Actual source code: plex.c
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/isimpl.h>
3: #include <petsc/private/vecimpl.h>
4: #include <petsc/private/glvisvecimpl.h>
5: #include <petscsf.h>
6: #include <petscds.h>
7: #include <petscdraw.h>
8: #include <petscdmfield.h>
9: #include <petscdmplextransform.h>
11: /* Logging support */
12: PetscLogEvent DMPLEX_Interpolate, DMPLEX_Partition, DMPLEX_Distribute, DMPLEX_DistributeCones, DMPLEX_DistributeLabels, DMPLEX_DistributeSF, DMPLEX_DistributeOverlap, DMPLEX_DistributeField, DMPLEX_DistributeData, DMPLEX_Migrate, DMPLEX_InterpolateSF, DMPLEX_GlobalToNaturalBegin, DMPLEX_GlobalToNaturalEnd, DMPLEX_NaturalToGlobalBegin, DMPLEX_NaturalToGlobalEnd, DMPLEX_Stratify, DMPLEX_Symmetrize, DMPLEX_Preallocate, DMPLEX_ResidualFEM, DMPLEX_JacobianFEM, DMPLEX_InterpolatorFEM, DMPLEX_InjectorFEM, DMPLEX_IntegralFEM, DMPLEX_CreateGmsh, DMPLEX_RebalanceSharedPoints, DMPLEX_PartSelf, DMPLEX_PartLabelInvert, DMPLEX_PartLabelCreateSF, DMPLEX_PartStratSF, DMPLEX_CreatePointSF,DMPLEX_LocatePoints,DMPLEX_TopologyView,DMPLEX_LabelsView,DMPLEX_CoordinatesView,DMPLEX_SectionView,DMPLEX_GlobalVectorView,DMPLEX_LocalVectorView,DMPLEX_TopologyLoad,DMPLEX_LabelsLoad,DMPLEX_CoordinatesLoad,DMPLEX_SectionLoad,DMPLEX_GlobalVectorLoad,DMPLEX_LocalVectorLoad;
14: PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);
16: /*@
17: DMPlexIsSimplex - Is the first cell in this mesh a simplex?
19: Input Parameter:
20: . dm - The DMPlex object
22: Output Parameter:
23: . simplex - Flag checking for a simplex
25: Note: This just gives the first range of cells found. If the mesh has several cell types, it will only give the first.
26: If the mesh has no cells, this returns PETSC_FALSE.
28: Level: intermediate
30: .seealso DMPlexGetSimplexOrBoxCells(), DMPlexGetCellType(), DMPlexGetHeightStratum(), DMPolytopeTypeGetNumVertices()
31: @*/
32: PetscErrorCode DMPlexIsSimplex(DM dm, PetscBool *simplex)
33: {
34: DMPolytopeType ct;
35: PetscInt cStart, cEnd;
37: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
38: if (cEnd <= cStart) {*simplex = PETSC_FALSE; return 0;}
39: DMPlexGetCellType(dm, cStart, &ct);
40: *simplex = DMPolytopeTypeGetNumVertices(ct) == DMPolytopeTypeGetDim(ct)+1 ? PETSC_TRUE : PETSC_FALSE;
41: return 0;
42: }
44: /*@
45: DMPlexGetSimplexOrBoxCells - Get the range of cells which are neither prisms nor ghost FV cells
47: Input Parameters:
48: + dm - The DMPlex object
49: - height - The cell height in the Plex, 0 is the default
51: Output Parameters:
52: + cStart - The first "normal" cell
53: - cEnd - The upper bound on "normal"" cells
55: Note: This just gives the first range of cells found. If the mesh has several cell types, it will only give the first.
57: Level: developer
59: .seealso DMPlexConstructGhostCells(), DMPlexGetGhostCellStratum()
60: @*/
61: PetscErrorCode DMPlexGetSimplexOrBoxCells(DM dm, PetscInt height, PetscInt *cStart, PetscInt *cEnd)
62: {
63: DMPolytopeType ct = DM_POLYTOPE_UNKNOWN;
64: PetscInt cS, cE, c;
66: DMPlexGetHeightStratum(dm, PetscMax(height, 0), &cS, &cE);
67: for (c = cS; c < cE; ++c) {
68: DMPolytopeType cct;
70: DMPlexGetCellType(dm, c, &cct);
71: if ((PetscInt) cct < 0) break;
72: switch (cct) {
73: case DM_POLYTOPE_POINT:
74: case DM_POLYTOPE_SEGMENT:
75: case DM_POLYTOPE_TRIANGLE:
76: case DM_POLYTOPE_QUADRILATERAL:
77: case DM_POLYTOPE_TETRAHEDRON:
78: case DM_POLYTOPE_HEXAHEDRON:
79: ct = cct;
80: break;
81: default: break;
82: }
83: if (ct != DM_POLYTOPE_UNKNOWN) break;
84: }
85: if (ct != DM_POLYTOPE_UNKNOWN) {
86: DMLabel ctLabel;
88: DMPlexGetCellTypeLabel(dm, &ctLabel);
89: DMLabelGetStratumBounds(ctLabel, ct, &cS, &cE);
90: }
91: if (cStart) *cStart = cS;
92: if (cEnd) *cEnd = cE;
93: return 0;
94: }
96: PetscErrorCode DMPlexGetFieldType_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *sStart, PetscInt *sEnd, PetscViewerVTKFieldType *ft)
97: {
98: PetscInt cdim, pStart, pEnd, vStart, vEnd, cStart, cEnd;
99: PetscInt vcdof[2] = {0,0}, globalvcdof[2];
101: *ft = PETSC_VTK_INVALID;
102: DMGetCoordinateDim(dm, &cdim);
103: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
104: DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
105: PetscSectionGetChart(section, &pStart, &pEnd);
106: if (field >= 0) {
107: if ((vStart >= pStart) && (vStart < pEnd)) PetscSectionGetFieldDof(section, vStart, field, &vcdof[0]);
108: if ((cStart >= pStart) && (cStart < pEnd)) PetscSectionGetFieldDof(section, cStart, field, &vcdof[1]);
109: } else {
110: if ((vStart >= pStart) && (vStart < pEnd)) PetscSectionGetDof(section, vStart, &vcdof[0]);
111: if ((cStart >= pStart) && (cStart < pEnd)) PetscSectionGetDof(section, cStart, &vcdof[1]);
112: }
113: MPI_Allreduce(vcdof, globalvcdof, 2, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm));
114: if (globalvcdof[0]) {
115: *sStart = vStart;
116: *sEnd = vEnd;
117: if (globalvcdof[0] == cdim) *ft = PETSC_VTK_POINT_VECTOR_FIELD;
118: else *ft = PETSC_VTK_POINT_FIELD;
119: } else if (globalvcdof[1]) {
120: *sStart = cStart;
121: *sEnd = cEnd;
122: if (globalvcdof[1] == cdim) *ft = PETSC_VTK_CELL_VECTOR_FIELD;
123: else *ft = PETSC_VTK_CELL_FIELD;
124: } else {
125: if (field >= 0) {
126: const char *fieldname;
128: PetscSectionGetFieldName(section, field, &fieldname);
129: PetscInfo((PetscObject) dm, "Could not classify VTK output type of section field %D \"%s\"\n", field, fieldname);
130: } else {
131: PetscInfo((PetscObject) dm, "Could not classify VTK output type of section\"%s\"\n");
132: }
133: }
134: return 0;
135: }
137: /*@
138: DMPlexVecView1D - Plot many 1D solutions on the same line graph
140: Collective on dm
142: Input Parameters:
143: + dm - The DMPlex
144: . n - The number of vectors
145: . u - The array of local vectors
146: - viewer - The Draw viewer
148: Level: advanced
150: .seealso: VecViewFromOptions(), VecView()
151: @*/
152: PetscErrorCode DMPlexVecView1D(DM dm, PetscInt n, Vec u[], PetscViewer viewer)
153: {
154: PetscDS ds;
155: PetscDraw draw = NULL;
156: PetscDrawLG lg;
157: Vec coordinates;
158: const PetscScalar *coords, **sol;
159: PetscReal *vals;
160: PetscInt *Nc;
161: PetscInt Nf, f, c, Nl, l, i, vStart, vEnd, v;
162: char **names;
164: DMGetDS(dm, &ds);
165: PetscDSGetNumFields(ds, &Nf);
166: PetscDSGetTotalComponents(ds, &Nl);
167: PetscDSGetComponents(ds, &Nc);
169: PetscViewerDrawGetDraw(viewer, 0, &draw);
170: if (!draw) return 0;
171: PetscDrawLGCreate(draw, n*Nl, &lg);
173: PetscMalloc3(n, &sol, n*Nl, &names, n*Nl, &vals);
174: for (i = 0, l = 0; i < n; ++i) {
175: const char *vname;
177: PetscObjectGetName((PetscObject) u[i], &vname);
178: for (f = 0; f < Nf; ++f) {
179: PetscObject disc;
180: const char *fname;
181: char tmpname[PETSC_MAX_PATH_LEN];
183: PetscDSGetDiscretization(ds, f, &disc);
184: /* TODO Create names for components */
185: for (c = 0; c < Nc[f]; ++c, ++l) {
186: PetscObjectGetName(disc, &fname);
187: PetscStrcpy(tmpname, vname);
188: PetscStrlcat(tmpname, ":", PETSC_MAX_PATH_LEN);
189: PetscStrlcat(tmpname, fname, PETSC_MAX_PATH_LEN);
190: PetscStrallocpy(tmpname, &names[l]);
191: }
192: }
193: }
194: PetscDrawLGSetLegend(lg, (const char *const *) names);
195: /* Just add P_1 support for now */
196: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
197: DMGetCoordinatesLocal(dm, &coordinates);
198: VecGetArrayRead(coordinates, &coords);
199: for (i = 0; i < n; ++i) VecGetArrayRead(u[i], &sol[i]);
200: for (v = vStart; v < vEnd; ++v) {
201: PetscScalar *x, *svals;
203: DMPlexPointLocalRead(dm, v, coords, &x);
204: for (i = 0; i < n; ++i) {
205: DMPlexPointLocalRead(dm, v, sol[i], &svals);
206: for (l = 0; l < Nl; ++l) vals[i*Nl + l] = PetscRealPart(svals[l]);
207: }
208: PetscDrawLGAddCommonPoint(lg, PetscRealPart(x[0]), vals);
209: }
210: VecRestoreArrayRead(coordinates, &coords);
211: for (i = 0; i < n; ++i) VecRestoreArrayRead(u[i], &sol[i]);
212: for (l = 0; l < n*Nl; ++l) PetscFree(names[l]);
213: PetscFree3(sol, names, vals);
215: PetscDrawLGDraw(lg);
216: PetscDrawLGDestroy(&lg);
217: return 0;
218: }
220: static PetscErrorCode VecView_Plex_Local_Draw_1D(Vec u, PetscViewer viewer)
221: {
222: DM dm;
224: VecGetDM(u, &dm);
225: DMPlexVecView1D(dm, 1, &u, viewer);
226: return 0;
227: }
229: static PetscErrorCode VecView_Plex_Local_Draw_2D(Vec v, PetscViewer viewer)
230: {
231: DM dm;
232: PetscSection s;
233: PetscDraw draw, popup;
234: DM cdm;
235: PetscSection coordSection;
236: Vec coordinates;
237: const PetscScalar *coords, *array;
238: PetscReal bound[4] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
239: PetscReal vbound[2], time;
240: PetscBool flg;
241: PetscInt dim, Nf, f, Nc, comp, vStart, vEnd, cStart, cEnd, c, N, level, step, w = 0;
242: const char *name;
243: char title[PETSC_MAX_PATH_LEN];
245: PetscViewerDrawGetDraw(viewer, 0, &draw);
246: VecGetDM(v, &dm);
247: DMGetCoordinateDim(dm, &dim);
248: DMGetLocalSection(dm, &s);
249: PetscSectionGetNumFields(s, &Nf);
250: DMGetCoarsenLevel(dm, &level);
251: DMGetCoordinateDM(dm, &cdm);
252: DMGetLocalSection(cdm, &coordSection);
253: DMGetCoordinatesLocal(dm, &coordinates);
254: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
255: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
257: PetscObjectGetName((PetscObject) v, &name);
258: DMGetOutputSequenceNumber(dm, &step, &time);
260: VecGetLocalSize(coordinates, &N);
261: VecGetArrayRead(coordinates, &coords);
262: for (c = 0; c < N; c += dim) {
263: bound[0] = PetscMin(bound[0], PetscRealPart(coords[c])); bound[2] = PetscMax(bound[2], PetscRealPart(coords[c]));
264: bound[1] = PetscMin(bound[1], PetscRealPart(coords[c+1])); bound[3] = PetscMax(bound[3], PetscRealPart(coords[c+1]));
265: }
266: VecRestoreArrayRead(coordinates, &coords);
267: PetscDrawClear(draw);
269: /* Could implement something like DMDASelectFields() */
270: for (f = 0; f < Nf; ++f) {
271: DM fdm = dm;
272: Vec fv = v;
273: IS fis;
274: char prefix[PETSC_MAX_PATH_LEN];
275: const char *fname;
277: PetscSectionGetFieldComponents(s, f, &Nc);
278: PetscSectionGetFieldName(s, f, &fname);
280: if (v->hdr.prefix) PetscStrncpy(prefix, v->hdr.prefix,sizeof(prefix));
281: else {prefix[0] = '\0';}
282: if (Nf > 1) {
283: DMCreateSubDM(dm, 1, &f, &fis, &fdm);
284: VecGetSubVector(v, fis, &fv);
285: PetscStrlcat(prefix, fname,sizeof(prefix));
286: PetscStrlcat(prefix, "_",sizeof(prefix));
287: }
288: for (comp = 0; comp < Nc; ++comp, ++w) {
289: PetscInt nmax = 2;
291: PetscViewerDrawGetDraw(viewer, w, &draw);
292: if (Nc > 1) PetscSNPrintf(title, sizeof(title), "%s:%s_%D Step: %D Time: %.4g", name, fname, comp, step, time);
293: else PetscSNPrintf(title, sizeof(title), "%s:%s Step: %D Time: %.4g", name, fname, step, time);
294: PetscDrawSetTitle(draw, title);
296: /* TODO Get max and min only for this component */
297: PetscOptionsGetRealArray(NULL, prefix, "-vec_view_bounds", vbound, &nmax, &flg);
298: if (!flg) {
299: VecMin(fv, NULL, &vbound[0]);
300: VecMax(fv, NULL, &vbound[1]);
301: if (vbound[1] <= vbound[0]) vbound[1] = vbound[0] + 1.0;
302: }
303: PetscDrawGetPopup(draw, &popup);
304: PetscDrawScalePopup(popup, vbound[0], vbound[1]);
305: PetscDrawSetCoordinates(draw, bound[0], bound[1], bound[2], bound[3]);
307: VecGetArrayRead(fv, &array);
308: for (c = cStart; c < cEnd; ++c) {
309: PetscScalar *coords = NULL, *a = NULL;
310: PetscInt numCoords, color[4] = {-1,-1,-1,-1};
312: DMPlexPointLocalRead(fdm, c, array, &a);
313: if (a) {
314: color[0] = PetscDrawRealToColor(PetscRealPart(a[comp]), vbound[0], vbound[1]);
315: color[1] = color[2] = color[3] = color[0];
316: } else {
317: PetscScalar *vals = NULL;
318: PetscInt numVals, va;
320: DMPlexVecGetClosure(fdm, NULL, fv, c, &numVals, &vals);
322: switch (numVals/Nc) {
323: case 3: /* P1 Triangle */
324: case 4: /* P1 Quadrangle */
325: for (va = 0; va < numVals/Nc; ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va*Nc+comp]), vbound[0], vbound[1]);
326: break;
327: case 6: /* P2 Triangle */
328: case 8: /* P2 Quadrangle */
329: for (va = 0; va < numVals/(Nc*2); ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va*Nc+comp + numVals/(Nc*2)]), vbound[0], vbound[1]);
330: break;
331: default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of values for cell closure %D cannot be handled", numVals/Nc);
332: }
333: DMPlexVecRestoreClosure(fdm, NULL, fv, c, &numVals, &vals);
334: }
335: DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
336: switch (numCoords) {
337: case 6:
338: case 12: /* Localized triangle */
339: PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), color[0], color[1], color[2]);
340: break;
341: case 8:
342: case 16: /* Localized quadrilateral */
343: PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), color[0], color[1], color[2]);
344: PetscDrawTriangle(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), color[2], color[3], color[0]);
345: break;
346: default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D coordinates", numCoords);
347: }
348: DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
349: }
350: VecRestoreArrayRead(fv, &array);
351: PetscDrawFlush(draw);
352: PetscDrawPause(draw);
353: PetscDrawSave(draw);
354: }
355: if (Nf > 1) {
356: VecRestoreSubVector(v, fis, &fv);
357: ISDestroy(&fis);
358: DMDestroy(&fdm);
359: }
360: }
361: return 0;
362: }
364: static PetscErrorCode VecView_Plex_Local_Draw(Vec v, PetscViewer viewer)
365: {
366: DM dm;
367: PetscDraw draw;
368: PetscInt dim;
369: PetscBool isnull;
371: PetscViewerDrawGetDraw(viewer, 0, &draw);
372: PetscDrawIsNull(draw, &isnull);
373: if (isnull) return 0;
375: VecGetDM(v, &dm);
376: DMGetCoordinateDim(dm, &dim);
377: switch (dim) {
378: case 1: VecView_Plex_Local_Draw_1D(v, viewer);break;
379: case 2: VecView_Plex_Local_Draw_2D(v, viewer);break;
380: default: SETERRQ(PetscObjectComm((PetscObject) v), PETSC_ERR_SUP, "Cannot draw meshes of dimension %" PetscInt_FMT ". Try PETSCVIEWERGLVIS", dim);
381: }
382: return 0;
383: }
385: static PetscErrorCode VecView_Plex_Local_VTK(Vec v, PetscViewer viewer)
386: {
387: DM dm;
388: Vec locv;
389: const char *name;
390: PetscSection section;
391: PetscInt pStart, pEnd;
392: PetscInt numFields;
393: PetscViewerVTKFieldType ft;
395: VecGetDM(v, &dm);
396: DMCreateLocalVector(dm, &locv); /* VTK viewer requires exclusive ownership of the vector */
397: PetscObjectGetName((PetscObject) v, &name);
398: PetscObjectSetName((PetscObject) locv, name);
399: VecCopy(v, locv);
400: DMGetLocalSection(dm, §ion);
401: PetscSectionGetNumFields(section, &numFields);
402: if (!numFields) {
403: DMPlexGetFieldType_Internal(dm, section, PETSC_DETERMINE, &pStart, &pEnd, &ft);
404: PetscViewerVTKAddField(viewer, (PetscObject) dm, DMPlexVTKWriteAll, PETSC_DEFAULT, ft, PETSC_TRUE,(PetscObject) locv);
405: } else {
406: PetscInt f;
408: for (f = 0; f < numFields; f++) {
409: DMPlexGetFieldType_Internal(dm, section, f, &pStart, &pEnd, &ft);
410: if (ft == PETSC_VTK_INVALID) continue;
411: PetscObjectReference((PetscObject)locv);
412: PetscViewerVTKAddField(viewer, (PetscObject) dm, DMPlexVTKWriteAll, f, ft, PETSC_TRUE,(PetscObject) locv);
413: }
414: VecDestroy(&locv);
415: }
416: return 0;
417: }
419: PetscErrorCode VecView_Plex_Local(Vec v, PetscViewer viewer)
420: {
421: DM dm;
422: PetscBool isvtk, ishdf5, isdraw, isglvis;
424: VecGetDM(v, &dm);
426: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);
427: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
428: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);
429: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);
430: if (isvtk || ishdf5 || isdraw || isglvis) {
431: PetscInt i,numFields;
432: PetscObject fe;
433: PetscBool fem = PETSC_FALSE;
434: Vec locv = v;
435: const char *name;
436: PetscInt step;
437: PetscReal time;
439: DMGetNumFields(dm, &numFields);
440: for (i=0; i<numFields; i++) {
441: DMGetField(dm, i, NULL, &fe);
442: if (fe->classid == PETSCFE_CLASSID) { fem = PETSC_TRUE; break; }
443: }
444: if (fem) {
445: PetscObject isZero;
447: DMGetLocalVector(dm, &locv);
448: PetscObjectGetName((PetscObject) v, &name);
449: PetscObjectSetName((PetscObject) locv, name);
450: PetscObjectQuery((PetscObject) v, "__Vec_bc_zero__", &isZero);
451: PetscObjectCompose((PetscObject) locv, "__Vec_bc_zero__", isZero);
452: VecCopy(v, locv);
453: DMGetOutputSequenceNumber(dm, NULL, &time);
454: DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL);
455: }
456: if (isvtk) {
457: VecView_Plex_Local_VTK(locv, viewer);
458: } else if (ishdf5) {
459: #if defined(PETSC_HAVE_HDF5)
460: VecView_Plex_Local_HDF5_Internal(locv, viewer);
461: #else
462: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
463: #endif
464: } else if (isdraw) {
465: VecView_Plex_Local_Draw(locv, viewer);
466: } else if (isglvis) {
467: DMGetOutputSequenceNumber(dm, &step, NULL);
468: PetscViewerGLVisSetSnapId(viewer, step);
469: VecView_GLVis(locv, viewer);
470: }
471: if (fem) {
472: PetscObjectCompose((PetscObject) locv, "__Vec_bc_zero__", NULL);
473: DMRestoreLocalVector(dm, &locv);
474: }
475: } else {
476: PetscBool isseq;
478: PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
479: if (isseq) VecView_Seq(v, viewer);
480: else VecView_MPI(v, viewer);
481: }
482: return 0;
483: }
485: PetscErrorCode VecView_Plex(Vec v, PetscViewer viewer)
486: {
487: DM dm;
488: PetscBool isvtk, ishdf5, isdraw, isglvis, isexodusii;
490: VecGetDM(v, &dm);
492: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);
493: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
494: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);
495: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);
496: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWEREXODUSII, &isexodusii);
497: if (isvtk || isdraw || isglvis) {
498: Vec locv;
499: PetscObject isZero;
500: const char *name;
502: DMGetLocalVector(dm, &locv);
503: PetscObjectGetName((PetscObject) v, &name);
504: PetscObjectSetName((PetscObject) locv, name);
505: DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv);
506: DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv);
507: PetscObjectQuery((PetscObject) v, "__Vec_bc_zero__", &isZero);
508: PetscObjectCompose((PetscObject) locv, "__Vec_bc_zero__", isZero);
509: VecView_Plex_Local(locv, viewer);
510: PetscObjectCompose((PetscObject) locv, "__Vec_bc_zero__", NULL);
511: DMRestoreLocalVector(dm, &locv);
512: } else if (ishdf5) {
513: #if defined(PETSC_HAVE_HDF5)
514: VecView_Plex_HDF5_Internal(v, viewer);
515: #else
516: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
517: #endif
518: } else if (isexodusii) {
519: #if defined(PETSC_HAVE_EXODUSII)
520: VecView_PlexExodusII_Internal(v, viewer);
521: #else
522: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "ExodusII not supported in this build.\nPlease reconfigure using --download-exodusii");
523: #endif
524: } else {
525: PetscBool isseq;
527: PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
528: if (isseq) VecView_Seq(v, viewer);
529: else VecView_MPI(v, viewer);
530: }
531: return 0;
532: }
534: PetscErrorCode VecView_Plex_Native(Vec originalv, PetscViewer viewer)
535: {
536: DM dm;
537: MPI_Comm comm;
538: PetscViewerFormat format;
539: Vec v;
540: PetscBool isvtk, ishdf5;
542: VecGetDM(originalv, &dm);
543: PetscObjectGetComm((PetscObject) originalv, &comm);
545: PetscViewerGetFormat(viewer, &format);
546: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
547: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);
548: if (format == PETSC_VIEWER_NATIVE) {
549: /* Natural ordering is the common case for DMDA, NATIVE means plain vector, for PLEX is the opposite */
550: /* this need a better fix */
551: if (dm->useNatural) {
552: if (dm->sfNatural) {
553: const char *vecname;
554: PetscInt n, nroots;
556: VecGetLocalSize(originalv, &n);
557: PetscSFGetGraph(dm->sfNatural, &nroots, NULL, NULL, NULL);
558: if (n == nroots) {
559: DMGetGlobalVector(dm, &v);
560: DMPlexGlobalToNaturalBegin(dm, originalv, v);
561: DMPlexGlobalToNaturalEnd(dm, originalv, v);
562: PetscObjectGetName((PetscObject) originalv, &vecname);
563: PetscObjectSetName((PetscObject) v, vecname);
564: } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "DM global to natural SF only handles global vectors");
565: } else SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created");
566: } else v = originalv;
567: } else v = originalv;
569: if (ishdf5) {
570: #if defined(PETSC_HAVE_HDF5)
571: VecView_Plex_HDF5_Native_Internal(v, viewer);
572: #else
573: SETERRQ(comm, PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
574: #endif
575: } else if (isvtk) {
576: SETERRQ(comm, PETSC_ERR_SUP, "VTK format does not support viewing in natural order. Please switch to HDF5.");
577: } else {
578: PetscBool isseq;
580: PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
581: if (isseq) VecView_Seq(v, viewer);
582: else VecView_MPI(v, viewer);
583: }
584: if (v != originalv) DMRestoreGlobalVector(dm, &v);
585: return 0;
586: }
588: PetscErrorCode VecLoad_Plex_Local(Vec v, PetscViewer viewer)
589: {
590: DM dm;
591: PetscBool ishdf5;
593: VecGetDM(v, &dm);
595: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
596: if (ishdf5) {
597: DM dmBC;
598: Vec gv;
599: const char *name;
601: DMGetOutputDM(dm, &dmBC);
602: DMGetGlobalVector(dmBC, &gv);
603: PetscObjectGetName((PetscObject) v, &name);
604: PetscObjectSetName((PetscObject) gv, name);
605: VecLoad_Default(gv, viewer);
606: DMGlobalToLocalBegin(dmBC, gv, INSERT_VALUES, v);
607: DMGlobalToLocalEnd(dmBC, gv, INSERT_VALUES, v);
608: DMRestoreGlobalVector(dmBC, &gv);
609: } else {
610: VecLoad_Default(v, viewer);
611: }
612: return 0;
613: }
615: PetscErrorCode VecLoad_Plex(Vec v, PetscViewer viewer)
616: {
617: DM dm;
618: PetscBool ishdf5,isexodusii;
620: VecGetDM(v, &dm);
622: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
623: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWEREXODUSII, &isexodusii);
624: if (ishdf5) {
625: #if defined(PETSC_HAVE_HDF5)
626: VecLoad_Plex_HDF5_Internal(v, viewer);
627: #else
628: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
629: #endif
630: } else if (isexodusii) {
631: #if defined(PETSC_HAVE_EXODUSII)
632: VecLoad_PlexExodusII_Internal(v, viewer);
633: #else
634: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "ExodusII not supported in this build.\nPlease reconfigure using --download-exodusii");
635: #endif
636: } else {
637: VecLoad_Default(v, viewer);
638: }
639: return 0;
640: }
642: PetscErrorCode VecLoad_Plex_Native(Vec originalv, PetscViewer viewer)
643: {
644: DM dm;
645: PetscViewerFormat format;
646: PetscBool ishdf5;
648: VecGetDM(originalv, &dm);
650: PetscViewerGetFormat(viewer, &format);
651: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
652: if (format == PETSC_VIEWER_NATIVE) {
653: if (dm->useNatural) {
654: if (dm->sfNatural) {
655: if (ishdf5) {
656: #if defined(PETSC_HAVE_HDF5)
657: Vec v;
658: const char *vecname;
660: DMGetGlobalVector(dm, &v);
661: PetscObjectGetName((PetscObject) originalv, &vecname);
662: PetscObjectSetName((PetscObject) v, vecname);
663: VecLoad_Plex_HDF5_Native_Internal(v, viewer);
664: DMPlexNaturalToGlobalBegin(dm, v, originalv);
665: DMPlexNaturalToGlobalEnd(dm, v, originalv);
666: DMRestoreGlobalVector(dm, &v);
667: #else
668: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
669: #endif
670: } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Reading in natural order is not supported for anything but HDF5.");
671: }
672: } else {
673: VecLoad_Default(originalv, viewer);
674: }
675: }
676: return 0;
677: }
679: PETSC_UNUSED static PetscErrorCode DMPlexView_Ascii_Geometry(DM dm, PetscViewer viewer)
680: {
681: PetscSection coordSection;
682: Vec coordinates;
683: DMLabel depthLabel, celltypeLabel;
684: const char *name[4];
685: const PetscScalar *a;
686: PetscInt dim, pStart, pEnd, cStart, cEnd, c;
688: DMGetDimension(dm, &dim);
689: DMGetCoordinatesLocal(dm, &coordinates);
690: DMGetCoordinateSection(dm, &coordSection);
691: DMPlexGetDepthLabel(dm, &depthLabel);
692: DMPlexGetCellTypeLabel(dm, &celltypeLabel);
693: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
694: PetscSectionGetChart(coordSection, &pStart, &pEnd);
695: VecGetArrayRead(coordinates, &a);
696: name[0] = "vertex";
697: name[1] = "edge";
698: name[dim-1] = "face";
699: name[dim] = "cell";
700: for (c = cStart; c < cEnd; ++c) {
701: PetscInt *closure = NULL;
702: PetscInt closureSize, cl, ct;
704: DMLabelGetValue(celltypeLabel, c, &ct);
705: PetscViewerASCIIPrintf(viewer, "Geometry for cell %D polytope type %s:\n", c, DMPolytopeTypes[ct]);
706: DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
707: PetscViewerASCIIPushTab(viewer);
708: for (cl = 0; cl < closureSize*2; cl += 2) {
709: PetscInt point = closure[cl], depth, dof, off, d, p;
711: if ((point < pStart) || (point >= pEnd)) continue;
712: PetscSectionGetDof(coordSection, point, &dof);
713: if (!dof) continue;
714: DMLabelGetValue(depthLabel, point, &depth);
715: PetscSectionGetOffset(coordSection, point, &off);
716: PetscViewerASCIIPrintf(viewer, "%s %D coords:", name[depth], point);
717: for (p = 0; p < dof/dim; ++p) {
718: PetscViewerASCIIPrintf(viewer, " (");
719: for (d = 0; d < dim; ++d) {
720: if (d > 0) PetscViewerASCIIPrintf(viewer, ", ");
721: PetscViewerASCIIPrintf(viewer, "%g", (double) PetscRealPart(a[off+p*dim+d]));
722: }
723: PetscViewerASCIIPrintf(viewer, ")");
724: }
725: PetscViewerASCIIPrintf(viewer, "\n");
726: }
727: DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
728: PetscViewerASCIIPopTab(viewer);
729: }
730: VecRestoreArrayRead(coordinates, &a);
731: return 0;
732: }
734: typedef enum {CS_CARTESIAN, CS_POLAR, CS_CYLINDRICAL, CS_SPHERICAL} CoordSystem;
735: const char *CoordSystems[] = {"cartesian", "polar", "cylindrical", "spherical", "CoordSystem", "CS_", NULL};
737: static PetscErrorCode DMPlexView_Ascii_Coordinates(PetscViewer viewer, CoordSystem cs, PetscInt dim, const PetscScalar x[])
738: {
739: PetscInt i;
741: if (dim > 3) {
742: for (i = 0; i < dim; ++i) PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double) PetscRealPart(x[i]));
743: } else {
744: PetscReal coords[3], trcoords[3];
746: for (i = 0; i < dim; ++i) coords[i] = PetscRealPart(x[i]);
747: switch (cs) {
748: case CS_CARTESIAN: for (i = 0; i < dim; ++i) trcoords[i] = coords[i];break;
749: case CS_POLAR:
751: trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1]));
752: trcoords[1] = PetscAtan2Real(coords[1], coords[0]);
753: break;
754: case CS_CYLINDRICAL:
756: trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1]));
757: trcoords[1] = PetscAtan2Real(coords[1], coords[0]);
758: trcoords[2] = coords[2];
759: break;
760: case CS_SPHERICAL:
762: trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1]) + PetscSqr(coords[2]));
763: trcoords[1] = PetscAtan2Real(PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1])), coords[2]);
764: trcoords[2] = PetscAtan2Real(coords[1], coords[0]);
765: break;
766: }
767: for (i = 0; i < dim; ++i) PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double) trcoords[i]);
768: }
769: return 0;
770: }
772: static PetscErrorCode DMPlexView_Ascii(DM dm, PetscViewer viewer)
773: {
774: DM_Plex *mesh = (DM_Plex*) dm->data;
775: DM cdm;
776: PetscSection coordSection;
777: Vec coordinates;
778: PetscViewerFormat format;
780: DMGetCoordinateDM(dm, &cdm);
781: DMGetLocalSection(cdm, &coordSection);
782: DMGetCoordinatesLocal(dm, &coordinates);
783: PetscViewerGetFormat(viewer, &format);
784: if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
785: const char *name;
786: PetscInt dim, cellHeight, maxConeSize, maxSupportSize;
787: PetscInt pStart, pEnd, p, numLabels, l;
788: PetscMPIInt rank, size;
790: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
791: MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);
792: PetscObjectGetName((PetscObject) dm, &name);
793: DMPlexGetChart(dm, &pStart, &pEnd);
794: DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
795: DMGetDimension(dm, &dim);
796: DMPlexGetVTKCellHeight(dm, &cellHeight);
797: if (name) PetscViewerASCIIPrintf(viewer, "%s in %D dimension%s:\n", name, dim, dim == 1 ? "" : "s");
798: else PetscViewerASCIIPrintf(viewer, "Mesh in %D dimension%s:\n", dim, dim == 1 ? "" : "s");
799: if (cellHeight) PetscViewerASCIIPrintf(viewer, " Cells are at height %D\n", cellHeight);
800: PetscViewerASCIIPrintf(viewer, "Supports:\n", name);
801: PetscViewerASCIIPushSynchronized(viewer);
802: PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max support size: %D\n", rank, maxSupportSize);
803: for (p = pStart; p < pEnd; ++p) {
804: PetscInt dof, off, s;
806: PetscSectionGetDof(mesh->supportSection, p, &dof);
807: PetscSectionGetOffset(mesh->supportSection, p, &off);
808: for (s = off; s < off+dof; ++s) {
809: PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %D ----> %D\n", rank, p, mesh->supports[s]);
810: }
811: }
812: PetscViewerFlush(viewer);
813: PetscViewerASCIIPrintf(viewer, "Cones:\n", name);
814: PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max cone size: %D\n", rank, maxConeSize);
815: for (p = pStart; p < pEnd; ++p) {
816: PetscInt dof, off, c;
818: PetscSectionGetDof(mesh->coneSection, p, &dof);
819: PetscSectionGetOffset(mesh->coneSection, p, &off);
820: for (c = off; c < off+dof; ++c) {
821: PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %D <---- %D (%D)\n", rank, p, mesh->cones[c], mesh->coneOrientations[c]);
822: }
823: }
824: PetscViewerFlush(viewer);
825: PetscViewerASCIIPopSynchronized(viewer);
826: if (coordSection && coordinates) {
827: CoordSystem cs = CS_CARTESIAN;
828: const PetscScalar *array;
829: PetscInt Nf, Nc, pStart, pEnd, p;
830: PetscMPIInt rank;
831: const char *name;
833: PetscOptionsGetEnum(((PetscObject) viewer)->options, ((PetscObject) viewer)->prefix, "-dm_plex_view_coord_system", CoordSystems, (PetscEnum *) &cs, NULL);
834: MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank);
835: PetscSectionGetNumFields(coordSection, &Nf);
837: PetscSectionGetFieldComponents(coordSection, 0, &Nc);
838: PetscSectionGetChart(coordSection, &pStart, &pEnd);
839: PetscObjectGetName((PetscObject) coordinates, &name);
840: PetscViewerASCIIPrintf(viewer, "%s with %D fields\n", name, Nf);
841: PetscViewerASCIIPrintf(viewer, " field 0 with %D components\n", Nc);
842: if (cs != CS_CARTESIAN) PetscViewerASCIIPrintf(viewer, " output coordinate system: %s\n", CoordSystems[cs]);
844: VecGetArrayRead(coordinates, &array);
845: PetscViewerASCIIPushSynchronized(viewer);
846: PetscViewerASCIISynchronizedPrintf(viewer, "Process %d:\n", rank);
847: for (p = pStart; p < pEnd; ++p) {
848: PetscInt dof, off;
850: PetscSectionGetDof(coordSection, p, &dof);
851: PetscSectionGetOffset(coordSection, p, &off);
852: PetscViewerASCIISynchronizedPrintf(viewer, " (%4D) dim %2D offset %3D", p, dof, off);
853: DMPlexView_Ascii_Coordinates(viewer, cs, dof, &array[off]);
854: PetscViewerASCIISynchronizedPrintf(viewer, "\n");
855: }
856: PetscViewerFlush(viewer);
857: PetscViewerASCIIPopSynchronized(viewer);
858: VecRestoreArrayRead(coordinates, &array);
859: }
860: DMGetNumLabels(dm, &numLabels);
861: if (numLabels) PetscViewerASCIIPrintf(viewer, "Labels:\n");
862: for (l = 0; l < numLabels; ++l) {
863: DMLabel label;
864: PetscBool isdepth;
865: const char *name;
867: DMGetLabelName(dm, l, &name);
868: PetscStrcmp(name, "depth", &isdepth);
869: if (isdepth) continue;
870: DMGetLabel(dm, name, &label);
871: DMLabelView(label, viewer);
872: }
873: if (size > 1) {
874: PetscSF sf;
876: DMGetPointSF(dm, &sf);
877: PetscSFView(sf, viewer);
878: }
879: PetscViewerFlush(viewer);
880: } else if (format == PETSC_VIEWER_ASCII_LATEX) {
881: const char *name, *color;
882: const char *defcolors[3] = {"gray", "orange", "green"};
883: const char *deflcolors[4] = {"blue", "cyan", "red", "magenta"};
884: char lname[PETSC_MAX_PATH_LEN];
885: PetscReal scale = 2.0;
886: PetscReal tikzscale = 1.0;
887: PetscBool useNumbers = PETSC_TRUE, drawNumbers[4], drawColors[4], useLabels, useColors, plotEdges, drawHasse = PETSC_FALSE;
888: double tcoords[3];
889: PetscScalar *coords;
890: PetscInt numLabels, l, numColors, numLColors, dim, d, depth, cStart, cEnd, c, vStart, vEnd, v, eStart = 0, eEnd = 0, e, p, n;
891: PetscMPIInt rank, size;
892: char **names, **colors, **lcolors;
893: PetscBool flg, lflg;
894: PetscBT wp = NULL;
895: PetscInt pEnd, pStart;
897: DMGetDimension(dm, &dim);
898: DMPlexGetDepth(dm, &depth);
899: DMGetNumLabels(dm, &numLabels);
900: numLabels = PetscMax(numLabels, 10);
901: numColors = 10;
902: numLColors = 10;
903: PetscCalloc3(numLabels, &names, numColors, &colors, numLColors, &lcolors);
904: PetscOptionsGetReal(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_scale", &scale, NULL);
905: PetscOptionsGetReal(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_tikzscale", &tikzscale, NULL);
906: PetscOptionsGetBool(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_numbers", &useNumbers, NULL);
907: for (d = 0; d < 4; ++d) drawNumbers[d] = useNumbers;
908: for (d = 0; d < 4; ++d) drawColors[d] = PETSC_TRUE;
909: n = 4;
910: PetscOptionsGetBoolArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_numbers_depth", drawNumbers, &n, &flg);
912: PetscOptionsGetBoolArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_colors_depth", drawColors, &n, &flg);
914: PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_labels", names, &numLabels, &useLabels);
915: if (!useLabels) numLabels = 0;
916: PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_colors", colors, &numColors, &useColors);
917: if (!useColors) {
918: numColors = 3;
919: for (c = 0; c < numColors; ++c) PetscStrallocpy(defcolors[c], &colors[c]);
920: }
921: PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_lcolors", lcolors, &numLColors, &useColors);
922: if (!useColors) {
923: numLColors = 4;
924: for (c = 0; c < numLColors; ++c) PetscStrallocpy(deflcolors[c], &lcolors[c]);
925: }
926: PetscOptionsGetString(((PetscObject) viewer)->options, ((PetscObject) viewer)->prefix, "-dm_plex_view_label_filter", lname, sizeof(lname), &lflg);
927: plotEdges = (PetscBool)(depth > 1 && drawNumbers[1] && dim < 3);
928: PetscOptionsGetBool(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_edges", &plotEdges, &flg);
930: if (depth < dim) plotEdges = PETSC_FALSE;
931: PetscOptionsGetBool(((PetscObject) viewer)->options, ((PetscObject) viewer)->prefix, "-dm_plex_view_hasse", &drawHasse, NULL);
933: /* filter points with labelvalue != labeldefaultvalue */
934: DMPlexGetChart(dm, &pStart, &pEnd);
935: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
936: DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);
937: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
938: if (lflg) {
939: DMLabel lbl;
941: DMGetLabel(dm, lname, &lbl);
942: if (lbl) {
943: PetscInt val, defval;
945: DMLabelGetDefaultValue(lbl, &defval);
946: PetscBTCreate(pEnd-pStart, &wp);
947: for (c = pStart; c < pEnd; c++) {
948: PetscInt *closure = NULL;
949: PetscInt closureSize;
951: DMLabelGetValue(lbl, c, &val);
952: if (val == defval) continue;
954: DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
955: for (p = 0; p < closureSize*2; p += 2) {
956: PetscBTSet(wp, closure[p] - pStart);
957: }
958: DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
959: }
960: }
961: }
963: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
964: MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);
965: PetscObjectGetName((PetscObject) dm, &name);
966: PetscCall(PetscViewerASCIIPrintf(viewer, "\
967: \\documentclass[tikz]{standalone}\n\n\
968: \\usepackage{pgflibraryshapes}\n\
969: \\usetikzlibrary{backgrounds}\n\
970: \\usetikzlibrary{arrows}\n\
971: \\begin{document}\n"));
972: if (size > 1) {
973: PetscViewerASCIIPrintf(viewer, "%s for process ", name);
974: for (p = 0; p < size; ++p) {
975: if (p > 0 && p == size-1) {
976: PetscViewerASCIIPrintf(viewer, ", and ", colors[p%numColors], p);
977: } else if (p > 0) {
978: PetscViewerASCIIPrintf(viewer, ", ", colors[p%numColors], p);
979: }
980: PetscViewerASCIIPrintf(viewer, "{\\textcolor{%s}%D}", colors[p%numColors], p);
981: }
982: PetscViewerASCIIPrintf(viewer, ".\n\n\n");
983: }
984: if (drawHasse) {
985: PetscInt maxStratum = PetscMax(vEnd-vStart, PetscMax(eEnd-eStart, cEnd-cStart));
987: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vStart}{%D}\n", vStart);
988: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vEnd}{%D}\n", vEnd-1);
989: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numVertices}{%D}\n", vEnd-vStart);
990: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vShift}{%.2f}\n", 3 + (maxStratum-(vEnd-vStart))/2.);
991: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eStart}{%D}\n", eStart);
992: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eEnd}{%D}\n", eEnd-1);
993: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eShift}{%.2f}\n", 3 + (maxStratum-(eEnd-eStart))/2.);
994: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numEdges}{%D}\n", eEnd-eStart);
995: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cStart}{%D}\n", cStart);
996: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cEnd}{%D}\n", cEnd-1);
997: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numCells}{%D}\n", cEnd-cStart);
998: PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cShift}{%.2f}\n", 3 + (maxStratum-(cEnd-cStart))/2.);
999: }
1000: PetscViewerASCIIPrintf(viewer, "\\begin{tikzpicture}[scale = %g,font=\\fontsize{8}{8}\\selectfont]\n", (double) tikzscale);
1002: /* Plot vertices */
1003: VecGetArray(coordinates, &coords);
1004: PetscViewerASCIIPushSynchronized(viewer);
1005: for (v = vStart; v < vEnd; ++v) {
1006: PetscInt off, dof, d;
1007: PetscBool isLabeled = PETSC_FALSE;
1009: if (wp && !PetscBTLookup(wp,v - pStart)) continue;
1010: PetscSectionGetDof(coordSection, v, &dof);
1011: PetscSectionGetOffset(coordSection, v, &off);
1012: PetscViewerASCIISynchronizedPrintf(viewer, "\\path (");
1014: for (d = 0; d < dof; ++d) {
1015: tcoords[d] = (double) (scale*PetscRealPart(coords[off+d]));
1016: tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d];
1017: }
1018: /* Rotate coordinates since PGF makes z point out of the page instead of up */
1019: if (dim == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;}
1020: for (d = 0; d < dof; ++d) {
1021: if (d > 0) PetscViewerASCIISynchronizedPrintf(viewer, ",");
1022: PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double) tcoords[d]);
1023: }
1024: if (drawHasse) color = colors[0%numColors];
1025: else color = colors[rank%numColors];
1026: for (l = 0; l < numLabels; ++l) {
1027: PetscInt val;
1028: DMGetLabelValue(dm, names[l], v, &val);
1029: if (val >= 0) {color = lcolors[l%numLColors]; isLabeled = PETSC_TRUE; break;}
1030: }
1031: if (drawNumbers[0]) {
1032: PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D};\n", v, rank, color, v);
1033: } else if (drawColors[0]) {
1034: PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", v, rank, !isLabeled ? 1 : 2, color);
1035: } else {
1036: PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [] {};\n", v, rank);
1037: }
1038: }
1039: VecRestoreArray(coordinates, &coords);
1040: PetscViewerFlush(viewer);
1041: /* Plot edges */
1042: if (plotEdges) {
1043: VecGetArray(coordinates, &coords);
1044: PetscViewerASCIIPrintf(viewer, "\\path\n");
1045: for (e = eStart; e < eEnd; ++e) {
1046: const PetscInt *cone;
1047: PetscInt coneSize, offA, offB, dof, d;
1049: if (wp && !PetscBTLookup(wp,e - pStart)) continue;
1050: DMPlexGetConeSize(dm, e, &coneSize);
1052: DMPlexGetCone(dm, e, &cone);
1053: PetscSectionGetDof(coordSection, cone[0], &dof);
1054: PetscSectionGetOffset(coordSection, cone[0], &offA);
1055: PetscSectionGetOffset(coordSection, cone[1], &offB);
1056: PetscViewerASCIISynchronizedPrintf(viewer, "(");
1057: for (d = 0; d < dof; ++d) {
1058: tcoords[d] = (double) (0.5*scale*PetscRealPart(coords[offA+d]+coords[offB+d]));
1059: tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d];
1060: }
1061: /* Rotate coordinates since PGF makes z point out of the page instead of up */
1062: if (dim == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;}
1063: for (d = 0; d < dof; ++d) {
1064: if (d > 0) PetscViewerASCIISynchronizedPrintf(viewer, ",");
1065: PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)tcoords[d]);
1066: }
1067: if (drawHasse) color = colors[1%numColors];
1068: else color = colors[rank%numColors];
1069: for (l = 0; l < numLabels; ++l) {
1070: PetscInt val;
1071: DMGetLabelValue(dm, names[l], v, &val);
1072: if (val >= 0) {color = lcolors[l%numLColors]; break;}
1073: }
1074: PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D} --\n", e, rank, color, e);
1075: }
1076: VecRestoreArray(coordinates, &coords);
1077: PetscViewerFlush(viewer);
1078: PetscViewerASCIIPrintf(viewer, "(0,0);\n");
1079: }
1080: /* Plot cells */
1081: if (dim == 3 || !drawNumbers[1]) {
1082: for (e = eStart; e < eEnd; ++e) {
1083: const PetscInt *cone;
1085: if (wp && !PetscBTLookup(wp,e - pStart)) continue;
1086: color = colors[rank%numColors];
1087: for (l = 0; l < numLabels; ++l) {
1088: PetscInt val;
1089: DMGetLabelValue(dm, names[l], e, &val);
1090: if (val >= 0) {color = lcolors[l%numLColors]; break;}
1091: }
1092: DMPlexGetCone(dm, e, &cone);
1093: PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] (%D_%d) -- (%D_%d);\n", color, cone[0], rank, cone[1], rank);
1094: }
1095: } else {
1096: DMPolytopeType ct;
1098: /* Drawing a 2D polygon */
1099: for (c = cStart; c < cEnd; ++c) {
1100: if (wp && !PetscBTLookup(wp, c - pStart)) continue;
1101: DMPlexGetCellType(dm, c, &ct);
1102: if (ct == DM_POLYTOPE_SEG_PRISM_TENSOR ||
1103: ct == DM_POLYTOPE_TRI_PRISM_TENSOR ||
1104: ct == DM_POLYTOPE_QUAD_PRISM_TENSOR) {
1105: const PetscInt *cone;
1106: PetscInt coneSize, e;
1108: DMPlexGetCone(dm, c, &cone);
1109: DMPlexGetConeSize(dm, c, &coneSize);
1110: for (e = 0; e < coneSize; ++e) {
1111: const PetscInt *econe;
1113: DMPlexGetCone(dm, cone[e], &econe);
1114: PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] (%D_%d) -- (%D_%d) -- (%D_%d);\n", colors[rank%numColors], econe[0], rank, cone[e], rank, econe[1], rank);
1115: }
1116: } else {
1117: PetscInt *closure = NULL;
1118: PetscInt closureSize, Nv = 0, v;
1120: DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
1121: for (p = 0; p < closureSize*2; p += 2) {
1122: const PetscInt point = closure[p];
1124: if ((point >= vStart) && (point < vEnd)) closure[Nv++] = point;
1125: }
1126: PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] ", colors[rank%numColors]);
