Actual source code: plexhdf5.c
petsc-3.13.6 2020-09-29
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/isimpl.h>
3: #include <petsc/private/vecimpl.h>
4: #include <petsc/private/viewerhdf5impl.h>
5: #include <petsclayouthdf5.h>
7: PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);
9: #if defined(PETSC_HAVE_HDF5)
10: static PetscErrorCode DMSequenceView_HDF5(DM dm, const char *seqname, PetscInt seqnum, PetscScalar value, PetscViewer viewer)
11: {
12: Vec stamp;
13: PetscMPIInt rank;
17: if (seqnum < 0) return(0);
18: MPI_Comm_rank(PetscObjectComm((PetscObject) viewer), &rank);
19: VecCreateMPI(PetscObjectComm((PetscObject) viewer), rank ? 0 : 1, 1, &stamp);
20: VecSetBlockSize(stamp, 1);
21: PetscObjectSetName((PetscObject) stamp, seqname);
22: if (!rank) {
23: PetscReal timeScale;
24: PetscBool istime;
26: PetscStrncmp(seqname, "time", 5, &istime);
27: if (istime) {DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale); value *= timeScale;}
28: VecSetValue(stamp, 0, value, INSERT_VALUES);
29: }
30: VecAssemblyBegin(stamp);
31: VecAssemblyEnd(stamp);
32: PetscViewerHDF5PushGroup(viewer, "/");
33: PetscViewerHDF5SetTimestep(viewer, seqnum);
34: VecView(stamp, viewer);
35: PetscViewerHDF5PopGroup(viewer);
36: VecDestroy(&stamp);
37: return(0);
38: }
40: PetscErrorCode DMSequenceLoad_HDF5_Internal(DM dm, const char *seqname, PetscInt seqnum, PetscScalar *value, PetscViewer viewer)
41: {
42: Vec stamp;
43: PetscMPIInt rank;
47: if (seqnum < 0) return(0);
48: MPI_Comm_rank(PetscObjectComm((PetscObject) viewer), &rank);
49: VecCreateMPI(PetscObjectComm((PetscObject) viewer), rank ? 0 : 1, 1, &stamp);
50: VecSetBlockSize(stamp, 1);
51: PetscObjectSetName((PetscObject) stamp, seqname);
52: PetscViewerHDF5PushGroup(viewer, "/");
53: PetscViewerHDF5SetTimestep(viewer, seqnum);
54: VecLoad(stamp, viewer);
55: PetscViewerHDF5PopGroup(viewer);
56: if (!rank) {
57: const PetscScalar *a;
58: PetscReal timeScale;
59: PetscBool istime;
61: VecGetArrayRead(stamp, &a);
62: *value = a[0];
63: VecRestoreArrayRead(stamp, &a);
64: PetscStrncmp(seqname, "time", 5, &istime);
65: if (istime) {DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale); *value /= timeScale;}
66: }
67: VecDestroy(&stamp);
68: return(0);
69: }
71: static PetscErrorCode DMPlexCreateCutVertexLabel_Private(DM dm, DMLabel cutLabel, DMLabel *cutVertexLabel)
72: {
73: IS cutcells = NULL;
74: const PetscInt *cutc;
75: PetscInt cellHeight, vStart, vEnd, cStart, cEnd, c;
76: PetscErrorCode ierr;
79: if (!cutLabel) return(0);
80: DMPlexGetVTKCellHeight(dm, &cellHeight);
81: DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
82: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
83: /* Label vertices that should be duplicated */
84: DMLabelCreate(PETSC_COMM_SELF, "Cut Vertices", cutVertexLabel);
85: DMLabelGetStratumIS(cutLabel, 2, &cutcells);
86: if (cutcells) {
87: PetscInt n;
89: ISGetIndices(cutcells, &cutc);
90: ISGetLocalSize(cutcells, &n);
91: for (c = 0; c < n; ++c) {
92: if ((cutc[c] >= cStart) && (cutc[c] < cEnd)) {
93: PetscInt *closure = NULL;
94: PetscInt closureSize, cl, value;
96: DMPlexGetTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure);
97: for (cl = 0; cl < closureSize*2; cl += 2) {
98: if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) {
99: DMLabelGetValue(cutLabel, closure[cl], &value);
100: if (value == 1) {
101: DMLabelSetValue(*cutVertexLabel, closure[cl], 1);
102: }
103: }
104: }
105: DMPlexRestoreTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure);
106: }
107: }
108: ISRestoreIndices(cutcells, &cutc);
109: }
110: ISDestroy(&cutcells);
111: return(0);
112: }
114: PetscErrorCode VecView_Plex_Local_HDF5_Internal(Vec v, PetscViewer viewer)
115: {
116: DM dm;
117: DM dmBC;
118: PetscSection section, sectionGlobal;
119: Vec gv;
120: const char *name;
121: PetscViewerVTKFieldType ft;
122: PetscViewerFormat format;
123: PetscInt seqnum;
124: PetscReal seqval;
125: PetscBool isseq;
126: PetscErrorCode ierr;
129: PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
130: VecGetDM(v, &dm);
131: DMGetLocalSection(dm, §ion);
132: DMGetOutputSequenceNumber(dm, &seqnum, &seqval);
133: PetscViewerHDF5SetTimestep(viewer, seqnum);
134: DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar) seqval, viewer);
135: PetscViewerGetFormat(viewer, &format);
136: DMGetOutputDM(dm, &dmBC);
137: DMGetGlobalSection(dmBC, §ionGlobal);
138: DMGetGlobalVector(dmBC, &gv);
139: PetscObjectGetName((PetscObject) v, &name);
140: PetscObjectSetName((PetscObject) gv, name);
141: DMLocalToGlobalBegin(dmBC, v, INSERT_VALUES, gv);
142: DMLocalToGlobalEnd(dmBC, v, INSERT_VALUES, gv);
143: PetscObjectTypeCompare((PetscObject) gv, VECSEQ, &isseq);
144: if (isseq) {VecView_Seq(gv, viewer);}
