xref: /petsc/src/dm/impls/plex/plexgenerate.c (revision 44b85a236d0c752951b0573ba76bfb3134d48c1e) 
1 #include <petsc-private/dmpleximpl.h>   /*I      "petscdmplex.h"   I*/
2 
3 #undef __FUNCT__
4 #define __FUNCT__ "DMPlexInvertCell_Internal"
5 PetscErrorCode DMPlexInvertCell_Internal(PetscInt dim, PetscInt numCorners, PetscInt cone[])
6 {
7   int tmpc;
8 
9   PetscFunctionBegin;
10   if (dim != 3) PetscFunctionReturn(0);
11   switch (numCorners) {
12   case 4:
13     tmpc    = cone[0];
14     cone[0] = cone[1];
15     cone[1] = tmpc;
16     break;
17   case 8:
18     tmpc    = cone[1];
19     cone[1] = cone[3];
20     cone[3] = tmpc;
21     break;
22   default: break;
23   }
24   PetscFunctionReturn(0);
25 }
26 
27 #undef __FUNCT__
28 #define __FUNCT__ "DMPlexInvertCell"
29 /*@C
30   DMPlexInvertCell - This flips tetrahedron and hexahedron orientation since Plex stores them internally with outward normals. Other cells are left untouched.
31 
32   Input Parameters:
33 + numCorners - The number of vertices in a cell
34 - cone - The incoming cone
35 
36   Output Parameter:
37 . cone - The inverted cone (in-place)
38 
39   Level: developer
40 
41 .seealso: DMPlexGenerate()
42 @*/
43 PetscErrorCode DMPlexInvertCell(PetscInt dim, PetscInt numCorners, int cone[])
44 {
45   int tmpc;
46 
47   PetscFunctionBegin;
48   if (dim != 3) PetscFunctionReturn(0);
49   switch (numCorners) {
50   case 4:
51     tmpc    = cone[0];
52     cone[0] = cone[1];
53     cone[1] = tmpc;
54     break;
55   case 8:
56     tmpc    = cone[1];
57     cone[1] = cone[3];
58     cone[3] = tmpc;
59     break;
60   default: break;
61   }
62   PetscFunctionReturn(0);
63 }
64 
65 #undef __FUNCT__
66 #define __FUNCT__ "DMPlexInvertCells_Internal"
67 /* This is to fix the tetrahedron orientation from TetGen */
68 PETSC_UNUSED static PetscErrorCode DMPlexInvertCells_Internal(PetscInt dim, PetscInt numCells, PetscInt numCorners, int cells[])
69 {
70   PetscInt       bound = numCells*numCorners, coff;
71   PetscErrorCode ierr;
72 
73   PetscFunctionBegin;
74   for (coff = 0; coff < bound; coff += numCorners) {
75     ierr = DMPlexInvertCell(dim, numCorners, &cells[coff]);CHKERRQ(ierr);
76   }
77   PetscFunctionReturn(0);
78 }
79 
80 #undef __FUNCT__
81 #define __FUNCT__ "DMPlexTriangleSetOptions"
82 /*@
83   DMPlexTriangleSetOptions - Set the options used for the Triangle mesh generator
84 
85   Not Collective
86 
87   Inputs Parameters:
88 + dm - The DMPlex object
89 - opts - The command line options
90 
91   Level: developer
92 
93 .keywords: mesh, points
94 .seealso: DMPlexTetgenSetOptions(), DMPlexGenerate()
95 @*/
96 PetscErrorCode DMPlexTriangleSetOptions(DM dm, const char *opts)
97 {
98   DM_Plex       *mesh = (DM_Plex*) dm->data;
99   PetscErrorCode ierr;
100 
101   PetscFunctionBegin;
102   PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
103   PetscValidPointer(opts, 2);
104   ierr = PetscFree(mesh->triangleOpts);CHKERRQ(ierr);
105   ierr = PetscStrallocpy(opts, &mesh->triangleOpts);CHKERRQ(ierr);
106   PetscFunctionReturn(0);
107 }
108 
109 #undef __FUNCT__
110 #define __FUNCT__ "DMPlexTetgenSetOptions"
111 /*@
112   DMPlexTetgenSetOptions - Set the options used for the Tetgen mesh generator
113 
114   Not Collective
115 
116   Inputs Parameters:
117 + dm - The DMPlex object
118 - opts - The command line options
119 
120   Level: developer
121 
122 .keywords: mesh, points
123 .seealso: DMPlexTriangleSetOptions(), DMPlexGenerate()
124 @*/
125 PetscErrorCode DMPlexTetgenSetOptions(DM dm, const char *opts)
126 {
127   DM_Plex       *mesh = (DM_Plex*) dm->data;
128   PetscErrorCode ierr;
129 
130   PetscFunctionBegin;
131   PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
132   PetscValidPointer(opts, 2);
133   ierr = PetscFree(mesh->tetgenOpts);CHKERRQ(ierr);
134   ierr = PetscStrallocpy(opts, &mesh->tetgenOpts);CHKERRQ(ierr);
135   PetscFunctionReturn(0);
136 }
137 
138 #if defined(PETSC_HAVE_TRIANGLE)
139 #include <triangle.h>
140 
141 #undef __FUNCT__
142 #define __FUNCT__ "InitInput_Triangle"
143 PetscErrorCode InitInput_Triangle(struct triangulateio *inputCtx)
144 {
145   PetscFunctionBegin;
146   inputCtx->numberofpoints             = 0;
147   inputCtx->numberofpointattributes    = 0;
148   inputCtx->pointlist                  = NULL;
149   inputCtx->pointattributelist         = NULL;
150   inputCtx->pointmarkerlist            = NULL;
151   inputCtx->numberofsegments           = 0;
152   inputCtx->segmentlist                = NULL;
153   inputCtx->segmentmarkerlist          = NULL;
154   inputCtx->numberoftriangleattributes = 0;
155   inputCtx->trianglelist               = NULL;
156   inputCtx->numberofholes              = 0;
157   inputCtx->holelist                   = NULL;
158   inputCtx->numberofregions            = 0;
159   inputCtx->regionlist                 = NULL;
160   PetscFunctionReturn(0);
161 }
162 
163 #undef __FUNCT__
164 #define __FUNCT__ "InitOutput_Triangle"
165 PetscErrorCode InitOutput_Triangle(struct triangulateio *outputCtx)
166 {
167   PetscFunctionBegin;
168   outputCtx->numberofpoints        = 0;
169   outputCtx->pointlist             = NULL;
170   outputCtx->pointattributelist    = NULL;
171   outputCtx->pointmarkerlist       = NULL;
172   outputCtx->numberoftriangles     = 0;
173   outputCtx->trianglelist          = NULL;
174   outputCtx->triangleattributelist = NULL;
175   outputCtx->neighborlist          = NULL;
176   outputCtx->segmentlist           = NULL;
177   outputCtx->segmentmarkerlist     = NULL;
178   outputCtx->numberofedges         = 0;
179   outputCtx->edgelist              = NULL;
180   outputCtx->edgemarkerlist        = NULL;
181   PetscFunctionReturn(0);
182 }
183 
184 #undef __FUNCT__
185 #define __FUNCT__ "FiniOutput_Triangle"
186 PetscErrorCode FiniOutput_Triangle(struct triangulateio *outputCtx)
187 {
188   PetscFunctionBegin;
189   free(outputCtx->pointlist);
190   free(outputCtx->pointmarkerlist);
191   free(outputCtx->segmentlist);
192   free(outputCtx->segmentmarkerlist);
193   free(outputCtx->edgelist);
194   free(outputCtx->edgemarkerlist);
195   free(outputCtx->trianglelist);
196   free(outputCtx->neighborlist);
