Actual source code: plexcreate.c
petsc-3.7.1 2016-05-15
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      1: #define PETSCDM_DLL
      2: #include <petsc/private/dmpleximpl.h>    /*I   "petscdmplex.h"   I*/
      3: #include <petscdmda.h>
      4: #include <petscsf.h>

      8: /*@
      9:   DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement.

     11:   Collective on MPI_Comm

     13:   Input Parameters:
     14: + comm - The communicator for the DM object
     15: . dim - The spatial dimension
     16: . simplex - Flag for simplicial cells, otherwise they are tensor product cells
     17: . interpolate - Flag to create intermediate mesh pieces (edges, faces)
     18: . refinementUniform - Flag for uniform parallel refinement
     19: - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell

     21:   Output Parameter:
     22: . dm  - The DM object

     24:   Level: beginner

     26: .keywords: DM, create
     27: .seealso: DMSetType(), DMCreate()
     28: @*/
     29: PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm)
     30: {
     31:   DM             dm;
     32:   PetscInt       p;
     33:   PetscMPIInt    rank;

     37:   DMCreate(comm, &dm);
     38:   DMSetType(dm, DMPLEX);
     39:   DMSetDimension(dm, dim);
     40:   MPI_Comm_rank(comm, &rank);
     41:   switch (dim) {
     42:   case 2:
     43:     if (simplex) {PetscObjectSetName((PetscObject) dm, "triangular");}
     44:     else         {PetscObjectSetName((PetscObject) dm, "quadrilateral");}
     45:     break;
     46:   case 3:
     47:     if (simplex) {PetscObjectSetName((PetscObject) dm, "tetrahedral");}
     48:     else         {PetscObjectSetName((PetscObject) dm, "hexahedral");}
     49:     break;
     50:   default:
     51:     SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
     52:   }
     53:   if (rank) {
     54:     PetscInt numPoints[2] = {0, 0};
     55:     DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);
     56:   } else {
     57:     switch (dim) {
     58:     case 2:
     59:       if (simplex) {
     60:         PetscInt    numPoints[2]        = {4, 2};
     61:         PetscInt    coneSize[6]         = {3, 3, 0, 0, 0, 0};
     62:         PetscInt    cones[6]            = {2, 3, 4,  5, 4, 3};
     63:         PetscInt    coneOrientations[6] = {0, 0, 0,  0, 0, 0};
     64:         PetscScalar vertexCoords[8]     = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
     65:         PetscInt    markerPoints[8]     = {2, 1, 3, 1, 4, 1, 5, 1};

     67:         DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
     68:         for (p = 0; p < 4; ++p) {DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);}
     69:       } else {
     70:         PetscInt    numPoints[2]        = {6, 2};
     71:         PetscInt    coneSize[8]         = {4, 4, 0, 0, 0, 0, 0, 0};
     72:         PetscInt    cones[8]            = {2, 3, 4, 5,  3, 6, 7, 4};
     73:         PetscInt    coneOrientations[8] = {0, 0, 0, 0,  0, 0, 0, 0};
     74:         PetscScalar vertexCoords[12]    = {-1.0, -0.5,  0.0, -0.5,  0.0, 0.5,  -1.0, 0.5,  1.0, -0.5,  1.0, 0.5};

     76:         DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
     77:       }
     78:       break;
     79:     case 3:
     80:       if (simplex) {
     81:         PetscInt    numPoints[2]        = {5, 2};
     82:         PetscInt    coneSize[7]         = {4, 4, 0, 0, 0, 0, 0};
     83:         PetscInt    cones[8]            = {4, 3, 5, 2,  5, 3, 4, 6};
     84:         PetscInt    coneOrientations[8] = {0, 0, 0, 0,  0, 0, 0, 0};
     85:         PetscScalar vertexCoords[15]    = {-1.0, 0.0, 0.0,  0.0, -1.0, 0.0,  0.0, 0.0, 1.0,  0.0, 1.0, 0.0,  1.0, 0.0, 0.0};
     86:         PetscInt    markerPoints[10]    = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1};

     88:         DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
     89:         for (p = 0; p < 5; ++p) {DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);}
     90:       } else {
     91:         PetscInt    numPoints[2]         = {12, 2};
     92:         PetscInt    coneSize[14]         = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
     93:         PetscInt    cones[16]            = {2, 3, 4, 5, 6, 7, 8, 9,  5, 4, 10, 11, 7, 12, 13, 8};
     94:         PetscInt    coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0,  0, 0,  0,  0, 0,  0,  0, 0};
     95:         PetscScalar vertexCoords[36]     = {-1.0, -0.5, -0.5,  -1.0,  0.5, -0.5,  0.0,  0.5, -0.5,   0.0, -0.5, -0.5,
     96:                                             -1.0, -0.5,  0.5,   0.0, -0.5,  0.5,  0.0,  0.5,  0.5,  -1.0,  0.5,  0.5,
     97:                                              1.0,  0.5, -0.5,   1.0, -0.5, -0.5,  1.0, -0.5,  0.5,   1.0,  0.5,  0.5};

     99:         DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
    100:       }
    101:       break;
    102:     default:
    103:       SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
    104:     }
    105:   }
    106:   *newdm = dm;
    107:   if (refinementLimit > 0.0) {
    108:     DM rdm;
    109:     const char *name;

    111:     DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);
    112:     DMPlexSetRefinementLimit(*newdm, refinementLimit);
    113:     DMRefine(*newdm, comm, &rdm);
    114:     PetscObjectGetName((PetscObject) *newdm, &name);
    115:     PetscObjectSetName((PetscObject)    rdm,  name);
    116:     DMDestroy(newdm);
    117:     *newdm = rdm;
    118:   }
    119:   if (interpolate) {
    120:     DM idm = NULL;
    121:     const char *name;

    123:     DMPlexInterpolate(*newdm, &idm);
    124:     PetscObjectGetName((PetscObject) *newdm, &name);
    125:     PetscObjectSetName((PetscObject)    idm,  name);
    126:     DMPlexCopyCoordinates(*newdm, idm);
    127:     DMCopyLabels(*newdm, idm);
    128:     DMDestroy(newdm);
    129:     *newdm = idm;
    130:   }
    131:   {
    132:     DM refinedMesh     = NULL;
    133:     DM distributedMesh = NULL;

    135:     /* Distribute mesh over processes */
    136:     DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);
    137:     if (distributedMesh) {
    138:       DMDestroy(newdm);
    139:       *newdm = distributedMesh;
    140:     }
    141:     if (refinementUniform) {
    142:       DMPlexSetRefinementUniform(*newdm, refinementUniform);
    143:       DMRefine(*newdm, comm, &refinedMesh);
    144:       if (refinedMesh) {
    145:         DMDestroy(newdm);
    146:         *newdm = refinedMesh;
    147:       }
    148:     }
    149:   }
    150:   return(0);
    151: }

    155: /*@
    156:   DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice.

    158:   Collective on MPI_Comm

    160:   Input Parameters:
    161: + comm  - The communicator for the DM object
    162: . lower - The lower left corner coordinates
    163: . upper - The upper right corner coordinates
    164: - edges - The number of cells in each direction

    166:   Output Parameter:
    167: . dm  - The DM object

    169:   Note: Here is the numbering returned for 2 cells in each direction:
    170: $ 18--5-17--4--16
    171: $  |     |     |
    172: $  6    10     3
    173: $  |     |     |
    174: $ 19-11-20--9--15
    175: $  |     |     |
    176: $  7     8     2
    177: $  |     |     |
    178: $ 12--0-13--1--14

    180:   Level: beginner

    182: .keywords: DM, create
    183: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate()
    184: @*/
    185: PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
    186: {
    187:   const PetscInt numVertices    = (edges[0]+1)*(edges[1]+1);
    188:   const PetscInt numEdges       = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
    189:   PetscInt       markerTop      = 1;
    190:   PetscInt       markerBottom   = 1;
    191:   PetscInt       markerRight    = 1;
    192:   PetscInt       markerLeft     = 1;
    193:   PetscBool      markerSeparate = PETSC_FALSE;
    194:   Vec            coordinates;
    195:   PetscSection   coordSection;
    196:   PetscScalar    *coords;
    197:   PetscInt       coordSize;
    198:   PetscMPIInt    rank;
    199:   PetscInt       v, vx, vy;

    203:   PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
    204:   if (markerSeparate) {
    205:     markerTop    = 3;
    206:     markerBottom = 1;
    207:     markerRight  = 2;
    208:     markerLeft   = 4;
    209:   }
    210:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
    211:   if (!rank) {
    212:     PetscInt e, ex, ey;

    214:     DMPlexSetChart(dm, 0, numEdges+numVertices);
    215:     for (e = 0; e < numEdges; ++e) {
    216:       DMPlexSetConeSize(dm, e, 2);
    217:     }
    218:     DMSetUp(dm); /* Allocate space for cones */
    219:     for (vx = 0; vx <= edges[0]; vx++) {
    220:       for (ey = 0; ey < edges[1]; ey++) {
    221:         PetscInt edge   = vx*edges[1] + ey + edges[0]*(edges[1]+1);
    222:         PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
    223:         PetscInt cone[2];

