Actual source code: dmmbutil.cxx

      1: #include <petsc/private/dmmbimpl.h>
      2: #include <petsc/private/vecimpl.h>

      4: #include <petscdmmoab.h>
      5: #include <MBTagConventions.hpp>
      6: #include <moab/ReadUtilIface.hpp>
      7: #include <moab/MergeMesh.hpp>
      8: #include <moab/CN.hpp>

     10: typedef struct {
     11:   // options
     12:   PetscInt  A, B, C, M, N, K, dim;
     13:   PetscInt  blockSizeVertexXYZ[3];              // Number of element blocks per partition
     14:   PetscInt  blockSizeElementXYZ[3];
     15:   PetscReal xyzbounds[6]; // the physical size of the domain
     16:   bool      newMergeMethod, keep_skins, simplex, adjEnts;

     18:   // compute params
     19:   PetscReal dx, dy, dz;
     20:   PetscInt  NX, NY, NZ, nex, ney, nez;
     21:   PetscInt  q, xstride, ystride, zstride;
     22:   PetscBool usrxyzgrid, usrprocgrid, usrrefgrid;
     23:   PetscInt  fraction, remainder, cumfraction;
     24:   PetscLogEvent generateMesh, generateElements, generateVertices, parResolve;

     26: } DMMoabMeshGeneratorCtx;

     29: PetscInt DMMoab_SetTensorElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, PetscInt offset, PetscInt corner, std::vector<PetscInt>& subent_conn, moab::EntityHandle *connectivity)
     30: {
     31:   switch (genCtx.dim) {
     32:   case 1:
     33:     subent_conn.resize(2);
     34:     moab::CN::SubEntityVertexIndices(moab::MBEDGE, 1, 0, subent_conn.data());
     35:     connectivity[offset + subent_conn[0]] = corner;
     36:     connectivity[offset + subent_conn[1]] = corner + 1;
     37:     break;
     38:   case 2:
     39:     subent_conn.resize(4);
     40:     moab::CN::SubEntityVertexIndices(moab::MBQUAD, 2, 0, subent_conn.data());
     41:     connectivity[offset + subent_conn[0]] = corner;
     42:     connectivity[offset + subent_conn[1]] = corner + 1;
     43:     connectivity[offset + subent_conn[2]] = corner + 1 + genCtx.ystride;
     44:     connectivity[offset + subent_conn[3]] = corner + genCtx.ystride;
     45:     break;
     46:   case 3:
     47:   default:
     48:     subent_conn.resize(8);
     49:     moab::CN::SubEntityVertexIndices(moab::MBHEX, 3, 0, subent_conn.data());
     50:     connectivity[offset + subent_conn[0]] = corner;
     51:     connectivity[offset + subent_conn[1]] = corner + 1;
     52:     connectivity[offset + subent_conn[2]] = corner + 1 + genCtx.ystride;
     53:     connectivity[offset + subent_conn[3]] = corner + genCtx.ystride;
     54:     connectivity[offset + subent_conn[4]] = corner + genCtx.zstride;
     55:     connectivity[offset + subent_conn[5]] = corner + 1 + genCtx.zstride;
     56:     connectivity[offset + subent_conn[6]] = corner + 1 + genCtx.ystride + genCtx.zstride;
     57:     connectivity[offset + subent_conn[7]] = corner + genCtx.ystride + genCtx.zstride;
     58:     break;
     59:   }
     60:   return subent_conn.size();
     61: }

     64: PetscInt DMMoab_SetSimplexElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, PetscInt subelem, PetscInt offset, PetscInt corner, std::vector<PetscInt>& subent_conn, moab::EntityHandle *connectivity)
     65: {
     66:   PetscInt A, B, C, D, E, F, G, H, M;
     67:   const PetscInt trigen_opts = 1; /* 1 - Aligned diagonally to right, 2 - Aligned diagonally to left, 3 - 4 elements per quad */
     68:   A = corner;
     69:   B = corner + 1;
     70:   switch (genCtx.dim) {
     71:   case 1:
     72:     subent_conn.resize(2);  /* only linear EDGE supported now */
     73:     moab::CN::SubEntityVertexIndices(moab::MBEDGE, 1, 0, subent_conn.data());
     74:     connectivity[offset + subent_conn[0]] = A;
     75:     connectivity[offset + subent_conn[1]] = B;
     76:     break;
     77:   case 2:
     78:     C = corner + 1 + genCtx.ystride;
     79:     D = corner +     genCtx.ystride;
     80:     M = corner + 0.5; /* technically -- need to modify vertex generation */
     81:     subent_conn.resize(3);  /* only linear TRI supported */
     82:     moab::CN::SubEntityVertexIndices(moab::MBTRI, 2, 0, subent_conn.data());
     83:     if (trigen_opts == 1) {
     84:       if (subelem) { /* 0 1 2 of a QUAD */
     85:         connectivity[offset + subent_conn[0]] = B;
     86:         connectivity[offset + subent_conn[1]] = C;
     87:         connectivity[offset + subent_conn[2]] = A;
     88:       }
     89:       else {        /* 2 3 0 of a QUAD */
     90:         connectivity[offset + subent_conn[0]] = D;
     91:         connectivity[offset + subent_conn[1]] = A;
     92:         connectivity[offset + subent_conn[2]] = C;
     93:       }
     94:     }
     95:     else if (trigen_opts == 2) {
     96:       if (subelem) { /* 0 1 2 of a QUAD */
     97:         connectivity[offset + subent_conn[0]] = A;
     98:         connectivity[offset + subent_conn[1]] = B;
     99:         connectivity[offset + subent_conn[2]] = D;
    100:       }
    101:       else {        /* 2 3 0 of a QUAD */
    102:         connectivity[offset + subent_conn[0]] = C;
    103:         connectivity[offset + subent_conn[1]] = D;
    104:         connectivity[offset + subent_conn[2]] = B;
    105:       }
    106:     }
    107:     else {
    108:       switch (subelem) { /* 0 1 2 of a QUAD */
    109:       case 0:
    110:         connectivity[offset + subent_conn[0]] = A;
    111:         connectivity[offset + subent_conn[1]] = B;
    112:         connectivity[offset + subent_conn[2]] = M;
    113:         break;
    114:       case 1:
    115:         connectivity[offset + subent_conn[0]] = B;
    116:         connectivity[offset + subent_conn[1]] = C;
    117:         connectivity[offset + subent_conn[2]] = M;
    118:         break;
    119:       case 2:
    120:         connectivity[offset + subent_conn[0]] = C;
    121:         connectivity[offset + subent_conn[1]] = D;
    122:         connectivity[offset + subent_conn[2]] = M;
    123:         break;
    124:       case 3:
    125:         connectivity[offset + subent_conn[0]] = D;
    126:         connectivity[offset + subent_conn[1]] = A;
    127:         connectivity[offset + subent_conn[2]] = M;
    128:         break;
    129:       }
    130:     }
    131:     break;
    132:   case 3:
    133:   default:
    134:     C = corner + 1 + genCtx.ystride;
    135:     D = corner +     genCtx.ystride;
    136:     E = corner +                      genCtx.zstride;
    137:     F = corner + 1 +                  genCtx.zstride;
    138:     G = corner + 1 + genCtx.ystride + genCtx.zstride;
    139:     H = corner +     genCtx.ystride + genCtx.zstride;
    140:     subent_conn.resize(4);  /* only linear TET supported */
    141:     moab::CN::SubEntityVertexIndices(moab::MBTET, 3, 0, subent_conn.data());
    142:     switch (subelem) {
    143:     case 0: /* 4 3 7 6 of a HEX */
    144:       connectivity[offset + subent_conn[0]] = E;
    145:       connectivity[offset + subent_conn[1]] = D;
    146:       connectivity[offset + subent_conn[2]] = H;
    147:       connectivity[offset + subent_conn[3]] = G;
    148:       break;
    149:     case 1: /* 0 1 2 5 of a HEX */
    150:       connectivity[offset + subent_conn[0]] = A;
    151:       connectivity[offset + subent_conn[1]] = B;
    152:       connectivity[offset + subent_conn[2]] = C;
    153:       connectivity[offset + subent_conn[3]] = F;
    154:       break;
    155:     case 2: /* 0 3 4 5 of a HEX */
    156:       connectivity[offset + subent_conn[0]] = A;
    157:       connectivity[offset + subent_conn[1]] = D;
    158:       connectivity[offset + subent_conn[2]] = E;
    159:       connectivity[offset + subent_conn[3]] = F;
    160:       break;
    161:     case 3: /* 2 6 3 5 of a HEX */
    162:       connectivity[offset + subent_conn[0]] = C;
    163:       connectivity[offset + subent_conn[1]] = G;
    164:       connectivity[offset + subent_conn[2]] = D;
    165:       connectivity[offset + subent_conn[3]] = F;
    166:       break;
    167:     case 4: /* 0 2 3 5 of a HEX */
    168:       connectivity[offset + subent_conn[0]] = A;
    169:       connectivity[offset + subent_conn[1]] = C;
    170:       connectivity[offset + subent_conn[2]] = D;
    171:       connectivity[offset + subent_conn[3]] = F;
    172:       break;
    173:     case 5: /* 3 6 4 5 of a HEX */
    174:       connectivity[offset + subent_conn[0]] = D;
    175:       connectivity[offset + subent_conn[1]] = G;
    176:       connectivity[offset + subent_conn[2]] = E;
    177:       connectivity[offset + subent_conn[3]] = F;
    178:       break;
    179:     }
    180:     break;
    181:   }
    182:   return subent_conn.size();
    183: }

