Actual source code: plexcgns.c

  1: #define PETSCDM_DLL
  2: #include <petsc/private/dmpleximpl.h>

  4: #undef I /* Very old CGNS stupidly uses I as a variable, which fails when using complex. Curse you idiot package managers */
  5: #if defined(PETSC_HAVE_CGNS)
  6: #include <cgnslib.h>
  7: #include <cgns_io.h>
  8: #endif
  9: #if !defined(CGNS_ENUMT)
 10: #define CGNS_ENUMT(a) a
 11: #endif
 12: #if !defined(CGNS_ENUMV)
 13: #define CGNS_ENUMV(a) a
 14: #endif

 16: #define PetscCallCGNS(ierr) \
 17: do { \
 18:   int _cgns_ier = (ierr); \
 20: } while (0)

 22: /*@C
 23:   DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file.

 25:   Collective

 27:   Input Parameters:
 28: + comm  - The MPI communicator
 29: . filename - The name of the CGNS file
 30: - interpolate - Create faces and edges in the mesh

 32:   Output Parameter:
 33: . dm  - The DM object representing the mesh

 35:   Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html

 37:   Level: beginner

 39: .seealso: DMPlexCreate(), DMPlexCreateCGNS(), DMPlexCreateExodus()
 40: @*/
 41: PetscErrorCode DMPlexCreateCGNSFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
 42: {
 43:   PetscMPIInt    rank;
 44: #if defined(PETSC_HAVE_CGNS)
 45:   int cgid = -1;
 46: #endif

 49:   MPI_Comm_rank(comm, &rank);
 50: #if defined(PETSC_HAVE_CGNS)
 51:   if (rank == 0) {
 52:     cg_open(filename, CG_MODE_READ, &cgid);
 54:   }
 55:   DMPlexCreateCGNS(comm, cgid, interpolate, dm);
 56:   if (rank == 0) cg_close(cgid);
 57:   return 0;
 58: #else
 59:   SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir");
 60: #endif
 61: }

 63: /*@
 64:   DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file ID.

 66:   Collective

 68:   Input Parameters:
 69: + comm  - The MPI communicator
 70: . cgid - The CG id associated with a file and obtained using cg_open
 71: - interpolate - Create faces and edges in the mesh

 73:   Output Parameter:
 74: . dm  - The DM object representing the mesh

 76:   Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html

 78:   Level: beginner

 80: .seealso: DMPlexCreate(), DMPlexCreateExodus()
 81: @*/
 82: PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm)
 83: {
 84: #if defined(PETSC_HAVE_CGNS)
 85:   PetscMPIInt    num_proc, rank;
 86:   DM             cdm;
 87:   DMLabel        label;
 88:   PetscSection   coordSection;
 89:   Vec            coordinates;
 90:   PetscScalar   *coords;
 91:   PetscInt      *cellStart, *vertStart, v;
 92:   PetscInt       labelIdRange[2], labelId;
 93:   /* Read from file */
 94:   char basename[CGIO_MAX_NAME_LENGTH+1];
 95:   char buffer[CGIO_MAX_NAME_LENGTH+1];
 96:   int  dim    = 0, physDim = 0, coordDim =0, numVertices = 0, numCells = 0;
 97:   int  nzones = 0;
 98: #endif

100: #if defined(PETSC_HAVE_CGNS)
101:   MPI_Comm_rank(comm, &rank);
102:   MPI_Comm_size(comm, &num_proc);
103:   DMCreate(comm, dm);
104:   DMSetType(*dm, DMPLEX);

106:   /* Open CGNS II file and read basic information on rank 0, then broadcast to all processors */
107:   if (rank == 0) {
108:     int nbases, z;

110:     cg_nbases(cgid, &nbases);
112:     cg_base_read(cgid, 1, basename, &dim, &physDim);
113:     cg_nzones(cgid, 1, &nzones);
114:     PetscCalloc2(nzones+1, &cellStart, nzones+1, &vertStart);
115:     for (z = 1; z <= nzones; ++z) {
116:       cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */

118:       cg_zone_read(cgid, 1, z, buffer, sizes);
119:       numVertices += sizes[0];
120:       numCells    += sizes[1];
121:       cellStart[z] += sizes[1] + cellStart[z-1];
122:       vertStart[z] += sizes[0] + vertStart[z-1];
123:     }
124:     for (z = 1; z <= nzones; ++z) {
125:       vertStart[z] += numCells;
126:     }
127:     coordDim = dim;
128:   }
129:   MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH+1, MPI_CHAR, 0, comm);
130:   MPI_Bcast(&dim, 1, MPI_INT, 0, comm);
131:   MPI_Bcast(&coordDim, 1, MPI_INT, 0, comm);
132:   MPI_Bcast(&nzones, 1, MPI_INT, 0, comm);