197   PetscFunctionReturn(0);
198 }
199 
200 #undef __FUNCT__
201 #define __FUNCT__ "DMPlexGenerate_Triangle"
202 PetscErrorCode DMPlexGenerate_Triangle(DM boundary, PetscBool interpolate, DM *dm)
203 {
204   MPI_Comm             comm;
205   DM_Plex             *mesh             = (DM_Plex *) boundary->data;
206   PetscInt             dim              = 2;
207   const PetscBool      createConvexHull = PETSC_FALSE;
208   const PetscBool      constrained      = PETSC_FALSE;
209   struct triangulateio in;
210   struct triangulateio out;
211   PetscInt             vStart, vEnd, v, eStart, eEnd, e;
212   PetscMPIInt          rank;
213   PetscErrorCode       ierr;
214 
215   PetscFunctionBegin;
216   ierr = PetscObjectGetComm((PetscObject)boundary,&comm);CHKERRQ(ierr);
217   ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
218   ierr = InitInput_Triangle(&in);CHKERRQ(ierr);
219   ierr = InitOutput_Triangle(&out);CHKERRQ(ierr);
220   ierr = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);CHKERRQ(ierr);
221 
222   in.numberofpoints = vEnd - vStart;
223   if (in.numberofpoints > 0) {
224     PetscSection coordSection;
225     Vec          coordinates;
226     PetscScalar *array;
227 
228     ierr = PetscMalloc1(in.numberofpoints*dim, &in.pointlist);CHKERRQ(ierr);
229     ierr = PetscMalloc1(in.numberofpoints, &in.pointmarkerlist);CHKERRQ(ierr);
230     ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr);
231     ierr = DMGetCoordinateSection(boundary, &coordSection);CHKERRQ(ierr);
232     ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
233     for (v = vStart; v < vEnd; ++v) {
234       const PetscInt idx = v - vStart;
235       PetscInt       off, d;
236 
237       ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
238       for (d = 0; d < dim; ++d) {
239         in.pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
240       }
241       ierr = DMPlexGetLabelValue(boundary, "marker", v, &in.pointmarkerlist[idx]);CHKERRQ(ierr);
242     }
243     ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
244   }
245   ierr  = DMPlexGetHeightStratum(boundary, 0, &eStart, &eEnd);CHKERRQ(ierr);
246   in.numberofsegments = eEnd - eStart;
247   if (in.numberofsegments > 0) {
248     ierr = PetscMalloc1(in.numberofsegments*2, &in.segmentlist);CHKERRQ(ierr);
249     ierr = PetscMalloc1(in.numberofsegments, &in.segmentmarkerlist);CHKERRQ(ierr);
250     for (e = eStart; e < eEnd; ++e) {
251       const PetscInt  idx = e - eStart;
252       const PetscInt *cone;
253 
254       ierr = DMPlexGetCone(boundary, e, &cone);CHKERRQ(ierr);
255 
256       in.segmentlist[idx*2+0] = cone[0] - vStart;
257       in.segmentlist[idx*2+1] = cone[1] - vStart;
258 
259       ierr = DMPlexGetLabelValue(boundary, "marker", e, &in.segmentmarkerlist[idx]);CHKERRQ(ierr);
260     }
261   }
262 #if 0 /* Do not currently support holes */
263   PetscReal *holeCoords;
264   PetscInt   h, d;
265 
266   ierr = DMPlexGetHoles(boundary, &in.numberofholes, &holeCords);CHKERRQ(ierr);
267   if (in.numberofholes > 0) {
268     ierr = PetscMalloc1(in.numberofholes*dim, &in.holelist);CHKERRQ(ierr);
269     for (h = 0; h < in.numberofholes; ++h) {
270       for (d = 0; d < dim; ++d) {
271         in.holelist[h*dim+d] = holeCoords[h*dim+d];
272       }
273     }
274   }
275 #endif
276   if (!rank) {
277     char args[32];
278 
279     /* Take away 'Q' for verbose output */
280     ierr = PetscStrcpy(args, "pqezQ");CHKERRQ(ierr);
281     if (createConvexHull)   {ierr = PetscStrcat(args, "c");CHKERRQ(ierr);}
282     if (constrained)        {ierr = PetscStrcpy(args, "zepDQ");CHKERRQ(ierr);}
283     if (mesh->triangleOpts) {triangulate(mesh->triangleOpts, &in, &out, NULL);}
284     else                    {triangulate(args, &in, &out, NULL);}
285   }
286   ierr = PetscFree(in.pointlist);CHKERRQ(ierr);
287   ierr = PetscFree(in.pointmarkerlist);CHKERRQ(ierr);
288   ierr = PetscFree(in.segmentlist);CHKERRQ(ierr);
289   ierr = PetscFree(in.segmentmarkerlist);CHKERRQ(ierr);
290   ierr = PetscFree(in.holelist);CHKERRQ(ierr);
291 
292   {
293     const PetscInt numCorners  = 3;
294     const PetscInt numCells    = out.numberoftriangles;
295     const PetscInt numVertices = out.numberofpoints;
296     const int     *cells      = out.trianglelist;
297     const double  *meshCoords = out.pointlist;
298 
299     ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dm);CHKERRQ(ierr);
300     /* Set labels */
301     for (v = 0; v < numVertices; ++v) {
302       if (out.pointmarkerlist[v]) {
303         ierr = DMPlexSetLabelValue(*dm, "marker", v+numCells, out.pointmarkerlist[v]);CHKERRQ(ierr);
304       }
305     }
306     if (interpolate) {
307       for (e = 0; e < out.numberofedges; e++) {
308         if (out.edgemarkerlist[e]) {
309           const PetscInt  vertices[2] = {out.edgelist[e*2+0]+numCells, out.edgelist[e*2+1]+numCells};
310           const PetscInt *edges;
311           PetscInt        numEdges;
312 
313           ierr = DMPlexGetJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
314           if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
315           ierr = DMPlexSetLabelValue(*dm, "marker", edges[0], out.edgemarkerlist[e]);CHKERRQ(ierr);
316           ierr = DMPlexRestoreJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
317         }
318       }
319     }
320     ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
321   }
322 #if 0 /* Do not currently support holes */
323   ierr = DMPlexCopyHoles(*dm, boundary);CHKERRQ(ierr);
324 #endif
325   ierr = FiniOutput_Triangle(&out);CHKERRQ(ierr);
326   PetscFunctionReturn(0);
327 }
328 
329 #undef __FUNCT__
330 #define __FUNCT__ "DMPlexRefine_Triangle"
331 PetscErrorCode DMPlexRefine_Triangle(DM dm, double *maxVolumes, DM *dmRefined)
332 {
333   MPI_Comm             comm;
334   PetscInt             dim  = 2;
335   struct triangulateio in;
336   struct triangulateio out;
337   PetscInt             vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal;
338   PetscMPIInt          rank;
339   PetscErrorCode       ierr;
340 
341   PetscFunctionBegin;
342   ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