1127: for (v = 0; v <= Nv; ++v) {
1128: const PetscInt vertex = closure[v%Nv];
1130: if (v > 0) {
1131: if (plotEdges) {
1132: const PetscInt *edge;
1133: PetscInt endpoints[2], ne;
1135: endpoints[0] = closure[v-1]; endpoints[1] = vertex;
1136: DMPlexGetJoin(dm, 2, endpoints, &ne, &edge);
1138: PetscViewerASCIISynchronizedPrintf(viewer, " -- (%D_%d) -- ", edge[0], rank);
1139: DMPlexRestoreJoin(dm, 2, endpoints, &ne, &edge);
1140: } else {
1141: PetscViewerASCIISynchronizedPrintf(viewer, " -- ");
1142: }
1143: }
1144: PetscViewerASCIISynchronizedPrintf(viewer, "(%D_%d)", vertex, rank);
1145: }
1146: PetscViewerASCIISynchronizedPrintf(viewer, ";\n");
1147: DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
1148: }
1149: }
1150: }
1151: VecGetArray(coordinates, &coords);
1152: for (c = cStart; c < cEnd; ++c) {
1153: double ccoords[3] = {0.0, 0.0, 0.0};
1154: PetscBool isLabeled = PETSC_FALSE;
1155: PetscInt *closure = NULL;
1156: PetscInt closureSize, dof, d, n = 0;
1158: if (wp && !PetscBTLookup(wp,c - pStart)) continue;
1159: DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
1160: PetscViewerASCIISynchronizedPrintf(viewer, "\\path (");
1161: for (p = 0; p < closureSize*2; p += 2) {
1162: const PetscInt point = closure[p];
1163: PetscInt off;
1165: if ((point < vStart) || (point >= vEnd)) continue;
1166: PetscSectionGetDof(coordSection, point, &dof);
1167: PetscSectionGetOffset(coordSection, point, &off);
1168: for (d = 0; d < dof; ++d) {
1169: tcoords[d] = (double) (scale*PetscRealPart(coords[off+d]));
1170: tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d];
1171: }
1172: /* Rotate coordinates since PGF makes z point out of the page instead of up */
1173: if (dof == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;}
1174: for (d = 0; d < dof; ++d) {ccoords[d] += tcoords[d];}
1175: ++n;
1176: }
1177: for (d = 0; d < dof; ++d) {ccoords[d] /= n;}
1178: DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
1179: for (d = 0; d < dof; ++d) {
1180: if (d > 0) PetscViewerASCIISynchronizedPrintf(viewer, ",");
1181: PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double) ccoords[d]);
1182: }
1183: if (drawHasse) color = colors[depth%numColors];
1184: else color = colors[rank%numColors];
1185: for (l = 0; l < numLabels; ++l) {
1186: PetscInt val;
1187: DMGetLabelValue(dm, names[l], c, &val);
1188: if (val >= 0) {color = lcolors[l%numLColors]; isLabeled = PETSC_TRUE; break;}
1189: }
1190: if (drawNumbers[dim]) {
1191: PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D};\n", c, rank, color, c);
1192: } else if (drawColors[dim]) {
1193: PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", c, rank, !isLabeled ? 1 : 2, color);
1194: } else {
1195: PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [] {};\n", c, rank);
1196: }
1197: }
1198: VecRestoreArray(coordinates, &coords);
1199: if (drawHasse) {
1200: color = colors[depth%numColors];
1201: PetscViewerASCIIPrintf(viewer, "%% Cells\n");
1202: PetscViewerASCIIPrintf(viewer, "\\foreach \\c in {\\cStart,...,\\cEnd}\n");
1203: PetscViewerASCIIPrintf(viewer, "{\n");
1204: PetscViewerASCIIPrintf(viewer, " \\node(\\c_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\cShift+\\c-\\cStart,0) {\\c};\n", rank, color);
1205: PetscViewerASCIIPrintf(viewer, "}\n");
1207: color = colors[1%numColors];
1208: PetscViewerASCIIPrintf(viewer, "%% Edges\n");
1209: PetscViewerASCIIPrintf(viewer, "\\foreach \\e in {\\eStart,...,\\eEnd}\n");
1210: PetscViewerASCIIPrintf(viewer, "{\n");
1211: PetscViewerASCIIPrintf(viewer, " \\node(\\e_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\eShift+\\e-\\eStart,1) {\\e};\n", rank, color);
1212: PetscViewerASCIIPrintf(viewer, "}\n");
1214: color = colors[0%numColors];
1215: PetscViewerASCIIPrintf(viewer, "%% Vertices\n");
1216: PetscViewerASCIIPrintf(viewer, "\\foreach \\v in {\\vStart,...,\\vEnd}\n");
1217: PetscViewerASCIIPrintf(viewer, "{\n");
1218: PetscViewerASCIIPrintf(viewer, " \\node(\\v_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\vShift+\\v-\\vStart,2) {\\v};\n", rank, color);
1219: PetscViewerASCIIPrintf(viewer, "}\n");
1221: for (p = pStart; p < pEnd; ++p) {
1222: const PetscInt *cone;
1223: PetscInt coneSize, cp;
1225: DMPlexGetCone(dm, p, &cone);
1226: DMPlexGetConeSize(dm, p, &coneSize);
1227: for (cp = 0; cp < coneSize; ++cp) {
1228: PetscViewerASCIIPrintf(viewer, "\\draw[->, shorten >=1pt] (%D_%d) -- (%D_%d);\n", cone[cp], rank, p, rank);
1229: }
1230: }
1231: }
1232: PetscViewerFlush(viewer);
1233: PetscViewerASCIIPopSynchronized(viewer);
1234: PetscViewerASCIIPrintf(viewer, "\\end{tikzpicture}\n");
1235: PetscViewerASCIIPrintf(viewer, "\\end{document}\n", name);
1236: for (l = 0; l < numLabels; ++l) PetscFree(names[l]);
1237: for (c = 0; c < numColors; ++c) PetscFree(colors[c]);
1238: for (c = 0; c < numLColors; ++c) PetscFree(lcolors[c]);
1239: PetscFree3(names, colors, lcolors);
1240: PetscBTDestroy(&wp);
1241: } else if (format == PETSC_VIEWER_LOAD_BALANCE) {
1242: Vec cown,acown;
1243: VecScatter sct;
1244: ISLocalToGlobalMapping g2l;
1245: IS gid,acis;
1246: MPI_Comm comm,ncomm = MPI_COMM_NULL;
1247: MPI_Group ggroup,ngroup;
1248: PetscScalar *array,nid;
1249: const PetscInt *idxs;
1250: PetscInt *idxs2,*start,*adjacency,*work;
1251: PetscInt64 lm[3],gm[3];
1252: PetscInt i,c,cStart,cEnd,cum,numVertices,ect,ectn,cellHeight;
1253: PetscMPIInt d1,d2,rank;
1255: PetscObjectGetComm((PetscObject)dm,&comm);
1256: MPI_Comm_rank(comm,&rank);
1257: #if defined(PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY)
1258: MPI_Comm_split_type(comm,MPI_COMM_TYPE_SHARED,rank,MPI_INFO_NULL,&ncomm);
1259: #endif
1260: if (ncomm != MPI_COMM_NULL) {
1261: MPI_Comm_group(comm,&ggroup);
1262: MPI_Comm_group(ncomm,&ngroup);
1263: d1 = 0;
1264: MPI_Group_translate_ranks(ngroup,1,&d1,ggroup,&d2);
1265: nid = d2;
1266: MPI_Group_free(&ggroup);
1267: MPI_Group_free(&ngroup);
1268: MPI_Comm_free(&ncomm);
1269: } else nid = 0.0;
1271: /* Get connectivity */
1272: DMPlexGetVTKCellHeight(dm,&cellHeight);
1273: DMPlexCreatePartitionerGraph(dm,cellHeight,&numVertices,&start,&adjacency,&gid);
1275: /* filter overlapped local cells */
1276: DMPlexGetHeightStratum(dm,cellHeight,&cStart,&cEnd);
1277: ISGetIndices(gid,&idxs);
1278: ISGetLocalSize(gid,&cum);
1279: PetscMalloc1(cum,&idxs2);
1280: for (c = cStart, cum = 0; c < cEnd; c++) {
1281: if (idxs[c-cStart] < 0) continue;
1282: idxs2[cum++] = idxs[c-cStart];
1283: }
1284: ISRestoreIndices(gid,&idxs);
1286: ISDestroy(&gid);
1287: ISCreateGeneral(comm,numVertices,idxs2,PETSC_OWN_POINTER,&gid);
1289: /* support for node-aware cell locality */
1290: ISCreateGeneral(comm,start[numVertices],adjacency,PETSC_USE_POINTER,&acis);
1291: VecCreateSeq(PETSC_COMM_SELF,start[numVertices],&acown);
1292: VecCreateMPI(comm,numVertices,PETSC_DECIDE,&cown);
1293: VecGetArray(cown,&array);
1294: for (c = 0; c < numVertices; c++) array[c] = nid;
1295: VecRestoreArray(cown,&array);
1296: VecScatterCreate(cown,acis,acown,NULL,&sct);
1297: VecScatterBegin(sct,cown,acown,INSERT_VALUES,SCATTER_FORWARD);
1298: VecScatterEnd(sct,cown,acown,INSERT_VALUES,SCATTER_FORWARD);
1299: ISDestroy(&acis);
1300: VecScatterDestroy(&sct);
1301: VecDestroy(&cown);
1303: /* compute edgeCut */
1304: for (c = 0, cum = 0; c < numVertices; c++) cum = PetscMax(cum,start[c+1]-start[c]);
1305: PetscMalloc1(cum,&work);
1306: ISLocalToGlobalMappingCreateIS(gid,&g2l);
1307: ISLocalToGlobalMappingSetType(g2l,ISLOCALTOGLOBALMAPPINGHASH);
1308: ISDestroy(&gid);
1309: VecGetArray(acown,&array);
1310: for (c = 0, ect = 0, ectn = 0; c < numVertices; c++) {
1311: PetscInt totl;
1313: totl = start[c+1]-start[c];
1314: ISGlobalToLocalMappingApply(g2l,IS_GTOLM_MASK,totl,adjacency+start[c],NULL,work);
1315: for (i = 0; i < totl; i++) {
1316: if (work[i] < 0) {
1317: ect += 1;
1318: ectn += (array[i + start[c]] != nid) ? 0 : 1;
1319: }
1320: }
1321: }
1322: PetscFree(work);
1323: VecRestoreArray(acown,&array);
1324: lm[0] = numVertices > 0 ? numVertices : PETSC_MAX_INT;
1325: lm[1] = -numVertices;
1326: MPIU_Allreduce(lm,gm,2,MPIU_INT64,MPI_MIN,comm);
1327: PetscViewerASCIIPrintf(viewer," Cell balance: %.2f (max %D, min %D",-((double)gm[1])/((double)gm[0]),-(PetscInt)gm[1],(PetscInt)gm[0]);
1328: lm[0] = ect; /* edgeCut */
1329: lm[1] = ectn; /* node-aware edgeCut */
1330: lm[2] = numVertices > 0 ? 0 : 1; /* empty processes */
1331: MPIU_Allreduce(lm,gm,3,MPIU_INT64,MPI_SUM,comm);
1332: PetscViewerASCIIPrintf(viewer,", empty %D)\n",(PetscInt)gm[2]);
1333: #if defined(PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY)
1334: PetscViewerASCIIPrintf(viewer," Edge Cut: %D (on node %.3f)\n",(PetscInt)(gm[0]/2),gm[0] ? ((double)(gm[1]))/((double)gm[0]) : 1.);
1335: #else
1336: PetscViewerASCIIPrintf(viewer," Edge Cut: %D (on node %.3f)\n",(PetscInt)(gm[0]/2),0.0);
1337: #endif
1338: ISLocalToGlobalMappingDestroy(&g2l);
1339: PetscFree(start);
1340: PetscFree(adjacency);
1341: VecDestroy(&acown);
1342: } else {
1343: const char *name;
1344: PetscInt *sizes, *hybsizes, *ghostsizes;
1345: PetscInt locDepth, depth, cellHeight, dim, d;
1346: PetscInt pStart, pEnd, p, gcStart, gcEnd, gcNum;
1347: PetscInt numLabels, l, maxSize = 17;
1348: DMPolytopeType ct0 = DM_POLYTOPE_UNKNOWN;
1349: MPI_Comm comm;
1350: PetscMPIInt size, rank;
1352: PetscObjectGetComm((PetscObject) dm, &comm);
1353: MPI_Comm_size(comm, &size);
1354: MPI_Comm_rank(comm, &rank);
1355: DMGetDimension(dm, &dim);
1356: DMPlexGetVTKCellHeight(dm, &cellHeight);
1357: PetscObjectGetName((PetscObject) dm, &name);
1358: if (name) PetscViewerASCIIPrintf(viewer, "%s in %D dimension%s:\n", name, dim, dim == 1 ? "" : "s");
1359: else PetscViewerASCIIPrintf(viewer, "Mesh in %D dimension%s:\n", dim, dim == 1 ? "" : "s");
1360: if (cellHeight) PetscViewerASCIIPrintf(viewer, " Cells are at height %D\n", cellHeight);
1361: DMPlexGetDepth(dm, &locDepth);
1362: MPIU_Allreduce(&locDepth, &depth, 1, MPIU_INT, MPI_MAX, comm);
1363: DMPlexGetGhostCellStratum(dm, &gcStart, &gcEnd);
1364: gcNum = gcEnd - gcStart;
1365: if (size < maxSize) PetscCalloc3(size, &sizes, size, &hybsizes, size, &ghostsizes);
1366: else PetscCalloc3(3, &sizes, 3, &hybsizes, 3, &ghostsizes);
1367: for (d = 0; d <= depth; d++) {
1368: PetscInt Nc[2] = {0, 0}, ict;
1370: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
1371: if (pStart < pEnd) DMPlexGetCellType(dm, pStart, &ct0);
1372: ict = ct0;
1373: MPI_Bcast(&ict, 1, MPIU_INT, 0, comm);
1374: ct0 = (DMPolytopeType) ict;
1375: for (p = pStart; p < pEnd; ++p) {
1376: DMPolytopeType ct;
1378: DMPlexGetCellType(dm, p, &ct);
1379: if (ct == ct0) ++Nc[0];
1380: else ++Nc[1];
1381: }
1382: if (size < maxSize) {
1383: MPI_Gather(&Nc[0], 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);
1384: MPI_Gather(&Nc[1], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm);
1385: if (d == depth) MPI_Gather(&gcNum, 1, MPIU_INT, ghostsizes, 1, MPIU_INT, 0, comm);
1386: PetscViewerASCIIPrintf(viewer, " Number of %D-cells per rank:", (depth == 1) && d ? dim : d);
1387: for (p = 0; p < size; ++p) {
1388: if (rank == 0) {
1389: PetscViewerASCIIPrintf(viewer, " %D", sizes[p]+hybsizes[p]);
1390: if (hybsizes[p] > 0) PetscViewerASCIIPrintf(viewer, " (%D)", hybsizes[p]);
1391: if (ghostsizes[p] > 0) PetscViewerASCIIPrintf(viewer, " [%D]", ghostsizes[p]);
1392: }
1393: }
1394: } else {
1395: PetscInt locMinMax[2];
1397: locMinMax[0] = Nc[0]+Nc[1]; locMinMax[1] = Nc[0]+Nc[1];
1398: PetscGlobalMinMaxInt(comm, locMinMax, sizes);
1399: locMinMax[0] = Nc[1]; locMinMax[1] = Nc[1];
1400: PetscGlobalMinMaxInt(comm, locMinMax, hybsizes);
1401: if (d == depth) {
1402: locMinMax[0] = gcNum; locMinMax[1] = gcNum;
1403: PetscGlobalMinMaxInt(comm, locMinMax, ghostsizes);
1404: }
1405: PetscViewerASCIIPrintf(viewer, " Min/Max of %D-cells per rank:", (depth == 1) && d ? dim : d);
1406: PetscViewerASCIIPrintf(viewer, " %" PetscInt_FMT "/%" PetscInt_FMT, sizes[0], sizes[1]);
1407: if (hybsizes[0] > 0) PetscViewerASCIIPrintf(viewer, " (%" PetscInt_FMT "/%" PetscInt_FMT ")", hybsizes[0], hybsizes[1]);
1408: if (ghostsizes[0] > 0) PetscViewerASCIIPrintf(viewer, " [%" PetscInt_FMT "/%" PetscInt_FMT "]", ghostsizes[0], ghostsizes[1]);
1409: }
1410: PetscViewerASCIIPrintf(viewer, "\n");
1411: }
1412: PetscFree3(sizes, hybsizes, ghostsizes);
1413: {
1414: const PetscReal *maxCell;
1415: const PetscReal *L;
1416: const DMBoundaryType *bd;
1417: PetscBool per, localized;
1419: DMGetPeriodicity(dm, &per, &maxCell, &L, &bd);
1420: DMGetCoordinatesLocalized(dm, &localized);
1421: if (per) {
1422: PetscViewerASCIIPrintf(viewer, "Periodic mesh (");
1423: PetscViewerASCIIUseTabs(viewer, PETSC_FALSE);
1424: for (d = 0; d < dim; ++d) {
1425: if (bd && d > 0) PetscViewerASCIIPrintf(viewer, ", ");
1426: if (bd) PetscViewerASCIIPrintf(viewer, "%s", DMBoundaryTypes[bd[d]]);
1427: }
1428: PetscViewerASCIIPrintf(viewer, ") coordinates %s\n", localized ? "localized" : "not localized");
1429: PetscViewerASCIIUseTabs(viewer, PETSC_TRUE);
1430: }
1431: }
1432: DMGetNumLabels(dm, &numLabels);
1433: if (numLabels) PetscViewerASCIIPrintf(viewer, "Labels:\n");
1434: for (l = 0; l < numLabels; ++l) {
1435: DMLabel label;
1436: const char *name;
1437: IS valueIS;
1438: const PetscInt *values;
1439: PetscInt numValues, v;
1441: DMGetLabelName(dm, l, &name);
1442: DMGetLabel(dm, name, &label);
1443: DMLabelGetNumValues(label, &numValues);
1444: PetscViewerASCIIPrintf(viewer, " %s: %D strata with value/size (", name, numValues);
1445: DMLabelGetValueIS(label, &valueIS);
1446: ISGetIndices(valueIS, &values);
1447: PetscViewerASCIIUseTabs(viewer, PETSC_FALSE);
1448: for (v = 0; v < numValues; ++v) {
1449: PetscInt size;
1451: DMLabelGetStratumSize(label, values[v], &size);
1452: if (v > 0) PetscViewerASCIIPrintf(viewer, ", ");
1453: PetscViewerASCIIPrintf(viewer, "%D (%D)", values[v], size);
1454: }
1455: PetscViewerASCIIPrintf(viewer, ")\n");
1456: PetscViewerASCIIUseTabs(viewer, PETSC_TRUE);
1457: ISRestoreIndices(valueIS, &values);
1458: ISDestroy(&valueIS);
1459: }
1460: {
1461: char **labelNames;
1462: PetscInt Nl = numLabels;
1463: PetscBool flg;
1465: PetscMalloc1(Nl, &labelNames);
1466: PetscOptionsGetStringArray(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_plex_view_labels", labelNames, &Nl, &flg);
1467: for (l = 0; l < Nl; ++l) {
1468: DMLabel label;
1470: DMHasLabel(dm, labelNames[l], &flg);
1471: if (flg) {
1472: DMGetLabel(dm, labelNames[l], &label);
1473: DMLabelView(label, viewer);
1474: }
1475: PetscFree(labelNames[l]);
1476: }
1477: PetscFree(labelNames);
1478: }
1479: /* If no fields are specified, people do not want to see adjacency */
1480: if (dm->Nf) {
1481: PetscInt f;
1483: for (f = 0; f < dm->Nf; ++f) {
1484: const char *name;
1486: PetscObjectGetName(dm->fields[f].disc, &name);
1487: if (numLabels) PetscViewerASCIIPrintf(viewer, "Field %s:\n", name);
1488: PetscViewerASCIIPushTab(viewer);
1489: if (dm->fields[f].label) DMLabelView(dm->fields[f].label, viewer);
1490: if (dm->fields[f].adjacency[0]) {
1491: if (dm->fields[f].adjacency[1]) PetscViewerASCIIPrintf(viewer, "adjacency FVM++\n");
1492: else PetscViewerASCIIPrintf(viewer, "adjacency FVM\n");
1493: } else {
1494: if (dm->fields[f].adjacency[1]) PetscViewerASCIIPrintf(viewer, "adjacency FEM\n");
1495: else PetscViewerASCIIPrintf(viewer, "adjacency FUNKY\n");
1496: }
1497: PetscViewerASCIIPopTab(viewer);
1498: }
1499: }
1500: DMGetCoarseDM(dm, &cdm);
1501: if (cdm) {
1502: PetscViewerASCIIPushTab(viewer);
1503: DMPlexView_Ascii(cdm, viewer);
1504: PetscViewerASCIIPopTab(viewer);
1505: }
1506: }
1507: return 0;
1508: }
1510: static PetscErrorCode DMPlexDrawCell(DM dm, PetscDraw draw, PetscInt cell, const PetscScalar coords[])
1511: {
1512: DMPolytopeType ct;
1513: PetscMPIInt rank;
1514: PetscInt cdim;
1516: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1517: DMPlexGetCellType(dm, cell, &ct);
1518: DMGetCoordinateDim(dm, &cdim);
1519: switch (ct) {
1520: case DM_POLYTOPE_SEGMENT:
1521: case DM_POLYTOPE_POINT_PRISM_TENSOR:
1522: switch (cdim) {
1523: case 1:
1524: {
1525: const PetscReal y = 0.5; /* TODO Put it in the middle of the viewport */
1526: const PetscReal dy = 0.05; /* TODO Make it a fraction of the total length */
1528: PetscDrawLine(draw, PetscRealPart(coords[0]), y, PetscRealPart(coords[1]), y, PETSC_DRAW_BLACK);
1529: PetscDrawLine(draw, PetscRealPart(coords[0]), y+dy, PetscRealPart(coords[0]), y-dy, PETSC_DRAW_BLACK);
1530: PetscDrawLine(draw, PetscRealPart(coords[1]), y+dy, PetscRealPart(coords[1]), y-dy, PETSC_DRAW_BLACK);
1531: }
1532: break;
1533: case 2:
1534: {
1535: const PetscReal dx = (PetscRealPart(coords[3]) - PetscRealPart(coords[1]));
1536: const PetscReal dy = (PetscRealPart(coords[2]) - PetscRealPart(coords[0]));
1537: const PetscReal l = 0.1/PetscSqrtReal(dx*dx + dy*dy);
1539: PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);
1540: PetscDrawLine(draw, PetscRealPart(coords[0])+l*dx, PetscRealPart(coords[1])+l*dy, PetscRealPart(coords[0])-l*dx, PetscRealPart(coords[1])-l*dy, PETSC_DRAW_BLACK);
1541: PetscDrawLine(draw, PetscRealPart(coords[2])+l*dx, PetscRealPart(coords[3])+l*dy, PetscRealPart(coords[2])-l*dx, PetscRealPart(coords[3])-l*dy, PETSC_DRAW_BLACK);
1542: }
1543: break;
1544: default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of dimension %D", cdim);
1545: }
1546: break;
1547: case DM_POLYTOPE_TRIANGLE:
1548: PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]),
1549: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1550: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1551: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2));
1552: PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);
1553: PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK);
1554: PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK);
1555: break;
1556: case DM_POLYTOPE_QUADRILATERAL:
1557: PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]),
1558: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1559: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1560: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2));
1561: PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]),
1562: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1563: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1564: PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2));
1565: PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);
1566: PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK);
1567: PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_BLACK);
1568: PetscDrawLine(draw, PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK);
1569: break;
1570: default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of type %s", DMPolytopeTypes[ct]);
1571: }
1572: return 0;
1573: }
1575: static PetscErrorCode DMPlexDrawCellHighOrder(DM dm, PetscDraw draw, PetscInt cell, const PetscScalar coords[], PetscInt edgeDiv, PetscReal refCoords[], PetscReal edgeCoords[])
1576: {
1577: DMPolytopeType ct;
1578: PetscReal centroid[2] = {0., 0.};
1579: PetscMPIInt rank;
1580: PetscInt fillColor, v, e, d;
1582: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1583: DMPlexGetCellType(dm, cell, &ct);
1584: fillColor = PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2;
1585: switch (ct) {
1586: case DM_POLYTOPE_TRIANGLE:
1587: {
1588: PetscReal refVertices[6] = {-1., -1., 1., -1., -1., 1.};
1590: for (v = 0; v < 3; ++v) {centroid[0] += PetscRealPart(coords[v*2+0])/3.;centroid[1] += PetscRealPart(coords[v*2+1])/3.;}
1591: for (e = 0; e < 3; ++e) {
1592: refCoords[0] = refVertices[e*2+0];
1593: refCoords[1] = refVertices[e*2+1];
1594: for (d = 1; d <= edgeDiv; ++d) {
1595: refCoords[d*2+0] = refCoords[0] + (refVertices[(e+1)%3 * 2 + 0] - refCoords[0])*d/edgeDiv;
1596: refCoords[d*2+1] = refCoords[1] + (refVertices[(e+1)%3 * 2 + 1] - refCoords[1])*d/edgeDiv;
1597: }
1598: DMPlexReferenceToCoordinates(dm, cell, edgeDiv+1, refCoords, edgeCoords);
1599: for (d = 0; d < edgeDiv; ++d) {
1600: PetscDrawTriangle(draw, centroid[0], centroid[1], edgeCoords[d*2+0], edgeCoords[d*2+1], edgeCoords[(d+1)*2+0], edgeCoords[(d+1)*2+1], fillColor, fillColor, fillColor);
1601: PetscDrawLine(draw, edgeCoords[d*2+0], edgeCoords[d*2+1], edgeCoords[(d+1)*2+0], edgeCoords[(d+1)*2+1], PETSC_DRAW_BLACK);
1602: }
1603: }
1604: }
1605: break;
1606: default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of type %s", DMPolytopeTypes[ct]);
1607: }
1608: return 0;
1609: }
1611: static PetscErrorCode DMPlexView_Draw(DM dm, PetscViewer viewer)
1612: {
1613: PetscDraw draw;
1614: DM cdm;
1615: PetscSection coordSection;
1616: Vec coordinates;
1617: const PetscScalar *coords;
1618: PetscReal xyl[2],xyr[2],bound[4] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
1619: PetscReal *refCoords, *edgeCoords;
1620: PetscBool isnull, drawAffine = PETSC_TRUE;
1621: PetscInt dim, vStart, vEnd, cStart, cEnd, c, N, edgeDiv = 4;
1623: DMGetCoordinateDim(dm, &dim);
1625: PetscOptionsGetBool(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_view_draw_affine", &drawAffine, NULL);
1626: if (!drawAffine) PetscMalloc2((edgeDiv+1)*dim, &refCoords, (edgeDiv+1)*dim, &edgeCoords);
1627: DMGetCoordinateDM(dm, &cdm);
1628: DMGetLocalSection(cdm, &coordSection);
1629: DMGetCoordinatesLocal(dm, &coordinates);
1630: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
1631: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
1633: PetscViewerDrawGetDraw(viewer, 0, &draw);
1634: PetscDrawIsNull(draw, &isnull);
1635: if (isnull) return 0;
1636: PetscDrawSetTitle(draw, "Mesh");
1638: VecGetLocalSize(coordinates, &N);
1639: VecGetArrayRead(coordinates, &coords);
1640: for (c = 0; c < N; c += dim) {
1641: bound[0] = PetscMin(bound[0], PetscRealPart(coords[c])); bound[2] = PetscMax(bound[2], PetscRealPart(coords[c]));
1642: bound[1] = PetscMin(bound[1], PetscRealPart(coords[c+1])); bound[3] = PetscMax(bound[3], PetscRealPart(coords[c+1]));
1643: }
1644: VecRestoreArrayRead(coordinates, &coords);
1645: MPIU_Allreduce(&bound[0],xyl,2,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)dm));
1646: MPIU_Allreduce(&bound[2],xyr,2,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)dm));
1647: PetscDrawSetCoordinates(draw, xyl[0], xyl[1], xyr[0], xyr[1]);
1648: PetscDrawClear(draw);
1650: for (c = cStart; c < cEnd; ++c) {
1651: PetscScalar *coords = NULL;
1652: PetscInt numCoords;
1654: DMPlexVecGetClosureAtDepth_Internal(dm, coordSection, coordinates, c, 0, &numCoords, &coords);
1655: if (drawAffine) {
1656: DMPlexDrawCell(dm, draw, c, coords);
1657: } else {
1658: DMPlexDrawCellHighOrder(dm, draw, c, coords, edgeDiv, refCoords, edgeCoords);
1659: }
1660: DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
1661: }
1662: if (!drawAffine) PetscFree2(refCoords, edgeCoords);
1663: PetscDrawFlush(draw);
1664: PetscDrawPause(draw);
1665: PetscDrawSave(draw);
1666: return 0;
1667: }
1669: #if defined(PETSC_HAVE_EXODUSII)
1670: #include <exodusII.h>
1671: #include <petscviewerexodusii.h>
1672: #endif
1674: PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer)
1675: {
1676: PetscBool iascii, ishdf5, isvtk, isdraw, flg, isglvis, isexodus;
1677: char name[PETSC_MAX_PATH_LEN];
1681: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
1682: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);
1683: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
1684: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);
1685: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);
1686: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWEREXODUSII, &isexodus);
1687: if (iascii) {
1688: PetscViewerFormat format;
1689: PetscViewerGetFormat(viewer, &format);
1690: if (format == PETSC_VIEWER_ASCII_GLVIS) {
1691: DMPlexView_GLVis(dm, viewer);
1692: } else {
1693: DMPlexView_Ascii(dm, viewer);
1694: }
1695: } else if (ishdf5) {
1696: #if defined(PETSC_HAVE_HDF5)
1697: DMPlexView_HDF5_Internal(dm, viewer);
1698: #else
1699: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
1700: #endif
1701: } else if (isvtk) {
1702: DMPlexVTKWriteAll((PetscObject) dm,viewer);
1703: } else if (isdraw) {
1704: DMPlexView_Draw(dm, viewer);
1705: } else if (isglvis) {
1706: DMPlexView_GLVis(dm, viewer);
1707: #if defined(PETSC_HAVE_EXODUSII)
1708: } else if (isexodus) {
1709: /*
1710: exodusII requires that all sets be part of exactly one cell set.
1711: If the dm does not have a "Cell Sets" label defined, we create one
1712: with ID 1, containig all cells.
1713: Note that if the Cell Sets label is defined but does not cover all cells,
1714: we may still have a problem. This should probably be checked here or in the viewer;
1715: */
1716: PetscInt numCS;
1717: DMGetLabelSize(dm,"Cell Sets",&numCS);
1718: if (!numCS) {
1719: PetscInt cStart, cEnd, c;
1720: DMCreateLabel(dm, "Cell Sets");
1721: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
1722: for (c = cStart; c < cEnd; ++c) DMSetLabelValue(dm, "Cell Sets", c, 1);
1723: }
1724: DMView_PlexExodusII(dm, viewer);
1725: #endif
1726: } else {
1727: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex writing", ((PetscObject)viewer)->type_name);
1728: }
1729: /* Optionally view the partition */
1730: PetscOptionsHasName(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_partition_view", &flg);
1731: if (flg) {
1732: Vec ranks;
1733: DMPlexCreateRankField(dm, &ranks);
1734: VecView(ranks, viewer);
1735: VecDestroy(&ranks);
1736: }
1737: /* Optionally view a label */
1738: PetscOptionsGetString(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_label_view", name, sizeof(name), &flg);
1739: if (flg) {
1740: DMLabel label;
1741: Vec val;
1743: DMGetLabel(dm, name, &label);
1745: DMPlexCreateLabelField(dm, label, &val);
1746: VecView(val, viewer);
1747: VecDestroy(&val);
1748: }
1749: return 0;
1750: }
1752: /*@
1753: DMPlexTopologyView - Saves a DMPlex topology into a file
1755: Collective on DM
1757: Input Parameters:
1758: + dm - The DM whose topology is to be saved
1759: - viewer - The PetscViewer for saving
1761: Level: advanced
1763: .seealso: DMView(), DMPlexCoordinatesView(), DMPlexLabelsView(), DMPlexTopologyLoad()
1764: @*/
1765: PetscErrorCode DMPlexTopologyView(DM dm, PetscViewer viewer)
1766: {
1767: PetscBool ishdf5;
1771: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
1772: PetscLogEventBegin(DMPLEX_TopologyView,viewer,0,0,0);
1773: if (ishdf5) {
1774: #if defined(PETSC_HAVE_HDF5)
1775: PetscViewerFormat format;
1776: PetscViewerGetFormat(viewer, &format);
1777: if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) {
1778: IS globalPointNumbering;
1780: DMPlexCreatePointNumbering(dm, &globalPointNumbering);
1781: DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbering, viewer);
1782: ISDestroy(&globalPointNumbering);
1783: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]);
1784: #else
1785: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
1786: #endif
1787: }
1788: PetscLogEventEnd(DMPLEX_TopologyView,viewer,0,0,0);
1789: return 0;
1790: }
1792: /*@
1793: DMPlexCoordinatesView - Saves DMPlex coordinates into a file
1795: Collective on DM
1797: Input Parameters:
1798: + dm - The DM whose coordinates are to be saved
1799: - viewer - The PetscViewer for saving
1801: Level: advanced
1803: .seealso: DMView(), DMPlexTopologyView(), DMPlexLabelsView(), DMPlexCoordinatesLoad()
1804: @*/
1805: PetscErrorCode DMPlexCoordinatesView(DM dm, PetscViewer viewer)
1806: {
1807: PetscBool ishdf5;
1811: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
1812: PetscLogEventBegin(DMPLEX_CoordinatesView,viewer,0,0,0);
1813: if (ishdf5) {
1814: #if defined(PETSC_HAVE_HDF5)
1815: PetscViewerFormat format;
1816: PetscViewerGetFormat(viewer, &format);
1817: if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) {
1818: DMPlexCoordinatesView_HDF5_Internal(dm, viewer);
1819: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
1820: #else
1821: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
1822: #endif
1823: }
1824: PetscLogEventEnd(DMPLEX_CoordinatesView,viewer,0,0,0);
1825: return 0;
1826: }
1828: /*@
1829: DMPlexLabelsView - Saves DMPlex labels into a file
1831: Collective on DM
1833: Input Parameters:
1834: + dm - The DM whose labels are to be saved
1835: - viewer - The PetscViewer for saving
1837: Level: advanced
1839: .seealso: DMView(), DMPlexTopologyView(), DMPlexCoordinatesView(), DMPlexLabelsLoad()
1840: @*/
1841: PetscErrorCode DMPlexLabelsView(DM dm, PetscViewer viewer)
1842: {
1843: PetscBool ishdf5;
1847: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
1848: PetscLogEventBegin(DMPLEX_LabelsView,viewer,0,0,0);
1849: if (ishdf5) {
1850: #if defined(PETSC_HAVE_HDF5)
1851: IS globalPointNumbering;
1852: PetscViewerFormat format;
1854: PetscViewerGetFormat(viewer, &format);
1855: if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) {
1856: DMPlexCreatePointNumbering(dm, &globalPointNumbering);
1857: DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbering, viewer);
1858: ISDestroy(&globalPointNumbering);
1859: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
1860: #else
1861: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
1862: #endif
1863: }
1864: PetscLogEventEnd(DMPLEX_LabelsView,viewer,0,0,0);
1865: return 0;
1866: }
1868: /*@
1869: DMPlexSectionView - Saves a section associated with a DMPlex
1871: Collective on DM
1873: Input Parameters:
1874: + dm - The DM that contains the topology on which the section to be saved is defined
1875: . viewer - The PetscViewer for saving
1876: - sectiondm - The DM that contains the section to be saved
1878: Level: advanced
1880: Notes:
1881: This function is a wrapper around PetscSectionView(); in addition to the raw section, it saves information that associates the section points to the topology (dm) points. When the topology (dm) and the section are later loaded with DMPlexTopologyLoad() and DMPlexSectionLoad(), respectively, this information is used to match section points with topology points.
1883: In general dm and sectiondm are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with PetscObjectSetName(). In practice, however, they can be the same object if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name.
1885: .seealso: DMView(), DMPlexTopologyView(), DMPlexCoordinatesView(), DMPlexLabelsView(), DMPlexGlobalVectorView(), DMPlexLocalVectorView(), PetscSectionView(), DMPlexSectionLoad()
1886: @*/
1887: PetscErrorCode DMPlexSectionView(DM dm, PetscViewer viewer, DM sectiondm)
1888: {
1889: PetscBool ishdf5;
1894: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
1895: PetscLogEventBegin(DMPLEX_SectionView,viewer,0,0,0);
1896: if (ishdf5) {
1897: #if defined(PETSC_HAVE_HDF5)
1898: DMPlexSectionView_HDF5_Internal(dm, viewer, sectiondm);
1899: #else
1900: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
1901: #endif
1902: }
1903: PetscLogEventEnd(DMPLEX_SectionView,viewer,0,0,0);
1904: return 0;
1905: }
1907: /*@
1908: DMPlexGlobalVectorView - Saves a global vector
1910: Collective on DM
1912: Input Parameters:
1913: + dm - The DM that represents the topology
1914: . viewer - The PetscViewer to save data with
1915: . sectiondm - The DM that contains the global section on which vec is defined
1916: - vec - The global vector to be saved
1918: Level: advanced
1920: Notes:
1921: In general dm and sectiondm are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with PetscObjectSetName(). In practice, however, they can be the same object if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name.
1923: Typical calling sequence
1924: $ DMCreate(PETSC_COMM_WORLD, &dm);
1925: $ DMSetType(dm, DMPLEX);
1926: $ PetscObjectSetName((PetscObject)dm, "topologydm_name");
1927: $ DMClone(dm, §iondm);
1928: $ PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name");
1929: $ PetscSectionCreate(PETSC_COMM_WORLD, §ion);
1930: $ DMPlexGetChart(sectiondm, &pStart, &pEnd);
1931: $ PetscSectionSetChart(section, pStart, pEnd);
1932: $ PetscSectionSetUp(section);
1933: $ DMSetLocalSection(sectiondm, section);
1934: $ PetscSectionDestroy(§ion);
1935: $ DMGetGlobalVector(sectiondm, &vec);
1936: $ PetscObjectSetName((PetscObject)vec, "vec_name");
1937: $ DMPlexTopologyView(dm, viewer);
1938: $ DMPlexSectionView(dm, viewer, sectiondm);
1939: $ DMPlexGlobalVectorView(dm, viewer, sectiondm, vec);
1940: $ DMRestoreGlobalVector(sectiondm, &vec);
1941: $ DMDestroy(§iondm);
1942: $ DMDestroy(&dm);
1944: .seealso: DMPlexTopologyView(), DMPlexSectionView(), DMPlexLocalVectorView(), DMPlexGlobalVectorLoad(), DMPlexLocalVectorLoad()
1945: @*/
1946: PetscErrorCode DMPlexGlobalVectorView(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1947: {
1948: PetscBool ishdf5;
1954: /* Check consistency */
1955: {
1956: PetscSection section;
1957: PetscBool includesConstraints;
1958: PetscInt m, m1;
1960: VecGetLocalSize(vec, &m1);
1961: DMGetGlobalSection(sectiondm, §ion);
1962: PetscSectionGetIncludesConstraints(section, &includesConstraints);
1963: if (includesConstraints) PetscSectionGetStorageSize(section, &m);
1964: else PetscSectionGetConstrainedStorageSize(section, &m);
1966: }
1967: PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5);
1968: PetscLogEventBegin(DMPLEX_GlobalVectorView,viewer,0,0,0);
1969: if (ishdf5) {
1970: #if defined(PETSC_HAVE_HDF5)
1971: DMPlexGlobalVectorView_HDF5_Internal(dm, viewer, sectiondm, vec);
1972: #else
1973: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
1974: #endif
1975: }
1976: PetscLogEventEnd(DMPLEX_GlobalVectorView,viewer,0,0,0);
1977: return 0;
1978: }
1980: /*@
1981: DMPlexLocalVectorView - Saves a local vector
1983: Collective on DM
1985: Input Parameters:
1986: + dm - The DM that represents the topology
1987: . viewer - The PetscViewer to save data with
1988: . sectiondm - The DM that contains the local section on which vec is defined; may be the same as dm
1989: - vec - The local vector to be saved
1991: Level: advanced
1993: Notes:
1994: In general dm and sectiondm are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with PetscObjectSetName(). In practice, however, they can be the same object if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name.
1996: Typical calling sequence
1997: $ DMCreate(PETSC_COMM_WORLD, &dm);
1998: $ DMSetType(dm, DMPLEX);
1999: $ PetscObjectSetName((PetscObject)dm, "topologydm_name");
2000: $ DMClone(dm, §iondm);
2001: $ PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name");
2002: $ PetscSectionCreate(PETSC_COMM_WORLD, §ion);
2003: $ DMPlexGetChart(sectiondm, &pStart, &pEnd);
2004: $ PetscSectionSetChart(section, pStart, pEnd);
2005: $ PetscSectionSetUp(section);
2006: $ DMSetLocalSection(sectiondm, section);
2007: $ DMGetLocalVector(sectiondm, &vec);
2008: $ PetscObjectSetName((PetscObject)vec, "vec_name");
2009: $ DMPlexTopologyView(dm, viewer);
2010: $ DMPlexSectionView(dm, viewer, sectiondm);
2011: $ DMPlexLocalVectorView(dm, viewer, sectiondm, vec);
2012: $ DMRestoreLocalVector(sectiondm, &vec);
2013: $ DMDestroy(§iondm);
2014: $ DMDestroy(&dm);
2016: .seealso: DMPlexTopologyView(), DMPlexSectionView(), DMPlexGlobalVectorView(), DMPlexGlobalVectorLoad(), DMPlexLocalVectorLoad()
2017: @*/
2018: PetscErrorCode DMPlexLocalVectorView(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
2019: {
2020: PetscBool ishdf5;
2026: /* Check consistency */
2027: {
2028: PetscSection section;
2029: PetscBool includesConstraints;
2030: PetscInt m, m1;
2032: VecGetLocalSize(vec, &m1);
2033: DMGetLocalSection(sectiondm, §ion);
2034: PetscSectionGetIncludesConstraints(section, &includesConstraints);
2035: if (includesConstraints) PetscSectionGetStorageSize(section, &m);
2036: else PetscSectionGetConstrainedStorageSize(section, &m);
2038: }
2039: PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5);
2040: PetscLogEventBegin(DMPLEX_LocalVectorView,viewer,0,0,0);
2041: if (ishdf5) {
2042: #if defined(PETSC_HAVE_HDF5)
2043: DMPlexLocalVectorView_HDF5_Internal(dm, viewer, sectiondm, vec);
2044: #else
2045: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2046: #endif
2047: }
2048: PetscLogEventEnd(DMPLEX_LocalVectorView,viewer,0,0,0);
2049: return 0;
2050: }
2052: PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer)
2053: {
2054: PetscBool ishdf5;
2058: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
2059: if (ishdf5) {
2060: #if defined(PETSC_HAVE_HDF5)
2061: PetscViewerFormat format;
2062: PetscViewerGetFormat(viewer, &format);
2063: if (format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) {
2064: DMPlexLoad_HDF5_Xdmf_Internal(dm, viewer);
2065: } else if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) {
2066: DMPlexLoad_HDF5_Internal(dm, viewer);
2067: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
2068: return 0;
2069: #else
2070: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2071: #endif
2072: } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex loading", ((PetscObject)viewer)->type_name);
2073: }
2075: /*@
2076: DMPlexTopologyLoad - Loads a topology into a DMPlex
2078: Collective on DM
2080: Input Parameters:
2081: + dm - The DM into which the topology is loaded
2082: - viewer - The PetscViewer for the saved topology
2084: Output Parameters:
2085: . globalToLocalPointSF - The PetscSF that pushes points in [0, N) to the associated points in the loaded plex, where N is the global number of points; NULL if unneeded
2087: Level: advanced
2089: .seealso: DMLoad(), DMPlexCoordinatesLoad(), DMPlexLabelsLoad(), DMView(), PetscViewerHDF5Open(), PetscViewerPushFormat()
2090: @*/
2091: PetscErrorCode DMPlexTopologyLoad(DM dm, PetscViewer viewer, PetscSF *globalToLocalPointSF)
2092: {
2093: PetscBool ishdf5;
2098: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
2099: PetscLogEventBegin(DMPLEX_TopologyLoad,viewer,0,0,0);
2100: if (ishdf5) {
2101: #if defined(PETSC_HAVE_HDF5)
2102: PetscViewerFormat format;
2103: PetscViewerGetFormat(viewer, &format);
2104: if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) {
2105: DMPlexTopologyLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF);
2106: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
2107: #else
2108: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2109: #endif
2110: }
2111: PetscLogEventEnd(DMPLEX_TopologyLoad,viewer,0,0,0);
2112: return 0;
2113: }
2115: /*@
2116: DMPlexCoordinatesLoad - Loads coordinates into a DMPlex
2118: Collective on DM
2120: Input Parameters:
2121: + dm - The DM into which the coordinates are loaded
2122: . viewer - The PetscViewer for the saved coordinates
2123: - globalToLocalPointSF - The SF returned by DMPlexTopologyLoad() when loading dm from viewer
2125: Level: advanced
2127: .seealso: DMLoad(), DMPlexTopologyLoad(), DMPlexLabelsLoad(), DMView(), PetscViewerHDF5Open(), PetscViewerPushFormat()
2128: @*/
2129: PetscErrorCode DMPlexCoordinatesLoad(DM dm, PetscViewer viewer, PetscSF globalToLocalPointSF)
2130: {
2131: PetscBool ishdf5;
2136: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
2137: PetscLogEventBegin(DMPLEX_CoordinatesLoad,viewer,0,0,0);
2138: if (ishdf5) {
2139: #if defined(PETSC_HAVE_HDF5)
2140: PetscViewerFormat format;
2141: PetscViewerGetFormat(viewer, &format);
2142: if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) {
2143: DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF);
2144: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
2145: #else
2146: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2147: #endif
2148: }
2149: PetscLogEventEnd(DMPLEX_CoordinatesLoad,viewer,0,0,0);
2150: return 0;
2151: }
2153: /*@
2154: DMPlexLabelsLoad - Loads labels into a DMPlex
2156: Collective on DM
2158: Input Parameters:
2159: + dm - The DM into which the labels are loaded
2160: . viewer - The PetscViewer for the saved labels
2161: - globalToLocalPointSF - The SF returned by DMPlexTopologyLoad() when loading dm from viewer
2163: Level: advanced
2165: Notes:
2166: The PetscSF argument must not be NULL if the DM is distributed, otherwise an error occurs.
2168: .seealso: DMLoad(), DMPlexTopologyLoad(), DMPlexCoordinatesLoad(), DMView(), PetscViewerHDF5Open(), PetscViewerPushFormat()
2169: @*/
2170: PetscErrorCode DMPlexLabelsLoad(DM dm, PetscViewer viewer, PetscSF globalToLocalPointSF)
2171: {
2172: PetscBool ishdf5;
2177: PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
2178: PetscLogEventBegin(DMPLEX_LabelsLoad,viewer,0,0,0);
2179: if (ishdf5) {
2180: #if defined(PETSC_HAVE_HDF5)
2181: PetscViewerFormat format;
2183: PetscViewerGetFormat(viewer, &format);
2184: if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) {
2185: DMPlexLabelsLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF);
2186: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
2187: #else
2188: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2189: #endif
2190: }
2191: PetscLogEventEnd(DMPLEX_LabelsLoad,viewer,0,0,0);
2192: return 0;
2193: }
2195: /*@
2196: DMPlexSectionLoad - Loads section into a DMPlex
2198: Collective on DM
2200: Input Parameters:
2201: + dm - The DM that represents the topology
2202: . viewer - The PetscViewer that represents the on-disk section (sectionA)
2203: . sectiondm - The DM into which the on-disk section (sectionA) is migrated
2204: - globalToLocalPointSF - The SF returned by DMPlexTopologyLoad() when loading dm from viewer
2206: Output Parameters
2207: + globalDofSF - The SF that migrates any on-disk Vec data associated with sectionA into a global Vec associated with the sectiondm's global section (NULL if not needed)
2208: - localDofSF - The SF that migrates any on-disk Vec data associated with sectionA into a local Vec associated with the sectiondm's local section (NULL if not needed)
2210: Level: advanced
2212: Notes:
2213: This function is a wrapper around PetscSectionLoad(); it loads, in addition to the raw section, a list of global point numbers that associates each on-disk section point with a global point number in [0, NX), where NX is the number of topology points in dm. Noting that globalToLocalPointSF associates each topology point in dm with a global number in [0, NX), one can readily establish an association of the on-disk section points with the topology points.
2215: In general dm and sectiondm are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with PetscObjectSetName(). In practice, however, they can be the same object if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name.
2217: The output parameter, globalDofSF (localDofSF), can later be used with DMPlexGlobalVectorLoad() (DMPlexLocalVectorLoad()) to load on-disk vectors into global (local) vectors associated with sectiondm's global (local) section.