145: else {VecView_MPI(gv, viewer);}
146: if (format == PETSC_VIEWER_HDF5_VIZ) {
147: /* Output visualization representation */
148: PetscInt numFields, f;
149: DMLabel cutLabel, cutVertexLabel = NULL;
151: PetscSectionGetNumFields(section, &numFields);
152: DMGetLabel(dm, "periodic_cut", &cutLabel);
153: for (f = 0; f < numFields; ++f) {
154: Vec subv;
155: IS is;
156: const char *fname, *fgroup;
157: char subname[PETSC_MAX_PATH_LEN];
158: PetscInt pStart, pEnd;
160: DMPlexGetFieldType_Internal(dm, section, f, &pStart, &pEnd, &ft);
161: fgroup = (ft == PETSC_VTK_POINT_VECTOR_FIELD) || (ft == PETSC_VTK_POINT_FIELD) ? "/vertex_fields" : "/cell_fields";
162: PetscSectionGetFieldName(section, f, &fname);
163: if (!fname) continue;
164: PetscViewerHDF5PushGroup(viewer, fgroup);
165: if (cutLabel) {
166: const PetscScalar *ga;
167: PetscScalar *suba;
168: PetscInt Nc, gstart, subSize = 0, extSize = 0, subOff = 0, newOff = 0, p;
170: DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel);
171: PetscSectionGetFieldComponents(section, f, &Nc);
172: for (p = pStart; p < pEnd; ++p) {
173: PetscInt gdof, fdof = 0, val;
175: PetscSectionGetDof(sectionGlobal, p, &gdof);
176: if (gdof > 0) {PetscSectionGetFieldDof(section, p, f, &fdof);}
177: subSize += fdof;
178: DMLabelGetValue(cutVertexLabel, p, &val);
179: if (val == 1) extSize += fdof;
180: }
181: VecCreate(PetscObjectComm((PetscObject) gv), &subv);
182: VecSetSizes(subv, subSize+extSize, PETSC_DETERMINE);
183: VecSetBlockSize(subv, Nc);
184: VecSetType(subv, VECSTANDARD);
185: VecGetOwnershipRange(gv, &gstart, NULL);
186: VecGetArrayRead(gv, &ga);
187: VecGetArray(subv, &suba);
188: for (p = pStart; p < pEnd; ++p) {
189: PetscInt gdof, goff, val;
191: PetscSectionGetDof(sectionGlobal, p, &gdof);
192: if (gdof > 0) {
193: PetscInt fdof, fc, f2, poff = 0;
195: PetscSectionGetOffset(sectionGlobal, p, &goff);
196: /* Can get rid of this loop by storing field information in the global section */
197: for (f2 = 0; f2 < f; ++f2) {
198: PetscSectionGetFieldDof(section, p, f2, &fdof);
199: poff += fdof;
200: }
201: PetscSectionGetFieldDof(section, p, f, &fdof);
202: for (fc = 0; fc < fdof; ++fc, ++subOff) suba[subOff] = ga[goff+poff+fc - gstart];
203: DMLabelGetValue(cutVertexLabel, p, &val);
204: if (val == 1) {
205: for (fc = 0; fc < fdof; ++fc, ++newOff) suba[subSize+newOff] = ga[goff+poff+fc - gstart];
206: }
207: }
208: }
209: VecRestoreArrayRead(gv, &ga);
210: VecRestoreArray(subv, &suba);
211: DMLabelDestroy(&cutVertexLabel);
212: } else {
213: PetscSectionGetField_Internal(section, sectionGlobal, gv, f, pStart, pEnd, &is, &subv);
214: }
215: PetscStrncpy(subname, name,sizeof(subname));
216: PetscStrlcat(subname, "_",sizeof(subname));
217: PetscStrlcat(subname, fname,sizeof(subname));
218: PetscObjectSetName((PetscObject) subv, subname);
219: if (isseq) {VecView_Seq(subv, viewer);}
220: else {VecView_MPI(subv, viewer);}
221: if ((ft == PETSC_VTK_POINT_VECTOR_FIELD) || (ft == PETSC_VTK_CELL_VECTOR_FIELD)) {
222: PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject) subv, "vector_field_type", PETSC_STRING, "vector");
223: } else {
224: PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject) subv, "vector_field_type", PETSC_STRING, "scalar");
225: }
226: if (cutLabel) {VecDestroy(&subv);}
227: else {PetscSectionRestoreField_Internal(section, sectionGlobal, gv, f, pStart, pEnd, &is, &subv);}
228: PetscViewerHDF5PopGroup(viewer);
229: }
230: }
231: DMRestoreGlobalVector(dmBC, &gv);
232: return(0);
233: }
235: PetscErrorCode VecView_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
236: {
237: DM dm;
238: Vec locv;
239: const char *name;
240: PetscReal time;
244: VecGetDM(v, &dm);
245: DMGetLocalVector(dm, &locv);
246: PetscObjectGetName((PetscObject) v, &name);
247: PetscObjectSetName((PetscObject) locv, name);
248: DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv);
249: DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv);
250: DMGetOutputSequenceNumber(dm, NULL, &time);
251: DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL);
252: PetscViewerHDF5PushGroup(viewer, "/fields");
253: PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_VIZ);
254: VecView_Plex_Local_HDF5_Internal(locv, viewer);
255: PetscViewerPopFormat(viewer);
256: PetscViewerHDF5PopGroup(viewer);
257: DMRestoreLocalVector(dm, &locv);
258: return(0);
259: }
261: PetscErrorCode VecView_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
262: {
263: PetscBool isseq;
267: PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
268: PetscViewerHDF5PushGroup(viewer, "/fields");
269: if (isseq) {VecView_Seq(v, viewer);}
270: else {VecView_MPI(v, viewer);}
271: PetscViewerHDF5PopGroup(viewer);
272: return(0);