343   ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
344   ierr = InitInput_Triangle(&in);CHKERRQ(ierr);
345   ierr = InitOutput_Triangle(&out);CHKERRQ(ierr);
346   ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
347   ierr = MPI_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
348   ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
349 
350   in.numberofpoints = vEnd - vStart;
351   if (in.numberofpoints > 0) {
352     PetscSection coordSection;
353     Vec          coordinates;
354     PetscScalar *array;
355 
356     ierr = PetscMalloc1(in.numberofpoints*dim, &in.pointlist);CHKERRQ(ierr);
357     ierr = PetscMalloc1(in.numberofpoints, &in.pointmarkerlist);CHKERRQ(ierr);
358     ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
359     ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
360     ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
361     for (v = vStart; v < vEnd; ++v) {
362       const PetscInt idx = v - vStart;
363       PetscInt       off, d;
364 
365       ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
366       for (d = 0; d < dim; ++d) {
367         in.pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
368       }
369       ierr = DMPlexGetLabelValue(dm, "marker", v, &in.pointmarkerlist[idx]);CHKERRQ(ierr);
370     }
371     ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
372   }
373   ierr  = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
374 
375   in.numberofcorners   = 3;
376   in.numberoftriangles = cEnd - cStart;
377 
378   in.trianglearealist  = (double*) maxVolumes;
379   if (in.numberoftriangles > 0) {
380     ierr = PetscMalloc1(in.numberoftriangles*in.numberofcorners, &in.trianglelist);CHKERRQ(ierr);
381     for (c = cStart; c < cEnd; ++c) {
382       const PetscInt idx      = c - cStart;
383       PetscInt      *closure = NULL;
384       PetscInt       closureSize;
385 
386       ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
387       if ((closureSize != 4) && (closureSize != 7)) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Mesh has cell which is not a triangle, %D vertices in closure", closureSize);
388       for (v = 0; v < 3; ++v) {
389         in.trianglelist[idx*in.numberofcorners + v] = closure[(v+closureSize-3)*2] - vStart;
390       }
391       ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
392     }
393   }
394   /* TODO: Segment markers are missing on input */
395 #if 0 /* Do not currently support holes */
396   PetscReal *holeCoords;
397   PetscInt   h, d;
398 
399   ierr = DMPlexGetHoles(boundary, &in.numberofholes, &holeCords);CHKERRQ(ierr);
400   if (in.numberofholes > 0) {
401     ierr = PetscMalloc1(in.numberofholes*dim, &in.holelist);CHKERRQ(ierr);
402     for (h = 0; h < in.numberofholes; ++h) {
403       for (d = 0; d < dim; ++d) {
404         in.holelist[h*dim+d] = holeCoords[h*dim+d];
405       }
406     }
407   }
408 #endif
409   if (!rank) {
410     char args[32];
411 
412     /* Take away 'Q' for verbose output */
413     ierr = PetscStrcpy(args, "pqezQra");CHKERRQ(ierr);
414     triangulate(args, &in, &out, NULL);
415   }
416   ierr = PetscFree(in.pointlist);CHKERRQ(ierr);
417   ierr = PetscFree(in.pointmarkerlist);CHKERRQ(ierr);
418   ierr = PetscFree(in.segmentlist);CHKERRQ(ierr);
419   ierr = PetscFree(in.segmentmarkerlist);CHKERRQ(ierr);
420   ierr = PetscFree(in.trianglelist);CHKERRQ(ierr);
421 
422   {
423     const PetscInt numCorners  = 3;
424     const PetscInt numCells    = out.numberoftriangles;
425     const PetscInt numVertices = out.numberofpoints;
426     const int     *cells      = out.trianglelist;
427     const double  *meshCoords = out.pointlist;
428     PetscBool      interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE;
429 
430     ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dmRefined);CHKERRQ(ierr);
431     /* Set labels */
432     for (v = 0; v < numVertices; ++v) {
433       if (out.pointmarkerlist[v]) {
434         ierr = DMPlexSetLabelValue(*dmRefined, "marker", v+numCells, out.pointmarkerlist[v]);CHKERRQ(ierr);
435       }
436     }
437     if (interpolate) {
438       PetscInt e;
439 
440       for (e = 0; e < out.numberofedges; e++) {
441         if (out.edgemarkerlist[e]) {
442           const PetscInt  vertices[2] = {out.edgelist[e*2+0]+numCells, out.edgelist[e*2+1]+numCells};
443           const PetscInt *edges;
444           PetscInt        numEdges;
445 
446           ierr = DMPlexGetJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
447           if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
448           ierr = DMPlexSetLabelValue(*dmRefined, "marker", edges[0], out.edgemarkerlist[e]);CHKERRQ(ierr);
449           ierr = DMPlexRestoreJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
450         }
451       }
452     }
453     ierr = DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE);CHKERRQ(ierr);
454   }
455 #if 0 /* Do not currently support holes */
456   ierr = DMPlexCopyHoles(*dm, boundary);CHKERRQ(ierr);
457 #endif
458   ierr = FiniOutput_Triangle(&out);CHKERRQ(ierr);
459   PetscFunctionReturn(0);
460 }
461 #endif /* PETSC_HAVE_TRIANGLE */
462 
463 #if defined(PETSC_HAVE_TETGEN)
464 #include <tetgen.h>
465 #undef __FUNCT__
466 #define __FUNCT__ "DMPlexGenerate_Tetgen"
467 PetscErrorCode DMPlexGenerate_Tetgen(DM boundary, PetscBool interpolate, DM *dm)
468 {
469   MPI_Comm       comm;
470   const PetscInt dim  = 3;
471   ::tetgenio     in;
472   ::tetgenio     out;
473   PetscInt       vStart, vEnd, v, fStart, fEnd, f;
474   PetscMPIInt    rank;
475   PetscErrorCode ierr;
476 
477   PetscFunctionBegin;
478   ierr              = PetscObjectGetComm((PetscObject)boundary,&comm);CHKERRQ(ierr);
479   ierr              = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
480   ierr              = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);CHKERRQ(ierr);
481   in.numberofpoints = vEnd - vStart;
482   if (in.numberofpoints > 0) {
483     PetscSection coordSection;
484     Vec          coordinates;
485     PetscScalar *array;
486 
487     in.pointlist       = new double[in.numberofpoints*dim];
488     in.pointmarkerlist = new int[in.numberofpoints];