    225:         cone[0] = vertex; cone[1] = vertex+edges[0]+1;
    226:         DMPlexSetCone(dm, edge, cone);
    227:         if (vx == edges[0]) {
    228:           DMSetLabelValue(dm, "marker", edge,    markerRight);
    229:           DMSetLabelValue(dm, "marker", cone[0], markerRight);
    230:           if (ey == edges[1]-1) {
    231:             DMSetLabelValue(dm, "marker", cone[1], markerRight);
    232:           }
    233:         } else if (vx == 0) {
    234:           DMSetLabelValue(dm, "marker", edge,    markerLeft);
    235:           DMSetLabelValue(dm, "marker", cone[0], markerLeft);
    236:           if (ey == edges[1]-1) {
    237:             DMSetLabelValue(dm, "marker", cone[1], markerLeft);
    238:           }
    239:         }
    240:       }
    241:     }
    242:     for (vy = 0; vy <= edges[1]; vy++) {
    243:       for (ex = 0; ex < edges[0]; ex++) {
    244:         PetscInt edge   = vy*edges[0]     + ex;
    245:         PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
    246:         PetscInt cone[2];

    248:         cone[0] = vertex; cone[1] = vertex+1;
    249:         DMPlexSetCone(dm, edge, cone);
    250:         if (vy == edges[1]) {
    251:           DMSetLabelValue(dm, "marker", edge,    markerTop);
    252:           DMSetLabelValue(dm, "marker", cone[0], markerTop);
    253:           if (ex == edges[0]-1) {
    254:             DMSetLabelValue(dm, "marker", cone[1], markerTop);
    255:           }
    256:         } else if (vy == 0) {
    257:           DMSetLabelValue(dm, "marker", edge,    markerBottom);
    258:           DMSetLabelValue(dm, "marker", cone[0], markerBottom);
    259:           if (ex == edges[0]-1) {
    260:             DMSetLabelValue(dm, "marker", cone[1], markerBottom);
    261:           }
    262:         }
    263:       }
    264:     }
    265:   }
    266:   DMPlexSymmetrize(dm);
    267:   DMPlexStratify(dm);
    268:   /* Build coordinates */
    269:   DMGetCoordinateSection(dm, &coordSection);
    270:   PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);
    271:   for (v = numEdges; v < numEdges+numVertices; ++v) {
    272:     PetscSectionSetDof(coordSection, v, 2);
    273:   }
    274:   PetscSectionSetUp(coordSection);
    275:   PetscSectionGetStorageSize(coordSection, &coordSize);
    276:   VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
    277:   VecSetBlockSize(coordinates, 2);
    278:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    279:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    280:   VecSetType(coordinates,VECSTANDARD);
    281:   VecGetArray(coordinates, &coords);
    282:   for (vy = 0; vy <= edges[1]; ++vy) {
    283:     for (vx = 0; vx <= edges[0]; ++vx) {
    284:       coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
    285:       coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
    286:     }
    287:   }
    288:   VecRestoreArray(coordinates, &coords);
    289:   DMSetCoordinatesLocal(dm, coordinates);
    290:   VecDestroy(&coordinates);
    291:   return(0);
    292: }

    296: /*@
    297:   DMPlexCreateCubeBoundary - Creates a 2D mesh the is the boundary of a cubic lattice.

    299:   Collective on MPI_Comm

    301:   Input Parameters:
    302: + comm  - The communicator for the DM object
    303: . lower - The lower left front corner coordinates
    304: . upper - The upper right back corner coordinates
    305: - edges - The number of cells in each direction

    307:   Output Parameter:
    308: . dm  - The DM object

    310:   Level: beginner

    312: .keywords: DM, create
    313: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate()
    314: @*/
    315: PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
    316: {
    317:   PetscInt       vertices[3], numVertices;
    318:   PetscInt       numFaces    = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2];
    319:   Vec            coordinates;
    320:   PetscSection   coordSection;
    321:   PetscScalar    *coords;
    322:   PetscInt       coordSize;
    323:   PetscMPIInt    rank;
    324:   PetscInt       v, vx, vy, vz;
    325:   PetscInt       voffset, iface=0, cone[4];

    329:   if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side");
    330:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
    331:   vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1;
    332:   numVertices = vertices[0]*vertices[1]*vertices[2];
    333:   if (!rank) {
    334:     PetscInt f;

    336:     DMPlexSetChart(dm, 0, numFaces+numVertices);
    337:     for (f = 0; f < numFaces; ++f) {
    338:       DMPlexSetConeSize(dm, f, 4);
    339:     }
    340:     DMSetUp(dm); /* Allocate space for cones */
    341:     for (v = 0; v < numFaces+numVertices; ++v) {
    342:       DMSetLabelValue(dm, "marker", v, 1);
    343:     }

    345:     /* Side 0 (Top) */
    346:     for (vy = 0; vy < faces[1]; vy++) {
    347:       for (vx = 0; vx < faces[0]; vx++) {
    348:         voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx;
    349:         cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0];
    350:         DMPlexSetCone(dm, iface, cone);
    351:         iface++;
    352:       }
    353:     }

    355:     /* Side 1 (Bottom) */
    356:     for (vy = 0; vy < faces[1]; vy++) {
    357:       for (vx = 0; vx < faces[0]; vx++) {
    358:         voffset = numFaces + vy*(faces[0]+1) + vx;
    359:         cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1;
    360:         DMPlexSetCone(dm, iface, cone);
    361:         iface++;
    362:       }
    363:     }

    365:     /* Side 2 (Front) */
    366:     for (vz = 0; vz < faces[2]; vz++) {
    367:       for (vx = 0; vx < faces[0]; vx++) {
    368:         voffset = numFaces + vz*vertices[0]*vertices[1] + vx;
    369:         cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1];
    370:         DMPlexSetCone(dm, iface, cone);
    371:         iface++;
    372:       }
    373:     }

    375:     /* Side 3 (Back) */
    376:     for (vz = 0; vz < faces[2]; vz++) {
    377:       for (vx = 0; vx < faces[0]; vx++) {
    378:         voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx;
    379:         cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1;
    380:         cone[2] = voffset+1; cone[3] = voffset;
    381:         DMPlexSetCone(dm, iface, cone);
    382:         iface++;
    383:       }
    384:     }

    386:     /* Side 4 (Left) */
    387:     for (vz = 0; vz < faces[2]; vz++) {
    388:       for (vy = 0; vy < faces[1]; vy++) {
    389:         voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0];
    390:         cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1];
    391:         cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0];
    392:         DMPlexSetCone(dm, iface, cone);
    393:         iface++;
    394:       }
    395:     }

    397:     /* Side 5 (Right) */
    398:     for (vz = 0; vz < faces[2]; vz++) {
    399:       for (vy = 0; vy < faces[1]; vy++) {
    400:         voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + vx;
    401:         cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset;
    402:         cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0];
    403:         DMPlexSetCone(dm, iface, cone);
    404:         iface++;
    405:       }
    406:     }
    407:   }
    408:   DMPlexSymmetrize(dm);
    409:   DMPlexStratify(dm);
    410:   /* Build coordinates */
    411:   DMGetCoordinateSection(dm, &coordSection);
    412:   PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);
    413:   for (v = numFaces; v < numFaces+numVertices; ++v) {
    414:     PetscSectionSetDof(coordSection, v, 3);
    415:   }
    416:   PetscSectionSetUp(coordSection);
    417:   PetscSectionGetStorageSize(coordSection, &coordSize);
    418:   VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
    419:   VecSetBlockSize(coordinates, 3);
    420:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    421:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    422:   VecSetType(coordinates,VECSTANDARD);
    423:   VecGetArray(coordinates, &coords);
    424:   for (vz = 0; vz <= faces[2]; ++vz) {
    425:     for (vy = 0; vy <= faces[1]; ++vy) {
    426:       for (vx = 0; vx <= faces[0]; ++vx) {
    427:         coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
    428:         coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
    429:         coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
    430:       }
    431:     }
    432:   }
    433:   VecRestoreArray(coordinates, &coords);
    434:   DMSetCoordinatesLocal(dm, coordinates);
    435:   VecDestroy(&coordinates);
    436:   return(0);
    437: }

    441: static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ)
    442: {
    443:   PetscInt       markerTop      = 1, faceMarkerTop      = 1;
    444:   PetscInt       markerBottom   = 1, faceMarkerBottom   = 1;
    445:   PetscInt       markerFront    = 1, faceMarkerFront    = 1;
    446:   PetscInt       markerBack     = 1, faceMarkerBack     = 1;
    447:   PetscInt       markerRight    = 1, faceMarkerRight    = 1;
    448:   PetscInt       markerLeft     = 1, faceMarkerLeft     = 1;
    449:   PetscInt       dim;
    450:   PetscBool      markerSeparate = PETSC_FALSE;
    451:   PetscMPIInt    rank;

