;
100 – typedef Polyhedron_3::Halfedge_handle Halfedge_handle;
101 – typedef Polyhedron_3::Facet_iterator Facet_iterator;
102 – typedef Polyhedron_3::Plane_iterator Plane_iterator;
103 – typedef Polyhedron_3::Vertex_iterator Vertex_iterator;
104 – typedef Polyhedron_3::Vertex_handle Vertex_handle;
105 – typedef Polyhedron_3::Point_iterator Point_iterator;
106 –
107 –
108 –
109 – class Enriched_Point_3 : public K::Point_3{
110 – public:
111 –  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
112 –
113 –  bool isMyPoint() const{ return yupMyPoint; }
114 –  void myPoint(){ yupMyPoint = true; }
115 –  void setSD(StuntDouble* SD){mySD = SD;}
116 –  StuntDouble* getStuntDouble(){return mySD;}
117 – private:
118 –  bool yupMyPoint;
119 –  StuntDouble* mySD;
120 –
121 – };
122 –
123 –
124 –
125 –
126 –
127 –    // compare Point_3's... used in setting up the STL map from points to indices
128 – template <typename Pt3>
129 – struct Point_3_comp {
130 –  bool operator() (const Pt3 & p, const Pt3 & q) const {
131 –    return CGAL::lexicographically_xyz_smaller(p,q); // this is defined inline & hence we had to create fn object & not ptrfun
132 –  }
133 – };
134 –
135 – // coordinate-based hashing inefficient but can we do better if pts are copied?
136 – typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
137 –
61   #ifdef IS_MPI
62 < struct {
140 <  double x,y,z;
141 < } surfacePt;
62 > #include <mpi.h>
63   #endif
64  
65 < ConvexHull::ConvexHull() : Hull(){
145 <  //If we are doing the mpi version, set up some vectors for data communication
146 < #ifdef IS_MPI
65 > using namespace oopse;
66  
67 <
68 < nproc_ = MPI::COMM_WORLD.Get_size();
150 < myrank_ = MPI::COMM_WORLD.Get_rank();
151 < NstoProc_ = new int[nproc_];
152 < vecdispls_   = new int[nproc_];
153 < displs_ = new int[nproc_];
154 < // Create a surface point type in MPI to send
155 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156 < surfacePtType.Commit();
157 <
158 <
159 < #endif
160 < }
161 <
162 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
67 > #ifdef HAVE_QHULL
68 > extern "C"
69   {
70 <
71 <  std::vector<Enriched_Point_3> points;
72 <  ptMapType myMap;
73 <  Point_iterator   hc;
74 <  
75 <  // Copy the positon vector into a points vector for cgal.
76 <  std::vector<StuntDouble*>::iterator SD;
77 <
78 <    for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
173 <    {
174 <      Vector3d pos = (*SD)->getPos();
175 <      Enriched_Point_3* pt = new Enriched_Point_3(pos.x(),pos.y(),pos.z());
176 <      pt->setSD(*SD);    
177 <      points.push_back(*pt);
178 <      // myMap[pt]=(*SD);
179 <    }
180 <  
181 <  // define object to hold convex hull
182 <  CGAL::Object ch_object_;
183 <  Polyhedron_3 polyhedron;
184 <
185 <  // compute convex hull
186 <  
187 <  std::vector<Enriched_Point_3>::iterator testpt;
188 <  
189 <  
190 <
191 <  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 <
193 <
194 <
195 <  Ns_ = polyhedron.size_of_vertices();
196 <
197 < #ifdef IS_MPI
198 <  /* Gather an array of the number of verticies on each processor */
199 <  
200 <
201 <  surfacePtsGlobal_.clear();
202 <  surfacePtsLocal_.clear();
203 <
204 <  MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
205 <
206 <  for (int i = 0; i < nproc_; i++){
207 <    Nsglobal_ += NstoProc_[i];
208 <  }
209 <  /*Reminder ideally, we would like to reserve size for the vectors here*/
210 <  surfacePtsLocal_.reserve(Ns_);
211 <  surfacePtsGlobal_.resize(Nsglobal_);
212 <  //  std::fill(surfacePtsGlobal_.begin(),surfacePtsGlobal_.end(),0);
213 <