273: }
275: PetscErrorCode VecLoad_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
276: {
277: DM dm;
278: Vec locv;
279: const char *name;
280: PetscInt seqnum;
284: VecGetDM(v, &dm);
285: DMGetLocalVector(dm, &locv);
286: PetscObjectGetName((PetscObject) v, &name);
287: PetscObjectSetName((PetscObject) locv, name);
288: DMGetOutputSequenceNumber(dm, &seqnum, NULL);
289: PetscViewerHDF5SetTimestep(viewer, seqnum);
290: PetscViewerHDF5PushGroup(viewer, "/fields");
291: VecLoad_Plex_Local(locv, viewer);
292: PetscViewerHDF5PopGroup(viewer);
293: DMLocalToGlobalBegin(dm, locv, INSERT_VALUES, v);
294: DMLocalToGlobalEnd(dm, locv, INSERT_VALUES, v);
295: DMRestoreLocalVector(dm, &locv);
296: return(0);
297: }
299: PetscErrorCode VecLoad_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
300: {
301: DM dm;
302: PetscInt seqnum;
306: VecGetDM(v, &dm);
307: DMGetOutputSequenceNumber(dm, &seqnum, NULL);
308: PetscViewerHDF5SetTimestep(viewer, seqnum);
309: PetscViewerHDF5PushGroup(viewer, "/fields");
310: VecLoad_Default(v, viewer);
311: PetscViewerHDF5PopGroup(viewer);
312: return(0);
313: }
315: static PetscErrorCode DMPlexWriteTopology_HDF5_Static(DM dm, IS globalPointNumbers, PetscViewer viewer)
316: {
317: IS orderIS, conesIS, cellsIS, orntsIS;
318: const PetscInt *gpoint;
319: PetscInt *order, *sizes, *cones, *ornts;
320: PetscInt dim, pStart, pEnd, p, conesSize = 0, cellsSize = 0, c = 0, s = 0;
321: PetscErrorCode ierr;
324: ISGetIndices(globalPointNumbers, &gpoint);
325: DMGetDimension(dm, &dim);
326: DMPlexGetChart(dm, &pStart, &pEnd);
327: for (p = pStart; p < pEnd; ++p) {
328: if (gpoint[p] >= 0) {
329: PetscInt coneSize;
331: DMPlexGetConeSize(dm, p, &coneSize);
332: conesSize += 1;
333: cellsSize += coneSize;
334: }
335: }
336: PetscMalloc1(conesSize, &order);
337: PetscMalloc1(conesSize, &sizes);
338: PetscMalloc1(cellsSize, &cones);
339: PetscMalloc1(cellsSize, &ornts);
340: for (p = pStart; p < pEnd; ++p) {
341: if (gpoint[p] >= 0) {
342: const PetscInt *cone, *ornt;
343: PetscInt coneSize, cp;
345: DMPlexGetConeSize(dm, p, &coneSize);
346: DMPlexGetCone(dm, p, &cone);
347: DMPlexGetConeOrientation(dm, p, &ornt);
348: order[s] = gpoint[p];
349: sizes[s++] = coneSize;
350: for (cp = 0; cp < coneSize; ++cp, ++c) {cones[c] = gpoint[cone[cp]] < 0 ? -(gpoint[cone[cp]]+1) : gpoint[cone[cp]]; ornts[c] = ornt[cp];}
351: }
352: }
353: if (s != conesSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of points %d != %d", s, conesSize);
354: if (c != cellsSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cone points %d != %d", c, cellsSize);
355: ISCreateGeneral(PetscObjectComm((PetscObject) dm), conesSize, order, PETSC_OWN_POINTER, &orderIS);
356: PetscObjectSetName((PetscObject) orderIS, "order");
357: ISCreateGeneral(PetscObjectComm((PetscObject) dm), conesSize, sizes, PETSC_OWN_POINTER, &conesIS);
358: PetscObjectSetName((PetscObject) conesIS, "cones");
359: ISCreateGeneral(PetscObjectComm((PetscObject) dm), cellsSize, cones, PETSC_OWN_POINTER, &cellsIS);
360: PetscObjectSetName((PetscObject) cellsIS, "cells");
361: ISCreateGeneral(PetscObjectComm((PetscObject) dm), cellsSize, ornts, PETSC_OWN_POINTER, &orntsIS);
362: PetscObjectSetName((PetscObject) orntsIS, "orientation");
363: PetscViewerHDF5PushGroup(viewer, "/topology");
364: ISView(orderIS, viewer);
365: ISView(conesIS, viewer);
366: ISView(cellsIS, viewer);
367: PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject) cellsIS, "cell_dim", PETSC_INT, (void *) &dim);
368: ISView(orntsIS, viewer);
369: PetscViewerHDF5PopGroup(viewer);
370: ISDestroy(&orderIS);
371: ISDestroy(&conesIS);
372: ISDestroy(&cellsIS);
373: ISDestroy(&orntsIS);
374: ISRestoreIndices(globalPointNumbers, &gpoint);
375: return(0);
376: }
378: static PetscErrorCode CreateConesIS_Private(DM dm, PetscInt cStart, PetscInt cEnd, PetscInt *numCorners, IS *cellIS)
379: {
380: PetscSF sfPoint;
381: DMLabel cutLabel, cutVertexLabel = NULL;
382: IS globalVertexNumbers, cutvertices = NULL;
383: const PetscInt *gvertex, *cutverts = NULL;
384: PetscInt *vertices;
385: PetscInt conesSize = 0;
386: PetscInt dim, numCornersLocal = 0, cell, vStart, vEnd, vExtra = 0, v;
387: PetscErrorCode ierr;
390: *numCorners = 0;
391: DMGetDimension(dm, &dim);
392: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
394: for (cell = cStart; cell < cEnd; ++cell) {
395: PetscInt *closure = NULL;
396: PetscInt closureSize, v, Nc = 0;
398: DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
399: for (v = 0; v < closureSize*2; v += 2) {
400: if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++Nc;
401: }
402: DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
403: conesSize += Nc;
404: if (!numCornersLocal) numCornersLocal = Nc;