    455:   DMGetDimension(dm,&dim);
    456:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
    457:   switch (dim) {
    458:   case 2:
    459:     faceMarkerTop    = 3;
    460:     faceMarkerBottom = 1;
    461:     faceMarkerRight  = 2;
    462:     faceMarkerLeft   = 4;
    463:     break;
    464:   case 3:
    465:     faceMarkerBottom = 1;
    466:     faceMarkerTop    = 2;
    467:     faceMarkerFront  = 3;
    468:     faceMarkerBack   = 4;
    469:     faceMarkerRight  = 5;
    470:     faceMarkerLeft   = 6;
    471:     break;
    472:   default:
    473:     SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim);
    474:     break;
    475:   }
    476:   PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
    477:   if (markerSeparate) {
    478:     markerBottom = faceMarkerBottom;
    479:     markerTop    = faceMarkerTop;
    480:     markerFront  = faceMarkerFront;
    481:     markerBack   = faceMarkerBack;
    482:     markerRight  = faceMarkerRight;
    483:     markerLeft   = faceMarkerLeft;
    484:   }
    485:   {
    486:     const PetscInt numXEdges    = !rank ? edges[0]   : 0;
    487:     const PetscInt numYEdges    = !rank ? edges[1]   : 0;
    488:     const PetscInt numZEdges    = !rank ? edges[2]   : 0;
    489:     const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0;
    490:     const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0;
    491:     const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0;
    492:     const PetscInt numCells     = numXEdges*numYEdges*numZEdges;
    493:     const PetscInt numXFaces    = numYEdges*numZEdges;
    494:     const PetscInt numYFaces    = numXEdges*numZEdges;
    495:     const PetscInt numZFaces    = numXEdges*numYEdges;
    496:     const PetscInt numTotXFaces = numXVertices*numXFaces;
    497:     const PetscInt numTotYFaces = numYVertices*numYFaces;
    498:     const PetscInt numTotZFaces = numZVertices*numZFaces;
    499:     const PetscInt numFaces     = numTotXFaces + numTotYFaces + numTotZFaces;
    500:     const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices;
    501:     const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices;
    502:     const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices;
    503:     const PetscInt numVertices  = numXVertices*numYVertices*numZVertices;
    504:     const PetscInt numEdges     = numTotXEdges + numTotYEdges + numTotZEdges;
    505:     const PetscInt firstVertex  = (dim == 2) ? numFaces : numCells;
    506:     const PetscInt firstXFace   = (dim == 2) ? 0 : numCells + numVertices;
    507:     const PetscInt firstYFace   = firstXFace + numTotXFaces;
    508:     const PetscInt firstZFace   = firstYFace + numTotYFaces;
    509:     const PetscInt firstXEdge   = numCells + numFaces + numVertices;
    510:     const PetscInt firstYEdge   = firstXEdge + numTotXEdges;
    511:     const PetscInt firstZEdge   = firstYEdge + numTotYEdges;
    512:     Vec            coordinates;
    513:     PetscSection   coordSection;
    514:     PetscScalar   *coords;
    515:     PetscInt       coordSize;
    516:     PetscInt       v, vx, vy, vz;
    517:     PetscInt       c, f, fx, fy, fz, e, ex, ey, ez;

    519:     DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);
    520:     for (c = 0; c < numCells; c++) {
    521:       DMPlexSetConeSize(dm, c, 6);
    522:     }
    523:     for (f = firstXFace; f < firstXFace+numFaces; ++f) {
    524:       DMPlexSetConeSize(dm, f, 4);
    525:     }
    526:     for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
    527:       DMPlexSetConeSize(dm, e, 2);
    528:     }
    529:     DMSetUp(dm); /* Allocate space for cones */
    530:     /* Build cells */
    531:     for (fz = 0; fz < numZEdges; ++fz) {
    532:       for (fy = 0; fy < numYEdges; ++fy) {
    533:         for (fx = 0; fx < numXEdges; ++fx) {
    534:           PetscInt cell    = (fz*numYEdges + fy)*numXEdges + fx;
    535:           PetscInt faceB   = firstZFace + (fy*numXEdges+fx)*numZVertices +   fz;
    536:           PetscInt faceT   = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices);
    537:           PetscInt faceF   = firstYFace + (fz*numXEdges+fx)*numYVertices +   fy;
    538:           PetscInt faceK   = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices);
    539:           PetscInt faceL   = firstXFace + (fz*numYEdges+fy)*numXVertices +   fx;
    540:           PetscInt faceR   = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices);
    541:                             /* B,  T,  F,  K,  R,  L */
    542:           PetscInt ornt[8] = {-4,  0,  0, -1,  0, -4}; /* ??? */
    543:           PetscInt cone[8];

    545:           /* no boundary twisting in 3D */
    546:           cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL;
    547:           DMPlexSetCone(dm, cell, cone);
    548:           DMPlexSetConeOrientation(dm, cell, ornt);
    549:         }
    550:       }
    551:     }
    552:     /* Build x faces */
    553:     for (fz = 0; fz < numZEdges; ++fz) {
    554:       for (fy = 0; fy < numYEdges; ++fy) {
    555:         for (fx = 0; fx < numXVertices; ++fx) {
    556:           PetscInt face    = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
    557:           PetscInt edgeL   = firstZEdge + (  fy*                 numXVertices+fx)*numZEdges + fz;
    558:           PetscInt edgeR   = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz;
    559:           PetscInt edgeB   = firstYEdge + (  fz*                 numXVertices+fx)*numYEdges + fy;
    560:           PetscInt edgeT   = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy;
    561:           PetscInt ornt[4] = {0, 0, -2, -2};
    562:           PetscInt cone[4];

    564:           if (dim == 3) {
    565:             /* markers */
    566:             if (bdX != DM_BOUNDARY_PERIODIC) {
    567:               if (fx == numXVertices-1) {
    568:                 DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);
    569:                 DMSetLabelValue(dm, "marker", face, markerRight);
    570:               }
    571:               else if (fx == 0) {
    572:                 DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);
    573:                 DMSetLabelValue(dm, "marker", face, markerLeft);
    574:               }
    575:             }
    576:           }
    577:           cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
    578:           DMPlexSetCone(dm, face, cone);
    579:           DMPlexSetConeOrientation(dm, face, ornt);
    580:         }
    581:       }
    582:     }
    583:     /* Build y faces */
    584:     for (fz = 0; fz < numZEdges; ++fz) {
    585:       for (fx = 0; fx < numYEdges; ++fx) {
    586:         for (fy = 0; fy < numYVertices; ++fy) {
    587:           PetscInt face    = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
    588:           PetscInt edgeL   = firstZEdge + (fy*numXVertices+  fx                 )*numZEdges + fz;
    589:           PetscInt edgeR   = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz;
    590:           PetscInt edgeB   = firstXEdge + (  fz                 *numYVertices+fy)*numXEdges + fx;
    591:           PetscInt edgeT   = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx;
    592:           PetscInt ornt[4] = {0, 0, -2, -2};
    593:           PetscInt cone[4];

    595:           if (dim == 3) {
    596:             /* markers */
    597:             if (bdY != DM_BOUNDARY_PERIODIC) {
    598:               if (fy == numYVertices-1) {
    599:                 DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);
    600:                 DMSetLabelValue(dm, "marker", face, markerBack);
    601:               }
    602:               else if (fy == 0) {
    603:                 DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);
    604:                 DMSetLabelValue(dm, "marker", face, markerFront);
    605:               }
    606:             }
    607:           }
    608:           cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
    609:           DMPlexSetCone(dm, face, cone);
    610:           DMPlexSetConeOrientation(dm, face, ornt);
    611:         }
    612:       }
    613:     }
    614:     /* Build z faces */
    615:     for (fy = 0; fy < numYEdges; ++fy) {
    616:       for (fx = 0; fx < numXEdges; ++fx) {
    617:         for (fz = 0; fz < numZVertices; fz++) {
    618:           PetscInt face    = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
    619:           PetscInt edgeL   = firstYEdge + (fz*numXVertices+  fx                 )*numYEdges + fy;
    620:           PetscInt edgeR   = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy;
    621:           PetscInt edgeB   = firstXEdge + (fz*numYVertices+  fy                 )*numXEdges + fx;
    622:           PetscInt edgeT   = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx;
    623:           PetscInt ornt[4] = {0, 0, -2, -2};
    624:           PetscInt cone[4];

    626:           if (dim == 2) {
    627:             if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;}
    628:             if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] =  0;}
    629:           }
    630:           else {
    631:             /* markers */
    632:             if (bdZ != DM_BOUNDARY_PERIODIC) {
    633:               if (fz == numZVertices-1) {
    634:                 DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);
    635:                 DMSetLabelValue(dm, "marker", face, markerTop);
    636:               }
    637:               else if (fz == 0) {
    638:                 DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);
    639:                 DMSetLabelValue(dm, "marker", face, markerBottom);
    640:               }
    641:             }
    642:           }
    643:           cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
    644:           DMPlexSetCone(dm, face, cone);
    645:           DMPlexSetConeOrientation(dm, face, ornt);
    646:         }
    647:       }
    648:     }
    649:     /* Build Z edges*/
    650:     for (vy = 0; vy < numYVertices; vy++) {
    651:       for (vx = 0; vx < numXVertices; vx++) {
    652:         for (ez = 0; ez < numZEdges; ez++) {
    653:           const PetscInt edge    = firstZEdge  + (vy*numXVertices+vx)*numZEdges + ez;
    654:           const PetscInt vertexB = firstVertex + (  ez                 *numYVertices+vy)*numXVertices + vx;
    655:           const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx;
    656:           PetscInt       cone[2];

