Actual source code: plexexodusii.c

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

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

      9: #include <petsc/private/viewerimpl.h>
     10: #include <petsc/private/viewerexodusiiimpl.h>
     11: #if defined(PETSC_HAVE_EXODUSII)
     12: /*
     13:   PETSC_VIEWER_EXODUSII_ - Creates an ExodusII PetscViewer shared by all processors in a communicator.

     15:   Collective

     17:   Input Parameter:
     18: . comm - the MPI communicator to share the ExodusII PetscViewer

     20:   Level: intermediate

     22:   Notes:
     23:     misses Fortran bindings

     25:   Notes:
     26:   Unlike almost all other PETSc routines, PETSC_VIEWER_EXODUSII_ does not return
     27:   an error code.  The GLVIS PetscViewer is usually used in the form
     28: $       XXXView(XXX object, PETSC_VIEWER_EXODUSII_(comm));

     30: .seealso: PetscViewerExodusIIOpen(), PetscViewerType, PetscViewerCreate(), PetscViewerDestroy()
     31: */
     32: PetscViewer PETSC_VIEWER_EXODUSII_(MPI_Comm comm)
     33: {
     34:   PetscViewer    viewer;

     37:   PetscViewerExodusIIOpen(comm, "mesh.exo", FILE_MODE_WRITE, &viewer);
     38:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_EXODUSII_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return 0;}
     39:   PetscObjectRegisterDestroy((PetscObject) viewer);
     40:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_EXODUSII_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return 0;}
     41:   return viewer;
     42: }

     44: static PetscErrorCode PetscViewerView_ExodusII(PetscViewer v, PetscViewer viewer)
     45: {
     46:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) v->data;

     48:   if (exo->filename) PetscViewerASCIIPrintf(viewer, "Filename:    %s\n", exo->filename);
     49:   if (exo->exoid)    PetscViewerASCIIPrintf(viewer, "exoid:       %d\n", exo->exoid);
     50:   if (exo->btype)    PetscViewerASCIIPrintf(viewer, "IO Mode:     %d\n", exo->btype);
     51:   if (exo->order)    PetscViewerASCIIPrintf(viewer, "Mesh order:  %d\n", exo->order);
     52:   return 0;
     53: }

     55: static PetscErrorCode PetscViewerSetFromOptions_ExodusII(PetscOptionItems *PetscOptionsObject, PetscViewer v)
     56: {
     57:   PetscOptionsHead(PetscOptionsObject, "ExodusII PetscViewer Options");
     58:   PetscOptionsTail();
     59:   return 0;
     60: }

     62: static PetscErrorCode PetscViewerSetUp_ExodusII(PetscViewer viewer)
     63: {
     64:   return 0;
     65: }

     67: static PetscErrorCode PetscViewerDestroy_ExodusII(PetscViewer viewer)
     68: {
     69:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

     71:   if (exo->exoid >= 0) {PetscStackCallStandard(ex_close,exo->exoid);}
     72:   PetscFree(exo->filename);
     73:   PetscFree(exo);
     74:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",NULL);
     75:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileGetName_C",NULL);
     76:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",NULL);
     77:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerGetId_C",NULL);
     78:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerGetOrder_C",NULL);
     79:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerSetOrder_C",NULL);
     80:   return 0;
     81: }

     83: static PetscErrorCode PetscViewerFileSetName_ExodusII(PetscViewer viewer, const char name[])
     84: {
     85:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;
     86:   PetscMPIInt           rank;
     87:   int                   CPU_word_size, IO_word_size, EXO_mode;
     88:   MPI_Info              mpi_info = MPI_INFO_NULL;
     89:   float                 EXO_version;

     91:   MPI_Comm_rank(PetscObjectComm((PetscObject) viewer), &rank);
     92:   CPU_word_size = sizeof(PetscReal);
     93:   IO_word_size  = sizeof(PetscReal);

     95:   if (exo->exoid >= 0) {
     96:     PetscStackCallStandard(ex_close,exo->exoid);
     97:     exo->exoid = -1;
     98:   }
     99:   if (exo->filename) PetscFree(exo->filename);
    100:   PetscStrallocpy(name, &exo->filename);
    101:   switch (exo->btype) {
    102:   case FILE_MODE_READ:
    103:     EXO_mode = EX_READ;
    104:     break;
    105:   case FILE_MODE_APPEND:
    106:   case FILE_MODE_UPDATE:
    107:   case FILE_MODE_APPEND_UPDATE:
    108:     /* Will fail if the file does not already exist */
    109:     EXO_mode = EX_WRITE;
    110:     break;
    111:   case FILE_MODE_WRITE:
    112:     /*
    113:       exodus only allows writing geometry upon file creation, so we will let DMView create the file.
    114:     */
    115:     return 0;
    116:     break;
    117:   default:
    118:     SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
    119:   }
    120:   #if defined(PETSC_USE_64BIT_INDICES)
    121:   EXO_mode += EX_ALL_INT64_API;
    122:   #endif
    123:   exo->exoid = ex_open_par(name,EXO_mode,&CPU_word_size,&IO_word_size,&EXO_version,PETSC_COMM_WORLD,mpi_info);
    125:   return 0;
    126: }

    128: static PetscErrorCode PetscViewerFileGetName_ExodusII(PetscViewer viewer, const char **name)
    129: {
    130:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    132:   *name = exo->filename;
    133:   return 0;
    134: }

    136: static PetscErrorCode PetscViewerFileSetMode_ExodusII(PetscViewer viewer, PetscFileMode type)
    137: {
    138:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    140:   exo->btype = type;
    141:   return 0;
    142: }

    144: static PetscErrorCode PetscViewerFileGetMode_ExodusII(PetscViewer viewer, PetscFileMode *type)
    145: {
    146:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    148:   *type = exo->btype;
    149:   return 0;
    150: }

    152: static PetscErrorCode PetscViewerExodusIIGetId_ExodusII(PetscViewer viewer, int *exoid)
    153: {
    154:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    156:   *exoid = exo->exoid;
    157:   return 0;
    158: }

    160: static PetscErrorCode PetscViewerExodusIIGetOrder_ExodusII(PetscViewer viewer, PetscInt *order)
    161: {
    162:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    164:   *order = exo->order;
    165:   return 0;
    166: }

    168: static PetscErrorCode PetscViewerExodusIISetOrder_ExodusII(PetscViewer viewer, PetscInt order)
    169: {
    170:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    172:   exo->order = order;
    173:   return 0;
    174: }

    176: /*MC
    177:    PETSCVIEWEREXODUSII - A viewer that writes to an Exodus II file

    179: .seealso:  PetscViewerExodusIIOpen(), PetscViewerCreate(), PETSCVIEWERBINARY, PETSCVIEWERHDF5, DMView(),
    180:            PetscViewerFileSetName(), PetscViewerFileSetMode(), PetscViewerFormat, PetscViewerType, PetscViewerSetType()

    182:   Level: beginner
    183: M*/

    185: PETSC_EXTERN PetscErrorCode PetscViewerCreate_ExodusII(PetscViewer v)
    186: {
    187:   PetscViewer_ExodusII *exo;

    189:   PetscNewLog(v,&exo);

    191:   v->data                = (void*) exo;
    192:   v->ops->destroy        = PetscViewerDestroy_ExodusII;
    193:   v->ops->setfromoptions = PetscViewerSetFromOptions_ExodusII;
    194:   v->ops->setup          = PetscViewerSetUp_ExodusII;
    195:   v->ops->view           = PetscViewerView_ExodusII;
    196:   v->ops->flush          = 0;
    197:   exo->btype             = (PetscFileMode) -1;
    198:   exo->filename          = 0;
    199:   exo->exoid             = -1;

    201:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_ExodusII);
    202:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetName_C",PetscViewerFileGetName_ExodusII);
    203:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_ExodusII);
    204:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetMode_C",PetscViewerFileGetMode_ExodusII);
    205:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerGetId_C",PetscViewerExodusIIGetId_ExodusII);
    206:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerSetOrder_C",PetscViewerExodusIISetOrder_ExodusII);
    207:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerGetOrder_C",PetscViewerExodusIIGetOrder_ExodusII);
    208:   return 0;
    209: }

    211: /*
    212:   EXOGetVarIndex - Locate a result in an exodus file based on its name

    214:   Collective

    216:   Input Parameters:
    217: + exoid    - the exodus id of a file (obtained from ex_open or ex_create for instance)
    218: . obj_type - the type of entity for instance EX_NODAL, EX_ELEM_BLOCK
    219: - name     - the name of the result

    221:   Output Parameters:
    222: . varIndex - the location in the exodus file of the result

    224:   Notes:
    225:   The exodus variable index is obtained by comparing name and the
    226:   names of zonal variables declared in the exodus file. For instance if name is "V"
    227:   the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
    228:   amongst all variables of type obj_type.

    230:   Level: beginner

    232: .seealso: EXOGetVarIndex(),DMPlexView_ExodusII_Internal(),VecViewPlex_ExodusII_Nodal_Internal(),VecLoadNodal_PlexEXO(),VecLoadZonal_PlexEXO()
    233: */
    234: PetscErrorCode EXOGetVarIndex_Internal(int exoid, ex_entity_type obj_type, const char name[], int *varIndex)
    235: {
    236:   int            num_vars, i, j;
    237:   char           ext_name[MAX_STR_LENGTH+1], var_name[MAX_STR_LENGTH+1];
    238:   const int      num_suffix = 5;
    239:   char          *suffix[5];
    240:   PetscBool      flg;

    242:   suffix[0] = (char *) "";
    243:   suffix[1] = (char *) "_X";
    244:   suffix[2] = (char *) "_XX";
    245:   suffix[3] = (char *) "_1";
    246:   suffix[4] = (char *) "_11";

    248:   *varIndex = -1;
    249:   PetscStackCallStandard(ex_get_variable_param,exoid, obj_type, &num_vars);
    250:   for (i = 0; i < num_vars; ++i) {
    251:     PetscStackCallStandard(ex_get_variable_name,exoid, obj_type, i+1, var_name);
    252:     for (j = 0; j < num_suffix; ++j) {
    253:       PetscStrncpy(ext_name, name, MAX_STR_LENGTH);
    254:       PetscStrlcat(ext_name, suffix[j], MAX_STR_LENGTH);
    255:       PetscStrcasecmp(ext_name, var_name, &flg);
    256:       if (flg) {
    257:         *varIndex = i+1;
    258:       }
    259:     }
    260:   }
    261:   return 0;
    262: }

    264: /*
    265:   DMView_PlexExodusII - Write a DM to disk in exodus format

    267:   Collective on dm

    269:   Input Parameters:
    270: + dm  - The dm to be written
    271: . viewer - an exodusII viewer

    273:   Notes:
    274:   Not all DM can be written to disk this way. For instance, exodus assume that element blocks (mapped to "Cell sets" labels)
    275:   consists of sequentially numbered cells. If this is not the case, the exodus file will be corrupted.