214 <  /* Build a displacements array */
215 <  for (int i = 1; i < nproc_; i++){
216 <    vecdispls_[i] = vecdispls_[i-1] + NstoProc_[i-1];
217 <  }
218 <  
219 <  int noffset = vecdispls_[myrank_];
220 <  /* gather the potential hull */
221 <  
222 <  
223 <  for (hc =polyhedron.points_begin();hc != polyhedron.points_end(); ++hc){
224 <    Point_3 mypoint = *hc;
225 <    surfacePt_ mpiSurfacePt;
226 <    mpiSurfacePt.x = CGAL::to_double(mypoint.x());
227 <    mpiSurfacePt.y = CGAL::to_double(mypoint.y());
228 <    mpiSurfacePt.z = CGAL::to_double(mypoint.z());
229 <    surfacePtsLocal_.push_back(mpiSurfacePt);
230 <  }
231 <
232 <  MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,vecdispls_,surfacePtType);
233 <  std::vector<surfacePt_>::iterator spt;
234 <  std::vector<Enriched_Point_3> gblpoints;
235 <
236 <  int mine = 0;
237 <  int pointidx = 0;
238 <  for (spt = surfacePtsGlobal_.begin(); spt != surfacePtsGlobal_.end(); ++spt)
239 <    {    
240 <      surfacePt_ thispos = *spt;
241 <      Enriched_Point_3 ept(thispos.x,thispos.y,thispos.z);
242 <      if (mine >= noffset && mine < noffset + Ns_){
243 <        ept.myPoint();
244 <        ept.setSD(points[pointidx].getStuntDouble());
245 <        pointidx++;
246 <      }
247 <      gblpoints.push_back(ept);
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  
249 –      mine++;
250 –    }
251 –
252 –  /* Compute the global hull */
253 –  polyhedron.clear();
254 –  CGAL::convex_hull_3(gblpoints.begin(), gblpoints.end(), polyhedron);
255 –
256 –
257 – #endif
258 –
259 –
260 –  
261 –  /* Loop over all of the surface triangles and build data structures for atoms and normals*/
262 –  Facet_iterator j;
263 –  area_ = 0;
264 –  for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) {
265 –    Halfedge_handle h = j->halfedge();
266 –
267 –    Point_3 r0=h->vertex()->point();
268 –    Point_3 r1=h->next()->vertex()->point();
269 –    Point_3 r2=h->next()->next()->vertex()->point();
270 –
271 –    Point_3* pr0 = &r0;
272 –    Point_3* pr1 = &r1;
273 –    Point_3* pr2 = &r2;
274 –
275 –    Enriched_Point_3* er0 = static_cast<Enriched_Point_3*>(pr0);
276 –    Enriched_Point_3* er1 = static_cast<Enriched_Point_3*>(pr1);
277 –    Enriched_Point_3* er2 = static_cast<Enriched_Point_3*>(pr2);
278 –
279 –    // StuntDouble* sd = er0->getStuntDouble();
280 –    std::cerr << "sd globalIndex = " << to_double(er0->x()) << "\n";
281 –  
282 –    Point_3 thisCentroid = CGAL::centroid(r0,r1,r2);
283 –
284 –    Vector_3 normal = CGAL::cross_product(r1-r0,r2-r0);
285 –
286 –    Triangle* face = new Triangle();
287 –    Vector3d V3dNormal(CGAL::to_double(normal.x()),CGAL::to_double(normal.y()),CGAL::to_double(normal.z()));
288 –    Vector3d V3dCentroid(CGAL::to_double(thisCentroid.x()),CGAL::to_double(thisCentroid.y()),CGAL::to_double(thisCentroid.z()));
289 –    face->setNormal(V3dNormal);
290 –    face->setCentroid(V3dCentroid);
291 –    RealType faceArea = 0.5*V3dNormal.length();
292 –    face->setArea(faceArea);
293 –    area_ += faceArea;
294 –    Triangles_.push_back(face);
295 –    //    ptMapType::const_iterator locn=myMap.find(mypoint);
296 –    //    int myIndex = locn->second;
297 –
298 –  }
299 –  
300 –  std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
301 –  
302 –
303 –
304 – }
305 – void ConvexHull::printHull(const std::string& geomFileName)
306 – {
307 –  /*
308 –  std::ofstream newGeomFile;
309 –  
310 –  //create new .md file based on old .md file
311 –  newGeomFile.open("testhull.off");
312 –  
313 –  // Write polyhedron in Object File Format (OFF).
