Date: 2013-07-02T14:45:59+00:00

Actual source code: plexexodusii.c
petsc-3.4.2 2013-07-02

      1: #define PETSCDM_DLL
      2: #include <petsc-private/dmpleximpl.h>    /*I   "petscdmplex.h"   I*/

      4: #if defined(PETSC_HAVE_EXODUSII)
      5: #include <netcdf.h>
      6: #include <exodusII.h>
      7: #endif

     11: /*@
     12:   DMPlexCreateExodus - Create a DMPlex mesh from an ExodusII file.

     14:   Collective on comm

     16:   Input Parameters:
     17: + comm  - The MPI communicator
     18: . exoid - The ExodusII id associated with a exodus file and obtained using ex_open
     19: - interpolate - Create faces and edges in the mesh

     21:   Output Parameter:
     22: . dm  - The DM object representing the mesh

     24:   Level: beginner

     26: .keywords: mesh,ExodusII
     27: .seealso: DMPLEX, DMCreate()
     28: @*/
     29: PetscErrorCode DMPlexCreateExodus(MPI_Comm comm, PetscInt exoid, PetscBool interpolate, DM *dm)
     30: {
     31: #if defined(PETSC_HAVE_EXODUSII)
     32:   PetscMPIInt    num_proc, rank;
     33:   PetscSection   coordSection;
     34:   Vec            coordinates;
     35:   PetscScalar    *coords;
     36:   PetscInt       coordSize, v;
     38:   /* Read from ex_get_init() */
     39:   char title[PETSC_MAX_PATH_LEN+1];
     40:   int  dim    = 0, numVertices = 0, numCells = 0;
     41:   int  num_cs = 0, num_vs = 0, num_fs = 0;
     42: #endif

     45: #if defined(PETSC_HAVE_EXODUSII)
     46:   MPI_Comm_rank(comm, &rank);
     47:   MPI_Comm_size(comm, &num_proc);
     48:   DMCreate(comm, dm);
     49:   DMSetType(*dm, DMPLEX);
     50:   /* Open EXODUS II file and read basic informations on rank 0, then broadcast to all processors */
     51:   if (!rank) {
     52:     ex_get_init(exoid, title, &dim, &numVertices, &numCells, &num_cs, &num_vs, &num_fs);
     53:     if (ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"ExodusII ex_get_init() failed with error code %D\n",ierr);
     54:     if (!num_cs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Exodus file does not contain any cell set\n");
     55:   }
     56:   MPI_Bcast(title, PETSC_MAX_PATH_LEN+1, MPI_CHAR, 0, comm);
     57:   MPI_Bcast(&dim, 1, MPI_INT, 0, comm);
     58:   PetscObjectSetName((PetscObject) *dm, title);
     59:   DMPlexSetDimension(*dm, dim);
     60:   DMPlexSetChart(*dm, 0, numCells+numVertices);

     62:   /* Read cell sets information */
     63:   if (!rank) {
     64:     PetscInt *cone;
     65:     int      c, cs, c_loc, v, v_loc;
     66:     /* Read from ex_get_elem_blk_ids() */
     67:     int *cs_id;
     68:     /* Read from ex_get_elem_block() */
     69:     char buffer[PETSC_MAX_PATH_LEN+1];
     70:     int  num_cell_in_set, num_vertex_per_cell, num_attr;
     71:     /* Read from ex_get_elem_conn() */
     72:     int *cs_connect;

     74:     /* Get cell sets IDs */
     75:     PetscMalloc(num_cs * sizeof(int), &cs_id);
     76:     ex_get_elem_blk_ids(exoid, cs_id);
     77:     /* Read the cell set connectivity table and build mesh topology
     78:        EXO standard requires that cells in cell sets be numbered sequentially and be pairwise disjoint. */
     79:     /* First set sizes */
     80:     for (cs = 0, c = 0; cs < num_cs; cs++) {
     81:       ex_get_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &num_attr);
     82:       for (c_loc = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
     83:         DMPlexSetConeSize(*dm, c, num_vertex_per_cell);
     84:       }
     85:     }
     86:     DMSetUp(*dm);
     87:     for (cs = 0, c = 0; cs < num_cs; cs++) {
     88:       ex_get_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &num_attr);
     89:       PetscMalloc2(num_vertex_per_cell*num_cell_in_set,int,&cs_connect,num_vertex_per_cell,PetscInt,&cone);
     90:       ex_get_elem_conn(exoid, cs_id[cs], cs_connect);
     91:       /* EXO uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
     92:       for (c_loc = 0, v = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
     93:         for (v_loc = 0; v_loc < num_vertex_per_cell; ++v_loc, ++v) {
     94:           cone[v_loc] = cs_connect[v]+numCells-1;
     95:         }
     96:         if (dim == 3) {
     97:           /* Tetrahedra are inverted */
     98:           if (num_vertex_per_cell == 4) {
     99:             PetscInt tmp = cone[0];
    100:             cone[0] = cone[1];
    101:             cone[1] = tmp;
    102:           }
    103:           /* Hexahedra are inverted */
    104:           if (num_vertex_per_cell == 8) {
    105:             PetscInt tmp = cone[1];
    106:             cone[1] = cone[3];
    107:             cone[3] = tmp;
    108:           }
    109:         }
    110:         DMPlexSetCone(*dm, c, cone);
    111:         DMPlexSetLabelValue(*dm, "Cell Sets", c, cs_id[cs]);
    112:       }
    113:       PetscFree2(cs_connect,cone);
    114:     }
    115:     PetscFree(cs_id);
    116:   }
    117:   DMPlexSymmetrize(*dm);
    118:   DMPlexStratify(*dm);
    119:   if (interpolate) {
    120:     DM idm;