    277:   If the dm has been distributed, only the part of the DM on MPI rank 0 (including "ghost" cells and vertices)
    278:   will be written.

    280:   DMPlex only represents geometry while most post-processing software expect that a mesh also provides information
    281:   on the discretization space. This function assumes that the file represents Lagrange finite elements of order 1 or 2.
    282:   The order of the mesh shall be set using PetscViewerExodusIISetOrder
    283:   It should be extended to use PetscFE objects.

    285:   This function will only handle TRI, TET, QUAD, and HEX cells.
    286:   Level: beginner

    288: .seealso:
    289: */
    290: PetscErrorCode DMView_PlexExodusII(DM dm, PetscViewer viewer)
    291: {
    292:   enum ElemType {TRI, QUAD, TET, HEX};
    293:   MPI_Comm        comm;
    294:   PetscInt        degree; /* the order of the mesh */
    295:   /* Connectivity Variables */
    296:   PetscInt        cellsNotInConnectivity;
    297:   /* Cell Sets */
    298:   DMLabel         csLabel;
    299:   IS              csIS;
    300:   const PetscInt *csIdx;
    301:   PetscInt        num_cs, cs;
    302:   enum ElemType  *type;
    303:   PetscBool       hasLabel;
    304:   /* Coordinate Variables */
    305:   DM              cdm;
    306:   PetscSection    coordSection;
    307:   Vec             coord;
    308:   PetscInt      **nodes;
    309:   PetscInt        depth, d, dim, skipCells = 0;
    310:   PetscInt        pStart, pEnd, p, cStart, cEnd, numCells, vStart, vEnd, numVertices, eStart, eEnd, numEdges, fStart, fEnd, numFaces, numNodes;
    311:   PetscInt        num_vs, num_fs;
    312:   PetscMPIInt     rank, size;
    313:   const char     *dmName;
    314:   PetscInt        nodesTriP1[4]  = {3,0,0,0};
    315:   PetscInt        nodesTriP2[4]  = {3,3,0,0};
    316:   PetscInt        nodesQuadP1[4] = {4,0,0,0};
    317:   PetscInt        nodesQuadP2[4] = {4,4,0,1};
    318:   PetscInt        nodesTetP1[4]  = {4,0,0,0};
    319:   PetscInt        nodesTetP2[4]  = {4,6,0,0};
    320:   PetscInt        nodesHexP1[4]  = {8,0,0,0};
    321:   PetscInt        nodesHexP2[4]  = {8,12,6,1};
    322:   PetscErrorCode  ierr;

    324:   int             CPU_word_size, IO_word_size, EXO_mode;
    325:   float           EXO_version;

    327:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    329:   PetscObjectGetComm((PetscObject)dm, &comm);
    330:   MPI_Comm_rank(comm, &rank);
    331:   MPI_Comm_size(comm, &size);

    333:   /*
    334:     Creating coordSection is a collective operation so we do it somewhat out of sequence
    335:   */
    336:   PetscSectionCreate(comm, &coordSection);
    337:   DMGetCoordinatesLocalSetUp(dm);
    338:   if (!rank) {
    339:     switch (exo->btype) {
    340:     case FILE_MODE_READ:
    341:     case FILE_MODE_APPEND:
    342:     case FILE_MODE_UPDATE:
    343:     case FILE_MODE_APPEND_UPDATE:
    344:       /* exodusII does not allow writing geometry to an existing file */
    345:       SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "cannot add geometry to existing file %s", exo->filename);
    346:     case FILE_MODE_WRITE:
    347:       /* Create an empty file if one already exists*/
    348:       EXO_mode = EX_CLOBBER;
    349: #if defined(PETSC_USE_64BIT_INDICES)
    350:       EXO_mode += EX_ALL_INT64_API;
    351: #endif
    352:         CPU_word_size = sizeof(PetscReal);
    353:         IO_word_size  = sizeof(PetscReal);
    354:         exo->exoid = ex_create(exo->filename, EXO_mode, &CPU_word_size, &IO_word_size);

    357:       break;
    358:     default:
    359:       SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
    360:     }

    362:     /* --- Get DM info --- */
    363:     PetscObjectGetName((PetscObject) dm, &dmName);
    364:     DMPlexGetDepth(dm, &depth);
    365:     DMGetDimension(dm, &dim);
    366:     DMPlexGetChart(dm, &pStart, &pEnd);
    367:     DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    368:     DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    369:     DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);
    370:     DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
    371:     numCells    = cEnd - cStart;
    372:     numEdges    = eEnd - eStart;
    373:     numVertices = vEnd - vStart;
    374:     if (depth == 3) {numFaces = fEnd - fStart;}
    375:     else            {numFaces = 0;}
    376:     DMGetLabelSize(dm, "Cell Sets", &num_cs);
    377:     DMGetLabelSize(dm, "Vertex Sets", &num_vs);
    378:     DMGetLabelSize(dm, "Face Sets", &num_fs);
    379:     DMGetCoordinatesLocal(dm, &coord);
    380:     DMGetCoordinateDM(dm, &cdm);
    381:     if (num_cs > 0) {
    382:       DMGetLabel(dm, "Cell Sets", &csLabel);
    383:       DMLabelGetValueIS(csLabel, &csIS);
    384:       ISGetIndices(csIS, &csIdx);
    385:     }
    386:     PetscMalloc1(num_cs, &nodes);
    387:     /* Set element type for each block and compute total number of nodes */
    388:     PetscMalloc1(num_cs, &type);
    389:     numNodes = numVertices;

    391:     PetscViewerExodusIIGetOrder(viewer, &degree);
    392:     if (degree == 2) {numNodes += numEdges;}
    393:     cellsNotInConnectivity = numCells;
    394:     for (cs = 0; cs < num_cs; ++cs) {
    395:       IS              stratumIS;
    396:       const PetscInt *cells;
    397:       PetscScalar    *xyz = NULL;
    398:       PetscInt        csSize, closureSize;

    400:       DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS);
    401:       ISGetIndices(stratumIS, &cells);
    402:       ISGetSize(stratumIS, &csSize);
    403:       DMPlexVecGetClosure(cdm, NULL, coord, cells[0], &closureSize, &xyz);
    404:       switch (dim) {
    405:         case 2:
    406:           if      (closureSize == 3*dim) {type[cs] = TRI;}
    407:           else if (closureSize == 4*dim) {type[cs] = QUAD;}
    408:           else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %D in dimension %D has no ExodusII type", closureSize/dim, dim);
    409:           break;
    410:         case 3:
    411:           if      (closureSize == 4*dim) {type[cs] = TET;}
    412:           else if (closureSize == 8*dim) {type[cs] = HEX;}
    413:           else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %D in dimension %D has no ExodusII type", closureSize/dim, dim);
    414:           break;
    415:         default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not handled by ExodusII viewer", dim);
    416:       }
    417:       if ((degree == 2) && (type[cs] == QUAD)) {numNodes += csSize;}
    418:       if ((degree == 2) && (type[cs] == HEX))  {numNodes += csSize; numNodes += numFaces;}
    419:       DMPlexVecRestoreClosure(cdm, NULL, coord, cells[0], &closureSize, &xyz);
    420:       /* Set nodes and Element type */
    421:       if (type[cs] == TRI) {
    422:         if      (degree == 1) nodes[cs] = nodesTriP1;
    423:         else if (degree == 2) nodes[cs] = nodesTriP2;
    424:       } else if (type[cs] == QUAD) {
    425:         if      (degree == 1) nodes[cs] = nodesQuadP1;
    426:         else if (degree == 2) nodes[cs] = nodesQuadP2;
    427:       } else if (type[cs] == TET) {
    428:         if      (degree == 1) nodes[cs] = nodesTetP1;
    429:         else if (degree == 2) nodes[cs] = nodesTetP2;
    430:       } else if (type[cs] == HEX) {
    431:         if      (degree == 1) nodes[cs] = nodesHexP1;
    432:         else if (degree == 2) nodes[cs] = nodesHexP2;
    433:       }
    434:       /* Compute the number of cells not in the connectivity table */
    435:       cellsNotInConnectivity -= nodes[cs][3]*csSize;

    437:       ISRestoreIndices(stratumIS, &cells);
    438:       ISDestroy(&stratumIS);
    439:     }
    440:     if (num_cs > 0) {PetscStackCallStandard(ex_put_init,exo->exoid, dmName, dim, numNodes, numCells, num_cs, num_vs, num_fs);}
    441:     /* --- Connectivity --- */
    442:     for (cs = 0; cs < num_cs; ++cs) {
    443:       IS              stratumIS;
    444:       const PetscInt *cells;
    445:       PetscInt       *connect, off = 0;
    446:       PetscInt        edgesInClosure = 0, facesInClosure = 0, verticesInClosure = 0;
    447:       PetscInt        csSize, c, connectSize, closureSize;
    448:       char           *elem_type = NULL;
    449:       char            elem_type_tri3[]  = "TRI3",  elem_type_quad4[] = "QUAD4";
    450:       char            elem_type_tri6[]  = "TRI6",  elem_type_quad9[] = "QUAD9";
    451:       char            elem_type_tet4[]  = "TET4",  elem_type_hex8[]  = "HEX8";
    452:       char            elem_type_tet10[] = "TET10", elem_type_hex27[] = "HEX27";