    186: std::pair<PetscInt, PetscInt> DMMoab_SetElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, PetscInt offset, PetscInt corner, moab::EntityHandle *connectivity)
    187: {
    188:   PetscInt vcount = 0;
    189:   PetscInt simplices_per_tensor[4] = {0, 1, 2, 6};
    190:   std::vector<PetscInt> subent_conn;  /* only linear edge, tri, tet supported now */
    191:   subent_conn.reserve(27);
    192:   PetscInt m, subelem;
    193:   if (genCtx.simplex) {
    194:     subelem = simplices_per_tensor[genCtx.dim];
    195:     for (m = 0; m < subelem; m++) {
    196:       vcount = DMMoab_SetSimplexElementConnectivity_Private(genCtx, m, offset, corner, subent_conn, connectivity);
    197:       offset += vcount;
    198:     }
    199:   }
    200:   else {
    201:     subelem = 1;
    202:     vcount = DMMoab_SetTensorElementConnectivity_Private(genCtx, offset, corner, subent_conn, connectivity);
    203:   }
    204:   return std::pair<PetscInt, PetscInt>(vcount * subelem, subelem);
    205: }

    208: PetscErrorCode DMMoab_GenerateVertices_Private(moab::Interface *mbImpl, moab::ReadUtilIface *iface, DMMoabMeshGeneratorCtx& genCtx, PetscInt m, PetscInt n, PetscInt k,
    209:     PetscInt a, PetscInt b, PetscInt c, moab::Tag& global_id_tag, moab::EntityHandle& startv, moab::Range& uverts)
    210: {
    211:   PetscInt x, y, z, ix, nnodes;
    213:   PetscInt ii, jj, kk;
    214:   std::vector<PetscReal*> arrays;
    215:   PetscInt* gids;
    216:   moab::ErrorCode merr;

    219:   /* we will generate (q*block+1)^3 vertices, and block^3 hexas; q is 1 for linear, 2 for quadratic
    220:    * the global id of the vertices will come from m, n, k, a, b, c
    221:    * x will vary from  m*A*q*block + a*q*block to m*A*q*block+(a+1)*q*block etc.
    222:    */
    223:   nnodes = genCtx.blockSizeVertexXYZ[0] * (genCtx.dim > 1 ? genCtx.blockSizeVertexXYZ[1] * (genCtx.dim > 2 ? genCtx.blockSizeVertexXYZ[2] : 1) : 1);
    224:   PetscMalloc1(nnodes, &gids);

    226:   merr = iface->get_node_coords(3, nnodes, 0, startv, arrays);MBERR("Can't get node coords.", merr);

    228:   /* will start with the lower corner: */
    229:   /* x = ( m * genCtx.A + a) * genCtx.q * genCtx.blockSizeElementXYZ[0]; */
    230:   /* y = ( n * genCtx.B + b) * genCtx.q * genCtx.blockSizeElementXYZ[1]; */
    231:   /* z = ( k * genCtx.C + c) * genCtx.q * genCtx.blockSizeElementXYZ[2]; */

    233:   x = ( m * genCtx.A + a) * genCtx.q;
    234:   y = ( n * genCtx.B + b) * genCtx.q;
    235:   z = ( k * genCtx.C + c) * genCtx.q;
    236:   PetscInfo3(NULL, "Starting offset for coordinates := %d, %d, %d\n", x, y, z);
    237:   ix = 0;
    238:   moab::Range verts(startv, startv + nnodes - 1);
    239:   for (kk = 0; kk < (genCtx.dim > 2 ? genCtx.blockSizeVertexXYZ[2] : 1); kk++) {
    240:     for (jj = 0; jj < (genCtx.dim > 1 ? genCtx.blockSizeVertexXYZ[1] : 1); jj++) {
    241:       for (ii = 0; ii < genCtx.blockSizeVertexXYZ[0]; ii++, ix++) {
    242:         /* set coordinates for the vertices */
    243:         arrays[0][ix] = (x + ii) * genCtx.dx + genCtx.xyzbounds[0];
    244:         arrays[1][ix] = (y + jj) * genCtx.dy + genCtx.xyzbounds[2];
    245:         arrays[2][ix] = (z + kk) * genCtx.dz + genCtx.xyzbounds[4];
    246:         PetscInfo3(NULL, "Creating vertex with coordinates := %f, %f, %f\n", arrays[0][ix], arrays[1][ix], arrays[2][ix]);