405: else if (numCornersLocal != Nc) numCornersLocal = 1;
406: }
407: MPIU_Allreduce(&numCornersLocal, numCorners, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));
408: if (numCornersLocal && (numCornersLocal != *numCorners || *numCorners == 1)) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Visualization topology currently only supports identical cell shapes");
409: /* Handle periodic cuts by identifying vertices which should be duplicated */
410: DMGetLabel(dm, "periodic_cut", &cutLabel);
411: DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel);
412: if (cutVertexLabel) {DMLabelGetStratumIS(cutVertexLabel, 1, &cutvertices);}
413: if (cutvertices) {
414: ISGetIndices(cutvertices, &cutverts);
415: ISGetLocalSize(cutvertices, &vExtra);
416: }
417: DMGetPointSF(dm, &sfPoint);
418: if (cutLabel) {
419: const PetscInt *ilocal;
420: const PetscSFNode *iremote;
421: PetscInt nroots, nleaves;
423: PetscSFGetGraph(sfPoint, &nroots, &nleaves, &ilocal, &iremote);
424: if (nleaves < 0) {
425: PetscObjectReference((PetscObject) sfPoint);
426: } else {
427: PetscSFCreate(PetscObjectComm((PetscObject) sfPoint), &sfPoint);
428: PetscSFSetGraph(sfPoint, nroots+vExtra, nleaves, ilocal, PETSC_USE_POINTER, iremote, PETSC_USE_POINTER);
429: }
430: } else {
431: PetscObjectReference((PetscObject) sfPoint);
432: }
433: /* Number all vertices */
434: DMPlexCreateNumbering_Plex(dm, vStart, vEnd+vExtra, 0, NULL, sfPoint, &globalVertexNumbers);
435: PetscSFDestroy(&sfPoint);
436: /* Create cones */
437: ISGetIndices(globalVertexNumbers, &gvertex);
438: PetscMalloc1(conesSize, &vertices);
439: for (cell = cStart, v = 0; cell < cEnd; ++cell) {
440: PetscInt *closure = NULL;
441: PetscInt closureSize, Nc = 0, p, value = -1;
442: PetscBool replace;
444: if (cutLabel) {DMLabelGetValue(cutLabel, cell, &value);}
445: replace = (value == 2) ? PETSC_TRUE : PETSC_FALSE;
446: DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
447: for (p = 0; p < closureSize*2; p += 2) {
448: if ((closure[p] >= vStart) && (closure[p] < vEnd)) {
449: closure[Nc++] = closure[p];
450: }
451: }
452: DMPlexReorderCell(dm, cell, closure);
453: for (p = 0; p < Nc; ++p) {
454: PetscInt nv, gv = gvertex[closure[p] - vStart];
456: if (replace) {
457: PetscFindInt(closure[p], vExtra, cutverts, &nv);
458: if (nv >= 0) gv = gvertex[vEnd - vStart + nv];
459: }
460: vertices[v++] = gv < 0 ? -(gv+1) : gv;
461: }
462: DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
463: }
464: ISRestoreIndices(globalVertexNumbers, &gvertex);
465: ISDestroy(&globalVertexNumbers);
466: if (cutvertices) {ISRestoreIndices(cutvertices, &cutverts);}
467: ISDestroy(&cutvertices);
468: DMLabelDestroy(&cutVertexLabel);
469: if (v != conesSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cell vertices %d != %d", v, conesSize);
470: ISCreateGeneral(PetscObjectComm((PetscObject) dm), conesSize, vertices, PETSC_OWN_POINTER, cellIS);
471: PetscLayoutSetBlockSize((*cellIS)->map, *numCorners);
472: PetscObjectSetName((PetscObject) *cellIS, "cells");
473: return(0);
474: }
476: static PetscErrorCode DMPlexWriteTopology_Vertices_HDF5_Static(DM dm, PetscViewer viewer)
477: {
478: DM cdm;
479: DMLabel depthLabel, ctLabel;
480: IS cellIS;
481: PetscInt dim, depth, cellHeight, c;
482: hid_t fileId, groupId;
483: PetscErrorCode ierr;
486: PetscViewerHDF5PushGroup(viewer, "/viz");
487: PetscViewerHDF5OpenGroup(viewer, &fileId, &groupId);
488: PetscStackCallHDF5(H5Gclose,(groupId));
490: PetscViewerHDF5PopGroup(viewer);
491: DMGetDimension(dm, &dim);
492: DMPlexGetDepth(dm, &depth);
493: DMGetCoordinateDM(dm, &cdm);
494: DMPlexGetVTKCellHeight(dm, &cellHeight);
495: DMPlexGetDepthLabel(dm, &depthLabel);
496: DMPlexGetCellTypeLabel(dm, &ctLabel);
497: for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
498: const DMPolytopeType ict = (DMPolytopeType) c;
499: PetscInt pStart, pEnd, dep, numCorners, n = 0;
500: PetscBool output = PETSC_FALSE, doOutput;
502: DMLabelGetStratumBounds(ctLabel, ict, &pStart, &pEnd);
503: if (pStart >= 0) {
504: DMLabelGetValue(depthLabel, pStart, &dep);
505: if (dep == depth - cellHeight) output = PETSC_TRUE;
506: }
507: MPI_Allreduce(&output, &doOutput, 1, MPIU_BOOL, MPI_LOR, PetscObjectComm((PetscObject) dm));
508: if (!doOutput) continue;
509: CreateConesIS_Private(dm, pStart, pEnd, &numCorners, &cellIS);
510: if (!n) {
511: PetscViewerHDF5PushGroup(viewer, "/viz/topology");
512: } else {
513: char group[PETSC_MAX_PATH_LEN];
515: PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/viz/topology_%D", n);
516: PetscViewerHDF5PushGroup(viewer, group);
517: }
518: ISView(cellIS, viewer);
519: PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject) cellIS, "cell_corners", PETSC_INT, (void *) &numCorners);