    454:       DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS);
    455:       ISGetIndices(stratumIS, &cells);
    456:       ISGetSize(stratumIS, &csSize);
    457:       /* Set Element type */
    458:       if (type[cs] == TRI) {
    459:         if      (degree == 1) elem_type = elem_type_tri3;
    460:         else if (degree == 2) elem_type = elem_type_tri6;
    461:       } else if (type[cs] == QUAD) {
    462:         if      (degree == 1) elem_type = elem_type_quad4;
    463:         else if (degree == 2) elem_type = elem_type_quad9;
    464:       } else if (type[cs] == TET) {
    465:         if      (degree == 1) elem_type = elem_type_tet4;
    466:         else if (degree == 2) elem_type = elem_type_tet10;
    467:       } else if (type[cs] == HEX) {
    468:         if      (degree == 1) elem_type = elem_type_hex8;
    469:         else if (degree == 2) elem_type = elem_type_hex27;
    470:       }
    471:       connectSize = nodes[cs][0] + nodes[cs][1] + nodes[cs][2] + nodes[cs][3];
    472:       PetscMalloc1(PetscMax(27,connectSize)*csSize, &connect);
    473:       PetscStackCallStandard(ex_put_block,exo->exoid, EX_ELEM_BLOCK, csIdx[cs], elem_type, csSize, connectSize, 0, 0, 1);
    474:       /* Find number of vertices, edges, and faces in the closure */
    475:       verticesInClosure = nodes[cs][0];
    476:       if (depth > 1) {
    477:         if (dim == 2) {
    478:           DMPlexGetConeSize(dm, cells[0], &edgesInClosure);
    479:         } else if (dim == 3) {
    480:           PetscInt *closure = NULL;

    482:           DMPlexGetConeSize(dm, cells[0], &facesInClosure);
    483:           DMPlexGetTransitiveClosure(dm, cells[0], PETSC_TRUE, &closureSize, &closure);
    484:           edgesInClosure = closureSize - facesInClosure - 1 - verticesInClosure;
    485:           DMPlexRestoreTransitiveClosure(dm, cells[0], PETSC_TRUE, &closureSize, &closure);
    486:         }
    487:       }
    488:       /* Get connectivity for each cell */
    489:       for (c = 0; c < csSize; ++c) {
    490:         PetscInt *closure = NULL;
    491:         PetscInt  temp, i;

    493:         DMPlexGetTransitiveClosure(dm, cells[c], PETSC_TRUE, &closureSize, &closure);
    494:         for (i = 0; i < connectSize; ++i) {
    495:           if (i < nodes[cs][0]) {/* Vertices */
    496:             connect[i+off] = closure[(i+edgesInClosure+facesInClosure+1)*2] + 1;
    497:             connect[i+off] -= cellsNotInConnectivity;
    498:           } else if (i < nodes[cs][0]+nodes[cs][1]) { /* Edges */
    499:             connect[i+off] = closure[(i-verticesInClosure+facesInClosure+1)*2] + 1;
    500:             if (nodes[cs][2] == 0) connect[i+off] -= numFaces;
    501:             connect[i+off] -= cellsNotInConnectivity;
    502:           } else if (i < nodes[cs][0]+nodes[cs][1]+nodes[cs][3]) { /* Cells */
    503:             connect[i+off] = closure[0] + 1;
    504:             connect[i+off] -= skipCells;
    505:           } else if (i < nodes[cs][0]+nodes[cs][1]+nodes[cs][3]+nodes[cs][2]) { /* Faces */
    506:             connect[i+off] = closure[(i-edgesInClosure-verticesInClosure)*2] + 1;
    507:             connect[i+off] -= cellsNotInConnectivity;
    508:           } else {
    509:             connect[i+off] = -1;
    510:           }
    511:         }
    512:         /* Tetrahedra are inverted */
    513:         if (type[cs] == TET) {
    514:           temp = connect[0+off]; connect[0+off] = connect[1+off]; connect[1+off] = temp;
    515:           if (degree == 2) {
    516:             temp = connect[5+off]; connect[5+off] = connect[6+off]; connect[6+off] = temp;
    517:             temp = connect[7+off]; connect[7+off] = connect[8+off]; connect[8+off] = temp;
    518:           }
    519:         }
    520:         /* Hexahedra are inverted */
    521:         if (type[cs] == HEX) {
    522:           temp = connect[1+off]; connect[1+off] = connect[3+off]; connect[3+off] = temp;
    523:           if (degree == 2) {
    524:             temp = connect[8+off];  connect[8+off]  = connect[11+off]; connect[11+off] = temp;
    525:             temp = connect[9+off];  connect[9+off]  = connect[10+off]; connect[10+off] = temp;
    526:             temp = connect[16+off]; connect[16+off] = connect[17+off]; connect[17+off] = temp;
    527:             temp = connect[18+off]; connect[18+off] = connect[19+off]; connect[19+off] = temp;

    529:             temp = connect[12+off]; connect[12+off] = connect[16+off]; connect[16+off] = temp;
    530:             temp = connect[13+off]; connect[13+off] = connect[17+off]; connect[17+off] = temp;
    531:             temp = connect[14+off]; connect[14+off] = connect[18+off]; connect[18+off] = temp;
    532:             temp = connect[15+off]; connect[15+off] = connect[19+off]; connect[19+off] = temp;

    534:             temp = connect[23+off]; connect[23+off] = connect[26+off]; connect[26+off] = temp;
    535:             temp = connect[24+off]; connect[24+off] = connect[25+off]; connect[25+off] = temp;
    536:             temp = connect[25+off]; connect[25+off] = connect[26+off]; connect[26+off] = temp;
    537:           }
    538:         }
    539:         off += connectSize;
    540:         DMPlexRestoreTransitiveClosure(dm, cells[c], PETSC_TRUE, &closureSize, &closure);
    541:       }
    542:       PetscStackCallStandard(ex_put_conn,exo->exoid, EX_ELEM_BLOCK, csIdx[cs], connect, 0, 0);
    543:       skipCells += (nodes[cs][3] == 0)*csSize;
    544:       PetscFree(connect);
    545:       ISRestoreIndices(stratumIS, &cells);
    546:       ISDestroy(&stratumIS);
    547:     }
    548:     PetscFree(type);
    549:     /* --- Coordinates --- */
    550:     PetscSectionSetChart(coordSection, pStart, pEnd);
    551:     if (num_cs) {
    552:       for (d = 0; d < depth; ++d) {
    553:         DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
    554:         for (p = pStart; p < pEnd; ++p) {
    555:           PetscSectionSetDof(coordSection, p, nodes[0][d] > 0);
    556:         }
    557:       }
    558:     }
    559:     for (cs = 0; cs < num_cs; ++cs) {
    560:       IS              stratumIS;
    561:       const PetscInt *cells;
    562:       PetscInt        csSize, c;

    564:       DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS);
    565:       ISGetIndices(stratumIS, &cells);
    566:       ISGetSize(stratumIS, &csSize);
    567:       for (c = 0; c < csSize; ++c) {
    568:         PetscSectionSetDof(coordSection, cells[c], nodes[cs][3] > 0);
    569:       }
    570:       ISRestoreIndices(stratumIS, &cells);
    571:       ISDestroy(&stratumIS);
    572:     }
    573:     if (num_cs > 0) {
    574:       ISRestoreIndices(csIS, &csIdx);
    575:       ISDestroy(&csIS);
    576:     }
    577:     PetscFree(nodes);
    578:     PetscSectionSetUp(coordSection);
    579:     if (numNodes > 0) {
    580:       const char  *coordNames[3] = {"x", "y", "z"};
    581:       PetscScalar *closure, *cval;
    582:       PetscReal   *coords;
    583:       PetscInt     hasDof, n = 0;

    585:       /* There can't be more than 24 values in the closure of a point for the coord coordSection */
    586:       PetscCalloc3(numNodes*3, &coords, dim, &cval, 24, &closure);
    587:       DMGetCoordinatesLocalNoncollective(dm, &coord);
    588:       DMPlexGetChart(dm, &pStart, &pEnd);
    589:       for (p = pStart; p < pEnd; ++p) {
    590:         PetscSectionGetDof(coordSection, p, &hasDof);
    591:         if (hasDof) {
    592:           PetscInt closureSize = 24, j;

    594:           DMPlexVecGetClosure(cdm, NULL, coord, p, &closureSize, &closure);
    595:           for (d = 0; d < dim; ++d) {
    596:             cval[d] = 0.0;
    597:             for (j = 0; j < closureSize/dim; j++) cval[d] += closure[j*dim+d];
    598:             coords[d*numNodes+n] = PetscRealPart(cval[d]) * dim / closureSize;
    599:           }
    600:           ++n;
    601:         }
    602:       }
    603:       PetscStackCallStandard(ex_put_coord,exo->exoid, &coords[0*numNodes], &coords[1*numNodes], &coords[2*numNodes]);
    604:       PetscFree3(coords, cval, closure);
    605:       PetscStackCallStandard(ex_put_coord_names,exo->exoid, (char **) coordNames);
    606:     }

