xref: /petsc/src/dm/impls/plex/plexcreate.c (revision 00de8ff0695ff394d09a2c60082aeaab5870b6e2) 
1 #define PETSCDM_DLL
2 #include <petsc-private/dmpleximpl.h>    /*I   "petscdmplex.h"   I*/
3 #include <petscdmda.h>
4 
5 #undef __FUNCT__
6 #define __FUNCT__ "DMSetFromOptions_Plex"
7 PetscErrorCode  DMSetFromOptions_Plex(DM dm)
8 {
9   DM_Plex        *mesh = (DM_Plex*) dm->data;
10   PetscErrorCode ierr;
11 
12   PetscFunctionBegin;
13   PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
14   ierr = PetscOptionsHead("DMPlex Options");CHKERRQ(ierr);
15   /* Handle DMPlex refinement */
16   /* Handle associated vectors */
17   /* Handle viewing */
18   ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr);
19   ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);CHKERRQ(ierr);
20   ierr = PetscOptionsTail();CHKERRQ(ierr);
21   PetscFunctionReturn(0);
22 }
23 
24 #undef __FUNCT__
25 #define __FUNCT__ "DMPlexCreateSquareBoundary"
26 /*
27  Simple square boundary:
28 
29  18--5-17--4--16
30   |     |     |
31   6    10     3
32   |     |     |
33  19-11-20--9--15
34   |     |     |
35   7     8     2
36   |     |     |
37  12--0-13--1--14
38 */
39 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
40 {
41   PetscInt       numVertices    = (edges[0]+1)*(edges[1]+1);
42   PetscInt       numEdges       = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
43   PetscInt       markerTop      = 1;
44   PetscInt       markerBottom   = 1;
45   PetscInt       markerRight    = 1;
46   PetscInt       markerLeft     = 1;
47   PetscBool      markerSeparate = PETSC_FALSE;
48   Vec            coordinates;
49   PetscSection   coordSection;
50   PetscScalar    *coords;
51   PetscInt       coordSize;
52   PetscMPIInt    rank;
53   PetscInt       v, vx, vy;
54   PetscErrorCode ierr;
55 
56   PetscFunctionBegin;
57   ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr);
58   if (markerSeparate) {
59     markerTop    = 1;
60     markerBottom = 0;
61     markerRight  = 0;
62     markerLeft   = 0;
63   }
64   ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
65   if (!rank) {
66     PetscInt e, ex, ey;
67 
68     ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr);
69     for (e = 0; e < numEdges; ++e) {
70       ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr);
71     }
72     ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
73     for (vx = 0; vx <= edges[0]; vx++) {
74       for (ey = 0; ey < edges[1]; ey++) {
75         PetscInt edge   = vx*edges[1] + ey + edges[0]*(edges[1]+1);
76         PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
77         PetscInt cone[2];
78 
79         cone[0] = vertex; cone[1] = vertex+edges[0]+1;
80         ierr    = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
81         if (vx == edges[0]) {
82           ierr = DMPlexSetLabelValue(dm, "marker", edge,    markerRight);CHKERRQ(ierr);
83           ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr);
84           if (ey == edges[1]-1) {
85             ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr);
86           }
87         } else if (vx == 0) {
88           ierr = DMPlexSetLabelValue(dm, "marker", edge,    markerLeft);CHKERRQ(ierr);
89           ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr);
90           if (ey == edges[1]-1) {
91             ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr);
92           }
93         }
94       }
95     }
96     for (vy = 0; vy <= edges[1]; vy++) {
97       for (ex = 0; ex < edges[0]; ex++) {
98         PetscInt edge   = vy*edges[0]     + ex;
99         PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
100         PetscInt cone[2];
101 
102         cone[0] = vertex; cone[1] = vertex+1;
103         ierr    = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
104         if (vy == edges[1]) {
105           ierr = DMPlexSetLabelValue(dm, "marker", edge,    markerTop);CHKERRQ(ierr);
106           ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr);
107           if (ex == edges[0]-1) {
108             ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr);
109           }
110         } else if (vy == 0) {
111           ierr = DMPlexSetLabelValue(dm, "marker", edge,    markerBottom);CHKERRQ(ierr);
112           ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr);
113           if (ex == edges[0]-1) {
114             ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr);
115           }
116         }
117       }
118     }
119   }
120   ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
121   ierr = DMPlexStratify(dm);CHKERRQ(ierr);
122   /* Build coordinates */
123   ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