    248:         /* If we want to set some tags on the vertices -> use the following entity handle definition:
    249:            moab::EntityHandle v = startv + ix;
    250:         */
    251:         /* compute the global ID for vertex */
    252:         gids[ix] = 1 + (x + ii) + (y + jj) * genCtx.NX + (z + kk) * (genCtx.NX * genCtx.NY);
    253:       }
    254:     }
    255:   }
    256:   /* set global ID data on vertices */
    257:   mbImpl->tag_set_data(global_id_tag, verts, &gids[0]);
    258:   verts.swap(uverts);
    259:   PetscFree(gids);
    260:   return(0);
    261: }

    263: PetscErrorCode DMMoab_GenerateElements_Private(moab::Interface* mbImpl, moab::ReadUtilIface* iface, DMMoabMeshGeneratorCtx& genCtx, PetscInt m, PetscInt n, PetscInt k,
    264:     PetscInt a, PetscInt b, PetscInt c, moab::Tag& global_id_tag, moab::EntityHandle startv, moab::Range& cells)
    265: {
    266:   moab::ErrorCode merr;
    267:   PetscInt ix, ie, xe, ye, ze;
    268:   PetscInt ii, jj, kk, nvperelem;
    269:   PetscInt simplices_per_tensor[4] = {0, 1, 2, 6};
    270:   PetscInt ntensorelems = genCtx.blockSizeElementXYZ[0] * (genCtx.dim > 1 ? genCtx.blockSizeElementXYZ[1] * (genCtx.dim > 2 ? genCtx.blockSizeElementXYZ[2] : 1) : 1); /*pow(genCtx.blockSizeElement,genCtx.dim);*/
    271:   PetscInt nelems = ntensorelems;
    272:   moab::EntityHandle starte; /* connectivity */
    273:   moab::EntityHandle* conn;

    276:   switch (genCtx.dim) {
    277:   case 1:
    278:     nvperelem = 2;
    279:     merr = iface->get_element_connect(nelems, 2, moab::MBEDGE, 0, starte, conn);MBERR("Can't get EDGE2 element connectivity.", merr);
    280:     break;
    281:   case 2:
    282:     if (genCtx.simplex) {
    283:       nvperelem = 3;
    284:       nelems = ntensorelems * simplices_per_tensor[genCtx.dim];
    285:       merr = iface->get_element_connect(nelems, 3, moab::MBTRI, 0, starte, conn);MBERR("Can't get TRI3 element connectivity.", merr);
    286:     }
    287:     else {
    288:       nvperelem = 4;
    289:       merr = iface->get_element_connect(nelems, 4, moab::MBQUAD, 0, starte, conn);MBERR("Can't get QUAD4 element connectivity.", merr);
    290:     }
    291:     break;
    292:   case 3:
    293:   default:
    294:     if (genCtx.simplex) {
    295:       nvperelem = 4;
    296:       nelems = ntensorelems * simplices_per_tensor[genCtx.dim];
    297:       merr = iface->get_element_connect(nelems, 4, moab::MBTET, 0, starte, conn);MBERR("Can't get TET4 element connectivity.", merr);
    298:     }
    299:     else {
    300:       nvperelem = 8;
    301:       merr = iface->get_element_connect(nelems, 8, moab::MBHEX, 0, starte, conn);MBERR("Can't get HEX8 element connectivity.", merr);
    302:     }
    303:     break;
    304:   }

    306:   ix = ie = 0; /* index now in the elements, for global ids */

    308:   /* create a temporary range to store local element handles */
    309:   moab::Range tmp(starte, starte + nelems - 1);
    310:   std::vector<PetscInt> gids(nelems);

    312:   /* identify the elements at the lower corner, for their global ids */
    313:   xe = m * genCtx.A * genCtx.blockSizeElementXYZ[0] + a * genCtx.blockSizeElementXYZ[0];
    314:   ye = (genCtx.dim > 1 ? n * genCtx.B * genCtx.blockSizeElementXYZ[1] + b * genCtx.blockSizeElementXYZ[1] : 0);
    315:   ze = (genCtx.dim > 2 ? k * genCtx.C * genCtx.blockSizeElementXYZ[2] + c * genCtx.blockSizeElementXYZ[2] : 0);

    317:   /* create owned elements requested by genCtx */
    318:   for (kk = 0; kk < (genCtx.dim > 2 ? genCtx.blockSizeElementXYZ[2] : 1); kk++) {
    319:     for (jj = 0; jj < (genCtx.dim > 1 ? genCtx.blockSizeElementXYZ[1] : 1); jj++) {
    320:       for (ii = 0; ii < genCtx.blockSizeElementXYZ[0]; ii++) {

    322:         moab::EntityHandle corner = startv + genCtx.q * ii + genCtx.q * jj * genCtx.ystride + genCtx.q * kk * genCtx.zstride;

    324:         std::pair<PetscInt, PetscInt> entoffset = DMMoab_SetElementConnectivity_Private(genCtx, ix, corner, conn);

    326:         for (PetscInt j = 0; j < entoffset.second; j++) {
    327:           /* The entity handle for the particular element -> if we want to set some tags is
    328:              moab::EntityHandle eh = starte + ie + j;
    329:           */
    330:           gids[ie + j] = 1 + ((xe + ii) + (ye + jj) * genCtx.nex + (ze + kk) * (genCtx.nex * genCtx.ney));
    331:           /* gids[ie+j] = ie + j + ((xe + ii) + (ye + jj) * genCtx.nex + (ze + kk) * (genCtx.nex * genCtx.ney)); */
    332:           /* gids[ie+j] = 1 + ie; */
    333:           /* ie++; */
    334:         }

    336:         ix += entoffset.first;
    337:         ie += entoffset.second;
    338:       }
    339:     }
    340:   }
    341:   if (genCtx.adjEnts) { /* we need to update adjacencies now, because some elements are new */
    342:     merr = iface->update_adjacencies(starte, nelems, nvperelem, conn);MBERR("Can't update adjacencies", merr);
    343:   }
    344:   tmp.swap(cells);
    345:   merr = mbImpl->tag_set_data(global_id_tag, cells, &gids[0]);MBERR("Can't set global ids to elements.", merr);
    346:   return(0);
    347: }

    349: PetscErrorCode DMMBUtil_InitializeOptions(DMMoabMeshGeneratorCtx& genCtx, PetscInt dim, PetscBool simplex, PetscInt rank, PetscInt nprocs, const PetscReal* bounds, PetscInt nelems)
    350: {
    352:   /* Initialize all genCtx data */
    353:   genCtx.dim = dim;
    354:   genCtx.simplex = simplex;
    355:   genCtx.newMergeMethod = genCtx.keep_skins = genCtx.adjEnts = true;
    356:   /* determine other global quantities for the mesh used for nodes increments */
    357:   genCtx.q = 1;
    358:   genCtx.fraction = genCtx.remainder = genCtx.cumfraction = 0;

