Date: 2016-07-24T17:01:32+00:00

Actual source code: dmmoab.cxx
petsc-3.7.3 2016-07-24
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      1: #include <petsc/private/dmmbimpl.h> /*I  "petscdmmoab.h"   I*/

      3: #include <petscdmmoab.h>
      4: #include <MBTagConventions.hpp>
      5: #include <moab/Skinner.hpp>

      8: /*MC
      9:   DMMOAB = "moab" - A DM object that encapsulates an unstructured mesh described by the MOAB mesh database.
     10:                     Direct access to the MOAB Interface and other mesh manipulation related objects are available
     11:                     through public API. Ability to create global and local representation of Vecs containing all
     12:                     unknowns in the interior and shared boundary via a transparent tag-data wrapper is provided
     13:                     along with utility functions to traverse the mesh and assemble a discrete system via
     14:                     field-based/blocked Vec(Get/Set) methods. Input from and output to different formats are
     15:                     available.

     17:   Reference: http://www.mcs.anl.gov/~fathom/moab-docs/html/contents.html

     19:   Level: intermediate

     21: .seealso: DMType, DMMoabCreate(), DMCreate(), DMSetType(), DMMoabCreateMoab()
     22: M*/

     27: /*@
     28:   DMMoabCreate - Creates a DMMoab object, which encapsulates a moab instance

     30:   Collective on MPI_Comm

     32:   Input Parameter:
     33: . comm - The communicator for the DMMoab object

     35:   Output Parameter:
     36: . dmb  - The DMMoab object

     38:   Level: beginner

     40: .keywords: DMMoab, create
     41: @*/
     42: PetscErrorCode DMMoabCreate(MPI_Comm comm, DM *dmb)
     43: {

     48:   DMCreate(comm, dmb);
     49:   DMSetType(*dmb, DMMOAB);
     50:   return(0);
     51: }

     55: /*@
     56:   DMMoabCreate - Creates a DMMoab object, optionally from an instance and other data

     58:   Collective on MPI_Comm

     60:   Input Parameter:
     61: . comm - The communicator for the DMMoab object
     62: . mbiface - (ptr to) the MOAB Instance; if passed in NULL, MOAB instance is created inside PETSc, and destroyed
     63:          along with the DMMoab
     64: . pcomm - (ptr to) a ParallelComm; if NULL, creates one internally for the whole communicator
     65: . ltog_tag - A tag to use to retrieve global id for an entity; if 0, will use GLOBAL_ID_TAG_NAME/tag
     66: . range - If non-NULL, contains range of entities to which DOFs will be assigned

     68:   Output Parameter:
     69: . dmb  - The DMMoab object

     71:   Level: intermediate

     73: .keywords: DMMoab, create
     74: @*/
     75: PetscErrorCode DMMoabCreateMoab(MPI_Comm comm, moab::Interface *mbiface, moab::ParallelComm *pcomm, moab::Tag *ltog_tag, moab::Range *range, DM *dmb)
     76: {
     78:   moab::ErrorCode merr;
     79:   moab::EntityHandle partnset;
     80:   PetscInt rank, nprocs;
     81:   DM             dmmb;
     82:   DM_Moab        *dmmoab;

     87:   DMMoabCreate(comm, &dmmb);
     88:   dmmoab = (DM_Moab*)(dmmb)->data;

     90:   if (!mbiface) {
     91:     dmmoab->mbiface = new moab::Core();
     92:     dmmoab->icreatedinstance = PETSC_TRUE;
     93:   }
     94:   else {
     95:     dmmoab->mbiface = mbiface;
     96:     dmmoab->icreatedinstance = PETSC_FALSE;
     97:   }

     99:   /* by default the fileset = root set. This set stores the hierarchy of entities belonging to current DM */
    100:   dmmoab->fileset=0;

    102:   if (!pcomm) {
    103:     MPI_Comm_rank(comm, &rank);
    104:     MPI_Comm_size(comm, &nprocs);

    106:     /* Create root sets for each mesh.  Then pass these
    107:        to the load_file functions to be populated. */
    108:     merr = dmmoab->mbiface->create_meshset(moab::MESHSET_SET, partnset);MBERR("Creating partition set failed", merr);

    110:     /* Create the parallel communicator object with the partition handle associated with MOAB */
    111:     dmmoab->pcomm = moab::ParallelComm::get_pcomm(dmmoab->mbiface, partnset, &comm);
    112:   }
    113:   else {
    114:     DMMoabSetParallelComm(dmmb, pcomm);
    115:   }

    117:   /* do the remaining initializations for DMMoab */
    118:   dmmoab->bs = 1;
    119:   dmmoab->numFields = 1;
    120:   dmmoab->rw_dbglevel = 0;
    121:   dmmoab->partition_by_rank = PETSC_FALSE;
    122:   dmmoab->extra_read_options[0] = '\0';
    123:   dmmoab->extra_write_options[0] = '\0';
    124:   dmmoab->read_mode = READ_PART;
    125:   dmmoab->write_mode = WRITE_PART;

    127:   /* set global ID tag handle */
    128:   if (ltog_tag && *ltog_tag) {
    129:     DMMoabSetLocalToGlobalTag(dmmb, *ltog_tag);
    130:   }
    131:   else {
    132:     merr = dmmoab->mbiface->tag_get_handle(GLOBAL_ID_TAG_NAME, dmmoab->ltog_tag);MBERRNM(merr);
    133:     if (ltog_tag) *ltog_tag = dmmoab->ltog_tag;
    134:   }

    136:   merr = dmmoab->mbiface->tag_get_handle(MATERIAL_SET_TAG_NAME, dmmoab->material_tag);MBERRNM(merr);

    138:   /* set the local range of entities (vertices) of interest */
    139:   if (range) {
    140:     DMMoabSetLocalVertices(dmmb, range);
    141:   }
    142:   *dmb=dmmb;
    143:   return(0);
    144: }

    148: /*@
    149:   DMMoabSetParallelComm - Set the ParallelComm used with this DMMoab

    151:   Collective on MPI_Comm

    153:   Input Parameter:
    154: . dm    - The DMMoab object being set
    155: . pcomm - The ParallelComm being set on the DMMoab

