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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1371 by chuckv, Mon Oct 19 17:44:18 2009 UTC vs.
Revision 1384 by gezelter, Thu Oct 22 19:43:10 2009 UTC

# 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 1.15 2009-10-19 17:44:18 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.20 2009-10-22 19:43:10 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  
61 + #ifdef IS_MPI
62 + #include <mpi.h>
63 + #endif
64  
65   using namespace oopse;
66  
67 < /* CGAL version of convex hull first then QHULL */
68 < #ifdef HAVE_CGAL
69 < //#include <CGAL/Homogeneous.h>
70 < #include <CGAL/basic.h>
71 < //#include <CGAL/Simple_cartesian.h>
72 < #include <CGAL/Cartesian.h>
73 < #include <CGAL/Origin.h>
74 < #include <CGAL/Exact_predicates_exact_constructions_kernel.h>
75 < #include <CGAL/Convex_hull_traits_3.h>
76 < #include <CGAL/convex_hull_3.h>
77 < #include <CGAL/Polyhedron_traits_with_normals_3.h>
78 < #include <CGAL/Polyhedron_3.h>
75 < #include <CGAL/double.h>
76 < #include <CGAL/number_utils.h>
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 + ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81 + }
82  
83 < //#include <CGAL/Quotient.h>
84 < #include <CGAL/MP_Float.h>
85 < //#include <CGAL/Lazy_exact_nt.h>
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 +  setT *vertices;
92 +  int curlong, totlong;
93 +  
94 +  std::vector<double> ptArray(numpoints*dim_);
95  
96 +  // Copy the positon vector into a points vector for qhull.
97 +  std::vector<StuntDouble*>::iterator SD;
98 +  int i = 0;
99 +  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
100 +    Vector3d pos = (*SD)->getPos();      
101 +    ptArray[dim_ * i] = pos.x();
102 +    ptArray[dim_ * i + 1] = pos.y();
103 +    ptArray[dim_ * i + 2] = pos.z();
104 +    i++;
105 +  }
106 +  
107 +  boolT ismalloc = False;
108 +  /* Clean up memory from previous convex hull calculations*/
109 +  
110 +  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
111 +                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
112  
113 < typedef CGAL::MP_Float RT;
114 < //typedef double RT;
115 < //typedef CGAL::Homogeneous<RT>                     K;
116 < typedef CGAL::Exact_predicates_exact_constructions_kernel K;
117 < 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;
113 >    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
114 >    painCave.isFatal = 1;
115 >    simError();
116 >    
117 >  } //qh_new_qhull
118  
119  
120 < typedef Polyhedron_3::HalfedgeDS             HalfedgeDS;
121 < typedef Polyhedron_3::Facet_iterator                   Facet_iterator;
122 < typedef Polyhedron_3::Halfedge_around_facet_circulator Halfedge_facet_circulator;
123 < typedef Polyhedron_3::Halfedge_handle Halfedge_handle;
124 < typedef Polyhedron_3::Facet_iterator Facet_iterator;
125 < 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 <
120 > #ifdef IS_MPI
121 >  //If we are doing the mpi version, set up some vectors for data communication
122 >  
123 >  int nproc = MPI::COMM_WORLD.Get_size();
124 >  int myrank = MPI::COMM_WORLD.Get_rank();
125 >  int localHullSites = 0;
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 < class Enriched_Point_3 : public K::Point_3{
133 < public:
134 <  Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
132 >  std::vector<double> coords;
133 >  std::vector<double> vels;
134 >  std::vector<int> indexMap;
135 >  std::vector<double> masses;
136  
137 <  bool isMyPoint() const{ return yupMyPoint; }
138 <  void myPoint(){ yupMyPoint = true; }
139 <  void setSD(StuntDouble* SD){mySD = SD;}
140 <  StuntDouble* getStuntDouble(){return mySD;}
117 < private:
118 <  bool yupMyPoint;
119 <  StuntDouble* mySD;
137 >  FORALLvertices{
138 >    localHullSites++;
139 >    
140 >    int idx = qh_pointid(vertex->point);
141  
142 < };
142 >    indexMap.push_back(idx);
143  
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 +    StuntDouble* sd = bodydoubles[idx];
149  
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 <
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
155 >    masses.push_back(sd->getMass());
156    }
133 – };
157  
158 < // coordinate-based hashing inefficient but can we do better if pts are copied?
