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Revision 1304 by chuckv, Wed Oct 15 18:26:01 2008 UTC vs.
Revision 1410 by chuckv, Wed Feb 24 15:22:03 2010 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2008 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 1.10 2008-10-15 18:26:01 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>
# 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 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 < nproc_ = MPI::COMM_WORLD.Get_size();
150 < myrank_ = MPI::COMM_WORLD.Get_rank();
151 < NstoProc_ = new int[nproc_];
152 < displs_   = new int[nproc_];
153 <
154 < // Create a surface point type in MPI to send
155 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156 < surfacePtType.Commit();
157 <
158 <
159 < #endif
80 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81   }
82  
83 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
163 < {
83 > void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84  
85 <  std::vector<Enriched_Point_3> points;
166 <  ptMapType myMap;
167 <  Point_iterator   hc;
168 <  
169 <  // Copy the positon vector into a points vector for cgal.
170 <  std::vector<StuntDouble*>::iterator SD;
85 >  int numpoints = bodydoubles.size();
86  
87 <    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 <    }
87 >  Triangles_.clear();
88    
89 <  // define object to hold convex hull
90 <  CGAL::Object ch_object_;
91 <  Polyhedron_3 polyhedron;
89 >  vertexT *vertex, **vertexp;
90 >  facetT *facet;
91 >  setT *vertices;
92 >  int curlong, totlong;
93 >  pointT *intPoint;
94 >  
95 >  std::vector<double> ptArray(numpoints*dim_);
96  
97 <  // compute convex hull
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 <  std::vector<Enriched_Point_3>::iterator testpt;
108 >  boolT ismalloc = False;
109 >  /* Clean up memory from previous convex hull calculations*/
110    
111 <  
112 <
191 <  CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192 <
111 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
112 >                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
113  
114 <
115 <  Ns_ = polyhedron.size_of_vertices();
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 <  /* Gather an array of the number of verticies on each processor */
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 <  surfacePtsGlobal_.clear();
129 <  surfacePtsLocal_.clear();
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 <  MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
133 >  std::vector<double> coords;
134 >  std::vector<double> vels;
135 >  std::vector<int> indexMap;
136 >  std::vector<double> masses;
137  
138 <  for (int i = 0; i < nproc_; i++){
139 <    Nsglobal_ += NstoProc_[i];
140 <  }
141 <  /*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);
138 >  FORALLvertices{
139 >    localHullSites++;
140 >    
141 >    int idx = qh_pointid(vertex->point);
142  
143 <  /* Build a displacements array */
215 <  for (int i = 1; i < nproc_; i++){
216 <    displs_[i] = displs_[i-1] + NstoProc_[i-1];
217 <  }
218 <  
219 <  int noffset = displs_[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 <  }
143 >    indexMap.push_back(idx);
144  
145 <  MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType);
146 <  std::vector<surfacePt_>::iterator spt;
147 <  std::vector<Enriched_Point_3> gblpoints;
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 <  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);
149 >    StuntDouble* sd = bodydoubles[idx];
150  
151 <      mine++;
152 <    }
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 <  /* Compute the global hull */
157 <  polyhedron.clear();
254 <  CGAL::convex_hull_3(gblpoints.begin(), gblpoints.end(), polyhedron);
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 < #endif
163 <
164 <
165 <  
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 <
162 >  int globalHullSites = 0;