    157:   Level: beginner

    159: .keywords: DMMoab, create
    160: @*/
    161: PetscErrorCode DMMoabSetParallelComm(DM dm,moab::ParallelComm *pcomm)
    162: {
    163:   DM_Moab        *dmmoab = (DM_Moab*)(dm)->data;

    168:   dmmoab->pcomm = pcomm;
    169:   dmmoab->mbiface = pcomm->get_moab();
    170:   dmmoab->icreatedinstance = PETSC_FALSE;
    171:   return(0);
    172: }

    177: /*@
    178:   DMMoabGetParallelComm - Get the ParallelComm used with this DMMoab

    180:   Collective on MPI_Comm

    182:   Input Parameter:
    183: . dm    - The DMMoab object being set

    185:   Output Parameter:
    186: . pcomm - The ParallelComm for the DMMoab

    188:   Level: beginner

    190: .keywords: DMMoab, create
    191: @*/
    192: PetscErrorCode DMMoabGetParallelComm(DM dm,moab::ParallelComm **pcomm)
    193: {
    196:   *pcomm = ((DM_Moab*)(dm)->data)->pcomm;
    197:   return(0);
    198: }

    203: /*@
    204:   DMMoabSetInterface - Set the MOAB instance used with this DMMoab

    206:   Collective on MPI_Comm

    208:   Input Parameter:
    209: . dm      - The DMMoab object being set
    210: . mbiface - The MOAB instance being set on this DMMoab

    212:   Level: beginner

    214: .keywords: DMMoab, create
    215: @*/
    216: PetscErrorCode DMMoabSetInterface(DM dm,moab::Interface *mbiface)
    217: {
    218:   DM_Moab        *dmmoab = (DM_Moab*)(dm)->data;

    223:   dmmoab->pcomm = NULL;
    224:   dmmoab->mbiface = mbiface;
    225:   dmmoab->icreatedinstance = PETSC_FALSE;
    226:   return(0);
    227: }

    232: /*@
    233:   DMMoabGetInterface - Get the MOAB instance used with this DMMoab

    235:   Collective on MPI_Comm

    237:   Input Parameter:
    238: . dm      - The DMMoab object being set

    240:   Output Parameter:
    241: . mbiface - The MOAB instance set on this DMMoab

    243:   Level: beginner

    245: .keywords: DMMoab, create
    246: @*/
    247: PetscErrorCode DMMoabGetInterface(DM dm,moab::Interface **mbiface)
    248: {
    249:   PetscErrorCode   ierr;
    250:   static PetscBool cite = PETSC_FALSE;

    254:   PetscCitationsRegister("@techreport{tautges_moab:_2004,\n  type = {{SAND2004-1592}},\n  title = {{MOAB:} A Mesh-Oriented Database},  institution = {Sandia National Laboratories},\n  author = {Tautges, T. J. and Meyers, R. and Merkley, K. and Stimpson, C. and Ernst, C.},\n  year = {2004},  note = {Report}\n}\n",&cite);
    255:   *mbiface = ((DM_Moab*)dm->data)->mbiface;
    256:   return(0);
    257: }

    262: /*@
    263:   DMMoabSetLocalVertices - Set the entities having DOFs on this DMMoab

    265:   Collective on MPI_Comm

    267:   Input Parameter:
    268: . dm    - The DMMoab object being set
    269: . range - The entities treated by this DMMoab

    271:   Level: beginner

    273: .keywords: DMMoab, create
    274: @*/
    275: PetscErrorCode DMMoabSetLocalVertices(DM dm,moab::Range *range)
    276: {
    277:   moab::ErrorCode merr;
    278:   PetscErrorCode  ierr;
    279:   moab::Range     tmpvtxs;
    280:   DM_Moab        *dmmoab = (DM_Moab*)(dm)->data;

    284:   dmmoab->vlocal->clear();
    285:   dmmoab->vowned->clear();

    287:   dmmoab->vlocal->insert(range->begin(), range->end());

    289:   /* filter based on parallel status */
    290:   merr = dmmoab->pcomm->filter_pstatus(*dmmoab->vlocal,PSTATUS_NOT_OWNED,PSTATUS_NOT,-1,dmmoab->vowned);MBERRNM(merr);

    292:   /* filter all the non-owned and shared entities out of the list */
    293:   tmpvtxs = moab::subtract(*dmmoab->vlocal, *dmmoab->vowned);
    294:   merr = dmmoab->pcomm->filter_pstatus(tmpvtxs,PSTATUS_INTERFACE,PSTATUS_OR,-1,dmmoab->vghost);MBERRNM(merr);
    295:   tmpvtxs = moab::subtract(tmpvtxs, *dmmoab->vghost);
    296:   *dmmoab->vlocal = moab::subtract(*dmmoab->vlocal, tmpvtxs);

    298:   /* compute and cache the sizes of local and ghosted entities */
    299:   dmmoab->nloc = dmmoab->vowned->size();
    300:   dmmoab->nghost = dmmoab->vghost->size();
    301:   MPIU_Allreduce(&dmmoab->nloc, &dmmoab->n, 1, MPI_INTEGER, MPI_SUM, ((PetscObject)dm)->comm);
    302:   return(0);
    303: }

    308: /*@
    309:   DMMoabGetAllVertices - Get the entities having DOFs on this DMMoab

    311:   Collective on MPI_Comm

    313:   Input Parameter:
    314: . dm    - The DMMoab object being set

    316:   Output Parameter:
    317: . owned - The local vertex entities in this DMMoab = (owned+ghosted)

    319:   Level: beginner

    321: .keywords: DMMoab, create
    322: @*/
    323: PetscErrorCode DMMoabGetAllVertices(DM dm,moab::Range *local)
    324: {
    327:   if (local) *local = *((DM_Moab*)dm->data)->vlocal;
    328:   return(0);
    329: }

    335: /*@
    336:   DMMoabGetLocalVertices - Get the entities having DOFs on this DMMoab

    338:   Collective on MPI_Comm

    340:   Input Parameter:
    341: . dm    - The DMMoab object being set

    343:   Output Parameter:
    344: . owned - The owned vertex entities in this DMMoab
    345: . ghost - The ghosted entities (non-owned) stored locally in this partition