    608:     /* --- Node Sets/Vertex Sets --- */
    609:     DMHasLabel(dm, "Vertex Sets", &hasLabel);
    610:     if (hasLabel) {
    611:       PetscInt        i, vs, vsSize;
    612:       const PetscInt *vsIdx, *vertices;
    613:       PetscInt       *nodeList;
    614:       IS              vsIS, stratumIS;
    615:       DMLabel         vsLabel;
    616:       DMGetLabel(dm, "Vertex Sets", &vsLabel);
    617:       DMLabelGetValueIS(vsLabel, &vsIS);
    618:       ISGetIndices(vsIS, &vsIdx);
    619:       for (vs=0; vs<num_vs; ++vs) {
    620:         DMLabelGetStratumIS(vsLabel, vsIdx[vs], &stratumIS);
    621:         ISGetIndices(stratumIS, &vertices);
    622:         ISGetSize(stratumIS, &vsSize);
    623:         PetscMalloc1(vsSize, &nodeList);
    624:         for (i=0; i<vsSize; ++i) {
    625:           nodeList[i] = vertices[i] - skipCells + 1;
    626:         }
    627:         PetscStackCallStandard(ex_put_set_param,exo->exoid, EX_NODE_SET, vsIdx[vs], vsSize, 0);
    628:         PetscStackCallStandard(ex_put_set,exo->exoid, EX_NODE_SET, vsIdx[vs], nodeList, NULL);
    629:         ISRestoreIndices(stratumIS, &vertices);
    630:         ISDestroy(&stratumIS);
    631:         PetscFree(nodeList);
    632:       }
    633:       ISRestoreIndices(vsIS, &vsIdx);
    634:       ISDestroy(&vsIS);
    635:     }
    636:     /* --- Side Sets/Face Sets --- */
    637:     DMHasLabel(dm, "Face Sets", &hasLabel);
    638:     if (hasLabel) {
    639:       PetscInt        i, j, fs, fsSize;
    640:       const PetscInt *fsIdx, *faces;
    641:       IS              fsIS, stratumIS;
    642:       DMLabel         fsLabel;
    643:       PetscInt        numPoints, *points;
    644:       PetscInt        elem_list_size = 0;
    645:       PetscInt       *elem_list, *elem_ind, *side_list;

    647:       DMGetLabel(dm, "Face Sets", &fsLabel);
    648:       /* Compute size of Node List and Element List */
    649:       DMLabelGetValueIS(fsLabel, &fsIS);
    650:       ISGetIndices(fsIS, &fsIdx);
    651:       for (fs=0; fs<num_fs; ++fs) {
    652:         DMLabelGetStratumIS(fsLabel, fsIdx[fs], &stratumIS);
    653:         ISGetSize(stratumIS, &fsSize);
    654:         elem_list_size += fsSize;
    655:         ISDestroy(&stratumIS);
    656:       }
    657:       PetscMalloc3(num_fs, &elem_ind,
    658:                           elem_list_size, &elem_list,
    659:                           elem_list_size, &side_list);
    660:       elem_ind[0] = 0;
    661:       for (fs=0; fs<num_fs; ++fs) {
    662:         DMLabelGetStratumIS(fsLabel, fsIdx[fs], &stratumIS);
    663:         ISGetIndices(stratumIS, &faces);
    664:         ISGetSize(stratumIS, &fsSize);
    665:         /* Set Parameters */
    666:         PetscStackCallStandard(ex_put_set_param,exo->exoid, EX_SIDE_SET, fsIdx[fs], fsSize, 0);
    667:         /* Indices */
    668:         if (fs<num_fs-1) {
    669:           elem_ind[fs+1] = elem_ind[fs] + fsSize;
    670:         }

    672:         for (i=0; i<fsSize; ++i) {
    673:           /* Element List */
    674:           points = NULL;
    675:           DMPlexGetTransitiveClosure(dm, faces[i], PETSC_FALSE, &numPoints, &points);
    676:           elem_list[elem_ind[fs] + i] = points[2] +1;
    677:           DMPlexRestoreTransitiveClosure(dm, faces[i], PETSC_FALSE, &numPoints, &points);

    679:           /* Side List */
    680:           points = NULL;
    681:           DMPlexGetTransitiveClosure(dm, elem_list[elem_ind[fs] + i]-1, PETSC_TRUE, &numPoints, &points);
    682:           for (j=1; j<numPoints; ++j) {
    683:             if (points[j*2]==faces[i]) {break;}
    684:           }
    685:           /* Convert HEX sides */
    686:           if (numPoints == 27) {
    687:             if      (j == 1) {j = 5;}
    688:             else if (j == 2) {j = 6;}
    689:             else if (j == 3) {j = 1;}
    690:             else if (j == 4) {j = 3;}
    691:             else if (j == 5) {j = 2;}
    692:             else if (j == 6) {j = 4;}
    693:           }
    694:           /* Convert TET sides */
    695:           if (numPoints == 15) {
    696:             --j;
    697:             if (j == 0) {j = 4;}
    698:           }
    699:           side_list[elem_ind[fs] + i] = j;
    700:           DMPlexRestoreTransitiveClosure(dm, elem_list[elem_ind[fs] + i]-1, PETSC_TRUE, &numPoints, &points);

    702:         }
    703:         ISRestoreIndices(stratumIS, &faces);
    704:         ISDestroy(&stratumIS);
    705:       }
    706:       ISRestoreIndices(fsIS, &fsIdx);
    707:       ISDestroy(&fsIS);

    709:       /* Put side sets */
    710:       for (fs=0; fs<num_fs; ++fs) {
    711:         PetscStackCallStandard(ex_put_set,exo->exoid, EX_SIDE_SET, fsIdx[fs], &elem_list[elem_ind[fs]], &side_list[elem_ind[fs]]);
    712:       }
    713:       PetscFree3(elem_ind,elem_list,side_list);
    714:     }
    715:     /*
    716:       close the exodus file
    717:     */
    718:     ex_close(exo->exoid);
    719:     exo->exoid = -1;
    720:   }
    721:   PetscSectionDestroy(&coordSection);

    723:   /*
    724:     reopen the file in parallel
    725:   */
    726:   EXO_mode = EX_WRITE;
    727: #if defined(PETSC_USE_64BIT_INDICES)
    728:   EXO_mode += EX_ALL_INT64_API;
    729: #endif
    730:   CPU_word_size = sizeof(PetscReal);
    731:   IO_word_size  = sizeof(PetscReal);
    732:   exo->exoid = ex_open_par(exo->filename,EXO_mode,&CPU_word_size,&IO_word_size,&EXO_version,comm,MPI_INFO_NULL);
    734:   return 0;
    735: }

    737: /*
    738:   VecView_PlexExodusII_Internal - Write a Vec corresponding in an exodus file

    740:   Collective on v

    742:   Input Parameters:
    743: + v  - The vector to be written
    744: - viewer - The PetscViewerExodusII viewer associate to an exodus file

    746:   Notes:
    747:   The exodus result variable index is obtained by comparing the Vec name and the
    748:   names of variables declared in the exodus file. For instance for a Vec named "V"
    749:   the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
    750:   amongst all variables.
    751:   In the event where a nodal and zonal variable both match, the function will return an error instead of
    752:   possibly corrupting the file

    754:   Level: beginner

    756: .seealso: EXOGetVarIndex_Internal(),DMPlexView_ExodusII(),VecView_PlexExodusII()
    757: @*/
    758: PetscErrorCode VecView_PlexExodusII_Internal(Vec v, PetscViewer viewer)
    759: {
    760:   DM                 dm;
    761:   MPI_Comm           comm;
    762:   PetscMPIInt        rank;

    764:   int                exoid,offsetN = 0, offsetZ = 0;
    765:   const char        *vecname;
    766:   PetscInt           step;

    768:   PetscObjectGetComm((PetscObject) v, &comm);
    769:   MPI_Comm_rank(comm, &rank);
    770:   PetscViewerExodusIIGetId(viewer,&exoid);
    771:   VecGetDM(v, &dm);
    772:   PetscObjectGetName((PetscObject) v, &vecname);

    774:   DMGetOutputSequenceNumber(dm,&step,NULL);
    775:   EXOGetVarIndex_Internal(exoid,EX_NODAL,vecname,&offsetN);
    776:   EXOGetVarIndex_Internal(exoid,EX_ELEM_BLOCK,vecname,&offsetZ);
    778:   if (offsetN > 0) {
    779:     VecViewPlex_ExodusII_Nodal_Internal(v,exoid,(int) step+1,offsetN);
    780:   } else if (offsetZ > 0) {
    781:     VecViewPlex_ExodusII_Zonal_Internal(v,exoid,(int) step+1,offsetZ);
    782:   } else SETERRQ(comm, PETSC_ERR_FILE_UNEXPECTED, "Could not find nodal or zonal variable %s in exodus file. ", vecname);
    783:   return 0;
    784: }

    786: /*
    787:   VecLoad_PlexExodusII_Internal - Write a Vec corresponding in an exodus file

    789:   Collective on v

    791:   Input Parameters:
    792: + v  - The vector to be written
    793: - viewer - The PetscViewerExodusII viewer associate to an exodus file

    795:   Notes:
    796:   The exodus result variable index is obtained by comparing the Vec name and the
    797:   names of variables declared in the exodus file. For instance for a Vec named "V"
    798:   the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
    799:   amongst all variables.
    800:   In the event where a nodal and zonal variable both match, the function will return an error instead of
    801:   possibly corrupting the file

    803:   Level: beginner

    805: .seealso: EXOGetVarIndex_Internal(),DMPlexView_ExodusII(),VecView_PlexExodusII()
    806: @*/
    807: PetscErrorCode VecLoad_PlexExodusII_Internal(Vec v, PetscViewer viewer)
    808: {
    809:   DM                 dm;
    810:   MPI_Comm           comm;
    811:   PetscMPIInt        rank;

    813:   int                exoid,offsetN = 0, offsetZ = 0;
    814:   const char        *vecname;
    815:   PetscInt           step;

    817:   PetscObjectGetComm((PetscObject) v, &comm);
    818:   MPI_Comm_rank(comm, &rank);
    819:   PetscViewerExodusIIGetId(viewer,&exoid);
    820:   VecGetDM(v, &dm);
    821:   PetscObjectGetName((PetscObject) v, &vecname);

    823:   DMGetOutputSequenceNumber(dm,&step,NULL);
    824:   EXOGetVarIndex_Internal(exoid,EX_NODAL,vecname,&offsetN);
    825:   EXOGetVarIndex_Internal(exoid,EX_ELEM_BLOCK,vecname,&offsetZ);
    827:   if (offsetN > 0) {
    828:     VecLoadPlex_ExodusII_Nodal_Internal(v,exoid,(int) step+1,offsetN);
    829:   } else if (offsetZ > 0) {
    830:     VecLoadPlex_ExodusII_Zonal_Internal(v,exoid,(int) step+1,offsetZ);
    831:   } else SETERRQ(comm, PETSC_ERR_FILE_UNEXPECTED, "Could not find nodal or zonal variable %s in exodus file. ", vecname);
    832:   return 0;
    833: }

    835: /*
    836:   VecViewPlex_ExodusII_Nodal_Internal - Write a Vec corresponding to a nodal field to an exodus file

    838:   Collective on v

    840:   Input Parameters:
    841: + v  - The vector to be written
    842: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    843: . step - the time step to write at (exodus steps are numbered starting from 1)
    844: - offset - the location of the variable in the file

    846:   Notes:
    847:   The exodus result nodal variable index is obtained by comparing the Vec name and the
    848:   names of nodal variables declared in the exodus file. For instance for a Vec named "V"
    849:   the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
    850:   amongst all nodal variables.