    360:   if (!genCtx.usrxyzgrid) { /* not overridden by genCtx - assume nele equally and that genCtx wants a uniform cube mesh */

    362:     genCtx.fraction = nelems / nprocs; /* partition only by the largest dimension */
    363:     genCtx.remainder = nelems % nprocs; /* remainder after partition which gets evenly distributed by round-robin */
    364:     genCtx.cumfraction = (rank > 0 ? (genCtx.fraction) * (rank) + (rank - 1 < genCtx.remainder ? rank : genCtx.remainder) : 0);
    365:     if (rank < genCtx.remainder)    /* This process gets "fraction+1" elements */
    366:       genCtx.fraction++;

    368:     PetscInfo3(NULL, "Fraction = %D, Remainder = %D, Cumulative fraction = %D\n", genCtx.fraction, genCtx.remainder, genCtx.cumfraction);
    369:     switch (genCtx.dim) {
    370:     case 1:
    371:       genCtx.blockSizeElementXYZ[0] = genCtx.fraction;
    372:       genCtx.blockSizeElementXYZ[1] = 1;
    373:       genCtx.blockSizeElementXYZ[2] = 1;
    374:       break;
    375:     case 2:
    376:       genCtx.blockSizeElementXYZ[0] = nelems;
    377:       genCtx.blockSizeElementXYZ[1] = genCtx.fraction;
    378:       genCtx.blockSizeElementXYZ[2] = 1;
    379:       break;
    380:     case 3:
    381:     default:
    382:       genCtx.blockSizeElementXYZ[0] = nelems;
    383:       genCtx.blockSizeElementXYZ[1] = nelems;
    384:       genCtx.blockSizeElementXYZ[2] = genCtx.fraction;
    385:       break;
    386:     }
    387:   }

    389:   /* partition only by the largest dimension */
    390:   /* Total number of local elements := genCtx.blockSizeElementXYZ[0]*(genCtx.dim>1? genCtx.blockSizeElementXYZ[1]*(genCtx.dim>2 ? genCtx.blockSizeElementXYZ[2]:1) :1); */
    391:   if (bounds) {
    392:     for (PetscInt i = 0; i < 6; i++)
    393:       genCtx.xyzbounds[i] = bounds[i];
    394:   }
    395:   else {
    396:     genCtx.xyzbounds[0] = genCtx.xyzbounds[2] = genCtx.xyzbounds[4] = 0.0;
    397:     genCtx.xyzbounds[1] = genCtx.xyzbounds[3] = genCtx.xyzbounds[5] = 1.0;
    398:   }

    400:   if (!genCtx.usrprocgrid) {
    401:     switch (genCtx.dim) {
    402:     case 1:
    403:       genCtx.M = nprocs;
    404:       genCtx.N = genCtx.K = 1;
    405:       break;
    406:     case 2:
    407:       genCtx.N = nprocs;
    408:       genCtx.M = genCtx.K = 1;
    409:       break;
    410:     default:
    411:       genCtx.K = nprocs;
    412:       genCtx.M = genCtx.N = 1;
    413:       break;
    414:     }
    415:   }

    417:   if (!genCtx.usrrefgrid) {
    418:     genCtx.A = genCtx.B = genCtx.C = 1;
    419:   }

    421:   /* more default values */
    422:   genCtx.nex = genCtx.ney = genCtx.nez = 0;
    423:   genCtx.xstride = genCtx.ystride = genCtx.zstride = 0;
    424:   genCtx.NX = genCtx.NY = genCtx.NZ = 0;
    425:   genCtx.nex = genCtx.ney = genCtx.nez = 0;
    426:   genCtx.blockSizeVertexXYZ[0] = genCtx.blockSizeVertexXYZ[1] = genCtx.blockSizeVertexXYZ[2] = 1;

    428:   switch (genCtx.dim) {
    429:   case 3:
    430:     genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;
    431:     genCtx.blockSizeVertexXYZ[1] = genCtx.q * genCtx.blockSizeElementXYZ[1] + 1;
    432:     genCtx.blockSizeVertexXYZ[2] = genCtx.q * genCtx.blockSizeElementXYZ[2] + 1;

    434:     genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0];   /* number of elements in x direction, used for global id on element */
    435:     genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (nelems * genCtx.q); /* distance between 2 nodes in x direction */
    436:     genCtx.NX = (genCtx.q * genCtx.nex + 1);
    437:     genCtx.xstride = 1;
    438:     genCtx.ney = genCtx.N * genCtx.B * genCtx.blockSizeElementXYZ[1];  /* number of elements in y direction  .... */
    439:     genCtx.dy = (genCtx.xyzbounds[3] - genCtx.xyzbounds[2]) / (nelems * genCtx.q); /* distance between 2 nodes in y direction */
    440:     genCtx.NY = (genCtx.q * genCtx.ney + 1);
    441:     genCtx.ystride = genCtx.blockSizeVertexXYZ[0];
    442:     genCtx.nez = genCtx.K * genCtx.C * genCtx.blockSizeElementXYZ[2];  /* number of elements in z direction  .... */
    443:     genCtx.dz = (genCtx.xyzbounds[5] - genCtx.xyzbounds[4]) / (nelems * genCtx.q); /* distance between 2 nodes in z direction */
    444:     genCtx.NZ = (genCtx.q * genCtx.nez + 1);
    445:     genCtx.zstride = genCtx.blockSizeVertexXYZ[0] * genCtx.blockSizeVertexXYZ[1];
    446:     break;
    447:   case 2:
    448:     genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;
    449:     genCtx.blockSizeVertexXYZ[1] = genCtx.q * genCtx.blockSizeElementXYZ[1] + 1;
    450:     genCtx.blockSizeVertexXYZ[2] = 0;

    452:     genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0];   /* number of elements in x direction, used for global id on element */
    453:     genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (genCtx.nex * genCtx.q); /* distance between 2 nodes in x direction */
    454:     genCtx.NX = (genCtx.q * genCtx.nex + 1);
    455:     genCtx.xstride = 1;
    456:     genCtx.ney = genCtx.N * genCtx.B * genCtx.blockSizeElementXYZ[1];  /* number of elements in y direction  .... */
    457:     genCtx.dy = (genCtx.xyzbounds[3] - genCtx.xyzbounds[2]) / (nelems * genCtx.q); /* distance between 2 nodes in y direction */
    458:     genCtx.NY = (genCtx.q * genCtx.ney + 1);
    459:     genCtx.ystride = genCtx.blockSizeVertexXYZ[0];
    460:     break;
    461:   case 1:
    462:     genCtx.blockSizeVertexXYZ[1] = genCtx.blockSizeVertexXYZ[2] = 0;
    463:     genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;