163 >  for (int iproc = 0; iproc < nproc; iproc++){
164 >    globalHullSites += hullSitesOnProc[iproc];
165 >    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
166    }
299 –  
300 –  std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
301 –  
167  
168 <
169 < }
305 < void ConvexHull::printHull(const std::string& geomFileName)
306 < {
307 <  /*
308 <  std::ofstream newGeomFile;
168 >  displacements[0] = 0;
169 >  vectorDisplacements[0] = 0;
170    
171 <  //create new .md file based on old .md file
172 <  newGeomFile.open("testhull.off");
173 <  
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;
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    }
329 –  
330 –  newGeomFile.close();
331 –  */
332 – /*
333 –  std::ofstream newGeomFile;
175  
176 <  //create new .md file based on old .md file
177 <  newGeomFile.open(geomFileName.c_str());
176 >  std::vector<double> globalCoords(dim_ * globalHullSites);
177 >  std::vector<double> globalVels(dim_ * globalHullSites);
178 >  std::vector<double> globalMasses(globalHullSites);
179  
180 <  // 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
371 < /* Old options Qt Qu Qg QG0 FA */
372 < /* More old opts Qc Qi Pp*/
373 < ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200) {
374 <  //If we are doing the mpi version, set up some vectors for data communication
375 < #ifdef IS_MPI
376 <
377 <
378 < nproc_ = MPI::COMM_WORLD.Get_size();
379 < myrank_ = MPI::COMM_WORLD.Get_rank();
380 < NstoProc_ = new int[nproc_];
381 < displs_   = new int[nproc_];
382 <
383 < // Create a surface point type in MPI to send
384 < //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
385 < // surfacePtType.Commit();
386 <
387 <
388 < #endif
389 < }
390 <
391 <
392 <
393 < void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
394 < {
180 >  int count = coordsOnProc[myrank];
181    
182 <  std::vector<int> surfaceIDs;
183 <  std::vector<int> surfaceIDsGlobal;
184 <  std::vector<int> localPtsMap;
399 <  int numpoints = bodydoubles.size();
182 >  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
183 >                             &coordsOnProc[0], &vectorDisplacements[0],
184 >                             MPI::DOUBLE);
185  
186 <  //coordT* pt_array;
187 <  coordT* surfpt_array;
188 <  vertexT *vertex, **vertexp;
404 <  facetT *facet;
405 <  setT *vertices;
406 <  int curlong,totlong;
407 <  int id;
408 <  
409 <  coordT *point,**pointp;
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 <  FILE *outdummy = NULL;
195 <  FILE *errdummy = NULL;
194 >  // Free previous hull
195 >  qh_freeqhull(!qh_ALL);
196 >  qh_memfreeshort(&curlong, &totlong);
197 >  if (curlong || totlong)
198 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
199 >              << totlong << curlong << std::endl;
200    
201 <  //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
202 <
203 < //  double* ptArray = new double[numpoints * 3];
204 <  std::vector<double> ptArray(numpoints*3);
205 <  std::vector<bool> isSurfaceID(numpoints);
206 <
207 <  // Copy the positon vector into a points vector for qhull.
422 <  std::vector<StuntDouble*>::iterator SD;
423 <  int i = 0;
424 <  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
425 <    {
426 <      Vector3d pos = (*SD)->getPos();
427 <      
428 <      ptArray[dim_ * i] = pos.x();
429 <      ptArray[dim_ * i + 1] = pos.y();
430 <      ptArray[dim_ * i + 2] = pos.z();
431 <      i++;
432 <    }
433 <  
434 <
435 <  
436 <  
437 <  
438 <  
439 <  boolT ismalloc = False;
440 <  /* Clean up memory from previous convex hull calculations*/
441 <  Triangles_.clear();
442 <  surfaceSDs_.clear();
443 <  surfaceSDs_.reserve(Ns_);
444 <
445 <  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
446 <                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
447 <
448 <      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
449 <      painCave.isFatal = 0;