520: PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject) cellIS, "cell_dim", PETSC_INT, (void *) &dim);
521: ISDestroy(&cellIS);
522: PetscViewerHDF5PopGroup(viewer);
523: ++n;
524: }
525: return(0);
526: }
528: static PetscErrorCode DMPlexWriteCoordinates_HDF5_Static(DM dm, PetscViewer viewer)
529: {
530: DM cdm;
531: Vec coordinates, newcoords;
532: PetscReal lengthScale;
533: PetscInt m, M, bs;
537: DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);
538: DMGetCoordinateDM(dm, &cdm);
539: DMGetCoordinates(dm, &coordinates);
540: VecCreate(PetscObjectComm((PetscObject) coordinates), &newcoords);
541: PetscObjectSetName((PetscObject) newcoords, "vertices");
542: VecGetSize(coordinates, &M);
543: VecGetLocalSize(coordinates, &m);
544: VecSetSizes(newcoords, m, M);
545: VecGetBlockSize(coordinates, &bs);
546: VecSetBlockSize(newcoords, bs);
547: VecSetType(newcoords,VECSTANDARD);
548: VecCopy(coordinates, newcoords);
549: VecScale(newcoords, lengthScale);
550: /* Did not use DMGetGlobalVector() in order to bypass default group assignment */
551: PetscViewerHDF5PushGroup(viewer, "/geometry");
552: PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE);
553: VecView(newcoords, viewer);
554: PetscViewerPopFormat(viewer);
555: PetscViewerHDF5PopGroup(viewer);
556: VecDestroy(&newcoords);
557: return(0);
558: }
560: static PetscErrorCode DMPlexWriteCoordinates_Vertices_HDF5_Static(DM dm, PetscViewer viewer)
561: {
562: DM cdm;
563: Vec coordinatesLocal, newcoords;
564: PetscSection cSection, cGlobalSection;
565: PetscScalar *coords, *ncoords;
566: DMLabel cutLabel, cutVertexLabel = NULL;
567: const PetscReal *L;
568: const DMBoundaryType *bd;
569: PetscReal lengthScale;
570: PetscInt vStart, vEnd, v, bs, N, coordSize, dof, off, d;
571: PetscBool localized, embedded;
572: hid_t fileId, groupId;
573: PetscErrorCode ierr;
576: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
577: DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);
578: DMGetCoordinatesLocal(dm, &coordinatesLocal);
579: VecGetBlockSize(coordinatesLocal, &bs);
580: DMGetCoordinatesLocalized(dm, &localized);
581: if (localized == PETSC_FALSE) return(0);
582: DMGetPeriodicity(dm, NULL, NULL, &L, &bd);
583: DMGetCoordinateDM(dm, &cdm);
584: DMGetLocalSection(cdm, &cSection);
585: DMGetGlobalSection(cdm, &cGlobalSection);
586: DMGetLabel(dm, "periodic_cut", &cutLabel);
587: N = 0;
589: DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel);
590: VecCreate(PetscObjectComm((PetscObject) dm), &newcoords);
591: PetscSectionGetDof(cSection, vStart, &dof);
592: PetscPrintf(PETSC_COMM_SELF, "DOF: %D\n", dof);
593: embedded = (PetscBool) (L && dof == 2 && !cutLabel);
594: if (cutVertexLabel) {
595: DMLabelGetStratumSize(cutVertexLabel, 1, &v);
596: N += dof*v;
597: }
598: for (v = vStart; v < vEnd; ++v) {
599: PetscSectionGetDof(cGlobalSection, v, &dof);
600: if (dof < 0) continue;
601: if (embedded) N += dof+1;
602: else N += dof;
603: }
604: if (embedded) {VecSetBlockSize(newcoords, bs+1);}
605: else {VecSetBlockSize(newcoords, bs);}
606: VecSetSizes(newcoords, N, PETSC_DETERMINE);
607: VecSetType(newcoords, VECSTANDARD);
608: VecGetArray(coordinatesLocal, &coords);
609: VecGetArray(newcoords, &ncoords);
610: coordSize = 0;
611: for (v = vStart; v < vEnd; ++v) {
612: PetscSectionGetDof(cGlobalSection, v, &dof);
613: PetscSectionGetOffset(cSection, v, &off);
614: if (dof < 0) continue;
615: if (embedded) {
616: if ((bd[0] == DM_BOUNDARY_PERIODIC) && (bd[1] == DM_BOUNDARY_PERIODIC)) {
617: PetscReal theta, phi, r, R;
618: /* XY-periodic */
619: /* Suppose its an y-z circle, then
620: \hat r = (0, cos(th), sin(th)) \hat x = (1, 0, 0)
621: and the circle in that plane is
622: \hat r cos(phi) + \hat x sin(phi) */
623: theta = 2.0*PETSC_PI*PetscRealPart(coords[off+1])/L[1];
624: phi = 2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0];
625: r = L[0]/(2.0*PETSC_PI * 2.0*L[1]);
626: R = L[1]/(2.0*PETSC_PI);
627: ncoords[coordSize++] = PetscSinReal(phi) * r;
628: ncoords[coordSize++] = -PetscCosReal(theta) * (R + r * PetscCosReal(phi));
629: ncoords[coordSize++] = PetscSinReal(theta) * (R + r * PetscCosReal(phi));
630: } else if ((bd[0] == DM_BOUNDARY_PERIODIC)) {
631: /* X-periodic */
632: ncoords[coordSize++] = -PetscCosReal(2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0])*(L[0]/(2.0*PETSC_PI));
633: ncoords[coordSize++] = coords[off+1];
634: ncoords[coordSize++] = PetscSinReal(2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0])*(L[0]/(2.0*PETSC_PI));
635: } else if ((bd[1] == DM_BOUNDARY_PERIODIC)) {
636: /* Y-periodic */
637: ncoords[coordSize++] = coords[off+0];
638: ncoords[coordSize++] = PetscSinReal(2.0*PETSC_PI*PetscRealPart(coords[off+1])/L[1])*(L[1]/(2.0*PETSC_PI));