    658:           if (dim == 3) {
    659:             if (bdX != DM_BOUNDARY_PERIODIC) {
    660:               if (vx == numXVertices-1) {
    661:                 DMSetLabelValue(dm, "marker", edge, markerRight);
    662:               }
    663:               else if (vx == 0) {
    664:                 DMSetLabelValue(dm, "marker", edge, markerLeft);
    665:               }
    666:             }
    667:             if (bdY != DM_BOUNDARY_PERIODIC) {
    668:               if (vy == numYVertices-1) {
    669:                 DMSetLabelValue(dm, "marker", edge, markerBack);
    670:               }
    671:               else if (vy == 0) {
    672:                 DMSetLabelValue(dm, "marker", edge, markerFront);
    673:               }
    674:             }
    675:           }
    676:           cone[0] = vertexB; cone[1] = vertexT;
    677:           DMPlexSetCone(dm, edge, cone);
    678:         }
    679:       }
    680:     }
    681:     /* Build Y edges*/
    682:     for (vz = 0; vz < numZVertices; vz++) {
    683:       for (vx = 0; vx < numXVertices; vx++) {
    684:         for (ey = 0; ey < numYEdges; ey++) {
    685:           const PetscInt nextv   = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx;
    686:           const PetscInt edge    = firstYEdge  + (vz*numXVertices+vx)*numYEdges + ey;
    687:           const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx;
    688:           const PetscInt vertexK = firstVertex + nextv;
    689:           PetscInt       cone[2];

    691:           cone[0] = vertexF; cone[1] = vertexK;
    692:           DMPlexSetCone(dm, edge, cone);
    693:           if (dim == 2) {
    694:             if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
    695:               if (vx == numXVertices-1) {
    696:                 DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);
    697:                 DMSetLabelValue(dm, "marker", edge,    markerRight);
    698:                 DMSetLabelValue(dm, "marker", cone[0], markerRight);
    699:                 if (ey == numYEdges-1) {
    700:                   DMSetLabelValue(dm, "marker", cone[1], markerRight);
    701:                 }
    702:               }
    703:               else if (vx == 0) {
    704:                 DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);
    705:                 DMSetLabelValue(dm, "marker", edge,    markerLeft);
    706:                 DMSetLabelValue(dm, "marker", cone[0], markerLeft);
    707:                 if (ey == numYEdges-1) {
    708:                   DMSetLabelValue(dm, "marker", cone[1], markerLeft);
    709:                 }
    710:               }
    711:             }
    712:           }
    713:           else {
    714:             if (bdX != DM_BOUNDARY_PERIODIC) {
    715:               if (vx == numXVertices-1) {
    716:                 DMSetLabelValue(dm, "marker", edge, markerRight);
    717:               }
    718:               else if (vx == 0) {
    719:                 DMSetLabelValue(dm, "marker", edge, markerLeft);
    720:               }
    721:             }
    722:             if (bdZ != DM_BOUNDARY_PERIODIC) {
    723:               if (vz == numZVertices-1) {
    724:                 DMSetLabelValue(dm, "marker", edge, markerTop);
    725:               }
    726:               else if (vz == 0) {
    727:                 DMSetLabelValue(dm, "marker", edge, markerBottom);
    728:               }
    729:             }
    730:           }
    731:         }
    732:       }
    733:     }
    734:     /* Build X edges*/
    735:     for (vz = 0; vz < numZVertices; vz++) {
    736:       for (vy = 0; vy < numYVertices; vy++) {
    737:         for (ex = 0; ex < numXEdges; ex++) {
    738:           const PetscInt nextv   = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices;
    739:           const PetscInt edge    = firstXEdge  + (vz*numYVertices+vy)*numXEdges + ex;
    740:           const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex;
    741:           const PetscInt vertexR = firstVertex + nextv;
    742:           PetscInt       cone[2];

    744:           cone[0] = vertexL; cone[1] = vertexR;
    745:           DMPlexSetCone(dm, edge, cone);
    746:           if (dim == 2) {
    747:             if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
    748:               if (vy == numYVertices-1) {
    749:                 DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);
    750:                 DMSetLabelValue(dm, "marker", edge,    markerTop);
    751:                 DMSetLabelValue(dm, "marker", cone[0], markerTop);
    752:                 if (ex == numXEdges-1) {
    753:                   DMSetLabelValue(dm, "marker", cone[1], markerTop);
    754:                 }
    755:               }
    756:               else if (vy == 0) {
    757:                 DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);
    758:                 DMSetLabelValue(dm, "marker", edge,    markerBottom);
    759:                 DMSetLabelValue(dm, "marker", cone[0], markerBottom);
    760:                 if (ex == numXEdges-1) {
    761:                   DMSetLabelValue(dm, "marker", cone[1], markerBottom);
    762:                 }
    763:               }
    764:             }
    765:           }
    766:           else {
    767:             if (bdY != DM_BOUNDARY_PERIODIC) {
    768:               if (vy == numYVertices-1) {
    769:                 DMSetLabelValue(dm, "marker", edge, markerBack);
    770:               }
    771:               else if (vy == 0) {
    772:                 DMSetLabelValue(dm, "marker", edge, markerFront);
    773:               }
    774:             }
    775:             if (bdZ != DM_BOUNDARY_PERIODIC) {
    776:               if (vz == numZVertices-1) {
    777:                 DMSetLabelValue(dm, "marker", edge, markerTop);
    778:               }
    779:               else if (vz == 0) {
    780:                 DMSetLabelValue(dm, "marker", edge, markerBottom);
    781:               }
    782:             }
    783:           }
    784:         }
    785:       }
    786:     }
    787:     DMPlexSymmetrize(dm);
    788:     DMPlexStratify(dm);
    789:     /* Build coordinates */
    790:     DMGetCoordinateSection(dm, &coordSection);
    791:     PetscSectionSetNumFields(coordSection, 1);
    792:     PetscSectionSetFieldComponents(coordSection, 0, dim);
    793:     PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);
    794:     for (v = firstVertex; v < firstVertex+numVertices; ++v) {
    795:       PetscSectionSetDof(coordSection, v, dim);
    796:       PetscSectionSetFieldDof(coordSection, v, 0, dim);
    797:     }
    798:     PetscSectionSetUp(coordSection);
    799:     PetscSectionGetStorageSize(coordSection, &coordSize);
    800:     VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
    801:     VecSetBlockSize(coordinates, dim);
    802:     PetscObjectSetName((PetscObject) coordinates, "coordinates");
    803:     VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    804:     VecSetType(coordinates,VECSTANDARD);
    805:     VecGetArray(coordinates, &coords);
    806:     for (vz = 0; vz < numZVertices; ++vz) {
    807:       for (vy = 0; vy < numYVertices; ++vy) {
    808:         for (vx = 0; vx < numXVertices; ++vx) {
    809:           coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
    810:           coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
    811:           if (dim == 3) {
    812:             coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz;
    813:           }
    814:         }
    815:       }
    816:     }
    817:     VecRestoreArray(coordinates, &coords);
    818:     DMSetCoordinatesLocal(dm, coordinates);
    819:     VecDestroy(&coordinates);
    820:   }
    821:   return(0);
    822: }

    826: /*@
    827:   DMPlexCreateSquareMesh - Creates a 2D mesh for a square lattice.

    829:   Collective on MPI_Comm

    831:   Input Parameters:
    832: + comm  - The communicator for the DM object
    833: . lower - The lower left corner coordinates
    834: . upper - The upper right corner coordinates
    835: . edges - The number of cells in each direction
    836: . bdX   - The boundary type for the X direction
    837: - bdY   - The boundary type for the Y direction

    839:   Output Parameter:
    840: . dm  - The DM object

    842:   Note: Here is the numbering returned for 2 cells in each direction:
    843: $ 22--8-23--9--24
    844: $  |     |     |
    845: $ 13  2 14  3  15
    846: $  |     |     |
    847: $ 19--6-20--7--21
    848: $  |     |     |
    849: $ 10  0 11  1 12
    850: $  |     |     |
    851: $ 16--4-17--5--18

    853:   Level: beginner

    855: .keywords: DM, create
    856: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate()
    857: @*/
    858: PetscErrorCode DMPlexCreateSquareMesh(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY)
    859: {
    860:   PetscReal      lower3[3], upper3[3];
    861:   PetscInt       edges3[3];

    865:   lower3[0] = lower[0]; lower3[1] = lower[1]; lower3[2] = 0.;
    866:   upper3[0] = upper[0]; upper3[1] = upper[1]; upper3[2] = 0.;
    867:   edges3[0] = edges[0]; edges3[1] = edges[1]; edges3[2] = 0;
    868:   DMPlexCreateCubeMesh_Internal(dm, lower3, upper3, edges3, bdX, bdY, DM_BOUNDARY_NONE);
    869:   return(0);
    870: }

    874: /*@
    875:   DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices.