159 < typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
158 >  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
159 >                            1, MPI::INT);
160  
161 < #ifdef IS_MPI
162 < struct {
163 <  double x,y,z;
164 < } surfacePt;
165 < #endif
161 >  int globalHullSites = 0;
162 >  for (int iproc = 0; iproc < nproc; iproc++){
163 >    globalHullSites += hullSitesOnProc[iproc];
164 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
165 >  }
166  
167 < ConvexHull::ConvexHull() : Hull(){
168 <  //If we are doing the mpi version, set up some vectors for data communication
169 < #ifdef IS_MPI
167 >  displacements[0] = 0;
168 >  vectorDisplacements[0] = 0;
169 >  
170 >  for (int iproc = 1; iproc < nproc; iproc++){
171 >    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
172 >    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
173 >  }
174  
175 +  std::vector<double> globalCoords(dim_ * globalHullSites);
176 +  std::vector<double> globalVels(dim_ * globalHullSites);
177 +  std::vector<double> globalMasses(globalHullSites);
178  
179 < 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)
163 < {
164 <
165 <  std::vector<Enriched_Point_3> points;
166 <  ptMapType myMap;
167 <  Point_iterator   hc;
179 >  int count = coordsOnProc[myrank];
180    
181 <  // Copy the positon vector into a points vector for cgal.
182 <  std::vector<StuntDouble*>::iterator SD;
181 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
182 >                             &coordsOnProc[0], &vectorDisplacements[0],
183 >                             MPI::DOUBLE);
184  
185 <    for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
186 <    {
187 <      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;
185 >  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
186 >                             &coordsOnProc[0], &vectorDisplacements[0],
187 >                             MPI::DOUBLE);
188  
189 <  // compute convex hull
190 <  
191 <  std::vector<Enriched_Point_3>::iterator testpt;
188 <  
189 <  
190 <
191 <  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 <
189 >  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
190 >                             &globalMasses[0], &hullSitesOnProc[0],
191 >                             &displacements[0], MPI::DOUBLE);
192  
193 <
194 <  Ns_ = polyhedron.size_of_vertices();
195 <
196 < #ifdef IS_MPI
197 <  /* Gather an array of the number of verticies on each processor */
193 >  // Free previous hull
194 >  qh_freeqhull(!qh_ALL);
195 >  qh_memfreeshort(&curlong, &totlong);
196 >  if (curlong || totlong)
197 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
198 >              << totlong << curlong << std::endl;
199    
200 +  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
201 +                   const_cast<char *>(options_.c_str()), NULL, stderr)){
202 +    
203 +    sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
204 +    painCave.isFatal = 1;
205 +    simError();
206 +    
207 +  } //qh_new_qhull
208  
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);
248 –
249 –      mine++;
250 –    }
251 –
252 –  /* Compute the global hull */
253 –  polyhedron.clear();
254 –  CGAL::convex_hull_3(gblpoints.begin(), gblpoints.end(), polyhedron);
255 –
256 –
209   #endif
210  
211 +  FORALLfacets {  
212 +    Triangle face;
213  
214 <  
215 <  /* Loop over all of the surface triangles and build data structures for atoms and normals*/
216 <  Facet_iterator j;
217 <  area_ = 0;
218 <  for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) {
219 <    Halfedge_handle h = j->halfedge();
220 <
221 <    Point_3 r0=h->vertex()->point();
222 <    Point_3 r1=h->next()->vertex()->point();
223 <    Point_3 r2=h->next()->next()->vertex()->point();
224 <
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 <  
301 <
302 <
303 < }
304 < void ConvexHull::printHull(const std::string& geomFileName)
305 < {
306 <  /*
307 <  std::ofstream newGeomFile;
308 <  
309 <  //create new .md file based on old .md file
310 <  newGeomFile.open("testhull.off");
311 <  
312 <  // Write polyhedron in Object File Format (OFF).