489 
490     ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr);
491     ierr = DMGetCoordinateSection(boundary, &coordSection);CHKERRQ(ierr);
492     ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
493     for (v = vStart; v < vEnd; ++v) {
494       const PetscInt idx = v - vStart;
495       PetscInt       off, d;
496 
497       ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
498       for (d = 0; d < dim; ++d) in.pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
499       ierr = DMPlexGetLabelValue(boundary, "marker", v, &in.pointmarkerlist[idx]);CHKERRQ(ierr);
500     }
501     ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
502   }
503   ierr  = DMPlexGetHeightStratum(boundary, 0, &fStart, &fEnd);CHKERRQ(ierr);
504 
505   in.numberoffacets = fEnd - fStart;
506   if (in.numberoffacets > 0) {
507     in.facetlist       = new tetgenio::facet[in.numberoffacets];
508     in.facetmarkerlist = new int[in.numberoffacets];
509     for (f = fStart; f < fEnd; ++f) {
510       const PetscInt idx     = f - fStart;
511       PetscInt      *points = NULL, numPoints, p, numVertices = 0, v;
512 
513       in.facetlist[idx].numberofpolygons = 1;
514       in.facetlist[idx].polygonlist      = new tetgenio::polygon[in.facetlist[idx].numberofpolygons];
515       in.facetlist[idx].numberofholes    = 0;
516       in.facetlist[idx].holelist         = NULL;
517 
518       ierr = DMPlexGetTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
519       for (p = 0; p < numPoints*2; p += 2) {
520         const PetscInt point = points[p];
521         if ((point >= vStart) && (point < vEnd)) points[numVertices++] = point;
522       }
523 
524       tetgenio::polygon *poly = in.facetlist[idx].polygonlist;
525       poly->numberofvertices = numVertices;
526       poly->vertexlist       = new int[poly->numberofvertices];
527       for (v = 0; v < numVertices; ++v) {
528         const PetscInt vIdx = points[v] - vStart;
529         poly->vertexlist[v] = vIdx;
530       }
531       ierr = DMPlexGetLabelValue(boundary, "marker", f, &in.facetmarkerlist[idx]);CHKERRQ(ierr);
532       ierr = DMPlexRestoreTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
533     }
534   }
535   if (!rank) {
536     char args[32];
537 
538     /* Take away 'Q' for verbose output */
539     ierr = PetscStrcpy(args, "pqezQ");CHKERRQ(ierr);
540     if (mesh->tetgenOpts) {::tetrahedralize(mesh->tetgenOpts, &in, &out);}
541     else                  {::tetrahedralize(args, &in, &out);}
542   }
543   {
544     const PetscInt numCorners  = 4;
545     const PetscInt numCells    = out.numberoftetrahedra;
546     const PetscInt numVertices = out.numberofpoints;
547     const double   *meshCoords = out.pointlist;
548     int            *cells      = out.tetrahedronlist;
549 
550     ierr = DMPlexInvertCells_Internal(dim, numCells, numCorners, cells);CHKERRQ(ierr);
551     ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dm);CHKERRQ(ierr);
552     /* Set labels */
553     for (v = 0; v < numVertices; ++v) {
554       if (out.pointmarkerlist[v]) {
555         ierr = DMPlexSetLabelValue(*dm, "marker", v+numCells, out.pointmarkerlist[v]);CHKERRQ(ierr);
556       }
557     }
558     if (interpolate) {
559       PetscInt e;
560 
561       for (e = 0; e < out.numberofedges; e++) {
562         if (out.edgemarkerlist[e]) {
563           const PetscInt  vertices[2] = {out.edgelist[e*2+0]+numCells, out.edgelist[e*2+1]+numCells};
564           const PetscInt *edges;
565           PetscInt        numEdges;
566 
567           ierr = DMPlexGetJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
568           if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
569           ierr = DMPlexSetLabelValue(*dm, "marker", edges[0], out.edgemarkerlist[e]);CHKERRQ(ierr);
570           ierr = DMPlexRestoreJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
571         }
572       }
573       for (f = 0; f < out.numberoftrifaces; f++) {
574         if (out.trifacemarkerlist[f]) {
575           const PetscInt  vertices[3] = {out.trifacelist[f*3+0]+numCells, out.trifacelist[f*3+1]+numCells, out.trifacelist[f*3+2]+numCells};
576           const PetscInt *faces;
577           PetscInt        numFaces;
578 
579           ierr = DMPlexGetJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
580           if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
581           ierr = DMPlexSetLabelValue(*dm, "marker", faces[0], out.trifacemarkerlist[f]);CHKERRQ(ierr);
582           ierr = DMPlexRestoreJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
583         }
584       }
585     }
586     ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
587   }
588   PetscFunctionReturn(0);
589 }
590 
591 #undef __FUNCT__
592 #define __FUNCT__ "DMPlexRefine_Tetgen"
593 PetscErrorCode DMPlexRefine_Tetgen(DM dm, double *maxVolumes, DM *dmRefined)
594 {
595   MPI_Comm       comm;
596   const PetscInt dim  = 3;
597   ::tetgenio     in;
598   ::tetgenio     out;
599   PetscInt       vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal;
600   PetscMPIInt    rank;
601   PetscErrorCode ierr;
602 
603   PetscFunctionBegin;
604   ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
605   ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
606   ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
607   ierr = MPI_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
608   ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
609 
610   in.numberofpoints = vEnd - vStart;
611   if (in.numberofpoints > 0) {
612     PetscSection coordSection;
613     Vec          coordinates;
614     PetscScalar *array;
615 
616     in.pointlist       = new double[in.numberofpoints*dim];
617     in.pointmarkerlist = new int[in.numberofpoints];
618 
619     ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
620     ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
621     ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
622     for (v = vStart; v < vEnd; ++v) {
623       const PetscInt idx = v - vStart;
624       PetscInt       off, d;
625 
626       ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