2219: Example using 2 processes:
2220: $ NX (number of points on dm): 4
2221: $ sectionA : the on-disk section
2222: $ vecA : a vector associated with sectionA
2223: $ sectionB : sectiondm's local section constructed in this function
2224: $ vecB (local) : a vector associated with sectiondm's local section
2225: $ vecB (global) : a vector associated with sectiondm's global section
2226: $
2227: $ rank 0 rank 1
2228: $ vecA (global) : [.0 .4 .1 | .2 .3] <- to be loaded in DMPlexGlobalVectorLoad() or DMPlexLocalVectorLoad()
2229: $ sectionA->atlasOff : 0 2 | 1 <- loaded in PetscSectionLoad()
2230: $ sectionA->atlasDof : 1 3 | 1 <- loaded in PetscSectionLoad()
2231: $ sectionA's global point numbers: 0 2 | 3 <- loaded in DMPlexSectionLoad()
2232: $ [0, NX) : 0 1 | 2 3 <- conceptual partition used in globalToLocalPointSF
2233: $ sectionB's global point numbers: 0 1 3 | 3 2 <- associated with [0, NX) by globalToLocalPointSF
2234: $ sectionB->atlasDof : 1 0 1 | 1 3
2235: $ sectionB->atlasOff (no perm) : 0 1 1 | 0 1
2236: $ vecB (local) : [.0 .4] | [.4 .1 .2 .3] <- to be constructed by calling DMPlexLocalVectorLoad() with localDofSF
2237: $ vecB (global) : [.0 .4 | .1 .2 .3] <- to be constructed by calling DMPlexGlobalVectorLoad() with globalDofSF
2238: $
2239: $ where "|" represents a partition of loaded data, and global point 3 is assumed to be owned by rank 0.
2241: .seealso: DMLoad(), DMPlexTopologyLoad(), DMPlexCoordinatesLoad(), DMPlexLabelsLoad(), DMPlexGlobalVectorLoad(), DMPlexLocalVectorLoad(), PetscSectionLoad(), DMPlexSectionView()
2242: @*/
2243: PetscErrorCode DMPlexSectionLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF globalToLocalPointSF, PetscSF *globalDofSF, PetscSF *localDofSF)
2244: {
2245: PetscBool ishdf5;
2253: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
2254: PetscLogEventBegin(DMPLEX_SectionLoad,viewer,0,0,0);
2255: if (ishdf5) {
2256: #if defined(PETSC_HAVE_HDF5)
2257: DMPlexSectionLoad_HDF5_Internal(dm, viewer, sectiondm, globalToLocalPointSF, globalDofSF, localDofSF);
2258: #else
2259: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2260: #endif
2261: }
2262: PetscLogEventEnd(DMPLEX_SectionLoad,viewer,0,0,0);
2263: return 0;
2264: }
2266: /*@
2267: DMPlexGlobalVectorLoad - Loads on-disk vector data into a global vector
2269: Collective on DM
2271: Input Parameters:
2272: + dm - The DM that represents the topology
2273: . viewer - The PetscViewer that represents the on-disk vector data
2274: . sectiondm - The DM that contains the global section on which vec is defined
2275: . sf - The SF that migrates the on-disk vector data into vec
2276: - vec - The global vector to set values of
2278: Level: advanced
2280: Notes:
2281: In general dm and sectiondm are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with PetscObjectSetName(). In practice, however, they can be the same object if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name.
2283: Typical calling sequence
2284: $ DMCreate(PETSC_COMM_WORLD, &dm);
2285: $ DMSetType(dm, DMPLEX);
2286: $ PetscObjectSetName((PetscObject)dm, "topologydm_name");
2287: $ DMPlexTopologyLoad(dm, viewer, &sfX);
2288: $ DMClone(dm, §iondm);
2289: $ PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name");
2290: $ DMPlexSectionLoad(dm, viewer, sectiondm, sfX, &gsf, NULL);
2291: $ DMGetGlobalVector(sectiondm, &vec);
2292: $ PetscObjectSetName((PetscObject)vec, "vec_name");
2293: $ DMPlexGlobalVectorLoad(dm, viewer, sectiondm, gsf, vec);
2294: $ DMRestoreGlobalVector(sectiondm, &vec);
2295: $ PetscSFDestroy(&gsf);
2296: $ PetscSFDestroy(&sfX);
2297: $ DMDestroy(§iondm);
2298: $ DMDestroy(&dm);
2300: .seealso: DMPlexTopologyLoad(), DMPlexSectionLoad(), DMPlexLocalVectorLoad(), DMPlexGlobalVectorView(), DMPlexLocalVectorView()
2301: @*/
2302: PetscErrorCode DMPlexGlobalVectorLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec)
2303: {
2304: PetscBool ishdf5;
2311: /* Check consistency */
2312: {
2313: PetscSection section;
2314: PetscBool includesConstraints;
2315: PetscInt m, m1;
2317: VecGetLocalSize(vec, &m1);
2318: DMGetGlobalSection(sectiondm, §ion);
2319: PetscSectionGetIncludesConstraints(section, &includesConstraints);
2320: if (includesConstraints) PetscSectionGetStorageSize(section, &m);
2321: else PetscSectionGetConstrainedStorageSize(section, &m);
2323: }
2324: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
2325: PetscLogEventBegin(DMPLEX_GlobalVectorLoad,viewer,0,0,0);
2326: if (ishdf5) {
2327: #if defined(PETSC_HAVE_HDF5)
2328: DMPlexVecLoad_HDF5_Internal(dm, viewer, sectiondm, sf, vec);
2329: #else
2330: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2331: #endif
2332: }
2333: PetscLogEventEnd(DMPLEX_GlobalVectorLoad,viewer,0,0,0);
2334: return 0;
2335: }
2337: /*@
2338: DMPlexLocalVectorLoad - Loads on-disk vector data into a local vector
2340: Collective on DM
2342: Input Parameters:
2343: + dm - The DM that represents the topology
2344: . viewer - The PetscViewer that represents the on-disk vector data
2345: . sectiondm - The DM that contains the local section on which vec is defined
2346: . sf - The SF that migrates the on-disk vector data into vec
2347: - vec - The local vector to set values of
2349: Level: advanced
2351: Notes:
2352: In general dm and sectiondm are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with PetscObjectSetName(). In practice, however, they can be the same object if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name.
2354: Typical calling sequence
2355: $ DMCreate(PETSC_COMM_WORLD, &dm);
2356: $ DMSetType(dm, DMPLEX);
2357: $ PetscObjectSetName((PetscObject)dm, "topologydm_name");
2358: $ DMPlexTopologyLoad(dm, viewer, &sfX);
2359: $ DMClone(dm, §iondm);
2360: $ PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name");
2361: $ DMPlexSectionLoad(dm, viewer, sectiondm, sfX, NULL, &lsf);
2362: $ DMGetLocalVector(sectiondm, &vec);
2363: $ PetscObjectSetName((PetscObject)vec, "vec_name");
2364: $ DMPlexLocalVectorLoad(dm, viewer, sectiondm, lsf, vec);
2365: $ DMRestoreLocalVector(sectiondm, &vec);
2366: $ PetscSFDestroy(&lsf);
2367: $ PetscSFDestroy(&sfX);
2368: $ DMDestroy(§iondm);
2369: $ DMDestroy(&dm);
2371: .seealso: DMPlexTopologyLoad(), DMPlexSectionLoad(), DMPlexGlobalVectorLoad(), DMPlexGlobalVectorView(), DMPlexLocalVectorView()
2372: @*/
2373: PetscErrorCode DMPlexLocalVectorLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec)
2374: {
2375: PetscBool ishdf5;
2382: /* Check consistency */
2383: {
2384: PetscSection section;
2385: PetscBool includesConstraints;
2386: PetscInt m, m1;
2388: VecGetLocalSize(vec, &m1);
2389: DMGetLocalSection(sectiondm, §ion);
2390: PetscSectionGetIncludesConstraints(section, &includesConstraints);
2391: if (includesConstraints) PetscSectionGetStorageSize(section, &m);
2392: else PetscSectionGetConstrainedStorageSize(section, &m);
2394: }
2395: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
2396: PetscLogEventBegin(DMPLEX_LocalVectorLoad,viewer,0,0,0);
2397: if (ishdf5) {
2398: #if defined(PETSC_HAVE_HDF5)
2399: DMPlexVecLoad_HDF5_Internal(dm, viewer, sectiondm, sf, vec);
2400: #else
2401: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2402: #endif
2403: }
2404: PetscLogEventEnd(DMPLEX_LocalVectorLoad,viewer,0,0,0);
2405: return 0;
2406: }
2408: PetscErrorCode DMDestroy_Plex(DM dm)
2409: {
2410: DM_Plex *mesh = (DM_Plex*) dm->data;
2412: PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",NULL);
2413: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C", NULL);
2414: PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C", NULL);
2415: PetscObjectComposeFunction((PetscObject)dm,"DMInterpolateSolution_C", NULL);
2416: if (--mesh->refct > 0) return 0;
2417: PetscSectionDestroy(&mesh->coneSection);
2418: PetscFree(mesh->cones);
2419: PetscFree(mesh->coneOrientations);
2420: PetscSectionDestroy(&mesh->supportSection);
2421: PetscSectionDestroy(&mesh->subdomainSection);
2422: PetscFree(mesh->supports);
2423: PetscFree(mesh->facesTmp);
2424: PetscFree(mesh->tetgenOpts);
2425: PetscFree(mesh->triangleOpts);
2426: PetscFree(mesh->transformType);
2427: PetscPartitionerDestroy(&mesh->partitioner);
2428: DMLabelDestroy(&mesh->subpointMap);
2429: ISDestroy(&mesh->subpointIS);
2430: ISDestroy(&mesh->globalVertexNumbers);
2431: ISDestroy(&mesh->globalCellNumbers);
2432: PetscSectionDestroy(&mesh->anchorSection);
2433: ISDestroy(&mesh->anchorIS);
2434: PetscSectionDestroy(&mesh->parentSection);
2435: PetscFree(mesh->parents);
2436: PetscFree(mesh->childIDs);
2437: PetscSectionDestroy(&mesh->childSection);
2438: PetscFree(mesh->children);
2439: DMDestroy(&mesh->referenceTree);
2440: PetscGridHashDestroy(&mesh->lbox);
2441: PetscFree(mesh->neighbors);
2442: if (mesh->metricCtx) PetscFree(mesh->metricCtx);
2443: /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */
2444: PetscFree(mesh);
2445: return 0;
2446: }
2448: PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J)
2449: {
2450: PetscSection sectionGlobal;
2451: PetscInt bs = -1, mbs;
2452: PetscInt localSize;
2453: PetscBool isShell, isBlock, isSeqBlock, isMPIBlock, isSymBlock, isSymSeqBlock, isSymMPIBlock, isMatIS;
2454: MatType mtype;
2455: ISLocalToGlobalMapping ltog;
2457: MatInitializePackage();
2458: mtype = dm->mattype;
2459: DMGetGlobalSection(dm, §ionGlobal);
2460: /* PetscSectionGetStorageSize(sectionGlobal, &localSize); */
2461: PetscSectionGetConstrainedStorageSize(sectionGlobal, &localSize);
2462: MatCreate(PetscObjectComm((PetscObject)dm), J);
2463: MatSetSizes(*J, localSize, localSize, PETSC_DETERMINE, PETSC_DETERMINE);
2464: MatSetType(*J, mtype);
2465: MatSetFromOptions(*J);
2466: MatGetBlockSize(*J, &mbs);
2467: if (mbs > 1) bs = mbs;
2468: PetscStrcmp(mtype, MATSHELL, &isShell);
2469: PetscStrcmp(mtype, MATBAIJ, &isBlock);
2470: PetscStrcmp(mtype, MATSEQBAIJ, &isSeqBlock);
2471: PetscStrcmp(mtype, MATMPIBAIJ, &isMPIBlock);
2472: PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);
2473: PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);
2474: PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);
2475: PetscStrcmp(mtype, MATIS, &isMatIS);
2476: if (!isShell) {
2477: PetscBool fillMatrix = (PetscBool)(!dm->prealloc_only && !isMatIS);
2478: PetscInt *dnz, *onz, *dnzu, *onzu, bsLocal[2], bsMinMax[2];
2479: PetscInt pStart, pEnd, p, dof, cdof;
2481: DMGetLocalToGlobalMapping(dm,<og);
2482: PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);
2483: for (p = pStart; p < pEnd; ++p) {
2484: PetscInt bdof;
2486: PetscSectionGetDof(sectionGlobal, p, &dof);
2487: PetscSectionGetConstraintDof(sectionGlobal, p, &cdof);
2488: dof = dof < 0 ? -(dof+1) : dof;
2489: bdof = cdof && (dof-cdof) ? 1 : dof;
2490: if (dof) {
2491: if (bs < 0) {bs = bdof;}
2492: else if (bs != bdof) {bs = 1; break;}
2493: }
2494: }
2495: /* Must have same blocksize on all procs (some might have no points) */
2496: bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs;
2497: bsLocal[1] = bs;
2498: PetscGlobalMinMaxInt(PetscObjectComm((PetscObject) dm), bsLocal, bsMinMax);
2499: if (bsMinMax[0] != bsMinMax[1]) bs = 1;
2500: else bs = bsMinMax[0];
2501: bs = PetscMax(1,bs);
2502: MatSetLocalToGlobalMapping(*J,ltog,ltog);
2503: if (dm->prealloc_skip) { // User will likely use MatSetPreallocationCOO(), but still set structural parameters
2504: MatSetBlockSize(*J, bs);
2505: MatSetUp(*J);
2506: } else {
2507: PetscCalloc4(localSize/bs, &dnz, localSize/bs, &onz, localSize/bs, &dnzu, localSize/bs, &onzu);
2508: DMPlexPreallocateOperator(dm, bs, dnz, onz, dnzu, onzu, *J, fillMatrix);
2509: PetscFree4(dnz, onz, dnzu, onzu);
2510: }
2511: }
2512: MatSetDM(*J, dm);
2513: return 0;
2514: }
2516: /*@
2517: DMPlexGetSubdomainSection - Returns the section associated with the subdomain
2519: Not collective
2521: Input Parameter:
2522: . mesh - The DMPlex
2524: Output Parameters:
2525: . subsection - The subdomain section
2527: Level: developer
2529: .seealso:
2530: @*/
2531: PetscErrorCode DMPlexGetSubdomainSection(DM dm, PetscSection *subsection)
2532: {
2533: DM_Plex *mesh = (DM_Plex*) dm->data;
2536: if (!mesh->subdomainSection) {
2537: PetscSection section;
2538: PetscSF sf;
2540: PetscSFCreate(PETSC_COMM_SELF,&sf);
2541: DMGetLocalSection(dm,§ion);
2542: PetscSectionCreateGlobalSection(section,sf,PETSC_FALSE,PETSC_TRUE,&mesh->subdomainSection);
2543: PetscSFDestroy(&sf);
2544: }
2545: *subsection = mesh->subdomainSection;
2546: return 0;
2547: }
2549: /*@
2550: DMPlexGetChart - Return the interval for all mesh points [pStart, pEnd)
2552: Not collective
2554: Input Parameter:
2555: . mesh - The DMPlex
2557: Output Parameters:
2558: + pStart - The first mesh point
2559: - pEnd - The upper bound for mesh points
2561: Level: beginner
2563: .seealso: DMPlexCreate(), DMPlexSetChart()
2564: @*/
2565: PetscErrorCode DMPlexGetChart(DM dm, PetscInt *pStart, PetscInt *pEnd)
2566: {
2567: DM_Plex *mesh = (DM_Plex*) dm->data;
2570: PetscSectionGetChart(mesh->coneSection, pStart, pEnd);
2571: return 0;
2572: }
2574: /*@
2575: DMPlexSetChart - Set the interval for all mesh points [pStart, pEnd)
2577: Not collective
2579: Input Parameters:
2580: + mesh - The DMPlex
2581: . pStart - The first mesh point
2582: - pEnd - The upper bound for mesh points
2584: Output Parameters:
2586: Level: beginner
2588: .seealso: DMPlexCreate(), DMPlexGetChart()
2589: @*/
2590: PetscErrorCode DMPlexSetChart(DM dm, PetscInt pStart, PetscInt pEnd)
2591: {
2592: DM_Plex *mesh = (DM_Plex*) dm->data;
2595: PetscSectionSetChart(mesh->coneSection, pStart, pEnd);
2596: PetscSectionSetChart(mesh->supportSection, pStart, pEnd);
2597: return 0;
2598: }
2600: /*@
2601: DMPlexGetConeSize - Return the number of in-edges for this point in the DAG
2603: Not collective
2605: Input Parameters:
2606: + mesh - The DMPlex
2607: - p - The point, which must lie in the chart set with DMPlexSetChart()
2609: Output Parameter:
2610: . size - The cone size for point p
2612: Level: beginner
2614: .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart()
2615: @*/
2616: PetscErrorCode DMPlexGetConeSize(DM dm, PetscInt p, PetscInt *size)
2617: {
2618: DM_Plex *mesh = (DM_Plex*) dm->data;
2622: PetscSectionGetDof(mesh->coneSection, p, size);
2623: return 0;
2624: }
2626: /*@
2627: DMPlexSetConeSize - Set the number of in-edges for this point in the DAG
2629: Not collective
2631: Input Parameters:
2632: + mesh - The DMPlex
2633: . p - The point, which must lie in the chart set with DMPlexSetChart()
2634: - size - The cone size for point p
2636: Output Parameter:
2638: Note:
2639: This should be called after DMPlexSetChart().
2641: Level: beginner
2643: .seealso: DMPlexCreate(), DMPlexGetConeSize(), DMPlexSetChart()
2644: @*/
2645: PetscErrorCode DMPlexSetConeSize(DM dm, PetscInt p, PetscInt size)
2646: {
2647: DM_Plex *mesh = (DM_Plex*) dm->data;
2650: PetscSectionSetDof(mesh->coneSection, p, size);
2651: return 0;
2652: }
2654: /*@
2655: DMPlexAddConeSize - Add the given number of in-edges to this point in the DAG
2657: Not collective
2659: Input Parameters:
2660: + mesh - The DMPlex
2661: . p - The point, which must lie in the chart set with DMPlexSetChart()
2662: - size - The additional cone size for point p
2664: Output Parameter:
2666: Note:
2667: This should be called after DMPlexSetChart().
2669: Level: beginner
2671: .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexGetConeSize(), DMPlexSetChart()
2672: @*/
2673: PetscErrorCode DMPlexAddConeSize(DM dm, PetscInt p, PetscInt size)
2674: {
2675: DM_Plex *mesh = (DM_Plex*) dm->data;
2677: PetscSectionAddDof(mesh->coneSection, p, size);
2678: return 0;
2679: }
2681: /*@C
2682: DMPlexGetCone - Return the points on the in-edges for this point in the DAG
2684: Not collective
2686: Input Parameters:
2687: + dm - The DMPlex
2688: - p - The point, which must lie in the chart set with DMPlexSetChart()
2690: Output Parameter:
2691: . cone - An array of points which are on the in-edges for point p
2693: Level: beginner
2695: Fortran Notes:
2696: Since it returns an array, this routine is only available in Fortran 90, and you must
2697: include petsc.h90 in your code.
2698: You must also call DMPlexRestoreCone() after you finish using the returned array.
2699: DMPlexRestoreCone() is not needed/available in C.
2701: .seealso: DMPlexGetConeSize(), DMPlexSetCone(), DMPlexGetConeTuple(), DMPlexSetChart()
2702: @*/
2703: PetscErrorCode DMPlexGetCone(DM dm, PetscInt p, const PetscInt *cone[])
2704: {
2705: DM_Plex *mesh = (DM_Plex*) dm->data;
2706: PetscInt off;
2710: PetscSectionGetOffset(mesh->coneSection, p, &off);
2711: *cone = &mesh->cones[off];
2712: return 0;
2713: }
2715: /*@C
2716: DMPlexGetConeTuple - Return the points on the in-edges of several points in the DAG
2718: Not collective
2720: Input Parameters:
2721: + dm - The DMPlex
2722: - p - The IS of points, which must lie in the chart set with DMPlexSetChart()
2724: Output Parameters:
2725: + pConesSection - PetscSection describing the layout of pCones
2726: - pCones - An array of points which are on the in-edges for the point set p
2728: Level: intermediate
2730: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeRecursive(), DMPlexSetChart()
2731: @*/
2732: PetscErrorCode DMPlexGetConeTuple(DM dm, IS p, PetscSection *pConesSection, IS *pCones)
2733: {
2734: PetscSection cs, newcs;
2735: PetscInt *cones;
2736: PetscInt *newarr=NULL;
2737: PetscInt n;
2739: DMPlexGetCones(dm, &cones);
2740: DMPlexGetConeSection(dm, &cs);
2741: PetscSectionExtractDofsFromArray(cs, MPIU_INT, cones, p, &newcs, pCones ? ((void**)&newarr) : NULL);
2742: if (pConesSection) *pConesSection = newcs;
2743: if (pCones) {
2744: PetscSectionGetStorageSize(newcs, &n);
2745: ISCreateGeneral(PetscObjectComm((PetscObject)p), n, newarr, PETSC_OWN_POINTER, pCones);
2746: }
2747: return 0;
2748: }
2750: /*@
2751: DMPlexGetConeRecursiveVertices - Expand each given point into its cone points and do that recursively until we end up just with vertices.
2753: Not collective
2755: Input Parameters:
2756: + dm - The DMPlex
2757: - points - The IS of points, which must lie in the chart set with DMPlexSetChart()
2759: Output Parameter:
2760: . expandedPoints - An array of vertices recursively expanded from input points
2762: Level: advanced
2764: Notes:
2765: Like DMPlexGetConeRecursive but returns only the 0-depth IS (i.e. vertices only) and no sections.
2766: There is no corresponding Restore function, just call ISDestroy() on the returned IS to deallocate.
2768: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexGetConeRecursive(), DMPlexRestoreConeRecursive(), DMPlexGetDepth()
2769: @*/
2770: PetscErrorCode DMPlexGetConeRecursiveVertices(DM dm, IS points, IS *expandedPoints)
2771: {
2772: IS *expandedPointsAll;
2773: PetscInt depth;
2778: DMPlexGetConeRecursive(dm, points, &depth, &expandedPointsAll, NULL);
2779: *expandedPoints = expandedPointsAll[0];
2780: PetscObjectReference((PetscObject)expandedPointsAll[0]);
2781: DMPlexRestoreConeRecursive(dm, points, &depth, &expandedPointsAll, NULL);
2782: return 0;
2783: }
2785: /*@
2786: DMPlexGetConeRecursive - Expand each given point into its cone points and do that recursively until we end up just with vertices (DAG points of depth 0, i.e. without cones).
2788: Not collective
2790: Input Parameters:
2791: + dm - The DMPlex
2792: - points - The IS of points, which must lie in the chart set with DMPlexSetChart()
2794: Output Parameters:
2795: + depth - (optional) Size of the output arrays, equal to DMPlex depth, returned by DMPlexGetDepth()
2796: . expandedPoints - (optional) An array of index sets with recursively expanded cones
2797: - sections - (optional) An array of sections which describe mappings from points to their cone points
2799: Level: advanced
2801: Notes:
2802: Like DMPlexGetConeTuple() but recursive.
2804: Array expandedPoints has size equal to depth. Each expandedPoints[d] contains DAG points with maximum depth d, recursively cone-wise expanded from the input points.
2805: For example, for d=0 it contains only vertices, for d=1 it can contain vertices and edges, etc.
2807: Array section has size equal to depth. Each PetscSection sections[d] realizes mapping from expandedPoints[d+1] (section points) to expandedPoints[d] (section dofs) as follows:
2808: (1) DAG points in expandedPoints[d+1] with depth d+1 to their cone points in expandedPoints[d];
2809: (2) DAG points in expandedPoints[d+1] with depth in [0,d] to the same points in expandedPoints[d].
2811: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexRestoreConeRecursive(), DMPlexGetConeRecursiveVertices(), DMPlexGetDepth()
2812: @*/
2813: PetscErrorCode DMPlexGetConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[])
2814: {
2815: const PetscInt *arr0=NULL, *cone=NULL;
2816: PetscInt *arr=NULL, *newarr=NULL;
2817: PetscInt d, depth_, i, n, newn, cn, co, start, end;
2818: IS *expandedPoints_;
2819: PetscSection *sections_;
2826: ISGetLocalSize(points, &n);
2827: ISGetIndices(points, &arr0);
2828: DMPlexGetDepth(dm, &depth_);
2829: PetscCalloc1(depth_, &expandedPoints_);
2830: PetscCalloc1(depth_, §ions_);
2831: arr = (PetscInt*) arr0; /* this is ok because first generation of arr is not modified */
2832: for (d=depth_-1; d>=0; d--) {
2833: PetscSectionCreate(PETSC_COMM_SELF, §ions_[d]);
2834: PetscSectionSetChart(sections_[d], 0, n);
2835: for (i=0; i<n; i++) {
2836: DMPlexGetDepthStratum(dm, d+1, &start, &end);
2837: if (arr[i] >= start && arr[i] < end) {
2838: DMPlexGetConeSize(dm, arr[i], &cn);
2839: PetscSectionSetDof(sections_[d], i, cn);
2840: } else {
2841: PetscSectionSetDof(sections_[d], i, 1);
2842: }
2843: }
2844: PetscSectionSetUp(sections_[d]);
2845: PetscSectionGetStorageSize(sections_[d], &newn);
2846: PetscMalloc1(newn, &newarr);
2847: for (i=0; i<n; i++) {
2848: PetscSectionGetDof(sections_[d], i, &cn);
2849: PetscSectionGetOffset(sections_[d], i, &co);
2850: if (cn > 1) {
2851: DMPlexGetCone(dm, arr[i], &cone);
2852: PetscMemcpy(&newarr[co], cone, cn*sizeof(PetscInt));
2853: } else {
2854: newarr[co] = arr[i];
2855: }
2856: }
2857: ISCreateGeneral(PETSC_COMM_SELF, newn, newarr, PETSC_OWN_POINTER, &expandedPoints_[d]);
2858: arr = newarr;
2859: n = newn;
2860: }
2861: ISRestoreIndices(points, &arr0);
2862: *depth = depth_;
2863: if (expandedPoints) *expandedPoints = expandedPoints_;
2864: else {
2865: for (d=0; d<depth_; d++) ISDestroy(&expandedPoints_[d]);
2866: PetscFree(expandedPoints_);
2867: }
2868: if (sections) *sections = sections_;
2869: else {
2870: for (d=0; d<depth_; d++) PetscSectionDestroy(§ions_[d]);
2871: PetscFree(sections_);
2872: }
2873: return 0;
2874: }
2876: /*@
2877: DMPlexRestoreConeRecursive - Deallocates arrays created by DMPlexGetConeRecursive
2879: Not collective
2881: Input Parameters:
2882: + dm - The DMPlex
2883: - points - The IS of points, which must lie in the chart set with DMPlexSetChart()
2885: Output Parameters:
2886: + depth - (optional) Size of the output arrays, equal to DMPlex depth, returned by DMPlexGetDepth()
2887: . expandedPoints - (optional) An array of recursively expanded cones
2888: - sections - (optional) An array of sections which describe mappings from points to their cone points
2890: Level: advanced
2892: Notes:
2893: See DMPlexGetConeRecursive() for details.
2895: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexGetConeRecursive(), DMPlexGetConeRecursiveVertices(), DMPlexGetDepth()
2896: @*/
2897: PetscErrorCode DMPlexRestoreConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[])
2898: {
2899: PetscInt d, depth_;
2901: DMPlexGetDepth(dm, &depth_);
2903: if (depth) *depth = 0;
2904: if (expandedPoints) {
2905: for (d=0; d<depth_; d++) ISDestroy(&((*expandedPoints)[d]));
2906: PetscFree(*expandedPoints);
2907: }
2908: if (sections) {
2909: for (d=0; d<depth_; d++) PetscSectionDestroy(&((*sections)[d]));
2910: PetscFree(*sections);
2911: }
2912: return 0;
2913: }
2915: /*@
2916: DMPlexSetCone - Set the points on the in-edges for this point in the DAG; that is these are the points that cover the specific point
2918: Not collective
2920: Input Parameters:
2921: + mesh - The DMPlex
2922: . p - The point, which must lie in the chart set with DMPlexSetChart()
2923: - cone - An array of points which are on the in-edges for point p
2925: Output Parameter:
2927: Note:
2928: This should be called after all calls to DMPlexSetConeSize() and DMSetUp().
2930: Level: beginner
2932: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp(), DMPlexSetSupport(), DMPlexSetSupportSize()
2933: @*/
2934: PetscErrorCode DMPlexSetCone(DM dm, PetscInt p, const PetscInt cone[])
2935: {
2936: DM_Plex *mesh = (DM_Plex*) dm->data;
2937: PetscInt pStart, pEnd;
2938: PetscInt dof, off, c;
2941: PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);
2942: PetscSectionGetDof(mesh->coneSection, p, &dof);
2944: PetscSectionGetOffset(mesh->coneSection, p, &off);
2946: for (c = 0; c < dof; ++c) {
2948: mesh->cones[off+c] = cone[c];
2949: }
2950: return 0;
2951: }
2953: /*@C
2954: DMPlexGetConeOrientation - Return the orientations on the in-edges for this point in the DAG
2956: Not collective
2958: Input Parameters:
2959: + mesh - The DMPlex
2960: - p - The point, which must lie in the chart set with DMPlexSetChart()
2962: Output Parameter:
2963: . coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an
2964: integer giving the prescription for cone traversal.
2966: Level: beginner
2968: Notes:
2969: The number indexes the symmetry transformations for the cell type (see manual). Orientation 0 is always
2970: the identity transformation. Negative orientation indicates reflection so that -(o+1) is the reflection
2971: of o, however it is not necessarily the inverse. To get the inverse, use DMPolytopeTypeComposeOrientationInv()
2972: with the identity.
2974: Fortran Notes:
2975: Since it returns an array, this routine is only available in Fortran 90, and you must
2976: include petsc.h90 in your code.
2977: You must also call DMPlexRestoreConeOrientation() after you finish using the returned array.
2978: DMPlexRestoreConeOrientation() is not needed/available in C.
2980: .seealso: DMPolytopeTypeComposeOrientation(), DMPolytopeTypeComposeOrientationInv(), DMPlexCreate(), DMPlexGetCone(), DMPlexSetCone(), DMPlexSetChart()
2981: @*/
2982: PetscErrorCode DMPlexGetConeOrientation(DM dm, PetscInt p, const PetscInt *coneOrientation[])
2983: {
2984: DM_Plex *mesh = (DM_Plex*) dm->data;
2985: PetscInt off;
2988: if (PetscDefined(USE_DEBUG)) {
2989: PetscInt dof;
2990: PetscSectionGetDof(mesh->coneSection, p, &dof);
2992: }
2993: PetscSectionGetOffset(mesh->coneSection, p, &off);
2995: *coneOrientation = &mesh->coneOrientations[off];
2996: return 0;
2997: }
2999: /*@
3000: DMPlexSetConeOrientation - Set the orientations on the in-edges for this point in the DAG
3002: Not collective
3004: Input Parameters:
3005: + mesh - The DMPlex
3006: . p - The point, which must lie in the chart set with DMPlexSetChart()
3007: - coneOrientation - An array of orientations
3008: Output Parameter:
3010: Notes:
3011: This should be called after all calls to DMPlexSetConeSize() and DMSetUp().
3013: The meaning of coneOrientation is detailed in DMPlexGetConeOrientation().
3015: Level: beginner
3017: .seealso: DMPlexCreate(), DMPlexGetConeOrientation(), DMPlexSetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp()
3018: @*/
3019: PetscErrorCode DMPlexSetConeOrientation(DM dm, PetscInt p, const PetscInt coneOrientation[])
3020: {
3021: DM_Plex *mesh = (DM_Plex*) dm->data;
3022: PetscInt pStart, pEnd;
3023: PetscInt dof, off, c;
3026: PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);
3027: PetscSectionGetDof(mesh->coneSection, p, &dof);
3029: PetscSectionGetOffset(mesh->coneSection, p, &off);
3031: for (c = 0; c < dof; ++c) {
3032: PetscInt cdof, o = coneOrientation[c];
3034: PetscSectionGetDof(mesh->coneSection, mesh->cones[off+c], &cdof);
3036: mesh->coneOrientations[off+c] = o;
3037: }
3038: return 0;
3039: }
3041: /*@
3042: DMPlexInsertCone - Insert a point into the in-edges for the point p in the DAG
3044: Not collective
3046: Input Parameters:
3047: + mesh - The DMPlex
3048: . p - The point, which must lie in the chart set with DMPlexSetChart()
3049: . conePos - The local index in the cone where the point should be put
3050: - conePoint - The mesh point to insert
3052: Level: beginner
3054: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp()
3055: @*/
3056: PetscErrorCode DMPlexInsertCone(DM dm, PetscInt p, PetscInt conePos, PetscInt conePoint)
3057: {
3058: DM_Plex *mesh = (DM_Plex*) dm->data;
3059: PetscInt pStart, pEnd;
3060: PetscInt dof, off;
3063: PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);
3066: PetscSectionGetDof(mesh->coneSection, p, &dof);
3067: PetscSectionGetOffset(mesh->coneSection, p, &off);
3069: mesh->cones[off+conePos] = conePoint;
3070: return 0;
3071: }
3073: /*@
3074: DMPlexInsertConeOrientation - Insert a point orientation for the in-edge for the point p in the DAG
3076: Not collective
3078: Input Parameters:
3079: + mesh - The DMPlex
3080: . p - The point, which must lie in the chart set with DMPlexSetChart()
3081: . conePos - The local index in the cone where the point should be put
3082: - coneOrientation - The point orientation to insert
3084: Level: beginner
3086: Notes:
3087: The meaning of coneOrientation values is detailed in DMPlexGetConeOrientation().
3089: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp()
3090: @*/
3091: PetscErrorCode DMPlexInsertConeOrientation(DM dm, PetscInt p, PetscInt conePos, PetscInt coneOrientation)
3092: {
3093: DM_Plex *mesh = (DM_Plex*) dm->data;
3094: PetscInt pStart, pEnd;
3095: PetscInt dof, off;
3098: PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);
3100: PetscSectionGetDof(mesh->coneSection, p, &dof);
3101: PetscSectionGetOffset(mesh->coneSection, p, &off);
3103: mesh->coneOrientations[off+conePos] = coneOrientation;
3104: return 0;
3105: }
3107: /*@
3108: DMPlexGetSupportSize - Return the number of out-edges for this point in the DAG
3110: Not collective
3112: Input Parameters:
3113: + mesh - The DMPlex
3114: - p - The point, which must lie in the chart set with DMPlexSetChart()
3116: Output Parameter:
3117: . size - The support size for point p
3119: Level: beginner
3121: .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart(), DMPlexGetConeSize()
3122: @*/
3123: PetscErrorCode DMPlexGetSupportSize(DM dm, PetscInt p, PetscInt *size)
3124: {
3125: DM_Plex *mesh = (DM_Plex*) dm->data;
3129: PetscSectionGetDof(mesh->supportSection, p, size);
3130: return 0;
3131: }
3133: /*@
3134: DMPlexSetSupportSize - Set the number of out-edges for this point in the DAG
3136: Not collective
3138: Input Parameters:
3139: + mesh - The DMPlex
3140: . p - The point, which must lie in the chart set with DMPlexSetChart()
3141: - size - The support size for point p
3143: Output Parameter:
3145: Note:
3146: This should be called after DMPlexSetChart().
3148: Level: beginner
3150: .seealso: DMPlexCreate(), DMPlexGetSupportSize(), DMPlexSetChart()
3151: @*/
3152: PetscErrorCode DMPlexSetSupportSize(DM dm, PetscInt p, PetscInt size)
3153: {
3154: DM_Plex *mesh = (DM_Plex*) dm->data;
3157: PetscSectionSetDof(mesh->supportSection, p, size);
3158: return 0;
3159: }
3161: /*@C
3162: DMPlexGetSupport - Return the points on the out-edges for this point in the DAG
3164: Not collective
3166: Input Parameters:
3167: + mesh - The DMPlex
3168: - p - The point, which must lie in the chart set with DMPlexSetChart()
3170: Output Parameter:
3171: . support - An array of points which are on the out-edges for point p
3173: Level: beginner
3175: Fortran Notes:
3176: Since it returns an array, this routine is only available in Fortran 90, and you must
3177: include petsc.h90 in your code.
3178: You must also call DMPlexRestoreSupport() after you finish using the returned array.
3179: DMPlexRestoreSupport() is not needed/available in C.
3181: .seealso: DMPlexGetSupportSize(), DMPlexSetSupport(), DMPlexGetCone(), DMPlexSetChart()
3182: @*/
3183: PetscErrorCode DMPlexGetSupport(DM dm, PetscInt p, const PetscInt *support[])
3184: {
3185: DM_Plex *mesh = (DM_Plex*) dm->data;
3186: PetscInt off;
3190: PetscSectionGetOffset(mesh->supportSection, p, &off);
3191: *support = &mesh->supports[off];
3192: return 0;
3193: }
3195: /*@
3196: DMPlexSetSupport - Set the points on the out-edges for this point in the DAG, that is the list of points that this point covers
3198: Not collective
3200: Input Parameters:
3201: + mesh - The DMPlex
3202: . p - The point, which must lie in the chart set with DMPlexSetChart()
3203: - support - An array of points which are on the out-edges for point p
3205: Output Parameter:
3207: Note:
3208: This should be called after all calls to DMPlexSetSupportSize() and DMSetUp().
3210: Level: beginner
3212: .seealso: DMPlexSetCone(), DMPlexSetConeSize(), DMPlexCreate(), DMPlexGetSupport(), DMPlexSetChart(), DMPlexSetSupportSize(), DMSetUp()
3213: @*/
3214: PetscErrorCode DMPlexSetSupport(DM dm, PetscInt p, const PetscInt support[])
3215: {
3216: DM_Plex *mesh = (DM_Plex*) dm->data;
3217: PetscInt pStart, pEnd;
3218: PetscInt dof, off, c;
3221: PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);
3222: PetscSectionGetDof(mesh->supportSection, p, &dof);
3224: PetscSectionGetOffset(mesh->supportSection, p, &off);
3226: for (c = 0; c < dof; ++c) {
3228: mesh->supports[off+c] = support[c];
3229: }
3230: return 0;
3231: }
3233: /*@
3234: DMPlexInsertSupport - Insert a point into the out-edges for the point p in the DAG
3236: Not collective
3238: Input Parameters:
3239: + mesh - The DMPlex
3240: . p - The point, which must lie in the chart set with DMPlexSetChart()
3241: . supportPos - The local index in the cone where the point should be put
3242: - supportPoint - The mesh point to insert
3244: Level: beginner
3246: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp()
3247: @*/
3248: PetscErrorCode DMPlexInsertSupport(DM dm, PetscInt p, PetscInt supportPos, PetscInt supportPoint)
3249: {
3250: DM_Plex *mesh = (DM_Plex*) dm->data;
3251: PetscInt pStart, pEnd;
3252: PetscInt dof, off;
3255: PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);
3256: PetscSectionGetDof(mesh->supportSection, p, &dof);
3257: PetscSectionGetOffset(mesh->supportSection, p, &off);
3261: mesh->supports[off+supportPos] = supportPoint;
3262: return 0;
3263: }
3265: /* Converts an orientation o in the current numbering to the previous scheme used in Plex */
3266: PetscInt DMPolytopeConvertNewOrientation_Internal(DMPolytopeType ct, PetscInt o)
3267: {
3268: switch (ct) {
3269: case DM_POLYTOPE_SEGMENT:
3270: if (o == -1) return -2;
3271: break;
3272: case DM_POLYTOPE_TRIANGLE:
3273: if (o == -3) return -1;
3274: if (o == -2) return -3;
3275: if (o == -1) return -2;
3276: break;
3277: case DM_POLYTOPE_QUADRILATERAL:
3278: if (o == -4) return -2;
3279: if (o == -3) return -1;
3280: if (o == -2) return -4;
3281: if (o == -1) return -3;
3282: break;
3283: default: return o;
3284: }
3285: return o;
3286: }
3288: /* Converts an orientation o in the previous scheme used in Plex to the current numbering */
3289: PetscInt DMPolytopeConvertOldOrientation_Internal(DMPolytopeType ct, PetscInt o)
3290: {
3291: switch (ct) {
3292: case DM_POLYTOPE_SEGMENT:
3293: if ((o == -2) || (o == 1)) return -1;
3294: if (o == -1) return 0;
3295: break;
3296: case DM_POLYTOPE_TRIANGLE:
3297: if (o == -3) return -2;
3298: if (o == -2) return -1;
3299: if (o == -1) return -3;
3300: break;
3301: case DM_POLYTOPE_QUADRILATERAL:
3302: if (o == -4) return -2;
3303: if (o == -3) return -1;
3304: if (o == -2) return -4;
3305: if (o == -1) return -3;
3306: break;
3307: default: return o;
3308: }
3309: return o;
3310: }
3312: /* Takes in a mesh whose orientations are in the previous scheme and converts them all to the current numbering */
3313: PetscErrorCode DMPlexConvertOldOrientations_Internal(DM dm)
3314: {
3315: PetscInt pStart, pEnd, p;
3317: DMPlexGetChart(dm, &pStart, &pEnd);
3318: for (p = pStart; p < pEnd; ++p) {
3319: const PetscInt *cone, *ornt;
3320: PetscInt coneSize, c;
3322: DMPlexGetConeSize(dm, p, &coneSize);
3323: DMPlexGetCone(dm, p, &cone);
3324: DMPlexGetConeOrientation(dm, p, &ornt);
3325: for (c = 0; c < coneSize; ++c) {
3326: DMPolytopeType ct;
3327: const PetscInt o = ornt[c];
3329: DMPlexGetCellType(dm, cone[c], &ct);
3330: switch (ct) {
3331: case DM_POLYTOPE_SEGMENT:
3332: if ((o == -2) || (o == 1)) DMPlexInsertConeOrientation(dm, p, c, -1);
3333: if (o == -1) DMPlexInsertConeOrientation(dm, p, c, 0);
3334: break;
3335: case DM_POLYTOPE_TRIANGLE:
3336: if (o == -3) DMPlexInsertConeOrientation(dm, p, c, -2);
3337: if (o == -2) DMPlexInsertConeOrientation(dm, p, c, -1);
3338: if (o == -1) DMPlexInsertConeOrientation(dm, p, c, -3);
3339: break;
3340: case DM_POLYTOPE_QUADRILATERAL:
3341: if (o == -4) DMPlexInsertConeOrientation(dm, p, c, -2);
3342: if (o == -3) DMPlexInsertConeOrientation(dm, p, c, -1);
3343: if (o == -2) DMPlexInsertConeOrientation(dm, p, c, -4);
3344: if (o == -1) DMPlexInsertConeOrientation(dm, p, c, -3);
3345: break;
3346: default: break;
3347: }
3348: }
3349: }
3350: return 0;
3351: }
3353: static PetscErrorCode DMPlexGetTransitiveClosure_Depth1_Private(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[])
3354: {
3355: DMPolytopeType ct = DM_POLYTOPE_UNKNOWN;
3356: PetscInt *closure;
3357: const PetscInt *tmp = NULL, *tmpO = NULL;
3358: PetscInt off = 0, tmpSize, t;
3361: if (ornt) {
3362: DMPlexGetCellType(dm, p, &ct);
3363: if (ct == DM_POLYTOPE_FV_GHOST || ct == DM_POLYTOPE_INTERIOR_GHOST || ct == DM_POLYTOPE_UNKNOWN) ct = DM_POLYTOPE_UNKNOWN;
3364: }
3365: if (*points) {
3366: closure = *points;
3367: } else {
3368: PetscInt maxConeSize, maxSupportSize;
3369: DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
3370: DMGetWorkArray(dm, 2*(PetscMax(maxConeSize, maxSupportSize)+1), MPIU_INT, &closure);
3371: }
3372: if (useCone) {
3373: DMPlexGetConeSize(dm, p, &tmpSize);
3374: DMPlexGetCone(dm, p, &tmp);
3375: DMPlexGetConeOrientation(dm, p, &tmpO);
3376: } else {
3377: DMPlexGetSupportSize(dm, p, &tmpSize);
3378: DMPlexGetSupport(dm, p, &tmp);
3379: }
3380: if (ct == DM_POLYTOPE_UNKNOWN) {
3381: closure[off++] = p;
3382: closure[off++] = 0;
3383: for (t = 0; t < tmpSize; ++t) {
3384: closure[off++] = tmp[t];
3385: closure[off++] = tmpO ? tmpO[t] : 0;
3386: }
3387: } else {
3388: const PetscInt *arr = DMPolytopeTypeGetArrangment(ct, ornt);
3390: /* We assume that cells with a valid type have faces with a valid type */
3391: closure[off++] = p;
3392: closure[off++] = ornt;
3393: for (t = 0; t < tmpSize; ++t) {
3394: DMPolytopeType ft;
3396: DMPlexGetCellType(dm, tmp[t], &ft);
3397: closure[off++] = tmp[arr[t]];
3398: closure[off++] = tmpO ? DMPolytopeTypeComposeOrientation(ft, ornt, tmpO[t]) : 0;
3399: }
3400: }
3401: if (numPoints) *numPoints = tmpSize+1;
3402: if (points) *points = closure;
3403: return 0;
3404: }
3406: /* We need a special tensor verison becasue we want to allow duplicate points in the endcaps for hybrid cells */
3407: static PetscErrorCode DMPlexTransitiveClosure_Tensor_Internal(DM dm, PetscInt point, DMPolytopeType ct, PetscInt o, PetscBool useCone, PetscInt *numPoints, PetscInt **points)
3408: {
3409: const PetscInt *arr = DMPolytopeTypeGetArrangment(ct, o);
3410: const PetscInt *cone, *ornt;
3411: PetscInt *pts, *closure = NULL;
3412: DMPolytopeType ft;
3413: PetscInt maxConeSize, maxSupportSize, coneSeries, supportSeries, maxSize;
3414: PetscInt dim, coneSize, c, d, clSize, cl;
3417: DMGetDimension(dm, &dim);
3418: DMPlexGetConeSize(dm, point, &coneSize);
3419: DMPlexGetCone(dm, point, &cone);
3420: DMPlexGetConeOrientation(dm, point, &ornt);
3421: DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
3422: coneSeries = (maxConeSize > 1) ? ((PetscPowInt(maxConeSize, dim+1)-1)/(maxConeSize-1)) : dim+1;
3423: supportSeries = (maxSupportSize > 1) ? ((PetscPowInt(maxSupportSize, dim+1)-1)/(maxSupportSize-1)) : dim+1;
3424: maxSize = PetscMax(coneSeries, supportSeries);
3425: if (*points) {pts = *points;}
3426: else DMGetWorkArray(dm, 2*maxSize, MPIU_INT, &pts);
3427: c = 0;
3428: pts[c++] = point;
3429: pts[c++] = o;
3430: DMPlexGetCellType(dm, cone[arr[0*2+0]], &ft);
3431: DMPlexGetTransitiveClosure_Internal(dm, cone[arr[0*2+0]], DMPolytopeTypeComposeOrientation(ft, arr[0*2+1], ornt[0]), useCone, &clSize, &closure);
3432: for (cl = 0; cl < clSize*2; cl += 2) {pts[c++] = closure[cl]; pts[c++] = closure[cl+1];}
3433: DMPlexGetTransitiveClosure_Internal(dm, cone[arr[1*2+0]], DMPolytopeTypeComposeOrientation(ft, arr[1*2+1], ornt[1]), useCone, &clSize, &closure);
3434: for (cl = 0; cl < clSize*2; cl += 2) {pts[c++] = closure[cl]; pts[c++] = closure[cl+1];}
3435: DMPlexRestoreTransitiveClosure(dm, cone[0], useCone, &clSize, &closure);
3436: for (d = 2; d < coneSize; ++d) {
3437: DMPlexGetCellType(dm, cone[arr[d*2+0]], &ft);
3438: pts[c++] = cone[arr[d*2+0]];
3439: pts[c++] = DMPolytopeTypeComposeOrientation(ft, arr[d*2+1], ornt[d]);
3440: }
3441: if (dim >= 3) {
3442: for (d = 2; d < coneSize; ++d) {
3443: const PetscInt fpoint = cone[arr[d*2+0]];
3444: const PetscInt *fcone, *fornt;
3445: PetscInt fconeSize, fc, i;
3447: DMPlexGetCellType(dm, fpoint, &ft);
3448: const PetscInt *farr = DMPolytopeTypeGetArrangment(ft, DMPolytopeTypeComposeOrientation(ft, arr[d*2+1], ornt[d]));
3449: DMPlexGetConeSize(dm, fpoint, &fconeSize);
3450: DMPlexGetCone(dm, fpoint, &fcone);
3451: DMPlexGetConeOrientation(dm, fpoint, &fornt);
3452: for (fc = 0; fc < fconeSize; ++fc) {
3453: const PetscInt cp = fcone[farr[fc*2+0]];
3454: const PetscInt co = farr[fc*2+1];
3456: for (i = 0; i < c; i += 2) if (pts[i] == cp) break;
3457: if (i == c) {
3458: DMPlexGetCellType(dm, cp, &ft);
3459: pts[c++] = cp;
3460: pts[c++] = DMPolytopeTypeComposeOrientation(ft, co, fornt[farr[fc*2+0]]);
3461: }
3462: }
3463: }
3464: }
3465: *numPoints = c/2;
3466: *points = pts;
3467: return 0;
3468: }
3470: PetscErrorCode DMPlexGetTransitiveClosure_Internal(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[])
3471: {
3472: DMPolytopeType ct;
3473: PetscInt *closure, *fifo;
3474: PetscInt closureSize = 0, fifoStart = 0, fifoSize = 0;
3475: PetscInt maxConeSize, maxSupportSize, coneSeries, supportSeries;
3476: PetscInt depth, maxSize;
3479: DMPlexGetDepth(dm, &depth);
3480: if (depth == 1) {
3481: DMPlexGetTransitiveClosure_Depth1_Private(dm, p, ornt, useCone, numPoints, points);
3482: return 0;
3483: }
3484: DMPlexGetCellType(dm, p, &ct);
3485: if (ct == DM_POLYTOPE_FV_GHOST || ct == DM_POLYTOPE_INTERIOR_GHOST || ct == DM_POLYTOPE_UNKNOWN) ct = DM_POLYTOPE_UNKNOWN;
3486: if (ct == DM_POLYTOPE_SEG_PRISM_TENSOR || ct == DM_POLYTOPE_TRI_PRISM_TENSOR || ct == DM_POLYTOPE_QUAD_PRISM_TENSOR) {
3487: DMPlexTransitiveClosure_Tensor_Internal(dm, p, ct, ornt, useCone, numPoints, points);
3488: return 0;
3489: }
3490: DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
3491: coneSeries = (maxConeSize > 1) ? ((PetscPowInt(maxConeSize, depth+1)-1)/(maxConeSize-1)) : depth+1;
3492: supportSeries = (maxSupportSize > 1) ? ((PetscPowInt(maxSupportSize, depth+1)-1)/(maxSupportSize-1)) : depth+1;
3493: maxSize = PetscMax(coneSeries, supportSeries);
3494: DMGetWorkArray(dm, 3*maxSize, MPIU_INT, &fifo);
3495: if (*points) {closure = *points;}
3496: else DMGetWorkArray(dm, 2*maxSize, MPIU_INT, &closure);
3497: closure[closureSize++] = p;
3498: closure[closureSize++] = ornt;
3499: fifo[fifoSize++] = p;
3500: fifo[fifoSize++] = ornt;
3501: fifo[fifoSize++] = ct;
3502: /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */
3503: while (fifoSize - fifoStart) {
3504: const PetscInt q = fifo[fifoStart++];
3505: const PetscInt o = fifo[fifoStart++];
3506: const DMPolytopeType qt = (DMPolytopeType) fifo[fifoStart++];
3507: const PetscInt *qarr = DMPolytopeTypeGetArrangment(qt, o);
3508: const PetscInt *tmp, *tmpO;
3509: PetscInt tmpSize, t;
3511: if (PetscDefined(USE_DEBUG)) {
3512: PetscInt nO = DMPolytopeTypeGetNumArrangments(qt)/2;
3514: }
3515: if (useCone) {
3516: DMPlexGetConeSize(dm, q, &tmpSize);
3517: DMPlexGetCone(dm, q, &tmp);
3518: DMPlexGetConeOrientation(dm, q, &tmpO);
3519: } else {
3520: DMPlexGetSupportSize(dm, q, &tmpSize);
3521: DMPlexGetSupport(dm, q, &tmp);
3522: tmpO = NULL;
3523: }
3524: for (t = 0; t < tmpSize; ++t) {
3525: const PetscInt ip = useCone && qarr ? qarr[t*2] : t;
3526: const PetscInt io = useCone && qarr ? qarr[t*2+1] : 0;
3527: const PetscInt cp = tmp[ip];
3528: DMPlexGetCellType(dm, cp, &ct);
3529: const PetscInt co = tmpO ? DMPolytopeTypeComposeOrientation(ct, io, tmpO[ip]) : 0;
3530: PetscInt c;
3532: /* Check for duplicate */
3533: for (c = 0; c < closureSize; c += 2) {
3534: if (closure[c] == cp) break;
3535: }
3536: if (c == closureSize) {
3537: closure[closureSize++] = cp;
3538: closure[closureSize++] = co;
3539: fifo[fifoSize++] = cp;
3540: fifo[fifoSize++] = co;
3541: fifo[fifoSize++] = ct;
3542: }
3543: }
3544: }
3545: DMRestoreWorkArray(dm, 3*maxSize, MPIU_INT, &fifo);
3546: if (numPoints) *numPoints = closureSize/2;
3547: if (points) *points = closure;
3548: return 0;
3549: }
3551: /*@C
3552: DMPlexGetTransitiveClosure - Return the points on the transitive closure of the in-edges or out-edges for this point in the DAG
3554: Not collective
3556: Input Parameters:
3557: + dm - The DMPlex
3558: . p - The mesh point
3559: - useCone - PETSC_TRUE for the closure, otherwise return the star
3561: Input/Output Parameter:
3562: . points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...];
3563: if NULL on input, internal storage will be returned, otherwise the provided array is used
3565: Output Parameter:
3566: . numPoints - The number of points in the closure, so points[] is of size 2*numPoints
3568: Note:
3569: If using internal storage (points is NULL on input), each call overwrites the last output.