313 <  CGAL::set_ascii_mode( std::cout);
314 <  newGeomFile << "OFF" << std::endl << polyhedron.size_of_vertices() << ' '
315 <              << polyhedron.size_of_facets() << " 0" << std::endl;
316 <  std::copy( polyhedron.points_begin(), polyhedron.points_end(),
317 <             std::ostream_iterator<Point_3>( newGeomFile, "\n"));
318 <  for (  Facet_iterator i = polyhedron.facets_begin(); i != polyhedron.facets_end(); ++i) {
319 <    Halfedge_facet_circulator j = i->facet_begin();
320 <    // Facets in polyhedral surfaces are at least triangles.
321 <    CGAL_assertion( CGAL::circulator_size(j) >= 3);
322 <    newGeomFile << CGAL::circulator_size(j) << ' ';
323 <    do {
324 <      newGeomFile << ' ' << std::distance(polyhedron.vertices_begin(), j->vertex());
325 <    } while ( ++j != i->facet_begin());
326 <    newGeomFile << std::endl;
327 <  }
328 <  
329 <  newGeomFile.close();
330 <  */
331 < /*
332 <  std::ofstream newGeomFile;
333 <
334 <  //create new .md file based on old .md file
335 <  newGeomFile.open(geomFileName.c_str());
336 <
337 <  // Write polyhedron in Object File Format (OFF).
338 <  CGAL::set_ascii_mode( std::cout);
339 <  newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
340 <  << ch_polyhedron.size_of_facets() << " 0" << std::endl;
341 <  std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
342 <             std::ostream_iterator<Point_3>( newGeomFile, "\n"));
343 <  for (  Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
344 <    {
345 <      Halfedge_facet_circulator j = i->facet_begin();
346 <      // Facets in polyhedral surfaces are at least triangles.
347 <      CGAL_assertion( CGAL::circulator_size(j) >= 3);
348 <      newGeomFile << CGAL::circulator_size(j) << ' ';
349 <      do
350 <        {
351 <          newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
352 <        }
353 <      while ( ++j != i->facet_begin());
354 <      newGeomFile << std::endl;
355 <    }
356 <
357 <  newGeomFile.close();
358 < */
359 <
360 < }
361 <
362 <
363 <
364 <
214 >    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
215 >    face.setNormal(V3dNormal);
216 >    
217 >    RealType faceArea = qh_facetarea(facet);
218 >    face.setArea(faceArea);
219 >    
220 >    vertices = qh_facet3vertex(facet);
221 >      
222 >    coordT *center = qh_getcenter(vertices);
223 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
224 >    face.setCentroid(V3dCentroid);
225  
226 +    Vector3d faceVel = V3Zero;
227 +    Vector3d p[3];
228 +    RealType faceMass = 0.0;
229  
230 +    int ver = 0;
231  
232 < #else
233 < #ifdef HAVE_QHULL
234 < /* Old options Qt Qu Qg QG0 FA */
235 < /* More old opts Qc Qi Pp*/
236 < ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
237 <  //If we are doing the mpi version, set up some vectors for data communication
232 >    FOREACHvertex_(vertices){
233 >      int id = qh_pointid(vertex->point);
234 >      p[ver][0] = vertex->point[0];
235 >      p[ver][1] = vertex->point[1];
236 >      p[ver][2] = vertex->point[2];
237 >      
238 >      Vector3d vel;
239 >      RealType mass;
240 >
241   #ifdef IS_MPI
242 +      vel = Vector3d(globalVels[dim_ * id],
243 +                     globalVels[dim_ * id + 1],
244 +                     globalVels[dim_ * id + 2]);
245 +      mass = globalMasses[id];
246  
247 +      // localID will be between 0 and hullSitesOnProc[myrank] if we
248 +      // own this guy.