627       for (d = 0; d < dim; ++d) in.pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
628       ierr = DMPlexGetLabelValue(dm, "marker", v, &in.pointmarkerlist[idx]);CHKERRQ(ierr);
629     }
630     ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
631   }
632   ierr  = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
633 
634   in.numberofcorners       = 4;
635   in.numberoftetrahedra    = cEnd - cStart;
636   in.tetrahedronvolumelist = (double*) maxVolumes;
637   if (in.numberoftetrahedra > 0) {
638     in.tetrahedronlist = new int[in.numberoftetrahedra*in.numberofcorners];
639     for (c = cStart; c < cEnd; ++c) {
640       const PetscInt idx      = c - cStart;
641       PetscInt      *closure = NULL;
642       PetscInt       closureSize;
643 
644       ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
645       if ((closureSize != 5) && (closureSize != 15)) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Mesh has cell which is not a tetrahedron, %D vertices in closure", closureSize);
646       for (v = 0; v < 4; ++v) {
647         in.tetrahedronlist[idx*in.numberofcorners + v] = closure[(v+closureSize-4)*2] - vStart;
648       }
649       ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
650     }
651   }
652   /* TODO: Put in boundary faces with markers */
653   if (!rank) {
654     char args[32];
655 
656     /* Take away 'Q' for verbose output */
657     /*ierr = PetscStrcpy(args, "qezQra");CHKERRQ(ierr); */
658     ierr = PetscStrcpy(args, "qezraVVVV");CHKERRQ(ierr);
659     ::tetrahedralize(args, &in, &out);
660   }
661   in.tetrahedronvolumelist = NULL;
662 
663   {
664     const PetscInt numCorners  = 4;
665     const PetscInt numCells    = out.numberoftetrahedra;
666     const PetscInt numVertices = out.numberofpoints;
667     const double   *meshCoords = out.pointlist;
668     int            *cells      = out.tetrahedronlist;
669 
670     PetscBool      interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE;
671 
672     ierr = DMPlexInvertCells_Internal(dim, numCells, numCorners, cells);CHKERRQ(ierr);
673     ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dmRefined);CHKERRQ(ierr);
674     /* Set labels */
675     for (v = 0; v < numVertices; ++v) {
676       if (out.pointmarkerlist[v]) {
677         ierr = DMPlexSetLabelValue(*dmRefined, "marker", v+numCells, out.pointmarkerlist[v]);CHKERRQ(ierr);
678       }
679     }
680     if (interpolate) {
681       PetscInt e, f;
682 
683       for (e = 0; e < out.numberofedges; e++) {
684         if (out.edgemarkerlist[e]) {
685           const PetscInt  vertices[2] = {out.edgelist[e*2+0]+numCells, out.edgelist[e*2+1]+numCells};
686           const PetscInt *edges;
687           PetscInt        numEdges;
688 
689           ierr = DMPlexGetJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
690           if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
691           ierr = DMPlexSetLabelValue(*dmRefined, "marker", edges[0], out.edgemarkerlist[e]);CHKERRQ(ierr);
692           ierr = DMPlexRestoreJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
693         }
694       }
695       for (f = 0; f < out.numberoftrifaces; f++) {
696         if (out.trifacemarkerlist[f]) {
697           const PetscInt  vertices[3] = {out.trifacelist[f*3+0]+numCells, out.trifacelist[f*3+1]+numCells, out.trifacelist[f*3+2]+numCells};
698           const PetscInt *faces;
699           PetscInt        numFaces;
700 
701           ierr = DMPlexGetJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
702           if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
703           ierr = DMPlexSetLabelValue(*dmRefined, "marker", faces[0], out.trifacemarkerlist[f]);CHKERRQ(ierr);
704           ierr = DMPlexRestoreJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
705         }
706       }
707     }
708     ierr = DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE);CHKERRQ(ierr);
709   }
710   PetscFunctionReturn(0);
711 }
712 #endif /* PETSC_HAVE_TETGEN */
713 
714 #if defined(PETSC_HAVE_CTETGEN)
715 #include <ctetgen.h>
716 
717 #undef __FUNCT__
718 #define __FUNCT__ "DMPlexGenerate_CTetgen"
719 PetscErrorCode DMPlexGenerate_CTetgen(DM boundary, PetscBool interpolate, DM *dm)
720 {
721   MPI_Comm       comm;
722   const PetscInt dim  = 3;
723   PLC           *in, *out;
724   PetscInt       verbose = 0, vStart, vEnd, v, fStart, fEnd, f;
725   PetscMPIInt    rank;
726   PetscErrorCode ierr;
727 
728   PetscFunctionBegin;
729   ierr = PetscObjectGetComm((PetscObject)boundary,&comm);CHKERRQ(ierr);
730   ierr = PetscOptionsGetInt(((PetscObject) boundary)->prefix, "-ctetgen_verbose", &verbose, NULL);CHKERRQ(ierr);
731   ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
732   ierr = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);CHKERRQ(ierr);
733   ierr = PLCCreate(&in);CHKERRQ(ierr);
734   ierr = PLCCreate(&out);CHKERRQ(ierr);
735 
736   in->numberofpoints = vEnd - vStart;
737   if (in->numberofpoints > 0) {
738     PetscSection coordSection;
739     Vec          coordinates;
740     PetscScalar *array;
741 
742     ierr = PetscMalloc1(in->numberofpoints*dim, &in->pointlist);CHKERRQ(ierr);
743     ierr = PetscMalloc1(in->numberofpoints,       &in->pointmarkerlist);CHKERRQ(ierr);
744     ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr);
745     ierr = DMGetCoordinateSection(boundary, &coordSection);CHKERRQ(ierr);
746     ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
747     for (v = vStart; v < vEnd; ++v) {
748       const PetscInt idx = v - vStart;
749       PetscInt       off, d, m;
750 
751       ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
752       for (d = 0; d < dim; ++d) {
753         in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
754       }
755       ierr = DMPlexGetLabelValue(boundary, "marker", v, &m);CHKERRQ(ierr);
756 
757       in->pointmarkerlist[idx] = (int) m;
758     }
759     ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
760   }
761   ierr  = DMPlexGetHeightStratum(boundary, 0, &fStart, &fEnd);CHKERRQ(ierr);
762 
763   in->numberoffacets = fEnd - fStart;
764   if (in->numberoffacets > 0) {