124   ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr);
125   for (v = numEdges; v < numEdges+numVertices; ++v) {
126     ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
127   }
128   ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
129   ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
130   ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
131   ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
132   ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
133   ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
134   for (vy = 0; vy <= edges[1]; ++vy) {
135     for (vx = 0; vx <= edges[0]; ++vx) {
136       coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
137       coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
138     }
139   }
140   ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
141   ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
142   ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
143   PetscFunctionReturn(0);
144 }
145 
146 #undef __FUNCT__
147 #define __FUNCT__ "DMPlexCreateCubeBoundary"
148 /*
149  Simple cubic boundary:
150 
151      2-------3
152     /|      /|
153    6-------7 |
154    | |     | |
155    | 0-----|-1
156    |/      |/
157    4-------5
158 */
159 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
160 {
161   PetscInt       numVertices = (faces[0]+1)*(faces[1]+1)*(faces[2]+1);
162   PetscInt       numFaces    = 6;
163   Vec            coordinates;
164   PetscSection   coordSection;
165   PetscScalar    *coords;
166   PetscInt       coordSize;
167   PetscMPIInt    rank;
168   PetscInt       v, vx, vy, vz;
169   PetscErrorCode ierr;
170 
171   PetscFunctionBegin;
172   if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side");
173   if ((faces[0] > 1) || (faces[1] > 1) || (faces[2] > 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Currently can't handle more than 1 face per side");
174   ierr = PetscMalloc(numVertices*2 * sizeof(PetscReal), &coords);CHKERRQ(ierr);
175   ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
176   if (!rank) {
177     PetscInt f;
178 
179     ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr);
180     for (f = 0; f < numFaces; ++f) {
181       ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr);
182     }
183     ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
184     for (v = 0; v < numFaces+numVertices; ++v) {
185       ierr = DMPlexSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr);
186     }
187     { /* Side 0 (Front) */
188       PetscInt cone[4];
189       cone[0] = numFaces+4; cone[1] = numFaces+5; cone[2] = numFaces+7; cone[3] = numFaces+6;
190       ierr    = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr);
191     }
192     { /* Side 1 (Back) */
193       PetscInt cone[4];
194       cone[0] = numFaces+1; cone[1] = numFaces+0; cone[2] = numFaces+2; cone[3] = numFaces+3;
195       ierr    = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr);
196     }
197     { /* Side 2 (Bottom) */
198       PetscInt cone[4];
199       cone[0] = numFaces+0; cone[1] = numFaces+1; cone[2] = numFaces+5; cone[3] = numFaces+4;
200       ierr    = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr);
201     }
202     { /* Side 3 (Top) */
203       PetscInt cone[4];
204       cone[0] = numFaces+6; cone[1] = numFaces+7; cone[2] = numFaces+3; cone[3] = numFaces+2;
205       ierr    = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr);
206     }
207     { /* Side 4 (Left) */
208       PetscInt cone[4];
209       cone[0] = numFaces+0; cone[1] = numFaces+4; cone[2] = numFaces+6; cone[3] = numFaces+2;
210       ierr    = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr);
211     }
212     { /* Side 5 (Right) */
213       PetscInt cone[4];
214       cone[0] = numFaces+5; cone[1] = numFaces+1; cone[2] = numFaces+3; cone[3] = numFaces+7;
215       ierr    = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr);
216     }
217   }
218   ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
219   ierr = DMPlexStratify(dm);CHKERRQ(ierr);
220   /* Build coordinates */
221   ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
222   ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr);
223   for (v = numFaces; v < numFaces+numVertices; ++v) {
224     ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr);
225   }
226   ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
227   ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
228   ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
229   ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
230   ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
231   ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
232   ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
