Actual source code: plexexodusii.c
petsc-3.13.6 2020-09-29
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      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;

     38:   PetscViewerExodusIIOpen(comm, "mesh.exo", FILE_MODE_WRITE, &viewer);
     39:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_EXODUSII_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
     40:   PetscObjectRegisterDestroy((PetscObject) viewer);
     41:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_EXODUSII_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
     42:   PetscFunctionReturn(viewer);
     43: }

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

     51:   if (exo->filename) {PetscViewerASCIIPrintf(viewer, "Filename: %s\n", exo->filename);}
     52:   return(0);
     53: }

     55: static PetscErrorCode PetscViewerSetFromOptions_ExodusII(PetscOptionItems *PetscOptionsObject, PetscViewer v)
     56: {

     60:   PetscOptionsHead(PetscOptionsObject, "ExodusII PetscViewer Options");
     61:   PetscOptionsTail();
     62:   return(0);
     63: }

     65: static PetscErrorCode PetscViewerSetUp_ExodusII(PetscViewer viewer)
     66: {
     68:   return(0);
     69: }

     71: static PetscErrorCode PetscViewerDestroy_ExodusII(PetscViewer viewer)
     72: {
     73:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;
     74:   PetscErrorCode        ierr;

     77:   if (exo->exoid >= 0) {ex_close(exo->exoid);}
     78:   PetscFree(exo);
     79:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",NULL);
     80:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileGetName_C",NULL);
     81:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",NULL);
     82:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerExodusIIGetId",NULL);
     83:   return(0);
     84: }

     86: static PetscErrorCode PetscViewerFileSetName_ExodusII(PetscViewer viewer, const char name[])
     87: {
     88:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;
     89:   PetscMPIInt           rank;
     90:   int                   CPU_word_size, IO_word_size, EXO_mode;
     91:   PetscErrorCode        ierr;

     94:   MPI_Comm_rank(PetscObjectComm((PetscObject) viewer), &rank);
     95:   CPU_word_size = sizeof(PetscReal);
     96:   IO_word_size  = sizeof(PetscReal);

     99:   if (exo->exoid >= 0) {ex_close(exo->exoid); exo->exoid = -1;}
    100:   if (exo->filename) {PetscFree(exo->filename);}
    101:   PetscStrallocpy(name, &exo->filename);
    102:   /* Create or open the file collectively */
    103:   switch (exo->btype) {
    104:   case FILE_MODE_READ:
    105:     EXO_mode = EX_CLOBBER;
    106:     break;
    107:   case FILE_MODE_APPEND:
    108:     EXO_mode = EX_CLOBBER;
    109:     break;
    110:   case FILE_MODE_WRITE:
    111:     EXO_mode = EX_CLOBBER;
    112:     break;
    113:   default:
    114:     SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
    115:   }
    116:   #if defined(PETSC_USE_64BIT_INDICES)
    117:   EXO_mode += EX_ALL_INT64_API;
    118:   #endif
    119:   exo->exoid = ex_create(name, EXO_mode, &CPU_word_size, &IO_word_size);
    120:   if (exo->exoid < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_create failed for %s", name);
    121:   return(0);
    122: }

    124: static PetscErrorCode PetscViewerFileGetName_ExodusII(PetscViewer viewer, const char **name)
    125: {
    126:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    129:   *name = exo->filename;
    130:   return(0);
    131: }

    133: static PetscErrorCode PetscViewerFileSetMode_ExodusII(PetscViewer viewer, PetscFileMode type)
    134: {
    135:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    138:   exo->btype = type;
    139:   return(0);
    140: }

    142: static PetscErrorCode PetscViewerFileGetMode_ExodusII(PetscViewer viewer, PetscFileMode *type)
    143: {
    144:   PetscViewer_ExodusII *exo = (PetscViewer_ExodusII *) viewer->data;

    147:   *type = exo->btype;
    148:   return(0);
    149: }

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

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

    160: /*@C
    161:    PetscViewerExodusIIOpen - Opens a file for ExodusII input/output.

    163:    Collective

    165:    Input Parameters:
    166: +  comm - MPI communicator
    167: .  name - name of file
    168: -  type - type of file
    169: $    FILE_MODE_WRITE - create new file for binary output
    170: $    FILE_MODE_READ - open existing file for binary input
    171: $    FILE_MODE_APPEND - open existing file for binary output

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

    176:    Level: beginner

    178:    Note:
    179:    This PetscViewer should be destroyed with PetscViewerDestroy().

    182: .seealso: PetscViewerPushFormat(), PetscViewerDestroy(),
    183:           DMLoad(), PetscFileMode, PetscViewer, PetscViewerSetType(), PetscViewerFileSetMode(), PetscViewerFileSetName()
    184: @*/
    185: PetscErrorCode PetscViewerExodusIIOpen(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *exo)
    186: {

    190:   PetscViewerCreate(comm, exo);
    191:   PetscViewerSetType(*exo, PETSCVIEWEREXODUSII);
    192:   PetscViewerFileSetMode(*exo, type);
    193:   PetscViewerFileSetName(*exo, name);
    194:   PetscViewerSetFromOptions(*exo);
    195:   return(0);
    196: }

    198: /*MC
    199:    PETSCVIEWEREXODUSII - A viewer that writes to an Exodus II file

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

    205:   Level: beginner
    206: M*/

    208: PETSC_EXTERN PetscErrorCode PetscViewerCreate_ExodusII(PetscViewer v)
    209: {
    210:   PetscViewer_ExodusII *exo;
    211:   PetscErrorCode        ierr;

    214:   PetscNewLog(v,&exo);

    216:   v->data                = (void*) exo;
    217:   v->ops->destroy        = PetscViewerDestroy_ExodusII;
    218:   v->ops->setfromoptions = PetscViewerSetFromOptions_ExodusII;
    219:   v->ops->setup          = PetscViewerSetUp_ExodusII;
    220:   v->ops->view           = PetscViewerView_ExodusII;
    221:   v->ops->flush          = 0;
    222:   exo->btype             = (PetscFileMode) -1;
    223:   exo->filename          = 0;
    224:   exo->exoid             = -1;

    226:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_ExodusII);
    227:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetName_C",PetscViewerFileGetName_ExodusII);
    228:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_ExodusII);
    229:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetMode_C",PetscViewerFileGetMode_ExodusII);
    230:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerExodusIIGetId_C",PetscViewerExodusIIGetId_ExodusII);
    231:   return(0);
    232: }

    234: /*
    235:   EXOGetVarIndex - Locate a result in an exodus file based on its name

    237:   Not collective

    239:   Input Parameters:
    240: + exoid    - the exodus id of a file (obtained from ex_open or ex_create for instance)
    241: . obj_type - the type of entity for instance EX_NODAL, EX_ELEM_BLOCK
    242: - name     - the name of the result

    244:   Output Parameters:
    245: . varIndex - the location in the exodus file of the result

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

    253:   Level: beginner

    255: .seealso: EXOGetVarIndex(),DMPlexView_ExodusII_Internal(),VecViewPlex_ExodusII_Nodal_Internal(),VecLoadNodal_PlexEXO(),VecLoadZonal_PlexEXO()
    256: */
    257: static PetscErrorCode EXOGetVarIndex_Private(int exoid, ex_entity_type obj_type, const char name[], int *varIndex)
    258: {
    259:   int            num_vars, i, j;
    260:   char           ext_name[MAX_STR_LENGTH+1], var_name[MAX_STR_LENGTH+1];
    261:   const int      num_suffix = 5;
    262:   char          *suffix[5];
    263:   PetscBool      flg;