    852:   Level: beginner

    854: .seealso: EXOGetVarIndex_Internal(),DMPlexView_ExodusII_Internal(),VecLoadNodal_PlexEXO(),VecViewZonal_PlexEXO(),VecLoadZonal_PlexEXO()
    855: @*/
    856: PetscErrorCode VecViewPlex_ExodusII_Nodal_Internal(Vec v, int exoid, int step, int offset)
    857: {
    858:   MPI_Comm           comm;
    859:   PetscMPIInt        size;
    860:   DM                 dm;
    861:   Vec                vNatural, vComp;
    862:   const PetscScalar *varray;
    863:   PetscInt           xs, xe, bs;
    864:   PetscBool          useNatural;

    866:   PetscObjectGetComm((PetscObject) v, &comm);
    867:   MPI_Comm_size(comm, &size);
    868:   VecGetDM(v, &dm);
    869:   DMGetUseNatural(dm, &useNatural);
    870:   useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
    871:   if (useNatural) {
    872:     DMGetGlobalVector(dm, &vNatural);
    873:     DMPlexGlobalToNaturalBegin(dm, v, vNatural);
    874:     DMPlexGlobalToNaturalEnd(dm, v, vNatural);
    875:   } else {
    876:     vNatural = v;
    877:   }

    879:   /* Write local chunk of the result in the exodus file
    880:      exodus stores each component of a vector-valued field as a separate variable.
    881:      We assume that they are stored sequentially */
    882:   VecGetOwnershipRange(vNatural, &xs, &xe);
    883:   VecGetBlockSize(vNatural, &bs);
    884:   if (bs == 1) {
    885:     VecGetArrayRead(vNatural, &varray);
    886:     PetscStackCallStandard(ex_put_partial_var,exoid, step, EX_NODAL, offset, 1, xs+1, xe-xs, varray);
    887:     VecRestoreArrayRead(vNatural, &varray);
    888:   } else {
    889:     IS       compIS;
    890:     PetscInt c;

    892:     ISCreateStride(comm, (xe-xs)/bs, xs, bs, &compIS);
    893:     for (c = 0; c < bs; ++c) {
    894:       ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);
    895:       VecGetSubVector(vNatural, compIS, &vComp);
    896:       VecGetArrayRead(vComp, &varray);
    897:       PetscStackCallStandard(ex_put_partial_var,exoid, step, EX_NODAL, offset+c, 1, xs/bs+1, (xe-xs)/bs, varray);
    898:       VecRestoreArrayRead(vComp, &varray);
    899:       VecRestoreSubVector(vNatural, compIS, &vComp);
    900:     }
    901:     ISDestroy(&compIS);
    902:   }
    903:   if (useNatural) DMRestoreGlobalVector(dm, &vNatural);
    904:   return 0;
    905: }

    907: /*
    908:   VecLoadPlex_ExodusII_Nodal_Internal - Read a Vec corresponding to a nodal field from an exodus file

    910:   Collective on v

    912:   Input Parameters:
    913: + v  - The vector to be written
    914: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    915: . step - the time step to read at (exodus steps are numbered starting from 1)
    916: - offset - the location of the variable in the file

    918:   Notes:
    919:   The exodus result nodal variable index is obtained by comparing the Vec name and the
    920:   names of nodal variables declared in the exodus file. For instance for a Vec named "V"
    921:   the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
    922:   amongst all nodal variables.

    924:   Level: beginner

    926: .seealso: EXOGetVarIndex_Internal(), DMPlexView_ExodusII_Internal(), VecViewPlex_ExodusII_Nodal_Internal(), VecViewZonal_PlexEXO(), VecLoadZonal_PlexEXO()
    927: */
    928: PetscErrorCode VecLoadPlex_ExodusII_Nodal_Internal(Vec v, int exoid, int step, int offset)
    929: {
    930:   MPI_Comm       comm;
    931:   PetscMPIInt    size;
    932:   DM             dm;
    933:   Vec            vNatural, vComp;
    934:   PetscScalar   *varray;
    935:   PetscInt       xs, xe, bs;
    936:   PetscBool      useNatural;

    938:   PetscObjectGetComm((PetscObject) v, &comm);
    939:   MPI_Comm_size(comm, &size);
    940:   VecGetDM(v,&dm);
    941:   DMGetUseNatural(dm, &useNatural);
    942:   useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
    943:   if (useNatural) DMGetGlobalVector(dm,&vNatural);
    944:   else            {vNatural = v;}

    946:   /* Read local chunk from the file */
    947:   VecGetOwnershipRange(vNatural, &xs, &xe);
    948:   VecGetBlockSize(vNatural, &bs);
    949:   if (bs == 1) {
    950:     VecGetArray(vNatural, &varray);
    951:     PetscStackCallStandard(ex_get_partial_var,exoid, step, EX_NODAL, offset, 1, xs+1, xe-xs, varray);
    952:     VecRestoreArray(vNatural, &varray);
    953:   } else {
    954:     IS       compIS;
    955:     PetscInt c;

    957:     ISCreateStride(comm, (xe-xs)/bs, xs, bs, &compIS);
    958:     for (c = 0; c < bs; ++c) {
    959:       ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);
    960:       VecGetSubVector(vNatural, compIS, &vComp);
    961:       VecGetArray(vComp, &varray);
    962:       PetscStackCallStandard(ex_get_partial_var,exoid, step, EX_NODAL, offset+c, 1, xs/bs+1, (xe-xs)/bs, varray);
    963:       VecRestoreArray(vComp, &varray);
    964:       VecRestoreSubVector(vNatural, compIS, &vComp);
    965:     }
    966:     ISDestroy(&compIS);
    967:   }
    968:   if (useNatural) {
    969:     DMPlexNaturalToGlobalBegin(dm, vNatural, v);
    970:     DMPlexNaturalToGlobalEnd(dm, vNatural, v);
    971:     DMRestoreGlobalVector(dm, &vNatural);
    972:   }
    973:   return 0;
    974: }

    976: /*
    977:   VecViewPlex_ExodusII_Zonal_Internal - Write a Vec corresponding to a zonal (cell based) field to an exodus file

    979:   Collective on v

    981:   Input Parameters:
    982: + v  - The vector to be written
    983: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    984: . step - the time step to write at (exodus steps are numbered starting from 1)
    985: - offset - the location of the variable in the file

    987:   Notes:
    988:   The exodus result zonal variable index is obtained by comparing the Vec name and the
    989:   names of zonal variables declared in the exodus file. For instance for a Vec named "V"
    990:   the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
    991:   amongst all zonal variables.

    993:   Level: beginner

    995: .seealso: EXOGetVarIndex_Internal(),DMPlexView_ExodusII_Internal(),VecViewPlex_ExodusII_Nodal_Internal(),VecLoadPlex_ExodusII_Nodal_Internal(),VecLoadPlex_ExodusII_Zonal_Internal()
    996: */
    997: PetscErrorCode VecViewPlex_ExodusII_Zonal_Internal(Vec v, int exoid, int step, int offset)
    998: {
    999:   MPI_Comm          comm;
    1000:   PetscMPIInt       size;
    1001:   DM                dm;
    1002:   Vec               vNatural, vComp;
    1003:   const PetscScalar *varray;
    1004:   PetscInt          xs, xe, bs;
    1005:   PetscBool         useNatural;
    1006:   IS                compIS;
    1007:   PetscInt         *csSize, *csID;
    1008:   PetscInt          numCS, set, csxs = 0;

    1010:   PetscObjectGetComm((PetscObject)v, &comm);
    1011:   MPI_Comm_size(comm, &size);
    1012:   VecGetDM(v, &dm);
    1013:   DMGetUseNatural(dm, &useNatural);
    1014:   useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
    1015:   if (useNatural) {
    1016:     DMGetGlobalVector(dm, &vNatural);
    1017:     DMPlexGlobalToNaturalBegin(dm, v, vNatural);
    1018:     DMPlexGlobalToNaturalEnd(dm, v, vNatural);
    1019:   } else {
    1020:     vNatural = v;
    1021:   }

    1023:   /* Write local chunk of the result in the exodus file
    1024:      exodus stores each component of a vector-valued field as a separate variable.
    1025:      We assume that they are stored sequentially
    1026:      Zonal variables are accessed one element block at a time, so we loop through the cell sets,
    1027:      but once the vector has been reordered to natural size, we cannot use the label information
    1028:      to figure out what to save where. */
    1029:   numCS = ex_inquire_int(exoid, EX_INQ_ELEM_BLK);
    1030:   PetscMalloc2(numCS, &csID, numCS, &csSize);
    1031:   PetscStackCallStandard(ex_get_ids,exoid, EX_ELEM_BLOCK, csID);
    1032:   for (set = 0; set < numCS; ++set) {
    1033:     ex_block block;