233   for (vz = 0; vz <= faces[2]; ++vz) {
234     for (vy = 0; vy <= faces[1]; ++vy) {
235       for (vx = 0; vx <= faces[0]; ++vx) {
236         coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
237         coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
238         coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
239       }
240     }
241   }
242   ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
243   ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
244   ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
245   PetscFunctionReturn(0);
246 }
247 
248 #undef __FUNCT__
249 #define __FUNCT__ "DMPlexCreateSquareMesh"
250 /*
251  Simple square mesh:
252 
253  22--8-23--9--24
254   |     |     |
255  13  2 14  3  15
256   |     |     |
257  19--6-20--7--21
258   |     |     |
259  10  0 11  1 12
260   |     |     |
261  16--4-17--5--18
262 */
263 PetscErrorCode DMPlexCreateSquareMesh(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
264 {
265   PetscInt       markerTop      = 1;
266   PetscInt       markerBottom   = 1;
267   PetscInt       markerRight    = 1;
268   PetscInt       markerLeft     = 1;
269   PetscBool      markerSeparate = PETSC_FALSE;
270   PetscMPIInt    rank;
271   PetscErrorCode ierr;
272 
273   PetscFunctionBegin;
274   ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
275   ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr);
276   if (markerSeparate) {
277     markerTop    = 3;
278     markerBottom = 1;
279     markerRight  = 2;
280     markerLeft   = 4;
281   }
282   {
283     const PetscInt numXEdges    = !rank ? edges[0]   : 0;
284     const PetscInt numYEdges    = !rank ? edges[1]   : 0;
285     const PetscInt numXVertices = !rank ? edges[0]+1 : 0;
286     const PetscInt numYVertices = !rank ? edges[1]+1 : 0;
287     const PetscInt numTotXEdges = numXEdges*numYVertices;
288     const PetscInt numTotYEdges = numYEdges*numXVertices;
289     const PetscInt numVertices  = numXVertices*numYVertices;
290     const PetscInt numEdges     = numTotXEdges + numTotYEdges;
291     const PetscInt numFaces     = numXEdges*numYEdges;
292     const PetscInt firstVertex  = numFaces;
293     const PetscInt firstXEdge   = numFaces + numVertices;
294     const PetscInt firstYEdge   = numFaces + numVertices + numTotXEdges;
295     Vec            coordinates;
296     PetscSection   coordSection;
297     PetscScalar    *coords;
298     PetscInt       coordSize;
299     PetscInt       v, vx, vy;
300     PetscInt       f, fx, fy, e, ex, ey;
301 
302     ierr = DMPlexSetChart(dm, 0, numFaces+numEdges+numVertices);CHKERRQ(ierr);
303     for (f = 0; f < numFaces; ++f) {
304       ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr);
305     }
306     for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
307       ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr);
308     }
309     ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
310     /* Build faces */
311     for (fy = 0; fy < numYEdges; fy++) {
312       for (fx = 0; fx < numXEdges; fx++) {
313         const PetscInt face    = fy*numXEdges + fx;
314         const PetscInt edgeL   = firstYEdge + fx*numYEdges + fy;
315         const PetscInt edgeB   = firstXEdge + fy*numXEdges + fx;
316         const PetscInt ornt[4] = {0,     0,               -2,              -2};
317         PetscInt       cone[4];
318 
319         cone[0] = edgeB; cone[1] = edgeL+numYEdges; cone[2] = edgeB+numXEdges; cone[3] = edgeL;
320         ierr    = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr);
321         ierr    = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr);
322       }
323     }
324     /* Build Y edges*/
325     for (vx = 0; vx < numXVertices; vx++) {
326       for (ey = 0; ey < numYEdges; ey++) {
327         const PetscInt edge   = firstYEdge  + vx*numYEdges + ey;
328         const PetscInt vertex = firstVertex + ey*numXVertices + vx;
329         PetscInt       cone[2];
330 
331         cone[0] = vertex; cone[1] = vertex+numXVertices;
332         ierr    = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
333         if (vx == numXVertices-1) {
334           ierr = DMPlexSetLabelValue(dm, "marker", edge,    markerRight);CHKERRQ(ierr);
335           ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr);
336           if (ey == numYEdges-1) {
337             ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr);
338           }
339         } else if (vx == 0) {
340           ierr = DMPlexSetLabelValue(dm, "marker", edge,    markerLeft);CHKERRQ(ierr);
341           ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr);
342           if (ey == numYEdges-1) {
343             ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr);