    877:   Collective on MPI_Comm

    879:   Input Parameters:
    880: + comm - The communicator for the DM object
    881: . dim - The spatial dimension
    882: - interpolate - Flag to create intermediate mesh pieces (edges, faces)

    884:   Output Parameter:
    885: . dm  - The DM object

    887:   Level: beginner

    889: .keywords: DM, create
    890: .seealso: DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate()
    891: @*/
    892: PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool interpolate, DM *dm)
    893: {
    894:   DM             boundary;

    899:   DMCreate(comm, &boundary);
    901:   DMSetType(boundary, DMPLEX);
    902:   DMSetDimension(boundary, dim-1);
    903:   switch (dim) {
    904:   case 2:
    905:   {
    906:     PetscReal lower[2] = {0.0, 0.0};
    907:     PetscReal upper[2] = {1.0, 1.0};
    908:     PetscInt  edges[2] = {2, 2};

    910:     DMPlexCreateSquareBoundary(boundary, lower, upper, edges);
    911:     break;
    912:   }
    913:   case 3:
    914:   {
    915:     PetscReal lower[3] = {0.0, 0.0, 0.0};
    916:     PetscReal upper[3] = {1.0, 1.0, 1.0};
    917:     PetscInt  faces[3] = {1, 1, 1};

    919:     DMPlexCreateCubeBoundary(boundary, lower, upper, faces);
    920:     break;
    921:   }
    922:   default:
    923:     SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
    924:   }
    925:   DMPlexGenerate(boundary, NULL, interpolate, dm);
    926:   DMDestroy(&boundary);
    927:   return(0);
    928: }

    932: /*@
    933:   DMPlexCreateHexBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using hexahedra.

    935:   Collective on MPI_Comm

    937:   Input Parameters:
    938: + comm  - The communicator for the DM object
    939: . dim   - The spatial dimension
    940: . periodicX - The boundary type for the X direction
    941: . periodicY - The boundary type for the Y direction
    942: . periodicZ - The boundary type for the Z direction
    943: - cells - The number of cells in each direction

    945:   Output Parameter:
    946: . dm  - The DM object

    948:   Level: beginner

    950: .keywords: DM, create
    951: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
    952: @*/
    953: PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DMBoundaryType periodicX, DMBoundaryType periodicY, DMBoundaryType periodicZ, DM *dm)
    954: {

    959:   DMCreate(comm, dm);
    961:   DMSetType(*dm, DMPLEX);
    962:   DMSetDimension(*dm, dim);
    963:   switch (dim) {
    964:   case 2:
    965:   {
    966:     PetscReal lower[2] = {0.0, 0.0};
    967:     PetscReal upper[2] = {1.0, 1.0};

    969:     DMPlexCreateSquareMesh(*dm, lower, upper, cells, periodicX, periodicY);
    970:     break;
    971:   }
    972:   case 3:
    973:   {
    974:     PetscReal lower[3] = {0.0, 0.0, 0.0};
    975:     PetscReal upper[3] = {1.0, 1.0, 1.0};

    977:     DMPlexCreateCubeMesh_Internal(*dm, lower, upper, cells, periodicX, periodicY, periodicZ);
    978:     break;
    979:   }
    980:   default:
    981:     SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
    982:   }
    983:   return(0);
    984: }

    986: /* External function declarations here */
    987: extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling);
    988: extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat);
    989: extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm);
    990: extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm);
    991: extern PetscErrorCode DMCreateMatrix_Plex(DM dm,  Mat *J);
    992: extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm);
    993: extern PetscErrorCode DMRefine_Plex(DM dm, MPI_Comm comm, DM *dmRefined);
    994: extern PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened);
    995: extern PetscErrorCode DMRefineHierarchy_Plex(DM dm, PetscInt nlevels, DM dmRefined[]);
    996: extern PetscErrorCode DMCoarsenHierarchy_Plex(DM dm, PetscInt nlevels, DM dmCoarsened[]);
    997: extern PetscErrorCode DMClone_Plex(DM dm, DM *newdm);
    998: extern PetscErrorCode DMSetUp_Plex(DM dm);
    999: extern PetscErrorCode DMDestroy_Plex(DM dm);
    1000: extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer);
    1001: extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer);
    1002: extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm);
    1003: extern PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, PetscSF cellSF);
    1004: extern PetscErrorCode DMProjectFunctionLocal_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,InsertMode,Vec);
    1005: extern PetscErrorCode DMProjectFunctionLabelLocal_Plex(DM,PetscReal,DMLabel,PetscInt,const PetscInt[],PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,InsertMode,Vec);
    1006: extern PetscErrorCode DMProjectFieldLocal_Plex(DM,Vec,void (**)(PetscInt,PetscInt,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[],const PetscScalar[],const PetscScalar[],const PetscInt[],const PetscInt[],const PetscScalar[],const PetscScalar[],const PetscScalar[],PetscReal,const PetscReal[],PetscScalar[]),InsertMode,Vec);
    1007: extern PetscErrorCode DMComputeL2Diff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,PetscReal *);
    1008: extern PetscErrorCode DMComputeL2GradientDiff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[], const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,const PetscReal [],PetscReal *);
    1009: extern PetscErrorCode DMComputeL2FieldDiff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,PetscReal *);

    1013: /* Replace dm with the contents of dmNew
    1014:    - Share the DM_Plex structure
    1015:    - Share the coordinates
    1016:    - Share the SF
    1017: */
    1018: static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew)
    1019: {
    1020:   PetscSF          sf;
    1021:   DM               coordDM, coarseDM;
    1022:   Vec              coords;
    1023:   const PetscReal *maxCell, *L;
    1024:   const DMBoundaryType *bd;
    1025:   PetscErrorCode   ierr;

    1028:   DMGetPointSF(dmNew, &sf);
    1029:   DMSetPointSF(dm, sf);
    1030:   DMGetCoordinateDM(dmNew, &coordDM);
    1031:   DMGetCoordinatesLocal(dmNew, &coords);
    1032:   DMSetCoordinateDM(dm, coordDM);
    1033:   DMSetCoordinatesLocal(dm, coords);
    1034:   DMGetPeriodicity(dm, &maxCell, &L, &bd);
    1035:   if (L) {DMSetPeriodicity(dmNew, maxCell, L, bd);}
    1036:   DMDestroy_Plex(dm);
    1037:   dm->data = dmNew->data;
    1038:   ((DM_Plex *) dmNew->data)->refct++;
    1039:   dmNew->labels->refct++;
    1040:   if (!--(dm->labels->refct)) {
    1041:     DMLabelLink next = dm->labels->next;

    1043:     /* destroy the labels */
    1044:     while (next) {
    1045:       DMLabelLink tmp = next->next;

    1047:       DMLabelDestroy(&next->label);
    1048:       PetscFree(next);
    1049:       next = tmp;
    1050:     }
    1051:     PetscFree(dm->labels);
    1052:   }
    1053:   dm->labels = dmNew->labels;
    1054:   dm->depthLabel = dmNew->depthLabel;
    1055:   DMGetCoarseDM(dmNew,&coarseDM);
    1056:   DMSetCoarseDM(dm,coarseDM);
    1057:   return(0);
    1058: }

    1062: /* Swap dm with the contents of dmNew
    1063:    - Swap the DM_Plex structure
    1064:    - Swap the coordinates
    1065:    - Swap the point PetscSF
    1066: */
    1067: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
    1068: {
    1069:   DM              coordDMA, coordDMB;
    1070:   Vec             coordsA,  coordsB;
    1071:   PetscSF         sfA,      sfB;
    1072:   void            *tmp;
    1073:   DMLabelLinkList listTmp;
    1074:   DMLabel         depthTmp;
    1075:   PetscErrorCode  ierr;

    1078:   DMGetPointSF(dmA, &sfA);
    1079:   DMGetPointSF(dmB, &sfB);
    1080:   PetscObjectReference((PetscObject) sfA);
    1081:   DMSetPointSF(dmA, sfB);
    1082:   DMSetPointSF(dmB, sfA);
    1083:   PetscObjectDereference((PetscObject) sfA);

    1085:   DMGetCoordinateDM(dmA, &coordDMA);
    1086:   DMGetCoordinateDM(dmB, &coordDMB);
    1087:   PetscObjectReference((PetscObject) coordDMA);
    1088:   DMSetCoordinateDM(dmA, coordDMB);
    1089:   DMSetCoordinateDM(dmB, coordDMA);
    1090:   PetscObjectDereference((PetscObject) coordDMA);

    1092:   DMGetCoordinatesLocal(dmA, &coordsA);
    1093:   DMGetCoordinatesLocal(dmB, &coordsB);
    1094:   PetscObjectReference((PetscObject) coordsA);
    1095:   DMSetCoordinatesLocal(dmA, coordsB);
    1096:   DMSetCoordinatesLocal(dmB, coordsA);
    1097:   PetscObjectDereference((PetscObject) coordsA);

    1099:   tmp       = dmA->data;
    1100:   dmA->data = dmB->data;
    1101:   dmB->data = tmp;
    1102:   listTmp   = dmA->labels;
    1103:   dmA->labels = dmB->labels;
    1104:   dmB->labels = listTmp;
    1105:   depthTmp  = dmA->depthLabel;
    1106:   dmA->depthLabel = dmB->depthLabel;
    1107:   dmB->depthLabel = depthTmp;
    1108:   return(0);
    1109: }

    1113: PetscErrorCode  DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
    1114: {
    1115:   DM_Plex       *mesh = (DM_Plex*) dm->data;
    1116:   DMBoundary     b;

    1120:   /* Handle boundary conditions */
    1121:   PetscOptionsBegin(PetscObjectComm((PetscObject) dm), NULL, "Boundary condition options", "");
    1122:   for (b = dm->boundary->next; b; b = b->next) {
    1123:     char      optname[1024];
    1124:     PetscInt  ids[1024], len = 1024, i;
    1125:     PetscBool flg;