314 –  CGAL::set_ascii_mode( std::cout);
315 –  newGeomFile << "OFF" << std::endl << polyhedron.size_of_vertices() << ' '
316 –              << polyhedron.size_of_facets() << " 0" << std::endl;
317 –  std::copy( polyhedron.points_begin(), polyhedron.points_end(),
318 –             std::ostream_iterator<Point_3>( newGeomFile, "\n"));
319 –  for (  Facet_iterator i = polyhedron.facets_begin(); i != polyhedron.facets_end(); ++i) {
320 –    Halfedge_facet_circulator j = i->facet_begin();
321 –    // Facets in polyhedral surfaces are at least triangles.
322 –    CGAL_assertion( CGAL::circulator_size(j) >= 3);
323 –    newGeomFile << CGAL::circulator_size(j) << ' ';
324 –    do {
325 –      newGeomFile << ' ' << std::distance(polyhedron.vertices_begin(), j->vertex());
326 –    } while ( ++j != i->facet_begin());
327 –    newGeomFile << std::endl;
328 –  }
329 –  
330 –  newGeomFile.close();
331 –  */
332 – /*
333 –  std::ofstream newGeomFile;
334 –
335 –  //create new .md file based on old .md file
336 –  newGeomFile.open(geomFileName.c_str());
337 –
338 –  // Write polyhedron in Object File Format (OFF).
339 –  CGAL::set_ascii_mode( std::cout);
340 –  newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
341 –  << ch_polyhedron.size_of_facets() << " 0" << std::endl;
342 –  std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
343 –             std::ostream_iterator<Point_3>( newGeomFile, "\n"));
344 –  for (  Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
345 –    {
346 –      Halfedge_facet_circulator j = i->facet_begin();
347 –      // Facets in polyhedral surfaces are at least triangles.
348 –      CGAL_assertion( CGAL::circulator_size(j) >= 3);
349 –      newGeomFile << CGAL::circulator_size(j) << ' ';
350 –      do
351 –        {
352 –          newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
353 –        }
354 –      while ( ++j != i->facet_begin());
355 –      newGeomFile << std::endl;
356 –    }
357 –
358 –  newGeomFile.close();
359 – */
360 –
361 – }
362 –
363 –
364 –
365 –
366 –
367 –
368 –
369 – #else
370 – #ifdef HAVE_QHULL
80   /* Old options Qt Qu Qg QG0 FA */
81   /* More old opts Qc Qi Pp*/
373 – ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
374 –  //If we are doing the mpi version, set up some vectors for data communication
375 – #ifdef IS_MPI
82  
83 <
378 < nproc_ = MPI::COMM_WORLD.Get_size();
379 < myrank_ = MPI::COMM_WORLD.Get_rank();
380 < NstoProc_ = new int[nproc_];
381 < vecdispls_   = new int[nproc_];
382 < vecNstoProc_ = new int[nproc_];
383 < displs_ = new int[nproc_];
384 <
385 < // Create a surface point type in MPI to send
386 < //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
387 < // surfacePtType.Commit();
388 <
389 <
390 < #endif
83 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
84   }
85  
86 <
87 <
395 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
396 < {
397 <  
398 <  std::vector<int> surfaceIDs;
399 <  std::vector<int> surfaceIDsGlobal;
400 <  std::vector<int> localPtsMap;
86 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
87 >
88    int numpoints = bodydoubles.size();
89  
90 <  //coordT* pt_array;
91 <  coordT* surfpt_array;
90 >  Triangles_.clear();
91 >  
92    vertexT *vertex, **vertexp;
93    facetT *facet;
94    setT *vertices;
95 <  int curlong,totlong;
409 <  int id;
95 >  int curlong, totlong;
96    
411 –  coordT *point,**pointp;
412 –
413 –
414 –  FILE *outdummy = NULL;
415 –  FILE *errdummy = NULL;
416 –  
417 –  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
418 –
419 – //  double* ptArray = new double[numpoints * 3];
97    std::vector<double> ptArray(numpoints*3);
98    std::vector<bool> isSurfaceID(numpoints);
99  
100    // Copy the positon vector into a points vector for qhull.