344           }
345         }
346       }
347     }
348     /* Build X edges*/
349     for (vy = 0; vy < numYVertices; vy++) {
350       for (ex = 0; ex < numXEdges; ex++) {
351         const PetscInt edge   = firstXEdge  + vy*numXEdges + ex;
352         const PetscInt vertex = firstVertex + vy*numXVertices + ex;
353         PetscInt       cone[2];
354 
355         cone[0] = vertex; cone[1] = vertex+1;
356         ierr    = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
357         if (vy == numYVertices-1) {
358           ierr = DMPlexSetLabelValue(dm, "marker", edge,    markerTop);CHKERRQ(ierr);
359           ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr);
360           if (ex == numXEdges-1) {
361             ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr);
362           }
363         } else if (vy == 0) {
364           ierr = DMPlexSetLabelValue(dm, "marker", edge,    markerBottom);CHKERRQ(ierr);
365           ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr);
366           if (ex == numXEdges-1) {
367             ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr);
368           }
369         }
370       }
371     }
372     ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
373     ierr = DMPlexStratify(dm);CHKERRQ(ierr);
374     /* Build coordinates */
375     ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
376     ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr);
377     for (v = firstVertex; v < firstVertex+numVertices; ++v) {
378       ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
379     }
380     ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
381     ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
382     ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
383     ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
384     ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
385     ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
386     for (vy = 0; vy < numYVertices; ++vy) {
387       for (vx = 0; vx < numXVertices; ++vx) {
388         coords[(vy*numXVertices+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
389         coords[(vy*numXVertices+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
390       }
391     }
392     ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
393     ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
394     ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
395   }
396   PetscFunctionReturn(0);
397 }
398 
399 #undef __FUNCT__
400 #define __FUNCT__ "DMPlexCreateBoxMesh"
401 PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool interpolate, DM *dm)
402 {
403   DM             boundary;
404   PetscErrorCode ierr;
405 
406   PetscFunctionBegin;
407   PetscValidPointer(dm, 4);
408   ierr = DMCreate(comm, &boundary);CHKERRQ(ierr);
409   PetscValidLogicalCollectiveInt(boundary,dim,2);
410   ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr);
411   ierr = DMPlexSetDimension(boundary, dim-1);CHKERRQ(ierr);
412   switch (dim) {
413   case 2:
414   {
415     PetscReal lower[2] = {0.0, 0.0};
416     PetscReal upper[2] = {1.0, 1.0};
417     PetscInt  edges[2] = {2, 2};
418 
419     ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, edges);CHKERRQ(ierr);
420     break;
421   }
422   case 3:
423   {
424     PetscReal lower[3] = {0.0, 0.0, 0.0};
425     PetscReal upper[3] = {1.0, 1.0, 1.0};
426     PetscInt  faces[3] = {1, 1, 1};
427 
428     ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);
429     break;
430   }
431   default:
432     SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
433   }
434   ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr);
435   ierr = DMDestroy(&boundary);CHKERRQ(ierr);
436   PetscFunctionReturn(0);
437 }
438 
439 #undef __FUNCT__
440 #define __FUNCT__ "DMPlexCreateHexBoxMesh"
441 PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DM *dm)
442 {
443   PetscErrorCode ierr;
444 
445   PetscFunctionBegin;
446   PetscValidPointer(dm, 4);
447   ierr = DMCreate(comm, dm);CHKERRQ(ierr);
448   PetscValidLogicalCollectiveInt(*dm,dim,2);
449   ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
450   ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr);
451   switch (dim) {
452   case 2:
453   {
454     PetscReal lower[2] = {0.0, 0.0};
455     PetscReal upper[2] = {1.0, 1.0};
456 
457     ierr = DMPlexCreateSquareMesh(*dm, lower, upper, cells);CHKERRQ(ierr);
458     break;
459   }
460 #if 0
461   case 3:
462   {
463     PetscReal lower[3] = {0.0, 0.0, 0.0};
464     PetscReal upper[3] = {1.0, 1.0, 1.0};
465 
466     ierr = DMPlexCreateCubeMesh(boundary, lower, upper, cells);CHKERRQ(ierr);
467     break;
468   }
469 #endif