    1127:     PetscSNPrintf(optname, sizeof(optname), "-bc_%s", b->name);
    1128:     PetscMemzero(ids, sizeof(ids));
    1129:     PetscOptionsIntArray(optname, "List of boundary IDs", "", ids, &len, &flg);
    1130:     if (flg) {
    1131:       DMLabel label;

    1133:       DMGetLabel(dm, b->labelname, &label);
    1134:       for (i = 0; i < len; ++i) {
    1135:         PetscBool has;

    1137:         DMLabelHasValue(label, ids[i], &has);
    1138:         if (!has) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Boundary id %D is not present in the label %s", ids[i], b->name);
    1139:       }
    1140:       b->numids = len;
    1141:       PetscFree(b->ids);
    1142:       PetscMalloc1(len, &b->ids);
    1143:       PetscMemcpy(b->ids, ids, len*sizeof(PetscInt));
    1144:     }
    1145:     PetscSNPrintf(optname, sizeof(optname), "-bc_%s_comp", b->name);
    1146:     PetscMemzero(ids, sizeof(ids));
    1147:     PetscOptionsIntArray(optname, "List of boundary field components", "", ids, &len, &flg);
    1148:     if (flg) {
    1149:       b->numcomps = len;
    1150:       PetscFree(b->comps);
    1151:       PetscMalloc1(len, &b->comps);
    1152:       PetscMemcpy(b->comps, ids, len*sizeof(PetscInt));
    1153:     }
    1154:   }
    1155:   PetscOptionsEnd();
    1156:   /* Handle viewing */
    1157:   PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);
    1158:   PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);
    1159:   PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", mesh->printTol, &mesh->printTol, NULL);
    1160:   /* Point Location */
    1161:   PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMView", PETSC_FALSE, &mesh->useHashLocation, NULL);
    1162:   /* Projection behavior */
    1163:   PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);
    1164:   PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);
    1165:   return(0);
    1166: }

    1170: PetscErrorCode  DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
    1171: {
    1172:   PetscInt       refine = 0, coarsen = 0, r;
    1173:   PetscBool      isHierarchy;

    1178:   PetscOptionsHead(PetscOptionsObject,"DMPlex Options");
    1179:   /* Handle DMPlex refinement */
    1180:   PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);
    1181:   PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);
    1182:   if (refine) {DMPlexSetRefinementUniform(dm, PETSC_TRUE);}
    1183:   if (refine && isHierarchy) {
    1184:     DM *dms, coarseDM;

    1186:     DMGetCoarseDM(dm, &coarseDM);
    1187:     PetscObjectReference((PetscObject)coarseDM);
    1188:     PetscMalloc1(refine,&dms);
    1189:     DMRefineHierarchy(dm, refine, dms);
    1190:     /* Total hack since we do not pass in a pointer */
    1191:     DMPlexSwap_Static(dm, dms[refine-1]);
    1192:     if (refine == 1) {
    1193:       DMSetCoarseDM(dm, dms[0]);
    1194:       DMPlexSetRegularRefinement(dm, PETSC_TRUE);
    1195:     } else {
    1196:       DMSetCoarseDM(dm, dms[refine-2]);
    1197:       DMPlexSetRegularRefinement(dm, PETSC_TRUE);
    1198:       DMSetCoarseDM(dms[0], dms[refine-1]);
    1199:       DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);
    1200:     }
    1201:     DMSetCoarseDM(dms[refine-1], coarseDM);
    1202:     PetscObjectDereference((PetscObject)coarseDM);
    1203:     /* Free DMs */
    1204:     for (r = 0; r < refine; ++r) {
    1205:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
    1206:       DMDestroy(&dms[r]);
    1207:     }
    1208:     PetscFree(dms);
    1209:   } else {
    1210:     for (r = 0; r < refine; ++r) {
    1211:       DM refinedMesh;

    1213:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
    1214:       DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);
    1215:       /* Total hack since we do not pass in a pointer */
    1216:       DMPlexReplace_Static(dm, refinedMesh);
    1217:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
    1218:       DMDestroy(&refinedMesh);
    1219:     }
    1220:   }
    1221:   /* Handle DMPlex coarsening */
    1222:   PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);
    1223:   PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);
    1224:   if (coarsen && isHierarchy) {
    1225:     DM *dms;

    1227:     PetscMalloc1(coarsen, &dms);
    1228:     DMCoarsenHierarchy(dm, coarsen, dms);
    1229:     /* Free DMs */
    1230:     for (r = 0; r < coarsen; ++r) {
    1231:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
    1232:       DMDestroy(&dms[r]);
    1233:     }
    1234:     PetscFree(dms);
    1235:   } else {
    1236:     for (r = 0; r < coarsen; ++r) {
    1237:       DM coarseMesh;

    1239:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
    1240:       DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);
    1241:       /* Total hack since we do not pass in a pointer */
    1242:       DMPlexReplace_Static(dm, coarseMesh);
    1243:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
    1244:       DMDestroy(&coarseMesh);
    1245:     }
    1246:   }
    1247:   /* Handle */
    1248:   DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
    1249:   PetscOptionsTail();
    1250:   return(0);
    1251: }

    1255: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
    1256: {

    1260:   DMCreateGlobalVector_Section_Private(dm,vec);
    1261:   /* VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM); */
    1262:   VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);
    1263:   VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);
    1264:   VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);
    1265:   VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);
    1266:   return(0);
    1267: }

    1271: static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
    1272: {

    1276:   DMCreateLocalVector_Section_Private(dm,vec);
    1277:   VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);
    1278:   VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);
    1279:   return(0);
    1280: }

    1284: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
    1285: {
    1286:   PetscInt       depth, d;

    1290:   DMPlexGetDepth(dm, &depth);
    1291:   if (depth == 1) {
    1292:     DMGetDimension(dm, &d);
    1293:     if (dim == 0)      {DMPlexGetDepthStratum(dm, dim, pStart, pEnd);}
    1294:     else if (dim == d) {DMPlexGetDepthStratum(dm, 1, pStart, pEnd);}
    1295:     else               {*pStart = 0; *pEnd = 0;}
    1296:   } else {
    1297:     DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
    1298:   }
    1299:   return(0);
    1300: }

    1304: PetscErrorCode DMInitialize_Plex(DM dm)
    1305: {
    1307:   dm->ops->view                            = DMView_Plex;
    1308:   dm->ops->load                            = DMLoad_Plex;
    1309:   dm->ops->setfromoptions                  = DMSetFromOptions_Plex;
    1310:   dm->ops->clone                           = DMClone_Plex;
    1311:   dm->ops->setup                           = DMSetUp_Plex;
    1312:   dm->ops->createdefaultsection            = DMCreateDefaultSection_Plex;
    1313:   dm->ops->createdefaultconstraints        = DMCreateDefaultConstraints_Plex;
    1314:   dm->ops->createglobalvector              = DMCreateGlobalVector_Plex;
    1315:   dm->ops->createlocalvector               = DMCreateLocalVector_Plex;
    1316:   dm->ops->getlocaltoglobalmapping         = NULL;
    1317:   dm->ops->createfieldis                   = NULL;
    1318:   dm->ops->createcoordinatedm              = DMCreateCoordinateDM_Plex;
    1319:   dm->ops->getcoloring                     = NULL;
    1320:   dm->ops->creatematrix                    = DMCreateMatrix_Plex;
    1321:   dm->ops->createinterpolation             = DMCreateInterpolation_Plex;
    1322:   dm->ops->getaggregates                   = NULL;
    1323:   dm->ops->getinjection                    = DMCreateInjection_Plex;
    1324:   dm->ops->refine                          = DMRefine_Plex;
    1325:   dm->ops->coarsen                         = DMCoarsen_Plex;
    1326:   dm->ops->refinehierarchy                 = DMRefineHierarchy_Plex;
    1327:   dm->ops->coarsenhierarchy                = DMCoarsenHierarchy_Plex;
    1328:   dm->ops->globaltolocalbegin              = NULL;
    1329:   dm->ops->globaltolocalend                = NULL;
    1330:   dm->ops->localtoglobalbegin              = NULL;
    1331:   dm->ops->localtoglobalend                = NULL;
    1332:   dm->ops->destroy                         = DMDestroy_Plex;
    1333:   dm->ops->createsubdm                     = DMCreateSubDM_Plex;
    1334:   dm->ops->getdimpoints                    = DMGetDimPoints_Plex;
    1335:   dm->ops->locatepoints                    = DMLocatePoints_Plex;
    1336:   dm->ops->projectfunctionlocal            = DMProjectFunctionLocal_Plex;
    1337:   dm->ops->projectfunctionlabellocal       = DMProjectFunctionLabelLocal_Plex;
    1338:   dm->ops->projectfieldlocal               = DMProjectFieldLocal_Plex;
    1339:   dm->ops->computel2diff                   = DMComputeL2Diff_Plex;
    1340:   dm->ops->computel2gradientdiff           = DMComputeL2GradientDiff_Plex;
    1341:   dm->ops->computel2fielddiff              = DMComputeL2FieldDiff_Plex;
    1342:   return(0);
    1343: }

    1347: PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
    1348: {
    1349:   DM_Plex        *mesh = (DM_Plex *) dm->data;

    1353:   mesh->refct++;
    1354:   (*newdm)->data = mesh;
    1355:   PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);
    1356:   DMInitialize_Plex(*newdm);
    1357:   return(0);
    1358: }

    1360: /*MC
    1361:   DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
    1362:                     In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is
    1363:                     specified by a PetscSection object. Ownership in the global representation is determined by
    1364:                     ownership of the underlying DMPlex points. This is specified by another PetscSection object.