    347:   Level: beginner

    349: .keywords: DMMoab, create
    350: @*/
    351: PetscErrorCode DMMoabGetLocalVertices(DM dm,const moab::Range **owned,const moab::Range **ghost)
    352: {
    355:   if (owned) *owned = ((DM_Moab*)dm->data)->vowned;
    356:   if (ghost) *ghost = ((DM_Moab*)dm->data)->vghost;
    357:   return(0);
    358: }

    362: /*@
    363:   DMMoabGetLocalElements - Get the higher-dimensional entities that are locally owned

    365:   Collective on MPI_Comm

    367:   Input Parameter:
    368: . dm    - The DMMoab object being set

    370:   Output Parameter:
    371: . range - The entities owned locally

    373:   Level: beginner

    375: .keywords: DMMoab, create
    376: @*/
    377: PetscErrorCode DMMoabGetLocalElements(DM dm,const moab::Range **range)
    378: {
    381:   if (range) *range = ((DM_Moab*)dm->data)->elocal;
    382:   return(0);
    383: }

    388: /*@
    389:   DMMoabSetLocalElements - Set the entities having DOFs on this DMMoab

    391:   Collective on MPI_Comm

    393:   Input Parameter:
    394: . dm    - The DMMoab object being set
    395: . range - The entities treated by this DMMoab

    397:   Level: beginner

    399: .keywords: DMMoab, create
    400: @*/
    401: PetscErrorCode DMMoabSetLocalElements(DM dm,moab::Range *range)
    402: {
    403:   moab::ErrorCode merr;
    404:   PetscErrorCode  ierr;
    405:   DM_Moab        *dmmoab = (DM_Moab*)(dm)->data;

    409:   dmmoab->elocal->clear();
    410:   dmmoab->eghost->clear();
    411:   dmmoab->elocal->insert(range->begin(), range->end());
    412:   merr = dmmoab->pcomm->filter_pstatus(*dmmoab->elocal,PSTATUS_NOT_OWNED,PSTATUS_NOT);MBERRNM(merr);
    413:   *dmmoab->eghost = moab::subtract(*range, *dmmoab->elocal);
    414:   dmmoab->neleloc=dmmoab->elocal->size();
    415:   dmmoab->neleghost=dmmoab->eghost->size();
    416:   MPIU_Allreduce(&dmmoab->nele, &dmmoab->neleloc, 1, MPI_INTEGER, MPI_SUM, ((PetscObject)dm)->comm);
    417:   PetscInfo2(dm, "Created %D local and %D global elements.\n", dmmoab->neleloc, dmmoab->nele);
    418:   return(0);
    419: }

    424: /*@
    425:   DMMoabSetLocalToGlobalTag - Set the tag used for local to global numbering

    427:   Collective on MPI_Comm

    429:   Input Parameter:
    430: . dm      - The DMMoab object being set
    431: . ltogtag - The MOAB tag used for local to global ids

    433:   Level: beginner

    435: .keywords: DMMoab, create
    436: @*/
    437: PetscErrorCode DMMoabSetLocalToGlobalTag(DM dm,moab::Tag ltogtag)
    438: {
    441:   ((DM_Moab*)dm->data)->ltog_tag = ltogtag;
    442:   return(0);
    443: }

    448: /*@
    449:   DMMoabGetLocalToGlobalTag - Get the tag used for local to global numbering

    451:   Collective on MPI_Comm

    453:   Input Parameter:
    454: . dm      - The DMMoab object being set

    456:   Output Parameter:
    457: . ltogtag - The MOAB tag used for local to global ids

    459:   Level: beginner

    461: .keywords: DMMoab, create
    462: @*/
    463: PetscErrorCode DMMoabGetLocalToGlobalTag(DM dm,moab::Tag *ltog_tag)
    464: {
    467:   *ltog_tag = ((DM_Moab*)dm->data)->ltog_tag;
    468:   return(0);
    469: }

    474: /*@
    475:   DMMoabSetBlockSize - Set the block size used with this DMMoab

    477:   Collective on MPI_Comm

    479:   Input Parameter:
    480: . dm - The DMMoab object being set
    481: . bs - The block size used with this DMMoab

    483:   Level: beginner

    485: .keywords: DMMoab, create
    486: @*/
    487: PetscErrorCode DMMoabSetBlockSize(DM dm,PetscInt bs)
    488: {
    491:   ((DM_Moab*)dm->data)->bs = bs;
    492:   return(0);
    493: }

    498: /*@
    499:   DMMoabGetBlockSize - Get the block size used with this DMMoab

    501:   Collective on MPI_Comm

    503:   Input Parameter:
    504: . dm - The DMMoab object being set

    506:   Output Parameter:
    507: . bs - The block size used with this DMMoab

    509:   Level: beginner

    511: .keywords: DMMoab, create
    512: @*/
    513: PetscErrorCode DMMoabGetBlockSize(DM dm,PetscInt *bs)
    514: {
    517:   *bs = ((DM_Moab*)dm->data)->bs;
    518:   return(0);
    519: }

    524: /*@
    525:   DMMoabGetSize - Get the global vertex size used with this DMMoab

    527:   Collective on DM

    529:   Input Parameter:
    530: . dm - The DMMoab object being set

    532:   Output Parameter:
    533: . neg - The number of global elements in the DMMoab instance
    534: . nvg - The number of global vertices in the DMMoab instance

    536:   Level: beginner

    538: .keywords: DMMoab, create
    539: @*/
    540: PetscErrorCode DMMoabGetSize(DM dm,PetscInt *neg,PetscInt *nvg)
    541: {
    544:   if(neg) *neg = ((DM_Moab*)dm->data)->nele;
    545:   if(nvg) *nvg = ((DM_Moab*)dm->data)->n;
    546:   return(0);
    547: }

    552: /*@
    553:   DMMoabGetLocalSize - Get the local and ghosted vertex size used with this DMMoab

    555:   Collective on DM

    557:   Input Parameter:
    558: . dm - The DMMoab object being set

    560:   Output Parameter:
    561: + nel - The number of owned elements in this processor
    562: . neg - The number of ghosted elements in this processor
    563: . nvl - The number of owned vertices in this processor
    564: . nvg - The number of ghosted vertices in this processor