470   default:
471     SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
472   }
473   PetscFunctionReturn(0);
474 }
475 
476 /* External function declarations here */
477 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling);
478 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, MatType mtype, Mat *J);
479 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm);
480 extern PetscErrorCode DMRefine_Plex(DM dm, MPI_Comm comm, DM *dmRefined);
481 extern PetscErrorCode DMSetUp_Plex(DM dm);
482 extern PetscErrorCode DMDestroy_Plex(DM dm);
483 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer);
484 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm);
485 extern PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, IS *cellIS);
486 
487 #undef __FUNCT__
488 #define __FUNCT__ "DMCreateGlobalVector_Plex"
489 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
490 {
491   PetscErrorCode ierr;
492 
493   PetscFunctionBegin;
494   ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr);
495   /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */
496   ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex);CHKERRQ(ierr);
497   PetscFunctionReturn(0);
498 }
499 
500 #undef __FUNCT__
501 #define __FUNCT__ "DMCreateLocalVector_Plex"
502 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
503 {
504   PetscErrorCode ierr;
505 
506   PetscFunctionBegin;
507   ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr);
508   ierr = VecSetOperation(*vec, VECOP_VIEW, (void(*)(void)) VecView_Plex_Local);CHKERRQ(ierr);
509   PetscFunctionReturn(0);
510 }
511 
512 
513 #undef __FUNCT__
514 #define __FUNCT__ "DMInitialize_Plex"
515 PetscErrorCode DMInitialize_Plex(DM dm)
516 {
517   PetscErrorCode ierr;
518 
519   PetscFunctionBegin;
520   ierr = PetscStrallocpy(VECSTANDARD, (char**)&dm->vectype);CHKERRQ(ierr);
521 
522   dm->ops->view                            = DMView_Plex;
523   dm->ops->setfromoptions                  = DMSetFromOptions_Plex;
524   dm->ops->setup                           = DMSetUp_Plex;
525   dm->ops->createglobalvector              = DMCreateGlobalVector_Plex;
526   dm->ops->createlocalvector               = DMCreateLocalVector_Plex;
527   dm->ops->createlocaltoglobalmapping      = NULL;
528   dm->ops->createlocaltoglobalmappingblock = NULL;
529   dm->ops->createfieldis                   = NULL;
530   dm->ops->createcoordinatedm              = DMCreateCoordinateDM_Plex;
531   dm->ops->getcoloring                     = 0;
532   dm->ops->creatematrix                    = DMCreateMatrix_Plex;
533   dm->ops->createinterpolation             = 0;
534   dm->ops->getaggregates                   = 0;
535   dm->ops->getinjection                    = 0;
536   dm->ops->refine                          = DMRefine_Plex;
537   dm->ops->coarsen                         = 0;
538   dm->ops->refinehierarchy                 = 0;
539   dm->ops->coarsenhierarchy                = 0;
540   dm->ops->globaltolocalbegin              = NULL;
541   dm->ops->globaltolocalend                = NULL;
542   dm->ops->localtoglobalbegin              = NULL;
543   dm->ops->localtoglobalend                = NULL;
544   dm->ops->destroy                         = DMDestroy_Plex;
545   dm->ops->createsubdm                     = DMCreateSubDM_Plex;
546   dm->ops->locatepoints                    = DMLocatePoints_Plex;
547   PetscFunctionReturn(0);
548 }
549 
550 EXTERN_C_BEGIN
551 #undef __FUNCT__
552 #define __FUNCT__ "DMCreate_Plex"
553 PetscErrorCode DMCreate_Plex(DM dm)
554 {
555   DM_Plex        *mesh;
556   PetscInt       unit, d;
557   PetscErrorCode ierr;
558 
559   PetscFunctionBegin;
560   PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
561   ierr     = PetscNewLog(dm, DM_Plex, &mesh);CHKERRQ(ierr);
562   dm->data = mesh;
563 
564   mesh->refct             = 1;
565   mesh->dim               = 0;
566   ierr                    = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr);
567   mesh->maxConeSize       = 0;
568   mesh->cones             = NULL;
569   mesh->coneOrientations  = NULL;
570   ierr                    = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr);
571   mesh->maxSupportSize    = 0;
572   mesh->supports          = NULL;
573   mesh->refinementUniform = PETSC_TRUE;
574   mesh->refinementLimit   = -1.0;
575 
576   mesh->facesTmp = NULL;
577 
578   mesh->subpointMap = NULL;
579 
580   for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
581 
582   mesh->labels              = NULL;
583   mesh->globalVertexNumbers = NULL;
584   mesh->globalCellNumbers   = NULL;
585   for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE;
586   mesh->vtkCellHeight     = 0;
587   mesh->preallocCenterDim = -1;
588 
