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root/OpenMD/trunk/src/math/ConvexHull.cpp
Revision: 1293
Committed: Sun Sep 14 01:32:26 2008 UTC (16 years, 7 months ago) by chuckv
File size: 18374 byte(s)
Log Message:
Added large quantities of code for convex hull and constant pressure langevin dynamics.

File Contents

# Content
1 /* Copyright (c) 2006 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 1.8 2008-09-14 01:32:25 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 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
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 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 }
231
232 MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,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 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
371 /* Old options Qt Qu Qg QG0 FA */
372 ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Qci Tcv Pp") {
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 displs_ = new int[nproc_];
381
382 // Create a surface point type in MPI to send
383 surfacePtType = MPI::DOUBLE.Create_contiguous(3);
384 surfacePtType.Commit();
385
386
387 #endif
388 }
389
390
391
392 void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
393 {
394
395 std::vector<int> surfaceIDs;
396 std::vector<int> surfaceIDsGlobal;
397 std::vector<int> localPtsMap;
398 int numpoints = bodydoubles.size();
399
400 //coordT* pt_array;
401 coordT* surfpt_array;
402 vertexT *vertex, **vertexp;
403 facetT *facet;
404 setT *vertices;
405 int curlong,totlong;
406 int id;
407
408 coordT *point,**pointp;
409
410
411 FILE *outdummy = NULL;
412 FILE *errdummy = NULL;
413
414 //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
415
416 double* ptArray = new double[numpoints * 3];
417 std::vector<bool> isSurfaceID(numpoints);
418
419 // Copy the positon vector into a points vector for qhull.
420 std::vector<StuntDouble*>::iterator SD;
421 int i = 0;
422 for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
423 {
424 Vector3d pos = (*SD)->getPos();
425
426 ptArray[dim_ * i] = pos.x();
427 ptArray[dim_ * i + 1] = pos.y();
428 ptArray[dim_ * i + 2] = pos.z();
429 i++;
430 }
431
432
433
434
435
436
437 boolT ismalloc = False;
438 Triangles_.clear();
439 surfaceSDs_.clear();
440
441 if (qh_new_qhull(dim_, numpoints, ptArray, ismalloc,
442 const_cast<char *>(options_.c_str()), NULL, stderr)) {
443
444 sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
445 painCave.isFatal = 0;
446 simError();
447
448 } //qh_new_qhull
449
450
451 #ifdef IS_MPI
452 std::vector<double> localPts;
453 int localPtArraySize;
454
455 std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
456
457 FORALLfacets {
458
459 if (!facet->simplicial){
460 // should never happen with Qt
461 sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
462 painCave.isFatal = 0;
463 simError();
464 }
465
466
467 vertices = qh_facet3vertex(facet);
468 FOREACHvertex_(vertices){
469 id = qh_pointid(vertex->point);
470
471 if( !isSurfaceID[id] ){
472 isSurfaceID[id] = true;
473 }
474 }
475 qh_settempfree(&vertices);
476
477 } //FORALLfacets
478
479
480
481 /*
482 std::sort(surfaceIDs.begin(),surfaceIDs.end());
483 surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
484 int localPtArraySize = surfaceIDs.size() * 3;
485 */
486
487 localPts.resize(localPtArraySize);
488 // std::fill(localPts.begin(),globalPts.end(),0.0);
489
490
491 int idx = 0;
492 // Copy the surface points into an array.
493 for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
494 list_iter != isSurfaceID.end(); list_iter++)
495 {
496 bool isIt = *list_iter;
497 if (isIt){
498 localPts.push_back(ptArray[dim_ * idx]);
499 localPts.push_back(ptArray[dim_ * idx + 1]);
500 localPts.push_back(ptArray[dim_ * idx + 2]);
501 localPtsMap.push_back(idx);
502 } //Isit
503 idx++;
504 } //isSurfaceID
505
506
507 localPtArraySize = localPts.size();
508 MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
509
510 for (int i = 0; i < nproc_; i++){
511 Nsglobal_ += NstoProc_[i];
512 }
513
514 std::vector<double> globalPts;
515 globalPts.resize(Nsglobal_);
516 isSurfaceID.resize(int(Nsglobal_/3));
517 std::fill(globalPts.begin(),globalPts.end(),0.0);
518 /* Build a displacements array */
519 for (int i = 1; i < nproc_; i++){
520 displs_[i] = displs_[i-1] + NstoProc_[i-1];
521 }
522
523 int noffset = displs_[myrank_];
524 /* gather the potential hull */
525
526 MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],NstoProc_,displs_,MPI::DOUBLE);
527
528
529
530
531 // Free previous hull
532 qh_freeqhull(!qh_ALL);
533 qh_memfreeshort(&curlong, &totlong);
534 if (curlong || totlong)
535 std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
536 << totlong << curlong << std::endl;
537
538 if (qh_new_qhull(dim_, numpoints, &globalPts[0], ismalloc,
539 const_cast<char *>(options_.c_str()), NULL, stderr)){
540
541 sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
542 painCave.isFatal = 0;
543 simError();
544
545 } //qh_new_qhull
546
547 #endif
548
549
550
551
552
553
554 unsigned int nf = qh num_facets;
555
556 /* Build Surface SD list first */
557
558 std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
559
560 FORALLfacets {
561
562 if (!facet->simplicial){
563 // should never happen with Qt
564 sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
565 painCave.isFatal = 0;
566 simError();
567 } //simplicical
568
569 Triangle* face = new Triangle();
570 Vector3d V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
571 face->setNormal(V3dNormal);
572 //face->setCentroid(V3dCentroid);
573 RealType faceArea = 0.5*V3dNormal.length();
574 face->setArea(faceArea);
575
576
577 vertices = qh_facet3vertex(facet);
578 FOREACHvertex_(vertices){
579 id = qh_pointid(vertex->point);
580 face->addVertex(bodydoubles[id]);
581 if( !isSurfaceID[id] ){
582 isSurfaceID[id] = true;
583 surfaceSDs_.push_back(bodydoubles[id]);
584 } //IF isSurfaceID
585 } //Foreachvertex
586
587
588 Triangles_.push_back(face);
589 qh_settempfree(&vertices);
590
591 } //FORALLfacets
592
593
594
595
596 /*
597 std::sort(surfaceIDs.begin(),surfaceIDs.end());
598 surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
599 for(std::vector<int>::iterator list_iter = surfaceIDs.begin();
600 list_iter != surfaceIDs.end(); list_iter++)
601 {
602 int i = *list_iter;
603 surfaceSDs_.push_back(bodydoubles[i]);
604 }
605 */
606
607
608
609
610
611
612 Ns_ = surfaceSDs_.size();
613
614
615 qh_getarea(qh facet_list);
616 volume_ = qh totvol;
617 area_ = qh totarea;
618
619
620
621 qh_freeqhull(!qh_ALL);
622 qh_memfreeshort(&curlong, &totlong);
623 if (curlong || totlong)
624 std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
625 << totlong << curlong << std::endl;
626
627
628 // free(pt_array);
629
630 }
631
632
633
634 void ConvexHull::printHull(const std::string& geomFileName)
635 {
636
637 FILE *newGeomFile;
638
639 //create new .md file based on old .md file
640 newGeomFile = fopen(geomFileName.c_str(), "w");
641 qh_findgood_all(qh facet_list);
642 for (int i = 0; i < qh_PRINTEND; i++)
643 qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
644
645 fclose(newGeomFile);
646 }
647 #endif //QHULL
648 #endif //CGAL
649
650
651