    465:     genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0];   /* number of elements in x direction, used for global id on element */
    466:     genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (nelems * genCtx.q); /* distance between 2 nodes in x direction */
    467:     genCtx.NX = (genCtx.q * genCtx.nex + 1);
    468:     genCtx.xstride = 1;
    469:     break;
    470:   }

    472:   /* Lets check for some valid input */
    473:   if (genCtx.dim < 1 || genCtx.dim > 3) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid topological dimension specified: %d.\n", genCtx.dim);
    474:   if (genCtx.M * genCtx.N * genCtx.K != nprocs) SETERRQ4(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid [m, n, k] data: %d, %d, %d. Product must be equal to global size = %d.\n", genCtx.M, genCtx.N, genCtx.K, nprocs);
    475:   /* validate the bounds data */
    476:   if (genCtx.xyzbounds[0] >= genCtx.xyzbounds[1]) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "X-dim: Left boundary cannot be greater than right. [%G >= %G]\n", genCtx.xyzbounds[0], genCtx.xyzbounds[1]);
    477:   if (genCtx.dim > 1 && (genCtx.xyzbounds[2] >= genCtx.xyzbounds[3])) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Y-dim: Left boundary cannot be greater than right. [%G >= %G]\n", genCtx.xyzbounds[2], genCtx.xyzbounds[3]);
    478:   if (genCtx.dim > 2 && (genCtx.xyzbounds[4] >= genCtx.xyzbounds[5])) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Z-dim: Left boundary cannot be greater than right. [%G >= %G]\n", genCtx.xyzbounds[4], genCtx.xyzbounds[5]);

    480:   PetscInfo3(NULL, "Local elements:= %d, %d, %d\n", genCtx.blockSizeElementXYZ[0], genCtx.blockSizeElementXYZ[1], genCtx.blockSizeElementXYZ[2]);
    481:   PetscInfo3(NULL, "Local vertices:= %d, %d, %d\n", genCtx.blockSizeVertexXYZ[0], genCtx.blockSizeVertexXYZ[1], genCtx.blockSizeVertexXYZ[2]);
    482:   PetscInfo3(NULL, "Local blocks/processors := %d, %d, %d\n", genCtx.A, genCtx.B, genCtx.C);
    483:   PetscInfo3(NULL, "Local processors := %d, %d, %d\n", genCtx.M, genCtx.N, genCtx.K);
    484:   PetscInfo3(NULL, "Local nexyz:= %d, %d, %d\n", genCtx.nex, genCtx.ney, genCtx.nez);
    485:   PetscInfo3(NULL, "Local delxyz:= %g, %g, %g\n", genCtx.dx, genCtx.dy, genCtx.dz);
    486:   PetscInfo3(NULL, "Local strides:= %d, %d, %d\n", genCtx.xstride, genCtx.ystride, genCtx.zstride);
    487:   return(0);
    488: }

    490: /*@C
    491:   DMMoabCreateBoxMesh - Creates a mesh on the tensor product (box) of intervals with genCtx specified bounds.

    493:   Collective

    495:   Input Parameters:
    496: + comm - The communicator for the DM object
    497: . dim - The spatial dimension
    498: . bounds - The bounds of the box specified with [x-left, x-right, y-bottom, y-top, z-bottom, z-top] depending on the spatial dimension
    499: . nele - The number of discrete elements in each direction
    500: - user_nghost - The number of ghosted layers needed in the partitioned mesh

    502:   Output Parameter:
    503: . dm  - The DM object

    505:   Level: beginner

    507: .seealso: DMSetType(), DMCreate(), DMMoabLoadFromFile()
    508: @*/
    509: PetscErrorCode DMMoabCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool useSimplex, const PetscReal* bounds, PetscInt nele, PetscInt nghost, DM *dm)
    510: {
    511:   PetscErrorCode         ierr;
    512:   moab::ErrorCode        merr;
    513:   PetscInt               a, b, c, n, global_size, global_rank;
    514:   DM_Moab               *dmmoab;
    515:   moab::Interface       *mbImpl;
    516: #ifdef MOAB_HAVE_MPI
    517:   moab::ParallelComm    *pcomm;
    518: #endif
    519:   moab::ReadUtilIface   *readMeshIface;
    520:   moab::Range            verts, cells, edges, faces, adj, dim3, dim2;
    521:   DMMoabMeshGeneratorCtx genCtx;
    522:   const PetscInt         npts = nele + 1;    /* Number of points in every dimension */

    524:   moab::Tag              global_id_tag, part_tag, geom_tag, mat_tag, dir_tag, neu_tag;
    525:   moab::Range            ownedvtx, ownedelms, localvtxs, localelms;
    526:   moab::EntityHandle     regionset;
    527:   PetscInt               ml = 0, nl = 0, kl = 0;

    530:   if (dim < 1 || dim > 3) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension argument for mesh: dim=[1,3].\n");

    532:   PetscLogEventRegister("GenerateMesh", DM_CLASSID,   &genCtx.generateMesh);
    533:   PetscLogEventRegister("AddVertices", DM_CLASSID,   &genCtx.generateVertices);
    534:   PetscLogEventRegister("AddElements", DM_CLASSID,   &genCtx.generateElements);
    535:   PetscLogEventRegister("ParResolve", DM_CLASSID,   &genCtx.parResolve);
    536:   PetscLogEventBegin(genCtx.generateMesh, 0, 0, 0, 0);
    537:   MPI_Comm_size(comm, &global_size);
    538:   /* total number of vertices in all dimensions */
    539:   n = pow(npts, dim);

    541:   /* do some error checking */
    542:   if (n < 2) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of points must be >= 2.\n");
    543:   if (global_size > n) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of processors must be less than or equal to number of elements.\n");
    544:   if (nghost < 0) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of ghost layers cannot be negative.\n");

    546:   /* Create the basic DMMoab object and keep the default parameters created by DM impls */
    547:   DMMoabCreateMoab(comm, NULL, NULL, NULL, dm);

    549:   /* get all the necessary handles from the private DM object */
    550:   dmmoab = (DM_Moab*)(*dm)->data;
    551:   mbImpl = dmmoab->mbiface;
    552: #ifdef MOAB_HAVE_MPI
    553:   pcomm = dmmoab->pcomm;
    554:   global_rank = pcomm->rank();
    555: #else
    556:   global_rank = 0;
    557:   global_size = 1;
    558: #endif
    559:   global_id_tag = dmmoab->ltog_tag;
    560:   dmmoab->dim = dim;
    561:   dmmoab->nghostrings = nghost;
    562:   dmmoab->refct = 1;

    564:   /* create a file set to associate all entities in current mesh */
    565:   merr = mbImpl->create_meshset(moab::MESHSET_SET, dmmoab->fileset);MBERR("Creating file set failed", merr);