101    std::vector<StuntDouble*>::iterator SD;
102    int i = 0;
103 <  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
104 <    {
105 <      Vector3d pos = (*SD)->getPos();
106 <      
107 <      ptArray[dim_ * i] = pos.x();
108 <      ptArray[dim_ * i + 1] = pos.y();
109 <      ptArray[dim_ * i + 2] = pos.z();
433 <      i++;
434 <    }
103 >  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
104 >    Vector3d pos = (*SD)->getPos();      
105 >    ptArray[dim_ * i] = pos.x();
106 >    ptArray[dim_ * i + 1] = pos.y();
107 >    ptArray[dim_ * i + 2] = pos.z();
108 >    i++;
109 >  }
110    
436 –
437 –  
438 –  
439 –  
440 –  
111    boolT ismalloc = False;
112    /* Clean up memory from previous convex hull calculations*/
113    
444 –  Triangles_.clear();
445 –  surfaceSDs_.clear();
446 –  surfaceSDs_.reserve(Ns_);
447 –
114    if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
115 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
115 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
116  
117 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
118 <      painCave.isFatal = 1;
119 <      simError();
120 <      
117 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
118 >    painCave.isFatal = 1;
119 >    simError();
120 >    
121    } //qh_new_qhull
122  
123  
124   #ifdef IS_MPI
125 <  std::vector<double> localPts;
460 <  std::vector<double> localVel;
461 <  std::vector<double> localMass;
462 <  int localPtArraySize;
125 >  //If we are doing the mpi version, set up some vectors for data communication
126    
127 <
128 <  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
129 <
127 >  int nproc = MPI::COMM_WORLD.Get_size();
128 >  int myrank = MPI::COMM_WORLD.Get_rank();
129 >  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];
134  
135 <  FORALLfacets {
135 >  std::vector<double> coords;
136 >  std::vector<double> vels;
137 >  std::vector<int> objectIDs;
138 >  std::vector<double> masses;
139 >
140 >  FORALLvertices{
141 >    localHullSites++;
142      
143 <    if (!facet->simplicial){
144 <      // should never happen with Qt
145 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
146 <      painCave.isFatal = 1;
474 <      simError();
475 <    }
476 <    
477 <    
478 <    vertices = qh_facet3vertex(facet);
479 <    FOREACHvertex_(vertices){
480 <      id = qh_pointid(vertex->point);
143 >    int idx = qh_pointid(vertex->point);
144 >    coords.push_back(ptArray[dim_  * idx]);
145 >    coords.push_back(ptArray[dim_  * idx + 1]);
146 >    coords.push_back(ptArray[dim_  * idx + 2]);
147  
148 <      if( !isSurfaceID[id] ){
483 <        isSurfaceID[id] = true;
484 <      }
485 <    }      
486 <    qh_settempfree(&vertices);      
487 <      
488 <  } //FORALLfacets
148 >    StuntDouble* sd = bodydoubles[idx];
149  
150 <
150 >    Vector3d vel = sd->getVel();
151 >    vels.push_back(vel.x());
152 >    vels.push_back(vel.y());
153 >    vels.push_back(vel.z());
154  
155 +    masses.push_back(sd->getMass());
156 +  }
157  
493 –  int idx = 0;
494 –  int nIsIts = 0;
495 –  FORALLvertices {
496 –    idx = qh_pointid(vertex->point);
497 –    localPts.push_back(ptArray[dim_ * idx]);    
498 –    localPts.push_back(ptArray[dim_ * idx + 1]);
499 –    localPts.push_back(ptArray[dim_ * idx + 2]);
158  
501 –    Vector3d vel = bodydoubles[idx]->getVel();
502 –    localVel.push_back(vel.x());
503 –    localVel.push_back(vel.y());
504 –    localVel.push_back(vel.z());
159  
160 <    RealType bdmass = bodydoubles[idx]->getMass();
161 <    localMass.push_back(bdmass);
160 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
161 >                            1, MPI::INT);
162  
163 <    localPtsMap.push_back(idx);
164 <
165 <
163 >  int globalHullSites = 0;
164 >  for (int iproc = 0; iproc < nproc; iproc++){
165 >    globalHullSites += hullSitesOnProc[iproc];
166 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
167    }
168  
169 <
170 <
516 <  localPtArraySize = int(localPts.size()/3.0);
517 <
518 <
519 <  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
169 >  displacements[0] = 0;
170 >  vectorDisplacements[0] = 0;
171    
172 <  Nsglobal_=0;
173 <  for (int i = 0; i < nproc_; i++){
174 <    Nsglobal_ += NstoProc_[i];
524 <    vecNstoProc_[i] = NstoProc_[i]*3;
172 >  for (int iproc = 1; iproc < nproc; iproc++){
173 >    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
174 >    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
