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 CHKERRCGNS(ierr) \
 17: do { \
 18:   int _cgns_ier = (ierr); \
 19:   if (PetscUnlikely(_cgns_ier)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS error %d %s",_cgns_ier,cg_get_error()); \
 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;
 45: #if defined(PETSC_HAVE_CGNS)
 46:   int cgid = -1;
 47: #endif

 51:   MPI_Comm_rank(comm, &rank);
 52: #if defined(PETSC_HAVE_CGNS)
 53:   if (rank == 0) {
 54:     cg_open(filename, CG_MODE_READ, &cgid);CHKERRCGNS(ierr);
 55:     if (cgid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename);
 56:   }
 57:   DMPlexCreateCGNS(comm, cgid, interpolate, dm);
 58:   if (rank == 0) {cg_close(cgid);CHKERRCGNS(ierr);}
 59:   return(0);
 60: #else
 61:   SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir");
 62: #endif
 63: }

 65: /*@
 66:   DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file ID.

 68:   Collective

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

 75:   Output Parameter:
 76: . dm  - The DM object representing the mesh

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

 80:   Level: beginner

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

104: #if defined(PETSC_HAVE_CGNS)
105:   MPI_Comm_rank(comm, &rank);
106:   MPI_Comm_size(comm, &num_proc);
107:   DMCreate(comm, dm);
108:   DMSetType(*dm, DMPLEX);

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

114:     cg_nbases(cgid, &nbases);CHKERRCGNS(ierr);
115:     if (nbases > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single base, not %d\n",nbases);
116:     cg_base_read(cgid, 1, basename, &dim, &physDim);CHKERRCGNS(ierr);
117:     cg_nzones(cgid, 1, &nzones);CHKERRCGNS(ierr);
118:     PetscCalloc2(nzones+1, &cellStart, nzones+1, &vertStart);
119:     for (z = 1; z <= nzones; ++z) {
120:       cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */

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

138:   PetscObjectSetName((PetscObject) *dm, basename);
139:   DMSetDimension(*dm, dim);
140:   DMCreateLabel(*dm, "celltype");
141:   DMPlexSetChart(*dm, 0, numCells+numVertices);

143:   /* Read zone information */
144:   if (rank == 0) {
145:     int z, c, c_loc;

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

159:       cg_zone_type(cgid, 1, z, &zonetype);CHKERRCGNS(ierr);
160:       if (zonetype == CGNS_ENUMV(Structured)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Can only handle Unstructured zones for CGNS");
161:       cg_nsections(cgid, 1, z, &nsections);CHKERRCGNS(ierr);
162:       if (nsections > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single section, not %d\n",nsections);
163:       cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRCGNS(ierr);
164:       /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
165:       if (cellType == CGNS_ENUMV(MIXED)) {
166:         cgsize_t elementDataSize, *elements;
167:         PetscInt off;

169:         cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRCGNS(ierr);
170:         PetscMalloc1(elementDataSize, &elements);
171:         cg_poly_elements_read(cgid, 1, z, 1, elements, NULL, NULL);CHKERRCGNS(ierr);
172:         for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) {
173:           switch (elements[off]) {
174:           case CGNS_ENUMV(BAR_2):   numCorners = 2; ctype = DM_POLYTOPE_SEGMENT;       break;
175:           case CGNS_ENUMV(TRI_3):   numCorners = 3; ctype = DM_POLYTOPE_TRIANGLE;      break;
176:           case CGNS_ENUMV(QUAD_4):  numCorners = 4; ctype = DM_POLYTOPE_QUADRILATERAL; break;
177:           case CGNS_ENUMV(TETRA_4): numCorners = 4; ctype = DM_POLYTOPE_TETRAHEDRON;   break;
178:           case CGNS_ENUMV(PENTA_6): numCorners = 6; ctype = DM_POLYTOPE_TRI_PRISM;     break;
179:           case CGNS_ENUMV(HEXA_8):  numCorners = 8; ctype = DM_POLYTOPE_HEXAHEDRON;    break;
180:           default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[off]);
181:           }
182:           DMPlexSetConeSize(*dm, c, numCorners);
183:           DMPlexSetCellType(*dm, c, ctype);
184:           off += numCorners+1;
185:         }
186:         PetscFree(elements);
187:       } else {
188:         switch (cellType) {
189:         case CGNS_ENUMV(BAR_2):   numCorners = 2; ctype = DM_POLYTOPE_SEGMENT;       break;
190:         case CGNS_ENUMV(TRI_3):   numCorners = 3; ctype = DM_POLYTOPE_TRIANGLE;      break;
191:         case CGNS_ENUMV(QUAD_4):  numCorners = 4; ctype = DM_POLYTOPE_QUADRILATERAL; break;
192:         case CGNS_ENUMV(TETRA_4): numCorners = 4; ctype = DM_POLYTOPE_TETRAHEDRON;   break;
193:         case CGNS_ENUMV(PENTA_6): numCorners = 6; ctype = DM_POLYTOPE_TRI_PRISM;     break;
194:         case CGNS_ENUMV(HEXA_8):  numCorners = 8; ctype = DM_POLYTOPE_HEXAHEDRON;    break;
195:         default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
196:         }
197:         for (c_loc = start; c_loc <= end; ++c_loc, ++c) {
198:           DMPlexSetConeSize(*dm, c, numCorners);
199:           DMPlexSetCellType(*dm, c, ctype);
200:         }
201:       }
202:     }
203:     for (v = numCells; v < numCells+numVertices; ++v) {
204:       DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);
205:     }
206:   }