    567:   /* No errors yet; proceed with building the mesh */
    568:   merr = mbImpl->query_interface(readMeshIface);MBERRNM(merr);

    570:   genCtx.M = genCtx.N = genCtx.K = 1;
    571:   genCtx.A = genCtx.B = genCtx.C = 1;
    572:   genCtx.blockSizeElementXYZ[0] = 0;
    573:   genCtx.blockSizeElementXYZ[1] = 0;
    574:   genCtx.blockSizeElementXYZ[2] = 0;

    576:   PetscOptionsBegin(comm, "", "DMMoab Creation Options", "DMMOAB");
    577:   /* Handle DMMoab spatial resolution */
    578:   PetscOptionsInt("-dmb_grid_x", "Number of grid points in x direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[0], &genCtx.blockSizeElementXYZ[0], &genCtx.usrxyzgrid);
    579:   if (dim > 1) {PetscOptionsInt("-dmb_grid_y", "Number of grid points in y direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[1], &genCtx.blockSizeElementXYZ[1], &genCtx.usrxyzgrid);}
    580:   if (dim > 2) {PetscOptionsInt("-dmb_grid_z", "Number of grid points in z direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[2], &genCtx.blockSizeElementXYZ[2], &genCtx.usrxyzgrid);}

    582:   /* Handle DMMoab parallel distibution */
    583:   PetscOptionsInt("-dmb_processors_x", "Number of processors in x direction", "DMMoabSetNumProcs", genCtx.M, &genCtx.M, &genCtx.usrprocgrid);
    584:   if (dim > 1) {PetscOptionsInt("-dmb_processors_y", "Number of processors in y direction", "DMMoabSetNumProcs", genCtx.N, &genCtx.N, &genCtx.usrprocgrid);}
    585:   if (dim > 2) {PetscOptionsInt("-dmb_processors_z", "Number of processors in z direction", "DMMoabSetNumProcs", genCtx.K, &genCtx.K, &genCtx.usrprocgrid);}

    587:   /* Handle DMMoab block refinement */
    588:   PetscOptionsInt("-dmb_refine_x", "Number of refinement blocks in x direction", "DMMoabSetRefinement", genCtx.A, &genCtx.A, &genCtx.usrrefgrid);
    589:   if (dim > 1) {PetscOptionsInt("-dmb_refine_y", "Number of refinement blocks in y direction", "DMMoabSetRefinement", genCtx.B, &genCtx.B, &genCtx.usrrefgrid);}
    590:   if (dim > 2) {PetscOptionsInt("-dmb_refine_z", "Number of refinement blocks in z direction", "DMMoabSetRefinement", genCtx.C, &genCtx.C, &genCtx.usrrefgrid);}
    591:   PetscOptionsEnd();

    593:   DMMBUtil_InitializeOptions(genCtx, dim, useSimplex, global_rank, global_size, bounds, nele);

    595:   //if (nele<nprocs) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The dimensional discretization size should be greater or equal to number of processors: %D < %D",nele,nprocs);

    597:   if (genCtx.adjEnts) genCtx.keep_skins = true; /* do not delete anything - consumes more memory */

    599:   /* determine m, n, k for processor rank */
    600:   ml = nl = kl = 0;
    601:   switch (genCtx.dim) {
    602:   case 1:
    603:     ml = (genCtx.cumfraction);
    604:     break;
    605:   case 2:
    606:     nl = (genCtx.cumfraction);
    607:     break;
    608:   default:
    609:     kl = (genCtx.cumfraction) / genCtx.q / genCtx.blockSizeElementXYZ[2] / genCtx.C; //genCtx.K
    610:     break;
    611:   }

    613:   /*
    614:    * so there are a total of M * A * blockSizeElement elements in x direction (so M * A * blockSizeElement + 1 verts in x direction)
    615:    * so there are a total of N * B * blockSizeElement elements in y direction (so N * B * blockSizeElement + 1 verts in y direction)
    616:    * so there are a total of K * C * blockSizeElement elements in z direction (so K * C * blockSizeElement + 1 verts in z direction)

    618:    * there are ( M * A blockSizeElement)      *  ( N * B * blockSizeElement)      * (K * C * blockSizeElement)    hexas
    619:    * there are ( M * A * blockSizeElement + 1) *  ( N * B * blockSizeElement + 1) * (K * C * blockSizeElement + 1) vertices
    620:    * x is the first dimension that varies
    621:    */

    623:   /* generate the block at (a, b, c); it will represent a partition , it will get a partition tag */
    624:   PetscInt dum_id = -1;
    625:   merr = mbImpl->tag_get_handle("GLOBAL_ID", 1, moab::MB_TYPE_INTEGER, global_id_tag);MBERR("Getting Global_ID Tag handle failed", merr);

    627:   merr = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, mat_tag);MBERR("Getting Material set Tag handle failed", merr);
    628:   merr = mbImpl->tag_get_handle(DIRICHLET_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, dir_tag);MBERR("Getting Dirichlet set Tag handle failed", merr);
    629:   merr = mbImpl->tag_get_handle(NEUMANN_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, neu_tag);MBERR("Getting Neumann set Tag handle failed", merr);

    631:   merr = mbImpl->tag_get_handle("PARALLEL_PARTITION", 1, moab::MB_TYPE_INTEGER, part_tag, moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE, &dum_id);MBERR("Getting Partition Tag handle failed", merr);

    633:   /* lets create some sets */
    634:   merr = mbImpl->tag_get_handle(GEOM_DIMENSION_TAG_NAME, 1, moab::MB_TYPE_INTEGER, geom_tag, moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE, &dum_id);MBERRNM(merr);
    635:   merr = mbImpl->create_meshset(moab::MESHSET_SET, regionset);MBERRNM(merr);
    636:   PetscLogEventEnd(genCtx.generateMesh, 0, 0, 0, 0);

    638:   for (a = 0; a < (genCtx.dim > 0 ? genCtx.A : genCtx.A); a++) {
    639:     for (b = 0; b < (genCtx.dim > 1 ? genCtx.B : 1); b++) {
    640:       for (c = 0; c < (genCtx.dim > 2 ? genCtx.C : 1); c++) {

    642:         moab::EntityHandle startv;

    644:         PetscLogEventBegin(genCtx.generateVertices, 0, 0, 0, 0);
    645:         DMMoab_GenerateVertices_Private(mbImpl, readMeshIface, genCtx, ml, nl, kl, a, b, c, global_id_tag, startv, verts);
    646:         PetscLogEventEnd(genCtx.generateVertices, 0, 0, 0, 0);

    648:         PetscLogEventBegin(genCtx.generateElements, 0, 0, 0, 0);
    649:         DMMoab_GenerateElements_Private(mbImpl, readMeshIface, genCtx, ml, nl, kl, a, b, c, global_id_tag, startv, cells);
    650:         PetscLogEventEnd(genCtx.generateElements, 0, 0, 0, 0);