3571: Fortran Notes:
3572: Since it returns an array, this routine is only available in Fortran 90, and you must include petsc.h90 in your code.
3574: The numPoints argument is not present in the Fortran 90 binding since it is internal to the array.
3576: Level: beginner
3578: .seealso: DMPlexRestoreTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone()
3579: @*/
3580: PetscErrorCode DMPlexGetTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[])
3581: {
3586: DMPlexGetTransitiveClosure_Internal(dm, p, 0, useCone, numPoints, points);
3587: return 0;
3588: }
3590: /*@C
3591: DMPlexRestoreTransitiveClosure - Restore the array of points on the transitive closure of the in-edges or out-edges for this point in the DAG
3593: Not collective
3595: Input Parameters:
3596: + dm - The DMPlex
3597: . p - The mesh point
3598: . useCone - PETSC_TRUE for the closure, otherwise return the star
3599: . numPoints - The number of points in the closure, so points[] is of size 2*numPoints
3600: - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...]
3602: Note:
3603: If not using internal storage (points is not NULL on input), this call is unnecessary
3605: Fortran Notes:
3606: Since it returns an array, this routine is only available in Fortran 90, and you must include petsc.h90 in your code.
3608: The numPoints argument is not present in the Fortran 90 binding since it is internal to the array.
3610: Level: beginner
3612: .seealso: DMPlexGetTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone()
3613: @*/
3614: PetscErrorCode DMPlexRestoreTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[])
3615: {
3618: if (numPoints) *numPoints = 0;
3619: DMRestoreWorkArray(dm, 0, MPIU_INT, points);
3620: return 0;
3621: }
3623: /*@
3624: DMPlexGetMaxSizes - Return the maximum number of in-edges (cone) and out-edges (support) for any point in the DAG
3626: Not collective
3628: Input Parameter:
3629: . mesh - The DMPlex
3631: Output Parameters:
3632: + maxConeSize - The maximum number of in-edges
3633: - maxSupportSize - The maximum number of out-edges
3635: Level: beginner
3637: .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart()
3638: @*/
3639: PetscErrorCode DMPlexGetMaxSizes(DM dm, PetscInt *maxConeSize, PetscInt *maxSupportSize)
3640: {
3641: DM_Plex *mesh = (DM_Plex*) dm->data;
3644: if (maxConeSize) {
3645: PetscSectionGetMaxDof(mesh->coneSection, maxConeSize);
3646: }
3647: if (maxSupportSize) {
3648: PetscSectionGetMaxDof(mesh->supportSection, maxSupportSize);
3649: }
3650: return 0;
3651: }
3653: PetscErrorCode DMSetUp_Plex(DM dm)
3654: {
3655: DM_Plex *mesh = (DM_Plex*) dm->data;
3656: PetscInt size, maxSupportSize;
3659: PetscSectionSetUp(mesh->coneSection);
3660: PetscSectionGetStorageSize(mesh->coneSection, &size);
3661: PetscMalloc1(size, &mesh->cones);
3662: PetscCalloc1(size, &mesh->coneOrientations);
3663: PetscLogObjectMemory((PetscObject) dm, size*2*sizeof(PetscInt));
3664: PetscSectionGetMaxDof(mesh->supportSection, &maxSupportSize);
3665: if (maxSupportSize) {
3666: PetscSectionSetUp(mesh->supportSection);
3667: PetscSectionGetStorageSize(mesh->supportSection, &size);
3668: PetscMalloc1(size, &mesh->supports);
3669: PetscLogObjectMemory((PetscObject) dm, size*sizeof(PetscInt));
3670: }
3671: return 0;
3672: }
3674: PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm)
3675: {
3676: if (subdm) DMClone(dm, subdm);
3677: DMCreateSectionSubDM(dm, numFields, fields, is, subdm);
3678: if (subdm) {(*subdm)->useNatural = dm->useNatural;}
3679: if (dm->useNatural && dm->sfMigration) {
3680: PetscSF sfMigrationInv,sfNatural;
3681: PetscSection section, sectionSeq;
3683: (*subdm)->sfMigration = dm->sfMigration;
3684: PetscObjectReference((PetscObject) dm->sfMigration);
3685: DMGetLocalSection((*subdm), §ion);
3686: PetscSFCreateInverseSF((*subdm)->sfMigration, &sfMigrationInv);
3687: PetscSectionCreate(PetscObjectComm((PetscObject) (*subdm)), §ionSeq);
3688: PetscSFDistributeSection(sfMigrationInv, section, NULL, sectionSeq);
3690: DMPlexCreateGlobalToNaturalSF(*subdm, sectionSeq, (*subdm)->sfMigration, &sfNatural);
3691: (*subdm)->sfNatural = sfNatural;
3692: PetscSectionDestroy(§ionSeq);
3693: PetscSFDestroy(&sfMigrationInv);
3694: }
3695: return 0;
3696: }
3698: PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm)
3699: {
3700: PetscInt i = 0;
3702: DMClone(dms[0], superdm);
3703: DMCreateSectionSuperDM(dms, len, is, superdm);
3704: (*superdm)->useNatural = PETSC_FALSE;
3705: for (i = 0; i < len; i++) {
3706: if (dms[i]->useNatural && dms[i]->sfMigration) {
3707: PetscSF sfMigrationInv,sfNatural;
3708: PetscSection section, sectionSeq;
3710: (*superdm)->sfMigration = dms[i]->sfMigration;
3711: PetscObjectReference((PetscObject) dms[i]->sfMigration);
3712: (*superdm)->useNatural = PETSC_TRUE;
3713: DMGetLocalSection((*superdm), §ion);
3714: PetscSFCreateInverseSF((*superdm)->sfMigration, &sfMigrationInv);
3715: PetscSectionCreate(PetscObjectComm((PetscObject) (*superdm)), §ionSeq);
3716: PetscSFDistributeSection(sfMigrationInv, section, NULL, sectionSeq);
3718: DMPlexCreateGlobalToNaturalSF(*superdm, sectionSeq, (*superdm)->sfMigration, &sfNatural);
3719: (*superdm)->sfNatural = sfNatural;
3720: PetscSectionDestroy(§ionSeq);
3721: PetscSFDestroy(&sfMigrationInv);
3722: break;
3723: }
3724: }
3725: return 0;
3726: }
3728: /*@
3729: DMPlexSymmetrize - Create support (out-edge) information from cone (in-edge) information
3731: Not collective
3733: Input Parameter:
3734: . mesh - The DMPlex
3736: Output Parameter:
3738: Note:
3739: This should be called after all calls to DMPlexSetCone()
3741: Level: beginner
3743: .seealso: DMPlexCreate(), DMPlexSetChart(), DMPlexSetConeSize(), DMPlexSetCone()
3744: @*/
3745: PetscErrorCode DMPlexSymmetrize(DM dm)
3746: {
3747: DM_Plex *mesh = (DM_Plex*) dm->data;
3748: PetscInt *offsets;
3749: PetscInt supportSize;
3750: PetscInt pStart, pEnd, p;
3754: PetscLogEventBegin(DMPLEX_Symmetrize,dm,0,0,0);
3755: /* Calculate support sizes */
3756: DMPlexGetChart(dm, &pStart, &pEnd);
3757: for (p = pStart; p < pEnd; ++p) {
3758: PetscInt dof, off, c;
3760: PetscSectionGetDof(mesh->coneSection, p, &dof);
3761: PetscSectionGetOffset(mesh->coneSection, p, &off);
3762: for (c = off; c < off+dof; ++c) {
3763: PetscSectionAddDof(mesh->supportSection, mesh->cones[c], 1);
3764: }
3765: }
3766: PetscSectionSetUp(mesh->supportSection);
3767: /* Calculate supports */
3768: PetscSectionGetStorageSize(mesh->supportSection, &supportSize);
3769: PetscMalloc1(supportSize, &mesh->supports);
3770: PetscCalloc1(pEnd - pStart, &offsets);
3771: for (p = pStart; p < pEnd; ++p) {
3772: PetscInt dof, off, c;
3774: PetscSectionGetDof(mesh->coneSection, p, &dof);
3775: PetscSectionGetOffset(mesh->coneSection, p, &off);
3776: for (c = off; c < off+dof; ++c) {
3777: const PetscInt q = mesh->cones[c];
3778: PetscInt offS;
3780: PetscSectionGetOffset(mesh->supportSection, q, &offS);
3782: mesh->supports[offS+offsets[q]] = p;
3783: ++offsets[q];
3784: }
3785: }
3786: PetscFree(offsets);
3787: PetscLogEventEnd(DMPLEX_Symmetrize,dm,0,0,0);
3788: return 0;
3789: }
3791: static PetscErrorCode DMPlexCreateDepthStratum(DM dm, DMLabel label, PetscInt depth, PetscInt pStart, PetscInt pEnd)
3792: {
3793: IS stratumIS;
3795: if (pStart >= pEnd) return 0;
3796: if (PetscDefined(USE_DEBUG)) {
3797: PetscInt qStart, qEnd, numLevels, level;
3798: PetscBool overlap = PETSC_FALSE;
3799: DMLabelGetNumValues(label, &numLevels);
3800: for (level = 0; level < numLevels; level++) {
3801: DMLabelGetStratumBounds(label, level, &qStart, &qEnd);
3802: if ((pStart >= qStart && pStart < qEnd) || (pEnd > qStart && pEnd <= qEnd)) {overlap = PETSC_TRUE; break;}
3803: }
3805: }
3806: ISCreateStride(PETSC_COMM_SELF, pEnd-pStart, pStart, 1, &stratumIS);
3807: DMLabelSetStratumIS(label, depth, stratumIS);
3808: ISDestroy(&stratumIS);
3809: return 0;
3810: }
3812: /*@
3813: DMPlexStratify - The DAG for most topologies is a graded poset (https://en.wikipedia.org/wiki/Graded_poset), and
3814: can be illustrated by a Hasse Diagram (https://en.wikipedia.org/wiki/Hasse_diagram). The strata group all points of the
3815: same grade, and this function calculates the strata. This grade can be seen as the height (or depth) of the point in
3816: the DAG.
3818: Collective on dm
3820: Input Parameter:
3821: . mesh - The DMPlex
3823: Output Parameter:
3825: Notes:
3826: Concretely, DMPlexStratify() creates a new label named "depth" containing the depth in the DAG of each point. For cell-vertex
3827: meshes, vertices are depth 0 and cells are depth 1. For fully interpolated meshes, depth 0 for vertices, 1 for edges, and so on
3828: until cells have depth equal to the dimension of the mesh. The depth label can be accessed through DMPlexGetDepthLabel() or DMPlexGetDepthStratum(), or
3829: manually via DMGetLabel(). The height is defined implicitly by height = maxDimension - depth, and can be accessed
3830: via DMPlexGetHeightStratum(). For example, cells have height 0 and faces have height 1.
3832: The depth of a point is calculated by executing a breadth-first search (BFS) on the DAG. This could produce surprising results
3833: if run on a partially interpolated mesh, meaning one that had some edges and faces, but not others. For example, suppose that
3834: we had a mesh consisting of one triangle (c0) and three vertices (v0, v1, v2), and only one edge is on the boundary so we choose
3835: to interpolate only that one (e0), so that
3836: $ cone(c0) = {e0, v2}
3837: $ cone(e0) = {v0, v1}
3838: If DMPlexStratify() is run on this mesh, it will give depths
3839: $ depth 0 = {v0, v1, v2}
3840: $ depth 1 = {e0, c0}
3841: where the triangle has been given depth 1, instead of 2, because it is reachable from vertex v2.
3843: DMPlexStratify() should be called after all calls to DMPlexSymmetrize()
3845: Level: beginner
3847: .seealso: DMPlexCreate(), DMPlexSymmetrize(), DMPlexComputeCellTypes()
3848: @*/
3849: PetscErrorCode DMPlexStratify(DM dm)
3850: {
3851: DM_Plex *mesh = (DM_Plex*) dm->data;
3852: DMLabel label;
3853: PetscInt pStart, pEnd, p;
3854: PetscInt numRoots = 0, numLeaves = 0;
3857: PetscLogEventBegin(DMPLEX_Stratify,dm,0,0,0);
3859: /* Create depth label */
3860: DMPlexGetChart(dm, &pStart, &pEnd);
3861: DMCreateLabel(dm, "depth");
3862: DMPlexGetDepthLabel(dm, &label);
3864: {
3865: /* Initialize roots and count leaves */
3866: PetscInt sMin = PETSC_MAX_INT;
3867: PetscInt sMax = PETSC_MIN_INT;
3868: PetscInt coneSize, supportSize;
3870: for (p = pStart; p < pEnd; ++p) {
3871: DMPlexGetConeSize(dm, p, &coneSize);
3872: DMPlexGetSupportSize(dm, p, &supportSize);
3873: if (!coneSize && supportSize) {
3874: sMin = PetscMin(p, sMin);
3875: sMax = PetscMax(p, sMax);
3876: ++numRoots;
3877: } else if (!supportSize && coneSize) {
3878: ++numLeaves;
3879: } else if (!supportSize && !coneSize) {
3880: /* Isolated points */
3881: sMin = PetscMin(p, sMin);
3882: sMax = PetscMax(p, sMax);
3883: }
3884: }
3885: DMPlexCreateDepthStratum(dm, label, 0, sMin, sMax+1);
3886: }
3888: if (numRoots + numLeaves == (pEnd - pStart)) {
3889: PetscInt sMin = PETSC_MAX_INT;
3890: PetscInt sMax = PETSC_MIN_INT;
3891: PetscInt coneSize, supportSize;
3893: for (p = pStart; p < pEnd; ++p) {
3894: DMPlexGetConeSize(dm, p, &coneSize);
3895: DMPlexGetSupportSize(dm, p, &supportSize);
3896: if (!supportSize && coneSize) {
3897: sMin = PetscMin(p, sMin);
3898: sMax = PetscMax(p, sMax);
3899: }
3900: }
3901: DMPlexCreateDepthStratum(dm, label, 1, sMin, sMax+1);
3902: } else {
3903: PetscInt level = 0;
3904: PetscInt qStart, qEnd, q;
3906: DMLabelGetStratumBounds(label, level, &qStart, &qEnd);
3907: while (qEnd > qStart) {
3908: PetscInt sMin = PETSC_MAX_INT;
3909: PetscInt sMax = PETSC_MIN_INT;
3911: for (q = qStart; q < qEnd; ++q) {
3912: const PetscInt *support;
3913: PetscInt supportSize, s;
3915: DMPlexGetSupportSize(dm, q, &supportSize);
3916: DMPlexGetSupport(dm, q, &support);
3917: for (s = 0; s < supportSize; ++s) {
3918: sMin = PetscMin(support[s], sMin);
3919: sMax = PetscMax(support[s], sMax);
3920: }
3921: }
3922: DMLabelGetNumValues(label, &level);
3923: DMPlexCreateDepthStratum(dm, label, level, sMin, sMax+1);
3924: DMLabelGetStratumBounds(label, level, &qStart, &qEnd);
3925: }
3926: }
3927: { /* just in case there is an empty process */
3928: PetscInt numValues, maxValues = 0, v;
3930: DMLabelGetNumValues(label, &numValues);
3931: MPI_Allreduce(&numValues,&maxValues,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)dm));
3932: for (v = numValues; v < maxValues; v++) {
3933: DMLabelAddStratum(label, v);
3934: }
3935: }
3936: PetscObjectStateGet((PetscObject) label, &mesh->depthState);
3937: PetscLogEventEnd(DMPLEX_Stratify,dm,0,0,0);
3938: return 0;
3939: }
3941: PetscErrorCode DMPlexComputeCellType_Internal(DM dm, PetscInt p, PetscInt pdepth, DMPolytopeType *pt)
3942: {
3943: DMPolytopeType ct = DM_POLYTOPE_UNKNOWN;
3944: PetscInt dim, depth, pheight, coneSize;
3947: DMGetDimension(dm, &dim);
3948: DMPlexGetDepth(dm, &depth);
3949: DMPlexGetConeSize(dm, p, &coneSize);
3950: pheight = depth - pdepth;
3951: if (depth <= 1) {
3952: switch (pdepth) {
3953: case 0: ct = DM_POLYTOPE_POINT;break;
3954: case 1:
3955: switch (coneSize) {
3956: case 2: ct = DM_POLYTOPE_SEGMENT;break;
3957: case 3: ct = DM_POLYTOPE_TRIANGLE;break;
3958: case 4:
3959: switch (dim) {
3960: case 2: ct = DM_POLYTOPE_QUADRILATERAL;break;
3961: case 3: ct = DM_POLYTOPE_TETRAHEDRON;break;
3962: default: break;
3963: }
3964: break;
3965: case 5: ct = DM_POLYTOPE_PYRAMID;break;
3966: case 6: ct = DM_POLYTOPE_TRI_PRISM_TENSOR;break;
3967: case 8: ct = DM_POLYTOPE_HEXAHEDRON;break;
3968: default: break;
3969: }
3970: }
3971: } else {
3972: if (pdepth == 0) {
3973: ct = DM_POLYTOPE_POINT;
3974: } else if (pheight == 0) {
3975: switch (dim) {
3976: case 1:
3977: switch (coneSize) {
3978: case 2: ct = DM_POLYTOPE_SEGMENT;break;
3979: default: break;
3980: }
3981: break;
3982: case 2:
3983: switch (coneSize) {
3984: case 3: ct = DM_POLYTOPE_TRIANGLE;break;
3985: case 4: ct = DM_POLYTOPE_QUADRILATERAL;break;
3986: default: break;
3987: }
3988: break;
3989: case 3:
3990: switch (coneSize) {
3991: case 4: ct = DM_POLYTOPE_TETRAHEDRON;break;
3992: case 5:
3993: {
3994: const PetscInt *cone;
3995: PetscInt faceConeSize;
3997: DMPlexGetCone(dm, p, &cone);
3998: DMPlexGetConeSize(dm, cone[0], &faceConeSize);
3999: switch (faceConeSize) {
4000: case 3: ct = DM_POLYTOPE_TRI_PRISM_TENSOR;break;
4001: case 4: ct = DM_POLYTOPE_PYRAMID;break;
4002: }
4003: }
4004: break;
4005: case 6: ct = DM_POLYTOPE_HEXAHEDRON;break;
4006: default: break;
4007: }
4008: break;
4009: default: break;
4010: }
4011: } else if (pheight > 0) {
4012: switch (coneSize) {
4013: case 2: ct = DM_POLYTOPE_SEGMENT;break;
4014: case 3: ct = DM_POLYTOPE_TRIANGLE;break;
4015: case 4: ct = DM_POLYTOPE_QUADRILATERAL;break;
4016: default: break;
4017: }
4018: }
4019: }
4020: *pt = ct;
4021: return 0;
4022: }
4024: /*@
4025: DMPlexComputeCellTypes - Infer the polytope type of every cell using its dimension and cone size.
4027: Collective on dm
4029: Input Parameter:
4030: . mesh - The DMPlex
4032: DMPlexComputeCellTypes() should be called after all calls to DMPlexSymmetrize() and DMPlexStratify()
4034: Level: developer
4036: Note: This function is normally called automatically by Plex when a cell type is requested. It creates an
4037: internal DMLabel named "celltype" which can be directly accessed using DMGetLabel(). A user may disable
4038: automatic creation by creating the label manually, using DMCreateLabel(dm, "celltype").
4040: .seealso: DMPlexCreate(), DMPlexSymmetrize(), DMPlexStratify(), DMGetLabel(), DMCreateLabel()
4041: @*/
4042: PetscErrorCode DMPlexComputeCellTypes(DM dm)
4043: {
4044: DM_Plex *mesh;
4045: DMLabel ctLabel;
4046: PetscInt pStart, pEnd, p;
4049: mesh = (DM_Plex *) dm->data;
4050: DMCreateLabel(dm, "celltype");
4051: DMPlexGetCellTypeLabel(dm, &ctLabel);
4052: DMPlexGetChart(dm, &pStart, &pEnd);
4053: for (p = pStart; p < pEnd; ++p) {
4054: DMPolytopeType ct = DM_POLYTOPE_UNKNOWN;
4055: PetscInt pdepth;
4057: DMPlexGetPointDepth(dm, p, &pdepth);
4058: DMPlexComputeCellType_Internal(dm, p, pdepth, &ct);
4060: DMLabelSetValue(ctLabel, p, ct);
4061: }
4062: PetscObjectStateGet((PetscObject) ctLabel, &mesh->celltypeState);
4063: PetscObjectViewFromOptions((PetscObject) ctLabel, NULL, "-dm_plex_celltypes_view");
4064: return 0;
4065: }
4067: /*@C
4068: DMPlexGetJoin - Get an array for the join of the set of points
4070: Not Collective
4072: Input Parameters:
4073: + dm - The DMPlex object
4074: . numPoints - The number of input points for the join
4075: - points - The input points
4077: Output Parameters:
4078: + numCoveredPoints - The number of points in the join
4079: - coveredPoints - The points in the join
4081: Level: intermediate
4083: Note: Currently, this is restricted to a single level join
4085: Fortran Notes:
4086: Since it returns an array, this routine is only available in Fortran 90, and you must
4087: include petsc.h90 in your code.
4089: The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.
4091: .seealso: DMPlexRestoreJoin(), DMPlexGetMeet()
4092: @*/
4093: PetscErrorCode DMPlexGetJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
4094: {
4095: DM_Plex *mesh = (DM_Plex*) dm->data;
4096: PetscInt *join[2];
4097: PetscInt joinSize, i = 0;
4098: PetscInt dof, off, p, c, m;
4099: PetscInt maxSupportSize;
4105: PetscSectionGetMaxDof(mesh->supportSection, &maxSupportSize);
4106: DMGetWorkArray(dm, maxSupportSize, MPIU_INT, &join[0]);
4107: DMGetWorkArray(dm, maxSupportSize, MPIU_INT, &join[1]);
4108: /* Copy in support of first point */
4109: PetscSectionGetDof(mesh->supportSection, points[0], &dof);
4110: PetscSectionGetOffset(mesh->supportSection, points[0], &off);
4111: for (joinSize = 0; joinSize < dof; ++joinSize) {
4112: join[i][joinSize] = mesh->supports[off+joinSize];
4113: }
4114: /* Check each successive support */
4115: for (p = 1; p < numPoints; ++p) {
4116: PetscInt newJoinSize = 0;
4118: PetscSectionGetDof(mesh->supportSection, points[p], &dof);
4119: PetscSectionGetOffset(mesh->supportSection, points[p], &off);
4120: for (c = 0; c < dof; ++c) {
4121: const PetscInt point = mesh->supports[off+c];
4123: for (m = 0; m < joinSize; ++m) {
4124: if (point == join[i][m]) {
4125: join[1-i][newJoinSize++] = point;
4126: break;
4127: }
4128: }
4129: }
4130: joinSize = newJoinSize;
4131: i = 1-i;
4132: }
4133: *numCoveredPoints = joinSize;
4134: *coveredPoints = join[i];
4135: DMRestoreWorkArray(dm, maxSupportSize, MPIU_INT, &join[1-i]);
4136: return 0;
4137: }
4139: /*@C
4140: DMPlexRestoreJoin - Restore an array for the join of the set of points
4142: Not Collective
4144: Input Parameters:
4145: + dm - The DMPlex object
4146: . numPoints - The number of input points for the join
4147: - points - The input points
4149: Output Parameters:
4150: + numCoveredPoints - The number of points in the join
4151: - coveredPoints - The points in the join
4153: Fortran Notes:
4154: Since it returns an array, this routine is only available in Fortran 90, and you must
4155: include petsc.h90 in your code.
4157: The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.
4159: Level: intermediate
4161: .seealso: DMPlexGetJoin(), DMPlexGetFullJoin(), DMPlexGetMeet()
4162: @*/
4163: PetscErrorCode DMPlexRestoreJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
4164: {
4169: DMRestoreWorkArray(dm, 0, MPIU_INT, (void*) coveredPoints);
4170: if (numCoveredPoints) *numCoveredPoints = 0;
4171: return 0;
4172: }
4174: /*@C
4175: DMPlexGetFullJoin - Get an array for the join of the set of points
4177: Not Collective
4179: Input Parameters:
4180: + dm - The DMPlex object
4181: . numPoints - The number of input points for the join
4182: - points - The input points
4184: Output Parameters:
4185: + numCoveredPoints - The number of points in the join
4186: - coveredPoints - The points in the join
4188: Fortran Notes:
4189: Since it returns an array, this routine is only available in Fortran 90, and you must
4190: include petsc.h90 in your code.
4192: The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.
4194: Level: intermediate
4196: .seealso: DMPlexGetJoin(), DMPlexRestoreJoin(), DMPlexGetMeet()
4197: @*/
4198: PetscErrorCode DMPlexGetFullJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
4199: {
4200: PetscInt *offsets, **closures;
4201: PetscInt *join[2];
4202: PetscInt depth = 0, maxSize, joinSize = 0, i = 0;
4203: PetscInt p, d, c, m, ms;
4210: DMPlexGetDepth(dm, &depth);
4211: PetscCalloc1(numPoints, &closures);
4212: DMGetWorkArray(dm, numPoints*(depth+2), MPIU_INT, &offsets);
4213: DMPlexGetMaxSizes(dm, NULL, &ms);
4214: maxSize = (ms > 1) ? ((PetscPowInt(ms,depth+1)-1)/(ms-1)) : depth + 1;
4215: DMGetWorkArray(dm, maxSize, MPIU_INT, &join[0]);
4216: DMGetWorkArray(dm, maxSize, MPIU_INT, &join[1]);
4218: for (p = 0; p < numPoints; ++p) {
4219: PetscInt closureSize;
4221: DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closures[p]);
4223: offsets[p*(depth+2)+0] = 0;
4224: for (d = 0; d < depth+1; ++d) {
4225: PetscInt pStart, pEnd, i;
4227: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
4228: for (i = offsets[p*(depth+2)+d]; i < closureSize; ++i) {
4229: if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) {
4230: offsets[p*(depth+2)+d+1] = i;
4231: break;
4232: }
4233: }
4234: if (i == closureSize) offsets[p*(depth+2)+d+1] = i;
4235: }
4237: }
4238: for (d = 0; d < depth+1; ++d) {
4239: PetscInt dof;
4241: /* Copy in support of first point */
4242: dof = offsets[d+1] - offsets[d];
4243: for (joinSize = 0; joinSize < dof; ++joinSize) {
4244: join[i][joinSize] = closures[0][(offsets[d]+joinSize)*2];
4245: }
4246: /* Check each successive cone */
4247: for (p = 1; p < numPoints && joinSize; ++p) {
4248: PetscInt newJoinSize = 0;
4250: dof = offsets[p*(depth+2)+d+1] - offsets[p*(depth+2)+d];
4251: for (c = 0; c < dof; ++c) {
4252: const PetscInt point = closures[p][(offsets[p*(depth+2)+d]+c)*2];
4254: for (m = 0; m < joinSize; ++m) {
4255: if (point == join[i][m]) {
4256: join[1-i][newJoinSize++] = point;
4257: break;
4258: }
4259: }
4260: }
4261: joinSize = newJoinSize;
4262: i = 1-i;
4263: }
4264: if (joinSize) break;
4265: }
4266: *numCoveredPoints = joinSize;
4267: *coveredPoints = join[i];
4268: for (p = 0; p < numPoints; ++p) {
4269: DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, NULL, &closures[p]);
4270: }
4271: PetscFree(closures);
4272: DMRestoreWorkArray(dm, numPoints*(depth+2), MPIU_INT, &offsets);
4273: DMRestoreWorkArray(dm, ms, MPIU_INT, &join[1-i]);
4274: return 0;
4275: }
4277: /*@C
4278: DMPlexGetMeet - Get an array for the meet of the set of points
4280: Not Collective
4282: Input Parameters:
4283: + dm - The DMPlex object
4284: . numPoints - The number of input points for the meet
4285: - points - The input points
4287: Output Parameters:
4288: + numCoveredPoints - The number of points in the meet
4289: - coveredPoints - The points in the meet
4291: Level: intermediate
4293: Note: Currently, this is restricted to a single level meet
4295: Fortran Notes:
4296: Since it returns an array, this routine is only available in Fortran 90, and you must
4297: include petsc.h90 in your code.
4299: The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.
4301: .seealso: DMPlexRestoreMeet(), DMPlexGetJoin()
4302: @*/
4303: PetscErrorCode DMPlexGetMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveringPoints, const PetscInt **coveringPoints)
4304: {
4305: DM_Plex *mesh = (DM_Plex*) dm->data;
4306: PetscInt *meet[2];
4307: PetscInt meetSize, i = 0;
4308: PetscInt dof, off, p, c, m;
4309: PetscInt maxConeSize;
4315: PetscSectionGetMaxDof(mesh->coneSection, &maxConeSize);
4316: DMGetWorkArray(dm, maxConeSize, MPIU_INT, &meet[0]);
4317: DMGetWorkArray(dm, maxConeSize, MPIU_INT, &meet[1]);
4318: /* Copy in cone of first point */
4319: PetscSectionGetDof(mesh->coneSection, points[0], &dof);
4320: PetscSectionGetOffset(mesh->coneSection, points[0], &off);
4321: for (meetSize = 0; meetSize < dof; ++meetSize) {
4322: meet[i][meetSize] = mesh->cones[off+meetSize];
4323: }
4324: /* Check each successive cone */
4325: for (p = 1; p < numPoints; ++p) {
4326: PetscInt newMeetSize = 0;
4328: PetscSectionGetDof(mesh->coneSection, points[p], &dof);
4329: PetscSectionGetOffset(mesh->coneSection, points[p], &off);
4330: for (c = 0; c < dof; ++c) {
4331: const PetscInt point = mesh->cones[off+c];
4333: for (m = 0; m < meetSize; ++m) {
4334: if (point == meet[i][m]) {
4335: meet[1-i][newMeetSize++] = point;
4336: break;
4337: }
4338: }
4339: }
4340: meetSize = newMeetSize;
4341: i = 1-i;
4342: }
4343: *numCoveringPoints = meetSize;
4344: *coveringPoints = meet[i];
4345: DMRestoreWorkArray(dm, maxConeSize, MPIU_INT, &meet[1-i]);
4346: return 0;
4347: }
4349: /*@C
4350: DMPlexRestoreMeet - Restore an array for the meet of the set of points
4352: Not Collective
4354: Input Parameters:
4355: + dm - The DMPlex object
4356: . numPoints - The number of input points for the meet
4357: - points - The input points
4359: Output Parameters:
4360: + numCoveredPoints - The number of points in the meet
4361: - coveredPoints - The points in the meet
4363: Level: intermediate
4365: Fortran Notes:
4366: Since it returns an array, this routine is only available in Fortran 90, and you must
4367: include petsc.h90 in your code.
4369: The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.
4371: .seealso: DMPlexGetMeet(), DMPlexGetFullMeet(), DMPlexGetJoin()
4372: @*/
4373: PetscErrorCode DMPlexRestoreMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
4374: {
4379: DMRestoreWorkArray(dm, 0, MPIU_INT, (void*) coveredPoints);
4380: if (numCoveredPoints) *numCoveredPoints = 0;
4381: return 0;
4382: }
4384: /*@C
4385: DMPlexGetFullMeet - Get an array for the meet of the set of points
4387: Not Collective
4389: Input Parameters:
4390: + dm - The DMPlex object
4391: . numPoints - The number of input points for the meet
4392: - points - The input points
4394: Output Parameters:
4395: + numCoveredPoints - The number of points in the meet
4396: - coveredPoints - The points in the meet
4398: Level: intermediate
4400: Fortran Notes:
4401: Since it returns an array, this routine is only available in Fortran 90, and you must
4402: include petsc.h90 in your code.
4404: The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.
4406: .seealso: DMPlexGetMeet(), DMPlexRestoreMeet(), DMPlexGetJoin()
4407: @*/
4408: PetscErrorCode DMPlexGetFullMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
4409: {
4410: PetscInt *offsets, **closures;
4411: PetscInt *meet[2];
4412: PetscInt height = 0, maxSize, meetSize = 0, i = 0;
4413: PetscInt p, h, c, m, mc;
4420: DMPlexGetDepth(dm, &height);
4421: PetscMalloc1(numPoints, &closures);
4422: DMGetWorkArray(dm, numPoints*(height+2), MPIU_INT, &offsets);
4423: DMPlexGetMaxSizes(dm, &mc, NULL);
4424: maxSize = (mc > 1) ? ((PetscPowInt(mc,height+1)-1)/(mc-1)) : height + 1;
4425: DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[0]);
4426: DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[1]);
4428: for (p = 0; p < numPoints; ++p) {
4429: PetscInt closureSize;
4431: DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closures[p]);
4433: offsets[p*(height+2)+0] = 0;
4434: for (h = 0; h < height+1; ++h) {
4435: PetscInt pStart, pEnd, i;
4437: DMPlexGetHeightStratum(dm, h, &pStart, &pEnd);
4438: for (i = offsets[p*(height+2)+h]; i < closureSize; ++i) {
4439: if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) {
4440: offsets[p*(height+2)+h+1] = i;
4441: break;
4442: }
4443: }
4444: if (i == closureSize) offsets[p*(height+2)+h+1] = i;
4445: }
4447: }
4448: for (h = 0; h < height+1; ++h) {
4449: PetscInt dof;
4451: /* Copy in cone of first point */
4452: dof = offsets[h+1] - offsets[h];
4453: for (meetSize = 0; meetSize < dof; ++meetSize) {
4454: meet[i][meetSize] = closures[0][(offsets[h]+meetSize)*2];
4455: }
4456: /* Check each successive cone */
4457: for (p = 1; p < numPoints && meetSize; ++p) {
4458: PetscInt newMeetSize = 0;
4460: dof = offsets[p*(height+2)+h+1] - offsets[p*(height+2)+h];
4461: for (c = 0; c < dof; ++c) {
4462: const PetscInt point = closures[p][(offsets[p*(height+2)+h]+c)*2];
4464: for (m = 0; m < meetSize; ++m) {
4465: if (point == meet[i][m]) {
4466: meet[1-i][newMeetSize++] = point;
4467: break;
4468: }
4469: }
4470: }
4471: meetSize = newMeetSize;
4472: i = 1-i;
4473: }
4474: if (meetSize) break;
4475: }
4476: *numCoveredPoints = meetSize;
4477: *coveredPoints = meet[i];
4478: for (p = 0; p < numPoints; ++p) {
4479: DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, NULL, &closures[p]);
4480: }
4481: PetscFree(closures);
4482: DMRestoreWorkArray(dm, numPoints*(height+2), MPIU_INT, &offsets);
4483: DMRestoreWorkArray(dm, mc, MPIU_INT, &meet[1-i]);
4484: return 0;
4485: }
4487: /*@C
4488: DMPlexEqual - Determine if two DMs have the same topology
4490: Not Collective
4492: Input Parameters:
4493: + dmA - A DMPlex object
4494: - dmB - A DMPlex object
4496: Output Parameters:
4497: . equal - PETSC_TRUE if the topologies are identical
4499: Level: intermediate
4501: Notes:
4502: We are not solving graph isomorphism, so we do not permutation.
4504: .seealso: DMPlexGetCone()
4505: @*/
4506: PetscErrorCode DMPlexEqual(DM dmA, DM dmB, PetscBool *equal)
4507: {
4508: PetscInt depth, depthB, pStart, pEnd, pStartB, pEndB, p;
4514: *equal = PETSC_FALSE;
4515: DMPlexGetDepth(dmA, &depth);
4516: DMPlexGetDepth(dmB, &depthB);
4517: if (depth != depthB) return 0;
4518: DMPlexGetChart(dmA, &pStart, &pEnd);
4519: DMPlexGetChart(dmB, &pStartB, &pEndB);
4520: if ((pStart != pStartB) || (pEnd != pEndB)) return 0;
4521: for (p = pStart; p < pEnd; ++p) {
4522: const PetscInt *cone, *coneB, *ornt, *orntB, *support, *supportB;
4523: PetscInt coneSize, coneSizeB, c, supportSize, supportSizeB, s;
4525: DMPlexGetConeSize(dmA, p, &coneSize);
4526: DMPlexGetCone(dmA, p, &cone);
4527: DMPlexGetConeOrientation(dmA, p, &ornt);
4528: DMPlexGetConeSize(dmB, p, &coneSizeB);
4529: DMPlexGetCone(dmB, p, &coneB);
4530: DMPlexGetConeOrientation(dmB, p, &orntB);
4531: if (coneSize != coneSizeB) return 0;
4532: for (c = 0; c < coneSize; ++c) {
4533: if (cone[c] != coneB[c]) return 0;
4534: if (ornt[c] != orntB[c]) return 0;
4535: }
4536: DMPlexGetSupportSize(dmA, p, &supportSize);
4537: DMPlexGetSupport(dmA, p, &support);
4538: DMPlexGetSupportSize(dmB, p, &supportSizeB);
4539: DMPlexGetSupport(dmB, p, &supportB);
4540: if (supportSize != supportSizeB) return 0;
4541: for (s = 0; s < supportSize; ++s) {
4542: if (support[s] != supportB[s]) return 0;
4543: }
4544: }
4545: *equal = PETSC_TRUE;
4546: return 0;
4547: }
4549: /*@C
4550: DMPlexGetNumFaceVertices - Returns the number of vertices on a face
4552: Not Collective
4554: Input Parameters:
4555: + dm - The DMPlex
4556: . cellDim - The cell dimension
4557: - numCorners - The number of vertices on a cell
4559: Output Parameters:
4560: . numFaceVertices - The number of vertices on a face
4562: Level: developer
4564: Notes:
4565: Of course this can only work for a restricted set of symmetric shapes
4567: .seealso: DMPlexGetCone()
4568: @*/
4569: PetscErrorCode DMPlexGetNumFaceVertices(DM dm, PetscInt cellDim, PetscInt numCorners, PetscInt *numFaceVertices)
4570: {
4571: MPI_Comm comm;
4573: PetscObjectGetComm((PetscObject)dm,&comm);
4575: switch (cellDim) {
4576: case 0:
4577: *numFaceVertices = 0;
4578: break;
4579: case 1:
4580: *numFaceVertices = 1;
4581: break;
4582: case 2:
4583: switch (numCorners) {
4584: case 3: /* triangle */
4585: *numFaceVertices = 2; /* Edge has 2 vertices */
4586: break;
4587: case 4: /* quadrilateral */
4588: *numFaceVertices = 2; /* Edge has 2 vertices */
4589: break;
4590: case 6: /* quadratic triangle, tri and quad cohesive Lagrange cells */
4591: *numFaceVertices = 3; /* Edge has 3 vertices */
4592: break;
4593: case 9: /* quadratic quadrilateral, quadratic quad cohesive Lagrange cells */
4594: *numFaceVertices = 3; /* Edge has 3 vertices */
4595: break;
4596: default:
4597: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %D for dimension %D", numCorners, cellDim);
4598: }
4599: break;
4600: case 3:
4601: switch (numCorners) {
4602: case 4: /* tetradehdron */
4603: *numFaceVertices = 3; /* Face has 3 vertices */
4604: break;
4605: case 6: /* tet cohesive cells */
4606: *numFaceVertices = 4; /* Face has 4 vertices */
4607: break;
4608: case 8: /* hexahedron */
4609: *numFaceVertices = 4; /* Face has 4 vertices */
4610: break;
4611: case 9: /* tet cohesive Lagrange cells */
4612: *numFaceVertices = 6; /* Face has 6 vertices */
4613: break;
4614: case 10: /* quadratic tetrahedron */
4615: *numFaceVertices = 6; /* Face has 6 vertices */
4616: break;
4617: case 12: /* hex cohesive Lagrange cells */
4618: *numFaceVertices = 6; /* Face has 6 vertices */
4619: break;
4620: case 18: /* quadratic tet cohesive Lagrange cells */
4621: *numFaceVertices = 6; /* Face has 6 vertices */
4622: break;
4623: case 27: /* quadratic hexahedron, quadratic hex cohesive Lagrange cells */
4624: *numFaceVertices = 9; /* Face has 9 vertices */
4625: break;
4626: default:
4627: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %D for dimension %D", numCorners, cellDim);
4628: }
4629: break;
4630: default:
4631: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid cell dimension %D", cellDim);
4632: }
4633: return 0;
4634: }
4636: /*@
4637: DMPlexGetDepthLabel - Get the DMLabel recording the depth of each point
4639: Not Collective
4641: Input Parameter:
4642: . dm - The DMPlex object
4644: Output Parameter:
4645: . depthLabel - The DMLabel recording point depth
4647: Level: developer
4649: .seealso: DMPlexGetDepth(), DMPlexGetHeightStratum(), DMPlexGetDepthStratum(), DMPlexGetPointDepth(),
4650: @*/
4651: PetscErrorCode DMPlexGetDepthLabel(DM dm, DMLabel *depthLabel)
4652: {
4655: *depthLabel = dm->depthLabel;
4656: return 0;
4657: }
4659: /*@
4660: DMPlexGetDepth - Get the depth of the DAG representing this mesh
4662: Not Collective
4664: Input Parameter:
4665: . dm - The DMPlex object
4667: Output Parameter:
4668: . depth - The number of strata (breadth first levels) in the DAG
4670: Level: developer
4672: Notes:
4673: This returns maximum of point depths over all points, i.e. maximum value of the label returned by DMPlexGetDepthLabel().
4674: The point depth is described more in detail in DMPlexGetDepthStratum().
4675: An empty mesh gives -1.
4677: .seealso: DMPlexGetDepthLabel(), DMPlexGetDepthStratum(), DMPlexGetPointDepth(), DMPlexSymmetrize()
4678: @*/
4679: PetscErrorCode DMPlexGetDepth(DM dm, PetscInt *depth)
4680: {
4681: DMLabel label;
4682: PetscInt d = 0;
4686: DMPlexGetDepthLabel(dm, &label);
4687: if (label) DMLabelGetNumValues(label, &d);
4688: *depth = d-1;
4689: return 0;
4690: }
4692: /*@
4693: DMPlexGetDepthStratum - Get the bounds [start, end) for all points at a certain depth.
4695: Not Collective
4697: Input Parameters:
4698: + dm - The DMPlex object
4699: - stratumValue - The requested depth
4701: Output Parameters:
4702: + start - The first point at this depth
4703: - end - One beyond the last point at this depth
4705: Notes:
4706: Depth indexing is related to topological dimension. Depth stratum 0 contains the lowest topological dimension points,
4707: often "vertices". If the mesh is "interpolated" (see DMPlexInterpolate()), then depth stratum 1 contains the next
4708: higher dimension, e.g., "edges".
4710: Level: developer
4712: .seealso: DMPlexGetHeightStratum(), DMPlexGetDepth(), DMPlexGetDepthLabel(), DMPlexGetPointDepth(), DMPlexSymmetrize(), DMPlexInterpolate()
4713: @*/
4714: PetscErrorCode DMPlexGetDepthStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end)
4715: {
4716: DMLabel label;
4717: PetscInt pStart, pEnd;
4722: DMPlexGetChart(dm, &pStart, &pEnd);
4723: if (pStart == pEnd) return 0;
4724: if (stratumValue < 0) {
4725: if (start) *start = pStart;
4726: if (end) *end = pEnd;
4727: return 0;
4728: }
4729: DMPlexGetDepthLabel(dm, &label);
4731: DMLabelGetStratumBounds(label, stratumValue, start, end);
4732: return 0;
4733: }
4735: /*@
4736: DMPlexGetHeightStratum - Get the bounds [start, end) for all points at a certain height.
4738: Not Collective
4740: Input Parameters:
4741: + dm - The DMPlex object
4742: - stratumValue - The requested height
4744: Output Parameters:
4745: + start - The first point at this height
4746: - end - One beyond the last point at this height
4748: Notes:
4749: Height indexing is related to topological codimension. Height stratum 0 contains the highest topological dimension
4750: points, often called "cells" or "elements". If the mesh is "interpolated" (see DMPlexInterpolate()), then height
4751: stratum 1 contains the boundary of these "cells", often called "faces" or "facets".
4753: Level: developer
4755: .seealso: DMPlexGetDepthStratum(), DMPlexGetDepth(), DMPlexGetPointHeight()
4756: @*/
4757: PetscErrorCode DMPlexGetHeightStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end)
4758: {
4759: DMLabel label;
4760: PetscInt depth, pStart, pEnd;
4765: DMPlexGetChart(dm, &pStart, &pEnd);
4766: if (pStart == pEnd) return 0;
4767: if (stratumValue < 0) {
4768: if (start) *start = pStart;
4769: if (end) *end = pEnd;
4770: return 0;
4771: }
4772: DMPlexGetDepthLabel(dm, &label);
4774: DMLabelGetNumValues(label, &depth);
4775: DMLabelGetStratumBounds(label, depth-1-stratumValue, start, end);
4776: return 0;
4777: }
4779: /*@
4780: DMPlexGetPointDepth - Get the depth of a given point
4782: Not Collective
4784: Input Parameters:
4785: + dm - The DMPlex object
4786: - point - The point
4788: Output Parameter:
4789: . depth - The depth of the point
4791: Level: intermediate
4793: .seealso: DMPlexGetCellType(), DMPlexGetDepthLabel(), DMPlexGetDepth(), DMPlexGetPointHeight()
4794: @*/
4795: PetscErrorCode DMPlexGetPointDepth(DM dm, PetscInt point, PetscInt *depth)
4796: {
4799: DMLabelGetValue(dm->depthLabel, point, depth);
4800: return 0;
4801: }
4803: /*@
4804: DMPlexGetPointHeight - Get the height of a given point
4806: Not Collective
4808: Input Parameters:
4809: + dm - The DMPlex object
4810: - point - The point
4812: Output Parameter:
4813: . height - The height of the point
4815: Level: intermediate
4817: .seealso: DMPlexGetCellType(), DMPlexGetDepthLabel(), DMPlexGetDepth(), DMPlexGetPointDepth()
4818: @*/
4819: PetscErrorCode DMPlexGetPointHeight(DM dm, PetscInt point, PetscInt *height)
4820: {
4821: PetscInt n, pDepth;
4825: DMLabelGetNumValues(dm->depthLabel, &n);
4826: DMLabelGetValue(dm->depthLabel, point, &pDepth);
4827: *height = n - 1 - pDepth; /* DAG depth is n-1 */
4828: return 0;
4829: }
4831: /*@
4832: DMPlexGetCellTypeLabel - Get the DMLabel recording the polytope type of each cell
4834: Not Collective
4836: Input Parameter:
4837: . dm - The DMPlex object
4839: Output Parameter:
4840: . celltypeLabel - The DMLabel recording cell polytope type
4842: Note: This function will trigger automatica computation of cell types. This can be disabled by calling
4843: DMCreateLabel(dm, "celltype") beforehand.