765     ierr = PetscMalloc1(in->numberoffacets, &in->facetlist);CHKERRQ(ierr);
766     ierr = PetscMalloc1(in->numberoffacets,   &in->facetmarkerlist);CHKERRQ(ierr);
767     for (f = fStart; f < fEnd; ++f) {
768       const PetscInt idx     = f - fStart;
769       PetscInt      *points = NULL, numPoints, p, numVertices = 0, v, m;
770       polygon       *poly;
771 
772       in->facetlist[idx].numberofpolygons = 1;
773 
774       ierr = PetscMalloc1(in->facetlist[idx].numberofpolygons, &in->facetlist[idx].polygonlist);CHKERRQ(ierr);
775 
776       in->facetlist[idx].numberofholes    = 0;
777       in->facetlist[idx].holelist         = NULL;
778 
779       ierr = DMPlexGetTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
780       for (p = 0; p < numPoints*2; p += 2) {
781         const PetscInt point = points[p];
782         if ((point >= vStart) && (point < vEnd)) points[numVertices++] = point;
783       }
784 
785       poly                   = in->facetlist[idx].polygonlist;
786       poly->numberofvertices = numVertices;
787       ierr                   = PetscMalloc1(poly->numberofvertices, &poly->vertexlist);CHKERRQ(ierr);
788       for (v = 0; v < numVertices; ++v) {
789         const PetscInt vIdx = points[v] - vStart;
790         poly->vertexlist[v] = vIdx;
791       }
792       ierr                     = DMPlexGetLabelValue(boundary, "marker", f, &m);CHKERRQ(ierr);
793       in->facetmarkerlist[idx] = (int) m;
794       ierr                     = DMPlexRestoreTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
795     }
796   }
797   if (!rank) {
798     TetGenOpts t;
799 
800     ierr        = TetGenOptsInitialize(&t);CHKERRQ(ierr);
801     t.in        = boundary; /* Should go away */
802     t.plc       = 1;
803     t.quality   = 1;
804     t.edgesout  = 1;
805     t.zeroindex = 1;
806     t.quiet     = 1;
807     t.verbose   = verbose;
808     ierr        = TetGenCheckOpts(&t);CHKERRQ(ierr);
809     ierr        = TetGenTetrahedralize(&t, in, out);CHKERRQ(ierr);
810   }
811   {
812     const PetscInt numCorners  = 4;
813     const PetscInt numCells    = out->numberoftetrahedra;
814     const PetscInt numVertices = out->numberofpoints;
815     const double   *meshCoords = out->pointlist;
816     int            *cells      = out->tetrahedronlist;
817 
818     ierr = DMPlexInvertCells_Internal(dim, numCells, numCorners, cells);CHKERRQ(ierr);
819     ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dm);CHKERRQ(ierr);
820     /* Set labels */
821     for (v = 0; v < numVertices; ++v) {
822       if (out->pointmarkerlist[v]) {
823         ierr = DMPlexSetLabelValue(*dm, "marker", v+numCells, out->pointmarkerlist[v]);CHKERRQ(ierr);
824       }
825     }
826     if (interpolate) {
827       PetscInt e;
828 
829       for (e = 0; e < out->numberofedges; e++) {
830         if (out->edgemarkerlist[e]) {
831           const PetscInt  vertices[2] = {out->edgelist[e*2+0]+numCells, out->edgelist[e*2+1]+numCells};
832           const PetscInt *edges;
833           PetscInt        numEdges;
834 
835           ierr = DMPlexGetJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
836           if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
837           ierr = DMPlexSetLabelValue(*dm, "marker", edges[0], out->edgemarkerlist[e]);CHKERRQ(ierr);
838           ierr = DMPlexRestoreJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
839         }
840       }
841       for (f = 0; f < out->numberoftrifaces; f++) {
842         if (out->trifacemarkerlist[f]) {
843           const PetscInt  vertices[3] = {out->trifacelist[f*3+0]+numCells, out->trifacelist[f*3+1]+numCells, out->trifacelist[f*3+2]+numCells};
844           const PetscInt *faces;
845           PetscInt        numFaces;
846 
847           ierr = DMPlexGetFullJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
848           if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
849           ierr = DMPlexSetLabelValue(*dm, "marker", faces[0], out->trifacemarkerlist[f]);CHKERRQ(ierr);
850           ierr = DMPlexRestoreJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
851         }
852       }
853     }
854     ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
855   }
856 
857   ierr = PLCDestroy(&in);CHKERRQ(ierr);
858   ierr = PLCDestroy(&out);CHKERRQ(ierr);
859   PetscFunctionReturn(0);
860 }
861 
862 #undef __FUNCT__
863 #define __FUNCT__ "DMPlexRefine_CTetgen"
864 PetscErrorCode DMPlexRefine_CTetgen(DM dm, PetscReal *maxVolumes, DM *dmRefined)
865 {
866   MPI_Comm       comm;
867   const PetscInt dim  = 3;
868   PLC           *in, *out;
869   PetscInt       verbose = 0, vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal;
870   PetscMPIInt    rank;
871   PetscErrorCode ierr;
872 
873   PetscFunctionBegin;
874   ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
875   ierr = PetscOptionsGetInt(((PetscObject) dm)->prefix, "-ctetgen_verbose", &verbose, NULL);CHKERRQ(ierr);
876   ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
877   ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
878   ierr = MPI_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
879   ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
880   ierr = PLCCreate(&in);CHKERRQ(ierr);
881   ierr = PLCCreate(&out);CHKERRQ(ierr);
882 
883   in->numberofpoints = vEnd - vStart;
884   if (in->numberofpoints > 0) {
885     PetscSection coordSection;
886     Vec          coordinates;
887     PetscScalar *array;
888 
889     ierr = PetscMalloc1(in->numberofpoints*dim, &in->pointlist);CHKERRQ(ierr);
890     ierr = PetscMalloc1(in->numberofpoints,       &in->pointmarkerlist);CHKERRQ(ierr);
891     ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
892     ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
893     ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
894     for (v = vStart; v < vEnd; ++v) {
895       const PetscInt idx = v - vStart;
896       PetscInt       off, d, m;
897 
898       ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
899       for (d = 0; d < dim; ++d) {
900         in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
901       }