    1366:   Level: intermediate

    1368: .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType()
    1369: M*/

    1373: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
    1374: {
    1375:   DM_Plex        *mesh;
    1376:   PetscInt       unit, d;

    1381:   PetscNewLog(dm,&mesh);
    1382:   dm->dim  = 0;
    1383:   dm->data = mesh;

    1385:   mesh->refct             = 1;
    1386:   PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);
    1387:   mesh->maxConeSize       = 0;
    1388:   mesh->cones             = NULL;
    1389:   mesh->coneOrientations  = NULL;
    1390:   PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);
    1391:   mesh->maxSupportSize    = 0;
    1392:   mesh->supports          = NULL;
    1393:   mesh->refinementUniform = PETSC_TRUE;
    1394:   mesh->refinementLimit   = -1.0;

    1396:   mesh->facesTmp = NULL;

    1398:   mesh->tetgenOpts   = NULL;
    1399:   mesh->triangleOpts = NULL;
    1400:   PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);
    1401:   PetscPartitionerSetTypeFromOptions_Internal(mesh->partitioner);

    1403:   mesh->subpointMap = NULL;

    1405:   for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;

    1407:   mesh->regularRefinement   = PETSC_FALSE;
    1408:   mesh->depthState          = -1;
    1409:   mesh->globalVertexNumbers = NULL;
    1410:   mesh->globalCellNumbers   = NULL;
    1411:   mesh->anchorSection       = NULL;
    1412:   mesh->anchorIS            = NULL;
    1413:   mesh->createanchors       = NULL;
    1414:   mesh->computeanchormatrix = NULL;
    1415:   mesh->parentSection       = NULL;
    1416:   mesh->parents             = NULL;
    1417:   mesh->childIDs            = NULL;
    1418:   mesh->childSection        = NULL;
    1419:   mesh->children            = NULL;
    1420:   mesh->referenceTree       = NULL;
    1421:   mesh->getchildsymmetry    = NULL;
    1422:   for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE;
    1423:   mesh->vtkCellHeight       = 0;
    1424:   mesh->useCone             = PETSC_FALSE;
    1425:   mesh->useClosure          = PETSC_TRUE;
    1426:   mesh->useAnchors          = PETSC_FALSE;

    1428:   mesh->maxProjectionHeight = 0;

    1430:   mesh->printSetValues = PETSC_FALSE;
    1431:   mesh->printFEM       = 0;
    1432:   mesh->printTol       = 1.0e-10;

    1434:   DMInitialize_Plex(dm);
    1435:   return(0);
    1436: }

    1440: /*@
    1441:   DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.

    1443:   Collective on MPI_Comm

    1445:   Input Parameter:
    1446: . comm - The communicator for the DMPlex object

    1448:   Output Parameter:
    1449: . mesh  - The DMPlex object

    1451:   Level: beginner

    1453: .keywords: DMPlex, create
    1454: @*/
    1455: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
    1456: {

    1461:   DMCreate(comm, mesh);
    1462:   DMSetType(*mesh, DMPLEX);
    1463:   return(0);
    1464: }

    1468: /*
    1469:   This takes as input the common mesh generator output, a list of the vertices for each cell
    1470: */
    1471: PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[])
    1472: {
    1473:   PetscInt      *cone, c, p;

    1477:   DMPlexSetChart(dm, 0, numCells+numVertices);
    1478:   for (c = 0; c < numCells; ++c) {
    1479:     DMPlexSetConeSize(dm, c, numCorners);
    1480:   }
    1481:   DMSetUp(dm);
    1482:   DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);
    1483:   for (c = 0; c < numCells; ++c) {
    1484:     for (p = 0; p < numCorners; ++p) {
    1485:       cone[p] = cells[c*numCorners+p]+numCells;
    1486:     }
    1487:     DMPlexSetCone(dm, c, cone);
    1488:   }
    1489:   DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);
    1490:   DMPlexSymmetrize(dm);
    1491:   DMPlexStratify(dm);
    1492:   return(0);
    1493: }

    1497: /*
    1498:   This takes as input the coordinates for each vertex
    1499: */
    1500: PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
    1501: {
    1502:   PetscSection   coordSection;
    1503:   Vec            coordinates;
    1504:   PetscScalar   *coords;
    1505:   PetscInt       coordSize, v, d;

    1509:   DMGetCoordinateSection(dm, &coordSection);
    1510:   PetscSectionSetNumFields(coordSection, 1);
    1511:   PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
    1512:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
    1513:   for (v = numCells; v < numCells+numVertices; ++v) {
    1514:     PetscSectionSetDof(coordSection, v, spaceDim);
    1515:     PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
    1516:   }
    1517:   PetscSectionSetUp(coordSection);
    1518:   PetscSectionGetStorageSize(coordSection, &coordSize);
    1519:   VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
    1520:   VecSetBlockSize(coordinates, spaceDim);
    1521:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    1522:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    1523:   VecSetType(coordinates,VECSTANDARD);
    1524:   VecGetArray(coordinates, &coords);
    1525:   for (v = 0; v < numVertices; ++v) {
    1526:     for (d = 0; d < spaceDim; ++d) {
    1527:       coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
    1528:     }
    1529:   }
    1530:   VecRestoreArray(coordinates, &coords);
    1531:   DMSetCoordinatesLocal(dm, coordinates);
    1532:   VecDestroy(&coordinates);
    1533:   return(0);
    1534: }

    1538: /*@C
    1539:   DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM

    1541:   Input Parameters:
    1542: + comm - The communicator
    1543: . dim - The topological dimension of the mesh
    1544: . numCells - The number of cells
    1545: . numVertices - The number of vertices
    1546: . numCorners - The number of vertices for each cell
    1547: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
    1548: . cells - An array of numCells*numCorners numbers, the vertices for each cell
    1549: . spaceDim - The spatial dimension used for coordinates
    1550: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex

    1552:   Output Parameter:
    1553: . dm - The DM

    1555:   Note: Two triangles sharing a face
    1556: $
    1557: $        2
    1558: $      / | \
    1559: $     /  |  \
    1560: $    /   |   \
    1561: $   0  0 | 1  3
    1562: $    \   |   /
    1563: $     \  |  /
    1564: $      \ | /
    1565: $        1
    1566: would have input
    1567: $  numCells = 2, numVertices = 4
    1568: $  cells = [0 1 2  1 3 2]
    1569: $
    1570: which would result in the DMPlex
    1571: $
    1572: $        4
    1573: $      / | \
    1574: $     /  |  \
    1575: $    /   |   \
    1576: $   2  0 | 1  5
    1577: $    \   |   /
    1578: $     \  |  /
    1579: $      \ | /
    1580: $        3

    1582:   Level: beginner

    1584: .seealso: DMPlexCreateFromDAG(), DMPlexCreate()
    1585: @*/
    1586: PetscErrorCode DMPlexCreateFromCellList(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const int cells[], PetscInt spaceDim, const double vertexCoords[], DM *dm)
    1587: {

    1591:   DMCreate(comm, dm);
    1592:   DMSetType(*dm, DMPLEX);
    1593:   DMSetDimension(*dm, dim);
    1594:   DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);
    1595:   if (interpolate) {
    1596:     DM idm = NULL;

    1598:     DMPlexInterpolate(*dm, &idm);
    1599:     DMDestroy(dm);
    1600:     *dm  = idm;
    1601:   }
    1602:   DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);
    1603:   return(0);
    1604: }

    1608: /*@
    1609:   DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM

    1611:   Input Parameters:
    1612: + dm - The empty DM object, usually from DMCreate() and DMSetDimension()
    1613: . depth - The depth of the DAG
    1614: . numPoints - The number of points at each depth
    1615: . coneSize - The cone size of each point
    1616: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
    1617: . coneOrientations - The orientation of each cone point
    1618: - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex

    1620:   Output Parameter:
    1621: . dm - The DM

    1623:   Note: Two triangles sharing a face would have input
    1624: $  depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
    1625: $  cones = [2 3 4  3 5 4], coneOrientations = [0 0 0  0 0 0]
    1626: $ vertexCoords = [-1.0 0.0  0.0 -1.0  0.0 1.0  1.0 0.0]
    1627: $
    1628: which would result in the DMPlex
    1629: $
    1630: $        4
    1631: $      / | \
    1632: $     /  |  \
    1633: $    /   |   \
    1634: $   2  0 | 1  5
    1635: $    \   |   /
    1636: $     \  |  /
    1637: $      \ | /
    1638: $        3
    1639: $
    1640: $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList()

    1642:   Level: advanced

    1644: .seealso: DMPlexCreateFromCellList(), DMPlexCreate()
    1645: @*/
    1646: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
    1647: {
    1648:   Vec            coordinates;
    1649:   PetscSection   coordSection;
    1650:   PetscScalar    *coords;
    1651:   PetscInt       coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;