639: ncoords[coordSize++] = -PetscCosReal(2.0*PETSC_PI*PetscRealPart(coords[off+1])/L[1])*(L[1]/(2.0*PETSC_PI));
640: } else if ((bd[0] == DM_BOUNDARY_TWIST)) {
641: PetscReal phi, r, R;
642: /* Mobius strip */
643: /* Suppose its an x-z circle, then
644: \hat r = (-cos(phi), 0, sin(phi)) \hat y = (0, 1, 0)
645: and in that plane we rotate by pi as we go around the circle
646: \hat r cos(phi/2) + \hat y sin(phi/2) */
647: phi = 2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0];
648: R = L[0];
649: r = PetscRealPart(coords[off+1]) - L[1]/2.0;
650: ncoords[coordSize++] = -PetscCosReal(phi) * (R + r * PetscCosReal(phi/2.0));
651: ncoords[coordSize++] = PetscSinReal(phi/2.0) * r;
652: ncoords[coordSize++] = PetscSinReal(phi) * (R + r * PetscCosReal(phi/2.0));
653: } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Cannot handle periodicity in this domain");
654: } else {
655: for (d = 0; d < dof; ++d, ++coordSize) ncoords[coordSize] = coords[off+d];
656: }
657: }
658: if (cutVertexLabel) {
659: IS vertices;
660: const PetscInt *verts;
661: PetscInt n;
663: DMLabelGetStratumIS(cutVertexLabel, 1, &vertices);
664: if (vertices) {
665: ISGetIndices(vertices, &verts);
666: ISGetLocalSize(vertices, &n);
667: for (v = 0; v < n; ++v) {
668: PetscSectionGetDof(cSection, verts[v], &dof);
669: PetscSectionGetOffset(cSection, verts[v], &off);
670: for (d = 0; d < dof; ++d) ncoords[coordSize++] = coords[off+d] + ((bd[d] == DM_BOUNDARY_PERIODIC) ? L[d] : 0.0);
671: }
672: ISRestoreIndices(vertices, &verts);
673: ISDestroy(&vertices);
674: }
675: }
676: if (coordSize != N) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatched sizes: %D != %D", coordSize, N);
677: DMLabelDestroy(&cutVertexLabel);
678: VecRestoreArray(coordinatesLocal, &coords);
679: VecRestoreArray(newcoords, &ncoords);
680: PetscObjectSetName((PetscObject) newcoords, "vertices");
681: VecScale(newcoords, lengthScale);
682: PetscViewerHDF5PushGroup(viewer, "/viz");
683: PetscViewerHDF5OpenGroup(viewer, &fileId, &groupId);
684: PetscStackCallHDF5(H5Gclose,(groupId));
685: PetscViewerHDF5PopGroup(viewer);
686: PetscViewerHDF5PushGroup(viewer, "/viz/geometry");
687: VecView(newcoords, viewer);
688: PetscViewerHDF5PopGroup(viewer);
689: VecDestroy(&newcoords);
690: return(0);
691: }
694: static PetscErrorCode DMPlexWriteLabels_HDF5_Static(DM dm, IS globalPointNumbers, PetscViewer viewer)
695: {
696: const PetscInt *gpoint;
697: PetscInt numLabels, l;
698: hid_t fileId, groupId;
699: PetscErrorCode ierr;
702: ISGetIndices(globalPointNumbers, &gpoint);
703: PetscViewerHDF5PushGroup(viewer, "/labels");
704: PetscViewerHDF5OpenGroup(viewer, &fileId, &groupId);
705: if (groupId != fileId) PetscStackCallHDF5(H5Gclose,(groupId));
706: PetscViewerHDF5PopGroup(viewer);
707: DMGetNumLabels(dm, &numLabels);
708: for (l = 0; l < numLabels; ++l) {
709: DMLabel label;
710: const char *name;
711: IS valueIS, pvalueIS, globalValueIS;
712: const PetscInt *values;
713: PetscInt numValues, v;
714: PetscBool isDepth, output;
715: char group[PETSC_MAX_PATH_LEN];
717: DMGetLabelName(dm, l, &name);
718: DMGetLabelOutput(dm, name, &output);
719: PetscStrncmp(name, "depth", 10, &isDepth);
720: if (isDepth || !output) continue;
721: DMGetLabel(dm, name, &label);
722: PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/labels/%s", name);
723: PetscViewerHDF5PushGroup(viewer, group);
724: PetscViewerHDF5OpenGroup(viewer, &fileId, &groupId);
725: if (groupId != fileId) PetscStackCallHDF5(H5Gclose,(groupId));
726: PetscViewerHDF5PopGroup(viewer);
727: DMLabelGetValueIS(label, &valueIS);
728: /* Must copy to a new IS on the global comm */
729: ISGetLocalSize(valueIS, &numValues);
730: ISGetIndices(valueIS, &values);
731: ISCreateGeneral(PetscObjectComm((PetscObject) dm), numValues, values, PETSC_COPY_VALUES, &pvalueIS);
732: ISRestoreIndices(valueIS, &values);
733: ISAllGather(pvalueIS, &globalValueIS);
734: ISDestroy(&pvalueIS);
735: ISSortRemoveDups(globalValueIS);
736: ISGetLocalSize(globalValueIS, &numValues);
737: ISGetIndices(globalValueIS, &values);
738: for (v = 0; v < numValues; ++v) {
739: IS stratumIS, globalStratumIS;
740: const PetscInt *spoints = NULL;
741: PetscInt *gspoints, n = 0, gn, p;
742: const char *iname = "indices";
744: PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/labels/%s/%d", name, values[v]);
745: DMLabelGetStratumIS(label, values[v], &stratumIS);
747: if (stratumIS) {ISGetLocalSize(stratumIS, &n);}
748: if (stratumIS) {ISGetIndices(stratumIS, &spoints);}
749: for (gn = 0, p = 0; p < n; ++p) if (gpoint[spoints[p]] >= 0) ++gn;
750: PetscMalloc1(gn,&gspoints);
751: for (gn = 0, p = 0; p < n; ++p) if (gpoint[spoints[p]] >= 0) gspoints[gn++] = gpoint[spoints[p]];