134:   PetscObjectSetName((PetscObject) *dm, basename);
135:   DMSetDimension(*dm, dim);
136:   DMCreateLabel(*dm, "celltype");
137:   DMPlexSetChart(*dm, 0, numCells+numVertices);

139:   /* Read zone information */
140:   if (rank == 0) {
141:     int z, c, c_loc;

143:     /* Read the cell set connectivity table and build mesh topology
144:        CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */
145:     /* First set sizes */
146:     for (z = 1, c = 0; z <= nzones; ++z) {
147:       CGNS_ENUMT(ZoneType_t)    zonetype;
148:       int                       nsections;
149:       CGNS_ENUMT(ElementType_t) cellType;
150:       cgsize_t                  start, end;
151:       int                       nbndry, parentFlag;
152:       PetscInt                  numCorners;
153:       DMPolytopeType            ctype;

155:       cg_zone_type(cgid, 1, z, &zonetype);
157:       cg_nsections(cgid, 1, z, &nsections);
159:       cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);
160:       /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
161:       if (cellType == CGNS_ENUMV(MIXED)) {
162:         cgsize_t elementDataSize, *elements;
163:         PetscInt off;

165:         cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);
166:         PetscMalloc1(elementDataSize, &elements);
167:         cg_poly_elements_read(cgid, 1, z, 1, elements, NULL, NULL);
168:         for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) {
169:           switch (elements[off]) {
170:           case CGNS_ENUMV(BAR_2):   numCorners = 2; ctype = DM_POLYTOPE_SEGMENT;       break;
171:           case CGNS_ENUMV(TRI_3):   numCorners = 3; ctype = DM_POLYTOPE_TRIANGLE;      break;
172:           case CGNS_ENUMV(QUAD_4):  numCorners = 4; ctype = DM_POLYTOPE_QUADRILATERAL; break;
173:           case CGNS_ENUMV(TETRA_4): numCorners = 4; ctype = DM_POLYTOPE_TETRAHEDRON;   break;
174:           case CGNS_ENUMV(PENTA_6): numCorners = 6; ctype = DM_POLYTOPE_TRI_PRISM;     break;
175:           case CGNS_ENUMV(HEXA_8):  numCorners = 8; ctype = DM_POLYTOPE_HEXAHEDRON;    break;
176:           default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[off]);
177:           }
178:           DMPlexSetConeSize(*dm, c, numCorners);
179:           DMPlexSetCellType(*dm, c, ctype);
180:           off += numCorners+1;
181:         }
182:         PetscFree(elements);
183:       } else {
184:         switch (cellType) {
185:         case CGNS_ENUMV(BAR_2):   numCorners = 2; ctype = DM_POLYTOPE_SEGMENT;       break;
186:         case CGNS_ENUMV(TRI_3):   numCorners = 3; ctype = DM_POLYTOPE_TRIANGLE;      break;
187:         case CGNS_ENUMV(QUAD_4):  numCorners = 4; ctype = DM_POLYTOPE_QUADRILATERAL; break;
188:         case CGNS_ENUMV(TETRA_4): numCorners = 4; ctype = DM_POLYTOPE_TETRAHEDRON;   break;
189:         case CGNS_ENUMV(PENTA_6): numCorners = 6; ctype = DM_POLYTOPE_TRI_PRISM;     break;
190:         case CGNS_ENUMV(HEXA_8):  numCorners = 8; ctype = DM_POLYTOPE_HEXAHEDRON;    break;
191:         default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
192:         }
193:         for (c_loc = start; c_loc <= end; ++c_loc, ++c) {
194:           DMPlexSetConeSize(*dm, c, numCorners);
195:           DMPlexSetCellType(*dm, c, ctype);
196:         }
197:       }
198:     }
199:     for (v = numCells; v < numCells+numVertices; ++v) {
200:       DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);
201:     }
202:   }

204:   DMSetUp(*dm);

206:   DMCreateLabel(*dm, "zone");
207:   if (rank == 0) {
208:     int z, c, c_loc, v_loc;

210:     DMGetLabel(*dm, "zone", &label);
211:     for (z = 1, c = 0; z <= nzones; ++z) {
212:       CGNS_ENUMT(ElementType_t)   cellType;
213:       cgsize_t                    elementDataSize, *elements, start, end;
214:       int                          nbndry, parentFlag;
215:       PetscInt                    *cone, numc, numCorners, maxCorners = 27;