    566:   Level: beginner

    568: .keywords: DMMoab, create
    569: @*/
    570: PetscErrorCode DMMoabGetLocalSize(DM dm,PetscInt *nel,PetscInt *neg,PetscInt *nvl,PetscInt *nvg)
    571: {
    574:   if(nel) *nel = ((DM_Moab*)dm->data)->neleloc;
    575:   if(neg) *neg = ((DM_Moab*)dm->data)->neleghost;
    576:   if(nvl) *nvl = ((DM_Moab*)dm->data)->nloc;
    577:   if(nvg) *nvg = ((DM_Moab*)dm->data)->nghost;
    578:   return(0);
    579: }

    584: /*@
    585:   DMMoabGetOffset - Get the local offset for the global vector

    587:   Collective on MPI_Comm

    589:   Input Parameter:
    590: . dm - The DMMoab object being set

    592:   Output Parameter:
    593: . offset - The local offset for the global vector

    595:   Level: beginner

    597: .keywords: DMMoab, create
    598: @*/
    599: PetscErrorCode DMMoabGetOffset(DM dm,PetscInt *offset)
    600: {
    603:   *offset = ((DM_Moab*)dm->data)->vstart;
    604:   return(0);
    605: }

    610: /*@
    611:   DMMoabGetDimension - Get the dimension of the DM Mesh

    613:   Collective on MPI_Comm

    615:   Input Parameter:
    616: . dm - The DMMoab object

    618:   Output Parameter:
    619: . dim - The dimension of DM

    621:   Level: beginner

    623: .keywords: DMMoab, create
    624: @*/
    625: PetscErrorCode DMMoabGetDimension(DM dm,PetscInt *dim)
    626: {
    629:   *dim = ((DM_Moab*)dm->data)->dim;
    630:   return(0);
    631: }

    636: /*@
    637:   DMMoabGetMaterialBlock - Get the material ID corresponding to the current entity of the DM Mesh

    639:   Collective on MPI_Comm

    641:   Input Parameter:
    642: . dm - The DMMoab object
    643: . ehandle - The element entity handle

    645:   Output Parameter:
    646: . mat - The material ID for the current entity

    648:   Level: beginner

    650: .keywords: DMMoab, create
    651: @*/
    652: PetscErrorCode DMMoabGetMaterialBlock(DM dm,const moab::EntityHandle ehandle, PetscInt *mat)
    653: {
    654:   DM_Moab         *dmmoab;
    655:   moab::ErrorCode merr;

    659:   if (*mat) {
    660:     dmmoab = (DM_Moab*)(dm)->data;
    661:     merr=dmmoab->mbiface->tag_get_data(dmmoab->material_tag, &ehandle, 1, mat);MBERRNM(merr);
    662:   }
    663:   return(0);
    664: }

    669: /*@
    670:   DMMoabGetVertexCoordinates - Get the coordinates corresponding to the requested vertex entities

    672:   Collective on MPI_Comm

    674:   Input Parameter:
    675: . dm - The DMMoab object
    676: . nconn - Number of entities whose coordinates are needed
    677: . conn - The vertex entity handles

    679:   Output Parameter:
    680: . vpos - The coordinates of the requested vertex entities

    682:   Level: beginner

    684: .seealso: DMMoabGetVertexConnectivity()
    685: @*/
    686: PetscErrorCode DMMoabGetVertexCoordinates(DM dm,PetscInt nconn,const moab::EntityHandle *conn,PetscReal *vpos)
    687: {
    688:   DM_Moab         *dmmoab;
    689:   PetscErrorCode  ierr;
    690:   moab::ErrorCode merr;

    695:   dmmoab = (DM_Moab*)(dm)->data;

    697:   if (!vpos) {
    698:     PetscMalloc1(nconn*3, &vpos);
    699:   }

    701:   /* Get connectivity information in MOAB canonical ordering */
    702:   merr = dmmoab->mbiface->get_coords(conn, nconn, vpos);MBERRNM(merr);
    703:   return(0);
    704: }

    709: /*@
    710:   DMMoabGetVertexConnectivity - Get the vertex adjacency for the given entity

    712:   Collective on MPI_Comm

    714:   Input Parameter:
    715: . dm - The DMMoab object
    716: . vhandle - Vertex entity handle

    718:   Output Parameter:
    719: . nconn - Number of entities whose coordinates are needed
    720: . conn - The vertex entity handles

    722:   Level: beginner

    724: .seealso: DMMoabGetVertexCoordinates(), DMMoabRestoreVertexConnectivity()
    725: @*/
    726: PetscErrorCode DMMoabGetVertexConnectivity(DM dm,moab::EntityHandle vhandle,PetscInt* nconn, moab::EntityHandle **conn)
    727: {
    728:   DM_Moab        *dmmoab;
    729:   std::vector<moab::EntityHandle> adj_entities,connect;
    730:   PetscErrorCode  ierr;
    731:   moab::ErrorCode merr;

    736:   dmmoab = (DM_Moab*)(dm)->data;

    738:   /* Get connectivity information in MOAB canonical ordering */
    739:   merr = dmmoab->mbiface->get_adjacencies(&vhandle, 1, 1, true, adj_entities, moab::Interface::UNION);MBERRNM(merr);
    740:   merr = dmmoab->mbiface->get_connectivity(&adj_entities[0],adj_entities.size(),connect);MBERRNM(merr);

    742:   if (conn) {
    743:     PetscMalloc(sizeof(moab::EntityHandle)*connect.size(), conn);
    744:     PetscMemcpy(*conn, &connect[0], sizeof(moab::EntityHandle)*connect.size());
    745:   }
    746:   if (nconn) *nconn=connect.size();
    747:   return(0);
    748: }

    753: /*@
    754:   DMMoabRestoreVertexConnectivity - Restore the vertex connectivity for the given entity

    756:   Collective on MPI_Comm

    758:   Input Parameter:
    759: . dm - The DMMoab object
    760: . vhandle - Vertex entity handle
    761: . nconn - Number of entities whose coordinates are needed
    762: . conn - The vertex entity handles

    764:   Level: beginner

    766: .seealso: DMMoabGetVertexCoordinates(), DMMoabGetVertexConnectivity()
    767: @*/
    768: PetscErrorCode DMMoabRestoreVertexConnectivity(DM dm,moab::EntityHandle ehandle,PetscInt* nconn, moab::EntityHandle **conn)
    769: {
    770:   PetscErrorCode  ierr;