589   mesh->integrateResidualFEM       = NULL;
590   mesh->integrateJacobianActionFEM = NULL;
591   mesh->integrateJacobianFEM       = NULL;
592 
593   mesh->printSetValues = PETSC_FALSE;
594   mesh->printFEM       = 0;
595 
596   ierr = DMInitialize_Plex(dm);CHKERRQ(ierr);
597   PetscFunctionReturn(0);
598 }
599 EXTERN_C_END
600 
601 #undef __FUNCT__
602 #define __FUNCT__ "DMPlexCreate"
603 /*@
604   DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
605 
606   Collective on MPI_Comm
607 
608   Input Parameter:
609 . comm - The communicator for the DMPlex object
610 
611   Output Parameter:
612 . mesh  - The DMPlex object
613 
614   Level: beginner
615 
616 .keywords: DMPlex, create
617 @*/
618 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
619 {
620   PetscErrorCode ierr;
621 
622   PetscFunctionBegin;
623   PetscValidPointer(mesh,2);
624   ierr = DMCreate(comm, mesh);CHKERRQ(ierr);
625   ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr);
626   PetscFunctionReturn(0);
627 }
628 
629 #undef __FUNCT__
630 #define __FUNCT__ "DMPlexClone"
631 /*@
632   DMPlexClone - Creates a DMPlex object with the same mesh as the original.
633 
634   Collective on MPI_Comm
635 
636   Input Parameter:
637 . dm - The original DMPlex object
638 
639   Output Parameter:
640 . newdm  - The new DMPlex object
641 
642   Level: beginner
643 
644 .keywords: DMPlex, create
645 @*/
646 PetscErrorCode DMPlexClone(DM dm, DM *newdm)
647 {
648   DM_Plex        *mesh;
649   void           *ctx;
650   PetscErrorCode ierr;
651 
652   PetscFunctionBegin;
653   PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
654   PetscValidPointer(newdm,2);
655   ierr         = DMCreate(PetscObjectComm((PetscObject)dm), newdm);CHKERRQ(ierr);
656   ierr         = PetscSFDestroy(&(*newdm)->sf);CHKERRQ(ierr);
657   ierr         = PetscObjectReference((PetscObject) dm->sf);CHKERRQ(ierr);
658   (*newdm)->sf = dm->sf;
659   mesh         = (DM_Plex*) dm->data;
660   mesh->refct++;
661   (*newdm)->data = mesh;
662   ierr           = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr);
663   ierr           = DMInitialize_Plex(*newdm);CHKERRQ(ierr);
664   ierr           = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr);
665   ierr           = DMSetApplicationContext(*newdm, ctx);CHKERRQ(ierr);
666   PetscFunctionReturn(0);
667 }
668 
669 #undef __FUNCT__
670 #define __FUNCT__ "DMPlexBuildFromCellList_Private"
671 /*
672   This takes as input the common mesh generator output, a list of the vertices for each cell
673 */
674 PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[])
675 {
676   PetscInt      *cone, c, p;
677   PetscErrorCode ierr;
678 
679   PetscFunctionBegin;
680   ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr);
681   for (c = 0; c < numCells; ++c) {
682     ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);
683   }
684   ierr = DMSetUp(dm);CHKERRQ(ierr);
685   ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr);
686   for (c = 0; c < numCells; ++c) {
687     for (p = 0; p < numCorners; ++p) {
688       cone[p] = cells[c*numCorners+p]+numCells;
689     }
690     ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr);
691   }
692   ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr);
693   ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
694   ierr = DMPlexStratify(dm);CHKERRQ(ierr);
695   PetscFunctionReturn(0);
696 }
697 
698 #undef __FUNCT__
699 #define __FUNCT__ "DMPlexBuildCoordinates_Private"
700 /*
701   This takes as input the coordinates for each vertex
702 */
703 PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
704 {
705   PetscSection   coordSection;
706   Vec            coordinates;
707   PetscScalar   *coords;
708   PetscInt       coordSize, v, d;
709   PetscErrorCode ierr;
710 
711   PetscFunctionBegin;
712   ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
713   ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
714   ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr);
715   ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
716   for (v = numCells; v < numCells+numVertices; ++v) {
717     ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr);
718     ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr);
719   }
720   ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
721   ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
722   ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
723   ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
724   ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
725   ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
726   ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
727   for (v = 0; v < numVertices; ++v) {