4845: Level: developer
4847: .seealso: DMPlexGetCellType(), DMPlexGetDepthLabel(), DMCreateLabel()
4848: @*/
4849: PetscErrorCode DMPlexGetCellTypeLabel(DM dm, DMLabel *celltypeLabel)
4850: {
4853: if (!dm->celltypeLabel) DMPlexComputeCellTypes(dm);
4854: *celltypeLabel = dm->celltypeLabel;
4855: return 0;
4856: }
4858: /*@
4859: DMPlexGetCellType - Get the polytope type of a given cell
4861: Not Collective
4863: Input Parameters:
4864: + dm - The DMPlex object
4865: - cell - The cell
4867: Output Parameter:
4868: . celltype - The polytope type of the cell
4870: Level: intermediate
4872: .seealso: DMPlexGetCellTypeLabel(), DMPlexGetDepthLabel(), DMPlexGetDepth()
4873: @*/
4874: PetscErrorCode DMPlexGetCellType(DM dm, PetscInt cell, DMPolytopeType *celltype)
4875: {
4876: DMLabel label;
4877: PetscInt ct;
4881: DMPlexGetCellTypeLabel(dm, &label);
4882: DMLabelGetValue(label, cell, &ct);
4884: *celltype = (DMPolytopeType) ct;
4885: return 0;
4886: }
4888: /*@
4889: DMPlexSetCellType - Set the polytope type of a given cell
4891: Not Collective
4893: Input Parameters:
4894: + dm - The DMPlex object
4895: . cell - The cell
4896: - celltype - The polytope type of the cell
4898: Note: By default, cell types will be automatically computed using DMPlexComputeCellTypes() before this function
4899: is executed. This function will override the computed type. However, if automatic classification will not succeed
4900: and a user wants to manually specify all types, the classification must be disabled by calling
4901: DMCreaateLabel(dm, "celltype") before getting or setting any cell types.
4903: Level: advanced
4905: .seealso: DMPlexGetCellTypeLabel(), DMPlexGetDepthLabel(), DMPlexGetDepth(), DMPlexComputeCellTypes(), DMCreateLabel()
4906: @*/
4907: PetscErrorCode DMPlexSetCellType(DM dm, PetscInt cell, DMPolytopeType celltype)
4908: {
4909: DMLabel label;
4912: DMPlexGetCellTypeLabel(dm, &label);
4913: DMLabelSetValue(label, cell, celltype);
4914: return 0;
4915: }
4917: PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm)
4918: {
4919: PetscSection section, s;
4920: Mat m;
4921: PetscInt maxHeight;
4923: DMClone(dm, cdm);
4924: DMPlexGetMaxProjectionHeight(dm, &maxHeight);
4925: DMPlexSetMaxProjectionHeight(*cdm, maxHeight);
4926: PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion);
4927: DMSetLocalSection(*cdm, section);
4928: PetscSectionDestroy(§ion);
4929: PetscSectionCreate(PETSC_COMM_SELF, &s);
4930: MatCreate(PETSC_COMM_SELF, &m);
4931: DMSetDefaultConstraints(*cdm, s, m, NULL);
4932: PetscSectionDestroy(&s);
4933: MatDestroy(&m);
4935: DMSetNumFields(*cdm, 1);
4936: DMCreateDS(*cdm);
4937: return 0;
4938: }
4940: PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field)
4941: {
4942: Vec coordsLocal;
4943: DM coordsDM;
4945: *field = NULL;
4946: DMGetCoordinatesLocal(dm,&coordsLocal);
4947: DMGetCoordinateDM(dm,&coordsDM);
4948: if (coordsLocal && coordsDM) {
4949: DMFieldCreateDS(coordsDM, 0, coordsLocal, field);
4950: }
4951: return 0;
4952: }
4954: /*@C
4955: DMPlexGetConeSection - Return a section which describes the layout of cone data
4957: Not Collective
4959: Input Parameters:
4960: . dm - The DMPlex object
4962: Output Parameter:
4963: . section - The PetscSection object
4965: Level: developer
4967: .seealso: DMPlexGetSupportSection(), DMPlexGetCones(), DMPlexGetConeOrientations()
4968: @*/
4969: PetscErrorCode DMPlexGetConeSection(DM dm, PetscSection *section)
4970: {
4971: DM_Plex *mesh = (DM_Plex*) dm->data;
4974: if (section) *section = mesh->coneSection;
4975: return 0;
4976: }
4978: /*@C
4979: DMPlexGetSupportSection - Return a section which describes the layout of support data
4981: Not Collective
4983: Input Parameters:
4984: . dm - The DMPlex object
4986: Output Parameter:
4987: . section - The PetscSection object
4989: Level: developer
4991: .seealso: DMPlexGetConeSection()
4992: @*/
4993: PetscErrorCode DMPlexGetSupportSection(DM dm, PetscSection *section)
4994: {
4995: DM_Plex *mesh = (DM_Plex*) dm->data;
4998: if (section) *section = mesh->supportSection;
4999: return 0;
5000: }
5002: /*@C
5003: DMPlexGetCones - Return cone data
5005: Not Collective
5007: Input Parameters:
5008: . dm - The DMPlex object
5010: Output Parameter:
5011: . cones - The cone for each point
5013: Level: developer
5015: .seealso: DMPlexGetConeSection()
5016: @*/
5017: PetscErrorCode DMPlexGetCones(DM dm, PetscInt *cones[])
5018: {
5019: DM_Plex *mesh = (DM_Plex*) dm->data;
5022: if (cones) *cones = mesh->cones;
5023: return 0;
5024: }
5026: /*@C
5027: DMPlexGetConeOrientations - Return cone orientation data
5029: Not Collective
5031: Input Parameters:
5032: . dm - The DMPlex object
5034: Output Parameter:
5035: . coneOrientations - The array of cone orientations for all points
5037: Level: developer
5039: Notes:
5040: The PetscSection returned by DMPlexGetConeSection() partitions coneOrientations into cone orientations of particular points as returned by DMPlexGetConeOrientation().
5042: The meaning of coneOrientations values is detailed in DMPlexGetConeOrientation().
5044: .seealso: DMPlexGetConeSection(), DMPlexGetConeOrientation()
5045: @*/
5046: PetscErrorCode DMPlexGetConeOrientations(DM dm, PetscInt *coneOrientations[])
5047: {
5048: DM_Plex *mesh = (DM_Plex*) dm->data;
5051: if (coneOrientations) *coneOrientations = mesh->coneOrientations;
5052: return 0;
5053: }
5055: /******************************** FEM Support **********************************/
5057: /*
5058: Returns number of components and tensor degree for the field. For interpolated meshes, line should be a point
5059: representing a line in the section.
5060: */
5061: static PetscErrorCode PetscSectionFieldGetTensorDegree_Private(PetscSection section,PetscInt field,PetscInt line,PetscBool vertexchart,PetscInt *Nc,PetscInt *k)
5062: {
5064: PetscSectionGetFieldComponents(section, field, Nc);
5065: if (line < 0) {
5066: *k = 0;
5067: *Nc = 0;
5068: } else if (vertexchart) { /* If we only have a vertex chart, we must have degree k=1 */
5069: *k = 1;
5070: } else { /* Assume the full interpolated mesh is in the chart; lines in particular */
5071: /* An order k SEM disc has k-1 dofs on an edge */
5072: PetscSectionGetFieldDof(section, line, field, k);
5073: *k = *k / *Nc + 1;
5074: }
5075: return 0;
5076: }
5078: /*@
5080: DMPlexSetClosurePermutationTensor - Create a permutation from the default (BFS) point ordering in the closure, to a
5081: lexicographic ordering over the tensor product cell (i.e., line, quad, hex, etc.), and set this permutation in the
5082: section provided (or the section of the DM).
5084: Input Parameters:
5085: + dm - The DM
5086: . point - Either a cell (highest dim point) or an edge (dim 1 point), or PETSC_DETERMINE
5087: - section - The PetscSection to reorder, or NULL for the default section
5089: Note: The point is used to determine the number of dofs/field on an edge. For SEM, this is related to the polynomial
5090: degree of the basis.
5092: Example:
5093: A typical interpolated single-quad mesh might order points as
5094: .vb
5095: [c0, v1, v2, v3, v4, e5, e6, e7, e8]
5097: v4 -- e6 -- v3
5098: | |
5099: e7 c0 e8
5100: | |
5101: v1 -- e5 -- v2
5102: .ve
5104: (There is no significance to the ordering described here.) The default section for a Q3 quad might typically assign
5105: dofs in the order of points, e.g.,
5106: .vb
5107: c0 -> [0,1,2,3]
5108: v1 -> [4]
5109: ...
5110: e5 -> [8, 9]
5111: .ve
5113: which corresponds to the dofs
5114: .vb
5115: 6 10 11 7
5116: 13 2 3 15
5117: 12 0 1 14
5118: 4 8 9 5
5119: .ve
5121: The closure in BFS ordering works through height strata (cells, edges, vertices) to produce the ordering
5122: .vb
5123: 0 1 2 3 8 9 14 15 11 10 13 12 4 5 7 6
5124: .ve
5126: After calling DMPlexSetClosurePermutationTensor(), the closure will be ordered lexicographically,
5127: .vb
5128: 4 8 9 5 12 0 1 14 13 2 3 15 6 10 11 7
5129: .ve
5131: Level: developer
5133: .seealso: DMGetLocalSection(), PetscSectionSetClosurePermutation(), DMSetGlobalSection()
5134: @*/
5135: PetscErrorCode DMPlexSetClosurePermutationTensor(DM dm, PetscInt point, PetscSection section)
5136: {
5137: DMLabel label;
5138: PetscInt dim, depth = -1, eStart = -1, Nf;
5139: PetscBool vertexchart;
5141: DMGetDimension(dm, &dim);
5142: if (dim < 1) return 0;
5143: if (point < 0) {
5144: PetscInt sStart,sEnd;
5146: DMPlexGetDepthStratum(dm, 1, &sStart, &sEnd);
5147: point = sEnd-sStart ? sStart : point;
5148: }
5149: DMPlexGetDepthLabel(dm, &label);
5150: if (point >= 0) DMLabelGetValue(label, point, &depth);
5151: if (!section) DMGetLocalSection(dm, §ion);
5152: if (depth == 1) {eStart = point;}
5153: else if (depth == dim) {
5154: const PetscInt *cone;
5156: DMPlexGetCone(dm, point, &cone);
5157: if (dim == 2) eStart = cone[0];
5158: else if (dim == 3) {
5159: const PetscInt *cone2;
5160: DMPlexGetCone(dm, cone[0], &cone2);
5161: eStart = cone2[0];
5162: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Point %D of depth %D cannot be used to bootstrap spectral ordering for dim %D", point, depth, dim);
5164: { /* Determine whether the chart covers all points or just vertices. */
5165: PetscInt pStart,pEnd,cStart,cEnd;
5166: DMPlexGetDepthStratum(dm,0,&pStart,&pEnd);
5167: PetscSectionGetChart(section,&cStart,&cEnd);
5168: if (pStart == cStart && pEnd == cEnd) vertexchart = PETSC_TRUE; /* Only vertices are in the chart */
5169: else if (cStart <= point && point < cEnd) vertexchart = PETSC_FALSE; /* Some interpolated points exist in the chart */
5170: else vertexchart = PETSC_TRUE; /* Some interpolated points are not in chart; assume dofs only at cells and vertices */
5171: }
5172: PetscSectionGetNumFields(section, &Nf);
5173: for (PetscInt d=1; d<=dim; d++) {
5174: PetscInt k, f, Nc, c, i, j, size = 0, offset = 0, foffset = 0;
5175: PetscInt *perm;
5177: for (f = 0; f < Nf; ++f) {
5178: PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);
5179: size += PetscPowInt(k+1, d)*Nc;
5180: }
5181: PetscMalloc1(size, &perm);
5182: for (f = 0; f < Nf; ++f) {
5183: switch (d) {
5184: case 1:
5185: PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);
5186: /*
5187: Original ordering is [ edge of length k-1; vtx0; vtx1 ]
5188: We want [ vtx0; edge of length k-1; vtx1 ]
5189: */
5190: for (c=0; c<Nc; c++,offset++) perm[offset] = (k-1)*Nc + c + foffset;
5191: for (i=0; i<k-1; i++) for (c=0; c<Nc; c++,offset++) perm[offset] = i*Nc + c + foffset;
5192: for (c=0; c<Nc; c++,offset++) perm[offset] = k*Nc + c + foffset;
5193: foffset = offset;
5194: break;
5195: case 2:
5196: /* The original quad closure is oriented clockwise, {f, e_b, e_r, e_t, e_l, v_lb, v_rb, v_tr, v_tl} */
5197: PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);
5198: /* The SEM order is
5200: v_lb, {e_b}, v_rb,
5201: e^{(k-1)-i}_l, {f^{i*(k-1)}}, e^i_r,
5202: v_lt, reverse {e_t}, v_rt
5203: */
5204: {
5205: const PetscInt of = 0;
5206: const PetscInt oeb = of + PetscSqr(k-1);
5207: const PetscInt oer = oeb + (k-1);
5208: const PetscInt oet = oer + (k-1);
5209: const PetscInt oel = oet + (k-1);
5210: const PetscInt ovlb = oel + (k-1);
5211: const PetscInt ovrb = ovlb + 1;
5212: const PetscInt ovrt = ovrb + 1;
5213: const PetscInt ovlt = ovrt + 1;
5214: PetscInt o;
5216: /* bottom */
5217: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlb*Nc + c + foffset;
5218: for (o = oeb; o < oer; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5219: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrb*Nc + c + foffset;
5220: /* middle */
5221: for (i = 0; i < k-1; ++i) {
5222: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oel+(k-2)-i)*Nc + c + foffset;
5223: for (o = of+(k-1)*i; o < of+(k-1)*(i+1); ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5224: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oer+i)*Nc + c + foffset;
5225: }
5226: /* top */
5227: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlt*Nc + c + foffset;
5228: for (o = oel-1; o >= oet; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5229: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrt*Nc + c + foffset;
5230: foffset = offset;
5231: }
5232: break;
5233: case 3:
5234: /* The original hex closure is
5236: {c,
5237: f_b, f_t, f_f, f_b, f_r, f_l,
5238: e_bl, e_bb, e_br, e_bf, e_tf, e_tr, e_tb, e_tl, e_rf, e_lf, e_lb, e_rb,
5239: v_blf, v_blb, v_brb, v_brf, v_tlf, v_trf, v_trb, v_tlb}
5240: */
5241: PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);
5242: /* The SEM order is
5243: Bottom Slice
5244: v_blf, {e^{(k-1)-n}_bf}, v_brf,
5245: e^{i}_bl, f^{n*(k-1)+(k-1)-i}_b, e^{(k-1)-i}_br,
5246: v_blb, {e_bb}, v_brb,
5248: Middle Slice (j)
5249: {e^{(k-1)-j}_lf}, {f^{j*(k-1)+n}_f}, e^j_rf,
5250: f^{i*(k-1)+j}_l, {c^{(j*(k-1) + i)*(k-1)+n}_t}, f^{j*(k-1)+i}_r,
5251: e^j_lb, {f^{j*(k-1)+(k-1)-n}_b}, e^{(k-1)-j}_rb,
5253: Top Slice
5254: v_tlf, {e_tf}, v_trf,
5255: e^{(k-1)-i}_tl, {f^{i*(k-1)}_t}, e^{i}_tr,
5256: v_tlb, {e^{(k-1)-n}_tb}, v_trb,
5257: */
5258: {
5259: const PetscInt oc = 0;
5260: const PetscInt ofb = oc + PetscSqr(k-1)*(k-1);
5261: const PetscInt oft = ofb + PetscSqr(k-1);
5262: const PetscInt off = oft + PetscSqr(k-1);
5263: const PetscInt ofk = off + PetscSqr(k-1);
5264: const PetscInt ofr = ofk + PetscSqr(k-1);
5265: const PetscInt ofl = ofr + PetscSqr(k-1);
5266: const PetscInt oebl = ofl + PetscSqr(k-1);
5267: const PetscInt oebb = oebl + (k-1);
5268: const PetscInt oebr = oebb + (k-1);
5269: const PetscInt oebf = oebr + (k-1);
5270: const PetscInt oetf = oebf + (k-1);
5271: const PetscInt oetr = oetf + (k-1);
5272: const PetscInt oetb = oetr + (k-1);
5273: const PetscInt oetl = oetb + (k-1);
5274: const PetscInt oerf = oetl + (k-1);
5275: const PetscInt oelf = oerf + (k-1);
5276: const PetscInt oelb = oelf + (k-1);
5277: const PetscInt oerb = oelb + (k-1);
5278: const PetscInt ovblf = oerb + (k-1);
5279: const PetscInt ovblb = ovblf + 1;
5280: const PetscInt ovbrb = ovblb + 1;
5281: const PetscInt ovbrf = ovbrb + 1;
5282: const PetscInt ovtlf = ovbrf + 1;
5283: const PetscInt ovtrf = ovtlf + 1;
5284: const PetscInt ovtrb = ovtrf + 1;
5285: const PetscInt ovtlb = ovtrb + 1;
5286: PetscInt o, n;
5288: /* Bottom Slice */
5289: /* bottom */
5290: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblf*Nc + c + foffset;
5291: for (o = oetf-1; o >= oebf; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5292: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrf*Nc + c + foffset;
5293: /* middle */
5294: for (i = 0; i < k-1; ++i) {
5295: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebl+i)*Nc + c + foffset;
5296: for (n = 0; n < k-1; ++n) {o = ofb+n*(k-1)+i; for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;}
5297: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebr+(k-2)-i)*Nc + c + foffset;
5298: }
5299: /* top */
5300: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblb*Nc + c + foffset;
5301: for (o = oebb; o < oebr; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5302: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrb*Nc + c + foffset;
5304: /* Middle Slice */
5305: for (j = 0; j < k-1; ++j) {
5306: /* bottom */
5307: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelf+(k-2)-j)*Nc + c + foffset;
5308: for (o = off+j*(k-1); o < off+(j+1)*(k-1); ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5309: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerf+j)*Nc + c + foffset;
5310: /* middle */
5311: for (i = 0; i < k-1; ++i) {
5312: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofl+i*(k-1)+j)*Nc + c + foffset;
5313: for (n = 0; n < k-1; ++n) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oc+(j*(k-1)+i)*(k-1)+n)*Nc + c + foffset;
5314: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofr+j*(k-1)+i)*Nc + c + foffset;
5315: }
5316: /* top */
5317: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelb+j)*Nc + c + foffset;
5318: for (o = ofk+j*(k-1)+(k-2); o >= ofk+j*(k-1); --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5319: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerb+(k-2)-j)*Nc + c + foffset;
5320: }
5322: /* Top Slice */
5323: /* bottom */
5324: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlf*Nc + c + foffset;
5325: for (o = oetf; o < oetr; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5326: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrf*Nc + c + foffset;
5327: /* middle */
5328: for (i = 0; i < k-1; ++i) {
5329: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetl+(k-2)-i)*Nc + c + foffset;
5330: for (n = 0; n < k-1; ++n) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oft+i*(k-1)+n)*Nc + c + foffset;
5331: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetr+i)*Nc + c + foffset;
5332: }
5333: /* top */
5334: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlb*Nc + c + foffset;
5335: for (o = oetl-1; o >= oetb; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
5336: for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrb*Nc + c + foffset;
5338: foffset = offset;
5339: }
5340: break;
5341: default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No spectral ordering for dimension %D", d);
5342: }
5343: }
5345: /* Check permutation */
5346: {
5347: PetscInt *check;
5349: PetscMalloc1(size, &check);
5351: for (i = 0; i < size; ++i) check[perm[i]] = i;
5353: PetscFree(check);
5354: }
5355: PetscSectionSetClosurePermutation_Internal(section, (PetscObject) dm, d, size, PETSC_OWN_POINTER, perm);
5356: if (d == dim) { // Add permutation for localized (in case this is a coordinate DM)
5357: PetscInt *loc_perm;
5358: PetscMalloc1(size*2, &loc_perm);
5359: for (PetscInt i=0; i<size; i++) {
5360: loc_perm[i] = perm[i];
5361: loc_perm[size+i] = size + perm[i];
5362: }
5363: PetscSectionSetClosurePermutation_Internal(section, (PetscObject) dm, d, size*2, PETSC_OWN_POINTER, loc_perm);
5364: }
5365: }
5366: return 0;
5367: }
5369: PetscErrorCode DMPlexGetPointDualSpaceFEM(DM dm, PetscInt point, PetscInt field, PetscDualSpace *dspace)
5370: {
5371: PetscDS prob;
5372: PetscInt depth, Nf, h;
5373: DMLabel label;
5376: DMGetDS(dm, &prob);
5377: Nf = prob->Nf;
5378: label = dm->depthLabel;
5379: *dspace = NULL;
5380: if (field < Nf) {
5381: PetscObject disc = prob->disc[field];
5383: if (disc->classid == PETSCFE_CLASSID) {
5384: PetscDualSpace dsp;
5386: PetscFEGetDualSpace((PetscFE)disc,&dsp);
5387: DMLabelGetNumValues(label,&depth);
5388: DMLabelGetValue(label,point,&h);
5389: h = depth - 1 - h;
5390: if (h) {
5391: PetscDualSpaceGetHeightSubspace(dsp,h,dspace);
5392: } else {
5393: *dspace = dsp;
5394: }
5395: }
5396: }
5397: return 0;
5398: }
5400: static inline PetscErrorCode DMPlexVecGetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[])
5401: {
5402: PetscScalar *array, *vArray;
5403: const PetscInt *cone, *coneO;
5404: PetscInt pStart, pEnd, p, numPoints, size = 0, offset = 0;
5407: PetscSectionGetChart(section, &pStart, &pEnd);
5408: DMPlexGetConeSize(dm, point, &numPoints);
5409: DMPlexGetCone(dm, point, &cone);
5410: DMPlexGetConeOrientation(dm, point, &coneO);
5411: if (!values || !*values) {
5412: if ((point >= pStart) && (point < pEnd)) {
5413: PetscInt dof;
5415: PetscSectionGetDof(section, point, &dof);
5416: size += dof;
5417: }
5418: for (p = 0; p < numPoints; ++p) {
5419: const PetscInt cp = cone[p];
5420: PetscInt dof;
5422: if ((cp < pStart) || (cp >= pEnd)) continue;
5423: PetscSectionGetDof(section, cp, &dof);
5424: size += dof;
5425: }
5426: if (!values) {
5427: if (csize) *csize = size;
5428: return 0;
5429: }
5430: DMGetWorkArray(dm, size, MPIU_SCALAR, &array);
5431: } else {
5432: array = *values;
5433: }
5434: size = 0;
5435: VecGetArray(v, &vArray);
5436: if ((point >= pStart) && (point < pEnd)) {
5437: PetscInt dof, off, d;
5438: PetscScalar *varr;
5440: PetscSectionGetDof(section, point, &dof);
5441: PetscSectionGetOffset(section, point, &off);
5442: varr = &vArray[off];
5443: for (d = 0; d < dof; ++d, ++offset) {
5444: array[offset] = varr[d];
5445: }
5446: size += dof;
5447: }
5448: for (p = 0; p < numPoints; ++p) {
5449: const PetscInt cp = cone[p];
5450: PetscInt o = coneO[p];
5451: PetscInt dof, off, d;
5452: PetscScalar *varr;
5454: if ((cp < pStart) || (cp >= pEnd)) continue;
5455: PetscSectionGetDof(section, cp, &dof);
5456: PetscSectionGetOffset(section, cp, &off);
5457: varr = &vArray[off];
5458: if (o >= 0) {
5459: for (d = 0; d < dof; ++d, ++offset) {
5460: array[offset] = varr[d];
5461: }
5462: } else {
5463: for (d = dof-1; d >= 0; --d, ++offset) {
5464: array[offset] = varr[d];
5465: }
5466: }
5467: size += dof;
5468: }
5469: VecRestoreArray(v, &vArray);
5470: if (!*values) {
5471: if (csize) *csize = size;
5472: *values = array;
5473: } else {
5475: *csize = size;
5476: }
5477: return 0;
5478: }
5480: /* Compress out points not in the section */
5481: static inline PetscErrorCode CompressPoints_Private(PetscSection section, PetscInt *numPoints, PetscInt points[])
5482: {
5483: const PetscInt np = *numPoints;
5484: PetscInt pStart, pEnd, p, q;
5486: PetscSectionGetChart(section, &pStart, &pEnd);
5487: for (p = 0, q = 0; p < np; ++p) {
5488: const PetscInt r = points[p*2];
5489: if ((r >= pStart) && (r < pEnd)) {
5490: points[q*2] = r;
5491: points[q*2+1] = points[p*2+1];
5492: ++q;
5493: }
5494: }
5495: *numPoints = q;
5496: return 0;
5497: }
5499: /* Compressed closure does not apply closure permutation */
5500: PetscErrorCode DMPlexGetCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp)
5501: {
5502: const PetscInt *cla = NULL;
5503: PetscInt np, *pts = NULL;
5506: PetscSectionGetClosureIndex(section, (PetscObject) dm, clSec, clPoints);
5507: if (*clPoints) {
5508: PetscInt dof, off;
5510: PetscSectionGetDof(*clSec, point, &dof);
5511: PetscSectionGetOffset(*clSec, point, &off);
5512: ISGetIndices(*clPoints, &cla);
5513: np = dof/2;
5514: pts = (PetscInt *) &cla[off];
5515: } else {
5516: DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &np, &pts);
5517: CompressPoints_Private(section, &np, pts);
5518: }
5519: *numPoints = np;
5520: *points = pts;
5521: *clp = cla;
5522: return 0;
5523: }
5525: PetscErrorCode DMPlexRestoreCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp)
5526: {
5528: if (!*clPoints) {
5529: DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, numPoints, points);
5530: } else {
5531: ISRestoreIndices(*clPoints, clp);
5532: }
5533: *numPoints = 0;
5534: *points = NULL;
5535: *clSec = NULL;
5536: *clPoints = NULL;
5537: *clp = NULL;
5538: return 0;
5539: }
5541: static inline PetscErrorCode DMPlexVecGetClosure_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[])
5542: {
5543: PetscInt offset = 0, p;
5544: const PetscInt **perms = NULL;
5545: const PetscScalar **flips = NULL;
5548: *size = 0;
5549: PetscSectionGetPointSyms(section,numPoints,points,&perms,&flips);
5550: for (p = 0; p < numPoints; p++) {
5551: const PetscInt point = points[2*p];
5552: const PetscInt *perm = perms ? perms[p] : NULL;
5553: const PetscScalar *flip = flips ? flips[p] : NULL;
5554: PetscInt dof, off, d;
5555: const PetscScalar *varr;
5557: PetscSectionGetDof(section, point, &dof);
5558: PetscSectionGetOffset(section, point, &off);
5559: varr = &vArray[off];
5560: if (clperm) {
5561: if (perm) {
5562: for (d = 0; d < dof; d++) array[clperm[offset + perm[d]]] = varr[d];
5563: } else {
5564: for (d = 0; d < dof; d++) array[clperm[offset + d ]] = varr[d];
5565: }
5566: if (flip) {
5567: for (d = 0; d < dof; d++) array[clperm[offset + d ]] *= flip[d];
5568: }
5569: } else {
5570: if (perm) {
5571: for (d = 0; d < dof; d++) array[offset + perm[d]] = varr[d];
5572: } else {
5573: for (d = 0; d < dof; d++) array[offset + d ] = varr[d];
5574: }
5575: if (flip) {
5576: for (d = 0; d < dof; d++) array[offset + d ] *= flip[d];
5577: }
5578: }
5579: offset += dof;
5580: }
5581: PetscSectionRestorePointSyms(section,numPoints,points,&perms,&flips);
5582: *size = offset;
5583: return 0;
5584: }
5586: static inline PetscErrorCode DMPlexVecGetClosure_Fields_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], PetscInt numFields, const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[])
5587: {
5588: PetscInt offset = 0, f;
5591: *size = 0;
5592: for (f = 0; f < numFields; ++f) {
5593: PetscInt p;
5594: const PetscInt **perms = NULL;
5595: const PetscScalar **flips = NULL;
5597: PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);
5598: for (p = 0; p < numPoints; p++) {
5599: const PetscInt point = points[2*p];
5600: PetscInt fdof, foff, b;
5601: const PetscScalar *varr;
5602: const PetscInt *perm = perms ? perms[p] : NULL;
5603: const PetscScalar *flip = flips ? flips[p] : NULL;
5605: PetscSectionGetFieldDof(section, point, f, &fdof);
5606: PetscSectionGetFieldOffset(section, point, f, &foff);
5607: varr = &vArray[foff];
5608: if (clperm) {
5609: if (perm) {for (b = 0; b < fdof; b++) {array[clperm[offset + perm[b]]] = varr[b];}}
5610: else {for (b = 0; b < fdof; b++) {array[clperm[offset + b ]] = varr[b];}}
5611: if (flip) {for (b = 0; b < fdof; b++) {array[clperm[offset + b ]] *= flip[b];}}
5612: } else {
5613: if (perm) {for (b = 0; b < fdof; b++) {array[offset + perm[b]] = varr[b];}}
5614: else {for (b = 0; b < fdof; b++) {array[offset + b ] = varr[b];}}
5615: if (flip) {for (b = 0; b < fdof; b++) {array[offset + b ] *= flip[b];}}
5616: }
5617: offset += fdof;
5618: }
5619: PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);
5620: }
5621: *size = offset;
5622: return 0;
5623: }
5625: /*@C
5626: DMPlexVecGetClosure - Get an array of the values on the closure of 'point'
5628: Not collective
5630: Input Parameters:
5631: + dm - The DM
5632: . section - The section describing the layout in v, or NULL to use the default section
5633: . v - The local vector
5634: - point - The point in the DM
5636: Input/Output Parameters:
5637: + csize - The size of the input values array, or NULL; on output the number of values in the closure
5638: - values - An array to use for the values, or NULL to have it allocated automatically;
5639: if the user provided NULL, it is a borrowed array and should not be freed
5641: $ Note that DMPlexVecGetClosure/DMPlexVecRestoreClosure only allocates the values array if it set to NULL in the
5642: $ calling function. This is because DMPlexVecGetClosure() is typically called in the inner loop of a Vec or Mat
5643: $ assembly function, and a user may already have allocated storage for this operation.
5644: $
5645: $ A typical use could be
5646: $
5647: $ values = NULL;
5648: $ DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values);
5649: $ for (cl = 0; cl < clSize; ++cl) {
5650: $ <Compute on closure>
5651: $ }
5652: $ DMPlexVecRestoreClosure(dm, NULL, v, p, &clSize, &values);
5653: $
5654: $ or
5655: $
5656: $ PetscMalloc1(clMaxSize, &values);
5657: $ for (p = pStart; p < pEnd; ++p) {
5658: $ clSize = clMaxSize;
5659: $ DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values);
5660: $ for (cl = 0; cl < clSize; ++cl) {
5661: $ <Compute on closure>
5662: $ }
5663: $ }
5664: $ PetscFree(values);
5666: Fortran Notes:
5667: Since it returns an array, this routine is only available in Fortran 90, and you must
5668: include petsc.h90 in your code.
5670: The csize argument is not present in the Fortran 90 binding since it is internal to the array.
5672: Level: intermediate
5674: .seealso DMPlexVecRestoreClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure()
5675: @*/
5676: PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[])
5677: {
5678: PetscSection clSection;
5679: IS clPoints;
5680: PetscInt *points = NULL;
5681: const PetscInt *clp, *perm;
5682: PetscInt depth, numFields, numPoints, asize;
5686: if (!section) DMGetLocalSection(dm, §ion);
5689: DMPlexGetDepth(dm, &depth);
5690: PetscSectionGetNumFields(section, &numFields);
5691: if (depth == 1 && numFields < 2) {
5692: DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values);
5693: return 0;
5694: }
5695: /* Get points */
5696: DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5697: /* Get sizes */
5698: asize = 0;
5699: for (PetscInt p = 0; p < numPoints*2; p += 2) {
5700: PetscInt dof;
5701: PetscSectionGetDof(section, points[p], &dof);
5702: asize += dof;
5703: }
5704: if (values) {
5705: const PetscScalar *vArray;
5706: PetscInt size;
5708: if (*values) {
5710: } else DMGetWorkArray(dm, asize, MPIU_SCALAR, values);
5711: PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, depth, asize, &perm);
5712: VecGetArrayRead(v, &vArray);
5713: /* Get values */
5714: if (numFields > 0) DMPlexVecGetClosure_Fields_Static(dm, section, numPoints, points, numFields, perm, vArray, &size, *values);
5715: else DMPlexVecGetClosure_Static(dm, section, numPoints, points, perm, vArray, &size, *values);
5717: /* Cleanup array */
5718: VecRestoreArrayRead(v, &vArray);
5719: }
5720: if (csize) *csize = asize;
5721: /* Cleanup points */
5722: DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5723: return 0;
5724: }
5726: PetscErrorCode DMPlexVecGetClosureAtDepth_Internal(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt depth, PetscInt *csize, PetscScalar *values[])
5727: {
5728: DMLabel depthLabel;
5729: PetscSection clSection;
5730: IS clPoints;
5731: PetscScalar *array;
5732: const PetscScalar *vArray;
5733: PetscInt *points = NULL;
5734: const PetscInt *clp, *perm = NULL;
5735: PetscInt mdepth, numFields, numPoints, Np = 0, p, clsize, size;
5739: if (!section) DMGetLocalSection(dm, §ion);
5742: DMPlexGetDepth(dm, &mdepth);
5743: DMPlexGetDepthLabel(dm, &depthLabel);
5744: PetscSectionGetNumFields(section, &numFields);
5745: if (mdepth == 1 && numFields < 2) {
5746: DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values);
5747: return 0;
5748: }
5749: /* Get points */
5750: DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5751: for (clsize=0,p=0; p<Np; p++) {
5752: PetscInt dof;
5753: PetscSectionGetDof(section, points[2*p], &dof);
5754: clsize += dof;
5755: }
5756: PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, depth, clsize, &perm);
5757: /* Filter points */
5758: for (p = 0; p < numPoints*2; p += 2) {
5759: PetscInt dep;
5761: DMLabelGetValue(depthLabel, points[p], &dep);
5762: if (dep != depth) continue;
5763: points[Np*2+0] = points[p];
5764: points[Np*2+1] = points[p+1];
5765: ++Np;
5766: }
5767: /* Get array */
5768: if (!values || !*values) {
5769: PetscInt asize = 0, dof;
5771: for (p = 0; p < Np*2; p += 2) {
5772: PetscSectionGetDof(section, points[p], &dof);
5773: asize += dof;
5774: }
5775: if (!values) {
5776: DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5777: if (csize) *csize = asize;
5778: return 0;
5779: }
5780: DMGetWorkArray(dm, asize, MPIU_SCALAR, &array);
5781: } else {
5782: array = *values;
5783: }
5784: VecGetArrayRead(v, &vArray);
5785: /* Get values */
5786: if (numFields > 0) DMPlexVecGetClosure_Fields_Static(dm, section, Np, points, numFields, perm, vArray, &size, array);
5787: else DMPlexVecGetClosure_Static(dm, section, Np, points, perm, vArray, &size, array);
5788: /* Cleanup points */
5789: DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5790: /* Cleanup array */
5791: VecRestoreArrayRead(v, &vArray);
5792: if (!*values) {
5793: if (csize) *csize = size;
5794: *values = array;
5795: } else {
5797: *csize = size;
5798: }
5799: return 0;
5800: }
5802: /*@C
5803: DMPlexVecRestoreClosure - Restore the array of the values on the closure of 'point'
5805: Not collective
5807: Input Parameters:
5808: + dm - The DM
5809: . section - The section describing the layout in v, or NULL to use the default section
5810: . v - The local vector
5811: . point - The point in the DM
5812: . csize - The number of values in the closure, or NULL
5813: - values - The array of values, which is a borrowed array and should not be freed
5815: Note that the array values are discarded and not copied back into v. In order to copy values back to v, use DMPlexVecSetClosure()
5817: Fortran Notes:
5818: Since it returns an array, this routine is only available in Fortran 90, and you must
5819: include petsc.h90 in your code.
5821: The csize argument is not present in the Fortran 90 binding since it is internal to the array.
5823: Level: intermediate
5825: .seealso DMPlexVecGetClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure()
5826: @*/
5827: PetscErrorCode DMPlexVecRestoreClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[])
5828: {
5829: PetscInt size = 0;
5831: /* Should work without recalculating size */
5832: DMRestoreWorkArray(dm, size, MPIU_SCALAR, (void*) values);
5833: *values = NULL;
5834: return 0;
5835: }
5837: static inline void add (PetscScalar *x, PetscScalar y) {*x += y;}
5838: static inline void insert(PetscScalar *x, PetscScalar y) {*x = y;}
5840: static inline PetscErrorCode updatePoint_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar*, PetscScalar), PetscBool setBC, const PetscInt perm[], const PetscScalar flip[], const PetscInt clperm[], const PetscScalar values[], PetscInt offset, PetscScalar array[])
5841: {
5842: PetscInt cdof; /* The number of constraints on this point */
5843: const PetscInt *cdofs; /* The indices of the constrained dofs on this point */
5844: PetscScalar *a;
5845: PetscInt off, cind = 0, k;
5847: PetscSectionGetConstraintDof(section, point, &cdof);
5848: PetscSectionGetOffset(section, point, &off);
5849: a = &array[off];
5850: if (!cdof || setBC) {
5851: if (clperm) {
5852: if (perm) {for (k = 0; k < dof; ++k) {fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.));}}
5853: else {for (k = 0; k < dof; ++k) {fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.));}}
5854: } else {
5855: if (perm) {for (k = 0; k < dof; ++k) {fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.));}}
5856: else {for (k = 0; k < dof; ++k) {fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.));}}
5857: }
5858: } else {
5859: PetscSectionGetConstraintIndices(section, point, &cdofs);
5860: if (clperm) {
5861: if (perm) {for (k = 0; k < dof; ++k) {
5862: if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
5863: fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.));
5864: }
5865: } else {
5866: for (k = 0; k < dof; ++k) {
5867: if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
5868: fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.));
5869: }
5870: }
5871: } else {
5872: if (perm) {
5873: for (k = 0; k < dof; ++k) {
5874: if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
5875: fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.));
5876: }
5877: } else {
5878: for (k = 0; k < dof; ++k) {
5879: if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
5880: fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.));
5881: }
5882: }
5883: }
5884: }
5885: return 0;
5886: }
5888: static inline PetscErrorCode updatePointBC_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar*, PetscScalar), const PetscInt perm[], const PetscScalar flip[], const PetscInt clperm[], const PetscScalar values[], PetscInt offset, PetscScalar array[])
5889: {
5890: PetscInt cdof; /* The number of constraints on this point */
5891: const PetscInt *cdofs; /* The indices of the constrained dofs on this point */
5892: PetscScalar *a;
5893: PetscInt off, cind = 0, k;
5895: PetscSectionGetConstraintDof(section, point, &cdof);
5896: PetscSectionGetOffset(section, point, &off);
5897: a = &array[off];
5898: if (cdof) {
5899: PetscSectionGetConstraintIndices(section, point, &cdofs);
5900: if (clperm) {
5901: if (perm) {
5902: for (k = 0; k < dof; ++k) {
5903: if ((cind < cdof) && (k == cdofs[cind])) {
5904: fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.));
5905: cind++;
5906: }
5907: }
5908: } else {
5909: for (k = 0; k < dof; ++k) {
5910: if ((cind < cdof) && (k == cdofs[cind])) {
5911: fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.));
5912: cind++;
5913: }
5914: }
5915: }
5916: } else {
5917: if (perm) {
5918: for (k = 0; k < dof; ++k) {
5919: if ((cind < cdof) && (k == cdofs[cind])) {
5920: fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.));
5921: cind++;
5922: }
5923: }
5924: } else {
5925: for (k = 0; k < dof; ++k) {
5926: if ((cind < cdof) && (k == cdofs[cind])) {
5927: fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.));
5928: cind++;
5929: }
5930: }
5931: }
5932: }
5933: }
5934: return 0;
5935: }
5937: static inline PetscErrorCode updatePointFields_private(PetscSection section, PetscInt point, const PetscInt *perm, const PetscScalar *flip, PetscInt f, void (*fuse)(PetscScalar*, PetscScalar), PetscBool setBC, const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[])
5938: {
5939: PetscScalar *a;
5940: PetscInt fdof, foff, fcdof, foffset = *offset;
5941: const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */
5942: PetscInt cind = 0, b;
5944: PetscSectionGetFieldDof(section, point, f, &fdof);
5945: PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);
5946: PetscSectionGetFieldOffset(section, point, f, &foff);
5947: a = &array[foff];
5948: if (!fcdof || setBC) {
5949: if (clperm) {
5950: if (perm) {for (b = 0; b < fdof; b++) {fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));}}
5951: else {for (b = 0; b < fdof; b++) {fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.));}}
5952: } else {
5953: if (perm) {for (b = 0; b < fdof; b++) {fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));}}
5954: else {for (b = 0; b < fdof; b++) {fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.));}}
5955: }
5956: } else {
5957: PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);
5958: if (clperm) {
5959: if (perm) {
5960: for (b = 0; b < fdof; b++) {
5961: if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;}
5962: fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));
5963: }
5964: } else {
5965: for (b = 0; b < fdof; b++) {
5966: if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;}
5967: fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.));
5968: }
5969: }
5970: } else {
5971: if (perm) {
5972: for (b = 0; b < fdof; b++) {
5973: if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;}
5974: fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));
5975: }
5976: } else {
5977: for (b = 0; b < fdof; b++) {
5978: if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;}
5979: fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.));
5980: }
5981: }
5982: }
5983: }
5984: *offset += fdof;
5985: return 0;
5986: }
5988: static inline PetscErrorCode updatePointFieldsBC_private(PetscSection section, PetscInt point, const PetscInt perm[], const PetscScalar flip[], PetscInt f, PetscInt Ncc, const PetscInt comps[], void (*fuse)(PetscScalar*, PetscScalar), const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[])
5989: {
5990: PetscScalar *a;
5991: PetscInt fdof, foff, fcdof, foffset = *offset;
5992: const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */
5993: PetscInt Nc, cind = 0, ncind = 0, b;
5994: PetscBool ncSet, fcSet;
5996: PetscSectionGetFieldComponents(section, f, &Nc);
5997: PetscSectionGetFieldDof(section, point, f, &fdof);
5998: PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);
5999: PetscSectionGetFieldOffset(section, point, f, &foff);
6000: a = &array[foff];
6001: if (fcdof) {
6002: /* We just override fcdof and fcdofs with Ncc and comps */
6003: PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);
6004: if (clperm) {
6005: if (perm) {
6006: if (comps) {
6007: for (b = 0; b < fdof; b++) {
6008: ncSet = fcSet = PETSC_FALSE;
6009: if (b%Nc == comps[ncind]) {ncind = (ncind+1)%Ncc; ncSet = PETSC_TRUE;}
6010: if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; fcSet = PETSC_TRUE;}
6011: if (ncSet && fcSet) {fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));}
6012: }
6013: } else {
6014: for (b = 0; b < fdof; b++) {
6015: if ((cind < fcdof) && (b == fcdofs[cind])) {
6016: fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));
6017: ++cind;
6018: }
6019: }
6020: }
6021: } else {
6022: if (comps) {
6023: for (b = 0; b < fdof; b++) {
6024: ncSet = fcSet = PETSC_FALSE;
6025: if (b%Nc == comps[ncind]) {ncind = (ncind+1)%Ncc; ncSet = PETSC_TRUE;}
6026: if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; fcSet = PETSC_TRUE;}
6027: if (ncSet && fcSet) {fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.));}
6028: }
6029: } else {
6030: for (b = 0; b < fdof; b++) {
6031: if ((cind < fcdof) && (b == fcdofs[cind])) {
6032: fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.));
6033: ++cind;
6034: }
6035: }
6036: }
6037: }
6038: } else {
6039: if (perm) {
6040: if (comps) {
6041: for (b = 0; b < fdof; b++) {
6042: ncSet = fcSet = PETSC_FALSE;
6043: if (b%Nc == comps[ncind]) {ncind = (ncind+1)%Ncc; ncSet = PETSC_TRUE;}
6044: if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; fcSet = PETSC_TRUE;}
6045: if (ncSet && fcSet) {fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));}
6046: }
6047: } else {
6048: for (b = 0; b < fdof; b++) {
6049: if ((cind < fcdof) && (b == fcdofs[cind])) {
6050: fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));
6051: ++cind;
6052: }
6053: }
6054: }
6055: } else {
6056: if (comps) {
6057: for (b = 0; b < fdof; b++) {
6058: ncSet = fcSet = PETSC_FALSE;
6059: if (b%Nc == comps[ncind]) {ncind = (ncind+1)%Ncc; ncSet = PETSC_TRUE;}
6060: if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; fcSet = PETSC_TRUE;}
6061: if (ncSet && fcSet) {fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.));}
6062: }
6063: } else {
6064: for (b = 0; b < fdof; b++) {
6065: if ((cind < fcdof) && (b == fcdofs[cind])) {
6066: fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.));
6067: ++cind;
6068: }
6069: }
6070: }
6071: }
6072: }
6073: }
6074: *offset += fdof;
6075: return 0;
6076: }
6078: static inline PetscErrorCode DMPlexVecSetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode)
6079: {
6080: PetscScalar *array;
6081: const PetscInt *cone, *coneO;
6082: PetscInt pStart, pEnd, p, numPoints, off, dof;
6085: PetscSectionGetChart(section, &pStart, &pEnd);
6086: DMPlexGetConeSize(dm, point, &numPoints);
6087: DMPlexGetCone(dm, point, &cone);
6088: DMPlexGetConeOrientation(dm, point, &coneO);
6089: VecGetArray(v, &array);
6090: for (p = 0, off = 0; p <= numPoints; ++p, off += dof) {
6091: const PetscInt cp = !p ? point : cone[p-1];
6092: const PetscInt o = !p ? 0 : coneO[p-1];
6094: if ((cp < pStart) || (cp >= pEnd)) {dof = 0; continue;}
6095: PetscSectionGetDof(section, cp, &dof);
6096: /* ADD_VALUES */
6097: {
6098: const PetscInt *cdofs; /* The indices of the constrained dofs on this point */
6099: PetscScalar *a;
6100: PetscInt cdof, coff, cind = 0, k;
6102: PetscSectionGetConstraintDof(section, cp, &cdof);
6103: PetscSectionGetOffset(section, cp, &coff);
6104: a = &array[coff];
6105: if (!cdof) {
6106: if (o >= 0) {
6107: for (k = 0; k < dof; ++k) {
6108: a[k] += values[off+k];
6109: }
6110: } else {
6111: for (k = 0; k < dof; ++k) {
6112: a[k] += values[off+dof-k-1];
6113: }
6114: }
6115: } else {
6116: PetscSectionGetConstraintIndices(section, cp, &cdofs);
6117: if (o >= 0) {
6118: for (k = 0; k < dof; ++k) {
6119: if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
6120: a[k] += values[off+k];
6121: }
6122: } else {
6123: for (k = 0; k < dof; ++k) {
6124: if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
6125: a[k] += values[off+dof-k-1];
6126: }
6127: }
6128: }
6129: }
6130: }
6131: VecRestoreArray(v, &array);
6132: return 0;
6133: }
6135: /*@C
6136: DMPlexVecSetClosure - Set an array of the values on the closure of 'point'
6138: Not collective
6140: Input Parameters:
6141: + dm - The DM
6142: . section - The section describing the layout in v, or NULL to use the default section
6143: . v - The local vector
6144: . point - The point in the DM
6145: . values - The array of values
6146: - mode - The insert mode. One of INSERT_ALL_VALUES, ADD_ALL_VALUES, INSERT_VALUES, ADD_VALUES, INSERT_BC_VALUES, and ADD_BC_VALUES,
6147: where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions.
6149: Fortran Notes:
6150: This routine is only available in Fortran 90, and you must include petsc.h90 in your code.