450 <      simError();
451 <      
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 <
211 < #ifdef IS_MPI
212 <  std::vector<double> localPts;
213 <  int localPtArraySize;
214 <  
215 <
216 <  std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
217 <
462 <
463 <  FORALLfacets {
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 <    if (!facet->simplicial){
220 <      // should never happen with Qt
467 <      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
468 <      painCave.isFatal = 0;
469 <      simError();
470 <    }
219 >    RealType faceArea = qh_facetarea(facet);
220 >    face.setArea(faceArea);
221      
472 –    
222      vertices = qh_facet3vertex(facet);
474 –    FOREACHvertex_(vertices){
475 –      id = qh_pointid(vertex->point);
476 –
477 –      if( !isSurfaceID[id] ){
478 –        isSurfaceID[id] = true;
479 –      }
480 –    }      
481 –    qh_settempfree(&vertices);      
223        
224 <  } //FORALLfacets
224 >    coordT *center = qh_getcenter(vertices);
225 >    Vector3d V3dCentroid(center[0], center[1], center[2]);
226 >    face.setCentroid(V3dCentroid);
227  
228 <
228 >    Vector3d faceVel = V3Zero;
229 >    Vector3d p[3];
230 >    RealType faceMass = 0.0;
231  
232 <  /*
488 <  std::sort(surfaceIDs.begin(),surfaceIDs.end());
489 <  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
490 <  int localPtArraySize = surfaceIDs.size() * 3;
491 <  */
232 >    int ver = 0;
233  
234 <  //localPts.resize(localPtArraySize);
235 <  //std::fill(localPts.begin(),localPts.end(),0.0);
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 <  int idx = 0;
249 <  int nIsIts = 0;
499 < /*
500 <  // Copy the surface points into an array.
501 <  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
502 <      list_iter != isSurfaceID.end(); list_iter++)
503 <    {
504 <      bool isIt = *list_iter;
505 <      if (isIt){
506 <        localPts.push_back(ptArray[dim_ * idx]);    
507 <        localPts.push_back(ptArray[dim_ * idx + 1]);
508 <        localPts.push_back(ptArray[dim_ * idx + 2]);
509 <        localPtsMap.push_back(idx);
510 <        nIsIts++;
511 <      } //Isit
512 <      idx++;
513 <    } //isSurfaceID
514 <  */
515 <  FORALLvertices {
516 <    idx = qh_pointid(vertex->point);
517 <    localPts.push_back(ptArray[dim_ * idx]);    
518 <    localPts.push_back(ptArray[dim_ * idx + 1]);
519 <    localPts.push_back(ptArray[dim_ * idx + 2]);
520 <    localPtsMap.push_back(idx);
521 <  }
248 >      // localID will be between 0 and hullSitesOnProc[myrank] if we
249 >      // own this guy.
250  
251 +      int localID = id - displacements[myrank];
252  
524 –  localPtArraySize = localPts.size();
253  
254 <
255 <  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
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  
529 –  Nsglobal_=0;
530 –  for (int i = 0; i < nproc_; i++){
531 –    Nsglobal_ += NstoProc_[i];
532 –  }
533 –  
534 –
535 –  int nglobalPts = int(Nsglobal_/3);
536 –
264  
265 <  std::vector<double> globalPts;
266 <  globalPts.resize(Nsglobal_);
265 > #endif
266 >        
267 >      faceVel = faceVel + vel;
268 >      faceMass = faceMass + mass;
269 >      ver++;      
270 >    } //Foreachvertex
271  
272 <  isSurfaceID.resize(nglobalPts);
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 <
544 <  std::fill(globalPts.begin(),globalPts.end(),0.0);
545 <
546 <  displs_[0] = 0;
547 <  /* Build a displacements array */
548 <  for (int i = 1; i < nproc_; i++){
549 <    displs_[i] = displs_[i-1] + NstoProc_[i-1];
550 <  }
287 >  } //FORALLfacets
288    
289 <  
290 <  int noffset = displs_[myrank_];
291 <  /* gather the potential hull */
292 <  
556 <  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
557 <
558 <  /*
559 <  if (myrank_ == 0){
560 <    for (i = 0; i < globalPts.size(); i++){
561 <      std::cout << globalPts[i] << std::endl;
562 <    }
563 <  }
564 <  */
565 <  // Free previous hull