    267:   suffix[0] = (char *) "";
    268:   suffix[1] = (char *) "_X";
    269:   suffix[2] = (char *) "_XX";
    270:   suffix[3] = (char *) "_1";
    271:   suffix[4] = (char *) "_11";

    273:   *varIndex = 0;
    274:   PetscStackCallStandard(ex_get_variable_param,(exoid, obj_type, &num_vars));
    275:   for (i = 0; i < num_vars; ++i) {
    276:     PetscStackCallStandard(ex_get_variable_name,(exoid, obj_type, i+1, var_name));
    277:     for (j = 0; j < num_suffix; ++j){
    278:       PetscStrncpy(ext_name, name, MAX_STR_LENGTH);
    279:       PetscStrlcat(ext_name, suffix[j], MAX_STR_LENGTH);
    280:       PetscStrcasecmp(ext_name, var_name, &flg);
    281:       if (flg) {
    282:         *varIndex = i+1;
    283:         return(0);
    284:       }
    285:     }
    286:   }
    287:   SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to locate variable %s in ExodusII file.", name);
    288:  PetscFunctionReturn(-1);
    289: }

    291: /*
    292:   DMPlexView_ExodusII_Internal - Write a DM to disk in exodus format

    294:   Collective on dm

    296:   Input Parameters:
    297: + dm  - The dm to be written
    298: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    299: - degree - the degree of the interpolation space

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

    305:   If the dm has been distributed and exoid points to different files on each MPI rank, only the "local" part of the DM
    306:   (including "ghost" cells and vertices) will be written. If all exoid points to the same file, the resulting file will
    307:   probably be corrupted.

    309:   DMPlex only represents geometry while most post-processing software expect that a mesh also provides information
    310:   on the discretization space. This function assumes that the file represents Lagrange finite elements of order 1 or 2.
    311:   It should be extended to use PetscFE objects.

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

    316: .seealso: EXOGetVarIndex_Private(), VecViewPlex_ExodusII_Nodal_Internal(), VecLoadNodal_PlexEXO(), VecViewZonal_PlexEXO(), VecLoadZonal_PlexEXO()
    317: */
    318: PetscErrorCode DMPlexView_ExodusII_Internal(DM dm, int exoid, PetscInt degree)
    319: {
    320:   enum ElemType {TRI, QUAD, TET, HEX};
    321:   MPI_Comm        comm;
    322:   /* Connectivity Variables */
    323:   PetscInt        cellsNotInConnectivity;
    324:   /* Cell Sets */
    325:   DMLabel         csLabel;
    326:   IS              csIS;
    327:   const PetscInt *csIdx;
    328:   PetscInt        num_cs, cs;
    329:   enum ElemType  *type;
    330:   PetscBool       hasLabel;
    331:   /* Coordinate Variables */
    332:   DM              cdm;
    333:   PetscSection    section;
    334:   Vec             coord;
    335:   PetscInt      **nodes;
    336:   PetscInt        depth, d, dim, skipCells = 0;
    337:   PetscInt        pStart, pEnd, p, cStart, cEnd, numCells, vStart, vEnd, numVertices, eStart, eEnd, numEdges, fStart, fEnd, numFaces, numNodes;
    338:   PetscInt        num_vs, num_fs;
    339:   PetscMPIInt     rank, size;
    340:   const char     *dmName;
    341:   PetscInt        nodesTriP1[4]  = {3,0,0,0};
    342:   PetscInt        nodesTriP2[4]  = {3,3,0,0};
    343:   PetscInt        nodesQuadP1[4] = {4,0,0,0};
    344:   PetscInt        nodesQuadP2[4] = {4,4,0,1};
    345:   PetscInt        nodesTetP1[4]  = {4,0,0,0};
    346:   PetscInt        nodesTetP2[4]  = {4,6,0,0};
    347:   PetscInt        nodesHexP1[4]  = {8,0,0,0};
    348:   PetscInt        nodesHexP2[4]  = {8,12,6,1};
    349:   PetscErrorCode  ierr;

    352:   PetscObjectGetComm((PetscObject)dm, &comm);
    353:   MPI_Comm_rank(comm, &rank);
    354:   MPI_Comm_size(comm, &size);
    355:   /* --- Get DM info --- */
    356:   PetscObjectGetName((PetscObject) dm, &dmName);
    357:   DMPlexGetDepth(dm, &depth);
    358:   DMGetDimension(dm, &dim);
    359:   DMPlexGetChart(dm, &pStart, &pEnd);
    360:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    361:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    362:   DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);
    363:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
    364:   numCells    = cEnd - cStart;
    365:   numEdges    = eEnd - eStart;
    366:   numVertices = vEnd - vStart;
    367:   if (depth == 3) {numFaces = fEnd - fStart;}
    368:   else            {numFaces = 0;}
    369:   DMGetLabelSize(dm, "Cell Sets", &num_cs);
    370:   DMGetLabelSize(dm, "Vertex Sets", &num_vs);
    371:   DMGetLabelSize(dm, "Face Sets", &num_fs);
    372:   DMGetCoordinatesLocal(dm, &coord);
    373:   DMGetCoordinateDM(dm, &cdm);
    374:   if (num_cs > 0) {
    375:     DMGetLabel(dm, "Cell Sets", &csLabel);
    376:     DMLabelGetValueIS(csLabel, &csIS);
    377:     ISGetIndices(csIS, &csIdx);
    378:   }
    379:   PetscMalloc1(num_cs, &nodes);
    380:   /* Set element type for each block and compute total number of nodes */
    381:   PetscMalloc1(num_cs, &type);
    382:   numNodes = numVertices;
    383:   if (degree == 2) {numNodes += numEdges;}
    384:   cellsNotInConnectivity = numCells;
    385:   for (cs = 0; cs < num_cs; ++cs) {
    386:     IS              stratumIS;
    387:     const PetscInt *cells;
    388:     PetscScalar    *xyz = NULL;
    389:     PetscInt        csSize, closureSize;

    391:     DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS);
    392:     ISGetIndices(stratumIS, &cells);
    393:     ISGetSize(stratumIS, &csSize);
    394:     DMPlexVecGetClosure(cdm, NULL, coord, cells[0], &closureSize, &xyz);
    395:     switch (dim) {
    396:       case 2:
    397:         if      (closureSize == 3*dim) {type[cs] = TRI;}
    398:         else if (closureSize == 4*dim) {type[cs] = QUAD;}
    399:         else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %D in dimension %D has no ExodusII type", closureSize/dim, dim);
    400:         break;
    401:       case 3:
    402:         if      (closureSize == 4*dim) {type[cs] = TET;}
    403:         else if (closureSize == 8*dim) {type[cs] = HEX;}
    404:         else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %D in dimension %D has no ExodusII type", closureSize/dim, dim);
    405:         break;
    406:       default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not handled by ExodusII viewer", dim);
    407:     }
    408:     if ((degree == 2) && (type[cs] == QUAD)) {numNodes += csSize;}
    409:     if ((degree == 2) && (type[cs] == HEX))  {numNodes += csSize; numNodes += numFaces;}
    410:     DMPlexVecRestoreClosure(cdm, NULL, coord, cells[0], &closureSize, &xyz);
    411:     /* Set nodes and Element type */
    412:     if (type[cs] == TRI) {
    413:       if      (degree == 1) nodes[cs] = nodesTriP1;
    414:       else if (degree == 2) nodes[cs] = nodesTriP2;
    415:     } else if (type[cs] == QUAD) {
    416:       if      (degree == 1) nodes[cs] = nodesQuadP1;
    417:       else if (degree == 2) nodes[cs] = nodesQuadP2;
    418:     } else if (type[cs] == TET) {
    419:       if      (degree == 1) nodes[cs] = nodesTetP1;
    420:       else if (degree == 2) nodes[cs] = nodesTetP2;
    421:     } else if (type[cs] == HEX) {
    422:       if      (degree == 1) nodes[cs] = nodesHexP1;
    423:       else if (degree == 2) nodes[cs] = nodesHexP2;
    424:     }
    425:     /* Compute the number of cells not in the connectivity table */
    426:     cellsNotInConnectivity -= nodes[cs][3]*csSize;