208:   DMSetUp(*dm);

210:   DMCreateLabel(*dm, "zone");
211:   if (rank == 0) {
212:     int z, c, c_loc, v_loc;

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

221:       cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRCGNS(ierr);
222:       numc = end - start;
223:       /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
224:       cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRCGNS(ierr);
225:       PetscMalloc2(elementDataSize,&elements,maxCorners,&cone);
226:       cg_poly_elements_read(cgid, 1, z, 1, elements, NULL, NULL);CHKERRCGNS(ierr);
227:       if (cellType == CGNS_ENUMV(MIXED)) {
228:         /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
229:         for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
230:           switch (elements[v]) {
231:           case CGNS_ENUMV(BAR_2):   numCorners = 2; break;
232:           case CGNS_ENUMV(TRI_3):   numCorners = 3; break;
233:           case CGNS_ENUMV(QUAD_4):  numCorners = 4; break;
234:           case CGNS_ENUMV(TETRA_4): numCorners = 4; break;
235:           case CGNS_ENUMV(PENTA_6): numCorners = 6; break;
236:           case CGNS_ENUMV(HEXA_8):  numCorners = 8; break;
237:           default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[v]);
238:           }
239:           ++v;
240:           for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
241:             cone[v_loc] = elements[v]+numCells-1;
242:           }
243:           DMPlexReorderCell(*dm, c, cone);
244:           DMPlexSetCone(*dm, c, cone);
245:           DMLabelSetValue(label, c, z);
246:         }
247:       } else {
248:         switch (cellType) {
249:         case CGNS_ENUMV(BAR_2):   numCorners = 2; break;
250:         case CGNS_ENUMV(TRI_3):   numCorners = 3; break;
251:         case CGNS_ENUMV(QUAD_4):  numCorners = 4; break;
252:         case CGNS_ENUMV(TETRA_4): numCorners = 4; break;
253:         case CGNS_ENUMV(PENTA_6): numCorners = 6; break;
254:         case CGNS_ENUMV(HEXA_8):  numCorners = 8; break;
255:         default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
256:         }
257:         /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
258:         for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
259:           for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
260:             cone[v_loc] = elements[v]+numCells-1;
261:           }
262:           DMPlexReorderCell(*dm, c, cone);
263:           DMPlexSetCone(*dm, c, cone);
264:           DMLabelSetValue(label, c, z);
265:         }
266:       }
267:       PetscFree2(elements,cone);
268:     }
269:   }

271:   DMPlexSymmetrize(*dm);
272:   DMPlexStratify(*dm);
273:   if (interpolate) {
274:     DM idm;

276:     DMPlexInterpolate(*dm, &idm);
277:     DMDestroy(dm);
278:     *dm  = idm;
279:   }

281:   /* Read coordinates */
282:   DMSetCoordinateDim(*dm, coordDim);
283:   DMGetCoordinateDM(*dm, &cdm);
284:   DMGetLocalSection(cdm, &coordSection);
285:   PetscSectionSetNumFields(coordSection, 1);
286:   PetscSectionSetFieldComponents(coordSection, 0, coordDim);
287:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
288:   for (v = numCells; v < numCells+numVertices; ++v) {
289:     PetscSectionSetDof(coordSection, v, dim);
290:     PetscSectionSetFieldDof(coordSection, v, 0, coordDim);
291:   }
292:   PetscSectionSetUp(coordSection);

294:   DMCreateLocalVector(cdm, &coordinates);
295:   VecGetArray(coordinates, &coords);
296:   if (rank == 0) {
297:     PetscInt off = 0;
298:     float   *x[3];
299:     int      z, d;