217:       cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);
218:       numc = end - start;
219:       /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
220:       cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);
221:       PetscMalloc2(elementDataSize,&elements,maxCorners,&cone);
222:       cg_poly_elements_read(cgid, 1, z, 1, elements, NULL, NULL);
223:       if (cellType == CGNS_ENUMV(MIXED)) {
224:         /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
225:         for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
226:           switch (elements[v]) {
227:           case CGNS_ENUMV(BAR_2):   numCorners = 2; break;
228:           case CGNS_ENUMV(TRI_3):   numCorners = 3; break;
229:           case CGNS_ENUMV(QUAD_4):  numCorners = 4; break;
230:           case CGNS_ENUMV(TETRA_4): numCorners = 4; break;
231:           case CGNS_ENUMV(PENTA_6): numCorners = 6; break;
232:           case CGNS_ENUMV(HEXA_8):  numCorners = 8; break;
233:           default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[v]);
234:           }
235:           ++v;
236:           for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
237:             cone[v_loc] = elements[v]+numCells-1;
238:           }
239:           DMPlexReorderCell(*dm, c, cone);
240:           DMPlexSetCone(*dm, c, cone);
241:           DMLabelSetValue(label, c, z);
242:         }
243:       } else {
244:         switch (cellType) {
245:         case CGNS_ENUMV(BAR_2):   numCorners = 2; break;
246:         case CGNS_ENUMV(TRI_3):   numCorners = 3; break;
247:         case CGNS_ENUMV(QUAD_4):  numCorners = 4; break;
248:         case CGNS_ENUMV(TETRA_4): numCorners = 4; break;
249:         case CGNS_ENUMV(PENTA_6): numCorners = 6; break;
250:         case CGNS_ENUMV(HEXA_8):  numCorners = 8; break;
251:         default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
252:         }
253:         /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
254:         for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
255:           for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
256:             cone[v_loc] = elements[v]+numCells-1;
257:           }
258:           DMPlexReorderCell(*dm, c, cone);
259:           DMPlexSetCone(*dm, c, cone);
260:           DMLabelSetValue(label, c, z);
261:         }
262:       }
263:       PetscFree2(elements,cone);
264:     }
265:   }

267:   DMPlexSymmetrize(*dm);
268:   DMPlexStratify(*dm);
269:   if (interpolate) {
270:     DM idm;

272:     DMPlexInterpolate(*dm, &idm);
273:     DMDestroy(dm);
274:     *dm  = idm;
275:   }

277:   /* Read coordinates */
278:   DMSetCoordinateDim(*dm, coordDim);
279:   DMGetCoordinateDM(*dm, &cdm);
280:   DMGetLocalSection(cdm, &coordSection);
281:   PetscSectionSetNumFields(coordSection, 1);
282:   PetscSectionSetFieldComponents(coordSection, 0, coordDim);
283:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
284:   for (v = numCells; v < numCells+numVertices; ++v) {
285:     PetscSectionSetDof(coordSection, v, dim);
286:     PetscSectionSetFieldDof(coordSection, v, 0, coordDim);
287:   }
288:   PetscSectionSetUp(coordSection);

290:   DMCreateLocalVector(cdm, &coordinates);
291:   VecGetArray(coordinates, &coords);
292:   if (rank == 0) {
293:     PetscInt off = 0;
294:     float   *x[3];
295:     int      z, d;

297:     PetscMalloc3(numVertices,&x[0],numVertices,&x[1],numVertices,&x[2]);
298:     for (z = 1; z <= nzones; ++z) {
299:       CGNS_ENUMT(DataType_t) datatype;
300:       cgsize_t               sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
301:       cgsize_t               range_min[3] = {1, 1, 1};
302:       cgsize_t               range_max[3] = {1, 1, 1};
303:       int                    ngrids, ncoords;

305:       cg_zone_read(cgid, 1, z, buffer, sizes);
306:       range_max[0] = sizes[0];
307:       cg_ngrids(cgid, 1, z, &ngrids);
309:       cg_ncoords(cgid, 1, z, &ncoords);
311:       for (d = 0; d < coordDim; ++d) {
312:         cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);
313:         cg_coord_read(cgid, 1, z, buffer, CGNS_ENUMV(RealSingle), range_min, range_max, x[d]);
314:       }
315:       if (coordDim >= 1) {
316:         for (v = 0; v < sizes[0]; ++v) coords[(v+off)*coordDim+0] = x[0][v];
317:       }
318:       if (coordDim >= 2) {
319:         for (v = 0; v < sizes[0]; ++v) coords[(v+off)*coordDim+1] = x[1][v];
320:       }
321:       if (coordDim >= 3) {
322:         for (v = 0; v < sizes[0]; ++v) coords[(v+off)*coordDim+2] = x[2][v];
323:       }
324:       off += sizes[0];
325:     }
326:     PetscFree3(x[0],x[1],x[2]);
327:   }
328:   VecRestoreArray(coordinates, &coords);

330:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
331:   VecSetBlockSize(coordinates, coordDim);
332:   DMSetCoordinatesLocal(*dm, coordinates);
333:   VecDestroy(&coordinates);

335:   /* Read boundary conditions */
336:   DMGetNumLabels(*dm, &labelIdRange[0]);
337:   if (rank == 0) {
338:     CGNS_ENUMT(BCType_t)        bctype;
339:     CGNS_ENUMT(DataType_t)      datatype;
340:     CGNS_ENUMT(PointSetType_t)  pointtype;
341:     cgsize_t                    *points;
342:     PetscReal                   *normals;
343:     int                         normal[3];
344:     char                        *bcname = buffer;
345:     cgsize_t                    npoints, nnormals;
346:     int                         z, nbc, bc, c, ndatasets;

348:     for (z = 1; z <= nzones; ++z) {
349:       cg_nbocos(cgid, 1, z, &nbc);
350:       for (bc = 1; bc <= nbc; ++bc) {
351:         cg_boco_info(cgid, 1, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets);
352:         DMCreateLabel(*dm, bcname);
353:         DMGetLabel(*dm, bcname, &label);
354:         PetscMalloc2(npoints, &points, nnormals, &normals);
355:         cg_boco_read(cgid, 1, z, bc, points, (void *) normals);
356:         if (pointtype == CGNS_ENUMV(ElementRange)) {
357:           /* Range of cells: assuming half-open interval since the documentation sucks */
358:           for (c = points[0]; c < points[1]; ++c) {
359:             DMLabelSetValue(label, c - cellStart[z-1], 1);
360:           }
361:         } else if (pointtype == CGNS_ENUMV(ElementList)) {
362:           /* List of cells */
363:           for (c = 0; c < npoints; ++c) {
364:             DMLabelSetValue(label, points[c] - cellStart[z-1], 1);
365:           }
366:         } else if (pointtype == CGNS_ENUMV(PointRange)) {
367:           CGNS_ENUMT(GridLocation_t) gridloc;

369:           /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
370:           cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");
371:           cg_gridlocation_read(&gridloc);
372:           /* Range of points: assuming half-open interval since the documentation sucks */
373:           for (c = points[0]; c < points[1]; ++c) {
374:             if (gridloc == CGNS_ENUMV(Vertex)) DMLabelSetValue(label, c - vertStart[z-1], 1);
375:             else                               DMLabelSetValue(label, c - cellStart[z-1], 1);
376:           }
377:         } else if (pointtype == CGNS_ENUMV(PointList)) {
378:           CGNS_ENUMT(GridLocation_t) gridloc;

380:           /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
381:           cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");
382:           cg_gridlocation_read(&gridloc);
383:           for (c = 0; c < npoints; ++c) {
384:             if (gridloc == CGNS_ENUMV(Vertex)) DMLabelSetValue(label, points[c] - vertStart[z-1], 1);
385:             else                               DMLabelSetValue(label, points[c] - cellStart[z-1], 1);
386:           }
387:         } else SETERRQ(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int) pointtype);
388:         PetscFree2(points, normals);
389:       }
390:     }
391:     PetscFree2(cellStart, vertStart);
392:   }
393:   DMGetNumLabels(*dm, &labelIdRange[1]);
394:   MPI_Bcast(labelIdRange, 2, MPIU_INT, 0, comm);

396:   /* Create BC labels at all processes */
397:   for (labelId = labelIdRange[0]; labelId < labelIdRange[1]; ++labelId) {
398:     char *labelName = buffer;
399:     size_t len = sizeof(buffer);
400:     const char *locName;

402:     if (rank == 0) {
403:       DMGetLabelByNum(*dm, labelId, &label);
404:       PetscObjectGetName((PetscObject)label, &locName);
405:       PetscStrncpy(labelName, locName, len);
406:     }
407:     MPI_Bcast(labelName, (PetscMPIInt)len, MPIU_INT, 0, comm);
408:     DMCreateLabel(*dm, labelName);
409:   }
410:   return 0;
411: #else
412:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir");
413: #endif
414: }