    776:   if (conn) {
    777:     PetscFree(*conn);
    778:   }
    779:   if (nconn) *nconn=0;
    780:   return(0);
    781: }

    786: /*@
    787:   DMMoabGetElementConnectivity - Get the vertex adjacency for the given entity

    789:   Collective on MPI_Comm

    791:   Input Parameter:
    792: . dm - The DMMoab object
    793: . ehandle - Vertex entity handle

    795:   Output Parameter:
    796: . nconn - Number of entities whose coordinates are needed
    797: . conn - The vertex entity handles

    799:   Level: beginner

    801: .seealso: DMMoabGetVertexCoordinates(), DMMoabGetVertexConnectivity(), DMMoabRestoreVertexConnectivity()
    802: @*/
    803: PetscErrorCode DMMoabGetElementConnectivity(DM dm,moab::EntityHandle ehandle,PetscInt* nconn,const moab::EntityHandle **conn)
    804: {
    805:   DM_Moab        *dmmoab;
    806:   const moab::EntityHandle *connect;
    807:   moab::ErrorCode merr;
    808:   PetscInt nnodes;

    813:   dmmoab = (DM_Moab*)(dm)->data;

    815:   /* Get connectivity information in MOAB canonical ordering */
    816:   merr = dmmoab->mbiface->get_connectivity(ehandle, connect, nnodes);MBERRNM(merr);
    817:   if (conn) *conn=connect;
    818:   if (nconn) *nconn=nnodes;
    819:   return(0);
    820: }

    825: /*@
    826:   DMMoabIsEntityOnBoundary - Check whether a given entity is on the boundary (vertex, edge, face, element)

    828:   Collective on MPI_Comm

    830:   Input Parameter:
    831: . dm - The DMMoab object
    832: . ent - Entity handle

    834:   Output Parameter:
    835: . ent_on_boundary - PETSC_TRUE if entity on boundary; PETSC_FALSE otherwise

    837:   Level: beginner

    839: .seealso: DMMoabCheckBoundaryVertices()
    840: @*/
    841: PetscErrorCode DMMoabIsEntityOnBoundary(DM dm,const moab::EntityHandle ent,PetscBool* ent_on_boundary)
    842: {
    843:   moab::EntityType etype;
    844:   DM_Moab         *dmmoab;
    845:   PetscInt         edim;

    850:   dmmoab = (DM_Moab*)(dm)->data;

    852:   /* get the entity type and handle accordingly */
    853:   etype=dmmoab->mbiface->type_from_handle(ent);
    854:   if(etype >= moab::MBPOLYHEDRON) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Entity type on the boundary skin is invalid. EntityType = %D\n",etype);

    856:   /* get the entity dimension */
    857:   edim=dmmoab->mbiface->dimension_from_handle(ent);

    859:   *ent_on_boundary=PETSC_FALSE;
    860:   if(etype == moab::MBVERTEX && edim == 0) {
    861:     if (dmmoab->bndyvtx->index(ent) >= 0) *ent_on_boundary=PETSC_TRUE;
    862:   }
    863:   else {
    864:     if (edim == dmmoab->dim) {  /* check the higher-dimensional elements first */
    865:       if (dmmoab->bndyelems->index(ent) >= 0) *ent_on_boundary=PETSC_TRUE;
    866:     }
    867:     else {                      /* next check the lower-dimensional faces */
    868:       if (dmmoab->bndyfaces->index(ent) >= 0) *ent_on_boundary=PETSC_TRUE;
    869:     }
    870:   }
    871:   return(0);
    872: }

    877: /*@
    878:   DMMoabIsEntityOnBoundary - Check whether a given entity is on the boundary (vertex, edge, face, element)

    880:   Input Parameter:
    881: . dm - The DMMoab object
    882: . nconn - Number of handles
    883: . cnt - Array of entity handles

    885:   Output Parameter:
    886: . isbdvtx - Array of boundary markers - PETSC_TRUE if entity on boundary; PETSC_FALSE otherwise

    888:   Level: beginner

    890: .seealso: DMMoabIsEntityOnBoundary()
    891: @*/
    892: PetscErrorCode DMMoabCheckBoundaryVertices(DM dm,PetscInt nconn,const moab::EntityHandle *cnt,PetscBool* isbdvtx)
    893: {
    894:   DM_Moab        *dmmoab;
    895:   PetscInt       i;

    901:   dmmoab = (DM_Moab*)(dm)->data;

    903:   for (i=0; i < nconn; ++i) {
    904:     isbdvtx[i]=(dmmoab->bndyvtx->index(cnt[i]) >= 0 ? PETSC_TRUE:PETSC_FALSE);
    905:   }
    906:   return(0);
    907: }

    912: /*@
    913:   DMMoabGetBoundaryMarkers - Return references to the vertices, faces, elements on the boundary

    915:   Input Parameter:
    916: . dm - The DMMoab object

    918:   Output Parameter:
    919: . bdvtx - Boundary vertices
    920: . bdelems - Boundary elements
    921: . bdfaces - Boundary faces

    923:   Level: beginner

    925: .seealso: DMMoabCheckBoundaryVertices(), DMMoabIsEntityOnBoundary()
    926: @*/
    927: PetscErrorCode DMMoabGetBoundaryMarkers(DM dm,const moab::Range **bdvtx,const moab::Range** bdelems,const moab::Range** bdfaces)
    928: {
    929:   DM_Moab        *dmmoab;

    933:   dmmoab = (DM_Moab*)(dm)->data;

    935:   if (bdvtx)  *bdvtx = dmmoab->bndyvtx;
    936:   if (bdfaces)  *bdfaces = dmmoab->bndyfaces;
    937:   if (bdelems)  *bdfaces = dmmoab->bndyelems;
    938:   return(0);
    939: }

    944: PETSC_EXTERN PetscErrorCode DMDestroy_Moab(DM dm)
    945: {
    947:   PetscInt       i;
    948:   DM_Moab        *dmmoab = (DM_Moab*)dm->data;