902       ierr = DMPlexGetLabelValue(dm, "marker", v, &m);CHKERRQ(ierr);
903 
904       in->pointmarkerlist[idx] = (int) m;
905     }
906     ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
907   }
908   ierr  = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
909 
910   in->numberofcorners       = 4;
911   in->numberoftetrahedra    = cEnd - cStart;
912   in->tetrahedronvolumelist = maxVolumes;
913   if (in->numberoftetrahedra > 0) {
914     ierr = PetscMalloc1(in->numberoftetrahedra*in->numberofcorners, &in->tetrahedronlist);CHKERRQ(ierr);
915     for (c = cStart; c < cEnd; ++c) {
916       const PetscInt idx      = c - cStart;
917       PetscInt      *closure = NULL;
918       PetscInt       closureSize;
919 
920       ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
921       if ((closureSize != 5) && (closureSize != 15)) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Mesh has cell which is not a tetrahedron, %D vertices in closure", closureSize);
922       for (v = 0; v < 4; ++v) {
923         in->tetrahedronlist[idx*in->numberofcorners + v] = closure[(v+closureSize-4)*2] - vStart;
924       }
925       ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
926     }
927   }
928   if (!rank) {
929     TetGenOpts t;
930 
931     ierr = TetGenOptsInitialize(&t);CHKERRQ(ierr);
932 
933     t.in        = dm; /* Should go away */
934     t.refine    = 1;
935     t.varvolume = 1;
936     t.quality   = 1;
937     t.edgesout  = 1;
938     t.zeroindex = 1;
939     t.quiet     = 1;
940     t.verbose   = verbose; /* Change this */
941 
942     ierr = TetGenCheckOpts(&t);CHKERRQ(ierr);
943     ierr = TetGenTetrahedralize(&t, in, out);CHKERRQ(ierr);
944   }
945   {
946     const PetscInt numCorners  = 4;
947     const PetscInt numCells    = out->numberoftetrahedra;
948     const PetscInt numVertices = out->numberofpoints;
949     const double   *meshCoords = out->pointlist;
950     int            *cells      = out->tetrahedronlist;
951     PetscBool      interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE;
952 
953     ierr = DMPlexInvertCells_Internal(dim, numCells, numCorners, cells);CHKERRQ(ierr);
954     ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dmRefined);CHKERRQ(ierr);
955     /* Set labels */
956     for (v = 0; v < numVertices; ++v) {
957       if (out->pointmarkerlist[v]) {
958         ierr = DMPlexSetLabelValue(*dmRefined, "marker", v+numCells, out->pointmarkerlist[v]);CHKERRQ(ierr);
959       }
960     }
961     if (interpolate) {
962       PetscInt e, f;
963 
964       for (e = 0; e < out->numberofedges; e++) {
965         if (out->edgemarkerlist[e]) {
966           const PetscInt  vertices[2] = {out->edgelist[e*2+0]+numCells, out->edgelist[e*2+1]+numCells};
967           const PetscInt *edges;
968           PetscInt        numEdges;
969 
970           ierr = DMPlexGetJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
971           if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
972           ierr = DMPlexSetLabelValue(*dmRefined, "marker", edges[0], out->edgemarkerlist[e]);CHKERRQ(ierr);
973           ierr = DMPlexRestoreJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
974         }
975       }
976       for (f = 0; f < out->numberoftrifaces; f++) {
977         if (out->trifacemarkerlist[f]) {
978           const PetscInt  vertices[3] = {out->trifacelist[f*3+0]+numCells, out->trifacelist[f*3+1]+numCells, out->trifacelist[f*3+2]+numCells};
979           const PetscInt *faces;
980           PetscInt        numFaces;
981 
982           ierr = DMPlexGetFullJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
983           if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
984           ierr = DMPlexSetLabelValue(*dmRefined, "marker", faces[0], out->trifacemarkerlist[f]);CHKERRQ(ierr);
985           ierr = DMPlexRestoreJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
986         }
987       }
988     }
989     ierr = DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE);CHKERRQ(ierr);
990   }
991   ierr = PLCDestroy(&in);CHKERRQ(ierr);
992   ierr = PLCDestroy(&out);CHKERRQ(ierr);
993   PetscFunctionReturn(0);
994 }
995 #endif /* PETSC_HAVE_CTETGEN */
996 
997 #undef __FUNCT__
998 #define __FUNCT__ "DMPlexGenerate"
999 /*@C
1000   DMPlexGenerate - Generates a mesh.
1001 
1002   Not Collective
1003 
1004   Input Parameters:
1005 + boundary - The DMPlex boundary object
1006 . name - The mesh generation package name
1007 - interpolate - Flag to create intermediate mesh elements
1008 
1009   Output Parameter:
1010 . mesh - The DMPlex object
1011 
1012   Level: intermediate
1013 
1014 .keywords: mesh, elements
1015 .seealso: DMPlexCreate(), DMRefine()
1016 @*/
1017 PetscErrorCode DMPlexGenerate(DM boundary, const char name[], PetscBool interpolate, DM *mesh)
1018 {
1019   PetscInt       dim;
1020   char           genname[1024];
1021   PetscBool      isTriangle = PETSC_FALSE, isTetgen = PETSC_FALSE, isCTetgen = PETSC_FALSE, flg;
1022   PetscErrorCode ierr;
1023 
1024   PetscFunctionBegin;
1025   PetscValidHeaderSpecific(boundary, DM_CLASSID, 1);
1026   PetscValidLogicalCollectiveBool(boundary, interpolate, 2);
1027   ierr = DMGetDimension(boundary, &dim);CHKERRQ(ierr);
1028   ierr = PetscOptionsGetString(((PetscObject) boundary)->prefix, "-dm_plex_generator", genname, 1024, &flg);CHKERRQ(ierr);
1029   if (flg) name = genname;
1030   if (name) {
1031     ierr = PetscStrcmp(name, "triangle", &isTriangle);CHKERRQ(ierr);
1032     ierr = PetscStrcmp(name, "tetgen",   &isTetgen);CHKERRQ(ierr);
1033     ierr = PetscStrcmp(name, "ctetgen",  &isCTetgen);CHKERRQ(ierr);
1034   }
1035   switch (dim) {
1036   case 1:
1037     if (!name || isTriangle) {
1038 #if defined(PETSC_HAVE_TRIANGLE)
1039       ierr = DMPlexGenerate_Triangle(boundary, interpolate, mesh);CHKERRQ(ierr);
1040 #else
1041       SETERRQ(PetscObjectComm((PetscObject)boundary), PETSC_ERR_SUP, "Mesh generation needs external package support.\nPlease reconfigure with --download-triangle.");
1042 #endif
1043     } else SETERRQ1(PetscObjectComm((PetscObject)boundary), PETSC_ERR_SUP, "Unknown 2D mesh generation package %s", name);
1044     break;
1045   case 2:
1046     if (!name || isCTetgen) {
1047 #if defined(PETSC_HAVE_CTETGEN)
1048       ierr = DMPlexGenerate_CTetgen(boundary, interpolate, mesh);CHKERRQ(ierr);
1049 #else
1050       SETERRQ(PetscObjectComm((PetscObject)boundary), PETSC_ERR_SUP, "CTetgen needs external package support.\nPlease reconfigure with --download-ctetgen.");
1051 #endif
1052     } else if (isTetgen) {
1053 #if defined(PETSC_HAVE_TETGEN)
1054       ierr = DMPlexGenerate_Tetgen(boundary, interpolate, mesh);CHKERRQ(ierr);
1055 #else
1056       SETERRQ(PetscObjectComm((PetscObject)boundary), PETSC_ERR_SUP, "Tetgen needs external package support.\nPlease reconfigure with --with-c-language=cxx --download-tetgen.");
1057 #endif
1058     } else SETERRQ1(PetscObjectComm((PetscObject)boundary), PETSC_ERR_SUP, "Unknown 3D mesh generation package %s", name);
1059     break;
1060   default:
1061     SETERRQ1(PetscObjectComm((PetscObject)boundary), PETSC_ERR_SUP, "Mesh generation for a dimension %d boundary is not supported.", dim);
1062   }
1063   PetscFunctionReturn(0);
1064 }
1065 
1066 #undef __FUNCT__
1067 #define __FUNCT__ "DMRefine_Plex"
1068 PetscErrorCode DMRefine_Plex(DM dm, MPI_Comm comm, DM *dmRefined)
1069 {
1070   PetscReal      refinementLimit;
1071   PetscInt       dim, cStart, cEnd;
1072   char           genname[1024], *name = NULL;
1073   PetscBool      isUniform, isTriangle = PETSC_FALSE, isTetgen = PETSC_FALSE, isCTetgen = PETSC_FALSE, flg;
1074   PetscErrorCode ierr;
1075 
1076   PetscFunctionBegin;
1077   ierr = DMPlexGetRefinementUniform(dm, &isUniform);CHKERRQ(ierr);
1078   if (isUniform) {
1079     CellRefiner cellRefiner;
1080 
1081     ierr = DMPlexGetCellRefiner_Internal(dm, &cellRefiner);CHKERRQ(ierr);
1082     ierr = DMPlexRefineUniform_Internal(dm, cellRefiner, dmRefined);CHKERRQ(ierr);
1083     ierr = DMPlexCopyBoundary(dm, *dmRefined);CHKERRQ(ierr);
1084     PetscFunctionReturn(0);
1085   }
1086   ierr = DMPlexGetRefinementLimit(dm, &refinementLimit);CHKERRQ(ierr);
1087   if (refinementLimit == 0.0) PetscFunctionReturn(0);
1088   ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
1089   ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
1090   ierr = PetscOptionsGetString(((PetscObject) dm)->prefix, "-dm_plex_generator", genname, 1024, &flg);CHKERRQ(ierr);
1091   if (flg) name = genname;
1092   if (name) {
1093     ierr = PetscStrcmp(name, "triangle", &isTriangle);CHKERRQ(ierr);
1094     ierr = PetscStrcmp(name, "tetgen",   &isTetgen);CHKERRQ(ierr);
1095     ierr = PetscStrcmp(name, "ctetgen",  &isCTetgen);CHKERRQ(ierr);
1096   }
1097   switch (dim) {
1098   case 2:
1099     if (!name || isTriangle) {
1100 #if defined(PETSC_HAVE_TRIANGLE)
1101       double  *maxVolumes;
1102       PetscInt c;
1103 
1104       ierr = PetscMalloc1((cEnd - cStart), &maxVolumes);CHKERRQ(ierr);
1105       for (c = 0; c < cEnd-cStart; ++c) maxVolumes[c] = refinementLimit;
1106       ierr = DMPlexRefine_Triangle(dm, maxVolumes, dmRefined);CHKERRQ(ierr);
1107       ierr = PetscFree(maxVolumes);CHKERRQ(ierr);
1108 #else
1109       SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Mesh refinement needs external package support.\nPlease reconfigure with --download-triangle.");
1110 #endif
1111     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unknown 2D mesh generation package %s", name);
1112     break;
1113   case 3:
1114     if (!name || isCTetgen) {
1115 #if defined(PETSC_HAVE_CTETGEN)
1116       PetscReal *maxVolumes;
1117       PetscInt   c;
1118 
1119       ierr = PetscMalloc1((cEnd - cStart), &maxVolumes);CHKERRQ(ierr);
1120       for (c = 0; c < cEnd-cStart; ++c) maxVolumes[c] = refinementLimit;
1121       ierr = DMPlexRefine_CTetgen(dm, maxVolumes, dmRefined);CHKERRQ(ierr);
1122 #else
1123       SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "CTetgen needs external package support.\nPlease reconfigure with --download-ctetgen.");
1124 #endif
1125     } else if (isTetgen) {
1126 #if defined(PETSC_HAVE_TETGEN)
1127       double  *maxVolumes;
1128       PetscInt c;
1129 
1130       ierr = PetscMalloc1((cEnd - cStart), &maxVolumes);CHKERRQ(ierr);
1131       for (c = 0; c < cEnd-cStart; ++c) maxVolumes[c] = refinementLimit;
1132       ierr = DMPlexRefine_Tetgen(dm, maxVolumes, dmRefined);CHKERRQ(ierr);
1133 #else
1134       SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Tetgen needs external package support.\nPlease reconfigure with --with-c-language=cxx --download-tetgen.");
1135 #endif
1136     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unknown 3D mesh generation package %s", name);
1137     break;
1138   default:
1139     SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Mesh refinement in dimension %d is not supported.", dim);
1140   }
1141   ierr = DMPlexCopyBoundary(dm, *dmRefined);CHKERRQ(ierr);
1142   PetscFunctionReturn(0);
1143 }
1144 
1145 #undef __FUNCT__
1146 #define __FUNCT__ "DMRefineHierarchy_Plex"
1147 PetscErrorCode DMRefineHierarchy_Plex(DM dm, PetscInt nlevels, DM dmRefined[])
1148 {
1149   DM             cdm = dm;
1150   PetscInt       r;
1151   PetscBool      isUniform;
1152   PetscErrorCode ierr;
1153 
1154   PetscFunctionBegin;
1155   ierr = DMPlexGetRefinementUniform(dm, &isUniform);CHKERRQ(ierr);
1156   if (!isUniform) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Non-uniform refinement is incompatible with the hierarchy");
1157   for (r = 0; r < nlevels; ++r) {
1158     CellRefiner cellRefiner;
1159 
1160     ierr = DMPlexGetCellRefiner_Internal(cdm, &cellRefiner);CHKERRQ(ierr);
1161     ierr = DMPlexRefineUniform_Internal(cdm, cellRefiner, &dmRefined[r]);CHKERRQ(ierr);
1162     ierr = DMPlexSetCoarseDM(dmRefined[r], cdm);CHKERRQ(ierr);
1163     cdm  = dmRefined[r];
1164   }
1165   PetscFunctionReturn(0);
1166 }
1167 
1168 #undef __FUNCT__
1169 #define __FUNCT__ "DMCoarsen_Plex"
1170 PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened)
1171 {
1172   DM_Plex       *mesh = (DM_Plex*) dm->data;
1173   PetscErrorCode ierr;
1174 
1175   PetscFunctionBegin;
1176   ierr = PetscObjectReference((PetscObject) mesh->coarseMesh);CHKERRQ(ierr);
1177   *dmCoarsened = mesh->coarseMesh;
1178   PetscFunctionReturn(0);
1179 }
1180