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;
297 >              << totlong << curlong << std::endl;    
298 > }
299  
300 <  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
573 <                    const_cast<char *>(options_.c_str()), NULL, stderr)){
300 > void ConvexHull::printHull(const std::string& geomFileName) {
301  
575 –      sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
576 –      painCave.isFatal = 1;
577 –      simError();
578 –      
579 –  } //qh_new_qhull
580 –
581 – #endif
582 –
583 –
584 –
585 –
586 –
587 –
588 –    unsigned int nf = qh num_facets;
589 –    
590 –    /* Build Surface SD list first */
591 –
592 –    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
593 –
594 –    FORALLfacets {
595 –      
596 –      if (!facet->simplicial){
597 –      // should never happen with Qt
598 –        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
599 –        painCave.isFatal = 1;
600 –        simError();
601 –      } //simplicical
602 –      
603 –      Triangle* face = new Triangle();
604 –      Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
605 –      face->setNormal(V3dNormal);
606 –
607 –      
608 –
609 –      RealType faceArea = 0.5*V3dNormal.length();
610 –      face->setArea(faceArea);
611 –
612 –
613 –      vertices = qh_facet3vertex(facet);
614 –      
615 –      coordT *center = qh_getcenter(vertices);
616 –      Vector3d V3dCentroid(center[0], center[1], center[2]);
617 –      face->setCentroid(V3dCentroid);
618 –
619 –      FOREACHvertex_(vertices){
620 –        id = qh_pointid(vertex->point);
621 –        int localindex = id;
302   #ifdef IS_MPI
303 <        
624 <        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
625 <          localindex = localPtsMap[id-noffset/3];
303 >  if (worldRank == 0)  {
304   #endif
627 –          face->addVertex(bodydoubles[localindex]);
628 –          if( !isSurfaceID[id] ){
629 –            isSurfaceID[id] = true;
630 – #ifdef IS_MPI      
631 –            
632 – #endif
633 –            
634 –            surfaceSDs_.push_back(bodydoubles[localindex]);
635 –            
636 –          } //IF isSurfaceID
637 –
638 – #ifdef IS_MPI
639 –        
640 –        }else{
641 –          face->addVertex(NULL);
642 –          }
643 – #endif
644 –      } //Foreachvertex
645 –      /*
646 –      if (!SETempty_(facet->coplanarset)){
647 –        FOREACHpoint_(facet->coplanarset){
648 –          id = qh_pointid(point);
649 –          surfaceSDs_.push_back(bodydoubles[id]);
650 –        }
651 –      }
652 –
653 –      Triangles_.push_back(face);
654 –      qh_settempfree(&vertices);      
655 –      */
656 –    } //FORALLfacets
657 –
658 –    /*
659 –    std::cout << surfaceSDs_.size() << std::endl;
660 –    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
661 –      Vector3d thisatom = (*SD)->getPos();
662 –      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
663 –    }
664 –    */
665 –
666 –
667 –
668 –    Ns_ = surfaceSDs_.size();
669 –    
670 –    
671 –    qh_getarea(qh facet_list);
672 –    volume_ = qh totvol;
673 –    area_ = qh totarea;
674 –    
675 –    
676 –    
677 –    qh_freeqhull(!qh_ALL);
678 –    qh_memfreeshort(&curlong, &totlong);
679 –    if (curlong || totlong)
680 –      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
681 –                << totlong << curlong << std::endl;
682 –    
683 –    
684 –    
685 – }
686 –
687 –
688 –
689 – void ConvexHull::printHull(const std::string& geomFileName)
690 – {
691 –
305    FILE *newGeomFile;
306    
307    //create new .md file based on old .md file
# Line 698 | Line 311 | void ConvexHull::printHull(const std::string& geomFile
311      qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
312    
313    fclose(newGeomFile);
314 + #ifdef IS_MPI
315 +  }
316 + #endif
317   }
318   #endif //QHULL
703 – #endif //CGAL
704 –
705 –
706 –

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