1 #define PETSCDM_DLL 2 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 4 #if defined(PETSC_HAVE_CGNS) 5 #include <cgnslib.h> 6 #include <cgns_io.h> 7 #endif 8 9 #undef __FUNCT__ 10 #define __FUNCT__ "DMPlexCreateCGNSFromFile" 11 /*@C 12 DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file. 13 14 Collective on comm 15 16 Input Parameters: 17 + comm - The MPI communicator 18 . filename - The name of the CGNS file 19 - interpolate - Create faces and edges in the mesh 20 21 Output Parameter: 22 . dm - The DM object representing the mesh 23 24 Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html 25 26 Level: beginner 27 28 .keywords: mesh,CGNS 29 .seealso: DMPlexCreate(), DMPlexCreateCGNS(), DMPlexCreateExodus() 30 @*/ 31 PetscErrorCode DMPlexCreateCGNSFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 32 { 33 PetscMPIInt rank; 34 PetscErrorCode ierr; 35 #if defined(PETSC_HAVE_CGNS) 36 int cgid = -1; 37 #endif 38 39 PetscFunctionBegin; 40 PetscValidCharPointer(filename, 2); 41 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 42 #if defined(PETSC_HAVE_CGNS) 43 if (!rank) { 44 ierr = cg_open(filename, CG_MODE_READ, &cgid);CHKERRQ(ierr); 45 if (cgid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename); 46 } 47 ierr = DMPlexCreateCGNS(comm, cgid, interpolate, dm);CHKERRQ(ierr); 48 if (!rank) {ierr = cg_close(cgid);CHKERRQ(ierr);} 49 #else 50 SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir"); 51 #endif 52 PetscFunctionReturn(0); 53 } 54 55 #undef __FUNCT__ 56 #define __FUNCT__ "DMPlexCreateCGNS" 57 /*@ 58 DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file ID. 59 60 Collective on comm 61 62 Input Parameters: 63 + comm - The MPI communicator 64 . cgid - The CG id associated with a file and obtained using cg_open 65 - interpolate - Create faces and edges in the mesh 66 67 Output Parameter: 68 . dm - The DM object representing the mesh 69 70 Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html 71 72 Level: beginner 73 74 .keywords: mesh,CGNS 75 .seealso: DMPlexCreate(), DMPlexCreateExodus() 76 @*/ 77 PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm) 78 { 79 #if defined(PETSC_HAVE_CGNS) 80 PetscMPIInt num_proc, rank; 81 PetscSection coordSection; 82 Vec coordinates; 83 PetscScalar *coords; 84 PetscInt coordSize, v; 85 PetscErrorCode ierr; 86 /* Read from file */ 87 char basename[CGIO_MAX_NAME_LENGTH+1]; 88 char buffer[CGIO_MAX_NAME_LENGTH+1]; 89 int dim = 0, physDim = 0, numVertices = 0, numCells = 0; 90 int nzones = 0; 91 #endif 92 93 PetscFunctionBegin; 94 #if defined(PETSC_HAVE_CGNS) 95 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 96 ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr); 97 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 98 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 99 /* Open CGNS II file and read basic informations on rank 0, then broadcast to all processors */ 100 if (!rank) { 101 int nbases, z; 102 103 ierr = cg_nbases(cgid, &nbases);CHKERRQ(ierr); 104 if (nbases > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single base, not %d\n",nbases); 105 ierr = cg_base_read(cgid, 1, basename, &dim, &physDim);CHKERRQ(ierr); 106 ierr = cg_nzones(cgid, 1, &nzones);CHKERRQ(ierr); 107 for (z = 1; z <= nzones; ++z) { 108 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 109 110 ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr); 111 numVertices += sizes[0]; 112 numCells += sizes[1]; 113 } 114 } 115 ierr = MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH+1, MPI_CHAR, 0, comm);CHKERRQ(ierr); 116 ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr); 117 ierr = MPI_Bcast(&nzones, 1, MPI_INT, 0, comm);CHKERRQ(ierr); 118 ierr = PetscObjectSetName((PetscObject) *dm, basename);CHKERRQ(ierr); 119 ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); 120 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 121 122 /* Read zone information */ 123 if (!rank) { 124 int z, c, c_loc, v, v_loc; 125 126 /* Read the cell set connectivity table and build mesh topology 127 CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */ 128 /* First set sizes */ 129 for (z = 1, c = 0; z <= nzones; ++z) { 130 ZoneType_t zonetype; 131 int nsections; 132 ElementType_t cellType; 133 cgsize_t start, end; 134 int nbndry, parentFlag; 135 PetscInt numCorners; 136 137 ierr = cg_zone_type(cgid, 1, z, &zonetype);CHKERRQ(ierr); 138 if (zonetype == Structured) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Can only handle Unstructured zones for CGNS"); 139 ierr = cg_nsections(cgid, 1, z, &nsections);CHKERRQ(ierr); 140 if (nsections > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single section, not %d\n",nsections); 141 ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr); 142 /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */ 143 if (cellType == MIXED) { 144 cgsize_t elementDataSize, *elements; 145 PetscInt off; 146 147 ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr); 148 ierr = PetscMalloc1(elementDataSize, &elements);CHKERRQ(ierr); 149 ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr); 150 for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) { 151 switch (elements[off]) { 152 case TRI_3: numCorners = 3;break; 153 case QUAD_4: numCorners = 4;break; 154 case TETRA_4: numCorners = 4;break; 155 case HEXA_8: numCorners = 8;break; 156 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[off]); 157 } 158 ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); 159 off += numCorners+1; 160 } 161 ierr = PetscFree(elements);CHKERRQ(ierr); 162 } else { 163 switch (cellType) { 164 case TRI_3: numCorners = 3;break; 165 case QUAD_4: numCorners = 4;break; 166 case TETRA_4: numCorners = 4;break; 167 case HEXA_8: numCorners = 8;break; 168 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); 169 } 170 for (c_loc = start; c_loc <= end; ++c_loc, ++c) { 171 ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); 172 } 173 } 174 } 175 ierr = DMSetUp(*dm);CHKERRQ(ierr); 176 for (z = 1, c = 0; z <= nzones; ++z) { 177 ElementType_t cellType; 178 cgsize_t *elements, elementDataSize, start, end; 179 int nbndry, parentFlag; 180 PetscInt *cone, numc, numCorners, maxCorners = 27; 181 182 ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr); 183 numc = end - start; 184 /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */ 185 ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr); 186 ierr = PetscMalloc2(elementDataSize,&elements,maxCorners,&cone);CHKERRQ(ierr); 187 ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr); 188 if (cellType == MIXED) { 189 /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */ 190 for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) { 191 switch (elements[v]) { 192 case TRI_3: numCorners = 3;break; 193 case QUAD_4: numCorners = 4;break; 194 case TETRA_4: numCorners = 4;break; 195 case HEXA_8: numCorners = 8;break; 196 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[v]); 197 } 198 ++v; 199 for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) { 200 cone[v_loc] = elements[v]+numCells-1; 201 } 202 /* Tetrahedra are inverted */ 203 if (elements[v] == TETRA_4) { 204 PetscInt tmp = cone[0]; 205 cone[0] = cone[1]; 206 cone[1] = tmp; 207 } 208 /* Hexahedra are inverted */ 209 if (elements[v] == HEXA_8) { 210 PetscInt tmp = cone[1]; 211 cone[1] = cone[3]; 212 cone[3] = tmp; 213 } 214 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 215 ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr); 216 } 217 } else { 218 switch (cellType) { 219 case TRI_3: numCorners = 3;break; 220 case QUAD_4: numCorners = 4;break; 221 case TETRA_4: numCorners = 4;break; 222 case HEXA_8: numCorners = 8;break; 223 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); 224 } 225 226 /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */ 227 for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) { 228 for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) { 229 cone[v_loc] = elements[v]+numCells-1; 230 } 231 /* Tetrahedra are inverted */ 232 if (cellType == TETRA_4) { 233 PetscInt tmp = cone[0]; 234 cone[0] = cone[1]; 235 cone[1] = tmp; 236 } 237 /* Hexahedra are inverted */ 238 if (cellType == HEXA_8) { 239 PetscInt tmp = cone[1]; 240 cone[1] = cone[3]; 241 cone[3] = tmp; 242 } 243 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 244 ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr); 245 } 246 } 247 ierr = PetscFree2(elements,cone);CHKERRQ(ierr); 248 } 249 } 250 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 251 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 252 if (interpolate) { 253 DM idm = NULL; 254 255 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 256 /* Maintain zone label */ 257 { 258 DMLabel label; 259 260 ierr = DMPlexRemoveLabel(*dm, "zone", &label);CHKERRQ(ierr); 261 if (label) {ierr = DMPlexAddLabel(idm, label);CHKERRQ(ierr);} 262 } 263 ierr = DMDestroy(dm);CHKERRQ(ierr); 264 *dm = idm; 265 } 266 267 /* Read coordinates */ 268 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 269 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 270 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 271 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 272 for (v = numCells; v < numCells+numVertices; ++v) { 273 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 274 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 275 } 276 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 277 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 278 ierr = VecCreate(comm, &coordinates);CHKERRQ(ierr); 279 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 280 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 281 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 282 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 283 if (!rank) { 284 PetscInt off = 0; 285 float *x[3]; 286 int z, d; 287 288 ierr = PetscMalloc3(numVertices,&x[0],numVertices,&x[1],numVertices,&x[2]);CHKERRQ(ierr); 289 for (z = 1; z <= nzones; ++z) { 290 DataType_t datatype; 291 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 292 cgsize_t range_min[3] = {1, 1, 1}; 293 cgsize_t range_max[3] = {1, 1, 1}; 294 int ngrids, ncoords; 295 296 297 ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr); 298 range_max[0] = sizes[0]; 299 ierr = cg_ngrids(cgid, 1, z, &ngrids);CHKERRQ(ierr); 300 if (ngrids > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single grid, not %d\n",ngrids); 301 ierr = cg_ncoords(cgid, 1, z, &ncoords);CHKERRQ(ierr); 302 if (ncoords != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords); 303 for (d = 0; d < dim; ++d) { 304 ierr = cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);CHKERRQ(ierr); 305 ierr = cg_coord_read(cgid, 1, z, buffer, RealSingle, range_min, range_max, x[d]);CHKERRQ(ierr); 306 } 307 if (dim > 0) { 308 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+0] = x[0][v]; 309 } 310 if (dim > 1) { 311 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+1] = x[1][v]; 312 } 313 if (dim > 2) { 314 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+2] = x[2][v]; 315 } 316 off += sizes[0]; 317 } 318 ierr = PetscFree3(x[0],x[1],x[2]);CHKERRQ(ierr); 319 } 320 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 321 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 322 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 323 #else 324 SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir"); 325 #endif 326 PetscFunctionReturn(0); 327 } 328