752: if (stratumIS) {ISRestoreIndices(stratumIS, &spoints);}
753: ISCreateGeneral(PetscObjectComm((PetscObject) dm), gn, gspoints, PETSC_OWN_POINTER, &globalStratumIS);
754: if (stratumIS) {PetscObjectGetName((PetscObject) stratumIS, &iname);}
755: PetscObjectSetName((PetscObject) globalStratumIS, iname);
757: PetscViewerHDF5PushGroup(viewer, group);
758: ISView(globalStratumIS, viewer);
759: PetscViewerHDF5PopGroup(viewer);
760: ISDestroy(&globalStratumIS);
761: ISDestroy(&stratumIS);
762: }
763: ISRestoreIndices(globalValueIS, &values);
764: ISDestroy(&globalValueIS);
765: ISDestroy(&valueIS);
766: }
767: ISRestoreIndices(globalPointNumbers, &gpoint);
768: return(0);
769: }
771: /* We only write cells and vertices. Does this screw up parallel reading? */
772: PetscErrorCode DMPlexView_HDF5_Internal(DM dm, PetscViewer viewer)
773: {
774: IS globalPointNumbers;
775: PetscViewerFormat format;
776: PetscBool viz_geom=PETSC_FALSE, xdmf_topo=PETSC_FALSE, petsc_topo=PETSC_FALSE;
777: PetscErrorCode ierr;
780: DMPlexCreatePointNumbering(dm, &globalPointNumbers);
781: DMPlexWriteCoordinates_HDF5_Static(dm, viewer);
782: DMPlexWriteLabels_HDF5_Static(dm, globalPointNumbers, viewer);
784: PetscViewerGetFormat(viewer, &format);
785: switch (format) {
786: case PETSC_VIEWER_HDF5_VIZ:
787: viz_geom = PETSC_TRUE;
788: xdmf_topo = PETSC_TRUE;
789: break;
790: case PETSC_VIEWER_HDF5_XDMF:
791: xdmf_topo = PETSC_TRUE;
792: break;
793: case PETSC_VIEWER_HDF5_PETSC:
794: petsc_topo = PETSC_TRUE;
795: break;
796: case PETSC_VIEWER_DEFAULT:
797: case PETSC_VIEWER_NATIVE:
798: viz_geom = PETSC_TRUE;
799: xdmf_topo = PETSC_TRUE;
800: petsc_topo = PETSC_TRUE;
801: break;
802: default:
803: SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]);
804: }
806: if (viz_geom) {DMPlexWriteCoordinates_Vertices_HDF5_Static(dm, viewer);}
807: if (xdmf_topo) {DMPlexWriteTopology_Vertices_HDF5_Static(dm, viewer);}
808: if (petsc_topo) {DMPlexWriteTopology_HDF5_Static(dm, globalPointNumbers, viewer);}
810: ISDestroy(&globalPointNumbers);
811: return(0);
812: }
814: typedef struct {
815: PetscMPIInt rank;
816: DM dm;
817: PetscViewer viewer;
818: DMLabel label;
819: } LabelCtx;
821: static herr_t ReadLabelStratumHDF5_Static(hid_t g_id, const char *name, const H5L_info_t *info, void *op_data)
822: {
823: PetscViewer viewer = ((LabelCtx *) op_data)->viewer;
824: DMLabel label = ((LabelCtx *) op_data)->label;
825: IS stratumIS;
826: const PetscInt *ind;
827: PetscInt value, N, i;
828: const char *lname;
829: char group[PETSC_MAX_PATH_LEN];
830: PetscErrorCode ierr;
832: PetscOptionsStringToInt(name, &value);
833: ISCreate(PetscObjectComm((PetscObject) viewer), &stratumIS);
834: PetscObjectSetName((PetscObject) stratumIS, "indices");
835: PetscObjectGetName((PetscObject) label, &lname);
836: PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/labels/%s/%s", lname, name);
837: PetscViewerHDF5PushGroup(viewer, group);
838: {
839: /* Force serial load */
840: PetscViewerHDF5ReadSizes(viewer, "indices", NULL, &N);
841: PetscLayoutSetLocalSize(stratumIS->map, !((LabelCtx *) op_data)->rank ? N : 0);
842: PetscLayoutSetSize(stratumIS->map, N);
843: }
844: ISLoad(stratumIS, viewer);
845: PetscViewerHDF5PopGroup(viewer);
846: ISGetLocalSize(stratumIS, &N);
847: ISGetIndices(stratumIS, &ind);
848: for (i = 0; i < N; ++i) {DMLabelSetValue(label, ind[i], value);}
849: ISRestoreIndices(stratumIS, &ind);
850: ISDestroy(&stratumIS);
851: return 0;
852: }
854: static herr_t ReadLabelHDF5_Static(hid_t g_id, const char *name, const H5L_info_t *info, void *op_data)
855: {
856: DM dm = ((LabelCtx *) op_data)->dm;
857: hsize_t idx = 0;
859: herr_t err;
861: DMCreateLabel(dm, name); if (ierr) return (herr_t) ierr;
862: DMGetLabel(dm, name, &((LabelCtx *) op_data)->label); if (ierr) return (herr_t) ierr;
863: PetscStackCall("H5Literate_by_name",err = H5Literate_by_name(g_id, name, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelStratumHDF5_Static, op_data, 0));
864: return err;
865: }
867: PetscErrorCode DMPlexLoadLabels_HDF5_Internal(DM dm, PetscViewer viewer)
868: {
869: LabelCtx ctx;
870: hid_t fileId, groupId;
871: hsize_t idx = 0;
872: PetscErrorCode ierr;
875: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &ctx.rank);
876: ctx.dm = dm;
877: ctx.viewer = viewer;
878: PetscViewerHDF5PushGroup(viewer, "/labels");
879: PetscViewerHDF5OpenGroup(viewer, &fileId, &groupId);
880: PetscStackCallHDF5(H5Literate,(groupId, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelHDF5_Static, &ctx));
881: PetscStackCallHDF5(H5Gclose,(groupId));
882: PetscViewerHDF5PopGroup(viewer);
883: return(0);
884: }
886: /* The first version will read everything onto proc 0, letting the user distribute