    1035:     block.id   = csID[set];
    1036:     block.type = EX_ELEM_BLOCK;
    1037:     PetscStackCallStandard(ex_get_block_param,exoid, &block);
    1038:     csSize[set] = block.num_entry;
    1039:   }
    1040:   VecGetOwnershipRange(vNatural, &xs, &xe);
    1041:   VecGetBlockSize(vNatural, &bs);
    1042:   if (bs > 1) ISCreateStride(comm, (xe-xs)/bs, xs, bs, &compIS);
    1043:   for (set = 0; set < numCS; set++) {
    1044:     PetscInt csLocalSize, c;

    1046:     /* range of indices for set setID[set]: csxs:csxs + csSize[set]-1
    1047:        local slice of zonal values:         xs/bs,xm/bs-1
    1048:        intersection:                        max(xs/bs,csxs),min(xm/bs-1,csxs + csSize[set]-1) */
    1049:     csLocalSize = PetscMax(0, PetscMin(xe/bs, csxs+csSize[set]) - PetscMax(xs/bs, csxs));
    1050:     if (bs == 1) {
    1051:       VecGetArrayRead(vNatural, &varray);
    1052:       PetscStackCallStandard(ex_put_partial_var,exoid, step, EX_ELEM_BLOCK, offset, csID[set], PetscMax(xs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs)]);
    1053:       VecRestoreArrayRead(vNatural, &varray);
    1054:     } else {
    1055:       for (c = 0; c < bs; ++c) {
    1056:         ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);
    1057:         VecGetSubVector(vNatural, compIS, &vComp);
    1058:         VecGetArrayRead(vComp, &varray);
    1059:         PetscStackCallStandard(ex_put_partial_var,exoid, step, EX_ELEM_BLOCK, offset+c, csID[set], PetscMax(xs/bs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs/bs)]);
    1060:         VecRestoreArrayRead(vComp, &varray);
    1061:         VecRestoreSubVector(vNatural, compIS, &vComp);
    1062:       }
    1063:     }
    1064:     csxs += csSize[set];
    1065:   }
    1066:   PetscFree2(csID, csSize);
    1067:   if (bs > 1) ISDestroy(&compIS);
    1068:   if (useNatural) DMRestoreGlobalVector(dm,&vNatural);
    1069:   return 0;
    1070: }

    1072: /*
    1073:   VecLoadPlex_ExodusII_Zonal_Internal - Read a Vec corresponding to a zonal (cell based) field from an exodus file

    1075:   Collective on v

    1077:   Input Parameters:
    1078: + v  - The vector to be written
    1079: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    1080: . step - the time step to read at (exodus steps are numbered starting from 1)
    1081: - offset - the location of the variable in the file

    1083:   Notes:
    1084:   The exodus result zonal variable index is obtained by comparing the Vec name and the
    1085:   names of zonal variables declared in the exodus file. For instance for a Vec named "V"
    1086:   the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
    1087:   amongst all zonal variables.

    1089:   Level: beginner

    1091: .seealso: EXOGetVarIndex_Internal(), DMPlexView_ExodusII_Internal(), VecViewPlex_ExodusII_Nodal_Internal(), VecLoadPlex_ExodusII_Nodal_Internal(), VecLoadPlex_ExodusII_Zonal_Internal()
    1092: */
    1093: PetscErrorCode VecLoadPlex_ExodusII_Zonal_Internal(Vec v, int exoid, int step, int offset)
    1094: {
    1095:   MPI_Comm          comm;
    1096:   PetscMPIInt       size;
    1097:   DM                dm;
    1098:   Vec               vNatural, vComp;
    1099:   PetscScalar      *varray;
    1100:   PetscInt          xs, xe, bs;
    1101:   PetscBool         useNatural;
    1102:   IS                compIS;
    1103:   PetscInt         *csSize, *csID;
    1104:   PetscInt          numCS, set, csxs = 0;

    1106:   PetscObjectGetComm((PetscObject)v,&comm);
    1107:   MPI_Comm_size(comm, &size);
    1108:   VecGetDM(v, &dm);
    1109:   DMGetUseNatural(dm, &useNatural);
    1110:   useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
    1111:   if (useNatural) DMGetGlobalVector(dm,&vNatural);
    1112:   else            {vNatural = v;}

    1114:   /* Read local chunk of the result in the exodus file
    1115:      exodus stores each component of a vector-valued field as a separate variable.
    1116:      We assume that they are stored sequentially
    1117:      Zonal variables are accessed one element block at a time, so we loop through the cell sets,
    1118:      but once the vector has been reordered to natural size, we cannot use the label information
    1119:      to figure out what to save where. */
    1120:   numCS = ex_inquire_int(exoid, EX_INQ_ELEM_BLK);
    1121:   PetscMalloc2(numCS, &csID, numCS, &csSize);
    1122:   PetscStackCallStandard(ex_get_ids,exoid, EX_ELEM_BLOCK, csID);
    1123:   for (set = 0; set < numCS; ++set) {
    1124:     ex_block block;

    1126:     block.id   = csID[set];
    1127:     block.type = EX_ELEM_BLOCK;
    1128:     PetscStackCallStandard(ex_get_block_param,exoid, &block);
    1129:     csSize[set] = block.num_entry;
    1130:   }
    1131:   VecGetOwnershipRange(vNatural, &xs, &xe);
    1132:   VecGetBlockSize(vNatural, &bs);
    1133:   if (bs > 1) ISCreateStride(comm, (xe-xs)/bs, xs, bs, &compIS);
    1134:   for (set = 0; set < numCS; ++set) {
    1135:     PetscInt csLocalSize, c;

    1137:     /* range of indices for set setID[set]: csxs:csxs + csSize[set]-1
    1138:        local slice of zonal values:         xs/bs,xm/bs-1
    1139:        intersection:                        max(xs/bs,csxs),min(xm/bs-1,csxs + csSize[set]-1) */
    1140:     csLocalSize = PetscMax(0, PetscMin(xe/bs, csxs+csSize[set]) - PetscMax(xs/bs, csxs));
    1141:     if (bs == 1) {
    1142:       VecGetArray(vNatural, &varray);
    1143:       PetscStackCallStandard(ex_get_partial_var,exoid, step, EX_ELEM_BLOCK, offset, csID[set], PetscMax(xs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs)]);
    1144:       VecRestoreArray(vNatural, &varray);
    1145:     } else {
    1146:       for (c = 0; c < bs; ++c) {
    1147:         ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);
    1148:         VecGetSubVector(vNatural, compIS, &vComp);
    1149:         VecGetArray(vComp, &varray);
    1150:         PetscStackCallStandard(ex_get_partial_var,exoid, step, EX_ELEM_BLOCK, offset+c, csID[set], PetscMax(xs/bs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs/bs)]);
    1151:         VecRestoreArray(vComp, &varray);
    1152:         VecRestoreSubVector(vNatural, compIS, &vComp);
    1153:       }
    1154:     }
    1155:     csxs += csSize[set];
    1156:   }
    1157:   PetscFree2(csID, csSize);
    1158:   if (bs > 1) ISDestroy(&compIS);
    1159:   if (useNatural) {
    1160:     DMPlexNaturalToGlobalBegin(dm, vNatural, v);
    1161:     DMPlexNaturalToGlobalEnd(dm, vNatural, v);
    1162:     DMRestoreGlobalVector(dm, &vNatural);
    1163:   }
    1164:   return 0;
    1165: }
    1166: #endif

    1168: /*@
    1169:   PetscViewerExodusIIGetId - Get the file id of the ExodusII file

    1171:   Logically Collective on PetscViewer

    1173:   Input Parameter:
    1174: .  viewer - the PetscViewer

    1176:   Output Parameter:
    1177: .  exoid - The ExodusII file id

    1179:   Level: intermediate

    1181: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen()
    1182: @*/
    1183: PetscErrorCode PetscViewerExodusIIGetId(PetscViewer viewer, int *exoid)
    1184: {
    1186:   PetscTryMethod(viewer, "PetscViewerGetId_C",(PetscViewer,int*),(viewer,exoid));
    1187:   return 0;
    1188: }

    1190: /*@
    1191:    PetscViewerExodusIISetOrder - Set the elements order in the exodusII file.

    1193:    Collective

    1195:    Input Parameters:
    1196: +  viewer - the viewer
    1197: -  order - elements order

    1199:    Output Parameter:

    1201:    Level: beginner

    1203:    Note:

    1205: .seealso: PetscViewerExodusIIGetId(), PetscViewerExodusIIGetOrder(), PetscViewerExodusIISetOrder()
    1206: @*/
    1207: PetscErrorCode PetscViewerExodusIISetOrder(PetscViewer viewer, PetscInt order)
    1208: {
    1210:   PetscTryMethod(viewer, "PetscViewerSetOrder_C",(PetscViewer,PetscInt),(viewer,order));
    1211:   return 0;
    1212: }

    1214: /*@
    1215:    PetscViewerExodusIIGetOrder - Get the elements order in the exodusII file.

    1217:    Collective

    1219:    Input Parameters:
    1220: +  viewer - the viewer
    1221: -  order - elements order

    1223:    Output Parameter:

    1225:    Level: beginner

    1227:    Note:

    1229: .seealso: PetscViewerExodusIIGetId(), PetscViewerExodusIIGetOrder(), PetscViewerExodusIISetOrder()
    1230: @*/
    1231: PetscErrorCode PetscViewerExodusIIGetOrder(PetscViewer viewer, PetscInt *order)
    1232: {
    1234:   PetscTryMethod(viewer, "PetscViewerGetOrder_C",(PetscViewer,PetscInt*),(viewer,order));
    1235:   return 0;
    1236: }

    1238: /*@C
    1239:    PetscViewerExodusIIOpen - Opens a file for ExodusII input/output.