    428:     ISRestoreIndices(stratumIS, &cells);
    429:     ISDestroy(&stratumIS);
    430:   }
    431:   if (num_cs > 0) {PetscStackCallStandard(ex_put_init,(exoid, dmName, dim, numNodes, numCells, num_cs, num_vs, num_fs));}
    432:   /* --- Connectivity --- */
    433:   for (cs = 0; cs < num_cs; ++cs) {
    434:     IS              stratumIS;
    435:     const PetscInt *cells;
    436:     PetscInt       *connect, off = 0;
    437:     PetscInt        edgesInClosure = 0, facesInClosure = 0, verticesInClosure = 0;
    438:     PetscInt        csSize, c, connectSize, closureSize;
    439:     char           *elem_type = NULL;
    440:     char            elem_type_tri3[]  = "TRI3",  elem_type_quad4[] = "QUAD4";
    441:     char            elem_type_tri6[]  = "TRI6",  elem_type_quad9[] = "QUAD9";
    442:     char            elem_type_tet4[]  = "TET4",  elem_type_hex8[]  = "HEX8";
    443:     char            elem_type_tet10[] = "TET10", elem_type_hex27[] = "HEX27";

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

    473:         DMPlexGetConeSize(dm, cells[0], &facesInClosure);
    474:         DMPlexGetTransitiveClosure(dm, cells[0], PETSC_TRUE, &closureSize, &closure);
    475:         edgesInClosure = closureSize - facesInClosure - 1 - verticesInClosure;
    476:         DMPlexRestoreTransitiveClosure(dm, cells[0], PETSC_TRUE, &closureSize, &closure);
    477:       }
    478:     }
    479:     /* Get connectivity for each cell */
    480:     for (c = 0; c < csSize; ++c) {
    481:       PetscInt *closure = NULL;
    482:       PetscInt  temp, i;

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

    520:           temp = connect[12+off]; connect[12+off] = connect[16+off]; connect[16+off] = temp;
    521:           temp = connect[13+off]; connect[13+off] = connect[17+off]; connect[17+off] = temp;
    522:           temp = connect[14+off]; connect[14+off] = connect[18+off]; connect[18+off] = temp;
    523:           temp = connect[15+off]; connect[15+off] = connect[19+off]; connect[19+off] = temp;

    525:           temp = connect[23+off]; connect[23+off] = connect[26+off]; connect[26+off] = temp;
    526:           temp = connect[24+off]; connect[24+off] = connect[25+off]; connect[25+off] = temp;
    527:           temp = connect[25+off]; connect[25+off] = connect[26+off]; connect[26+off] = temp;
    528:         }
    529:       }
    530:       off += connectSize;
    531:       DMPlexRestoreTransitiveClosure(dm, cells[c], PETSC_TRUE, &closureSize, &closure);
    532:     }
    533:     PetscStackCallStandard(ex_put_conn,(exoid, EX_ELEM_BLOCK, csIdx[cs], connect, 0, 0));
    534:     skipCells += (nodes[cs][3] == 0)*csSize;
    535:     PetscFree(connect);
    536:     ISRestoreIndices(stratumIS, &cells);
    537:     ISDestroy(&stratumIS);
    538:   }
    539:   PetscFree(type);
    540:   /* --- Coordinates --- */
    541:   PetscSectionCreate(comm, &section);
    542:   PetscSectionSetChart(section, pStart, pEnd);
    543:   if (num_cs) {
    544:     for (d = 0; d < depth; ++d) {
    545:       DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
    546:       for (p = pStart; p < pEnd; ++p) {
    547:         PetscSectionSetDof(section, p, nodes[0][d] > 0);
    548:       }
    549:     }
    550:   }
    551:   for (cs = 0; cs < num_cs; ++cs) {
    552:     IS              stratumIS;
    553:     const PetscInt *cells;
    554:     PetscInt        csSize, c;

    556:     DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS);
    557:     ISGetIndices(stratumIS, &cells);
    558:     ISGetSize(stratumIS, &csSize);
    559:     for (c = 0; c < csSize; ++c) {
    560:       PetscSectionSetDof(section, cells[c], nodes[cs][3] > 0);
    561:     }
    562:     ISRestoreIndices(stratumIS, &cells);
    563:     ISDestroy(&stratumIS);
    564:   }
    565:   if (num_cs > 0) {
    566:     ISRestoreIndices(csIS, &csIdx);
    567:     ISDestroy(&csIS);
    568:   }
    569:   PetscFree(nodes);
    570:   PetscSectionSetUp(section);
    571:   if (numNodes > 0) {
    572:     const char  *coordNames[3] = {"x", "y", "z"};
    573:     PetscScalar *coords, *closure;
    574:     PetscReal   *cval;
    575:     PetscInt     hasDof, n = 0;

    577:     /* There can't be more than 24 values in the closure of a point for the coord section */
    578:     PetscCalloc3(numNodes*3, &coords, dim, &cval, 24, &closure);
    579:     DMGetCoordinatesLocal(dm, &coord);
    580:     DMPlexGetChart(dm, &pStart, &pEnd);
    581:     for (p = pStart; p < pEnd; ++p) {
    582:       PetscSectionGetDof(section, p, &hasDof);
    583:       if (hasDof) {
    584:         PetscInt closureSize = 24, j;