175    }
526 –  
527 –
528 –  int nglobalPts = Nsglobal_*3;
529 –
176  
177 <  std::vector<double> globalPts(nglobalPts);
178 <  std::vector<double> globalVel(nglobalPts);
179 <  std::vector<double> globalMass(Nsglobal_);
177 >  std::vector<double> globalCoords(dim_ * globalHullSites);
178 >  std::vector<double> globalVels(dim_ * globalHullSites);
179 >  std::vector<double> globalMasses(globalHullSites);
180  
181 <  isSurfaceID.resize(nglobalPts);
181 >  int count = coordsOnProc[myrank];
182 >  
183 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
184 >                             &coordsOnProc[0], &vectorDisplacements[0],
185 >                             MPI::DOUBLE);
186  
187 +  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
188 +                             &coordsOnProc[0], &vectorDisplacements[0],
189 +                             MPI::DOUBLE);
190  
191 <  std::fill(globalPts.begin(),globalPts.end(),0.0);
192 <
193 <  vecdispls_[0] = 0;
194 <  /* Build a displacements array */
542 <  for (int i = 1; i < nproc_; i++){
543 <    vecdispls_[i] = vecdispls_[i-1] + vecNstoProc_[i-1];
544 <  }
545 <  
546 <  displs_[0] = 0;
547 <  for (int i = 1; i < nproc_; i++){
548 <    displs_[i] = displs_[i-1] + NstoProc_[i-1];
549 <  }
550 <  
551 <  int noffset = vecdispls_[myrank_];
552 <  /* gather the potential hull */
553 <  
554 <  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
555 <  MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize,MPI::DOUBLE,&globalVel[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
556 <  MPI::COMM_WORLD.Allgatherv(&localMass[0],localPtArraySize,MPI::DOUBLE,&globalMass[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
557 <  /*
558 <  if (myrank_ == 0){
559 <    for (i = 0; i < globalPts.size(); i++){
560 <      std::cout << globalPts[i] << std::endl;
561 <    }
562 <  }
563 <  */
191 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
192 >                             &globalMasses[0], &hullSitesOnProc[0],
193 >                             &displacements[0], MPI::DOUBLE);
194 >
195    // Free previous hull
196    qh_freeqhull(!qh_ALL);
197    qh_memfreeshort(&curlong, &totlong);
198    if (curlong || totlong)
199      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
200                << totlong << curlong << std::endl;
201 <
202 <  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
203 <                    const_cast<char *>(options_.c_str()), NULL, stderr)){
204 <
205 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
206 <      painCave.isFatal = 1;
207 <      simError();
208 <      
201 >  
202 >  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
203 >                   const_cast<char *>(options_.c_str()), NULL, stderr)){
204 >    
205 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
206 >    painCave.isFatal = 1;
207 >    simError();
208 >    
209    } //qh_new_qhull
210  
211   #endif
212  
213 +  FORALLfacets {  
214 +    Triangle face;
215  
216 +    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
217 +    face.setNormal(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 +    Vector3d faceVel = V3Zero;
229 +    Vector3d p[3];
230 +    RealType faceMass = 0.0;
231  
232 +    int ver = 0;
233  
234 <
235 <    unsigned int nf = qh num_facets;
236 <    
237 <    /* Build Surface SD list first */
238 <
591 <    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
592 <
593 <    FORALLfacets {
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        
240 <      if (!facet->simplicial){
241 <      // should never happen with Qt
597 <        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
598 <        painCave.isFatal = 1;
599 <        simError();
600 <      } //simplicical
601 <      
602 <      Triangle face;
603 <      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
604 <      face.setNormal(V3dNormal);
605 <
606 <      
240 >      Vector3d vel;
241 >      RealType mass;
242  
243 <      //RealType faceArea = 0.5*V3dNormal.length();
244 <      RealType faceArea = qh_facetarea(facet);
245 <      face.setArea(faceArea);
243 > #ifdef IS_MPI
244 >      vel = Vector3d(globalVels[dim_ * id],
245 >                     globalVels[dim_ * id + 1],
246 >                     globalVels[dim_ * id + 2]);
247 >      mass = globalMasses[id];
248  
249 +      // localID will be between 0 and hullSitesOnProc[myrank] if we
250 +      // own this guy.