    1241:    Collective

    1243:    Input Parameters:
    1244: +  comm - MPI communicator
    1245: .  name - name of file
    1246: -  type - type of file
    1247: $    FILE_MODE_WRITE - create new file for binary output
    1248: $    FILE_MODE_READ - open existing file for binary input
    1249: $    FILE_MODE_APPEND - open existing file for binary output

    1251:    Output Parameter:
    1252: .  exo - PetscViewer for Exodus II input/output to use with the specified file

    1254:    Level: beginner

    1256:    Note:
    1257:    This PetscViewer should be destroyed with PetscViewerDestroy().

    1259: .seealso: PetscViewerPushFormat(), PetscViewerDestroy(),
    1260:           DMLoad(), PetscFileMode, PetscViewer, PetscViewerSetType(), PetscViewerFileSetMode(), PetscViewerFileSetName()
    1261: @*/
    1262: PetscErrorCode PetscViewerExodusIIOpen(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *exo)
    1263: {
    1264:   PetscViewerCreate(comm, exo);
    1265:   PetscViewerSetType(*exo, PETSCVIEWEREXODUSII);
    1266:   PetscViewerFileSetMode(*exo, type);
    1267:   PetscViewerFileSetName(*exo, name);
    1268:   PetscViewerSetFromOptions(*exo);
    1269:   return 0;
    1270: }

    1272: /*@C
    1273:   DMPlexCreateExodusFromFile - Create a DMPlex mesh from an ExodusII file.

    1275:   Collective

    1277:   Input Parameters:
    1278: + comm  - The MPI communicator
    1279: . filename - The name of the ExodusII file
    1280: - interpolate - Create faces and edges in the mesh

    1282:   Output Parameter:
    1283: . dm  - The DM object representing the mesh

    1285:   Level: beginner

    1287: .seealso: DMPLEX, DMCreate(), DMPlexCreateExodus()
    1288: @*/
    1289: PetscErrorCode DMPlexCreateExodusFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
    1290: {
    1291:   PetscMPIInt    rank;
    1292: #if defined(PETSC_HAVE_EXODUSII)
    1293:   int   CPU_word_size = sizeof(PetscReal), IO_word_size = 0, exoid = -1;
    1294:   float version;
    1295: #endif

    1298:   MPI_Comm_rank(comm, &rank);
    1299: #if defined(PETSC_HAVE_EXODUSII)
    1300:   if (rank == 0) {
    1301:     exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version);
    1303:   }
    1304:   DMPlexCreateExodus(comm, exoid, interpolate, dm);
    1305:   if (rank == 0) {PetscStackCallStandard(ex_close,exoid);}
    1306:   return 0;
    1307: #else
    1308:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
    1309: #endif
    1310: }

    1312: #if defined(PETSC_HAVE_EXODUSII)
    1313: static PetscErrorCode ExodusGetCellType_Internal(const char *elem_type, DMPolytopeType *ct)
    1314: {
    1315:   PetscBool      flg;

    1317:   *ct = DM_POLYTOPE_UNKNOWN;
    1318:   PetscStrcmp(elem_type, "TRI", &flg);
    1319:   if (flg) {*ct = DM_POLYTOPE_TRIANGLE; goto done;}
    1320:   PetscStrcmp(elem_type, "TRI3", &flg);
    1321:   if (flg) {*ct = DM_POLYTOPE_TRIANGLE; goto done;}
    1322:   PetscStrcmp(elem_type, "QUAD", &flg);
    1323:   if (flg) {*ct = DM_POLYTOPE_QUADRILATERAL; goto done;}
    1324:   PetscStrcmp(elem_type, "QUAD4", &flg);
    1325:   if (flg) {*ct = DM_POLYTOPE_QUADRILATERAL; goto done;}
    1326:   PetscStrcmp(elem_type, "SHELL4", &flg);
    1327:   if (flg) {*ct = DM_POLYTOPE_QUADRILATERAL; goto done;}
    1328:   PetscStrcmp(elem_type, "TETRA", &flg);
    1329:   if (flg) {*ct = DM_POLYTOPE_TETRAHEDRON; goto done;}
    1330:   PetscStrcmp(elem_type, "TET4", &flg);
    1331:   if (flg) {*ct = DM_POLYTOPE_TETRAHEDRON; goto done;}
    1332:   PetscStrcmp(elem_type, "WEDGE", &flg);
    1333:   if (flg) {*ct = DM_POLYTOPE_TRI_PRISM; goto done;}
    1334:   PetscStrcmp(elem_type, "HEX", &flg);
    1335:   if (flg) {*ct = DM_POLYTOPE_HEXAHEDRON; goto done;}
    1336:   PetscStrcmp(elem_type, "HEX8", &flg);
    1337:   if (flg) {*ct = DM_POLYTOPE_HEXAHEDRON; goto done;}
    1338:   PetscStrcmp(elem_type, "HEXAHEDRON", &flg);
    1339:   if (flg) {*ct = DM_POLYTOPE_HEXAHEDRON; goto done;}
    1340:   SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unrecognized element type %s", elem_type);
    1341:   done:
    1342:   return 0;
    1343: }
    1344: #endif

    1346: /*@
    1347:   DMPlexCreateExodus - Create a DMPlex mesh from an ExodusII file ID.

    1349:   Collective

    1351:   Input Parameters:
    1352: + comm  - The MPI communicator
    1353: . exoid - The ExodusII id associated with a exodus file and obtained using ex_open
    1354: - interpolate - Create faces and edges in the mesh

    1356:   Output Parameter:
    1357: . dm  - The DM object representing the mesh

    1359:   Level: beginner

    1361: .seealso: DMPLEX, DMCreate()
    1362: @*/
    1363: PetscErrorCode DMPlexCreateExodus(MPI_Comm comm, PetscInt exoid, PetscBool interpolate, DM *dm)
    1364: {
    1365: #if defined(PETSC_HAVE_EXODUSII)
    1366:   PetscMPIInt    num_proc, rank;
    1367:   DMLabel        cellSets = NULL, faceSets = NULL, vertSets = NULL;
    1368:   PetscSection   coordSection;
    1369:   Vec            coordinates;
    1370:   PetscScalar    *coords;
    1371:   PetscInt       coordSize, v;
    1372:   /* Read from ex_get_init() */
    1373:   char title[PETSC_MAX_PATH_LEN+1];
    1374:   int  dim    = 0, dimEmbed = 0, numVertices = 0, numCells = 0;
    1375:   int  num_cs = 0, num_vs = 0, num_fs = 0;
    1376: #endif

    1378: #if defined(PETSC_HAVE_EXODUSII)
    1379:   MPI_Comm_rank(comm, &rank);
    1380:   MPI_Comm_size(comm, &num_proc);
    1381:   DMCreate(comm, dm);
    1382:   DMSetType(*dm, DMPLEX);
    1383:   /* Open EXODUS II file and read basic information on rank 0, then broadcast to all processors */
    1384:   if (rank == 0) {
    1385:     PetscMemzero(title,PETSC_MAX_PATH_LEN+1);
    1386:     PetscStackCallStandard(ex_get_init,exoid, title, &dimEmbed, &numVertices, &numCells, &num_cs, &num_vs, &num_fs);
    1388:   }
    1389:   MPI_Bcast(title, PETSC_MAX_PATH_LEN+1, MPI_CHAR, 0, comm);
    1390:   MPI_Bcast(&dim, 1, MPI_INT, 0, comm);
    1391:   PetscObjectSetName((PetscObject) *dm, title);
    1392:   DMPlexSetChart(*dm, 0, numCells+numVertices);
    1393:   /*   We do not want this label automatically computed, instead we compute it here */
    1394:   DMCreateLabel(*dm, "celltype");

    1396:   /* Read cell sets information */
    1397:   if (rank == 0) {
    1398:     PetscInt *cone;
    1399:     int      c, cs, ncs, c_loc, v, v_loc;
    1400:     /* Read from ex_get_elem_blk_ids() */
    1401:     int *cs_id, *cs_order;
    1402:     /* Read from ex_get_elem_block() */
    1403:     char buffer[PETSC_MAX_PATH_LEN+1];
    1404:     int  num_cell_in_set, num_vertex_per_cell, num_hybrid, num_attr;
    1405:     /* Read from ex_get_elem_conn() */
    1406:     int *cs_connect;

    1408:     /* Get cell sets IDs */
    1409:     PetscMalloc2(num_cs, &cs_id, num_cs, &cs_order);
    1410:     PetscStackCallStandard(ex_get_ids,exoid, EX_ELEM_BLOCK, cs_id);
    1411:     /* Read the cell set connectivity table and build mesh topology
    1412:        EXO standard requires that cells in cell sets be numbered sequentially and be pairwise disjoint. */
    1413:     /* Check for a hybrid mesh */
    1414:     for (cs = 0, num_hybrid = 0; cs < num_cs; ++cs) {
    1415:       DMPolytopeType ct;
    1416:       char           elem_type[PETSC_MAX_PATH_LEN];

    1418:       PetscArrayzero(elem_type, sizeof(elem_type));
    1419:       PetscStackCallStandard(ex_get_elem_type,exoid, cs_id[cs], elem_type);
    1420:       ExodusGetCellType_Internal(elem_type, &ct);
    1421:       dim  = PetscMax(dim, DMPolytopeTypeGetDim(ct));
    1422:       PetscStackCallStandard(ex_get_block,exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set,&num_vertex_per_cell, 0, 0, &num_attr);
    1423:       switch (ct) {
    1424:         case DM_POLYTOPE_TRI_PRISM:
    1425:           cs_order[cs] = cs;
    1426:           ++num_hybrid;
    1427:           break;
    1428:         default:
    1429:           for (c = cs; c > cs-num_hybrid; --c) cs_order[c] = cs_order[c-1];
    1430:           cs_order[cs-num_hybrid] = cs;
    1431:       }
    1432:     }
    1433:     /* First set sizes */
    1434:     for (ncs = 0, c = 0; ncs < num_cs; ++ncs) {
    1435:       DMPolytopeType ct;
    1436:       char           elem_type[PETSC_MAX_PATH_LEN];
    1437:       const PetscInt cs = cs_order[ncs];

