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root/OpenMD/trunk/src/math/ConvexHull.cpp
Revision: 1371
Committed: Mon Oct 19 17:44:18 2009 UTC (15 years, 6 months ago) by chuckv
File size: 20642 byte(s)
Log Message:
More MPI convex hull bug fixes. noffset corresponds to the correct array indexs. Still mismatch in forces between serial and parallel versions.

File Contents

# Content
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
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
18 * notice, this list of conditions and the following disclaimer.
19 *
20 * 3. Redistributions in binary form must reproduce the above copyright
21 * notice, this list of conditions and the following disclaimer in the
22 * documentation and/or other materials provided with the
23 * distribution.
24 *
25 * This software is provided "AS IS," without a warranty of any
26 * kind. All express or implied conditions, representations and
27 * warranties, including any implied warranty of merchantability,
28 * fitness for a particular purpose or non-infringement, are hereby
29 * excluded. The University of Notre Dame and its licensors shall not
30 * be liable for any damages suffered by licensee as a result of
31 * using, modifying or distributing the software or its
32 * derivatives. In no event will the University of Notre Dame or its
33 * licensors be liable for any lost revenue, profit or data, or for
34 * direct, indirect, special, consequential, incidental or punitive
35 * damages, however caused and regardless of the theory of liability,
36 * arising out of the use of or inability to use software, even if the
37 * University of Notre Dame has been advised of the possibility of
38 * such damages.
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 1.15 2009-10-19 17:44:18 chuckv Exp $
48 *
49 */
50
51 /* Standard includes independent of library */
52 #include <iostream>
53 #include <fstream>
54 #include <list>
55 #include <algorithm>
56 #include <iterator>
57 #include "math/ConvexHull.hpp"
58 #include "utils/simError.h"
59
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
138 #ifdef IS_MPI
139 struct {
140 double x,y,z;
141 } surfacePt;
142 #endif
143
144 ConvexHull::ConvexHull() : Hull(){
145 //If we are doing the mpi version, set up some vectors for data communication
146 #ifdef IS_MPI
147
148
149 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;
168
169 // Copy the positon vector into a points vector for cgal.
170 std::vector<StuntDouble*>::iterator SD;
171
172 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);
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
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
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
365
366
367
368 #else
369 #ifdef HAVE_QHULL
370 /* Old options Qt Qu Qg QG0 FA */
371 /* More old opts Qc Qi Pp*/
372 ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
373 //If we are doing the mpi version, set up some vectors for data communication
374 #ifdef IS_MPI
375
376
377 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_];
383
384 // Create a surface point type in MPI to send
385 //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
386 // surfacePtType.Commit();
387
388
389 #endif
390 }
391
392
393
394 void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
395 {
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 }
485 qh_settempfree(&vertices);
486
487 } //FORALLfacets
488
489
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);
517
518 Nsglobal_=0;
519 for (int i = 0; i < nproc_; i++){
520 Nsglobal_ += NstoProc_[i];
521 vecNstoProc_[i] = NstoProc_[i]*3;
522 }
523
524
525 int nglobalPts = Nsglobal_*3;
526
527
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
569 qh_freeqhull(!qh_ALL);
570 qh_memfreeshort(&curlong, &totlong);
571 if (curlong || totlong)
572 std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
573 << totlong << curlong << std::endl;
574
575 if (qh_new_qhull(dim_, Nsglobal_, &globalPts[0], ismalloc,
576 const_cast<char *>(options_.c_str()), NULL, stderr)){
577
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;
632 #ifdef IS_MPI
633 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();
643 #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
714 FILE *newGeomFile;
715
716 //create new .md file based on old .md file
717 newGeomFile = fopen(geomFileName.c_str(), "w");
718 qh_findgood_all(qh facet_list);
719 for (int i = 0; i < qh_PRINTEND; i++)
720 qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
721
722 fclose(newGeomFile);
723 }
724 #endif //QHULL
725 #endif //CGAL
726
727
728