728     for (d = 0; d < spaceDim; ++d) {
729       coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
730     }
731   }
732   ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
733   ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
734   ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
735   PetscFunctionReturn(0);
736 }
737 
738 #undef __FUNCT__
739 #define __FUNCT__ "DMPlexCreateFromCellList"
740 /*@C
741   DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
742 
743   Input Parameters:
744 + comm - The communicator
745 . dim - The topological dimension of the mesh
746 . numCells - The number of cells
747 . numVertices - The number of vertices
748 . numCorners - The number of vertices for each cell
749 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
750 . cells - An array of numCells*numCorners numbers, the vertices for each cell
751 . spaceDim - The spatial dimension used for coordinates
752 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
753 
754   Output Parameter:
755 . dm - The DM
756 
757   Note: Two triangles sharing a face
758 $
759 $        2
760 $      / | \
761 $     /  |  \
762 $    /   |   \
763 $   0  0 | 1  3
764 $    \   |   /
765 $     \  |  /
766 $      \ | /
767 $        1
768 would have input
769 $  numCells = 2, numVertices = 4
770 $  cells = [0 1 2  1 3 2]
771 $
772 which would result in the DMPlex
773 $
774 $        4
775 $      / | \
776 $     /  |  \
777 $    /   |   \
778 $   2  0 | 1  5
779 $    \   |   /
780 $     \  |  /
781 $      \ | /
782 $        3
783 
784   Level: beginner
785 
786 .seealso: DMPlexCreate()
787 @*/
788 PetscErrorCode DMPlexCreateFromCellList(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const int cells[], PetscInt spaceDim, const double vertexCoords[], DM *dm)
789 {
790   PetscErrorCode ierr;
791 
792   PetscFunctionBegin;
793   ierr = DMCreate(comm, dm);CHKERRQ(ierr);
794   ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
795   ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr);
796   ierr = DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr);
797   if (interpolate) {
798     DM idm;
799 
800     ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
801     ierr = DMDestroy(dm);CHKERRQ(ierr);
802     *dm  = idm;
803   }
804   ierr = DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr);
805   PetscFunctionReturn(0);
806 }
807 
808 #undef __FUNCT__
809 #define __FUNCT__ "DMPlexCreateFromDAG"
810 /*
811   This takes as input the raw Hasse Diagram data
812 */
813 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
814 {
815   Vec            coordinates;
816   PetscSection   coordSection;
817   PetscScalar    *coords;
818   PetscInt       coordSize, firstVertex = numPoints[depth], pStart = 0, pEnd = 0, p, v, dim, d, off;
819   PetscErrorCode ierr;
820 
821   PetscFunctionBegin;
822   ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
823   for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
824   ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr);
825   for (p = pStart; p < pEnd; ++p) {
826     ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr);
827   }
828   ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
829   for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
830     ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr);
831     ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr);
832   }
833   ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
834   ierr = DMPlexStratify(dm);CHKERRQ(ierr);
835   /* Build coordinates */
836   ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
837   ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
838   ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
839   ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr);
840   for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
841     ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
842   }
843   ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
844   ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
845   ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
846   ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
847   ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
848   ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
849   for (v = 0; v < numPoints[0]; ++v) {
850     PetscInt off;
851 
852     ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr);
853     for (d = 0; d < dim; ++d) {
854       coords[off+d] = vertexCoords[v*dim+d];
855     }
856   }
857   ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
858   ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
859   ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
860   PetscFunctionReturn(0);
861 }
862