    1439:       PetscArrayzero(elem_type, sizeof(elem_type));
    1440:       PetscStackCallStandard(ex_get_elem_type,exoid, cs_id[cs], elem_type);
    1441:       ExodusGetCellType_Internal(elem_type, &ct);
    1442:       PetscStackCallStandard(ex_get_block,exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set,&num_vertex_per_cell, 0, 0, &num_attr);
    1443:       for (c_loc = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
    1444:         DMPlexSetConeSize(*dm, c, num_vertex_per_cell);
    1445:         DMPlexSetCellType(*dm, c, ct);
    1446:       }
    1447:     }
    1448:     for (v = numCells; v < numCells+numVertices; ++v) DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);
    1449:     DMSetUp(*dm);
    1450:     for (ncs = 0, c = 0; ncs < num_cs; ++ncs) {
    1451:       const PetscInt cs = cs_order[ncs];
    1452:       PetscStackCallStandard(ex_get_block,exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, 0, 0, &num_attr);
    1453:       PetscMalloc2(num_vertex_per_cell*num_cell_in_set,&cs_connect,num_vertex_per_cell,&cone);
    1454:       PetscStackCallStandard(ex_get_conn,exoid, EX_ELEM_BLOCK, cs_id[cs], cs_connect,NULL,NULL);
    1455:       /* EXO uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
    1456:       for (c_loc = 0, v = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
    1457:         DMPolytopeType ct;

    1459:         for (v_loc = 0; v_loc < num_vertex_per_cell; ++v_loc, ++v) {
    1460:           cone[v_loc] = cs_connect[v]+numCells-1;
    1461:         }
    1462:         DMPlexGetCellType(*dm, c, &ct);
    1463:         DMPlexInvertCell(ct, cone);
    1464:         DMPlexSetCone(*dm, c, cone);
    1465:         DMSetLabelValue_Fast(*dm, &cellSets, "Cell Sets", c, cs_id[cs]);
    1466:       }
    1467:       PetscFree2(cs_connect,cone);
    1468:     }
    1469:     PetscFree2(cs_id, cs_order);
    1470:   }
    1471:   {
    1472:     PetscInt ints[] = {dim, dimEmbed};

    1474:     MPI_Bcast(ints, 2, MPIU_INT, 0, comm);
    1475:     DMSetDimension(*dm, ints[0]);
    1476:     DMSetCoordinateDim(*dm, ints[1]);
    1477:     dim      = ints[0];
    1478:     dimEmbed = ints[1];
    1479:   }
    1480:   DMPlexSymmetrize(*dm);
    1481:   DMPlexStratify(*dm);
    1482:   if (interpolate) {
    1483:     DM idm;

    1485:     DMPlexInterpolate(*dm, &idm);
    1486:     DMDestroy(dm);
    1487:     *dm  = idm;
    1488:   }

    1490:   /* Create vertex set label */
    1491:   if (rank == 0 && (num_vs > 0)) {
    1492:     int vs, v;
    1493:     /* Read from ex_get_node_set_ids() */
    1494:     int *vs_id;
    1495:     /* Read from ex_get_node_set_param() */
    1496:     int num_vertex_in_set;
    1497:     /* Read from ex_get_node_set() */
    1498:     int *vs_vertex_list;

    1500:     /* Get vertex set ids */
    1501:     PetscMalloc1(num_vs, &vs_id);
    1502:     PetscStackCallStandard(ex_get_ids,exoid, EX_NODE_SET, vs_id);
    1503:     for (vs = 0; vs < num_vs; ++vs) {
    1504:       PetscStackCallStandard(ex_get_set_param,exoid, EX_NODE_SET, vs_id[vs], &num_vertex_in_set, NULL);
    1505:       PetscMalloc1(num_vertex_in_set, &vs_vertex_list);
    1506:       PetscStackCallStandard(ex_get_set,exoid, EX_NODE_SET, vs_id[vs], vs_vertex_list, NULL);
    1507:       for (v = 0; v < num_vertex_in_set; ++v) {
    1508:         DMSetLabelValue_Fast(*dm, &vertSets, "Vertex Sets", vs_vertex_list[v]+numCells-1, vs_id[vs]);
    1509:       }
    1510:       PetscFree(vs_vertex_list);
    1511:     }
    1512:     PetscFree(vs_id);
    1513:   }
    1514:   /* Read coordinates */
    1515:   DMGetCoordinateSection(*dm, &coordSection);
    1516:   PetscSectionSetNumFields(coordSection, 1);
    1517:   PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
    1518:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
    1519:   for (v = numCells; v < numCells+numVertices; ++v) {
    1520:     PetscSectionSetDof(coordSection, v, dimEmbed);
    1521:     PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
    1522:   }
    1523:   PetscSectionSetUp(coordSection);
    1524:   PetscSectionGetStorageSize(coordSection, &coordSize);
    1525:   VecCreate(PETSC_COMM_SELF, &coordinates);
    1526:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    1527:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    1528:   VecSetBlockSize(coordinates, dimEmbed);
    1529:   VecSetType(coordinates,VECSTANDARD);
    1530:   VecGetArray(coordinates, &coords);
    1531:   if (rank == 0) {
    1532:     PetscReal *x, *y, *z;

    1534:     PetscMalloc3(numVertices,&x,numVertices,&y,numVertices,&z);
    1535:     PetscStackCallStandard(ex_get_coord,exoid, x, y, z);
    1536:     if (dimEmbed > 0) {
    1537:       for (v = 0; v < numVertices; ++v) coords[v*dimEmbed+0] = x[v];
    1538:     }
    1539:     if (dimEmbed > 1) {
    1540:       for (v = 0; v < numVertices; ++v) coords[v*dimEmbed+1] = y[v];
    1541:     }
    1542:     if (dimEmbed > 2) {
    1543:       for (v = 0; v < numVertices; ++v) coords[v*dimEmbed+2] = z[v];
    1544:     }
    1545:     PetscFree3(x,y,z);
    1546:   }
    1547:   VecRestoreArray(coordinates, &coords);
    1548:   DMSetCoordinatesLocal(*dm, coordinates);
    1549:   VecDestroy(&coordinates);

    1551:   /* Create side set label */
    1552:   if (rank == 0 && interpolate && (num_fs > 0)) {
    1553:     int fs, f, voff;
    1554:     /* Read from ex_get_side_set_ids() */
    1555:     int *fs_id;
    1556:     /* Read from ex_get_side_set_param() */
    1557:     int num_side_in_set;
    1558:     /* Read from ex_get_side_set_node_list() */
    1559:     int *fs_vertex_count_list, *fs_vertex_list;
    1560:     /* Read side set labels */
    1561:     char fs_name[MAX_STR_LENGTH+1];

    1563:     /* Get side set ids */
    1564:     PetscMalloc1(num_fs, &fs_id);
    1565:     PetscStackCallStandard(ex_get_ids,exoid, EX_SIDE_SET, fs_id);
    1566:     for (fs = 0; fs < num_fs; ++fs) {
    1567:       PetscStackCallStandard(ex_get_set_param,exoid, EX_SIDE_SET, fs_id[fs], &num_side_in_set, NULL);
    1568:       PetscMalloc2(num_side_in_set,&fs_vertex_count_list,num_side_in_set*4,&fs_vertex_list);
    1569:       PetscStackCallStandard(ex_get_side_set_node_list,exoid, fs_id[fs], fs_vertex_count_list, fs_vertex_list);
    1570:       /* Get the specific name associated with this side set ID. */
    1571:       int fs_name_err = ex_get_name(exoid, EX_SIDE_SET, fs_id[fs], fs_name);
    1572:       for (f = 0, voff = 0; f < num_side_in_set; ++f) {
    1573:         const PetscInt *faces   = NULL;
    1574:         PetscInt       faceSize = fs_vertex_count_list[f], numFaces;
    1575:         PetscInt       faceVertices[4], v;

    1578:         for (v = 0; v < faceSize; ++v, ++voff) {
    1579:           faceVertices[v] = fs_vertex_list[voff]+numCells-1;
    1580:         }
    1581:         DMPlexGetFullJoin(*dm, faceSize, faceVertices, &numFaces, &faces);
    1583:         DMSetLabelValue_Fast(*dm, &faceSets, "Face Sets", faces[0], fs_id[fs]);
    1584:         /* Only add the label if one has been detected for this side set. */
    1585:         if (!fs_name_err) {
    1586:           DMSetLabelValue(*dm, fs_name, faces[0], fs_id[fs]);
    1587:         }
    1588:         DMPlexRestoreJoin(*dm, faceSize, faceVertices, &numFaces, &faces);
    1589:       }
    1590:       PetscFree2(fs_vertex_count_list,fs_vertex_list);
    1591:     }
    1592:     PetscFree(fs_id);
    1593:   }

    1595:   { /* Create Cell/Face/Vertex Sets labels at all processes */
    1596:     enum {n = 3};
    1597:     PetscBool flag[n];

    1599:     flag[0] = cellSets ? PETSC_TRUE : PETSC_FALSE;
    1600:     flag[1] = faceSets ? PETSC_TRUE : PETSC_FALSE;
    1601:     flag[2] = vertSets ? PETSC_TRUE : PETSC_FALSE;
    1602:     MPI_Bcast(flag, n, MPIU_BOOL, 0, comm);
    1603:     if (flag[0]) DMCreateLabel(*dm, "Cell Sets");
    1604:     if (flag[1]) DMCreateLabel(*dm, "Face Sets");
    1605:     if (flag[2]) DMCreateLabel(*dm, "Vertex Sets");
    1606:   }
    1607:   return 0;
    1608: #else
    1609:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
    1610: #endif
    1611: }