    586:         DMPlexVecGetClosure(cdm, NULL, coord, p, &closureSize, &closure);
    587:         for (d = 0; d < dim; ++d) {
    588:           cval[d] = 0.0;
    589:           for (j = 0; j < closureSize/dim; j++) cval[d] += closure[j*dim+d];
    590:           coords[d*numNodes+n] = cval[d] * dim / closureSize;
    591:         }
    592:         ++n;
    593:       }
    594:     }
    595:     PetscStackCallStandard(ex_put_coord,(exoid, &coords[0*numNodes], &coords[1*numNodes], &coords[2*numNodes]));
    596:     PetscFree3(coords, cval, closure);
    597:     PetscStackCallStandard(ex_put_coord_names,(exoid, (char **) coordNames));
    598:   }
    599:   PetscSectionDestroy(&section);
    600:   /* --- Node Sets/Vertex Sets --- */
    601:   DMHasLabel(dm, "Vertex Sets", &hasLabel);
    602:   if (hasLabel) {
    603:     PetscInt        i, vs, vsSize;
    604:     const PetscInt *vsIdx, *vertices;
    605:     PetscInt       *nodeList;
    606:     IS              vsIS, stratumIS;
    607:     DMLabel         vsLabel;
    608:     DMGetLabel(dm, "Vertex Sets", &vsLabel);
    609:     DMLabelGetValueIS(vsLabel, &vsIS);
    610:     ISGetIndices(vsIS, &vsIdx);
    611:     for (vs=0; vs<num_vs; ++vs) {
    612:       DMLabelGetStratumIS(vsLabel, vsIdx[vs], &stratumIS);
    613:       ISGetIndices(stratumIS, &vertices);
    614:       ISGetSize(stratumIS, &vsSize);
    615:       PetscMalloc1(vsSize, &nodeList);
    616:       for (i=0; i<vsSize; ++i) {
    617:         nodeList[i] = vertices[i] - skipCells + 1;
    618:       }
    619:       PetscStackCallStandard(ex_put_set_param,(exoid, EX_NODE_SET, vsIdx[vs], vsSize, 0));
    620:       PetscStackCallStandard(ex_put_set,(exoid, EX_NODE_SET, vsIdx[vs], nodeList, NULL));
    621:       ISRestoreIndices(stratumIS, &vertices);
    622:       ISDestroy(&stratumIS);
    623:       PetscFree(nodeList);
    624:     }
    625:     ISRestoreIndices(vsIS, &vsIdx);
    626:     ISDestroy(&vsIS);
    627:   }
    628:   /* --- Side Sets/Face Sets --- */
    629:   DMHasLabel(dm, "Face Sets", &hasLabel);
    630:   if (hasLabel) {
    631:     PetscInt        i, j, fs, fsSize;
    632:     const PetscInt *fsIdx, *faces;
    633:     IS              fsIS, stratumIS;
    634:     DMLabel         fsLabel;
    635:     PetscInt        numPoints, *points;
    636:     PetscInt        elem_list_size = 0;
    637:     PetscInt       *elem_list, *elem_ind, *side_list;

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

    664:       for (i=0; i<fsSize; ++i) {
    665:         /* Element List */
    666:         points = NULL;
    667:         DMPlexGetTransitiveClosure(dm, faces[i], PETSC_FALSE, &numPoints, &points);
    668:         elem_list[elem_ind[fs] + i] = points[2] +1;
    669:         DMPlexRestoreTransitiveClosure(dm, faces[i], PETSC_FALSE, &numPoints, &points);

    671:         /* Side List */
    672:         points = NULL;
    673:         DMPlexGetTransitiveClosure(dm, elem_list[elem_ind[fs] + i]-1, PETSC_TRUE, &numPoints, &points);
    674:         for (j=1; j<numPoints; ++j) {
    675:           if (points[j*2]==faces[i]) {break;}
    676:         }
    677:         /* Convert HEX sides */
    678:         if (numPoints == 27) {
    679:           if      (j == 1) {j = 5;}
    680:           else if (j == 2) {j = 6;}
    681:           else if (j == 3) {j = 1;}
    682:           else if (j == 4) {j = 3;}
    683:           else if (j == 5) {j = 2;}
    684:           else if (j == 6) {j = 4;}
    685:         }
    686:         /* Convert TET sides */
    687:         if (numPoints == 15) {
    688:           --j;
    689:           if (j == 0) {j = 4;}
    690:         }
    691:         side_list[elem_ind[fs] + i] = j;
    692:         DMPlexRestoreTransitiveClosure(dm, elem_list[elem_ind[fs] + i]-1, PETSC_TRUE, &numPoints, &points);

    694:       }
    695:       ISRestoreIndices(stratumIS, &faces);
    696:       ISDestroy(&stratumIS);
    697:     }
    698:     ISRestoreIndices(fsIS, &fsIdx);
    699:     ISDestroy(&fsIS);

    701:     /* Put side sets */
    702:     for (fs=0; fs<num_fs; ++fs) {
    703:       PetscStackCallStandard(ex_put_set,(exoid, EX_SIDE_SET, fsIdx[fs], &elem_list[elem_ind[fs]], &side_list[elem_ind[fs]]));
    704:     }
    705:     PetscFree3(elem_ind,elem_list,side_list);
    706:   }
    707:   return(0);
    708: }

    710: /*
    711:   VecViewPlex_ExodusII_Nodal_Internal - Write a Vec corresponding to a nodal field to an exodus file

    713:   Collective on v

    715:   Input Parameters:
    716: + v  - The vector to be written
    717: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    718: - step - the time step to write at (exodus steps are numbered starting from 1)

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

    726:   Level: beginner

    728: .seealso: EXOGetVarIndex_Private(),DMPlexView_ExodusII_Internal(),VecLoadNodal_PlexEXO(),VecViewZonal_PlexEXO(),VecLoadZonal_PlexEXO()
    729: @*/
    730: PetscErrorCode VecViewPlex_ExodusII_Nodal_Internal(Vec v, int exoid, int step)
    731: {
    732:   MPI_Comm         comm;
    733:   PetscMPIInt      size;
    734:   DM               dm;
    735:   Vec              vNatural, vComp;
    736:   const PetscScalar *varray;
    737:   const char      *vecname;
    738:   PetscInt         xs, xe, bs;
    739:   PetscBool        useNatural;
    740:   int              offset;
    741:   PetscErrorCode   ierr;

    744:   PetscObjectGetComm((PetscObject) v, &comm);
    745:   MPI_Comm_size(comm, &size);
    746:   VecGetDM(v, &dm);
    747:   DMGetUseNatural(dm, &useNatural);
    748:   useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
    749:   if (useNatural) {
    750:     DMGetGlobalVector(dm, &vNatural);
    751:     DMPlexGlobalToNaturalBegin(dm, v, vNatural);
    752:     DMPlexGlobalToNaturalEnd(dm, v, vNatural);
    753:   } else {
    754:     vNatural = v;
    755:   }
    756:   /* Get the location of the variable in the exodus file */
    757:   PetscObjectGetName((PetscObject) v, &vecname);
    758:   EXOGetVarIndex_Private(exoid, EX_NODAL, vecname, &offset);
    759:   if (!offset) SETERRQ1(comm, PETSC_ERR_FILE_UNEXPECTED, "Cannot locate nodal variable %s in exodus file\n", vecname);
    760:   /* Write local chunk of the result in the exodus file
    761:      exodus stores each component of a vector-valued field as a separate variable.
    762:      We assume that they are stored sequentially */
    763:   VecGetOwnershipRange(vNatural, &xs, &xe);
    764:   VecGetBlockSize(vNatural, &bs);
    765:   if (bs == 1) {
    766:     VecGetArrayRead(vNatural, &varray);
    767:     PetscStackCallStandard(ex_put_partial_var,(exoid, step, EX_NODAL, offset, 1, xs+1, xe-xs, varray));
    768:     VecRestoreArrayRead(vNatural, &varray);
    769:   } else {
    770:     IS       compIS;
    771:     PetscInt c;

    773:     ISCreateStride(PETSC_COMM_SELF, (xe-xs)/bs, xs, bs, &compIS);
    774:     for (c = 0; c < bs; ++c) {
    775:       ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);
    776:       VecGetSubVector(vNatural, compIS, &vComp);
    777:       VecGetArrayRead(vComp, &varray);
    778:       PetscStackCallStandard(ex_put_partial_var,(exoid, step, EX_NODAL, offset+c, 1, xs/bs+1, (xe-xs)/bs, varray));
    779:       VecRestoreArrayRead(vComp, &varray);
    780:       VecRestoreSubVector(vNatural, compIS, &vComp);
    781:     }
    782:     ISDestroy(&compIS);
    783:   }
    784:   if (useNatural) {DMRestoreGlobalVector(dm, &vNatural);}
    785:   return(0);
    786: }

    788: /*
    789:   VecLoadPlex_ExodusII_Nodal_Internal - Read a Vec corresponding to a nodal field from an exodus file