249  
250 < nproc_ = MPI::COMM_WORLD.Get_size();
378 < myrank_ = MPI::COMM_WORLD.Get_rank();
379 < NstoProc_ = new int[nproc_];
380 < vecdispls_   = new int[nproc_];
381 < vecNstoProc_ = new int[nproc_];
382 < displs_ = new int[nproc_];
250 >      int localID = id - displacements[myrank];
251  
252 < // Create a surface point type in MPI to send
253 < //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
254 < // surfacePtType.Commit();
255 <
256 <
252 >      if (localID >= 0 && localID < hullSitesOnProc[myrank])
253 >        face.addVertexSD(bodydoubles[indexMap[localID]]);
254 >      
255 > #else
256 >      vel = bodydoubles[id]->getVel();
257 >      mass = bodydoubles[id]->getMass();
258 >      face.addVertexSD(bodydoubles[id]);      
259   #endif
260 < }
260 >        
261 >      faceVel = faceVel + vel;
262 >      faceMass = faceMass + mass;
263 >      ver++;      
264 >    } //Foreachvertex
265  
266 <
267 <
268 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
269 < {
396 <  
397 <  std::vector<int> surfaceIDs;
398 <  std::vector<int> surfaceIDsGlobal;
399 <  std::vector<int> localPtsMap;
400 <  int numpoints = bodydoubles.size();
401 <
402 <  //coordT* pt_array;
403 <  coordT* surfpt_array;
404 <  vertexT *vertex, **vertexp;
405 <  facetT *facet;
406 <  setT *vertices;
407 <  int curlong,totlong;
408 <  int id;
409 <  
410 <  coordT *point,**pointp;
411 <
412 <
413 <  FILE *outdummy = NULL;
414 <  FILE *errdummy = NULL;
415 <  
416 <  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
417 <
418 < //  double* ptArray = new double[numpoints * 3];
419 <  std::vector<double> ptArray(numpoints*3);
420 <  std::vector<bool> isSurfaceID(numpoints);
421 <
422 <  // Copy the positon vector into a points vector for qhull.
423 <  std::vector<StuntDouble*>::iterator SD;
424 <  int i = 0;
425 <  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
426 <    {
427 <      Vector3d pos = (*SD)->getPos();
428 <      
429 <      ptArray[dim_ * i] = pos.x();
430 <      ptArray[dim_ * i + 1] = pos.y();
431 <      ptArray[dim_ * i + 2] = pos.z();
432 <      i++;
433 <    }
434 <  
435 <
436 <  
437 <  
438 <  
439 <  
440 <  boolT ismalloc = False;
441 <  /* Clean up memory from previous convex hull calculations*/
442 <  
443 <  Triangles_.clear();
444 <  surfaceSDs_.clear();
445 <  surfaceSDs_.reserve(Ns_);
446 <
447 <  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
448 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
449 <
450 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
451 <      painCave.isFatal = 1;
452 <      simError();
453 <      
454 <  } //qh_new_qhull
455 <
456 <
457 < #ifdef IS_MPI
458 <  std::vector<double> localPts;
459 <  std::vector<double> localVel;
460 <  std::vector<double> localMass;
461 <  int localPtArraySize;
462 <  
463 <
464 <  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
465 <
466 <
467 <  FORALLfacets {
468 <    
469 <    if (!facet->simplicial){
470 <      // should never happen with Qt
471 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
472 <      painCave.isFatal = 1;
473 <      simError();
474 <    }
475 <    
476 <    
477 <    vertices = qh_facet3vertex(facet);
478 <    FOREACHvertex_(vertices){
479 <      id = qh_pointid(vertex->point);
480 <
481 <      if( !isSurfaceID[id] ){
482 <        isSurfaceID[id] = true;
483 <      }
484 <    }      
266 >    face.addVertices(p[0], p[1], p[2]);
267 >    face.setFacetMass(faceMass);
268 >    face.setFacetVelocity(faceVel/3.0);
269 >    Triangles_.push_back(face);
270      qh_settempfree(&vertices);      
486 –      
487 –  } //FORALLfacets
271  
272 <
490 <
491 <
492 <  int idx = 0;
493 <  int nIsIts = 0;