6152: Level: intermediate
6154: .seealso DMPlexVecGetClosure(), DMPlexMatSetClosure()
6155: @*/
6156: PetscErrorCode DMPlexVecSetClosure(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode)
6157: {
6158: PetscSection clSection;
6159: IS clPoints;
6160: PetscScalar *array;
6161: PetscInt *points = NULL;
6162: const PetscInt *clp, *clperm = NULL;
6163: PetscInt depth, numFields, numPoints, p, clsize;
6167: if (!section) DMGetLocalSection(dm, §ion);
6170: DMPlexGetDepth(dm, &depth);
6171: PetscSectionGetNumFields(section, &numFields);
6172: if (depth == 1 && numFields < 2 && mode == ADD_VALUES) {
6173: DMPlexVecSetClosure_Depth1_Static(dm, section, v, point, values, mode);
6174: return 0;
6175: }
6176: /* Get points */
6177: DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
6178: for (clsize=0,p=0; p<numPoints; p++) {
6179: PetscInt dof;
6180: PetscSectionGetDof(section, points[2*p], &dof);
6181: clsize += dof;
6182: }
6183: PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, depth, clsize, &clperm);
6184: /* Get array */
6185: VecGetArray(v, &array);
6186: /* Get values */
6187: if (numFields > 0) {
6188: PetscInt offset = 0, f;
6189: for (f = 0; f < numFields; ++f) {
6190: const PetscInt **perms = NULL;
6191: const PetscScalar **flips = NULL;
6193: PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);
6194: switch (mode) {
6195: case INSERT_VALUES:
6196: for (p = 0; p < numPoints; p++) {
6197: const PetscInt point = points[2*p];
6198: const PetscInt *perm = perms ? perms[p] : NULL;
6199: const PetscScalar *flip = flips ? flips[p] : NULL;
6200: updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array);
6201: } break;
6202: case INSERT_ALL_VALUES:
6203: for (p = 0; p < numPoints; p++) {
6204: const PetscInt point = points[2*p];
6205: const PetscInt *perm = perms ? perms[p] : NULL;
6206: const PetscScalar *flip = flips ? flips[p] : NULL;
6207: updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array);
6208: } break;
6209: case INSERT_BC_VALUES:
6210: for (p = 0; p < numPoints; p++) {
6211: const PetscInt point = points[2*p];
6212: const PetscInt *perm = perms ? perms[p] : NULL;
6213: const PetscScalar *flip = flips ? flips[p] : NULL;
6214: updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, insert, clperm, values, &offset, array);
6215: } break;
6216: case ADD_VALUES:
6217: for (p = 0; p < numPoints; p++) {
6218: const PetscInt point = points[2*p];
6219: const PetscInt *perm = perms ? perms[p] : NULL;
6220: const PetscScalar *flip = flips ? flips[p] : NULL;
6221: updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array);
6222: } break;
6223: case ADD_ALL_VALUES:
6224: for (p = 0; p < numPoints; p++) {
6225: const PetscInt point = points[2*p];
6226: const PetscInt *perm = perms ? perms[p] : NULL;
6227: const PetscScalar *flip = flips ? flips[p] : NULL;
6228: updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array);
6229: } break;
6230: case ADD_BC_VALUES:
6231: for (p = 0; p < numPoints; p++) {
6232: const PetscInt point = points[2*p];
6233: const PetscInt *perm = perms ? perms[p] : NULL;
6234: const PetscScalar *flip = flips ? flips[p] : NULL;
6235: updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, add, clperm, values, &offset, array);
6236: } break;
6237: default:
6238: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode);
6239: }
6240: PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);
6241: }
6242: } else {
6243: PetscInt dof, off;
6244: const PetscInt **perms = NULL;
6245: const PetscScalar **flips = NULL;
6247: PetscSectionGetPointSyms(section,numPoints,points,&perms,&flips);
6248: switch (mode) {
6249: case INSERT_VALUES:
6250: for (p = 0, off = 0; p < numPoints; p++, off += dof) {
6251: const PetscInt point = points[2*p];
6252: const PetscInt *perm = perms ? perms[p] : NULL;
6253: const PetscScalar *flip = flips ? flips[p] : NULL;
6254: PetscSectionGetDof(section, point, &dof);
6255: updatePoint_private(section, point, dof, insert, PETSC_FALSE, perm, flip, clperm, values, off, array);
6256: } break;
6257: case INSERT_ALL_VALUES:
6258: for (p = 0, off = 0; p < numPoints; p++, off += dof) {
6259: const PetscInt point = points[2*p];
6260: const PetscInt *perm = perms ? perms[p] : NULL;
6261: const PetscScalar *flip = flips ? flips[p] : NULL;
6262: PetscSectionGetDof(section, point, &dof);
6263: updatePoint_private(section, point, dof, insert, PETSC_TRUE, perm, flip, clperm, values, off, array);
6264: } break;
6265: case INSERT_BC_VALUES:
6266: for (p = 0, off = 0; p < numPoints; p++, off += dof) {
6267: const PetscInt point = points[2*p];
6268: const PetscInt *perm = perms ? perms[p] : NULL;
6269: const PetscScalar *flip = flips ? flips[p] : NULL;
6270: PetscSectionGetDof(section, point, &dof);
6271: updatePointBC_private(section, point, dof, insert, perm, flip, clperm, values, off, array);
6272: } break;
6273: case ADD_VALUES:
6274: for (p = 0, off = 0; p < numPoints; p++, off += dof) {
6275: const PetscInt point = points[2*p];
6276: const PetscInt *perm = perms ? perms[p] : NULL;
6277: const PetscScalar *flip = flips ? flips[p] : NULL;
6278: PetscSectionGetDof(section, point, &dof);
6279: updatePoint_private(section, point, dof, add, PETSC_FALSE, perm, flip, clperm, values, off, array);
6280: } break;
6281: case ADD_ALL_VALUES:
6282: for (p = 0, off = 0; p < numPoints; p++, off += dof) {
6283: const PetscInt point = points[2*p];
6284: const PetscInt *perm = perms ? perms[p] : NULL;
6285: const PetscScalar *flip = flips ? flips[p] : NULL;
6286: PetscSectionGetDof(section, point, &dof);
6287: updatePoint_private(section, point, dof, add, PETSC_TRUE, perm, flip, clperm, values, off, array);
6288: } break;
6289: case ADD_BC_VALUES:
6290: for (p = 0, off = 0; p < numPoints; p++, off += dof) {
6291: const PetscInt point = points[2*p];
6292: const PetscInt *perm = perms ? perms[p] : NULL;
6293: const PetscScalar *flip = flips ? flips[p] : NULL;
6294: PetscSectionGetDof(section, point, &dof);
6295: updatePointBC_private(section, point, dof, add, perm, flip, clperm, values, off, array);
6296: } break;
6297: default:
6298: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode);
6299: }
6300: PetscSectionRestorePointSyms(section,numPoints,points,&perms,&flips);
6301: }
6302: /* Cleanup points */
6303: DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
6304: /* Cleanup array */
6305: VecRestoreArray(v, &array);
6306: return 0;
6307: }
6309: /* Check whether the given point is in the label. If not, update the offset to skip this point */
6310: static inline PetscErrorCode CheckPoint_Private(DMLabel label, PetscInt labelId, PetscSection section, PetscInt point, PetscInt f, PetscInt *offset)
6311: {
6312: if (label) {
6313: PetscInt val, fdof;
6315: /* There is a problem with this:
6316: Suppose we have two label values, defining surfaces, interecting along a line in 3D. When we add cells to the label, the cells that
6317: touch both surfaces must pick a label value. Thus we miss setting values for the surface with that other value intersecting that cell.
6318: Thus I am only going to check val != -1, not val != labelId
6319: */
6320: DMLabelGetValue(label, point, &val);
6321: if (val < 0) {
6322: PetscSectionGetFieldDof(section, point, f, &fdof);
6323: *offset += fdof;
6324: return 1;
6325: }
6326: }
6327: return 0;
6328: }
6330: /* Unlike DMPlexVecSetClosure(), this uses plex-native closure permutation, not a user-specified permutation such as DMPlexSetClosurePermutationTensor(). */
6331: PetscErrorCode DMPlexVecSetFieldClosure_Internal(DM dm, PetscSection section, Vec v, PetscBool fieldActive[], PetscInt point, PetscInt Ncc, const PetscInt comps[], DMLabel label, PetscInt labelId, const PetscScalar values[], InsertMode mode)
6332: {
6333: PetscSection clSection;
6334: IS clPoints;
6335: PetscScalar *array;
6336: PetscInt *points = NULL;
6337: const PetscInt *clp;
6338: PetscInt numFields, numPoints, p;
6339: PetscInt offset = 0, f;
6343: if (!section) DMGetLocalSection(dm, §ion);
6346: PetscSectionGetNumFields(section, &numFields);
6347: /* Get points */
6348: DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
6349: /* Get array */
6350: VecGetArray(v, &array);
6351: /* Get values */
6352: for (f = 0; f < numFields; ++f) {
6353: const PetscInt **perms = NULL;
6354: const PetscScalar **flips = NULL;
6356: if (!fieldActive[f]) {
6357: for (p = 0; p < numPoints*2; p += 2) {
6358: PetscInt fdof;
6359: PetscSectionGetFieldDof(section, points[p], f, &fdof);
6360: offset += fdof;
6361: }
6362: continue;
6363: }
6364: PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);
6365: switch (mode) {
6366: case INSERT_VALUES:
6367: for (p = 0; p < numPoints; p++) {
6368: const PetscInt point = points[2*p];
6369: const PetscInt *perm = perms ? perms[p] : NULL;
6370: const PetscScalar *flip = flips ? flips[p] : NULL;
6371: if (CheckPoint_Private(label, labelId, section, point, f, &offset)) continue;
6372: updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, NULL, values, &offset, array);
6373: } break;
6374: case INSERT_ALL_VALUES:
6375: for (p = 0; p < numPoints; p++) {
6376: const PetscInt point = points[2*p];
6377: const PetscInt *perm = perms ? perms[p] : NULL;
6378: const PetscScalar *flip = flips ? flips[p] : NULL;
6379: if (CheckPoint_Private(label, labelId, section, point, f, &offset)) continue;
6380: updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, NULL, values, &offset, array);
6381: } break;
6382: case INSERT_BC_VALUES:
6383: for (p = 0; p < numPoints; p++) {
6384: const PetscInt point = points[2*p];
6385: const PetscInt *perm = perms ? perms[p] : NULL;
6386: const PetscScalar *flip = flips ? flips[p] : NULL;
6387: if (CheckPoint_Private(label, labelId, section, point, f, &offset)) continue;
6388: updatePointFieldsBC_private(section, point, perm, flip, f, Ncc, comps, insert, NULL, values, &offset, array);
6389: } break;
6390: case ADD_VALUES:
6391: for (p = 0; p < numPoints; p++) {
6392: const PetscInt point = points[2*p];
6393: const PetscInt *perm = perms ? perms[p] : NULL;
6394: const PetscScalar *flip = flips ? flips[p] : NULL;
6395: if (CheckPoint_Private(label, labelId, section, point, f, &offset)) continue;
6396: updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, NULL, values, &offset, array);
6397: } break;
6398: case ADD_ALL_VALUES:
6399: for (p = 0; p < numPoints; p++) {
6400: const PetscInt point = points[2*p];
6401: const PetscInt *perm = perms ? perms[p] : NULL;
6402: const PetscScalar *flip = flips ? flips[p] : NULL;
6403: if (CheckPoint_Private(label, labelId, section, point, f, &offset)) continue;
6404: updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, NULL, values, &offset, array);
6405: } break;
6406: default:
6407: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode);
6408: }
6409: PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);
6410: }
6411: /* Cleanup points */
6412: DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
6413: /* Cleanup array */
6414: VecRestoreArray(v, &array);
6415: return 0;
6416: }
6418: static PetscErrorCode DMPlexPrintMatSetValues(PetscViewer viewer, Mat A, PetscInt point, PetscInt numRIndices, const PetscInt rindices[], PetscInt numCIndices, const PetscInt cindices[], const PetscScalar values[])
6419: {
6420: PetscMPIInt rank;
6421: PetscInt i, j;
6423: MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);
6424: PetscViewerASCIIPrintf(viewer, "[%d]mat for point %D\n", rank, point);
6425: for (i = 0; i < numRIndices; i++) PetscViewerASCIIPrintf(viewer, "[%d]mat row indices[%D] = %D\n", rank, i, rindices[i]);
6426: for (i = 0; i < numCIndices; i++) PetscViewerASCIIPrintf(viewer, "[%d]mat col indices[%D] = %D\n", rank, i, cindices[i]);
6427: numCIndices = numCIndices ? numCIndices : numRIndices;
6428: if (!values) return 0;
6429: for (i = 0; i < numRIndices; i++) {
6430: PetscViewerASCIIPrintf(viewer, "[%d]", rank);
6431: for (j = 0; j < numCIndices; j++) {
6432: #if defined(PETSC_USE_COMPLEX)
6433: PetscViewerASCIIPrintf(viewer, " (%g,%g)", (double)PetscRealPart(values[i*numCIndices+j]), (double)PetscImaginaryPart(values[i*numCIndices+j]));
6434: #else
6435: PetscViewerASCIIPrintf(viewer, " %g", (double)values[i*numCIndices+j]);
6436: #endif
6437: }
6438: PetscViewerASCIIPrintf(viewer, "\n");
6439: }
6440: return 0;
6441: }
6443: /*
6444: DMPlexGetIndicesPoint_Internal - Add the indices for dofs on a point to an index array
6446: Input Parameters:
6447: + section - The section for this data layout
6448: . islocal - Is the section (and thus indices being requested) local or global?
6449: . point - The point contributing dofs with these indices
6450: . off - The global offset of this point
6451: . loff - The local offset of each field
6452: . setBC - The flag determining whether to include indices of boundary values
6453: . perm - A permutation of the dofs on this point, or NULL
6454: - indperm - A permutation of the entire indices array, or NULL
6456: Output Parameter:
6457: . indices - Indices for dofs on this point
6459: Level: developer
6461: Note: The indices could be local or global, depending on the value of 'off'.
6462: */
6463: PetscErrorCode DMPlexGetIndicesPoint_Internal(PetscSection section, PetscBool islocal,PetscInt point, PetscInt off, PetscInt *loff, PetscBool setBC, const PetscInt perm[], const PetscInt indperm[], PetscInt indices[])
6464: {
6465: PetscInt dof; /* The number of unknowns on this point */
6466: PetscInt cdof; /* The number of constraints on this point */
6467: const PetscInt *cdofs; /* The indices of the constrained dofs on this point */
6468: PetscInt cind = 0, k;
6471: PetscSectionGetDof(section, point, &dof);
6472: PetscSectionGetConstraintDof(section, point, &cdof);
6473: if (!cdof || setBC) {
6474: for (k = 0; k < dof; ++k) {
6475: const PetscInt preind = perm ? *loff+perm[k] : *loff+k;
6476: const PetscInt ind = indperm ? indperm[preind] : preind;
6478: indices[ind] = off + k;
6479: }
6480: } else {
6481: PetscSectionGetConstraintIndices(section, point, &cdofs);
6482: for (k = 0; k < dof; ++k) {
6483: const PetscInt preind = perm ? *loff+perm[k] : *loff+k;
6484: const PetscInt ind = indperm ? indperm[preind] : preind;
6486: if ((cind < cdof) && (k == cdofs[cind])) {
6487: /* Insert check for returning constrained indices */
6488: indices[ind] = -(off+k+1);
6489: ++cind;
6490: } else {
6491: indices[ind] = off + k - (islocal ? 0 : cind);
6492: }
6493: }
6494: }
6495: *loff += dof;
6496: return 0;
6497: }
6499: /*
6500: DMPlexGetIndicesPointFields_Internal - gets section indices for a point in its canonical ordering.
6502: Input Parameters:
6503: + section - a section (global or local)
6504: - islocal - PETSC_TRUE if requesting local indices (i.e., section is local); PETSC_FALSE for global
6505: . point - point within section
6506: . off - The offset of this point in the (local or global) indexed space - should match islocal and (usually) the section
6507: . foffs - array of length numFields containing the offset in canonical point ordering (the location in indices) of each field
6508: . setBC - identify constrained (boundary condition) points via involution.
6509: . perms - perms[f][permsoff][:] is a permutation of dofs within each field
6510: . permsoff - offset
6511: - indperm - index permutation
6513: Output Parameter:
6514: . foffs - each entry is incremented by the number of (unconstrained if setBC=FALSE) dofs in that field
6515: . indices - array to hold indices (as defined by section) of each dof associated with point
6517: Notes:
6518: If section is local and setBC=true, there is no distinction between constrained and unconstrained dofs.
6519: If section is local and setBC=false, the indices for constrained points are the involution -(i+1) of their position
6520: in the local vector.
6522: If section is global and setBC=false, the indices for constrained points are negative (and their value is not
6523: significant). It is invalid to call with a global section and setBC=true.
6525: Developer Note:
6526: The section is only used for field layout, so islocal is technically a statement about the offset (off). At some point
6527: in the future, global sections may have fields set, in which case we could pass the global section and obtain the
6528: offset could be obtained from the section instead of passing it explicitly as we do now.
6530: Example:
6531: Suppose a point contains one field with three components, and for which the unconstrained indices are {10, 11, 12}.
6532: When the middle component is constrained, we get the array {10, -12, 12} for (islocal=TRUE, setBC=FALSE).
6533: Note that -12 is the involution of 11, so the user can involute negative indices to recover local indices.
6534: The global vector does not store constrained dofs, so when this function returns global indices, say {110, -112, 111}, the value of -112 is an arbitrary flag that should not be interpreted beyond its sign.
6536: Level: developer
6537: */
6538: PetscErrorCode DMPlexGetIndicesPointFields_Internal(PetscSection section, PetscBool islocal, PetscInt point, PetscInt off, PetscInt foffs[], PetscBool setBC, const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[])
6539: {
6540: PetscInt numFields, foff, f;
6543: PetscSectionGetNumFields(section, &numFields);
6544: for (f = 0, foff = 0; f < numFields; ++f) {
6545: PetscInt fdof, cfdof;
6546: const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */
6547: PetscInt cind = 0, b;
6548: const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL;
6550: PetscSectionGetFieldDof(section, point, f, &fdof);
6551: PetscSectionGetFieldConstraintDof(section, point, f, &cfdof);
6552: if (!cfdof || setBC) {
6553: for (b = 0; b < fdof; ++b) {
6554: const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b;
6555: const PetscInt ind = indperm ? indperm[preind] : preind;
6557: indices[ind] = off+foff+b;
6558: }
6559: } else {
6560: PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);
6561: for (b = 0; b < fdof; ++b) {
6562: const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b;
6563: const PetscInt ind = indperm ? indperm[preind] : preind;
6565: if ((cind < cfdof) && (b == fcdofs[cind])) {
6566: indices[ind] = -(off+foff+b+1);
6567: ++cind;
6568: } else {
6569: indices[ind] = off + foff + b - (islocal ? 0 : cind);
6570: }
6571: }
6572: }
6573: foff += (setBC || islocal ? fdof : (fdof - cfdof));
6574: foffs[f] += fdof;
6575: }
6576: return 0;
6577: }
6579: /*
6580: This version believes the globalSection offsets for each field, rather than just the point offset
6582: . foffs - The offset into 'indices' for each field, since it is segregated by field
6584: Notes:
6585: The semantics of this function relate to that of setBC=FALSE in DMPlexGetIndicesPointFields_Internal.
6586: Since this function uses global indices, setBC=TRUE would be invalid, so no such argument exists.
6587: */
6588: static PetscErrorCode DMPlexGetIndicesPointFieldsSplit_Internal(PetscSection section, PetscSection globalSection, PetscInt point, PetscInt foffs[], const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[])
6589: {
6590: PetscInt numFields, foff, f;
6592: PetscSectionGetNumFields(section, &numFields);
6593: for (f = 0; f < numFields; ++f) {
6594: PetscInt fdof, cfdof;
6595: const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */
6596: PetscInt cind = 0, b;
6597: const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL;
6599: PetscSectionGetFieldDof(section, point, f, &fdof);
6600: PetscSectionGetFieldConstraintDof(section, point, f, &cfdof);
6601: PetscSectionGetFieldOffset(globalSection, point, f, &foff);
6602: if (!cfdof) {
6603: for (b = 0; b < fdof; ++b) {
6604: const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b;
6605: const PetscInt ind = indperm ? indperm[preind] : preind;
6607: indices[ind] = foff+b;
6608: }
6609: } else {
6610: PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);
6611: for (b = 0; b < fdof; ++b) {
6612: const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b;
6613: const PetscInt ind = indperm ? indperm[preind] : preind;
6615: if ((cind < cfdof) && (b == fcdofs[cind])) {
6616: indices[ind] = -(foff+b+1);
6617: ++cind;
6618: } else {
6619: indices[ind] = foff+b-cind;
6620: }
6621: }
6622: }
6623: foffs[f] += fdof;
6624: }
6625: return 0;
6626: }
6628: PetscErrorCode DMPlexAnchorsModifyMat(DM dm, PetscSection section, PetscInt numPoints, PetscInt numIndices, const PetscInt points[], const PetscInt ***perms, const PetscScalar values[], PetscInt *outNumPoints, PetscInt *outNumIndices, PetscInt *outPoints[], PetscScalar *outValues[], PetscInt offsets[], PetscBool multiplyLeft)
6629: {
6630: Mat cMat;
6631: PetscSection aSec, cSec;
6632: IS aIS;
6633: PetscInt aStart = -1, aEnd = -1;
6634: const PetscInt *anchors;
6635: PetscInt numFields, f, p, q, newP = 0;
6636: PetscInt newNumPoints = 0, newNumIndices = 0;
6637: PetscInt *newPoints, *indices, *newIndices;
6638: PetscInt maxAnchor, maxDof;
6639: PetscInt newOffsets[32];
6640: PetscInt *pointMatOffsets[32];
6641: PetscInt *newPointOffsets[32];
6642: PetscScalar *pointMat[32];
6643: PetscScalar *newValues=NULL,*tmpValues;
6644: PetscBool anyConstrained = PETSC_FALSE;
6648: PetscSectionGetNumFields(section, &numFields);
6650: DMPlexGetAnchors(dm,&aSec,&aIS);
6651: /* if there are point-to-point constraints */
6652: if (aSec) {
6653: PetscArrayzero(newOffsets, 32);
6654: ISGetIndices(aIS,&anchors);
6655: PetscSectionGetChart(aSec,&aStart,&aEnd);
6656: /* figure out how many points are going to be in the new element matrix
6657: * (we allow double counting, because it's all just going to be summed
6658: * into the global matrix anyway) */
6659: for (p = 0; p < 2*numPoints; p+=2) {
6660: PetscInt b = points[p];
6661: PetscInt bDof = 0, bSecDof;
6663: PetscSectionGetDof(section,b,&bSecDof);
6664: if (!bSecDof) {
6665: continue;
6666: }
6667: if (b >= aStart && b < aEnd) {
6668: PetscSectionGetDof(aSec,b,&bDof);
6669: }
6670: if (bDof) {
6671: /* this point is constrained */
6672: /* it is going to be replaced by its anchors */
6673: PetscInt bOff, q;
6675: anyConstrained = PETSC_TRUE;
6676: newNumPoints += bDof;
6677: PetscSectionGetOffset(aSec,b,&bOff);
6678: for (q = 0; q < bDof; q++) {
6679: PetscInt a = anchors[bOff + q];
6680: PetscInt aDof;
6682: PetscSectionGetDof(section,a,&aDof);
6683: newNumIndices += aDof;
6684: for (f = 0; f < numFields; ++f) {
6685: PetscInt fDof;
6687: PetscSectionGetFieldDof(section, a, f, &fDof);
6688: newOffsets[f+1] += fDof;
6689: }
6690: }
6691: }
6692: else {
6693: /* this point is not constrained */
6694: newNumPoints++;
6695: newNumIndices += bSecDof;
6696: for (f = 0; f < numFields; ++f) {
6697: PetscInt fDof;
6699: PetscSectionGetFieldDof(section, b, f, &fDof);
6700: newOffsets[f+1] += fDof;
6701: }
6702: }
6703: }
6704: }
6705: if (!anyConstrained) {
6706: if (outNumPoints) *outNumPoints = 0;
6707: if (outNumIndices) *outNumIndices = 0;
6708: if (outPoints) *outPoints = NULL;
6709: if (outValues) *outValues = NULL;
6710: if (aSec) ISRestoreIndices(aIS,&anchors);
6711: return 0;
6712: }
6714: if (outNumPoints) *outNumPoints = newNumPoints;
6715: if (outNumIndices) *outNumIndices = newNumIndices;
6717: for (f = 0; f < numFields; ++f) newOffsets[f+1] += newOffsets[f];
6719: if (!outPoints && !outValues) {
6720: if (offsets) {
6721: for (f = 0; f <= numFields; f++) {
6722: offsets[f] = newOffsets[f];
6723: }
6724: }
6725: if (aSec) ISRestoreIndices(aIS,&anchors);
6726: return 0;
6727: }
6731: DMGetDefaultConstraints(dm, &cSec, &cMat, NULL);
6733: /* workspaces */
6734: if (numFields) {
6735: for (f = 0; f < numFields; f++) {
6736: DMGetWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[f]);
6737: DMGetWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[f]);
6738: }
6739: }
6740: else {
6741: DMGetWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[0]);
6742: DMGetWorkArray(dm,numPoints,MPIU_INT,&newPointOffsets[0]);
6743: }
6745: /* get workspaces for the point-to-point matrices */
6746: if (numFields) {
6747: PetscInt totalOffset, totalMatOffset;
6749: for (p = 0; p < numPoints; p++) {
6750: PetscInt b = points[2*p];
6751: PetscInt bDof = 0, bSecDof;
6753: PetscSectionGetDof(section,b,&bSecDof);
6754: if (!bSecDof) {
6755: for (f = 0; f < numFields; f++) {
6756: newPointOffsets[f][p + 1] = 0;
6757: pointMatOffsets[f][p + 1] = 0;
6758: }
6759: continue;
6760: }
6761: if (b >= aStart && b < aEnd) {
6762: PetscSectionGetDof(aSec, b, &bDof);
6763: }
6764: if (bDof) {
6765: for (f = 0; f < numFields; f++) {
6766: PetscInt fDof, q, bOff, allFDof = 0;
6768: PetscSectionGetFieldDof(section, b, f, &fDof);
6769: PetscSectionGetOffset(aSec, b, &bOff);
6770: for (q = 0; q < bDof; q++) {
6771: PetscInt a = anchors[bOff + q];
6772: PetscInt aFDof;
6774: PetscSectionGetFieldDof(section, a, f, &aFDof);
6775: allFDof += aFDof;
6776: }
6777: newPointOffsets[f][p+1] = allFDof;
6778: pointMatOffsets[f][p+1] = fDof * allFDof;
6779: }
6780: }
6781: else {
6782: for (f = 0; f < numFields; f++) {
6783: PetscInt fDof;
6785: PetscSectionGetFieldDof(section, b, f, &fDof);
6786: newPointOffsets[f][p+1] = fDof;
6787: pointMatOffsets[f][p+1] = 0;
6788: }
6789: }
6790: }
6791: for (f = 0, totalOffset = 0, totalMatOffset = 0; f < numFields; f++) {
6792: newPointOffsets[f][0] = totalOffset;
6793: pointMatOffsets[f][0] = totalMatOffset;
6794: for (p = 0; p < numPoints; p++) {
6795: newPointOffsets[f][p+1] += newPointOffsets[f][p];
6796: pointMatOffsets[f][p+1] += pointMatOffsets[f][p];
6797: }
6798: totalOffset = newPointOffsets[f][numPoints];
6799: totalMatOffset = pointMatOffsets[f][numPoints];
6800: DMGetWorkArray(dm,pointMatOffsets[f][numPoints],MPIU_SCALAR,&pointMat[f]);
6801: }
6802: }
6803: else {
6804: for (p = 0; p < numPoints; p++) {
6805: PetscInt b = points[2*p];
6806: PetscInt bDof = 0, bSecDof;
6808: PetscSectionGetDof(section,b,&bSecDof);
6809: if (!bSecDof) {
6810: newPointOffsets[0][p + 1] = 0;
6811: pointMatOffsets[0][p + 1] = 0;
6812: continue;
6813: }
6814: if (b >= aStart && b < aEnd) {
6815: PetscSectionGetDof(aSec, b, &bDof);
6816: }
6817: if (bDof) {
6818: PetscInt bOff, q, allDof = 0;
6820: PetscSectionGetOffset(aSec, b, &bOff);
6821: for (q = 0; q < bDof; q++) {
6822: PetscInt a = anchors[bOff + q], aDof;
6824: PetscSectionGetDof(section, a, &aDof);
6825: allDof += aDof;
6826: }
6827: newPointOffsets[0][p+1] = allDof;
6828: pointMatOffsets[0][p+1] = bSecDof * allDof;
6829: }
6830: else {
6831: newPointOffsets[0][p+1] = bSecDof;
6832: pointMatOffsets[0][p+1] = 0;
6833: }
6834: }
6835: newPointOffsets[0][0] = 0;
6836: pointMatOffsets[0][0] = 0;
6837: for (p = 0; p < numPoints; p++) {
6838: newPointOffsets[0][p+1] += newPointOffsets[0][p];
6839: pointMatOffsets[0][p+1] += pointMatOffsets[0][p];
6840: }
6841: DMGetWorkArray(dm,pointMatOffsets[0][numPoints],MPIU_SCALAR,&pointMat[0]);
6842: }
6844: /* output arrays */
6845: DMGetWorkArray(dm,2*newNumPoints,MPIU_INT,&newPoints);
6847: /* get the point-to-point matrices; construct newPoints */
6848: PetscSectionGetMaxDof(aSec, &maxAnchor);
6849: PetscSectionGetMaxDof(section, &maxDof);
6850: DMGetWorkArray(dm,maxDof,MPIU_INT,&indices);
6851: DMGetWorkArray(dm,maxAnchor*maxDof,MPIU_INT,&newIndices);
6852: if (numFields) {
6853: for (p = 0, newP = 0; p < numPoints; p++) {
6854: PetscInt b = points[2*p];
6855: PetscInt o = points[2*p+1];
6856: PetscInt bDof = 0, bSecDof;
6858: PetscSectionGetDof(section, b, &bSecDof);
6859: if (!bSecDof) {
6860: continue;
6861: }
6862: if (b >= aStart && b < aEnd) {
6863: PetscSectionGetDof(aSec, b, &bDof);
6864: }
6865: if (bDof) {
6866: PetscInt fStart[32], fEnd[32], fAnchorStart[32], fAnchorEnd[32], bOff, q;
6868: fStart[0] = 0;
6869: fEnd[0] = 0;
6870: for (f = 0; f < numFields; f++) {
6871: PetscInt fDof;
6873: PetscSectionGetFieldDof(cSec, b, f, &fDof);
6874: fStart[f+1] = fStart[f] + fDof;
6875: fEnd[f+1] = fStart[f+1];
6876: }
6877: PetscSectionGetOffset(cSec, b, &bOff);
6878: DMPlexGetIndicesPointFields_Internal(cSec, PETSC_TRUE, b, bOff, fEnd, PETSC_TRUE, perms, p, NULL, indices);
6880: fAnchorStart[0] = 0;
6881: fAnchorEnd[0] = 0;
6882: for (f = 0; f < numFields; f++) {
6883: PetscInt fDof = newPointOffsets[f][p + 1] - newPointOffsets[f][p];
6885: fAnchorStart[f+1] = fAnchorStart[f] + fDof;
6886: fAnchorEnd[f+1] = fAnchorStart[f + 1];
6887: }
6888: PetscSectionGetOffset(aSec, b, &bOff);
6889: for (q = 0; q < bDof; q++) {
6890: PetscInt a = anchors[bOff + q], aOff;
6892: /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */
6893: newPoints[2*(newP + q)] = a;
6894: newPoints[2*(newP + q) + 1] = 0;
6895: PetscSectionGetOffset(section, a, &aOff);
6896: DMPlexGetIndicesPointFields_Internal(section, PETSC_TRUE, a, aOff, fAnchorEnd, PETSC_TRUE, NULL, -1, NULL, newIndices);
6897: }
6898: newP += bDof;
6900: if (outValues) {
6901: /* get the point-to-point submatrix */
6902: for (f = 0; f < numFields; f++) {
6903: MatGetValues(cMat,fEnd[f]-fStart[f],indices + fStart[f],fAnchorEnd[f] - fAnchorStart[f],newIndices + fAnchorStart[f],pointMat[f] + pointMatOffsets[f][p]);
6904: }
6905: }
6906: }
6907: else {
6908: newPoints[2 * newP] = b;
6909: newPoints[2 * newP + 1] = o;
6910: newP++;
6911: }
6912: }
6913: } else {
6914: for (p = 0; p < numPoints; p++) {
6915: PetscInt b = points[2*p];
6916: PetscInt o = points[2*p+1];
6917: PetscInt bDof = 0, bSecDof;
6919: PetscSectionGetDof(section, b, &bSecDof);
6920: if (!bSecDof) {
6921: continue;
6922: }
6923: if (b >= aStart && b < aEnd) {
6924: PetscSectionGetDof(aSec, b, &bDof);
6925: }
6926: if (bDof) {
6927: PetscInt bEnd = 0, bAnchorEnd = 0, bOff;
6929: PetscSectionGetOffset(cSec, b, &bOff);
6930: DMPlexGetIndicesPoint_Internal(cSec, PETSC_TRUE, b, bOff, &bEnd, PETSC_TRUE, (perms && perms[0]) ? perms[0][p] : NULL, NULL, indices);
6932: PetscSectionGetOffset (aSec, b, &bOff);
6933: for (q = 0; q < bDof; q++) {
6934: PetscInt a = anchors[bOff + q], aOff;
6936: /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */
6938: newPoints[2*(newP + q)] = a;
6939: newPoints[2*(newP + q) + 1] = 0;
6940: PetscSectionGetOffset(section, a, &aOff);
6941: DMPlexGetIndicesPoint_Internal(section, PETSC_TRUE, a, aOff, &bAnchorEnd, PETSC_TRUE, NULL, NULL, newIndices);
6942: }
6943: newP += bDof;
6945: /* get the point-to-point submatrix */
6946: if (outValues) {
6947: MatGetValues(cMat,bEnd,indices,bAnchorEnd,newIndices,pointMat[0] + pointMatOffsets[0][p]);
6948: }
6949: }
6950: else {
6951: newPoints[2 * newP] = b;
6952: newPoints[2 * newP + 1] = o;
6953: newP++;
6954: }
6955: }
6956: }
6958: if (outValues) {
6959: DMGetWorkArray(dm,newNumIndices*numIndices,MPIU_SCALAR,&tmpValues);
6960: PetscArrayzero(tmpValues,newNumIndices*numIndices);
6961: /* multiply constraints on the right */
6962: if (numFields) {
6963: for (f = 0; f < numFields; f++) {
6964: PetscInt oldOff = offsets[f];
6966: for (p = 0; p < numPoints; p++) {
6967: PetscInt cStart = newPointOffsets[f][p];
6968: PetscInt b = points[2 * p];
6969: PetscInt c, r, k;
6970: PetscInt dof;
6972: PetscSectionGetFieldDof(section,b,f,&dof);
6973: if (!dof) {
6974: continue;
6975: }
6976: if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) {
6977: PetscInt nCols = newPointOffsets[f][p+1]-cStart;
6978: const PetscScalar *mat = pointMat[f] + pointMatOffsets[f][p];
6980: for (r = 0; r < numIndices; r++) {
6981: for (c = 0; c < nCols; c++) {
6982: for (k = 0; k < dof; k++) {
6983: tmpValues[r * newNumIndices + cStart + c] += values[r * numIndices + oldOff + k] * mat[k * nCols + c];
6984: }
6985: }
6986: }
6987: }
6988: else {
6989: /* copy this column as is */
6990: for (r = 0; r < numIndices; r++) {
6991: for (c = 0; c < dof; c++) {
6992: tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c];
6993: }
6994: }
6995: }
6996: oldOff += dof;
6997: }
6998: }
6999: }
7000: else {
7001: PetscInt oldOff = 0;
7002: for (p = 0; p < numPoints; p++) {
7003: PetscInt cStart = newPointOffsets[0][p];
7004: PetscInt b = points[2 * p];
7005: PetscInt c, r, k;
7006: PetscInt dof;
7008: PetscSectionGetDof(section,b,&dof);
7009: if (!dof) {
7010: continue;
7011: }
7012: if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) {
7013: PetscInt nCols = newPointOffsets[0][p+1]-cStart;
7014: const PetscScalar *mat = pointMat[0] + pointMatOffsets[0][p];
7016: for (r = 0; r < numIndices; r++) {
7017: for (c = 0; c < nCols; c++) {
7018: for (k = 0; k < dof; k++) {
7019: tmpValues[r * newNumIndices + cStart + c] += mat[k * nCols + c] * values[r * numIndices + oldOff + k];
7020: }
7021: }
7022: }
7023: }
7024: else {
7025: /* copy this column as is */
7026: for (r = 0; r < numIndices; r++) {
7027: for (c = 0; c < dof; c++) {
7028: tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c];
7029: }
7030: }
7031: }
7032: oldOff += dof;
7033: }
7034: }
7036: if (multiplyLeft) {
7037: DMGetWorkArray(dm,newNumIndices*newNumIndices,MPIU_SCALAR,&newValues);
7038: PetscArrayzero(newValues,newNumIndices*newNumIndices);
7039: /* multiply constraints transpose on the left */
7040: if (numFields) {
7041: for (f = 0; f < numFields; f++) {
7042: PetscInt oldOff = offsets[f];
7044: for (p = 0; p < numPoints; p++) {
7045: PetscInt rStart = newPointOffsets[f][p];
7046: PetscInt b = points[2 * p];
7047: PetscInt c, r, k;
7048: PetscInt dof;
7050: PetscSectionGetFieldDof(section,b,f,&dof);
7051: if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) {
7052: PetscInt nRows = newPointOffsets[f][p+1]-rStart;
7053: const PetscScalar *PETSC_RESTRICT mat = pointMat[f] + pointMatOffsets[f][p];
7055: for (r = 0; r < nRows; r++) {
7056: for (c = 0; c < newNumIndices; c++) {
7057: for (k = 0; k < dof; k++) {
7058: newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c];
7059: }
7060: }
7061: }
7062: }
7063: else {
7064: /* copy this row as is */
7065: for (r = 0; r < dof; r++) {
7066: for (c = 0; c < newNumIndices; c++) {
7067: newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c];
7068: }
7069: }
7070: }
7071: oldOff += dof;
7072: }
7073: }
7074: }
7075: else {
7076: PetscInt oldOff = 0;
7078: for (p = 0; p < numPoints; p++) {
7079: PetscInt rStart = newPointOffsets[0][p];
7080: PetscInt b = points[2 * p];
7081: PetscInt c, r, k;
7082: PetscInt dof;
7084: PetscSectionGetDof(section,b,&dof);
7085: if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) {
7086: PetscInt nRows = newPointOffsets[0][p+1]-rStart;
7087: const PetscScalar *PETSC_RESTRICT mat = pointMat[0] + pointMatOffsets[0][p];
7089: for (r = 0; r < nRows; r++) {
7090: for (c = 0; c < newNumIndices; c++) {
7091: for (k = 0; k < dof; k++) {
7092: newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c];
7093: }
7094: }
7095: }
7096: }
7097: else {
7098: /* copy this row as is */
7099: for (r = 0; r < dof; r++) {
7100: for (c = 0; c < newNumIndices; c++) {
7101: newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c];
7102: }
7103: }
7104: }
7105: oldOff += dof;
7106: }
7107: }
7109: DMRestoreWorkArray(dm,newNumIndices*numIndices,MPIU_SCALAR,&tmpValues);
7110: }
7111: else {
7112: newValues = tmpValues;
7113: }
7114: }
7116: /* clean up */
7117: DMRestoreWorkArray(dm,maxDof,MPIU_INT,&indices);
7118: DMRestoreWorkArray(dm,maxAnchor*maxDof,MPIU_INT,&newIndices);
7120: if (numFields) {
7121: for (f = 0; f < numFields; f++) {
7122: DMRestoreWorkArray(dm,pointMatOffsets[f][numPoints],MPIU_SCALAR,&pointMat[f]);
7123: DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[f]);
7124: DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[f]);
7125: }
7126: }
7127: else {
7128: DMRestoreWorkArray(dm,pointMatOffsets[0][numPoints],MPIU_SCALAR,&pointMat[0]);
7129: DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[0]);
7130: DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[0]);
7131: }
7132: ISRestoreIndices(aIS,&anchors);
7134: /* output */
7135: if (outPoints) {
7136: *outPoints = newPoints;
7137: }
7138: else {
7139: DMRestoreWorkArray(dm,2*newNumPoints,MPIU_INT,&newPoints);
7140: }
7141: if (outValues) {
7142: *outValues = newValues;
7143: }
7144: for (f = 0; f <= numFields; f++) {
7145: offsets[f] = newOffsets[f];
7146: }
7147: return 0;
7148: }
7150: /*@C
7151: DMPlexGetClosureIndices - Gets the global dof indices associated with the closure of the given point within the provided sections.
7153: Not collective
7155: Input Parameters:
7156: + dm - The DM
7157: . section - The PetscSection describing the points (a local section)
7158: . idxSection - The PetscSection from which to obtain indices (may be local or global)
7159: . point - The point defining the closure
7160: - useClPerm - Use the closure point permutation if available
7162: Output Parameters:
7163: + numIndices - The number of dof indices in the closure of point with the input sections
7164: . indices - The dof indices
7165: . outOffsets - Array to write the field offsets into, or NULL
7166: - values - The input values, which may be modified if sign flips are induced by the point symmetries, or NULL
7168: Notes:
7169: Must call DMPlexRestoreClosureIndices() to free allocated memory
7171: If idxSection is global, any constrained dofs (see DMAddBoundary(), for example) will get negative indices. The value
7172: of those indices is not significant. If idxSection is local, the constrained dofs will yield the involution -(idx+1)
7173: of their index in a local vector. A caller who does not wish to distinguish those points may recover the nonnegative
7174: indices via involution, -(-(idx+1)+1)==idx. Local indices are provided when idxSection == section, otherwise global
7175: indices (with the above semantics) are implied.
7177: Level: advanced
7179: .seealso DMPlexRestoreClosureIndices(), DMPlexVecGetClosure(), DMPlexMatSetClosure(), DMGetLocalSection(), DMGetGlobalSection()
7180: @*/
7181: PetscErrorCode DMPlexGetClosureIndices(DM dm, PetscSection section, PetscSection idxSection, PetscInt point, PetscBool useClPerm,
7182: PetscInt *numIndices, PetscInt *indices[], PetscInt outOffsets[], PetscScalar *values[])
7183: {
7184: /* Closure ordering */
7185: PetscSection clSection;
7186: IS clPoints;
7187: const PetscInt *clp;
7188: PetscInt *points;
7189: const PetscInt *clperm = NULL;
7190: /* Dof permutation and sign flips */
7191: const PetscInt **perms[32] = {NULL};
7192: const PetscScalar **flips[32] = {NULL};
7193: PetscScalar *valCopy = NULL;
7194: /* Hanging node constraints */
7195: PetscInt *pointsC = NULL;
7196: PetscScalar *valuesC = NULL;
7197: PetscInt NclC, NiC;
7199: PetscInt *idx;
7200: PetscInt Nf, Ncl, Ni = 0, offsets[32], p, f;
7201: PetscBool isLocal = (section == idxSection) ? PETSC_TRUE : PETSC_FALSE;
7211: PetscSectionGetNumFields(section, &Nf);
7213: PetscArrayzero(offsets, 32);
7214: /* 1) Get points in closure */
7215: DMPlexGetCompressedClosure(dm, section, point, &Ncl, &points, &clSection, &clPoints, &clp);
7216: if (useClPerm) {
7217: PetscInt depth, clsize;
7218: DMPlexGetPointDepth(dm, point, &depth);
7219: for (clsize=0,p=0; p<Ncl; p++) {
7220: PetscInt dof;
7221: PetscSectionGetDof(section, points[2*p], &dof);
7222: clsize += dof;
7223: }
7224: PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, depth, clsize, &clperm);
7225: }
7226: /* 2) Get number of indices on these points and field offsets from section */
7227: for (p = 0; p < Ncl*2; p += 2) {
7228: PetscInt dof, fdof;
7230: PetscSectionGetDof(section, points[p], &dof);
7231: for (f = 0; f < Nf; ++f) {
7232: PetscSectionGetFieldDof(section, points[p], f, &fdof);
7233: offsets[f+1] += fdof;
7234: }
7235: Ni += dof;
7236: }
7237: for (f = 1; f < Nf; ++f) offsets[f+1] += offsets[f];
7239: /* 3) Get symmetries and sign flips. Apply sign flips to values if passed in (only works for square values matrix) */
7240: for (f = 0; f < PetscMax(1, Nf); ++f) {
7241: if (Nf) PetscSectionGetFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f]);
7242: else PetscSectionGetPointSyms(section, Ncl, points, &perms[f], &flips[f]);
7243: /* may need to apply sign changes to the element matrix */
7244: if (values && flips[f]) {
7245: PetscInt foffset = offsets[f];
7247: for (p = 0; p < Ncl; ++p) {
7248: PetscInt pnt = points[2*p], fdof;
7249: const PetscScalar *flip = flips[f] ? flips[f][p] : NULL;
7251: if (!Nf) PetscSectionGetDof(section, pnt, &fdof);
7252: else PetscSectionGetFieldDof(section, pnt, f, &fdof);
7253: if (flip) {
7254: PetscInt i, j, k;
7256: if (!valCopy) {
7257: DMGetWorkArray(dm, Ni*Ni, MPIU_SCALAR, &valCopy);
7258: for (j = 0; j < Ni * Ni; ++j) valCopy[j] = (*values)[j];
7259: *values = valCopy;
7260: }
7261: for (i = 0; i < fdof; ++i) {
7262: PetscScalar fval = flip[i];
7264: for (k = 0; k < Ni; ++k) {
7265: valCopy[Ni * (foffset + i) + k] *= fval;
7266: valCopy[Ni * k + (foffset + i)] *= fval;
7267: }
7268: }
7269: }
7270: foffset += fdof;
7271: }
7272: }
7273: }
7274: /* 4) Apply hanging node constraints. Get new symmetries and replace all storage with constrained storage */
7275: DMPlexAnchorsModifyMat(dm, section, Ncl, Ni, points, perms, values ? *values : NULL, &NclC, &NiC, &pointsC, values ? &valuesC : NULL, offsets, PETSC_TRUE);
7276: if (NclC) {
7277: if (valCopy) DMRestoreWorkArray(dm, Ni*Ni, MPIU_SCALAR, &valCopy);
7278: for (f = 0; f < PetscMax(1, Nf); ++f) {
7279: if (Nf) PetscSectionRestoreFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f]);
7280: else PetscSectionRestorePointSyms(section, Ncl, points, &perms[f], &flips[f]);
7281: }
7282: for (f = 0; f < PetscMax(1, Nf); ++f) {
7283: if (Nf) PetscSectionGetFieldPointSyms(section, f, NclC, pointsC, &perms[f], &flips[f]);
7284: else PetscSectionGetPointSyms(section, NclC, pointsC, &perms[f], &flips[f]);
7285: }
7286: DMPlexRestoreCompressedClosure(dm, section, point, &Ncl, &points, &clSection, &clPoints, &clp);
7287: Ncl = NclC;
7288: Ni = NiC;
7289: points = pointsC;
7290: if (values) *values = valuesC;
7291: }
7292: /* 5) Calculate indices */
7293: DMGetWorkArray(dm, Ni, MPIU_INT, &idx);
7294: if (Nf) {
7295: PetscInt idxOff;
7296: PetscBool useFieldOffsets;
7298: if (outOffsets) {for (f = 0; f <= Nf; f++) outOffsets[f] = offsets[f];}
7299: PetscSectionGetUseFieldOffsets(idxSection, &useFieldOffsets);
7300: if (useFieldOffsets) {
7301: for (p = 0; p < Ncl; ++p) {
7302: const PetscInt pnt = points[p*2];
7304: DMPlexGetIndicesPointFieldsSplit_Internal(section, idxSection, pnt, offsets, perms, p, clperm, idx);
7305: }
7306: } else {
7307: for (p = 0; p < Ncl; ++p) {
7308: const PetscInt pnt = points[p*2];
7310: PetscSectionGetOffset(idxSection, pnt, &idxOff);
7311: /* Note that we pass a local section even though we're using global offsets. This is because global sections do
7312: * not (at the time of this writing) have fields set. They probably should, in which case we would pass the
7313: * global section. */
7314: DMPlexGetIndicesPointFields_Internal(section, isLocal, pnt, idxOff < 0 ? -(idxOff+1) : idxOff, offsets, PETSC_FALSE, perms, p, clperm, idx);
7315: }
7316: }
7317: } else {
7318: PetscInt off = 0, idxOff;
7320: for (p = 0; p < Ncl; ++p) {
7321: const PetscInt pnt = points[p*2];
7322: const PetscInt *perm = perms[0] ? perms[0][p] : NULL;
7324: PetscSectionGetOffset(idxSection, pnt, &idxOff);
7325: /* Note that we pass a local section even though we're using global offsets. This is because global sections do
7326: * not (at the time of this writing) have fields set. They probably should, in which case we would pass the global section. */
7327: DMPlexGetIndicesPoint_Internal(section, isLocal, pnt, idxOff < 0 ? -(idxOff+1) : idxOff, &off, PETSC_FALSE, perm, clperm, idx);
7328: }
7329: }
7330: /* 6) Cleanup */
7331: for (f = 0; f < PetscMax(1, Nf); ++f) {
7332: if (Nf) PetscSectionRestoreFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f]);
7333: else PetscSectionRestorePointSyms(section, Ncl, points, &perms[f], &flips[f]);
7334: }
7335: if (NclC) {
7336: DMRestoreWorkArray(dm, NclC*2, MPIU_INT, &pointsC);
7337: } else {
7338: DMPlexRestoreCompressedClosure(dm, section, point, &Ncl, &points, &clSection, &clPoints, &clp);
7339: }
7341: if (numIndices) *numIndices = Ni;
7342: if (indices) *indices = idx;
7343: return 0;
7344: }
7346: /*@C
7347: DMPlexRestoreClosureIndices - Restores the global dof indices associated with the closure of the given point within the provided sections.