    791:   Collective on v

    793:   Input Parameters:
    794: + v  - The vector to be written
    795: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    796: - step - the time step to read at (exodus steps are numbered starting from 1)

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

    804:   Level: beginner

    806: .seealso: EXOGetVarIndex_Private(), DMPlexView_ExodusII_Internal(), VecViewPlex_ExodusII_Nodal_Internal(), VecViewZonal_PlexEXO(), VecLoadZonal_PlexEXO()
    807: */
    808: PetscErrorCode VecLoadPlex_ExodusII_Nodal_Internal(Vec v, int exoid, int step)
    809: {
    810:   MPI_Comm       comm;
    811:   PetscMPIInt    size;
    812:   DM             dm;
    813:   Vec            vNatural, vComp;
    814:   PetscScalar   *varray;
    815:   const char    *vecname;
    816:   PetscInt       xs, xe, bs;
    817:   PetscBool      useNatural;
    818:   int            offset;

    822:   PetscObjectGetComm((PetscObject) v, &comm);
    823:   MPI_Comm_size(comm, &size);
    824:   VecGetDM(v,&dm);
    825:   DMGetUseNatural(dm, &useNatural);
    826:   useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
    827:   if (useNatural) {DMGetGlobalVector(dm,&vNatural);}
    828:   else            {vNatural = v;}
    829:   /* Get the location of the variable in the exodus file */
    830:   PetscObjectGetName((PetscObject) v, &vecname);
    831:   EXOGetVarIndex_Private(exoid, EX_NODAL, vecname, &offset);
    832:   if (!offset) SETERRQ1(comm, PETSC_ERR_FILE_UNEXPECTED, "Cannot locate nodal variable %s in exodus file", vecname);
    833:   /* Read local chunk from the file */
    834:   VecGetOwnershipRange(vNatural, &xs, &xe);
    835:   VecGetBlockSize(vNatural, &bs);
    836:   if (bs == 1) {
    837:     VecGetArray(vNatural, &varray);
    838:     PetscStackCallStandard(ex_get_partial_var,(exoid, step, EX_NODAL, offset, 1, xs+1, xe-xs, varray));
    839:     VecRestoreArray(vNatural, &varray);
    840:   } else {
    841:     IS       compIS;
    842:     PetscInt c;

    844:     ISCreateStride(PETSC_COMM_SELF, (xe-xs)/bs, xs, bs, &compIS);
    845:     for (c = 0; c < bs; ++c) {
    846:       ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);
    847:       VecGetSubVector(vNatural, compIS, &vComp);
    848:       VecGetArray(vComp, &varray);
    849:       PetscStackCallStandard(ex_get_partial_var,(exoid, step, EX_NODAL, offset+c, 1, xs/bs+1, (xe-xs)/bs, varray));
    850:       VecRestoreArray(vComp, &varray);
    851:       VecRestoreSubVector(vNatural, compIS, &vComp);
    852:     }
    853:     ISDestroy(&compIS);
    854:   }
    855:   if (useNatural) {
    856:     DMPlexNaturalToGlobalBegin(dm, vNatural, v);
    857:     DMPlexNaturalToGlobalEnd(dm, vNatural, v);
    858:     DMRestoreGlobalVector(dm, &vNatural);
    859:   }
    860:   return(0);
    861: }

    863: /*
    864:   VecViewPlex_ExodusII_Zonal_Internal - Write a Vec corresponding to a zonal (cell based) field to an exodus file

    866:   Collective on v

    868:   Input Parameters:
    869: + v  - The vector to be written
    870: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    871: - step - the time step to write at (exodus steps are numbered starting from 1)

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

    879:   Level: beginner

    881: .seealso: EXOGetVarIndex_Private(),DMPlexView_ExodusII_Internal(),VecViewPlex_ExodusII_Nodal_Internal(),VecLoadPlex_ExodusII_Nodal_Internal(),VecLoadPlex_ExodusII_Zonal_Internal()
    882: */
    883: PetscErrorCode VecViewPlex_ExodusII_Zonal_Internal(Vec v, int exoid, int step)
    884: {
    885:   MPI_Comm          comm;
    886:   PetscMPIInt       size;
    887:   DM                dm;
    888:   Vec               vNatural, vComp;
    889:   const PetscScalar *varray;
    890:   const char       *vecname;
    891:   PetscInt          xs, xe, bs;
    892:   PetscBool         useNatural;
    893:   int               offset;
    894:   IS                compIS;
    895:   PetscInt         *csSize, *csID;
    896:   PetscInt          numCS, set, csxs = 0;
    897:   PetscErrorCode    ierr;

    900:   PetscObjectGetComm((PetscObject)v, &comm);
    901:   MPI_Comm_size(comm, &size);
    902:   VecGetDM(v, &dm);
    903:   DMGetUseNatural(dm, &useNatural);
    904:   useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
    905:   if (useNatural) {
    906:     DMGetGlobalVector(dm, &vNatural);
    907:     DMPlexGlobalToNaturalBegin(dm, v, vNatural);
    908:     DMPlexGlobalToNaturalEnd(dm, v, vNatural);
    909:   } else {
    910:     vNatural = v;
    911:   }
    912:   /* Get the location of the variable in the exodus file */
    913:   PetscObjectGetName((PetscObject) v, &vecname);
    914:   EXOGetVarIndex_Private(exoid, EX_ELEM_BLOCK, vecname, &offset);
    915:   if (!offset) SETERRQ1(comm, PETSC_ERR_FILE_UNEXPECTED, "Cannot locate zonal variable %s in exodus file\n", vecname);
    916:   /* Write local chunk of the result in the exodus file
    917:      exodus stores each component of a vector-valued field as a separate variable.
    918:      We assume that they are stored sequentially
    919:      Zonal variables are accessed one element block at a time, so we loop through the cell sets,
    920:      but once the vector has been reordered to natural size, we cannot use the label informations
    921:      to figure out what to save where. */
    922:   numCS = ex_inquire_int(exoid, EX_INQ_ELEM_BLK);
    923:   PetscMalloc2(numCS, &csID, numCS, &csSize);
    924:   PetscStackCallStandard(ex_get_ids,(exoid, EX_ELEM_BLOCK, csID));
    925:   for (set = 0; set < numCS; ++set) {
    926:     ex_block block;

    928:     block.id   = csID[set];
    929:     block.type = EX_ELEM_BLOCK;
    930:     PetscStackCallStandard(ex_get_block_param,(exoid, &block));
    931:     csSize[set] = block.num_entry;
    932:   }
    933:   VecGetOwnershipRange(vNatural, &xs, &xe);
    934:   VecGetBlockSize(vNatural, &bs);
    935:   if (bs > 1) {ISCreateStride(comm, (xe-xs)/bs, xs, bs, &compIS);}
    936:   for (set = 0; set < numCS; set++) {
    937:     PetscInt csLocalSize, c;