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

309:       cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRCGNS(ierr);
310:       range_max[0] = sizes[0];
311:       cg_ngrids(cgid, 1, z, &ngrids);CHKERRCGNS(ierr);
312:       if (ngrids > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single grid, not %d\n",ngrids);
313:       cg_ncoords(cgid, 1, z, &ncoords);CHKERRCGNS(ierr);
314:       if (ncoords != coordDim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords);
315:       for (d = 0; d < coordDim; ++d) {
316:         cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);CHKERRCGNS(ierr);
317:         cg_coord_read(cgid, 1, z, buffer, CGNS_ENUMV(RealSingle), range_min, range_max, x[d]);CHKERRCGNS(ierr);
318:       }
319:       if (coordDim >= 1) {
320:         for (v = 0; v < sizes[0]; ++v) coords[(v+off)*coordDim+0] = x[0][v];
321:       }
322:       if (coordDim >= 2) {
323:         for (v = 0; v < sizes[0]; ++v) coords[(v+off)*coordDim+1] = x[1][v];
324:       }
325:       if (coordDim >= 3) {
326:         for (v = 0; v < sizes[0]; ++v) coords[(v+off)*coordDim+2] = x[2][v];
327:       }
328:       off += sizes[0];
329:     }
330:     PetscFree3(x[0],x[1],x[2]);
331:   }
332:   VecRestoreArray(coordinates, &coords);

334:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
335:   VecSetBlockSize(coordinates, coordDim);
336:   DMSetCoordinatesLocal(*dm, coordinates);
337:   VecDestroy(&coordinates);

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

352:     for (z = 1; z <= nzones; ++z) {
353:       cg_nbocos(cgid, 1, z, &nbc);CHKERRCGNS(ierr);
354:       for (bc = 1; bc <= nbc; ++bc) {
355:         cg_boco_info(cgid, 1, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets);CHKERRCGNS(ierr);
356:         DMCreateLabel(*dm, bcname);
357:         DMGetLabel(*dm, bcname, &label);
358:         PetscMalloc2(npoints, &points, nnormals, &normals);
359:         cg_boco_read(cgid, 1, z, bc, points, (void *) normals);CHKERRCGNS(ierr);
360:         if (pointtype == CGNS_ENUMV(ElementRange)) {
361:           /* Range of cells: assuming half-open interval since the documentation sucks */
362:           for (c = points[0]; c < points[1]; ++c) {
363:             DMLabelSetValue(label, c - cellStart[z-1], 1);
364:           }
365:         } else if (pointtype == CGNS_ENUMV(ElementList)) {
366:           /* List of cells */
367:           for (c = 0; c < npoints; ++c) {
368:             DMLabelSetValue(label, points[c] - cellStart[z-1], 1);
369:           }
370:         } else if (pointtype == CGNS_ENUMV(PointRange)) {
371:           CGNS_ENUMT(GridLocation_t) gridloc;

373:           /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
374:           cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");CHKERRCGNS(ierr);
375:           cg_gridlocation_read(&gridloc);CHKERRCGNS(ierr);
376:           /* Range of points: assuming half-open interval since the documentation sucks */
377:           for (c = points[0]; c < points[1]; ++c) {
378:             if (gridloc == CGNS_ENUMV(Vertex)) {DMLabelSetValue(label, c - vertStart[z-1], 1);}
379:             else                               {DMLabelSetValue(label, c - cellStart[z-1], 1);}
380:           }
381:         } else if (pointtype == CGNS_ENUMV(PointList)) {
382:           CGNS_ENUMT(GridLocation_t) gridloc;

384:           /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
385:           cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");CHKERRCGNS(ierr);
386:           cg_gridlocation_read(&gridloc);CHKERRCGNS(ierr);
387:           for (c = 0; c < npoints; ++c) {
388:             if (gridloc == CGNS_ENUMV(Vertex)) {DMLabelSetValue(label, points[c] - vertStart[z-1], 1);}
389:             else                               {DMLabelSetValue(label, points[c] - cellStart[z-1], 1);}
390:           }
391:         } else SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int) pointtype);
392:         PetscFree2(points, normals);
393:       }
394:     }
395:     PetscFree2(cellStart, vertStart);
396:   }
397:   DMGetNumLabels(*dm, &labelIdRange[1]);
398:   MPI_Bcast(labelIdRange, 2, MPIU_INT, 0, comm);

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

406:     if (rank == 0) {
407:       DMGetLabelByNum(*dm, labelId, &label);
408:       PetscObjectGetName((PetscObject)label, &locName);
409:       PetscStrncpy(labelName, locName, len);
410:     }
411:     MPI_Bcast(labelName, (PetscMPIInt)len, MPIU_INT, 0, comm);
412:     DMCreateLabel(*dm, labelName);
413:   }
414:   return(0);
415: #else
416:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir");
417: #endif
418: }