7349: Not collective
7351: Input Parameters:
7352: + dm - The DM
7353: . section - The PetscSection describing the points (a local section)
7354: . idxSection - The PetscSection from which to obtain indices (may be local or global)
7355: . point - The point defining the closure
7356: - useClPerm - Use the closure point permutation if available
7358: Output Parameters:
7359: + numIndices - The number of dof indices in the closure of point with the input sections
7360: . indices - The dof indices
7361: . outOffsets - Array to write the field offsets into, or NULL
7362: - values - The input values, which may be modified if sign flips are induced by the point symmetries, or NULL
7364: Notes:
7365: If values were modified, the user is responsible for calling DMRestoreWorkArray(dm, 0, MPIU_SCALAR, &values).
7367: If idxSection is global, any constrained dofs (see DMAddBoundary(), for example) will get negative indices. The value
7368: of those indices is not significant. If idxSection is local, the constrained dofs will yield the involution -(idx+1)
7369: of their index in a local vector. A caller who does not wish to distinguish those points may recover the nonnegative
7370: indices via involution, -(-(idx+1)+1)==idx. Local indices are provided when idxSection == section, otherwise global
7371: indices (with the above semantics) are implied.
7373: Level: advanced
7375: .seealso DMPlexGetClosureIndices(), DMPlexVecGetClosure(), DMPlexMatSetClosure(), DMGetLocalSection(), DMGetGlobalSection()
7376: @*/
7377: PetscErrorCode DMPlexRestoreClosureIndices(DM dm, PetscSection section, PetscSection idxSection, PetscInt point, PetscBool useClPerm,
7378: PetscInt *numIndices, PetscInt *indices[], PetscInt outOffsets[], PetscScalar *values[])
7379: {
7382: DMRestoreWorkArray(dm, 0, MPIU_INT, indices);
7383: return 0;
7384: }
7386: /*@C
7387: DMPlexMatSetClosure - Set an array of the values on the closure of 'point'
7389: Not collective
7391: Input Parameters:
7392: + dm - The DM
7393: . section - The section describing the layout in v, or NULL to use the default section
7394: . globalSection - The section describing the layout in v, or NULL to use the default global section
7395: . A - The matrix
7396: . point - The point in the DM
7397: . values - The array of values
7398: - mode - The insert mode, where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions
7400: Fortran Notes:
7401: This routine is only available in Fortran 90, and you must include petsc.h90 in your code.
7403: Level: intermediate
7405: .seealso DMPlexMatSetClosureGeneral(), DMPlexVecGetClosure(), DMPlexVecSetClosure()
7406: @*/
7407: PetscErrorCode DMPlexMatSetClosure(DM dm, PetscSection section, PetscSection globalSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode)
7408: {
7409: DM_Plex *mesh = (DM_Plex*) dm->data;
7410: PetscInt *indices;
7411: PetscInt numIndices;
7412: const PetscScalar *valuesOrig = values;
7413: PetscErrorCode ierr;
7416: if (!section) DMGetLocalSection(dm, §ion);
7418: if (!globalSection) DMGetGlobalSection(dm, &globalSection);
7422: DMPlexGetClosureIndices(dm, section, globalSection, point, PETSC_TRUE, &numIndices, &indices, NULL, (PetscScalar **) &values);
7424: if (mesh->printSetValues) DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndices, indices, 0, NULL, values);
7425: MatSetValues(A, numIndices, indices, numIndices, indices, values, mode);
7426: if (ierr) {
7427: PetscMPIInt rank;
7429: MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);
7430: (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);
7431: DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndices, indices, 0, NULL, values);
7432: DMPlexRestoreClosureIndices(dm, section, globalSection, point, PETSC_TRUE, &numIndices, &indices, NULL, (PetscScalar **) &values);
7433: if (values != valuesOrig) DMRestoreWorkArray(dm, 0, MPIU_SCALAR, &values);
7434: SETERRQ(PetscObjectComm((PetscObject)dm),ierr,"Not possible to set matrix values");
7435: }
7436: if (mesh->printFEM > 1) {
7437: PetscInt i;
7438: PetscPrintf(PETSC_COMM_SELF, " Indices:");
7439: for (i = 0; i < numIndices; ++i) PetscPrintf(PETSC_COMM_SELF, " %D", indices[i]);
7440: PetscPrintf(PETSC_COMM_SELF, "\n");
7441: }
7443: DMPlexRestoreClosureIndices(dm, section, globalSection, point, PETSC_TRUE, &numIndices, &indices, NULL, (PetscScalar **) &values);
7444: if (values != valuesOrig) DMRestoreWorkArray(dm, 0, MPIU_SCALAR, &values);
7445: return 0;
7446: }
7448: /*@C
7449: DMPlexMatSetClosure - Set an array of the values on the closure of 'point' using a different row and column section
7451: Not collective
7453: Input Parameters:
7454: + dmRow - The DM for the row fields
7455: . sectionRow - The section describing the layout, or NULL to use the default section in dmRow
7456: . globalSectionRow - The section describing the layout, or NULL to use the default global section in dmRow
7457: . dmCol - The DM for the column fields
7458: . sectionCol - The section describing the layout, or NULL to use the default section in dmCol
7459: . globalSectionCol - The section describing the layout, or NULL to use the default global section in dmCol
7460: . A - The matrix
7461: . point - The point in the DMs
7462: . values - The array of values
7463: - mode - The insert mode, where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions
7465: Level: intermediate
7467: .seealso DMPlexMatSetClosure(), DMPlexVecGetClosure(), DMPlexVecSetClosure()
7468: @*/
7469: PetscErrorCode DMPlexMatSetClosureGeneral(DM dmRow, PetscSection sectionRow, PetscSection globalSectionRow, DM dmCol, PetscSection sectionCol, PetscSection globalSectionCol, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode)
7470: {
7471: DM_Plex *mesh = (DM_Plex*) dmRow->data;
7472: PetscInt *indicesRow, *indicesCol;
7473: PetscInt numIndicesRow, numIndicesCol;
7474: const PetscScalar *valuesOrig = values;
7475: PetscErrorCode ierr;
7478: if (!sectionRow) DMGetLocalSection(dmRow, §ionRow);
7480: if (!globalSectionRow) DMGetGlobalSection(dmRow, &globalSectionRow);
7483: if (!sectionCol) DMGetLocalSection(dmCol, §ionCol);
7485: if (!globalSectionCol) DMGetGlobalSection(dmCol, &globalSectionCol);
7489: DMPlexGetClosureIndices(dmRow, sectionRow, globalSectionRow, point, PETSC_TRUE, &numIndicesRow, &indicesRow, NULL, (PetscScalar **) &values);
7490: DMPlexGetClosureIndices(dmCol, sectionCol, globalSectionCol, point, PETSC_TRUE, &numIndicesCol, &indicesCol, NULL, (PetscScalar **) &values);
7492: if (mesh->printSetValues) DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values);
7493: MatSetValues(A, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values, mode);
7494: if (ierr) {
7495: PetscMPIInt rank;
7497: MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);
7498: (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);
7499: DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values);
7500: DMPlexRestoreClosureIndices(dmRow, sectionRow, globalSectionRow, point, PETSC_TRUE, &numIndicesRow, &indicesRow, NULL, (PetscScalar **) &values);
7501: DMPlexRestoreClosureIndices(dmCol, sectionCol, globalSectionCol, point, PETSC_TRUE, &numIndicesCol, &indicesRow, NULL, (PetscScalar **) &values);
7502: if (values != valuesOrig) DMRestoreWorkArray(dmRow, 0, MPIU_SCALAR, &values);
7503: ierr;
7504: }
7506: DMPlexRestoreClosureIndices(dmRow, sectionRow, globalSectionRow, point, PETSC_TRUE, &numIndicesRow, &indicesRow, NULL, (PetscScalar **) &values);
7507: DMPlexRestoreClosureIndices(dmCol, sectionCol, globalSectionCol, point, PETSC_TRUE, &numIndicesCol, &indicesCol, NULL, (PetscScalar **) &values);
7508: if (values != valuesOrig) DMRestoreWorkArray(dmRow, 0, MPIU_SCALAR, &values);
7509: return 0;
7510: }
7512: PetscErrorCode DMPlexMatSetClosureRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode)
7513: {
7514: DM_Plex *mesh = (DM_Plex*) dmf->data;
7515: PetscInt *fpoints = NULL, *ftotpoints = NULL;
7516: PetscInt *cpoints = NULL;
7517: PetscInt *findices, *cindices;
7518: const PetscInt *fclperm = NULL, *cclperm = NULL; /* Closure permutations cannot work here */
7519: PetscInt foffsets[32], coffsets[32];
7520: DMPolytopeType ct;
7521: PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f;
7522: PetscErrorCode ierr;
7526: if (!fsection) DMGetLocalSection(dmf, &fsection);
7528: if (!csection) DMGetLocalSection(dmc, &csection);
7530: if (!globalFSection) DMGetGlobalSection(dmf, &globalFSection);
7532: if (!globalCSection) DMGetGlobalSection(dmc, &globalCSection);
7535: PetscSectionGetNumFields(fsection, &numFields);
7537: PetscArrayzero(foffsets, 32);
7538: PetscArrayzero(coffsets, 32);
7539: /* Column indices */
7540: DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);
7541: maxFPoints = numCPoints;
7542: /* Compress out points not in the section */
7543: /* TODO: Squeeze out points with 0 dof as well */
7544: PetscSectionGetChart(csection, &pStart, &pEnd);
7545: for (p = 0, q = 0; p < numCPoints*2; p += 2) {
7546: if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) {
7547: cpoints[q*2] = cpoints[p];
7548: cpoints[q*2+1] = cpoints[p+1];
7549: ++q;
7550: }
7551: }
7552: numCPoints = q;
7553: for (p = 0, numCIndices = 0; p < numCPoints*2; p += 2) {
7554: PetscInt fdof;
7556: PetscSectionGetDof(csection, cpoints[p], &dof);
7557: if (!dof) continue;
7558: for (f = 0; f < numFields; ++f) {
7559: PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof);
7560: coffsets[f+1] += fdof;
7561: }
7562: numCIndices += dof;
7563: }
7564: for (f = 1; f < numFields; ++f) coffsets[f+1] += coffsets[f];
7565: /* Row indices */
7566: DMPlexGetCellType(dmc, point, &ct);
7567: {
7568: DMPlexTransform tr;
7569: DMPolytopeType *rct;
7570: PetscInt *rsize, *rcone, *rornt, Nt;
7572: DMPlexTransformCreate(PETSC_COMM_SELF, &tr);
7573: DMPlexTransformSetType(tr, DMPLEXREFINEREGULAR);
7574: DMPlexTransformCellTransform(tr, ct, point, NULL, &Nt, &rct, &rsize, &rcone, &rornt);
7575: numSubcells = rsize[Nt-1];
7576: DMPlexTransformDestroy(&tr);
7577: }
7578: DMGetWorkArray(dmf, maxFPoints*2*numSubcells, MPIU_INT, &ftotpoints);
7579: for (r = 0, q = 0; r < numSubcells; ++r) {
7580: /* TODO Map from coarse to fine cells */
7581: DMPlexGetTransitiveClosure(dmf, point*numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints);
7582: /* Compress out points not in the section */
7583: PetscSectionGetChart(fsection, &pStart, &pEnd);
7584: for (p = 0; p < numFPoints*2; p += 2) {
7585: if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) {
7586: PetscSectionGetDof(fsection, fpoints[p], &dof);
7587: if (!dof) continue;
7588: for (s = 0; s < q; ++s) if (fpoints[p] == ftotpoints[s*2]) break;
7589: if (s < q) continue;
7590: ftotpoints[q*2] = fpoints[p];
7591: ftotpoints[q*2+1] = fpoints[p+1];
7592: ++q;
7593: }
7594: }
7595: DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints);
7596: }
7597: numFPoints = q;
7598: for (p = 0, numFIndices = 0; p < numFPoints*2; p += 2) {
7599: PetscInt fdof;
7601: PetscSectionGetDof(fsection, ftotpoints[p], &dof);
7602: if (!dof) continue;
7603: for (f = 0; f < numFields; ++f) {
7604: PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof);
7605: foffsets[f+1] += fdof;
7606: }
7607: numFIndices += dof;
7608: }
7609: for (f = 1; f < numFields; ++f) foffsets[f+1] += foffsets[f];
7613: DMGetWorkArray(dmf, numFIndices, MPIU_INT, &findices);
7614: DMGetWorkArray(dmc, numCIndices, MPIU_INT, &cindices);
7615: if (numFields) {
7616: const PetscInt **permsF[32] = {NULL};
7617: const PetscInt **permsC[32] = {NULL};
7619: for (f = 0; f < numFields; f++) {
7620: PetscSectionGetFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);
7621: PetscSectionGetFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);
7622: }
7623: for (p = 0; p < numFPoints; p++) {
7624: PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);
7625: DMPlexGetIndicesPointFields_Internal(fsection, PETSC_FALSE, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices);
7626: }
7627: for (p = 0; p < numCPoints; p++) {
7628: PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);
7629: DMPlexGetIndicesPointFields_Internal(csection, PETSC_FALSE, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices);
7630: }
7631: for (f = 0; f < numFields; f++) {
7632: PetscSectionRestoreFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);
7633: PetscSectionRestoreFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);
7634: }
7635: } else {
7636: const PetscInt **permsF = NULL;
7637: const PetscInt **permsC = NULL;
7639: PetscSectionGetPointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);
7640: PetscSectionGetPointSyms(csection,numCPoints,cpoints,&permsC,NULL);
7641: for (p = 0, off = 0; p < numFPoints; p++) {
7642: const PetscInt *perm = permsF ? permsF[p] : NULL;
7644: PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);
7645: DMPlexGetIndicesPoint_Internal(fsection, PETSC_FALSE, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices);
7646: }
7647: for (p = 0, off = 0; p < numCPoints; p++) {
7648: const PetscInt *perm = permsC ? permsC[p] : NULL;
7650: PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);
7651: DMPlexGetIndicesPoint_Internal(csection, PETSC_FALSE, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices);
7652: }
7653: PetscSectionRestorePointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);
7654: PetscSectionRestorePointSyms(csection,numCPoints,cpoints,&permsC,NULL);
7655: }
7656: if (mesh->printSetValues) DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numFIndices, findices, numCIndices, cindices, values);
7657: /* TODO: flips */
7658: MatSetValues(A, numFIndices, findices, numCIndices, cindices, values, mode);
7659: if (ierr) {
7660: PetscMPIInt rank;
7662: MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);
7663: (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);
7664: DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numFIndices, findices, numCIndices, cindices, values);
7665: DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices);
7666: DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices);
7667: ierr;
7668: }
7669: DMRestoreWorkArray(dmf, numCPoints*2*4, MPIU_INT, &ftotpoints);
7670: DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);
7671: DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices);
7672: DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices);
7673: return 0;
7674: }
7676: PetscErrorCode DMPlexMatGetClosureIndicesRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, PetscInt point, PetscInt cindices[], PetscInt findices[])
7677: {
7678: PetscInt *fpoints = NULL, *ftotpoints = NULL;
7679: PetscInt *cpoints = NULL;
7680: PetscInt foffsets[32], coffsets[32];
7681: const PetscInt *fclperm = NULL, *cclperm = NULL; /* Closure permutations cannot work here */
7682: DMPolytopeType ct;
7683: PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f;
7687: if (!fsection) DMGetLocalSection(dmf, &fsection);
7689: if (!csection) DMGetLocalSection(dmc, &csection);
7691: if (!globalFSection) DMGetGlobalSection(dmf, &globalFSection);
7693: if (!globalCSection) DMGetGlobalSection(dmc, &globalCSection);
7695: PetscSectionGetNumFields(fsection, &numFields);
7697: PetscArrayzero(foffsets, 32);
7698: PetscArrayzero(coffsets, 32);
7699: /* Column indices */
7700: DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);
7701: maxFPoints = numCPoints;
7702: /* Compress out points not in the section */
7703: /* TODO: Squeeze out points with 0 dof as well */
7704: PetscSectionGetChart(csection, &pStart, &pEnd);
7705: for (p = 0, q = 0; p < numCPoints*2; p += 2) {
7706: if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) {
7707: cpoints[q*2] = cpoints[p];
7708: cpoints[q*2+1] = cpoints[p+1];
7709: ++q;
7710: }
7711: }
7712: numCPoints = q;
7713: for (p = 0, numCIndices = 0; p < numCPoints*2; p += 2) {
7714: PetscInt fdof;
7716: PetscSectionGetDof(csection, cpoints[p], &dof);
7717: if (!dof) continue;
7718: for (f = 0; f < numFields; ++f) {
7719: PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof);
7720: coffsets[f+1] += fdof;
7721: }
7722: numCIndices += dof;
7723: }
7724: for (f = 1; f < numFields; ++f) coffsets[f+1] += coffsets[f];
7725: /* Row indices */
7726: DMPlexGetCellType(dmc, point, &ct);
7727: {
7728: DMPlexTransform tr;
7729: DMPolytopeType *rct;
7730: PetscInt *rsize, *rcone, *rornt, Nt;
7732: DMPlexTransformCreate(PETSC_COMM_SELF, &tr);
7733: DMPlexTransformSetType(tr, DMPLEXREFINEREGULAR);
7734: DMPlexTransformCellTransform(tr, ct, point, NULL, &Nt, &rct, &rsize, &rcone, &rornt);
7735: numSubcells = rsize[Nt-1];
7736: DMPlexTransformDestroy(&tr);
7737: }
7738: DMGetWorkArray(dmf, maxFPoints*2*numSubcells, MPIU_INT, &ftotpoints);
7739: for (r = 0, q = 0; r < numSubcells; ++r) {
7740: /* TODO Map from coarse to fine cells */
7741: DMPlexGetTransitiveClosure(dmf, point*numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints);
7742: /* Compress out points not in the section */
7743: PetscSectionGetChart(fsection, &pStart, &pEnd);
7744: for (p = 0; p < numFPoints*2; p += 2) {
7745: if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) {
7746: PetscSectionGetDof(fsection, fpoints[p], &dof);
7747: if (!dof) continue;
7748: for (s = 0; s < q; ++s) if (fpoints[p] == ftotpoints[s*2]) break;
7749: if (s < q) continue;
7750: ftotpoints[q*2] = fpoints[p];
7751: ftotpoints[q*2+1] = fpoints[p+1];
7752: ++q;
7753: }
7754: }
7755: DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints);
7756: }
7757: numFPoints = q;
7758: for (p = 0, numFIndices = 0; p < numFPoints*2; p += 2) {
7759: PetscInt fdof;
7761: PetscSectionGetDof(fsection, ftotpoints[p], &dof);
7762: if (!dof) continue;
7763: for (f = 0; f < numFields; ++f) {
7764: PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof);
7765: foffsets[f+1] += fdof;
7766: }
7767: numFIndices += dof;
7768: }
7769: for (f = 1; f < numFields; ++f) foffsets[f+1] += foffsets[f];
7773: if (numFields) {
7774: const PetscInt **permsF[32] = {NULL};
7775: const PetscInt **permsC[32] = {NULL};
7777: for (f = 0; f < numFields; f++) {
7778: PetscSectionGetFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);
7779: PetscSectionGetFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);
7780: }
7781: for (p = 0; p < numFPoints; p++) {
7782: PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);
7783: DMPlexGetIndicesPointFields_Internal(fsection, PETSC_FALSE, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices);
7784: }
7785: for (p = 0; p < numCPoints; p++) {
7786: PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);
7787: DMPlexGetIndicesPointFields_Internal(csection, PETSC_FALSE, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices);
7788: }
7789: for (f = 0; f < numFields; f++) {
7790: PetscSectionRestoreFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);
7791: PetscSectionRestoreFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);
7792: }
7793: } else {
7794: const PetscInt **permsF = NULL;
7795: const PetscInt **permsC = NULL;
7797: PetscSectionGetPointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);
7798: PetscSectionGetPointSyms(csection,numCPoints,cpoints,&permsC,NULL);
7799: for (p = 0, off = 0; p < numFPoints; p++) {
7800: const PetscInt *perm = permsF ? permsF[p] : NULL;
7802: PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);
7803: DMPlexGetIndicesPoint_Internal(fsection, PETSC_FALSE, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices);
7804: }
7805: for (p = 0, off = 0; p < numCPoints; p++) {
7806: const PetscInt *perm = permsC ? permsC[p] : NULL;
7808: PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);
7809: DMPlexGetIndicesPoint_Internal(csection, PETSC_FALSE, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices);
7810: }
7811: PetscSectionRestorePointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);
7812: PetscSectionRestorePointSyms(csection,numCPoints,cpoints,&permsC,NULL);
7813: }
7814: DMRestoreWorkArray(dmf, numCPoints*2*4, MPIU_INT, &ftotpoints);
7815: DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);
7816: return 0;
7817: }
7819: /*@C
7820: DMPlexGetVTKCellHeight - Returns the height in the DAG used to determine which points are cells (normally 0)
7822: Input Parameter:
7823: . dm - The DMPlex object
7825: Output Parameter:
7826: . cellHeight - The height of a cell
7828: Level: developer
7830: .seealso DMPlexSetVTKCellHeight()
7831: @*/
7832: PetscErrorCode DMPlexGetVTKCellHeight(DM dm, PetscInt *cellHeight)
7833: {
7834: DM_Plex *mesh = (DM_Plex*) dm->data;
7838: *cellHeight = mesh->vtkCellHeight;
7839: return 0;
7840: }
7842: /*@C
7843: DMPlexSetVTKCellHeight - Sets the height in the DAG used to determine which points are cells (normally 0)
7845: Input Parameters:
7846: + dm - The DMPlex object
7847: - cellHeight - The height of a cell
7849: Level: developer
7851: .seealso DMPlexGetVTKCellHeight()
7852: @*/
7853: PetscErrorCode DMPlexSetVTKCellHeight(DM dm, PetscInt cellHeight)
7854: {
7855: DM_Plex *mesh = (DM_Plex*) dm->data;
7858: mesh->vtkCellHeight = cellHeight;
7859: return 0;
7860: }
7862: /*@
7863: DMPlexGetGhostCellStratum - Get the range of cells which are used to enforce FV boundary conditions
7865: Input Parameter:
7866: . dm - The DMPlex object
7868: Output Parameters:
7869: + gcStart - The first ghost cell, or NULL
7870: - gcEnd - The upper bound on ghost cells, or NULL
7872: Level: advanced
7874: .seealso DMPlexConstructGhostCells(), DMPlexGetGhostCellStratum()
7875: @*/
7876: PetscErrorCode DMPlexGetGhostCellStratum(DM dm, PetscInt *gcStart, PetscInt *gcEnd)
7877: {
7878: DMLabel ctLabel;
7881: DMPlexGetCellTypeLabel(dm, &ctLabel);
7882: DMLabelGetStratumBounds(ctLabel, DM_POLYTOPE_FV_GHOST, gcStart, gcEnd);
7883: return 0;
7884: }
7886: PetscErrorCode DMPlexCreateNumbering_Plex(DM dm, PetscInt pStart, PetscInt pEnd, PetscInt shift, PetscInt *globalSize, PetscSF sf, IS *numbering)
7887: {
7888: PetscSection section, globalSection;
7889: PetscInt *numbers, p;
7891: PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion);
7892: PetscSectionSetChart(section, pStart, pEnd);
7893: for (p = pStart; p < pEnd; ++p) {
7894: PetscSectionSetDof(section, p, 1);
7895: }
7896: PetscSectionSetUp(section);
7897: PetscSectionCreateGlobalSection(section, sf, PETSC_FALSE, PETSC_FALSE, &globalSection);
7898: PetscMalloc1(pEnd - pStart, &numbers);
7899: for (p = pStart; p < pEnd; ++p) {
7900: PetscSectionGetOffset(globalSection, p, &numbers[p-pStart]);
7901: if (numbers[p-pStart] < 0) numbers[p-pStart] -= shift;
7902: else numbers[p-pStart] += shift;
7903: }
7904: ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd - pStart, numbers, PETSC_OWN_POINTER, numbering);
7905: if (globalSize) {
7906: PetscLayout layout;
7907: PetscSectionGetPointLayout(PetscObjectComm((PetscObject) dm), globalSection, &layout);
7908: PetscLayoutGetSize(layout, globalSize);
7909: PetscLayoutDestroy(&layout);
7910: }
7911: PetscSectionDestroy(§ion);
7912: PetscSectionDestroy(&globalSection);
7913: return 0;
7914: }
7916: PetscErrorCode DMPlexCreateCellNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalCellNumbers)
7917: {
7918: PetscInt cellHeight, cStart, cEnd;
7920: DMPlexGetVTKCellHeight(dm, &cellHeight);
7921: if (includeHybrid) DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
7922: else DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);
7923: DMPlexCreateNumbering_Plex(dm, cStart, cEnd, 0, NULL, dm->sf, globalCellNumbers);
7924: return 0;
7925: }
7927: /*@
7928: DMPlexGetCellNumbering - Get a global cell numbering for all cells on this process
7930: Input Parameter:
7931: . dm - The DMPlex object
7933: Output Parameter:
7934: . globalCellNumbers - Global cell numbers for all cells on this process
7936: Level: developer
7938: .seealso DMPlexGetVertexNumbering()
7939: @*/
7940: PetscErrorCode DMPlexGetCellNumbering(DM dm, IS *globalCellNumbers)
7941: {
7942: DM_Plex *mesh = (DM_Plex*) dm->data;
7945: if (!mesh->globalCellNumbers) DMPlexCreateCellNumbering_Internal(dm, PETSC_FALSE, &mesh->globalCellNumbers);
7946: *globalCellNumbers = mesh->globalCellNumbers;
7947: return 0;
7948: }
7950: PetscErrorCode DMPlexCreateVertexNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalVertexNumbers)
7951: {
7952: PetscInt vStart, vEnd;
7955: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
7956: DMPlexCreateNumbering_Plex(dm, vStart, vEnd, 0, NULL, dm->sf, globalVertexNumbers);
7957: return 0;
7958: }
7960: /*@
7961: DMPlexGetVertexNumbering - Get a global vertex numbering for all vertices on this process
7963: Input Parameter:
7964: . dm - The DMPlex object
7966: Output Parameter:
7967: . globalVertexNumbers - Global vertex numbers for all vertices on this process
7969: Level: developer
7971: .seealso DMPlexGetCellNumbering()
7972: @*/
7973: PetscErrorCode DMPlexGetVertexNumbering(DM dm, IS *globalVertexNumbers)
7974: {
7975: DM_Plex *mesh = (DM_Plex*) dm->data;
7978: if (!mesh->globalVertexNumbers) DMPlexCreateVertexNumbering_Internal(dm, PETSC_FALSE, &mesh->globalVertexNumbers);
7979: *globalVertexNumbers = mesh->globalVertexNumbers;
7980: return 0;
7981: }
7983: /*@
7984: DMPlexCreatePointNumbering - Create a global numbering for all points on this process
7986: Input Parameter:
7987: . dm - The DMPlex object
7989: Output Parameter:
7990: . globalPointNumbers - Global numbers for all points on this process
7992: Level: developer
7994: .seealso DMPlexGetCellNumbering()
7995: @*/
7996: PetscErrorCode DMPlexCreatePointNumbering(DM dm, IS *globalPointNumbers)
7997: {
7998: IS nums[4];
7999: PetscInt depths[4], gdepths[4], starts[4];
8000: PetscInt depth, d, shift = 0;
8003: DMPlexGetDepth(dm, &depth);
8004: /* For unstratified meshes use dim instead of depth */
8005: if (depth < 0) DMGetDimension(dm, &depth);
8006: for (d = 0; d <= depth; ++d) {
8007: PetscInt end;
8009: depths[d] = depth-d;
8010: DMPlexGetDepthStratum(dm, depths[d], &starts[d], &end);
8011: if (!(starts[d]-end)) { starts[d] = depths[d] = -1; }
8012: }
8013: PetscSortIntWithArray(depth+1, starts, depths);
8014: MPIU_Allreduce(depths, gdepths, depth+1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));
8015: for (d = 0; d <= depth; ++d) {
8017: }
8018: for (d = 0; d <= depth; ++d) {
8019: PetscInt pStart, pEnd, gsize;
8021: DMPlexGetDepthStratum(dm, gdepths[d], &pStart, &pEnd);
8022: DMPlexCreateNumbering_Plex(dm, pStart, pEnd, shift, &gsize, dm->sf, &nums[d]);
8023: shift += gsize;
8024: }
8025: ISConcatenate(PetscObjectComm((PetscObject) dm), depth+1, nums, globalPointNumbers);
8026: for (d = 0; d <= depth; ++d) ISDestroy(&nums[d]);
8027: return 0;
8028: }
8030: /*@
8031: DMPlexCreateRankField - Create a cell field whose value is the rank of the owner
8033: Input Parameter:
8034: . dm - The DMPlex object
8036: Output Parameter:
8037: . ranks - The rank field
8039: Options Database Keys:
8040: . -dm_partition_view - Adds the rank field into the DM output from -dm_view using the same viewer
8042: Level: intermediate
8044: .seealso: DMView()
8045: @*/
8046: PetscErrorCode DMPlexCreateRankField(DM dm, Vec *ranks)
8047: {
8048: DM rdm;
8049: PetscFE fe;
8050: PetscScalar *r;
8051: PetscMPIInt rank;
8052: DMPolytopeType ct;
8053: PetscInt dim, cStart, cEnd, c;
8054: PetscBool simplex;
8059: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
8060: DMClone(dm, &rdm);
8061: DMGetDimension(rdm, &dim);
8062: DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd);
8063: DMPlexGetCellType(dm, cStart, &ct);
8064: simplex = DMPolytopeTypeGetNumVertices(ct) == DMPolytopeTypeGetDim(ct)+1 ? PETSC_TRUE : PETSC_FALSE;
8065: PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, simplex, "PETSc___rank_", -1, &fe);
8066: PetscObjectSetName((PetscObject) fe, "rank");
8067: DMSetField(rdm, 0, NULL, (PetscObject) fe);
8068: PetscFEDestroy(&fe);
8069: DMCreateDS(rdm);
8070: DMCreateGlobalVector(rdm, ranks);
8071: PetscObjectSetName((PetscObject) *ranks, "partition");
8072: VecGetArray(*ranks, &r);
8073: for (c = cStart; c < cEnd; ++c) {
8074: PetscScalar *lr;
8076: DMPlexPointGlobalRef(rdm, c, r, &lr);
8077: if (lr) *lr = rank;
8078: }
8079: VecRestoreArray(*ranks, &r);
8080: DMDestroy(&rdm);
8081: return 0;
8082: }
8084: /*@
8085: DMPlexCreateLabelField - Create a cell field whose value is the label value for that cell
8087: Input Parameters:
8088: + dm - The DMPlex
8089: - label - The DMLabel
8091: Output Parameter:
8092: . val - The label value field
8094: Options Database Keys:
8095: . -dm_label_view - Adds the label value field into the DM output from -dm_view using the same viewer
8097: Level: intermediate
8099: .seealso: DMView()
8100: @*/
8101: PetscErrorCode DMPlexCreateLabelField(DM dm, DMLabel label, Vec *val)
8102: {
8103: DM rdm;
8104: PetscFE fe;
8105: PetscScalar *v;
8106: PetscInt dim, cStart, cEnd, c;
8112: DMClone(dm, &rdm);
8113: DMGetDimension(rdm, &dim);
8114: PetscFECreateDefault(PetscObjectComm((PetscObject) rdm), dim, 1, PETSC_TRUE, "PETSc___label_value_", -1, &fe);
8115: PetscObjectSetName((PetscObject) fe, "label_value");
8116: DMSetField(rdm, 0, NULL, (PetscObject) fe);
8117: PetscFEDestroy(&fe);
8118: DMCreateDS(rdm);
8119: DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd);
8120: DMCreateGlobalVector(rdm, val);
8121: PetscObjectSetName((PetscObject) *val, "label_value");
8122: VecGetArray(*val, &v);
8123: for (c = cStart; c < cEnd; ++c) {
8124: PetscScalar *lv;
8125: PetscInt cval;
8127: DMPlexPointGlobalRef(rdm, c, v, &lv);
8128: DMLabelGetValue(label, c, &cval);
8129: *lv = cval;
8130: }
8131: VecRestoreArray(*val, &v);
8132: DMDestroy(&rdm);
8133: return 0;
8134: }
8136: /*@
8137: DMPlexCheckSymmetry - Check that the adjacency information in the mesh is symmetric.
8139: Input Parameter:
8140: . dm - The DMPlex object
8142: Notes:
8143: This is a useful diagnostic when creating meshes programmatically.
8145: For the complete list of DMPlexCheck* functions, see DMSetFromOptions().
8147: Level: developer
8149: .seealso: DMCreate(), DMSetFromOptions()
8150: @*/
8151: PetscErrorCode DMPlexCheckSymmetry(DM dm)
8152: {
8153: PetscSection coneSection, supportSection;
8154: const PetscInt *cone, *support;
8155: PetscInt coneSize, c, supportSize, s;
8156: PetscInt pStart, pEnd, p, pp, csize, ssize;
8157: PetscBool storagecheck = PETSC_TRUE;
8160: DMViewFromOptions(dm, NULL, "-sym_dm_view");
8161: DMPlexGetConeSection(dm, &coneSection);
8162: DMPlexGetSupportSection(dm, &supportSection);
8163: /* Check that point p is found in the support of its cone points, and vice versa */
8164: DMPlexGetChart(dm, &pStart, &pEnd);
8165: for (p = pStart; p < pEnd; ++p) {
8166: DMPlexGetConeSize(dm, p, &coneSize);
8167: DMPlexGetCone(dm, p, &cone);
8168: for (c = 0; c < coneSize; ++c) {
8169: PetscBool dup = PETSC_FALSE;
8170: PetscInt d;
8171: for (d = c-1; d >= 0; --d) {
8172: if (cone[c] == cone[d]) {dup = PETSC_TRUE; break;}
8173: }
8174: DMPlexGetSupportSize(dm, cone[c], &supportSize);
8175: DMPlexGetSupport(dm, cone[c], &support);
8176: for (s = 0; s < supportSize; ++s) {
8177: if (support[s] == p) break;
8178: }
8179: if ((s >= supportSize) || (dup && (support[s+1] != p))) {
8180: PetscPrintf(PETSC_COMM_SELF, "p: %D cone: ", p);
8181: for (s = 0; s < coneSize; ++s) {
8182: PetscPrintf(PETSC_COMM_SELF, "%D, ", cone[s]);
8183: }
8184: PetscPrintf(PETSC_COMM_SELF, "\n");
8185: PetscPrintf(PETSC_COMM_SELF, "p: %D support: ", cone[c]);
8186: for (s = 0; s < supportSize; ++s) {
8187: PetscPrintf(PETSC_COMM_SELF, "%D, ", support[s]);
8188: }
8189: PetscPrintf(PETSC_COMM_SELF, "\n");
8191: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not found in support of cone point %D", p, cone[c]);
8192: }
8193: }
8194: DMPlexGetTreeParent(dm, p, &pp, NULL);
8195: if (p != pp) { storagecheck = PETSC_FALSE; continue; }
8196: DMPlexGetSupportSize(dm, p, &supportSize);
8197: DMPlexGetSupport(dm, p, &support);
8198: for (s = 0; s < supportSize; ++s) {
8199: DMPlexGetConeSize(dm, support[s], &coneSize);
8200: DMPlexGetCone(dm, support[s], &cone);
8201: for (c = 0; c < coneSize; ++c) {
8202: DMPlexGetTreeParent(dm, cone[c], &pp, NULL);
8203: if (cone[c] != pp) { c = 0; break; }
8204: if (cone[c] == p) break;
8205: }
8206: if (c >= coneSize) {
8207: PetscPrintf(PETSC_COMM_SELF, "p: %D support: ", p);
8208: for (c = 0; c < supportSize; ++c) {
8209: PetscPrintf(PETSC_COMM_SELF, "%D, ", support[c]);
8210: }
8211: PetscPrintf(PETSC_COMM_SELF, "\n");
8212: PetscPrintf(PETSC_COMM_SELF, "p: %D cone: ", support[s]);
8213: for (c = 0; c < coneSize; ++c) {
8214: PetscPrintf(PETSC_COMM_SELF, "%D, ", cone[c]);
8215: }
8216: PetscPrintf(PETSC_COMM_SELF, "\n");
8217: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not found in cone of support point %D", p, support[s]);
8218: }
8219: }
8220: }
8221: if (storagecheck) {
8222: PetscSectionGetStorageSize(coneSection, &csize);
8223: PetscSectionGetStorageSize(supportSection, &ssize);
8225: }
8226: return 0;
8227: }
8229: /*
8230: For submeshes with cohesive cells (see DMPlexConstructCohesiveCells()), we allow a special case where some of the boundary of a face (edges and vertices) are not duplicated. We call these special boundary points "unsplit", since the same edge or vertex appears in both copies of the face. These unsplit points throw off our counting, so we have to explicitly account for them here.
8231: */
8232: static PetscErrorCode DMPlexCellUnsplitVertices_Private(DM dm, PetscInt c, DMPolytopeType ct, PetscInt *unsplit)
8233: {
8234: DMPolytopeType cct;
8235: PetscInt ptpoints[4];
8236: const PetscInt *cone, *ccone, *ptcone;
8237: PetscInt coneSize, cp, cconeSize, ccp, npt = 0, pt;
8239: *unsplit = 0;
8240: switch (ct) {
8241: case DM_POLYTOPE_POINT_PRISM_TENSOR:
8242: ptpoints[npt++] = c;
8243: break;
8244: case DM_POLYTOPE_SEG_PRISM_TENSOR:
8245: DMPlexGetCone(dm, c, &cone);
8246: DMPlexGetConeSize(dm, c, &coneSize);
8247: for (cp = 0; cp < coneSize; ++cp) {
8248: DMPlexGetCellType(dm, cone[cp], &cct);
8249: if (cct == DM_POLYTOPE_POINT_PRISM_TENSOR) ptpoints[npt++] = cone[cp];
8250: }
8251: break;
8252: case DM_POLYTOPE_TRI_PRISM_TENSOR:
8253: case DM_POLYTOPE_QUAD_PRISM_TENSOR:
8254: DMPlexGetCone(dm, c, &cone);
8255: DMPlexGetConeSize(dm, c, &coneSize);
8256: for (cp = 0; cp < coneSize; ++cp) {
8257: DMPlexGetCone(dm, cone[cp], &ccone);
8258: DMPlexGetConeSize(dm, cone[cp], &cconeSize);
8259: for (ccp = 0; ccp < cconeSize; ++ccp) {
8260: DMPlexGetCellType(dm, ccone[ccp], &cct);
8261: if (cct == DM_POLYTOPE_POINT_PRISM_TENSOR) {
8262: PetscInt p;
8263: for (p = 0; p < npt; ++p) if (ptpoints[p] == ccone[ccp]) break;
8264: if (p == npt) ptpoints[npt++] = ccone[ccp];
8265: }
8266: }
8267: }
8268: break;
8269: default: break;
8270: }
8271: for (pt = 0; pt < npt; ++pt) {
8272: DMPlexGetCone(dm, ptpoints[pt], &ptcone);
8273: if (ptcone[0] == ptcone[1]) ++(*unsplit);
8274: }
8275: return 0;
8276: }
8278: /*@
8279: DMPlexCheckSkeleton - Check that each cell has the correct number of vertices
8281: Input Parameters:
8282: + dm - The DMPlex object
8283: - cellHeight - Normally 0
8285: Notes:
8286: This is a useful diagnostic when creating meshes programmatically.
8287: Currently applicable only to homogeneous simplex or tensor meshes.
8289: For the complete list of DMPlexCheck* functions, see DMSetFromOptions().
8291: Level: developer
8293: .seealso: DMCreate(), DMSetFromOptions()
8294: @*/
8295: PetscErrorCode DMPlexCheckSkeleton(DM dm, PetscInt cellHeight)
8296: {
8297: DMPlexInterpolatedFlag interp;
8298: DMPolytopeType ct;
8299: PetscInt vStart, vEnd, cStart, cEnd, c;
8302: DMPlexIsInterpolated(dm, &interp);
8303: DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
8304: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
8305: for (c = cStart; c < cEnd; ++c) {
8306: PetscInt *closure = NULL;
8307: PetscInt coneSize, closureSize, cl, Nv = 0;
8309: DMPlexGetCellType(dm, c, &ct);
8311: if (ct == DM_POLYTOPE_UNKNOWN) continue;
8312: if (interp == DMPLEX_INTERPOLATED_FULL) {
8313: DMPlexGetConeSize(dm, c, &coneSize);
8315: }
8316: DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
8317: for (cl = 0; cl < closureSize*2; cl += 2) {
8318: const PetscInt p = closure[cl];
8319: if ((p >= vStart) && (p < vEnd)) ++Nv;
8320: }
8321: DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
8322: /* Special Case: Tensor faces with identified vertices */
8323: if (Nv < DMPolytopeTypeGetNumVertices(ct)) {
8324: PetscInt unsplit;
8326: DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit);
8327: if (Nv + unsplit == DMPolytopeTypeGetNumVertices(ct)) continue;
8328: }
8330: }
8331: return 0;
8332: }
8334: /*@
8335: DMPlexCheckFaces - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type
8337: Not Collective
8339: Input Parameters:
8340: + dm - The DMPlex object
8341: - cellHeight - Normally 0
8343: Notes:
8344: This is a useful diagnostic when creating meshes programmatically.
8345: This routine is only relevant for meshes that are fully interpolated across all ranks.
8346: It will error out if a partially interpolated mesh is given on some rank.
8347: It will do nothing for locally uninterpolated mesh (as there is nothing to check).
8349: For the complete list of DMPlexCheck* functions, see DMSetFromOptions().
8351: Level: developer
8353: .seealso: DMCreate(), DMPlexGetVTKCellHeight(), DMSetFromOptions()
8354: @*/
8355: PetscErrorCode DMPlexCheckFaces(DM dm, PetscInt cellHeight)
8356: {
8357: PetscInt dim, depth, vStart, vEnd, cStart, cEnd, c, h;
8358: DMPlexInterpolatedFlag interpEnum;
8361: DMPlexIsInterpolated(dm, &interpEnum);
8362: if (interpEnum == DMPLEX_INTERPOLATED_NONE) return 0;
8363: if (interpEnum == DMPLEX_INTERPOLATED_PARTIAL) {
8364: PetscMPIInt rank;
8365: MPI_Comm comm;
8367: PetscObjectGetComm((PetscObject) dm, &comm);
8368: MPI_Comm_rank(comm, &rank);
8369: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Mesh is only partially interpolated on rank %d, this is currently not supported", rank);
8370: }
8372: DMGetDimension(dm, &dim);
8373: DMPlexGetDepth(dm, &depth);
8374: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
8375: for (h = cellHeight; h < PetscMin(depth, dim); ++h) {
8376: DMPlexGetHeightStratum(dm, h, &cStart, &cEnd);
8377: for (c = cStart; c < cEnd; ++c) {
8378: const PetscInt *cone, *ornt, *faceSizes, *faces;
8379: const DMPolytopeType *faceTypes;
8380: DMPolytopeType ct;
8381: PetscInt numFaces, coneSize, f;
8382: PetscInt *closure = NULL, closureSize, cl, numCorners = 0, fOff = 0, unsplit;
8384: DMPlexGetCellType(dm, c, &ct);
8385: DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit);
8386: if (unsplit) continue;
8387: DMPlexGetConeSize(dm, c, &coneSize);
8388: DMPlexGetCone(dm, c, &cone);
8389: DMPlexGetConeOrientation(dm, c, &ornt);
8390: DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
8391: for (cl = 0; cl < closureSize*2; cl += 2) {
8392: const PetscInt p = closure[cl];
8393: if ((p >= vStart) && (p < vEnd)) closure[numCorners++] = p;
8394: }
8395: DMPlexGetRawFaces_Internal(dm, ct, closure, &numFaces, &faceTypes, &faceSizes, &faces);
8397: for (f = 0; f < numFaces; ++f) {
8398: DMPolytopeType fct;
8399: PetscInt *fclosure = NULL, fclosureSize, cl, fnumCorners = 0, v;
8401: DMPlexGetCellType(dm, cone[f], &fct);
8402: DMPlexGetTransitiveClosure_Internal(dm, cone[f], ornt[f], PETSC_TRUE, &fclosureSize, &fclosure);
8403: for (cl = 0; cl < fclosureSize*2; cl += 2) {
8404: const PetscInt p = fclosure[cl];
8405: if ((p >= vStart) && (p < vEnd)) fclosure[fnumCorners++] = p;
8406: }
8408: for (v = 0; v < fnumCorners; ++v) {
8409: if (fclosure[v] != faces[fOff+v]) {
8410: PetscInt v1;
8412: PetscPrintf(PETSC_COMM_SELF, "face closure:");
8413: for (v1 = 0; v1 < fnumCorners; ++v1) PetscPrintf(PETSC_COMM_SELF, " %D", fclosure[v1]);
8414: PetscPrintf(PETSC_COMM_SELF, "\ncell face:");
8415: for (v1 = 0; v1 < fnumCorners; ++v1) PetscPrintf(PETSC_COMM_SELF, " %D", faces[fOff+v1]);
8416: PetscPrintf(PETSC_COMM_SELF, "\n");
8417: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D of type %s (cone idx %d, ornt %D) of cell %D of type %s vertex %D, %D != %D", cone[f], DMPolytopeTypes[fct], f, ornt[f], c, DMPolytopeTypes[ct], v, fclosure[v], faces[fOff+v]);
8418: }
8419: }
8420: DMPlexRestoreTransitiveClosure(dm, cone[f], PETSC_TRUE, &fclosureSize, &fclosure);
8421: fOff += faceSizes[f];
8422: }
8423: DMPlexRestoreRawFaces_Internal(dm, ct, closure, &numFaces, &faceTypes, &faceSizes, &faces);
8424: DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
8425: }
8426: }
8427: return 0;
8428: }
8430: /*@
8431: DMPlexCheckGeometry - Check the geometry of mesh cells
8433: Input Parameter:
8434: . dm - The DMPlex object
8436: Notes:
8437: This is a useful diagnostic when creating meshes programmatically.
8439: For the complete list of DMPlexCheck* functions, see DMSetFromOptions().
8441: Level: developer
8443: .seealso: DMCreate(), DMSetFromOptions()
8444: @*/
8445: PetscErrorCode DMPlexCheckGeometry(DM dm)
8446: {
8447: Vec coordinates;
8448: PetscReal detJ, J[9], refVol = 1.0;
8449: PetscReal vol;
8450: PetscBool periodic;
8451: PetscInt dim, depth, dE, d, cStart, cEnd, c;
8453: DMGetDimension(dm, &dim);
8454: DMGetCoordinateDim(dm, &dE);
8455: if (dim != dE) return 0;
8456: DMPlexGetDepth(dm, &depth);
8457: DMGetPeriodicity(dm, &periodic, NULL, NULL, NULL);
8458: for (d = 0; d < dim; ++d) refVol *= 2.0;
8459: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
8460: /* Make sure local coordinates are created, because that step is collective */
8461: DMGetCoordinatesLocal(dm, &coordinates);
8462: for (c = cStart; c < cEnd; ++c) {
8463: DMPolytopeType ct;
8464: PetscInt unsplit;
8465: PetscBool ignoreZeroVol = PETSC_FALSE;
8467: DMPlexGetCellType(dm, c, &ct);
8468: switch (ct) {
8469: case DM_POLYTOPE_SEG_PRISM_TENSOR:
8470: case DM_POLYTOPE_TRI_PRISM_TENSOR:
8471: case DM_POLYTOPE_QUAD_PRISM_TENSOR:
8472: ignoreZeroVol = PETSC_TRUE; break;
8473: default: break;
8474: }
8475: switch (ct) {
8476: case DM_POLYTOPE_TRI_PRISM:
8477: case DM_POLYTOPE_TRI_PRISM_TENSOR:
8478: case DM_POLYTOPE_QUAD_PRISM_TENSOR:
8479: case DM_POLYTOPE_PYRAMID:
8480: continue;
8481: default: break;
8482: }
8483: DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit);
8484: if (unsplit) continue;
8485: DMPlexComputeCellGeometryFEM(dm, c, NULL, NULL, J, NULL, &detJ);
8487: PetscInfo(dm, "Cell %D FEM Volume %g\n", c, (double) detJ*refVol);
8488: if (depth > 1 && !periodic) {
8489: DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);
8491: PetscInfo(dm, "Cell %D FVM Volume %g\n", c, (double) vol);
8492: }
8493: }
8494: return 0;
8495: }
8497: /*@
8498: DMPlexCheckPointSF - Check that several necessary conditions are met for the point SF of this plex.
8500: Input Parameters:
8501: . dm - The DMPlex object
8503: Notes:
8504: This is mainly intended for debugging/testing purposes.
8505: It currently checks only meshes with no partition overlapping.
8507: For the complete list of DMPlexCheck* functions, see DMSetFromOptions().