    939:     /* range of indices for set setID[set]: csxs:csxs + csSize[set]-1
    940:        local slice of zonal values:         xs/bs,xm/bs-1
    941:        intersection:                        max(xs/bs,csxs),min(xm/bs-1,csxs + csSize[set]-1) */
    942:     csLocalSize = PetscMax(0, PetscMin(xe/bs, csxs+csSize[set]) - PetscMax(xs/bs, csxs));
    943:     if (bs == 1) {
    944:       VecGetArrayRead(vNatural, &varray);
    945:       PetscStackCallStandard(ex_put_partial_var,(exoid, step, EX_ELEM_BLOCK, offset, csID[set], PetscMax(xs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs)]));
    946:       VecRestoreArrayRead(vNatural, &varray);
    947:     } else {
    948:       for (c = 0; c < bs; ++c) {
    949:         ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);
    950:         VecGetSubVector(vNatural, compIS, &vComp);
    951:         VecGetArrayRead(vComp, &varray);
    952:         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)]));
    953:         VecRestoreArrayRead(vComp, &varray);
    954:         VecRestoreSubVector(vNatural, compIS, &vComp);
    955:       }
    956:     }
    957:     csxs += csSize[set];
    958:   }
    959:   PetscFree2(csID, csSize);
    960:   if (bs > 1) {ISDestroy(&compIS);}
    961:   if (useNatural) {DMRestoreGlobalVector(dm,&vNatural);}
    962:   return(0);
    963: }

    965: /*
    966:   VecLoadPlex_ExodusII_Zonal_Internal - Read a Vec corresponding to a zonal (cell based) field from an exodus file

    968:   Collective on v

    970:   Input Parameters:
    971: + v  - The vector to be written
    972: . exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
    973: - step - the time step to read at (exodus steps are numbered starting from 1)

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

    981:   Level: beginner

    983: .seealso: EXOGetVarIndex_Private(), DMPlexView_ExodusII_Internal(), VecViewPlex_ExodusII_Nodal_Internal(), VecLoadPlex_ExodusII_Nodal_Internal(), VecLoadPlex_ExodusII_Zonal_Internal()
    984: */
    985: PetscErrorCode VecLoadPlex_ExodusII_Zonal_Internal(Vec v, int exoid, int step)
    986: {
    987:   MPI_Comm          comm;
    988:   PetscMPIInt       size;
    989:   DM                dm;
    990:   Vec               vNatural, vComp;
    991:   PetscScalar      *varray;
    992:   const char       *vecname;
    993:   PetscInt          xs, xe, bs;
    994:   PetscBool         useNatural;
    995:   int               offset;
    996:   IS                compIS;
    997:   PetscInt         *csSize, *csID;
    998:   PetscInt          numCS, set, csxs = 0;
    999:   PetscErrorCode    ierr;

    1002:   PetscObjectGetComm((PetscObject)v,&comm);
    1003:   MPI_Comm_size(comm, &size);
    1004:   VecGetDM(v, &dm);
    1005:   DMGetUseNatural(dm, &useNatural);
    1006:   useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
    1007:   if (useNatural) {DMGetGlobalVector(dm,&vNatural);}
    1008:   else            {vNatural = v;}
    1009:   /* Get the location of the variable in the exodus file */
    1010:   PetscObjectGetName((PetscObject) v, &vecname);
    1011:   EXOGetVarIndex_Private(exoid, EX_ELEM_BLOCK, vecname, &offset);
    1012:   if (!offset) SETERRQ1(comm, PETSC_ERR_FILE_UNEXPECTED, "Cannot locate zonal variable %s in exodus file\n", vecname);
    1013:   /* Read local chunk of the result in the exodus file
    1014:      exodus stores each component of a vector-valued field as a separate variable.
    1015:      We assume that they are stored sequentially
    1016:      Zonal variables are accessed one element block at a time, so we loop through the cell sets,
    1017:      but once the vector has been reordered to natural size, we cannot use the label informations
    1018:      to figure out what to save where. */
    1019:   numCS = ex_inquire_int(exoid, EX_INQ_ELEM_BLK);
    1020:   PetscMalloc2(numCS, &csID, numCS, &csSize);
    1021:   PetscStackCallStandard(ex_get_ids,(exoid, EX_ELEM_BLOCK, csID));
    1022:   for (set = 0; set < numCS; ++set) {
    1023:     ex_block block;

    1025:     block.id   = csID[set];
    1026:     block.type = EX_ELEM_BLOCK;
    1027:     PetscStackCallStandard(ex_get_block_param,(exoid, &block));
    1028:     csSize[set] = block.num_entry;
    1029:   }
    1030:   VecGetOwnershipRange(vNatural, &xs, &xe);
    1031:   VecGetBlockSize(vNatural, &bs);
    1032:   if (bs > 1) {ISCreateStride(comm, (xe-xs)/bs, xs, bs, &compIS);}
    1033:   for (set = 0; set < numCS; ++set) {
    1034:     PetscInt csLocalSize, c;

    1036:     /* range of indices for set setID[set]: csxs:csxs + csSize[set]-1
    1037:        local slice of zonal values:         xs/bs,xm/bs-1
    1038:        intersection:                        max(xs/bs,csxs),min(xm/bs-1,csxs + csSize[set]-1) */
    1039:     csLocalSize = PetscMax(0, PetscMin(xe/bs, csxs+csSize[set]) - PetscMax(xs/bs, csxs));
    1040:     if (bs == 1) {
    1041:       VecGetArray(vNatural, &varray);
    1042:       PetscStackCallStandard(ex_get_partial_var,(exoid, step, EX_ELEM_BLOCK, offset, csID[set], PetscMax(xs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs)]));
    1043:       VecRestoreArray(vNatural, &varray);
    1044:     } else {
    1045:       for (c = 0; c < bs; ++c) {
    1046:         ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);
    1047:         VecGetSubVector(vNatural, compIS, &vComp);
    1048:         VecGetArray(vComp, &varray);
    1049:         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)]));
    1050:         VecRestoreArray(vComp, &varray);
    1051:         VecRestoreSubVector(vNatural, compIS, &vComp);
    1052:       }
    1053:     }
    1054:     csxs += csSize[set];
    1055:   }
    1056:   PetscFree2(csID, csSize);
    1057:   if (bs > 1) {ISDestroy(&compIS);}
    1058:   if (useNatural) {
    1059:     DMPlexNaturalToGlobalBegin(dm, vNatural, v);
    1060:     DMPlexNaturalToGlobalEnd(dm, vNatural, v);
    1061:     DMRestoreGlobalVector(dm, &vNatural);
    1062:   }
    1063:   return(0);
    1064: }
    1065: #endif

    1067: /*@
    1068:   PetscViewerExodusIIGetId - Get the file id of the ExodusII file

    1070:   Logically Collective on PetscViewer

    1072:   Input Parameter:
    1073: .  viewer - the PetscViewer

    1075:   Output Parameter:
    1076: -  exoid - The ExodusII file id

    1078:   Level: intermediate

    1080: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen()
    1081: @*/
    1082: PetscErrorCode PetscViewerExodusIIGetId(PetscViewer viewer, int *exoid)
    1083: {

    1088:   PetscTryMethod(viewer, "PetscViewerExodusIIGetId_C",(PetscViewer,int*),(viewer,exoid));
    1089:   return(0);
    1090: }

    1092: /*@C
    1093:   DMPlexCreateExodusFromFile - Create a DMPlex mesh from an ExodusII file.