494 <  FORALLvertices {
495 <    idx = qh_pointid(vertex->point);
496 <    localPts.push_back(ptArray[dim_ * idx]);    
497 <    localPts.push_back(ptArray[dim_ * idx + 1]);
498 <    localPts.push_back(ptArray[dim_ * idx + 2]);
499 <
500 <    Vector3d vel = bodydoubles[idx]->getVel();
501 <    localVel.push_back(vel.x());
502 <    localVel.push_back(vel.y());
503 <    localVel.push_back(vel.z());
504 <
505 <
506 <    RealType bdmass = bodydoubles[idx]->getMass();
507 <    localMass.push_back(bdmass);
508 <
509 <    localPtsMap.push_back(idx);
510 <
511 <  }
512 <
513 <
514 <  localPtArraySize = int(localPts.size()/3.0);
515 <
516 <  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
272 >  } //FORALLfacets
273    
274 <  Nsglobal_=0;
275 <  for (int i = 0; i < nproc_; i++){
276 <    Nsglobal_ += NstoProc_[i];
521 <    vecNstoProc_[i] = NstoProc_[i]*3;
522 <  }
523 <  
524 <
525 <  int nglobalPts = Nsglobal_*3;
526 <
274 >  qh_getarea(qh facet_list);
275 >  volume_ = qh totvol;
276 >  area_ = qh totarea;
277  
528 –  std::vector<double> globalPts(nglobalPts);
529 –  std::vector<double> globalVel(nglobalPts);
530 –  std::vector<double> globalMass(Nsglobal_);
531 –
532 –
533 –  
534 –  isSurfaceID.resize(nglobalPts);
535 –
536 –
537 –  std::fill(globalPts.begin(),globalPts.end(),0.0);
538 –
539 –  vecdispls_[0] = 0;
540 –  /* Build a displacements array */
541 –  for (int i = 1; i < nproc_; i++){
542 –    vecdispls_[i] = vecdispls_[i-1] + vecNstoProc_[i-1];
543 –  }
544 –  
545 –  displs_[0] = 0;
546 –  for (int i = 1; i < nproc_; i++){
547 –    displs_[i] = displs_[i-1] + NstoProc_[i-1];
548 –  }
549 –  
550 –  int noffset = displs_[myrank_];
551 –  /* gather the potential hull */
552 –  
553 –  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize*3,MPI::DOUBLE,&globalPts[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
554 –  MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize*3,MPI::DOUBLE,&globalVel[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
555 –  MPI::COMM_WORLD.Allgatherv(&localMass[0],localPtArraySize,MPI::DOUBLE,&globalMass[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
556 –
557 –  /*
558 –  int tmpidx = 0;
559 –  
560 –  if (myrank_ == 0){
561 –    for (i = 0; i < nglobalPts-3; i++){      
562 –      std::cout << "Au   " << globalPts[tmpidx] << "  " << globalPts[tmpidx+1] << "  " << globalPts[tmpidx +2] << std::endl;
563 –      tmpidx = tmpidx + 3;
564 –    }
565 –  }
566 –  */
567 –  
568 –  // Free previous hull
278    qh_freeqhull(!qh_ALL);
279    qh_memfreeshort(&curlong, &totlong);
280    if (curlong || totlong)
281      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
282 <              << totlong << curlong << std::endl;
282 >              << totlong << curlong << std::endl;    
283 > }
284  
285 <  if (qh_new_qhull(dim_, Nsglobal_, &globalPts[0], ismalloc,
576 <                    const_cast<char *>(options_.c_str()), NULL, stderr)){
285 > void ConvexHull::printHull(const std::string& geomFileName) {
286  
578 –      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
579 –      painCave.isFatal = 1;
580 –      simError();
581 –      
582 –  } //qh_new_qhull
583 –
584 – #endif
585 –
586 –
587 –
588 –
589 –
590 –
591 –    unsigned int nf = qh num_facets;
592 –    
593 –    /* Build Surface SD list first */
594 –
595 –    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
596 –    int numvers = 0;
597 –    FORALLfacets {
598 –      
599 –      if (!facet->simplicial){
600 –      // should never happen with Qt
601 –        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
602 –        painCave.isFatal = 1;
603 –        simError();
604 –      } //simplicical
605 –      