    1655:   DMGetDimension(dm, &dim);
    1656:   DMGetCoordinateDim(dm, &dimEmbed);
    1657:   if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim);
    1658:   for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
    1659:   DMPlexSetChart(dm, pStart, pEnd);
    1660:   for (p = pStart; p < pEnd; ++p) {
    1661:     DMPlexSetConeSize(dm, p, coneSize[p-pStart]);
    1662:     if (firstVertex < 0 && !coneSize[p - pStart]) {
    1663:       firstVertex = p - pStart;
    1664:     }
    1665:   }
    1666:   if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]);
    1667:   DMSetUp(dm); /* Allocate space for cones */
    1668:   for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
    1669:     DMPlexSetCone(dm, p, &cones[off]);
    1670:     DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);
    1671:   }
    1672:   DMPlexSymmetrize(dm);
    1673:   DMPlexStratify(dm);
    1674:   /* Build coordinates */
    1675:   DMGetCoordinateSection(dm, &coordSection);
    1676:   PetscSectionSetNumFields(coordSection, 1);
    1677:   PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
    1678:   PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);
    1679:   for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
    1680:     PetscSectionSetDof(coordSection, v, dimEmbed);
    1681:     PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
    1682:   }
    1683:   PetscSectionSetUp(coordSection);
    1684:   PetscSectionGetStorageSize(coordSection, &coordSize);
    1685:   VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
    1686:   VecSetBlockSize(coordinates, dimEmbed);
    1687:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    1688:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    1689:   VecSetType(coordinates,VECSTANDARD);
    1690:   VecGetArray(coordinates, &coords);
    1691:   for (v = 0; v < numPoints[0]; ++v) {
    1692:     PetscInt off;

    1694:     PetscSectionGetOffset(coordSection, v+firstVertex, &off);
    1695:     for (d = 0; d < dimEmbed; ++d) {
    1696:       coords[off+d] = vertexCoords[v*dimEmbed+d];
    1697:     }
    1698:   }
    1699:   VecRestoreArray(coordinates, &coords);
    1700:   DMSetCoordinatesLocal(dm, coordinates);
    1701:   VecDestroy(&coordinates);
    1702:   return(0);
    1703: }

    1707: /*@C
    1708:   DMPlexCreateFromFile - This takes a filename and produces a DM

    1710:   Input Parameters:
    1711: + comm - The communicator
    1712: . filename - A file name
    1713: - interpolate - Flag to create intermediate mesh pieces (edges, faces)

    1715:   Output Parameter:
    1716: . dm - The DM

    1718:   Level: beginner

    1720: .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate()
    1721: @*/
    1722: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
    1723: {
    1724:   const char    *extGmsh   = ".msh";
    1725:   const char    *extCGNS   = ".cgns";
    1726:   const char    *extExodus = ".exo";
    1727:   const char    *extFluent = ".cas";
    1728:   const char    *extHDF5   = ".h5";
    1729:   size_t         len;
    1730:   PetscBool      isGmsh, isCGNS, isExodus, isFluent, isHDF5;
    1731:   PetscMPIInt    rank;

    1737:   MPI_Comm_rank(comm, &rank);
    1738:   PetscStrlen(filename, &len);
    1739:   if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
    1740:   PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh,   4, &isGmsh);
    1741:   PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS,   5, &isCGNS);
    1742:   PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);
    1743:   PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);
    1744:   PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5,   3, &isHDF5);
    1745:   if (isGmsh) {
    1746:     DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);
    1747:   } else if (isCGNS) {
    1748:     DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);
    1749:   } else if (isExodus) {
    1750:     DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);
    1751:   } else if (isFluent) {
    1752:     DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);
    1753:   } else if (isHDF5) {
    1754:     PetscViewer viewer;

    1756:     PetscViewerCreate(comm, &viewer);
    1757:     PetscViewerSetType(viewer, PETSCVIEWERHDF5);
    1758:     PetscViewerFileSetMode(viewer, FILE_MODE_READ);
    1759:     PetscViewerFileSetName(viewer, filename);
    1760:     DMCreate(comm, dm);
    1761:     DMSetType(*dm, DMPLEX);
    1762:     DMLoad(*dm, viewer);
    1763:     PetscViewerDestroy(&viewer);
    1764:   } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
    1765:   return(0);
    1766: }

    1770: /*@
    1771:   DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell

    1773:   Collective on comm

    1775:   Input Parameters:
    1776: + comm    - The communicator
    1777: . dim     - The spatial dimension
    1778: - simplex - Flag for simplex, otherwise use a tensor-product cell

    1780:   Output Parameter:
    1781: . refdm - The reference cell

    1783:   Level: intermediate

    1785: .keywords: reference cell
    1786: .seealso:
    1787: @*/
    1788: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm)
    1789: {
    1790:   DM             rdm;
    1791:   Vec            coords;

    1795:   DMCreate(comm, &rdm);
    1796:   DMSetType(rdm, DMPLEX);
    1797:   DMSetDimension(rdm, dim);
    1798:   switch (dim) {
    1799:   case 0:
    1800:   {
    1801:     PetscInt    numPoints[1]        = {1};
    1802:     PetscInt    coneSize[1]         = {0};
    1803:     PetscInt    cones[1]            = {0};
    1804:     PetscInt    coneOrientations[1] = {0};
    1805:     PetscScalar vertexCoords[1]     = {0.0};

    1807:     DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);
    1808:   }
    1809:   break;
    1810:   case 1:
    1811:   {
    1812:     PetscInt    numPoints[2]        = {2, 1};
    1813:     PetscInt    coneSize[3]         = {2, 0, 0};
    1814:     PetscInt    cones[2]            = {1, 2};
    1815:     PetscInt    coneOrientations[2] = {0, 0};
    1816:     PetscScalar vertexCoords[2]     = {-1.0,  1.0};

    1818:     DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
    1819:   }
    1820:   break;
    1821:   case 2:
    1822:     if (simplex) {
    1823:       PetscInt    numPoints[2]        = {3, 1};
    1824:       PetscInt    coneSize[4]         = {3, 0, 0, 0};
    1825:       PetscInt    cones[3]            = {1, 2, 3};
    1826:       PetscInt    coneOrientations[3] = {0, 0, 0};
    1827:       PetscScalar vertexCoords[6]     = {-1.0, -1.0,  1.0, -1.0,  -1.0, 1.0};

    1829:       DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
    1830:     } else {
    1831:       PetscInt    numPoints[2]        = {4, 1};
    1832:       PetscInt    coneSize[5]         = {4, 0, 0, 0, 0};
    1833:       PetscInt    cones[4]            = {1, 2, 3, 4};
    1834:       PetscInt    coneOrientations[4] = {0, 0, 0, 0};
    1835:       PetscScalar vertexCoords[8]     = {-1.0, -1.0,  1.0, -1.0,  1.0, 1.0,  -1.0, 1.0};

    1837:       DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
    1838:     }
    1839:   break;
    1840:   case 3:
    1841:     if (simplex) {
    1842:       PetscInt    numPoints[2]        = {4, 1};
    1843:       PetscInt    coneSize[5]         = {4, 0, 0, 0, 0};
    1844:       PetscInt    cones[4]            = {1, 3, 2, 4};
    1845:       PetscInt    coneOrientations[4] = {0, 0, 0, 0};
    1846:       PetscScalar vertexCoords[12]    = {-1.0, -1.0, -1.0,  1.0, -1.0, -1.0,  -1.0, 1.0, -1.0,  -1.0, -1.0, 1.0};

    1848:       DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
    1849:     } else {
    1850:       PetscInt    numPoints[2]        = {8, 1};
    1851:       PetscInt    coneSize[9]         = {8, 0, 0, 0, 0, 0, 0, 0, 0};
    1852:       PetscInt    cones[8]            = {1, 4, 3, 2, 5, 6, 7, 8};
    1853:       PetscInt    coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
    1854:       PetscScalar vertexCoords[24]    = {-1.0, -1.0, -1.0,  1.0, -1.0, -1.0,  1.0, 1.0, -1.0,  -1.0, 1.0, -1.0,
    1855:                                          -1.0, -1.0,  1.0,  1.0, -1.0,  1.0,  1.0, 1.0,  1.0,  -1.0, 1.0,  1.0};

    1857:       DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
    1858:     }
    1859:   break;
    1860:   default:
    1861:     SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim);
    1862:   }
    1863:   *refdm = NULL;
    1864:   DMPlexInterpolate(rdm, refdm);
    1865:   if (rdm->coordinateDM) {
    1866:     DM           ncdm;
    1867:     PetscSection cs;
    1868:     PetscInt     pEnd = -1;

    1870:     DMGetDefaultSection(rdm->coordinateDM, &cs);
    1871:     if (cs) {PetscSectionGetChart(cs, NULL, &pEnd);}
    1872:     if (pEnd >= 0) {
    1873:       DMClone(rdm->coordinateDM, &ncdm);
    1874:       DMSetDefaultSection(ncdm, cs);
    1875:       DMSetCoordinateDM(*refdm, ncdm);
    1876:       DMDestroy(&ncdm);
    1877:     }
    1878:   }
    1879:   DMGetCoordinatesLocal(rdm, &coords);
    1880:   if (coords) {
    1881:     DMSetCoordinatesLocal(*refdm, coords);
    1882:   } else {
    1883:     DMGetCoordinates(rdm, &coords);
    1884:     if (coords) {DMSetCoordinates(*refdm, coords);}
    1885:   }
    1886:   DMDestroy(&rdm);
    1887:   return(0);
    1888: }