    1095:   Collective

    1097:   Input Parameters:
    1098: + comm  - The MPI communicator
    1099: . filename - The name of the ExodusII file
    1100: - interpolate - Create faces and edges in the mesh

    1102:   Output Parameter:
    1103: . dm  - The DM object representing the mesh

    1105:   Level: beginner

    1107: .seealso: DMPLEX, DMCreate(), DMPlexCreateExodus()
    1108: @*/
    1109: PetscErrorCode DMPlexCreateExodusFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
    1110: {
    1111:   PetscMPIInt    rank;
    1113: #if defined(PETSC_HAVE_EXODUSII)
    1114:   int   CPU_word_size = sizeof(PetscReal), IO_word_size = 0, exoid = -1;
    1115:   float version;
    1116: #endif

    1120:   MPI_Comm_rank(comm, &rank);
    1121: #if defined(PETSC_HAVE_EXODUSII)
    1122:   if (!rank) {
    1123:     exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version);
    1124:     if (exoid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open(\"%s\",...) did not return a valid file ID", filename);
    1125:   }
    1126:   DMPlexCreateExodus(comm, exoid, interpolate, dm);
    1127:   if (!rank) {PetscStackCallStandard(ex_close,(exoid));}
    1128: #else
    1129:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
    1130: #endif
    1131:   return(0);
    1132: }

    1134: /*@
    1135:   DMPlexCreateExodus - Create a DMPlex mesh from an ExodusII file ID.

    1137:   Collective

    1139:   Input Parameters:
    1140: + comm  - The MPI communicator
    1141: . exoid - The ExodusII id associated with a exodus file and obtained using ex_open
    1142: - interpolate - Create faces and edges in the mesh

    1144:   Output Parameter:
    1145: . dm  - The DM object representing the mesh

    1147:   Level: beginner

    1149: .seealso: DMPLEX, DMCreate()
    1150: @*/
    1151: PetscErrorCode DMPlexCreateExodus(MPI_Comm comm, PetscInt exoid, PetscBool interpolate, DM *dm)
    1152: {
    1153: #if defined(PETSC_HAVE_EXODUSII)
    1154:   PetscMPIInt    num_proc, rank;
    1155:   PetscSection   coordSection;
    1156:   Vec            coordinates;
    1157:   PetscScalar    *coords;
    1158:   PetscInt       coordSize, v;
    1160:   /* Read from ex_get_init() */
    1161:   char title[PETSC_MAX_PATH_LEN+1];
    1162:   int  dim    = 0, numVertices = 0, numCells = 0, numHybridCells = 0;
    1163:   int  num_cs = 0, num_vs = 0, num_fs = 0;
    1164: #endif

    1167: #if defined(PETSC_HAVE_EXODUSII)
    1168:   MPI_Comm_rank(comm, &rank);
    1169:   MPI_Comm_size(comm, &num_proc);
    1170:   DMCreate(comm, dm);
    1171:   DMSetType(*dm, DMPLEX);
    1172:   /* Open EXODUS II file and read basic informations on rank 0, then broadcast to all processors */
    1173:   if (!rank) {
    1174:     PetscMemzero(title,PETSC_MAX_PATH_LEN+1);
    1175:     PetscStackCallStandard(ex_get_init,(exoid, title, &dim, &numVertices, &numCells, &num_cs, &num_vs, &num_fs));
    1176:     if (!num_cs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Exodus file does not contain any cell set\n");
    1177:   }
    1178:   MPI_Bcast(title, PETSC_MAX_PATH_LEN+1, MPI_CHAR, 0, comm);
    1179:   MPI_Bcast(&dim, 1, MPI_INT, 0, comm);
    1180:   PetscObjectSetName((PetscObject) *dm, title);
    1181:   DMSetDimension(*dm, dim);
    1182:   DMPlexSetChart(*dm, 0, numCells+numVertices);
    1183:   /*   We do not want this label automatically computed, instead we compute it here */
    1184:   DMCreateLabel(*dm, "celltype");

    1186:   /* Read cell sets information */
    1187:   if (!rank) {
    1188:     PetscInt *cone;
    1189:     int      c, cs, ncs, c_loc, v, v_loc;
    1190:     /* Read from ex_get_elem_blk_ids() */
    1191:     int *cs_id, *cs_order;
    1192:     /* Read from ex_get_elem_block() */
    1193:     char buffer[PETSC_MAX_PATH_LEN+1];
    1194:     int  num_cell_in_set, num_vertex_per_cell, num_hybrid, num_attr;
    1195:     /* Read from ex_get_elem_conn() */
    1196:     int *cs_connect;

    1198:     /* Get cell sets IDs */
    1199:     PetscMalloc2(num_cs, &cs_id, num_cs, &cs_order);
    1200:     PetscStackCallStandard(ex_get_ids,(exoid, EX_ELEM_BLOCK, cs_id));
    1201:     /* Read the cell set connectivity table and build mesh topology
    1202:        EXO standard requires that cells in cell sets be numbered sequentially and be pairwise disjoint. */
    1203:     /* Check for a hybrid mesh */
    1204:     for (cs = 0, num_hybrid = 0; cs < num_cs; ++cs) {
    1205:       PetscStackCallStandard(ex_get_block,(exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set,&num_vertex_per_cell, 0, 0, &num_attr));
    1206:       switch (dim) {
    1207:         case 3:
    1208:         switch (num_vertex_per_cell) {
    1209:           case 6:
    1210:             cs_order[cs] = cs;
    1211:             numHybridCells += num_cell_in_set;
    1212:             ++num_hybrid;
    1213:           break;
    1214:           default:
    1215:             for (c = cs; c > cs-num_hybrid; --c) cs_order[c] = cs_order[c-1];
    1216:             cs_order[cs-num_hybrid] = cs;
    1217:         }
    1218:         break;
    1219:       default:
    1220:         for (c = cs; c > cs-num_hybrid; --c) cs_order[c] = cs_order[c-1];
    1221:         cs_order[cs-num_hybrid] = cs;
    1222:       }
    1223:     }
    1224:     /* First set sizes */
    1225:     for (ncs = 0, c = 0; ncs < num_cs; ++ncs) {
    1226:       const PetscInt cs = cs_order[ncs];
    1227:       PetscStackCallStandard(ex_get_block,(exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set,&num_vertex_per_cell, 0, 0, &num_attr));
    1228:       for (c_loc = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
    1229:         DMPlexSetConeSize(*dm, c, num_vertex_per_cell);
    1230:         if (c >= numCells-numHybridCells) {
    1231:           DMPlexSetCellType(*dm, c, DM_POLYTOPE_TRI_PRISM);
    1232:         } else {
    1233:           DMPolytopeType ct;

    1235:           DMPlexComputeCellType_Internal(*dm, c, 1, &ct);
    1236:           DMPlexSetCellType(*dm, c, ct);
    1237:         }
    1238:       }
    1239:     }
    1240:     for (v = numCells; v < numCells+numVertices; ++v) {DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);}
    1241:     DMSetUp(*dm);
    1242:     for (ncs = 0, c = 0; ncs < num_cs; ++ncs) {
    1243:       const PetscInt cs = cs_order[ncs];
    1244:       PetscStackCallStandard(ex_get_block,(exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, 0, 0, &num_attr));
    1245:       PetscMalloc2(num_vertex_per_cell*num_cell_in_set,&cs_connect,num_vertex_per_cell,&cone);
    1246:       PetscStackCallStandard(ex_get_conn,(exoid, EX_ELEM_BLOCK, cs_id[cs], cs_connect,NULL,NULL));
    1247:       /* EXO uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
    1248:       for (c_loc = 0, v = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
    1249:         for (v_loc = 0; v_loc < num_vertex_per_cell; ++v_loc, ++v) {
    1250:           cone[v_loc] = cs_connect[v]+numCells-1;
    1251:         }
    1252:         if (dim == 3) {
    1253:           /* Tetrahedra are inverted */
    1254:           if (num_vertex_per_cell == 4) {
    1255:             PetscInt tmp = cone[0];
    1256:             cone[0] = cone[1];
    1257:             cone[1] = tmp;
    1258:           }
    1259:           /* Hexahedra are inverted */
    1260:           if (num_vertex_per_cell == 8) {
    1261:             PetscInt tmp = cone[1];
    1262:             cone[1] = cone[3];
    1263:             cone[3] = tmp;
    1264:           }
    1265:           /* Triangular prisms are inverted */
    1266:           if (num_vertex_per_cell == 6) {
    1267:             PetscInt tmp = cone[1];
    1268:             cone[1] = cone[2];
    1269:             cone[2] = tmp;
    1270:           }
    1271:         }
    1272:         DMPlexSetCone(*dm, c, cone);
    1273:         DMSetLabelValue(*dm, "Cell Sets", c, cs_id[cs]);
    1274:       }
    1275:       PetscFree2(cs_connect,cone);
    1276:     }
    1277:     PetscFree2(cs_id, cs_order);
    1278:   }
    1279:   DMPlexSymmetrize(*dm);
    1280:   DMPlexStratify(*dm);
    1281:   if (interpolate) {
    1282:     DM idm;