    652:         PetscInt part_num = 0;
    653:         switch (genCtx.dim) {
    654:         case 3:
    655:           part_num += (c + kl * genCtx.C) * (genCtx.M * genCtx.A * genCtx.N * genCtx.B);
    656:         case 2:
    657:           part_num += (b + nl * genCtx.B) * (genCtx.M * genCtx.A);
    658:         case 1:
    659:           part_num += (a + ml * genCtx.A);
    660:           break;
    661:         }

    663:         moab::EntityHandle part_set;
    664:         merr = mbImpl->create_meshset(moab::MESHSET_SET, part_set);MBERR("Can't create mesh set.", merr);

    666:         merr = mbImpl->add_entities(part_set, verts);MBERR("Can't add vertices to set.", merr);
    667:         merr = mbImpl->add_entities(part_set, cells);MBERR("Can't add entities to set.", merr);
    668:         merr = mbImpl->add_entities(regionset, cells);MBERR("Can't add entities to set.", merr);

    670:         /* if needed, add all edges and faces */
    671:         if (genCtx.adjEnts)
    672:         {
    673:           if (genCtx.dim > 1) {
    674:             merr = mbImpl->get_adjacencies(cells, 1, true, edges, moab::Interface::UNION);MBERR("Can't get edges", merr);
    675:             merr = mbImpl->add_entities(part_set, edges);MBERR("Can't add edges to partition set.", merr);
    676:           }
    677:           if (genCtx.dim > 2) {
    678:             merr = mbImpl->get_adjacencies(cells, 2, true, faces, moab::Interface::UNION);MBERR("Can't get faces", merr);
    679:             merr = mbImpl->add_entities(part_set, faces);MBERR("Can't add faces to partition set.", merr);
    680:           }
    681:           edges.clear();
    682:           faces.clear();
    683:         }
    684:         verts.clear(); cells.clear();

    686:         merr = mbImpl->tag_set_data(part_tag, &part_set, 1, &part_num);MBERR("Can't set part tag on set", merr);
    687:         if (dmmoab->fileset) {
    688:           merr = mbImpl->add_parent_child(dmmoab->fileset, part_set);MBERR("Can't add part set to file set.", merr);
    689:           merr = mbImpl->unite_meshset(dmmoab->fileset, part_set);MBERRNM(merr);
    690:         }
    691:         merr = mbImpl->add_entities(dmmoab->fileset, &part_set, 1);MBERRNM(merr);
    692:       }
    693:     }
    694:   }

    696:   merr = mbImpl->add_parent_child(dmmoab->fileset, regionset);MBERRNM(merr);

    698:   /* Only in parallel: resolve shared entities between processors and exchange ghost layers */
    699:   if (global_size > 1) {

    701:     PetscLogEventBegin(genCtx.parResolve, 0, 0, 0, 0);

    703:     merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, genCtx.dim, cells);MBERR("Can't get all d-dimensional elements.", merr);
    704:     merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 0, verts);MBERR("Can't get all vertices.", merr);

    706:     if (genCtx.A * genCtx.B * genCtx.C != 1) { //  merge needed
    707:       moab::MergeMesh mm(mbImpl);
    708:       if (genCtx.newMergeMethod) {
    709:         merr = mm.merge_using_integer_tag(verts, global_id_tag);MBERR("Can't merge with GLOBAL_ID tag", merr);
    710:       }
    711:       else {
    712:         merr = mm.merge_entities(cells, 0.0001);MBERR("Can't merge with coordinates", merr);
    713:       }
    714:     }

    716: #ifdef MOAB_HAVE_MPI
    717:     /* check the handles */
    718:     merr = pcomm->check_all_shared_handles();MBERRV(mbImpl, merr);

    720:     /* resolve the shared entities by exchanging information to adjacent processors */
    721:     merr = pcomm->resolve_shared_ents(dmmoab->fileset, cells, dim, dim - 1, NULL, &global_id_tag);MBERRV(mbImpl, merr);
    722:     if (dmmoab->fileset) {
    723:       merr = pcomm->exchange_ghost_cells(dim, 0, nghost, dim, true, false, &dmmoab->fileset);MBERRV(mbImpl, merr);
    724:     }
    725:     else {
    726:       merr = pcomm->exchange_ghost_cells(dim, 0, nghost, dim, true, false);MBERRV(mbImpl, merr);
    727:     }

    729:     /* Reassign global IDs on all entities. */
    730:     merr = pcomm->assign_global_ids(dmmoab->fileset, dim, 1, false, true, false);MBERRNM(merr);
    731: #endif

    733:     PetscLogEventEnd(genCtx.parResolve, 0, 0, 0, 0);
    734:   }

    736:   if (!genCtx.keep_skins) { // default is to delete the 1- and 2-dimensional entities
    737:     // delete all quads and edges
    738:     moab::Range toDelete;
    739:     if (genCtx.dim > 1) {
    740:       merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 1, toDelete);MBERR("Can't get edges", merr);
    741:     }

    743:     if (genCtx.dim > 2) {
    744:       merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 2, toDelete);MBERR("Can't get faces", merr);
    745:     }

    747: #ifdef MOAB_HAVE_MPI
    748:     merr = dmmoab->pcomm->delete_entities(toDelete) ;MBERR("Can't delete entities", merr);
    749: #endif
    750:   }

    752:   /* set geometric dimension tag for regions */
    753:   merr = mbImpl->tag_set_data(geom_tag, &regionset, 1, &dmmoab->dim);MBERRNM(merr);
    754:   /* set default material ID for regions */
    755:   int default_material = 1;
    756:   merr = mbImpl->tag_set_data(mat_tag, &regionset, 1, &default_material);MBERRNM(merr);
    757:   /*
    758:     int default_dbc = 0;
    759:     merr = mbImpl->tag_set_data(dir_tag, &vertexset, 1, &default_dbc);MBERRNM(merr);
    760:   */
    761:   return(0);
    762: }

    765: PetscErrorCode DMMoab_GetReadOptions_Private(PetscBool by_rank, PetscInt numproc, PetscInt dim, PetscInt nghost, MoabReadMode mode, PetscInt dbglevel, const char* dm_opts, const char* extra_opts, const char** read_opts)
    766: {
    767:   char           *ropts;
    768:   char           ropts_par[PETSC_MAX_PATH_LEN], ropts_pargh[PETSC_MAX_PATH_LEN];
    769:   char           ropts_dbg[PETSC_MAX_PATH_LEN];

    773:   PetscMalloc1(PETSC_MAX_PATH_LEN, &ropts);
    774:   PetscMemzero(&ropts_par, PETSC_MAX_PATH_LEN);
    775:   PetscMemzero(&ropts_pargh, PETSC_MAX_PATH_LEN);
    776:   PetscMemzero(&ropts_dbg, PETSC_MAX_PATH_LEN);