606 –      Triangle face;
607 –      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
608 –      face.setNormal(V3dNormal);
609 –
610 –      
611 –
612 –      //RealType faceArea = 0.5*V3dNormal.length();
613 –      RealType faceArea = qh_facetarea(facet);
614 –      face.setArea(faceArea);
615 –
616 –
617 –      vertices = qh_facet3vertex(facet);
618 –      
619 –      coordT *center = qh_getcenter(vertices);
620 –      Vector3d V3dCentroid(center[0], center[1], center[2]);
621 –      face.setCentroid(V3dCentroid);
622 –      Vector3d faceVel = V3Zero;
623 –      Vector3d p[3];
624 –      RealType faceMass = 0.0;
625 –      int ver = 0;
626 –      FOREACHvertex_(vertices){
627 –        id = qh_pointid(vertex->point);
628 –        p[ver][0] = vertex->point[0];
629 –        p[ver][1] = vertex->point[1];
630 –        p[ver][2] = vertex->point[2];
631 –        int localindex = id;
287   #ifdef IS_MPI
288 <        Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 2]);
634 <        
635 <        faceVel = faceVel + velVector;
636 <        faceMass = faceMass + globalMass[id];
637 <        if (id >= noffset && id < (noffset + localPtArraySize) ){
638 <          
639 <          localindex = localPtsMap[id-noffset];
640 < #else
641 <          faceVel = faceVel + bodydoubles[localindex]->getVel();
642 <          faceMass = faceMass + bodydoubles[localindex]->getMass();
288 >  if (worldRank == 0)  {
289   #endif
644 –          face.addVertexSD(bodydoubles[localindex]);
645 –          if( !isSurfaceID[id] ){
646 –            isSurfaceID[id] = true;
647 – #ifdef IS_MPI      
648 –            
649 – #endif
650 –            
651 –            surfaceSDs_.push_back(bodydoubles[localindex]);
652 –            //   std::cout <<"This ID is: " << bodydoubles[localindex]->getGlobalIndex() << std::endl;
653 –            
654 –          } //IF isSurfaceID
655 –
656 – #ifdef IS_MPI
657 –        
658 –        }else{
659 –          face.addVertexSD(NULL);
660 –          }
661 – #endif
662 –        numvers++;
663 –        ver++;
664 –      } //Foreachvertex
665 –      /*
666 –      if (!SETempty_(facet->coplanarset)){
667 –        FOREACHpoint_(facet->coplanarset){
668 –          id = qh_pointid(point);
669 –          surfaceSDs_.push_back(bodydoubles[id]);
670 –        }
671 –      }
672 –      */
673 –      face.addVertices(p[0],p[1],p[2]);
674 –      face.setFacetMass(faceMass);
675 –      face.setFacetVelocity(faceVel/3.0);
676 –      Triangles_.push_back(face);
677 –      qh_settempfree(&vertices);      
678 –
679 –    } //FORALLfacets
680 –
681 –    /*    
682 –    std::cout << surfaceSDs_.size() << std::endl;
683 –    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
684 –      Vector3d thisatom = (*SD)->getPos();
685 –      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
686 –    }
687 –    */
688 –
689 –
690 –    Ns_ = surfaceSDs_.size();
691 –    nTriangles_ = Triangles_.size();
692 –    
693 –    qh_getarea(qh facet_list);
694 –    volume_ = qh totvol;
695 –    area_ = qh totarea;
696 –    
697 –    
698 –    
699 –    qh_freeqhull(!qh_ALL);
700 –    qh_memfreeshort(&curlong, &totlong);
701 –    if (curlong || totlong)
702 –      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
703 –                << totlong << curlong << std::endl;
704 –    
705 –    
706 –    
707 – }
708 –
709 –
710 –
711 – void ConvexHull::printHull(const std::string& geomFileName)
712 – {
713 –
290    FILE *newGeomFile;
291    
292    //create new .md file based on old .md file
# Line 720 | 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
725 – #endif //CGAL
726 –
727 –
728 –

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