8509: Level: developer
8511: .seealso: DMGetPointSF(), DMSetFromOptions()
8512: @*/
8513: PetscErrorCode DMPlexCheckPointSF(DM dm)
8514: {
8515: PetscSF pointSF;
8516: PetscInt cellHeight, cStart, cEnd, l, nleaves, nroots, overlap;
8517: const PetscInt *locals, *rootdegree;
8518: PetscBool distributed;
8521: DMGetPointSF(dm, &pointSF);
8522: DMPlexIsDistributed(dm, &distributed);
8523: if (!distributed) return 0;
8524: DMPlexGetOverlap(dm, &overlap);
8525: if (overlap) {
8526: PetscPrintf(PetscObjectComm((PetscObject)dm), "Warning: DMPlexCheckPointSF() is currently not implemented for meshes with partition overlapping");
8527: return 0;
8528: }
8530: PetscSFGetGraph(pointSF, &nroots, &nleaves, &locals, NULL);
8532: PetscSFComputeDegreeBegin(pointSF, &rootdegree);
8533: PetscSFComputeDegreeEnd(pointSF, &rootdegree);
8535: /* 1) check there are no faces in 2D, cells in 3D, in interface */
8536: DMPlexGetVTKCellHeight(dm, &cellHeight);
8537: DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
8538: for (l = 0; l < nleaves; ++l) {
8539: const PetscInt point = locals[l];
8542: }
8544: /* 2) if some point is in interface, then all its cone points must be also in interface (either as leaves or roots) */
8545: for (l = 0; l < nleaves; ++l) {
8546: const PetscInt point = locals[l];
8547: const PetscInt *cone;
8548: PetscInt coneSize, c, idx;
8550: DMPlexGetConeSize(dm, point, &coneSize);
8551: DMPlexGetCone(dm, point, &cone);
8552: for (c = 0; c < coneSize; ++c) {
8553: if (!rootdegree[cone[c]]) {
8554: PetscFindInt(cone[c], nleaves, locals, &idx);
8556: }
8557: }
8558: }
8559: return 0;
8560: }
8562: PetscErrorCode DMPlexCheckAll_Internal(DM dm, PetscInt cellHeight)
8563: {
8564: DMPlexCheckSymmetry(dm);
8565: DMPlexCheckSkeleton(dm, cellHeight);
8566: DMPlexCheckFaces(dm, cellHeight);
8567: DMPlexCheckGeometry(dm);
8568: DMPlexCheckPointSF(dm);
8569: DMPlexCheckInterfaceCones(dm);
8570: return 0;
8571: }
8573: typedef struct cell_stats
8574: {
8575: PetscReal min, max, sum, squaresum;
8576: PetscInt count;
8577: } cell_stats_t;
8579: static void MPIAPI cell_stats_reduce(void *a, void *b, int * len, MPI_Datatype *datatype)
8580: {
8581: PetscInt i, N = *len;
8583: for (i = 0; i < N; i++) {
8584: cell_stats_t *A = (cell_stats_t *) a;
8585: cell_stats_t *B = (cell_stats_t *) b;
8587: B->min = PetscMin(A->min,B->min);
8588: B->max = PetscMax(A->max,B->max);
8589: B->sum += A->sum;
8590: B->squaresum += A->squaresum;
8591: B->count += A->count;
8592: }
8593: }
8595: /*@
8596: DMPlexCheckCellShape - Checks the Jacobian of the mapping from reference to real cells and computes some minimal statistics.
8598: Collective on dm
8600: Input Parameters:
8601: + dm - The DMPlex object
8602: . output - If true, statistics will be displayed on stdout
8603: - condLimit - Display all cells above this condition number, or PETSC_DETERMINE for no cell output
8605: Notes:
8606: This is mainly intended for debugging/testing purposes.
8608: For the complete list of DMPlexCheck* functions, see DMSetFromOptions().
8610: Level: developer
8612: .seealso: DMSetFromOptions(), DMPlexComputeOrthogonalQuality()
8613: @*/
8614: PetscErrorCode DMPlexCheckCellShape(DM dm, PetscBool output, PetscReal condLimit)
8615: {
8616: DM dmCoarse;
8617: cell_stats_t stats, globalStats;
8618: MPI_Comm comm = PetscObjectComm((PetscObject)dm);
8619: PetscReal *J, *invJ, min = 0, max = 0, mean = 0, stdev = 0;
8620: PetscReal limit = condLimit > 0 ? condLimit : PETSC_MAX_REAL;
8621: PetscInt cdim, cStart, cEnd, c, eStart, eEnd, count = 0;
8622: PetscMPIInt rank,size;
8625: stats.min = PETSC_MAX_REAL;
8626: stats.max = PETSC_MIN_REAL;
8627: stats.sum = stats.squaresum = 0.;
8628: stats.count = 0;
8630: MPI_Comm_size(comm, &size);
8631: MPI_Comm_rank(comm, &rank);
8632: DMGetCoordinateDim(dm,&cdim);
8633: PetscMalloc2(PetscSqr(cdim), &J, PetscSqr(cdim), &invJ);
8634: DMPlexGetSimplexOrBoxCells(dm,0,&cStart,&cEnd);
8635: DMPlexGetDepthStratum(dm,1,&eStart,&eEnd);
8636: for (c = cStart; c < cEnd; c++) {
8637: PetscInt i;
8638: PetscReal frobJ = 0., frobInvJ = 0., cond2, cond, detJ;
8640: DMPlexComputeCellGeometryAffineFEM(dm,c,NULL,J,invJ,&detJ);
8642: for (i = 0; i < PetscSqr(cdim); ++i) {
8643: frobJ += J[i] * J[i];
8644: frobInvJ += invJ[i] * invJ[i];
8645: }
8646: cond2 = frobJ * frobInvJ;
8647: cond = PetscSqrtReal(cond2);
8649: stats.min = PetscMin(stats.min,cond);
8650: stats.max = PetscMax(stats.max,cond);
8651: stats.sum += cond;
8652: stats.squaresum += cond2;
8653: stats.count++;
8654: if (output && cond > limit) {
8655: PetscSection coordSection;
8656: Vec coordsLocal;
8657: PetscScalar *coords = NULL;
8658: PetscInt Nv, d, clSize, cl, *closure = NULL;
8660: DMGetCoordinatesLocal(dm, &coordsLocal);
8661: DMGetCoordinateSection(dm, &coordSection);
8662: DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, &Nv, &coords);
8663: PetscSynchronizedPrintf(comm, "[%d] Cell %D cond %g\n", rank, c, (double) cond);
8664: for (i = 0; i < Nv/cdim; ++i) {
8665: PetscSynchronizedPrintf(comm, " Vertex %D: (", i);
8666: for (d = 0; d < cdim; ++d) {
8667: if (d > 0) PetscSynchronizedPrintf(comm, ", ");
8668: PetscSynchronizedPrintf(comm, "%g", (double) PetscRealPart(coords[i*cdim+d]));
8669: }
8670: PetscSynchronizedPrintf(comm, ")\n");
8671: }
8672: DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure);
8673: for (cl = 0; cl < clSize*2; cl += 2) {
8674: const PetscInt edge = closure[cl];
8676: if ((edge >= eStart) && (edge < eEnd)) {
8677: PetscReal len;
8679: DMPlexComputeCellGeometryFVM(dm, edge, &len, NULL, NULL);
8680: PetscSynchronizedPrintf(comm, " Edge %D: length %g\n", edge, (double) len);
8681: }
8682: }
8683: DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure);
8684: DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, &Nv, &coords);
8685: }
8686: }
8687: if (output) PetscSynchronizedFlush(comm, NULL);
8689: if (size > 1) {
8690: PetscMPIInt blockLengths[2] = {4,1};
8691: MPI_Aint blockOffsets[2] = {offsetof(cell_stats_t,min),offsetof(cell_stats_t,count)};
8692: MPI_Datatype blockTypes[2] = {MPIU_REAL,MPIU_INT}, statType;
8693: MPI_Op statReduce;
8695: MPI_Type_create_struct(2,blockLengths,blockOffsets,blockTypes,&statType);
8696: MPI_Type_commit(&statType);
8697: MPI_Op_create(cell_stats_reduce, PETSC_TRUE, &statReduce);
8698: MPI_Reduce(&stats,&globalStats,1,statType,statReduce,0,comm);
8699: MPI_Op_free(&statReduce);
8700: MPI_Type_free(&statType);
8701: } else {
8702: PetscArraycpy(&globalStats,&stats,1);
8703: }
8704: if (rank == 0) {
8705: count = globalStats.count;
8706: min = globalStats.min;
8707: max = globalStats.max;
8708: mean = globalStats.sum / globalStats.count;
8709: stdev = globalStats.count > 1 ? PetscSqrtReal(PetscMax((globalStats.squaresum - globalStats.count * mean * mean) / (globalStats.count - 1),0)) : 0.0;
8710: }
8712: if (output) {
8713: PetscPrintf(comm,"Mesh with %D cells, shape condition numbers: min = %g, max = %g, mean = %g, stddev = %g\n", count, (double) min, (double) max, (double) mean, (double) stdev);
8714: }
8715: PetscFree2(J,invJ);
8717: DMGetCoarseDM(dm,&dmCoarse);
8718: if (dmCoarse) {
8719: PetscBool isplex;
8721: PetscObjectTypeCompare((PetscObject)dmCoarse,DMPLEX,&isplex);
8722: if (isplex) {
8723: DMPlexCheckCellShape(dmCoarse,output,condLimit);
8724: }
8725: }
8726: return 0;
8727: }
8729: /*@
8730: DMPlexComputeOrthogonalQuality - Compute cell-wise orthogonal quality mesh statistic. Optionally tags all cells with
8731: orthogonal quality below given tolerance.
8733: Collective on dm
8735: Input Parameters:
8736: + dm - The DMPlex object
8737: . fv - Optional PetscFV object for pre-computed cell/face centroid information
8738: - atol - [0, 1] Absolute tolerance for tagging cells.
8740: Output Parameters:
8741: + OrthQual - Vec containing orthogonal quality per cell
8742: - OrthQualLabel - DMLabel tagging cells below atol with DM_ADAPT_REFINE
8744: Options Database Keys:
8745: + -dm_plex_orthogonal_quality_label_view - view OrthQualLabel if label is requested. Currently only PETSCVIEWERASCII is
8746: supported.
8747: - -dm_plex_orthogonal_quality_vec_view - view OrthQual vector.
8749: Notes:
8750: Orthogonal quality is given by the following formula:
8752: \min \left[ \frac{A_i \cdot f_i}{\|A_i\| \|f_i\|} , \frac{A_i \cdot c_i}{\|A_i\| \|c_i\|} \right]
8754: Where A_i is the i'th face-normal vector, f_i is the vector from the cell centroid to the i'th face centroid, and c_i
8755: is the vector from the current cells centroid to the centroid of its i'th neighbor (which shares a face with the
8756: current cell). This computes the vector similarity between each cell face and its corresponding neighbor centroid by
8757: calculating the cosine of the angle between these vectors.
8759: Orthogonal quality ranges from 1 (best) to 0 (worst).
8761: This routine is mainly useful for FVM, however is not restricted to only FVM. The PetscFV object is optionally used to check for
8762: pre-computed FVM cell data, but if it is not passed in then this data will be computed.
8764: Cells are tagged if they have an orthogonal quality less than or equal to the absolute tolerance.
8766: Level: intermediate
8768: .seealso: DMPlexCheckCellShape(), DMCreateLabel()
8769: @*/
8770: PetscErrorCode DMPlexComputeOrthogonalQuality(DM dm, PetscFV fv, PetscReal atol, Vec *OrthQual, DMLabel *OrthQualLabel)
8771: {
8772: PetscInt nc, cellHeight, cStart, cEnd, cell, cellIter = 0;
8773: PetscInt *idx;
8774: PetscScalar *oqVals;
8775: const PetscScalar *cellGeomArr, *faceGeomArr;
8776: PetscReal *ci, *fi, *Ai;
8777: MPI_Comm comm;
8778: Vec cellgeom, facegeom;
8779: DM dmFace, dmCell;
8780: IS glob;
8781: ISLocalToGlobalMapping ltog;
8782: PetscViewer vwr;
8788: PetscObjectGetComm((PetscObject) dm, &comm);
8789: DMGetDimension(dm, &nc);
8791: {
8792: DMPlexInterpolatedFlag interpFlag;
8794: DMPlexIsInterpolated(dm, &interpFlag);
8795: if (interpFlag != DMPLEX_INTERPOLATED_FULL) {
8796: PetscMPIInt rank;
8798: MPI_Comm_rank(comm, &rank);
8799: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM must be fully interpolated, DM on rank %d is not fully interpolated", rank);
8800: }
8801: }
8802: if (OrthQualLabel) {
8804: DMCreateLabel(dm, "Orthogonal_Quality");
8805: DMGetLabel(dm, "Orthogonal_Quality", OrthQualLabel);
8806: } else {*OrthQualLabel = NULL;}
8807: DMPlexGetVTKCellHeight(dm, &cellHeight);
8808: DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
8809: DMPlexCreateCellNumbering_Internal(dm, PETSC_TRUE, &glob);
8810: ISLocalToGlobalMappingCreateIS(glob, <og);
8811: ISLocalToGlobalMappingSetType(ltog, ISLOCALTOGLOBALMAPPINGHASH);
8812: VecCreate(comm, OrthQual);
8813: VecSetType(*OrthQual, VECSTANDARD);
8814: VecSetSizes(*OrthQual, cEnd-cStart, PETSC_DETERMINE);
8815: VecSetLocalToGlobalMapping(*OrthQual, ltog);
8816: VecSetUp(*OrthQual);
8817: ISDestroy(&glob);
8818: ISLocalToGlobalMappingDestroy(<og);
8819: DMPlexGetDataFVM(dm, fv, &cellgeom, &facegeom, NULL);
8820: VecGetArrayRead(cellgeom, &cellGeomArr);
8821: VecGetArrayRead(facegeom, &faceGeomArr);
8822: VecGetDM(cellgeom, &dmCell);
8823: VecGetDM(facegeom, &dmFace);
8824: PetscMalloc5(cEnd-cStart, &idx, cEnd-cStart, &oqVals, nc, &ci, nc, &fi, nc, &Ai);
8825: for (cell = cStart; cell < cEnd; cellIter++,cell++) {
8826: PetscInt cellneigh, cellneighiter = 0, adjSize = PETSC_DETERMINE;
8827: PetscInt cellarr[2], *adj = NULL;
8828: PetscScalar *cArr, *fArr;
8829: PetscReal minvalc = 1.0, minvalf = 1.0;
8830: PetscFVCellGeom *cg;
8832: idx[cellIter] = cell-cStart;
8833: cellarr[0] = cell;
8834: /* Make indexing into cellGeom easier */
8835: DMPlexPointLocalRead(dmCell, cell, cellGeomArr, &cg);
8836: DMPlexGetAdjacency_Internal(dm, cell, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, &adjSize, &adj);
8837: /* Technically 1 too big, but easier than fiddling with empty adjacency array */
8838: PetscCalloc2(adjSize, &cArr, adjSize, &fArr);
8839: for (cellneigh = 0; cellneigh < adjSize; cellneighiter++,cellneigh++) {
8840: PetscInt i;
8841: const PetscInt neigh = adj[cellneigh];
8842: PetscReal normci = 0, normfi = 0, normai = 0;
8843: PetscFVCellGeom *cgneigh;
8844: PetscFVFaceGeom *fg;
8846: /* Don't count ourselves in the neighbor list */
8847: if (neigh == cell) continue;
8848: DMPlexPointLocalRead(dmCell, neigh, cellGeomArr, &cgneigh);
8849: cellarr[1] = neigh;
8850: {
8851: PetscInt numcovpts;
8852: const PetscInt *covpts;
8854: DMPlexGetMeet(dm, 2, cellarr, &numcovpts, &covpts);
8855: DMPlexPointLocalRead(dmFace, covpts[0], faceGeomArr, &fg);
8856: DMPlexRestoreMeet(dm, 2, cellarr, &numcovpts, &covpts);
8857: }
8859: /* Compute c_i, f_i and their norms */
8860: for (i = 0; i < nc; i++) {
8861: ci[i] = cgneigh->centroid[i] - cg->centroid[i];
8862: fi[i] = fg->centroid[i] - cg->centroid[i];
8863: Ai[i] = fg->normal[i];
8864: normci += PetscPowReal(ci[i], 2);
8865: normfi += PetscPowReal(fi[i], 2);
8866: normai += PetscPowReal(Ai[i], 2);
8867: }
8868: normci = PetscSqrtReal(normci);
8869: normfi = PetscSqrtReal(normfi);
8870: normai = PetscSqrtReal(normai);
8872: /* Normalize and compute for each face-cell-normal pair */
8873: for (i = 0; i < nc; i++) {
8874: ci[i] = ci[i]/normci;
8875: fi[i] = fi[i]/normfi;
8876: Ai[i] = Ai[i]/normai;
8877: /* PetscAbs because I don't know if normals are guaranteed to point out */
8878: cArr[cellneighiter] += PetscAbs(Ai[i]*ci[i]);
8879: fArr[cellneighiter] += PetscAbs(Ai[i]*fi[i]);
8880: }
8881: if (PetscRealPart(cArr[cellneighiter]) < minvalc) {
8882: minvalc = PetscRealPart(cArr[cellneighiter]);
8883: }
8884: if (PetscRealPart(fArr[cellneighiter]) < minvalf) {
8885: minvalf = PetscRealPart(fArr[cellneighiter]);
8886: }
8887: }
8888: PetscFree(adj);
8889: PetscFree2(cArr, fArr);
8890: /* Defer to cell if they're equal */
8891: oqVals[cellIter] = PetscMin(minvalf, minvalc);
8892: if (OrthQualLabel) {
8893: if (PetscRealPart(oqVals[cellIter]) <= atol) DMLabelSetValue(*OrthQualLabel, cell, DM_ADAPT_REFINE);
8894: }
8895: }
8896: VecSetValuesLocal(*OrthQual, cEnd-cStart, idx, oqVals, INSERT_VALUES);
8897: VecAssemblyBegin(*OrthQual);
8898: VecAssemblyEnd(*OrthQual);
8899: VecRestoreArrayRead(cellgeom, &cellGeomArr);
8900: VecRestoreArrayRead(facegeom, &faceGeomArr);
8901: PetscOptionsGetViewer(comm, NULL, NULL, "-dm_plex_orthogonal_quality_label_view", &vwr, NULL, NULL);
8902: if (OrthQualLabel) {
8903: if (vwr) DMLabelView(*OrthQualLabel, vwr);
8904: }
8905: PetscFree5(idx, oqVals, ci, fi, Ai);
8906: PetscViewerDestroy(&vwr);
8907: VecViewFromOptions(*OrthQual, NULL, "-dm_plex_orthogonal_quality_vec_view");
8908: return 0;
8909: }
8911: /* this is here insead of DMGetOutputDM because output DM still has constraints in the local indices that affect
8912: * interpolator construction */
8913: static PetscErrorCode DMGetFullDM(DM dm, DM *odm)
8914: {
8915: PetscSection section, newSection, gsection;
8916: PetscSF sf;
8917: PetscBool hasConstraints, ghasConstraints;
8921: DMGetLocalSection(dm, §ion);
8922: PetscSectionHasConstraints(section, &hasConstraints);
8923: MPI_Allreduce(&hasConstraints, &ghasConstraints, 1, MPIU_BOOL, MPI_LOR, PetscObjectComm((PetscObject) dm));
8924: if (!ghasConstraints) {
8925: PetscObjectReference((PetscObject)dm);
8926: *odm = dm;
8927: return 0;
8928: }
8929: DMClone(dm, odm);
8930: DMCopyFields(dm, *odm);
8931: DMGetLocalSection(*odm, &newSection);
8932: DMGetPointSF(*odm, &sf);
8933: PetscSectionCreateGlobalSection(newSection, sf, PETSC_TRUE, PETSC_FALSE, &gsection);
8934: DMSetGlobalSection(*odm, gsection);
8935: PetscSectionDestroy(&gsection);
8936: return 0;
8937: }
8939: static PetscErrorCode DMCreateAffineInterpolationCorrection_Plex(DM dmc, DM dmf, Vec *shift)
8940: {
8941: DM dmco, dmfo;
8942: Mat interpo;
8943: Vec rscale;
8944: Vec cglobalo, clocal;
8945: Vec fglobal, fglobalo, flocal;
8946: PetscBool regular;
8948: DMGetFullDM(dmc, &dmco);
8949: DMGetFullDM(dmf, &dmfo);
8950: DMSetCoarseDM(dmfo, dmco);
8951: DMPlexGetRegularRefinement(dmf, ®ular);
8952: DMPlexSetRegularRefinement(dmfo, regular);
8953: DMCreateInterpolation(dmco, dmfo, &interpo, &rscale);
8954: DMCreateGlobalVector(dmco, &cglobalo);
8955: DMCreateLocalVector(dmc, &clocal);
8956: VecSet(cglobalo, 0.);
8957: VecSet(clocal, 0.);
8958: DMCreateGlobalVector(dmf, &fglobal);
8959: DMCreateGlobalVector(dmfo, &fglobalo);
8960: DMCreateLocalVector(dmf, &flocal);
8961: VecSet(fglobal, 0.);
8962: VecSet(fglobalo, 0.);
8963: VecSet(flocal, 0.);
8964: DMPlexInsertBoundaryValues(dmc, PETSC_TRUE, clocal, 0., NULL, NULL, NULL);
8965: DMLocalToGlobalBegin(dmco, clocal, INSERT_VALUES, cglobalo);
8966: DMLocalToGlobalEnd(dmco, clocal, INSERT_VALUES, cglobalo);
8967: MatMult(interpo, cglobalo, fglobalo);
8968: DMGlobalToLocalBegin(dmfo, fglobalo, INSERT_VALUES, flocal);
8969: DMGlobalToLocalEnd(dmfo, fglobalo, INSERT_VALUES, flocal);
8970: DMLocalToGlobalBegin(dmf, flocal, INSERT_VALUES, fglobal);
8971: DMLocalToGlobalEnd(dmf, flocal, INSERT_VALUES, fglobal);
8972: *shift = fglobal;
8973: VecDestroy(&flocal);
8974: VecDestroy(&fglobalo);
8975: VecDestroy(&clocal);
8976: VecDestroy(&cglobalo);
8977: VecDestroy(&rscale);
8978: MatDestroy(&interpo);
8979: DMDestroy(&dmfo);
8980: DMDestroy(&dmco);
8981: return 0;
8982: }
8984: PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM coarse, DM fine, Mat interp, Vec coarseSol, Vec fineSol)
8985: {
8986: PetscObject shifto;
8987: Vec shift;
8989: if (!interp) {
8990: Vec rscale;
8992: DMCreateInterpolation(coarse, fine, &interp, &rscale);
8993: VecDestroy(&rscale);
8994: } else {
8995: PetscObjectReference((PetscObject)interp);
8996: }
8997: PetscObjectQuery((PetscObject)interp, "_DMInterpolateSolution_Plex_Vec", &shifto);
8998: if (!shifto) {
8999: DMCreateAffineInterpolationCorrection_Plex(coarse, fine, &shift);
9000: PetscObjectCompose((PetscObject)interp, "_DMInterpolateSolution_Plex_Vec", (PetscObject) shift);
9001: shifto = (PetscObject) shift;
9002: VecDestroy(&shift);
9003: }
9004: shift = (Vec) shifto;
9005: MatInterpolate(interp, coarseSol, fineSol);
9006: VecAXPY(fineSol, 1.0, shift);
9007: MatDestroy(&interp);
9008: return 0;
9009: }
9011: /* Pointwise interpolation
9012: Just code FEM for now
9013: u^f = I u^c
9014: sum_k u^f_k phi^f_k = I sum_j u^c_j phi^c_j
9015: u^f_i = sum_j psi^f_i I phi^c_j u^c_j
9016: I_{ij} = psi^f_i phi^c_j
9017: */
9018: PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling)
9019: {
9020: PetscSection gsc, gsf;
9021: PetscInt m, n;
9022: void *ctx;
9023: DM cdm;
9024: PetscBool regular, ismatis, isRefined = dmCoarse->data == dmFine->data ? PETSC_FALSE : PETSC_TRUE;
9026: DMGetGlobalSection(dmFine, &gsf);
9027: PetscSectionGetConstrainedStorageSize(gsf, &m);
9028: DMGetGlobalSection(dmCoarse, &gsc);
9029: PetscSectionGetConstrainedStorageSize(gsc, &n);
9031: PetscStrcmp(dmCoarse->mattype, MATIS, &ismatis);
9032: MatCreate(PetscObjectComm((PetscObject) dmCoarse), interpolation);
9033: MatSetSizes(*interpolation, m, n, PETSC_DETERMINE, PETSC_DETERMINE);
9034: MatSetType(*interpolation, ismatis ? MATAIJ : dmCoarse->mattype);
9035: DMGetApplicationContext(dmFine, &ctx);
9037: DMGetCoarseDM(dmFine, &cdm);
9038: DMPlexGetRegularRefinement(dmFine, ®ular);
9039: if (!isRefined || (regular && cdm == dmCoarse)) DMPlexComputeInterpolatorNested(dmCoarse, dmFine, isRefined, *interpolation, ctx);
9040: else DMPlexComputeInterpolatorGeneral(dmCoarse, dmFine, *interpolation, ctx);
9041: MatViewFromOptions(*interpolation, NULL, "-interp_mat_view");
9042: if (scaling) {
9043: /* Use naive scaling */
9044: DMCreateInterpolationScale(dmCoarse, dmFine, *interpolation, scaling);
9045: }
9046: return 0;
9047: }
9049: PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat)
9050: {
9051: VecScatter ctx;
9053: DMPlexComputeInjectorFEM(dmCoarse, dmFine, &ctx, NULL);
9054: MatCreateScatter(PetscObjectComm((PetscObject)ctx), ctx, mat);
9055: VecScatterDestroy(&ctx);
9056: return 0;
9057: }
9059: static void g0_identity_private(PetscInt dim, PetscInt Nf, PetscInt NfAux,
9060: const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
9061: const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
9062: PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[])
9063: {
9064: const PetscInt Nc = uOff[1] - uOff[0];
9065: PetscInt c;
9066: for (c = 0; c < Nc; ++c) g0[c*Nc+c] = 1.0;
9067: }
9069: PetscErrorCode DMCreateMassMatrixLumped_Plex(DM dm, Vec *mass)
9070: {
9071: DM dmc;
9072: PetscDS ds;
9073: Vec ones, locmass;
9074: IS cellIS;
9075: PetscFormKey key;
9076: PetscInt depth;
9078: DMClone(dm, &dmc);
9079: DMCopyDisc(dm, dmc);
9080: DMGetDS(dmc, &ds);
9081: PetscDSSetJacobian(ds, 0, 0, g0_identity_private, NULL, NULL, NULL);
9082: DMCreateGlobalVector(dmc, mass);
9083: DMGetLocalVector(dmc, &ones);
9084: DMGetLocalVector(dmc, &locmass);
9085: DMPlexGetDepth(dmc, &depth);
9086: DMGetStratumIS(dmc, "depth", depth, &cellIS);
9087: VecSet(locmass, 0.0);
9088: VecSet(ones, 1.0);
9089: key.label = NULL;
9090: key.value = 0;
9091: key.field = 0;
9092: key.part = 0;
9093: DMPlexComputeJacobian_Action_Internal(dmc, key, cellIS, 0.0, 0.0, ones, NULL, ones, locmass, NULL);
9094: ISDestroy(&cellIS);
9095: VecSet(*mass, 0.0);
9096: DMLocalToGlobalBegin(dmc, locmass, ADD_VALUES, *mass);
9097: DMLocalToGlobalEnd(dmc, locmass, ADD_VALUES, *mass);
9098: DMRestoreLocalVector(dmc, &ones);
9099: DMRestoreLocalVector(dmc, &locmass);
9100: DMDestroy(&dmc);
9101: return 0;
9102: }
9104: PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mass)
9105: {
9106: PetscSection gsc, gsf;
9107: PetscInt m, n;
9108: void *ctx;
9109: DM cdm;
9110: PetscBool regular;
9112: if (dmFine == dmCoarse) {
9113: DM dmc;
9114: PetscDS ds;
9115: PetscWeakForm wf;
9116: Vec u;
9117: IS cellIS;
9118: PetscFormKey key;
9119: PetscInt depth;
9121: DMClone(dmFine, &dmc);
9122: DMCopyDisc(dmFine, dmc);
9123: DMGetDS(dmc, &ds);
9124: PetscDSGetWeakForm(ds, &wf);
9125: PetscWeakFormClear(wf);
9126: PetscDSSetJacobian(ds, 0, 0, g0_identity_private, NULL, NULL, NULL);
9127: DMCreateMatrix(dmc, mass);
9128: DMGetGlobalVector(dmc, &u);
9129: DMPlexGetDepth(dmc, &depth);
9130: DMGetStratumIS(dmc, "depth", depth, &cellIS);
9131: MatZeroEntries(*mass);
9132: key.label = NULL;
9133: key.value = 0;
9134: key.field = 0;
9135: key.part = 0;
9136: DMPlexComputeJacobian_Internal(dmc, key, cellIS, 0.0, 0.0, u, NULL, *mass, *mass, NULL);
9137: ISDestroy(&cellIS);
9138: DMRestoreGlobalVector(dmc, &u);
9139: DMDestroy(&dmc);
9140: } else {
9141: DMGetGlobalSection(dmFine, &gsf);
9142: PetscSectionGetConstrainedStorageSize(gsf, &m);
9143: DMGetGlobalSection(dmCoarse, &gsc);
9144: PetscSectionGetConstrainedStorageSize(gsc, &n);
9146: MatCreate(PetscObjectComm((PetscObject) dmCoarse), mass);
9147: MatSetSizes(*mass, m, n, PETSC_DETERMINE, PETSC_DETERMINE);
9148: MatSetType(*mass, dmCoarse->mattype);
9149: DMGetApplicationContext(dmFine, &ctx);
9151: DMGetCoarseDM(dmFine, &cdm);
9152: DMPlexGetRegularRefinement(dmFine, ®ular);
9153: if (regular && cdm == dmCoarse) DMPlexComputeMassMatrixNested(dmCoarse, dmFine, *mass, ctx);
9154: else DMPlexComputeMassMatrixGeneral(dmCoarse, dmFine, *mass, ctx);
9155: }
9156: MatViewFromOptions(*mass, NULL, "-mass_mat_view");
9157: return 0;
9158: }
9160: /*@
9161: DMPlexGetRegularRefinement - Get the flag indicating that this mesh was obtained by regular refinement from its coarse mesh
9163: Input Parameter:
9164: . dm - The DMPlex object
9166: Output Parameter:
9167: . regular - The flag
9169: Level: intermediate
9171: .seealso: DMPlexSetRegularRefinement()
9172: @*/
9173: PetscErrorCode DMPlexGetRegularRefinement(DM dm, PetscBool *regular)
9174: {
9177: *regular = ((DM_Plex *) dm->data)->regularRefinement;
9178: return 0;
9179: }
9181: /*@
9182: DMPlexSetRegularRefinement - Set the flag indicating that this mesh was obtained by regular refinement from its coarse mesh
9184: Input Parameters:
9185: + dm - The DMPlex object
9186: - regular - The flag
9188: Level: intermediate
9190: .seealso: DMPlexGetRegularRefinement()
9191: @*/
9192: PetscErrorCode DMPlexSetRegularRefinement(DM dm, PetscBool regular)
9193: {
9195: ((DM_Plex *) dm->data)->regularRefinement = regular;
9196: return 0;
9197: }
9199: /* anchors */
9200: /*@
9201: DMPlexGetAnchors - Get the layout of the anchor (point-to-point) constraints. Typically, the user will not have to
9202: call DMPlexGetAnchors() directly: if there are anchors, then DMPlexGetAnchors() is called during DMGetDefaultConstraints().
9204: not collective
9206: Input Parameter:
9207: . dm - The DMPlex object
9209: Output Parameters:
9210: + anchorSection - If not NULL, set to the section describing which points anchor the constrained points.
9211: - anchorIS - If not NULL, set to the list of anchors indexed by anchorSection
9213: Level: intermediate
9215: .seealso: DMPlexSetAnchors(), DMGetDefaultConstraints(), DMSetDefaultConstraints()
9216: @*/
9217: PetscErrorCode DMPlexGetAnchors(DM dm, PetscSection *anchorSection, IS *anchorIS)
9218: {
9219: DM_Plex *plex = (DM_Plex *)dm->data;
9222: if (!plex->anchorSection && !plex->anchorIS && plex->createanchors) (*plex->createanchors)(dm);
9223: if (anchorSection) *anchorSection = plex->anchorSection;
9224: if (anchorIS) *anchorIS = plex->anchorIS;
9225: return 0;
9226: }
9228: /*@
9229: DMPlexSetAnchors - Set the layout of the local anchor (point-to-point) constraints. Unlike boundary conditions,
9230: when a point's degrees of freedom in a section are constrained to an outside value, the anchor constraints set a
9231: point's degrees of freedom to be a linear combination of other points' degrees of freedom.
9233: After specifying the layout of constraints with DMPlexSetAnchors(), one specifies the constraints by calling
9234: DMGetDefaultConstraints() and filling in the entries in the constraint matrix.
9236: collective on dm
9238: Input Parameters:
9239: + dm - The DMPlex object
9240: . anchorSection - The section that describes the mapping from constrained points to the anchor points listed in anchorIS. Must have a local communicator (PETSC_COMM_SELF or derivative).
9241: - anchorIS - The list of all anchor points. Must have a local communicator (PETSC_COMM_SELF or derivative).
9243: The reference counts of anchorSection and anchorIS are incremented.
9245: Level: intermediate
9247: .seealso: DMPlexGetAnchors(), DMGetDefaultConstraints(), DMSetDefaultConstraints()
9248: @*/
9249: PetscErrorCode DMPlexSetAnchors(DM dm, PetscSection anchorSection, IS anchorIS)
9250: {
9251: DM_Plex *plex = (DM_Plex *)dm->data;
9252: PetscMPIInt result;
9255: if (anchorSection) {
9257: MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)anchorSection),&result);
9259: }
9260: if (anchorIS) {
9262: MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)anchorIS),&result);
9264: }
9266: PetscObjectReference((PetscObject)anchorSection);
9267: PetscSectionDestroy(&plex->anchorSection);
9268: plex->anchorSection = anchorSection;
9270: PetscObjectReference((PetscObject)anchorIS);
9271: ISDestroy(&plex->anchorIS);
9272: plex->anchorIS = anchorIS;
9274: if (PetscUnlikelyDebug(anchorIS && anchorSection)) {
9275: PetscInt size, a, pStart, pEnd;
9276: const PetscInt *anchors;
9278: PetscSectionGetChart(anchorSection,&pStart,&pEnd);
9279: ISGetLocalSize(anchorIS,&size);
9280: ISGetIndices(anchorIS,&anchors);
9281: for (a = 0; a < size; a++) {
9282: PetscInt p;
9284: p = anchors[a];
9285: if (p >= pStart && p < pEnd) {
9286: PetscInt dof;
9288: PetscSectionGetDof(anchorSection,p,&dof);
9289: if (dof) {
9291: ISRestoreIndices(anchorIS,&anchors);
9292: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Point %D cannot be constrained and an anchor",p);
9293: }
9294: }
9295: }
9296: ISRestoreIndices(anchorIS,&anchors);
9297: }
9298: /* reset the generic constraints */
9299: DMSetDefaultConstraints(dm,NULL,NULL,NULL);
9300: return 0;
9301: }
9303: static PetscErrorCode DMPlexCreateConstraintSection_Anchors(DM dm, PetscSection section, PetscSection *cSec)
9304: {
9305: PetscSection anchorSection;
9306: PetscInt pStart, pEnd, sStart, sEnd, p, dof, numFields, f;
9309: DMPlexGetAnchors(dm,&anchorSection,NULL);
9310: PetscSectionCreate(PETSC_COMM_SELF,cSec);
9311: PetscSectionGetNumFields(section,&numFields);
9312: if (numFields) {
9313: PetscInt f;
9314: PetscSectionSetNumFields(*cSec,numFields);
9316: for (f = 0; f < numFields; f++) {
9317: PetscInt numComp;
9319: PetscSectionGetFieldComponents(section,f,&numComp);
9320: PetscSectionSetFieldComponents(*cSec,f,numComp);
9321: }
9322: }
9323: PetscSectionGetChart(anchorSection,&pStart,&pEnd);
9324: PetscSectionGetChart(section,&sStart,&sEnd);
9325: pStart = PetscMax(pStart,sStart);
9326: pEnd = PetscMin(pEnd,sEnd);
9327: pEnd = PetscMax(pStart,pEnd);
9328: PetscSectionSetChart(*cSec,pStart,pEnd);
9329: for (p = pStart; p < pEnd; p++) {
9330: PetscSectionGetDof(anchorSection,p,&dof);
9331: if (dof) {
9332: PetscSectionGetDof(section,p,&dof);
9333: PetscSectionSetDof(*cSec,p,dof);
9334: for (f = 0; f < numFields; f++) {
9335: PetscSectionGetFieldDof(section,p,f,&dof);
9336: PetscSectionSetFieldDof(*cSec,p,f,dof);
9337: }
9338: }
9339: }
9340: PetscSectionSetUp(*cSec);
9341: PetscObjectSetName((PetscObject) *cSec, "Constraint Section");
9342: return 0;
9343: }
9345: static PetscErrorCode DMPlexCreateConstraintMatrix_Anchors(DM dm, PetscSection section, PetscSection cSec, Mat *cMat)
9346: {
9347: PetscSection aSec;
9348: PetscInt pStart, pEnd, p, sStart, sEnd, dof, aDof, aOff, off, nnz, annz, m, n, q, a, offset, *i, *j;
9349: const PetscInt *anchors;
9350: PetscInt numFields, f;
9351: IS aIS;
9352: MatType mtype;
9353: PetscBool iscuda,iskokkos;
9356: PetscSectionGetStorageSize(cSec, &m);
9357: PetscSectionGetStorageSize(section, &n);
9358: MatCreate(PETSC_COMM_SELF,cMat);
9359: MatSetSizes(*cMat,m,n,m,n);
9360: PetscStrcmp(dm->mattype,MATSEQAIJCUSPARSE,&iscuda);
9361: if (!iscuda) PetscStrcmp(dm->mattype,MATMPIAIJCUSPARSE,&iscuda);
9362: PetscStrcmp(dm->mattype,MATSEQAIJKOKKOS,&iskokkos);
9363: if (!iskokkos) PetscStrcmp(dm->mattype,MATMPIAIJKOKKOS,&iskokkos);
9364: if (iscuda) mtype = MATSEQAIJCUSPARSE;
9365: else if (iskokkos) mtype = MATSEQAIJKOKKOS;
9366: else mtype = MATSEQAIJ;
9367: MatSetType(*cMat,mtype);
9368: DMPlexGetAnchors(dm,&aSec,&aIS);
9369: ISGetIndices(aIS,&anchors);
9370: /* cSec will be a subset of aSec and section */
9371: PetscSectionGetChart(cSec,&pStart,&pEnd);
9372: PetscSectionGetChart(section,&sStart,&sEnd);
9373: PetscMalloc1(m+1,&i);
9374: i[0] = 0;
9375: PetscSectionGetNumFields(section,&numFields);
9376: for (p = pStart; p < pEnd; p++) {
9377: PetscInt rDof, rOff, r;
9379: PetscSectionGetDof(aSec,p,&rDof);
9380: if (!rDof) continue;
9381: PetscSectionGetOffset(aSec,p,&rOff);
9382: if (numFields) {
9383: for (f = 0; f < numFields; f++) {
9384: annz = 0;
9385: for (r = 0; r < rDof; r++) {
9386: a = anchors[rOff + r];
9387: if (a < sStart || a >= sEnd) continue;
9388: PetscSectionGetFieldDof(section,a,f,&aDof);
9389: annz += aDof;
9390: }
9391: PetscSectionGetFieldDof(cSec,p,f,&dof);
9392: PetscSectionGetFieldOffset(cSec,p,f,&off);
9393: for (q = 0; q < dof; q++) {
9394: i[off + q + 1] = i[off + q] + annz;
9395: }
9396: }
9397: } else {
9398: annz = 0;
9399: PetscSectionGetDof(cSec,p,&dof);
9400: for (q = 0; q < dof; q++) {
9401: a = anchors[rOff + q];
9402: if (a < sStart || a >= sEnd) continue;
9403: PetscSectionGetDof(section,a,&aDof);
9404: annz += aDof;
9405: }
9406: PetscSectionGetDof(cSec,p,&dof);
9407: PetscSectionGetOffset(cSec,p,&off);
9408: for (q = 0; q < dof; q++) {
9409: i[off + q + 1] = i[off + q] + annz;
9410: }
9411: }
9412: }
9413: nnz = i[m];
9414: PetscMalloc1(nnz,&j);
9415: offset = 0;
9416: for (p = pStart; p < pEnd; p++) {
9417: if (numFields) {
9418: for (f = 0; f < numFields; f++) {
9419: PetscSectionGetFieldDof(cSec,p,f,&dof);
9420: for (q = 0; q < dof; q++) {
9421: PetscInt rDof, rOff, r;
9422: PetscSectionGetDof(aSec,p,&rDof);
9423: PetscSectionGetOffset(aSec,p,&rOff);
9424: for (r = 0; r < rDof; r++) {
9425: PetscInt s;
9427: a = anchors[rOff + r];
9428: if (a < sStart || a >= sEnd) continue;
9429: PetscSectionGetFieldDof(section,a,f,&aDof);
9430: PetscSectionGetFieldOffset(section,a,f,&aOff);
9431: for (s = 0; s < aDof; s++) {
9432: j[offset++] = aOff + s;
9433: }
9434: }
9435: }
9436: }
9437: } else {
9438: PetscSectionGetDof(cSec,p,&dof);
9439: for (q = 0; q < dof; q++) {
9440: PetscInt rDof, rOff, r;
9441: PetscSectionGetDof(aSec,p,&rDof);
9442: PetscSectionGetOffset(aSec,p,&rOff);
9443: for (r = 0; r < rDof; r++) {
9444: PetscInt s;
9446: a = anchors[rOff + r];
9447: if (a < sStart || a >= sEnd) continue;
9448: PetscSectionGetDof(section,a,&aDof);
9449: PetscSectionGetOffset(section,a,&aOff);
9450: for (s = 0; s < aDof; s++) {
9451: j[offset++] = aOff + s;
9452: }
9453: }
9454: }
9455: }
9456: }
9457: MatSeqAIJSetPreallocationCSR(*cMat,i,j,NULL);
9458: PetscFree(i);
9459: PetscFree(j);
9460: ISRestoreIndices(aIS,&anchors);
9461: return 0;
9462: }
9464: PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm)
9465: {
9466: DM_Plex *plex = (DM_Plex *)dm->data;
9467: PetscSection anchorSection, section, cSec;
9468: Mat cMat;
9471: DMPlexGetAnchors(dm,&anchorSection,NULL);
9472: if (anchorSection) {
9473: PetscInt Nf;
9475: DMGetLocalSection(dm,§ion);
9476: DMPlexCreateConstraintSection_Anchors(dm,section,&cSec);
9477: DMPlexCreateConstraintMatrix_Anchors(dm,section,cSec,&cMat);
9478: DMGetNumFields(dm,&Nf);
9479: if (Nf && plex->computeanchormatrix) (*plex->computeanchormatrix)(dm,section,cSec,cMat);
9480: DMSetDefaultConstraints(dm,cSec,cMat,NULL);
9481: PetscSectionDestroy(&cSec);
9482: MatDestroy(&cMat);
9483: }
9484: return 0;
9485: }
9487: PetscErrorCode DMCreateSubDomainDM_Plex(DM dm, DMLabel label, PetscInt value, IS *is, DM *subdm)
9488: {
9489: IS subis;
9490: PetscSection section, subsection;
9492: DMGetLocalSection(dm, §ion);
9495: /* Create subdomain */
9496: DMPlexFilter(dm, label, value, subdm);
9497: /* Create submodel */
9498: DMPlexGetSubpointIS(*subdm, &subis);
9499: PetscSectionCreateSubmeshSection(section, subis, &subsection);
9500: DMSetLocalSection(*subdm, subsection);
9501: PetscSectionDestroy(&subsection);
9502: DMCopyDisc(dm, *subdm);
9503: /* Create map from submodel to global model */
9504: if (is) {
9505: PetscSection sectionGlobal, subsectionGlobal;
9506: IS spIS;
9507: const PetscInt *spmap;
9508: PetscInt *subIndices;
9509: PetscInt subSize = 0, subOff = 0, pStart, pEnd, p;
9510: PetscInt Nf, f, bs = -1, bsLocal[2], bsMinMax[2];
9512: DMPlexGetSubpointIS(*subdm, &spIS);
9513: ISGetIndices(spIS, &spmap);
9514: PetscSectionGetNumFields(section, &Nf);
9515: DMGetGlobalSection(dm, §ionGlobal);
9516: DMGetGlobalSection(*subdm, &subsectionGlobal);
9517: PetscSectionGetChart(subsection, &pStart, &pEnd);
9518: for (p = pStart; p < pEnd; ++p) {
9519: PetscInt gdof, pSubSize = 0;
9521: PetscSectionGetDof(sectionGlobal, p, &gdof);
9522: if (gdof > 0) {
9523: for (f = 0; f < Nf; ++f) {
9524: PetscInt fdof, fcdof;
9526: PetscSectionGetFieldDof(subsection, p, f, &fdof);
9527: PetscSectionGetFieldConstraintDof(subsection, p, f, &fcdof);
9528: pSubSize += fdof-fcdof;
9529: }
9530: subSize += pSubSize;
9531: if (pSubSize) {
9532: if (bs < 0) {
9533: bs = pSubSize;
9534: } else if (bs != pSubSize) {
9535: /* Layout does not admit a pointwise block size */
9536: bs = 1;
9537: }
9538: }
9539: }
9540: }
9541: /* Must have same blocksize on all procs (some might have no points) */
9542: bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; bsLocal[1] = bs;
9543: PetscGlobalMinMaxInt(PetscObjectComm((PetscObject) dm), bsLocal, bsMinMax);
9544: if (bsMinMax[0] != bsMinMax[1]) {bs = 1;}
9545: else {bs = bsMinMax[0];}
9546: PetscMalloc1(subSize, &subIndices);
9547: for (p = pStart; p < pEnd; ++p) {
9548: PetscInt gdof, goff;
9550: PetscSectionGetDof(subsectionGlobal, p, &gdof);
9551: if (gdof > 0) {
9552: const PetscInt point = spmap[p];
9554: PetscSectionGetOffset(sectionGlobal, point, &goff);
9555: for (f = 0; f < Nf; ++f) {
9556: PetscInt fdof, fcdof, fc, f2, poff = 0;
9558: /* Can get rid of this loop by storing field information in the global section */
9559: for (f2 = 0; f2 < f; ++f2) {
9560: PetscSectionGetFieldDof(section, p, f2, &fdof);
9561: PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);
9562: poff += fdof-fcdof;
9563: }
9564: PetscSectionGetFieldDof(section, p, f, &fdof);
9565: PetscSectionGetFieldConstraintDof(section, p, f, &fcdof);
9566: for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) {
9567: subIndices[subOff] = goff+poff+fc;
9568: }
9569: }
9570: }
9571: }
9572: ISRestoreIndices(spIS, &spmap);
9573: ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);
9574: if (bs > 1) {
9575: /* We need to check that the block size does not come from non-contiguous fields */
9576: PetscInt i, j, set = 1;
9577: for (i = 0; i < subSize; i += bs) {
9578: for (j = 0; j < bs; ++j) {
9579: if (subIndices[i+j] != subIndices[i]+j) {set = 0; break;}
9580: }
9581: }
9582: if (set) ISSetBlockSize(*is, bs);
9583: }
9584: /* Attach nullspace */
9585: for (f = 0; f < Nf; ++f) {
9586: (*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[f];
9587: if ((*subdm)->nullspaceConstructors[f]) break;
9588: }
9589: if (f < Nf) {
9590: MatNullSpace nullSpace;
9591: (*(*subdm)->nullspaceConstructors[f])(*subdm, f, f, &nullSpace);
9593: PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);
9594: MatNullSpaceDestroy(&nullSpace);
9595: }
9596: }
9597: return 0;
9598: }
9600: /*@
9601: DMPlexMonitorThroughput - Report the cell throughput of FE integration
9603: Input Parameter:
9604: - dm - The DM
9606: Level: developer
9608: Options Database Keys:
9609: . -dm_plex_monitor_throughput - Activate the monitor
9611: .seealso: DMSetFromOptions(), DMPlexCreate()
9612: @*/
9613: PetscErrorCode DMPlexMonitorThroughput(DM dm, void *dummy)
9614: {
9615: #if defined(PETSC_USE_LOG)
9616: PetscStageLog stageLog;
9617: PetscLogEvent event;
9618: PetscLogStage stage;
9619: PetscEventPerfInfo eventInfo;
9620: PetscReal cellRate, flopRate;
9621: PetscInt cStart, cEnd, Nf, N;
9622: const char *name;
9623: #endif
9626: #if defined(PETSC_USE_LOG)
9627: PetscObjectGetName((PetscObject) dm, &name);
9628: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
9629: DMGetNumFields(dm, &Nf);
9630: PetscLogGetStageLog(&stageLog);
9631: PetscStageLogGetCurrent(stageLog, &stage);
9632: PetscLogEventGetId("DMPlexResidualFE", &event);
9633: PetscLogEventGetPerfInfo(stage, event, &eventInfo);
9634: N = (cEnd - cStart)*Nf*eventInfo.count;
9635: flopRate = eventInfo.flops/eventInfo.time;
9636: cellRate = N/eventInfo.time;
9637: PetscPrintf(PetscObjectComm((PetscObject) dm), "DM (%s) FE Residual Integration: %D integrals %D reps\n Cell rate: %.2g/s flop rate: %.2g MF/s\n", name ? name : "unknown", N, eventInfo.count, (double) cellRate, (double) (flopRate/1.e6));
9638: #else
9639: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Plex Throughput Monitor is not supported if logging is turned off. Reconfigure using --with-log.");
9640: #endif
9641: return 0;
9642: }