    952:   if (dmmoab->icreatedinstance) {
    953:     delete dmmoab->mbiface;
    954:   }
    955:   dmmoab->mbiface = NULL;
    956:   dmmoab->pcomm = NULL;
    957:   delete dmmoab->vlocal;
    958:   delete dmmoab->vowned;
    959:   delete dmmoab->vghost;
    960:   delete dmmoab->elocal;
    961:   delete dmmoab->eghost;
    962:   delete dmmoab->bndyvtx;
    963:   delete dmmoab->bndyfaces;
    964:   delete dmmoab->bndyelems;

    966:   PetscFree(dmmoab->gsindices);
    967:   PetscFree2(dmmoab->gidmap,dmmoab->lidmap);
    968:   PetscFree2(dmmoab->lgmap,dmmoab->llmap);
    969:   PetscFree(dmmoab->dfill);
    970:   PetscFree(dmmoab->ofill);
    971:   if (dmmoab->fieldNames) {
    972:     for(i=0; i<dmmoab->numFields; i++) {
    973:       PetscFree(dmmoab->fieldNames[i]);
    974:     }
    975:     PetscFree(dmmoab->fieldNames);
    976:   }
    977:   VecScatterDestroy(&dmmoab->ltog_sendrecv);
    978:   ISLocalToGlobalMappingDestroy(&dmmoab->ltog_map);
    979:   PetscFree(dm->data);
    980:   return(0);
    981: }

    986: PETSC_EXTERN PetscErrorCode DMSetFromOptions_Moab(PetscOptionItems *PetscOptionsObject,DM dm)
    987: {
    989:   DM_Moab        *dmmoab = (DM_Moab*)dm->data;

    993:   PetscOptionsHead(PetscOptionsObject,"DMMoab Options");
    994:   PetscOptionsInt("-dm_moab_rw_dbg", "The verbosity level for reading and writing MOAB meshes", "DMView", dmmoab->rw_dbglevel, &dmmoab->rw_dbglevel, NULL);
    995:   PetscOptionsBool("-dm_moab_partiton_by_rank", "Use partition by rank when reading MOAB meshes from file", "DMView", dmmoab->partition_by_rank, &dmmoab->partition_by_rank, NULL);
    996:   /* TODO: typically, the read options are needed before a DM is completely created and available in which case, the options wont be available ?? */
    997:   PetscOptionsString("-dm_moab_read_opts", "Extra options to enable MOAB reader to load DM from file", "DMView", dmmoab->extra_read_options, dmmoab->extra_read_options, PETSC_MAX_PATH_LEN, NULL);
    998:   PetscOptionsString("-dm_moab_write_opts", "Extra options to enable MOAB writer to serialize DM to file", "DMView", dmmoab->extra_write_options, dmmoab->extra_write_options, PETSC_MAX_PATH_LEN, NULL);
    999:   PetscOptionsEnum("-dm_moab_read_mode", "MOAB parallel read mode", "DMView", MoabReadModes, (PetscEnum)dmmoab->read_mode, (PetscEnum*)&dmmoab->read_mode, NULL);
    1000:   PetscOptionsEnum("-dm_moab_write_mode", "MOAB parallel write mode", "DMView", MoabWriteModes, (PetscEnum)dmmoab->write_mode, (PetscEnum*)&dmmoab->write_mode, NULL);
    1001:   return(0);
    1002: }

    1007: PETSC_EXTERN PetscErrorCode DMSetUp_Moab(DM dm)
    1008: {
    1009:   PetscErrorCode          ierr;
    1010:   moab::ErrorCode         merr;
    1011:   Vec                     local, global;
    1012:   IS                      from,to;
    1013:   moab::Range::iterator   iter;
    1014:   PetscInt                i,j,f,bs,gmin,lmin,lmax,vent,totsize;
    1015:   DM_Moab                *dmmoab = (DM_Moab*)dm->data;
    1016:   moab::Range             adjs;

    1020:   /* Get the local and shared vertices and cache it */
    1021:   if (dmmoab->mbiface == PETSC_NULL || dmmoab->pcomm == PETSC_NULL) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ORDER, "Set the MOAB Interface and ParallelComm objects before calling SetUp.");

    1023:   /* Get the entities recursively in the current part of the mesh, if user did not set the local vertices explicitly */
    1024:   if (dmmoab->vlocal->empty())
    1025:   {
    1026:     merr = dmmoab->mbiface->get_entities_by_type(dmmoab->fileset,moab::MBVERTEX,*dmmoab->vlocal,true);MBERRNM(merr);

    1028:     /* filter based on parallel status */
    1029:     merr = dmmoab->pcomm->filter_pstatus(*dmmoab->vlocal,PSTATUS_NOT_OWNED,PSTATUS_NOT,-1,dmmoab->vowned);MBERRNM(merr);

    1031:     /* filter all the non-owned and shared entities out of the list */
    1032:     adjs = moab::subtract(*dmmoab->vlocal, *dmmoab->vowned);
    1033:     merr = dmmoab->pcomm->filter_pstatus(adjs,PSTATUS_INTERFACE,PSTATUS_OR,-1,dmmoab->vghost);MBERRNM(merr);
    1034:     adjs = moab::subtract(adjs, *dmmoab->vghost);
    1035:     *dmmoab->vlocal = moab::subtract(*dmmoab->vlocal, adjs);

    1037:     /* compute and cache the sizes of local and ghosted entities */
    1038:     dmmoab->nloc = dmmoab->vowned->size();
    1039:     dmmoab->nghost = dmmoab->vghost->size();
    1040:     MPIU_Allreduce(&dmmoab->nloc, &dmmoab->n, 1, MPI_INTEGER, MPI_SUM, ((PetscObject)dm)->comm);
    1041:   }

    1043:   {
    1044:     /* get the information about the local elements in the mesh */
    1045:     dmmoab->eghost->clear();

    1047:     /* first decipher the leading dimension */
    1048:     for (i=3;i>0;i--) {
    1049:       dmmoab->elocal->clear();
    1050:       merr = dmmoab->mbiface->get_entities_by_dimension(dmmoab->fileset, i, *dmmoab->elocal, true);CHKERRQ(merr);

    1052:       /* store the current mesh dimension */
    1053:       if (dmmoab->elocal->size()) {
    1054:         dmmoab->dim=i;
    1055:         break;
    1056:       }
    1057:     }