887: The next will create a naive partition, and then rebalance after reading
888: */
889: PetscErrorCode DMPlexLoad_HDF5_Internal(DM dm, PetscViewer viewer)
890: {
891: PetscSection coordSection;
892: Vec coordinates;
893: IS orderIS, conesIS, cellsIS, orntsIS;
894: const PetscInt *order, *cones, *cells, *ornts;
895: PetscReal lengthScale;
896: PetscInt *cone, *ornt;
897: PetscInt dim, spatialDim, N, numVertices, vStart, vEnd, v, pEnd, p, q, maxConeSize = 0, c;
898: PetscMPIInt rank;
899: PetscErrorCode ierr;
902: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
903: /* Read toplogy */
904: PetscViewerHDF5PushGroup(viewer, "/topology");
905: ISCreate(PetscObjectComm((PetscObject) dm), &orderIS);
906: PetscObjectSetName((PetscObject) orderIS, "order");
907: ISCreate(PetscObjectComm((PetscObject) dm), &conesIS);
908: PetscObjectSetName((PetscObject) conesIS, "cones");
909: ISCreate(PetscObjectComm((PetscObject) dm), &cellsIS);
910: PetscObjectSetName((PetscObject) cellsIS, "cells");
911: ISCreate(PetscObjectComm((PetscObject) dm), &orntsIS);
912: PetscObjectSetName((PetscObject) orntsIS, "orientation");
913: PetscViewerHDF5ReadObjectAttribute(viewer, (PetscObject) cellsIS, "cell_dim", PETSC_INT, (void *) &dim);
914: DMSetDimension(dm, dim);
915: {
916: /* Force serial load */
917: PetscViewerHDF5ReadSizes(viewer, "order", NULL, &pEnd);
918: PetscLayoutSetLocalSize(orderIS->map, !rank ? pEnd : 0);
919: PetscLayoutSetSize(orderIS->map, pEnd);
920: PetscViewerHDF5ReadSizes(viewer, "cones", NULL, &pEnd);
921: PetscLayoutSetLocalSize(conesIS->map, !rank ? pEnd : 0);
922: PetscLayoutSetSize(conesIS->map, pEnd);
923: pEnd = !rank ? pEnd : 0;
924: PetscViewerHDF5ReadSizes(viewer, "cells", NULL, &N);
925: PetscLayoutSetLocalSize(cellsIS->map, !rank ? N : 0);
926: PetscLayoutSetSize(cellsIS->map, N);
927: PetscViewerHDF5ReadSizes(viewer, "orientation", NULL, &N);
928: PetscLayoutSetLocalSize(orntsIS->map, !rank ? N : 0);
929: PetscLayoutSetSize(orntsIS->map, N);
930: }
931: ISLoad(orderIS, viewer);
932: ISLoad(conesIS, viewer);
933: ISLoad(cellsIS, viewer);
934: ISLoad(orntsIS, viewer);
935: PetscViewerHDF5PopGroup(viewer);
936: /* Read geometry */
937: PetscViewerHDF5PushGroup(viewer, "/geometry");
938: VecCreate(PetscObjectComm((PetscObject) dm), &coordinates);
939: PetscObjectSetName((PetscObject) coordinates, "vertices");
940: {
941: /* Force serial load */
942: PetscViewerHDF5ReadSizes(viewer, "vertices", &spatialDim, &N);
943: VecSetSizes(coordinates, !rank ? N : 0, N);
944: VecSetBlockSize(coordinates, spatialDim);
945: }
946: VecLoad(coordinates, viewer);
947: PetscViewerHDF5PopGroup(viewer);
948: DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);
949: VecScale(coordinates, 1.0/lengthScale);
950: VecGetLocalSize(coordinates, &numVertices);
951: VecGetBlockSize(coordinates, &spatialDim);
952: numVertices /= spatialDim;
953: /* Create Plex */
954: DMPlexSetChart(dm, 0, pEnd);
955: ISGetIndices(orderIS, &order);
956: ISGetIndices(conesIS, &cones);
957: for (p = 0; p < pEnd; ++p) {
958: DMPlexSetConeSize(dm, order[p], cones[p]);
959: maxConeSize = PetscMax(maxConeSize, cones[p]);
960: }
961: DMSetUp(dm);
962: ISGetIndices(cellsIS, &cells);
963: ISGetIndices(orntsIS, &ornts);
964: PetscMalloc2(maxConeSize,&cone,maxConeSize,&ornt);
965: for (p = 0, q = 0; p < pEnd; ++p) {
966: for (c = 0; c < cones[p]; ++c, ++q) {cone[c] = cells[q]; ornt[c] = ornts[q];}
967: DMPlexSetCone(dm, order[p], cone);
968: DMPlexSetConeOrientation(dm, order[p], ornt);
969: }
970: PetscFree2(cone,ornt);
971: ISRestoreIndices(orderIS, &order);
972: ISRestoreIndices(conesIS, &cones);
973: ISRestoreIndices(cellsIS, &cells);
974: ISRestoreIndices(orntsIS, &ornts);
975: ISDestroy(&orderIS);
976: ISDestroy(&conesIS);
977: ISDestroy(&cellsIS);
978: ISDestroy(&orntsIS);
979: DMPlexSymmetrize(dm);
980: DMPlexStratify(dm);
981: /* Create coordinates */
982: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
983: if (numVertices != vEnd - vStart) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of coordinates loaded %d does not match number of vertices %d", numVertices, vEnd - vStart);
984: DMGetCoordinateSection(dm, &coordSection);
985: PetscSectionSetNumFields(coordSection, 1);
986: PetscSectionSetFieldComponents(coordSection, 0, spatialDim);
987: PetscSectionSetChart(coordSection, vStart, vEnd);
988: for (v = vStart; v < vEnd; ++v) {
989: PetscSectionSetDof(coordSection, v, spatialDim);
990: PetscSectionSetFieldDof(coordSection, v, 0, spatialDim);
991: }
992: PetscSectionSetUp(coordSection);
993: DMSetCoordinates(dm, coordinates);
994: VecDestroy(&coordinates);
995: /* Read Labels */
996: DMPlexLoadLabels_HDF5_Internal(dm, viewer);
997: return(0);
998: }
999: #endif