251  
252 <      vertices = qh_facet3vertex(facet);
252 >      int localID = id - displacements[myrank];
253 >
254 >      if (localID >= 0 && localID < hullSitesOnProc[myrank])
255 >        face.addVertexSD(bodydoubles[localID]);
256        
615 –      coordT *center = qh_getcenter(vertices);
616 –      Vector3d V3dCentroid(center[0], center[1], center[2]);
617 –      face.setCentroid(V3dCentroid);
618 –      Vector3d faceVel = V3Zero;
619 –      Vector3d p[3];
620 –      RealType faceMass = 0.0;
621 –      int ver = 0;
622 –      FOREACHvertex_(vertices){
623 –        id = qh_pointid(vertex->point);
624 –        p[ver][0] = vertex->point[0];
625 –        p[ver][1] = vertex->point[1];
626 –        p[ver][2] = vertex->point[2];
627 –        int localindex = id;
628 – #ifdef IS_MPI
629 –        Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
630 –        
631 –        faceVel = faceVel + velVector;
632 –        faceMass = faceMass + globalMass[id];
633 –        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
634 –          localindex = localPtsMap[id-noffset/3];
257   #else
258 <          faceVel = faceVel + bodydoubles[localindex]->getVel();
259 <          faceMass = faceMass + bodydoubles[localindex]->getMass();
258 >      vel = bodydoubles[id]->getVel();
259 >      mass = bodydoubles[id]->getMass();
260 >      face.addVertexSD(bodydoubles[id]);      
261   #endif
262 <          face.addVertexSD(bodydoubles[localindex]);
263 <          if( !isSurfaceID[id] ){
264 <            isSurfaceID[id] = true;
265 < #ifdef IS_MPI      
266 <            
644 < #endif
645 <            
646 <            surfaceSDs_.push_back(bodydoubles[localindex]);
647 <            
648 <          } //IF isSurfaceID
262 >        
263 >      faceVel = faceVel + vel;
264 >      faceMass = faceMass + mass;
265 >      ver++;      
266 >    } //Foreachvertex
267  
268 < #ifdef IS_MPI
269 <        
270 <        }else{
271 <          face.addVertexSD(NULL);
272 <          }
655 < #endif
656 <        ver++;
657 <      } //Foreachvertex
658 <      /*
659 <      if (!SETempty_(facet->coplanarset)){
660 <        FOREACHpoint_(facet->coplanarset){
661 <          id = qh_pointid(point);
662 <          surfaceSDs_.push_back(bodydoubles[id]);
663 <        }
664 <      }
665 <      */
666 <      face.addVertices(p[0],p[1],p[2]);
667 <      face.setFacetMass(faceMass);
668 <      face.setFacetVelocity(faceVel/3.0);
669 <      Triangles_.push_back(face);
670 <      qh_settempfree(&vertices);      
268 >    face.addVertices(p[0], p[1], p[2]);
269 >    face.setFacetMass(faceMass);
270 >    face.setFacetVelocity(faceVel/3.0);
271 >    Triangles_.push_back(face);
272 >    qh_settempfree(&vertices);      
273  
274 <    } //FORALLfacets
274 >  } //FORALLfacets
275 >  
276 >  qh_getarea(qh facet_list);
277 >  volume_ = qh totvol;
278 >  area_ = qh totarea;
279  
280 <    /*
281 <    std::cout << surfaceSDs_.size() << std::endl;
282 <    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
283 <      Vector3d thisatom = (*SD)->getPos();
284 <      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
285 <    }
286 <    */
287 <
288 <
289 <
290 <    Ns_ = surfaceSDs_.size();
291 <    nTriangles_ = Triangles_.size();
686 <    
687 <    qh_getarea(qh facet_list);
688 <    volume_ = qh totvol;
689 <    area_ = qh totarea;
690 <    
691 <    
692 <    
693 <    qh_freeqhull(!qh_ALL);
694 <    qh_memfreeshort(&curlong, &totlong);
695 <    if (curlong || totlong)
696 <      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
697 <                << totlong << curlong << std::endl;
698 <    
699 <    
700 <    
280 > #ifdef IS_MPI
281 >  delete [] hullSitesOnProc;
282 >  delete [] coordsOnProc;
283 >  delete [] displacements;
284 >  delete [] vectorDisplacements;
285 > #endif
286 >  
287 >  qh_freeqhull(!qh_ALL);
288 >  qh_memfreeshort(&curlong, &totlong);
289 >  if (curlong || totlong)
290 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
291 >              << totlong << curlong << std::endl;    
292   }
293  
294 <
704 <
705 < void ConvexHull::printHull(const std::string& geomFileName)
706 < {
707 <
294 > void ConvexHull::printHull(const std::string& geomFileName) {
295    FILE *newGeomFile;
296    
297    //create new .md file based on old .md file
# Line 716 | Line 303 | void ConvexHull::printHull(const std::string& geomFile
303    fclose(newGeomFile);
304   }
305   #endif //QHULL
719 – #endif //CGAL
720 –
721 –
722 –

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