    1059:     /* filter the ghosted and owned element list */
    1060:     *dmmoab->eghost = *dmmoab->elocal;
    1061:     merr = dmmoab->pcomm->filter_pstatus(*dmmoab->elocal,PSTATUS_NOT_OWNED,PSTATUS_NOT);MBERRNM(merr);
    1062:     *dmmoab->eghost = moab::subtract(*dmmoab->eghost, *dmmoab->elocal);

    1064:     dmmoab->neleloc = dmmoab->elocal->size();
    1065:     dmmoab->neleghost = dmmoab->eghost->size();
    1066:     MPIU_Allreduce(&dmmoab->neleloc, &dmmoab->nele, 1, MPI_INTEGER, MPI_SUM, ((PetscObject)dm)->comm);
    1067:   }

    1069:   bs = dmmoab->bs;
    1070:   if (!dmmoab->ltog_tag) {
    1071:     /* Get the global ID tag. The global ID tag is applied to each
    1072:        vertex. It acts as an global identifier which MOAB uses to
    1073:        assemble the individual pieces of the mesh */
    1074:     merr = dmmoab->mbiface->tag_get_handle(GLOBAL_ID_TAG_NAME, dmmoab->ltog_tag);MBERRNM(merr);
    1075:   }

    1077:   totsize=dmmoab->vlocal->size();
    1078:   if (totsize != dmmoab->nloc+dmmoab->nghost) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Mismatch between local and owned+ghost vertices. %D != %D.",totsize,dmmoab->nloc+dmmoab->nghost);
    1079:   PetscMalloc1(totsize,&dmmoab->gsindices);
    1080:   {
    1081:     /* first get the local indices */
    1082:     merr = dmmoab->mbiface->tag_get_data(dmmoab->ltog_tag,*dmmoab->vowned,&dmmoab->gsindices[0]);MBERRNM(merr);
    1083:     /* next get the ghosted indices */
    1084:     if (dmmoab->nghost) {
    1085:       merr = dmmoab->mbiface->tag_get_data(dmmoab->ltog_tag,*dmmoab->vghost,&dmmoab->gsindices[dmmoab->nloc]);MBERRNM(merr);
    1086:     }

    1088:     /* find out the local and global minima of GLOBAL_ID */
    1089:     lmin=lmax=dmmoab->gsindices[0];
    1090:     for (i=0; i<totsize; ++i) {
    1091:       if(lmin>dmmoab->gsindices[i]) lmin=dmmoab->gsindices[i];
    1092:       if(lmax<dmmoab->gsindices[i]) lmax=dmmoab->gsindices[i];
    1093:     }

    1095:     MPIU_Allreduce(&lmin, &gmin, 1, MPI_INT, MPI_MIN, ((PetscObject)dm)->comm);

    1097:     /* set the GID map */
    1098:     for (i=0; i<totsize; ++i) {
    1099:       dmmoab->gsindices[i]-=gmin;   /* zero based index needed for IS */
    1100:     }
    1101:     lmin-=gmin;
    1102:     lmax-=gmin;

    1104:     PetscInfo3(NULL, "GLOBAL_ID: Local minima - %D, Local maxima - %D, Global minima - %D.\n", lmin, lmax, gmin);
    1105:   }
    1106:   if(!(dmmoab->bs==dmmoab->numFields || dmmoab->bs == 1)) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mismatch between block size and number of component fields. %D != 1 OR %D != %D.",dmmoab->bs,dmmoab->bs,dmmoab->numFields);

    1108:   {
    1109:     i=(PetscInt)dmmoab->vlocal->back()+1;
    1110:     //i=(PetscInt)(dmmoab->vlocal->back()-dmmoab->vlocal->front())+1;
    1111:     j=totsize*dmmoab->numFields;
    1112:     PetscMalloc2(i,&dmmoab->gidmap,i,&dmmoab->lidmap);
    1113:     PetscMalloc2(j,&dmmoab->lgmap,j,&dmmoab->llmap);

    1115:     i=j=0;
    1116:     /* set the owned vertex data first */
    1117:     for(moab::Range::iterator iter = dmmoab->vowned->begin(); iter != dmmoab->vowned->end(); iter++,i++) {
    1118:       vent=(PetscInt)(*iter);
    1119:       dmmoab->gidmap[vent]=dmmoab->gsindices[i];
    1120:       dmmoab->lidmap[vent]=i;
    1121:       if (bs > 1) {
    1122:         for (f=0;f<dmmoab->numFields;f++,j++) {
    1123:           dmmoab->lgmap[j]=dmmoab->gsindices[i]*dmmoab->numFields+f;
    1124:           dmmoab->llmap[j]=i*dmmoab->numFields+f;
    1125:         }
    1126:       }
    1127:       else {
    1128:         for (f=0;f<dmmoab->numFields;f++,j++) {
    1129:           dmmoab->lgmap[j]=totsize*f+dmmoab->gsindices[i];
    1130:           dmmoab->llmap[j]=totsize*f+i;
    1131:         }
    1132:       }
    1133:     }
    1134:     /* next arrange all the ghosted data information */
    1135:     for(moab::Range::iterator iter = dmmoab->vghost->begin(); iter != dmmoab->vghost->end(); iter++,i++) {
    1136:       vent=(PetscInt)(*iter);
    1137:       dmmoab->gidmap[vent]=dmmoab->gsindices[i];
    1138:       dmmoab->lidmap[vent]=i;
    1139:       if (bs > 1) {
    1140:         for (f=0;f<dmmoab->numFields;f++,j++) {
    1141:           dmmoab->lgmap[j]=dmmoab->gsindices[i]*dmmoab->numFields+f;
    1142:           dmmoab->llmap[j]=i*dmmoab->numFields+f;
    1143:         }
    1144:       }
    1145:       else {
    1146:         for (f=0;f<dmmoab->numFields;f++,j++) {
    1147:           dmmoab->lgmap[j]=totsize*f+dmmoab->gsindices[i];
    1148:           dmmoab->llmap[j]=totsize*f+i;
    1149:         }
    1150:       }
    1151:     }