    1284:     DMPlexInterpolate(*dm, &idm);
    1285:     DMDestroy(dm);
    1286:     *dm  = idm;
    1287:   }

    1289:   /* Create vertex set label */
    1290:   if (!rank && (num_vs > 0)) {
    1291:     int vs, v;
    1292:     /* Read from ex_get_node_set_ids() */
    1293:     int *vs_id;
    1294:     /* Read from ex_get_node_set_param() */
    1295:     int num_vertex_in_set;
    1296:     /* Read from ex_get_node_set() */
    1297:     int *vs_vertex_list;

    1299:     /* Get vertex set ids */
    1300:     PetscMalloc1(num_vs, &vs_id);
    1301:     PetscStackCallStandard(ex_get_ids,(exoid, EX_NODE_SET, vs_id));
    1302:     for (vs = 0; vs < num_vs; ++vs) {
    1303:       PetscStackCallStandard(ex_get_set_param,(exoid, EX_NODE_SET, vs_id[vs], &num_vertex_in_set, NULL));
    1304:       PetscMalloc1(num_vertex_in_set, &vs_vertex_list);
    1305:       PetscStackCallStandard(ex_get_set,(exoid, EX_NODE_SET, vs_id[vs], vs_vertex_list, NULL));
    1306:       for (v = 0; v < num_vertex_in_set; ++v) {
    1307:         DMSetLabelValue(*dm, "Vertex Sets", vs_vertex_list[v]+numCells-1, vs_id[vs]);
    1308:       }
    1309:       PetscFree(vs_vertex_list);
    1310:     }
    1311:     PetscFree(vs_id);
    1312:   }
    1313:   /* Read coordinates */
    1314:   DMGetCoordinateSection(*dm, &coordSection);
    1315:   PetscSectionSetNumFields(coordSection, 1);
    1316:   PetscSectionSetFieldComponents(coordSection, 0, dim);
    1317:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
    1318:   for (v = numCells; v < numCells+numVertices; ++v) {
    1319:     PetscSectionSetDof(coordSection, v, dim);
    1320:     PetscSectionSetFieldDof(coordSection, v, 0, dim);
    1321:   }
    1322:   PetscSectionSetUp(coordSection);
    1323:   PetscSectionGetStorageSize(coordSection, &coordSize);
    1324:   VecCreate(PETSC_COMM_SELF, &coordinates);
    1325:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    1326:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    1327:   VecSetBlockSize(coordinates, dim);
    1328:   VecSetType(coordinates,VECSTANDARD);
    1329:   VecGetArray(coordinates, &coords);
    1330:   if (!rank) {
    1331:     PetscReal *x, *y, *z;

    1333:     PetscMalloc3(numVertices,&x,numVertices,&y,numVertices,&z);
    1334:     PetscStackCallStandard(ex_get_coord,(exoid, x, y, z));
    1335:     if (dim > 0) {
    1336:       for (v = 0; v < numVertices; ++v) coords[v*dim+0] = x[v];
    1337:     }
    1338:     if (dim > 1) {
    1339:       for (v = 0; v < numVertices; ++v) coords[v*dim+1] = y[v];
    1340:     }
    1341:     if (dim > 2) {
    1342:       for (v = 0; v < numVertices; ++v) coords[v*dim+2] = z[v];
    1343:     }
    1344:     PetscFree3(x,y,z);
    1345:   }
    1346:   VecRestoreArray(coordinates, &coords);
    1347:   DMSetCoordinatesLocal(*dm, coordinates);
    1348:   VecDestroy(&coordinates);

    1350:   /* Create side set label */
    1351:   if (!rank && interpolate && (num_fs > 0)) {
    1352:     int fs, f, voff;
    1353:     /* Read from ex_get_side_set_ids() */
    1354:     int *fs_id;
    1355:     /* Read from ex_get_side_set_param() */
    1356:     int num_side_in_set;
    1357:     /* Read from ex_get_side_set_node_list() */
    1358:     int *fs_vertex_count_list, *fs_vertex_list;
    1359:     /* Read side set labels */
    1360:     char fs_name[MAX_STR_LENGTH+1];

    1362:     /* Get side set ids */
    1363:     PetscMalloc1(num_fs, &fs_id);
    1364:     PetscStackCallStandard(ex_get_ids,(exoid, EX_SIDE_SET, fs_id));
    1365:     for (fs = 0; fs < num_fs; ++fs) {
    1366:       PetscStackCallStandard(ex_get_set_param,(exoid, EX_SIDE_SET, fs_id[fs], &num_side_in_set, NULL));
    1367:       PetscMalloc2(num_side_in_set,&fs_vertex_count_list,num_side_in_set*4,&fs_vertex_list);
    1368:       PetscStackCallStandard(ex_get_side_set_node_list,(exoid, fs_id[fs], fs_vertex_count_list, fs_vertex_list));
    1369:       /* Get the specific name associated with this side set ID. */
    1370:       int fs_name_err = ex_get_name(exoid, EX_SIDE_SET, fs_id[fs], fs_name);
    1371:       for (f = 0, voff = 0; f < num_side_in_set; ++f) {
    1372:         const PetscInt *faces   = NULL;
    1373:         PetscInt       faceSize = fs_vertex_count_list[f], numFaces;
    1374:         PetscInt       faceVertices[4], v;

    1376:         if (faceSize > 4) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "ExodusII side cannot have %d > 4 vertices", faceSize);
    1377:         for (v = 0; v < faceSize; ++v, ++voff) {
    1378:           faceVertices[v] = fs_vertex_list[voff]+numCells-1;
    1379:         }
    1380:         DMPlexGetFullJoin(*dm, faceSize, faceVertices, &numFaces, &faces);
    1381:         if (numFaces != 1) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Invalid ExodusII side %d in set %d maps to %d faces", f, fs, numFaces);
    1382:         DMSetLabelValue(*dm, "Face Sets", faces[0], fs_id[fs]);
    1383:         /* Only add the label if one has been detected for this side set. */
    1384:         if (!fs_name_err) {
    1385:           DMSetLabelValue(*dm, fs_name, faces[0], fs_id[fs]);
    1386:         }
    1387:         DMPlexRestoreJoin(*dm, faceSize, faceVertices, &numFaces, &faces);
    1388:       }
    1389:       PetscFree2(fs_vertex_count_list,fs_vertex_list);
    1390:     }
    1391:     PetscFree(fs_id);
    1392:   }
    1393: #else
    1394:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
    1395: #endif
    1396:   return(0);
    1397: }