    122:     DMPlexInterpolate(*dm, &idm);
    123:     /* Maintain Cell Sets label */
    124:     {
    125:       DMLabel label;

    127:       DMPlexRemoveLabel(*dm, "Cell Sets", &label);
    128:       if (label) {DMPlexAddLabel(idm, label);}
    129:     }
    130:     DMDestroy(dm);
    131:     *dm  = idm;
    132:   }

    134:   /* Create vertex set label */
    135:   if (!rank && (num_vs > 0)) {
    136:     int vs, v;
    137:     /* Read from ex_get_node_set_ids() */
    138:     int *vs_id;
    139:     /* Read from ex_get_node_set_param() */
    140:     int num_vertex_in_set, num_attr;
    141:     /* Read from ex_get_node_set() */
    142:     int *vs_vertex_list;

    144:     /* Get vertex set ids */
    145:     PetscMalloc(num_vs * sizeof(int), &vs_id);
    146:     ex_get_node_set_ids(exoid, vs_id);
    147:     for (vs = 0; vs < num_vs; ++vs) {
    148:       ex_get_node_set_param(exoid, vs_id[vs], &num_vertex_in_set, &num_attr);
    149:       PetscMalloc(num_vertex_in_set * sizeof(int), &vs_vertex_list);
    150:       ex_get_node_set(exoid, vs_id[vs], vs_vertex_list);
    151:       for (v = 0; v < num_vertex_in_set; ++v) {
    152:         DMPlexSetLabelValue(*dm, "Vertex Sets", vs_vertex_list[v]+numCells-1, vs_id[vs]);
    153:       }
    154:       PetscFree(vs_vertex_list);
    155:     }
    156:     PetscFree(vs_id);
    157:   }
    158:   /* Read coordinates */
    159:   DMPlexGetCoordinateSection(*dm, &coordSection);
    160:   PetscSectionSetNumFields(coordSection, 1);
    161:   PetscSectionSetFieldComponents(coordSection, 0, dim);
    162:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
    163:   for (v = numCells; v < numCells+numVertices; ++v) {
    164:     PetscSectionSetDof(coordSection, v, dim);
    165:     PetscSectionSetFieldDof(coordSection, v, 0, dim);
    166:   }
    167:   PetscSectionSetUp(coordSection);
    168:   PetscSectionGetStorageSize(coordSection, &coordSize);
    169:   VecCreate(comm, &coordinates);
    170:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    171:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    172:   VecSetFromOptions(coordinates);
    173:   VecGetArray(coordinates, &coords);
    174:   if (!rank) {
    175:     float *x, *y, *z;

    177:     PetscMalloc3(numVertices,float,&x,numVertices,float,&y,numVertices,float,&z);
    178:     ex_get_coord(exoid, x, y, z);
    179:     if (dim > 0) {
    180:       for (v = 0; v < numVertices; ++v) coords[v*dim+0] = x[v];
    181:     }
    182:     if (dim > 1) {
    183:       for (v = 0; v < numVertices; ++v) coords[v*dim+1] = y[v];
    184:     }
    185:     if (dim > 2) {
    186:       for (v = 0; v < numVertices; ++v) coords[v*dim+2] = z[v];
    187:     }
    188:     PetscFree3(x,y,z);
    189:   }
    190:   VecRestoreArray(coordinates, &coords);
    191:   DMSetCoordinatesLocal(*dm, coordinates);
    192:   VecDestroy(&coordinates);

    194:   /* Create side set label */
    195:   if (!rank && interpolate && (num_fs > 0)) {
    196:     int fs, f, voff;
    197:     /* Read from ex_get_side_set_ids() */
    198:     int *fs_id;
    199:     /* Read from ex_get_side_set_param() */
    200:     int num_side_in_set, num_dist_fact_in_set;
    201:     /* Read from ex_get_side_set_node_list() */
    202:     int *fs_vertex_count_list, *fs_vertex_list;

    204:     /* Get side set ids */
    205:     PetscMalloc(num_fs * sizeof(int), &fs_id);
    206:     ex_get_side_set_ids(exoid, fs_id);
    207:     for (fs = 0; fs < num_fs; ++fs) {
    208:       ex_get_side_set_param(exoid, fs_id[fs], &num_side_in_set, &num_dist_fact_in_set);
    209:       PetscMalloc2(num_side_in_set,int,&fs_vertex_count_list,num_side_in_set*4,int,&fs_vertex_list);
    210:       ex_get_side_set_node_list(exoid, fs_id[fs], fs_vertex_count_list, fs_vertex_list);
    211:       for (f = 0, voff = 0; f < num_side_in_set; ++f) {
    212:         const PetscInt *faces   = NULL;
    213:         PetscInt       faceSize = fs_vertex_count_list[f], numFaces;
    214:         PetscInt       faceVertices[4], v;

    216:         if (faceSize > 4) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "ExodusII side cannot have %d > 4 vertices", faceSize);
    217:         for (v = 0; v < faceSize; ++v, ++voff) {
    218:           faceVertices[v] = fs_vertex_list[voff]+numCells-1;
    219:         }
    220:         DMPlexGetFullJoin(*dm, faceSize, faceVertices, &numFaces, &faces);
    221:         if (numFaces != 1) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Invalid ExodusII side %d in set %d maps to %d faces", f, fs, numFaces);
    222:         DMPlexSetLabelValue(*dm, "Face Sets", faces[0], fs_id[fs]);
    223:         DMPlexRestoreJoin(*dm, faceSize, faceVertices, &numFaces, &faces);
    224:       }
    225:       PetscFree2(fs_vertex_count_list,fs_vertex_list);
    226:     }
    227:     PetscFree(fs_id);
    228:   }
    229: #else
    230:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
    231: #endif
    232:   return(0);
    233: }