    778:   /* do parallel read unless using only one processor */
    779:   if (numproc > 1) {
    780:     // PetscSNPrintf(ropts_par, PETSC_MAX_PATH_LEN, "PARALLEL=%s;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=%d.0.1%s;",MoabReadModes[mode],dim,(by_rank ? ";PARTITION_BY_RANK":""));
    781:     PetscSNPrintf(ropts_par, PETSC_MAX_PATH_LEN, "PARALLEL=%s;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;%s", MoabReadModes[mode], (by_rank ? "PARTITION_BY_RANK;" : ""));
    782:     if (nghost) {
    783:       PetscSNPrintf(ropts_pargh, PETSC_MAX_PATH_LEN, "PARALLEL_GHOSTS=%d.0.%d;", dim, nghost);
    784:     }
    785:   }

    787:   if (dbglevel) {
    788:     if (numproc > 1) {
    789:       PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "CPUTIME;DEBUG_IO=%d;DEBUG_PIO=%d;", dbglevel, dbglevel);
    790:     }
    791:     else {
    792:       PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "CPUTIME;DEBUG_IO=%d;", dbglevel);
    793:     }
    794:   }

    796:   PetscSNPrintf(ropts, PETSC_MAX_PATH_LEN, "%s%s%s%s%s", ropts_par, (nghost ? ropts_pargh : ""), ropts_dbg, (extra_opts ? extra_opts : ""), (dm_opts ? dm_opts : ""));
    797:   *read_opts = ropts;
    798:   return(0);
    799: }

    802: /*@C
    803:   DMMoabLoadFromFile - Creates a DM object by loading the mesh from a user specified file.

    805:   Collective

    807:   Input Parameters:
    808: + comm - The communicator for the DM object
    809: . dim - The spatial dimension
    810: . filename - The name of the mesh file to be loaded
    811: - usrreadopts - The options string to read a MOAB mesh.

    813:   Reference (Parallel Mesh Initialization: https://www.mcs.anl.gov/~fathom/moab-docs/html/contents.html#fivetwo)

    815:   Output Parameter:
    816: . dm  - The DM object

    818:   Level: beginner

    820: .seealso: DMSetType(), DMCreate(), DMMoabCreateBoxMesh()
    821: @*/
    822: PetscErrorCode DMMoabLoadFromFile(MPI_Comm comm, PetscInt dim, PetscInt nghost, const char* filename, const char* usrreadopts, DM *dm)
    823: {
    824:   moab::ErrorCode     merr;
    825:   PetscInt            nprocs;
    826:   DM_Moab            *dmmoab;
    827:   moab::Interface    *mbiface;
    828: #ifdef MOAB_HAVE_MPI
    829:   moab::ParallelComm *pcomm;
    830: #endif
    831:   moab::Range         verts, elems;
    832:   const char         *readopts;
    833:   PetscErrorCode      ierr;

    838:   /* Create the basic DMMoab object and keep the default parameters created by DM impls */
    839:   DMMoabCreateMoab(comm, NULL, NULL, NULL, dm);

    841:   /* get all the necessary handles from the private DM object */
    842:   dmmoab = (DM_Moab*)(*dm)->data;
    843:   mbiface = dmmoab->mbiface;
    844: #ifdef MOAB_HAVE_MPI
    845:   pcomm = dmmoab->pcomm;
    846:   nprocs = pcomm->size();
    847: #else
    848:   nprocs = 1;
    849: #endif
    850:   /* TODO: Decipher dimension based on the loaded mesh instead of getting from user */
    851:   dmmoab->dim = dim;
    852:   dmmoab->nghostrings = nghost;
    853:   dmmoab->refct = 1;

    855:   /* create a file set to associate all entities in current mesh */
    856:   merr = dmmoab->mbiface->create_meshset(moab::MESHSET_SET, dmmoab->fileset);MBERR("Creating file set failed", merr);

    858:   /* add mesh loading options specific to the DM */
    859:   DMMoab_GetReadOptions_Private(dmmoab->partition_by_rank, nprocs, dim, nghost, dmmoab->read_mode,
    860:                                        dmmoab->rw_dbglevel, dmmoab->extra_read_options, usrreadopts, &readopts);

    862:   PetscInfo2(*dm, "Reading file %s with options: %s\n", filename, readopts);

    864:   /* Load the mesh from a file. */
    865:   if (dmmoab->fileset) {
    866:     merr = mbiface->load_file(filename, &dmmoab->fileset, readopts);MBERRVM(mbiface, "Reading MOAB file failed.", merr);
    867:   }
    868:   else {
    869:     merr = mbiface->load_file(filename, 0, readopts);MBERRVM(mbiface, "Reading MOAB file failed.", merr);
    870:   }

    872: #ifdef MOAB_HAVE_MPI
    873:   /* Reassign global IDs on all entities. */
    874:   /* merr = pcomm->assign_global_ids(dmmoab->fileset, dim, 1, true, true, true);MBERRNM(merr); */
    875: #endif

    877:   /* load the local vertices */
    878:   merr = mbiface->get_entities_by_type(dmmoab->fileset, moab::MBVERTEX, verts, true);MBERRNM(merr);
    879:   /* load the local elements */
    880:   merr = mbiface->get_entities_by_dimension(dmmoab->fileset, dim, elems, true);MBERRNM(merr);

    882: #ifdef MOAB_HAVE_MPI
    883:   /* Everything is set up, now just do a tag exchange to update tags
    884:      on all of the ghost vertexes */
    885:   merr = pcomm->exchange_tags(dmmoab->ltog_tag, verts);MBERRV(mbiface, merr);
    886:   merr = pcomm->exchange_tags(dmmoab->ltog_tag, elems);MBERRV(mbiface, merr);
    887:   merr = pcomm->collective_sync_partition();MBERR("Collective sync failed", merr);
    888: #endif

    890:   PetscInfo3(*dm, "MOAB file '%s' was successfully loaded. Found %D vertices and %D elements.\n", filename, verts.size(), elems.size());
    891:   PetscFree(readopts);
    892:   return(0);
    893: }

    896: /*@C
    897:   DMMoabRenumberMeshEntities - Order and number all entities (vertices->elements) to be contiguously ordered
    898:   in parallel

    900:   Collective

    902:   Input Parameters:
    903: . dm  - The DM object

    905:   Level: advanced

    907: .seealso: DMSetUp(), DMCreate()
    908: @*/
    909: PetscErrorCode DMMoabRenumberMeshEntities(DM dm)
    910: {
    911:   moab::Range         verts;

    916: #ifdef MOAB_HAVE_MPI
    917:   /* Insert new points */
    918:   moab::ErrorCode     merr;
    919:   merr = ((DM_Moab*) dm->data)->pcomm->assign_global_ids(((DM_Moab*) dm->data)->fileset, 3, 0, false, true, false);MBERRNM(merr);
    920: #endif
    921:   return(0);
    922: }