    1153:     /* We need to create the Global to Local Vector Scatter Contexts
    1154:        1) First create a local and global vector
    1155:        2) Create a local and global IS
    1156:        3) Create VecScatter and LtoGMapping objects
    1157:        4) Cleanup the IS and Vec objects
    1158:     */
    1159:     DMCreateGlobalVector(dm, &global);
    1160:     DMCreateLocalVector(dm, &local);

    1162:     VecGetOwnershipRange(global, &dmmoab->vstart, &dmmoab->vend);
    1163:     PetscInfo3(NULL, "Total-size = %D\t Owned = %D, Ghosted = %D.\n", totsize, dmmoab->nloc, dmmoab->nghost);

    1165:     /* global to local must retrieve ghost points */
    1166:     ISCreateStride(((PetscObject)dm)->comm,dmmoab->nloc*dmmoab->numFields,dmmoab->vstart,1,&from);
    1167:     ISSetBlockSize(from,bs);

    1169:     ISCreateGeneral(((PetscObject)dm)->comm,dmmoab->nloc*dmmoab->numFields,&dmmoab->lgmap[0],PETSC_COPY_VALUES,&to);
    1170:     ISSetBlockSize(to,bs);

    1172:     if (!dmmoab->ltog_map) {
    1173:       /* create to the local to global mapping for vectors in order to use VecSetValuesLocal */
    1174:       ISLocalToGlobalMappingCreate(((PetscObject)dm)->comm,dmmoab->bs,totsize*dmmoab->numFields,dmmoab->lgmap,
    1175:                                           PETSC_COPY_VALUES,&dmmoab->ltog_map);
    1176:     }

    1178:     /* now create the scatter object from local to global vector */
    1179:     VecScatterCreate(local,from,global,to,&dmmoab->ltog_sendrecv);

    1181:     /* clean up IS, Vec */
    1182:     ISDestroy(&from);
    1183:     ISDestroy(&to);
    1184:     VecDestroy(&local);
    1185:     VecDestroy(&global);
    1186:   }

    1188:   /* skin the boundary and store nodes */
    1189:   {
    1190:     /* get the skin vertices of boundary faces for the current partition and then filter
    1191:        the local, boundary faces, vertices and elements alone via PSTATUS flags;
    1192:        this should not give us any ghosted boundary, but if user needs such a functionality
    1193:        it would be easy to add it based on the find_skin query below */
    1194:     moab::Skinner skinner(dmmoab->mbiface);

    1196:     dmmoab->bndyvtx = new moab::Range();
    1197:     dmmoab->bndyfaces = new moab::Range();
    1198:     dmmoab->bndyelems = new moab::Range();

    1200:     /* get the entities on the skin - only the faces */
    1201:     merr = skinner.find_skin(dmmoab->fileset, *dmmoab->elocal, false, *dmmoab->bndyfaces, NULL, false, true, false);MBERRNM(merr); // 'false' param indicates we want faces back, not vertices

    1203:     /* filter all the non-owned and shared entities out of the list */
    1204:     merr = dmmoab->pcomm->filter_pstatus(*dmmoab->bndyfaces,PSTATUS_NOT_OWNED,PSTATUS_NOT);MBERRNM(merr);
    1205:     merr = dmmoab->pcomm->filter_pstatus(*dmmoab->bndyfaces,PSTATUS_SHARED,PSTATUS_NOT);MBERRNM(merr);

    1207:     /* get all the nodes via connectivity and the parent elements via adjacency information */
    1208:     merr = dmmoab->mbiface->get_connectivity(*dmmoab->bndyfaces, *dmmoab->bndyvtx, false);MBERRNM(ierr);
    1209:     merr = dmmoab->mbiface->get_adjacencies(*dmmoab->bndyfaces, dmmoab->dim, false, *dmmoab->bndyelems, moab::Interface::UNION);MBERRNM(ierr);
    1210:     PetscInfo3(NULL, "Found %D boundary vertices, %D boundary faces and %D boundary elements.\n", dmmoab->bndyvtx->size(), dmmoab->bndyvtx->size(), dmmoab->bndyelems->size());
    1211:   }
    1212:   return(0);
    1213: }

    1217: PETSC_EXTERN PetscErrorCode DMCreate_Moab(DM dm)
    1218: {

    1223:   PetscNewLog(dm,(DM_Moab**)&dm->data);

    1225:   ((DM_Moab*)dm->data)->bs = 1;
    1226:   ((DM_Moab*)dm->data)->numFields = 1;
    1227:   ((DM_Moab*)dm->data)->n = 0;
    1228:   ((DM_Moab*)dm->data)->nloc = 0;
    1229:   ((DM_Moab*)dm->data)->nghost = 0;
    1230:   ((DM_Moab*)dm->data)->nele = 0;
    1231:   ((DM_Moab*)dm->data)->neleloc = 0;
    1232:   ((DM_Moab*)dm->data)->neleghost = 0;
    1233:   ((DM_Moab*)dm->data)->ltog_map = PETSC_NULL;
    1234:   ((DM_Moab*)dm->data)->ltog_sendrecv = PETSC_NULL;

    1236:   ((DM_Moab*)dm->data)->vlocal = new moab::Range();
    1237:   ((DM_Moab*)dm->data)->vowned = new moab::Range();
    1238:   ((DM_Moab*)dm->data)->vghost = new moab::Range();
    1239:   ((DM_Moab*)dm->data)->elocal = new moab::Range();
    1240:   ((DM_Moab*)dm->data)->eghost = new moab::Range();

    1242:   dm->ops->createglobalvector       = DMCreateGlobalVector_Moab;
    1243:   dm->ops->createlocalvector        = DMCreateLocalVector_Moab;
    1244:   dm->ops->creatematrix             = DMCreateMatrix_Moab;
    1245:   dm->ops->setup                    = DMSetUp_Moab;
    1246:   dm->ops->destroy                  = DMDestroy_Moab;
    1247:   dm->ops->setfromoptions           = DMSetFromOptions_Moab;
    1248:   dm->ops->globaltolocalbegin       = DMGlobalToLocalBegin_Moab;
    1249:   dm->ops->globaltolocalend         = DMGlobalToLocalEnd_Moab;
    1250:   dm->ops->localtoglobalbegin       = DMLocalToGlobalBegin_Moab;
    1251:   dm->ops->localtoglobalend         = DMLocalToGlobalEnd_Moab;
    1252:   return(0);
    1253: }