Exemple #1
0
static PetscErrorCode CreateMesh(MPI_Comm comm, DM *dm, AppCtx *ctx)
{
    DM             pdm = NULL;
    const PetscInt dim = ctx->dim;
    PetscInt       cells[3] = {1, 1, 1}; /* coarse mesh is one cell; refine from there */
    PetscBool      hasLabel;
    PetscErrorCode ierr;

    PetscFunctionBeginUser;
    if (ctx->simplex) {
        ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_TRUE, dm);
        CHKERRQ(ierr);
    } else {
        ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);
        CHKERRQ(ierr);
    }
    ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");
    CHKERRQ(ierr);
    /* If no boundary marker exists, mark the whole boundary */
    ierr = DMHasLabel(*dm, "marker", &hasLabel);
    CHKERRQ(ierr);
    if (!hasLabel) {
        ierr = CreateBCLabel(*dm, "marker");
        CHKERRQ(ierr);
    }
    /* Distribute mesh over processes */
    ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);
    CHKERRQ(ierr);
    if (pdm) {
        ierr = DMDestroy(dm);
        CHKERRQ(ierr);
        *dm  = pdm;
    }
    ierr = DMSetFromOptions(*dm);
    CHKERRQ(ierr);
    ierr = DMViewFromOptions(*dm, NULL, "-dm_view");
    CHKERRQ(ierr);
    PetscFunctionReturn(0);
}
Exemple #2
0
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
  PetscInt       dim             = user->dim;
  PetscBool      interpolate     = user->interpolate;
  PetscReal      refinementLimit = user->refinementLimit;
  PetscBool      cellSimplex     = user->cellSimplex;
  const char    *filename        = user->filename;
  PetscInt       triSizes_n2[2]  = {4, 4};
  PetscInt       triPoints_n2[8] = {3, 5, 6, 7, 0, 1, 2, 4};
  PetscInt       triSizes_n8[8]  = {1, 1, 1, 1, 1, 1, 1, 1};
  PetscInt       triPoints_n8[8] = {0, 1, 2, 3, 4, 5, 6, 7};
  PetscInt       quadSizes[2]    = {2, 2};
  PetscInt       quadPoints[4]   = {2, 3, 0, 1};
  const PetscInt cells[3]        = {2, 2, 2};
  size_t         len;
  PetscMPIInt    rank, numProcs;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
  ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
  if (len)              {ierr = DMPlexCreateFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr);}
  else if (cellSimplex) {ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, interpolate, dm);CHKERRQ(ierr);}
  else                  {ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);CHKERRQ(ierr);}
  {
    DM refinedMesh     = NULL;
    DM distributedMesh = NULL;

    if (user->testPartition) {
      const PetscInt  *sizes = NULL;
      const PetscInt  *points = NULL;
      PetscPartitioner part;

      if (!rank) {
        if (dim == 2 && cellSimplex && numProcs == 2) {
           sizes = triSizes_n2; points = triPoints_n2;
        } else if (dim == 2 && cellSimplex && numProcs == 8) {
          sizes = triSizes_n8; points = triPoints_n8;
        } else if (dim == 2 && !cellSimplex && numProcs == 2) {
          sizes = quadSizes; points = quadPoints;
        }
      }
      ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
      ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr);
      ierr = PetscPartitionerShellSetPartition(part, numProcs, sizes, points);CHKERRQ(ierr);
    }
    /* Distribute mesh over processes */
    ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
    if (distributedMesh) {
      ierr = DMDestroy(dm);CHKERRQ(ierr);
      *dm  = distributedMesh;
    }
    /* Refine mesh using a volume constraint */
    ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
    ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
    ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
    if (refinedMesh) {
      ierr = DMDestroy(dm);CHKERRQ(ierr);
      *dm  = refinedMesh;
    }
  }
  ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
  if (user->overlap) {
    DM overlapMesh = NULL;
    /* Add the level-1 overlap to refined mesh */
    ierr = DMPlexDistributeOverlap(*dm, 1, NULL, &overlapMesh);CHKERRQ(ierr);
    if (overlapMesh) {
      ierr = DMView(overlapMesh, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
      ierr = DMDestroy(dm);CHKERRQ(ierr);
      *dm = overlapMesh;
    }
  }
  ierr = PetscObjectSetName((PetscObject) *dm, "Simplicial Mesh");CHKERRQ(ierr);
  ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
  ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
  user->dm = *dm;
  PetscFunctionReturn(0);
}
Exemple #3
0
int main(int argc,char **args)
{
  Mat            Amat;
  PetscErrorCode ierr;
  SNES           snes;
  KSP            ksp;
  MPI_Comm       comm;
  PetscMPIInt    npe,rank;
  PetscLogStage  stage[7];
  PetscBool      test_nonzero_cols=PETSC_FALSE,use_nearnullspace=PETSC_TRUE;
  Vec            xx,bb;
  PetscInt       iter,i,N,dim=3,cells[3]={1,1,1},max_conv_its,local_sizes[7],run_type=1;
  DM             dm,distdm,basedm;
  PetscBool      flg;
  char           convType[256];
  PetscReal      Lx,mdisp[10],err[10];
  const char * const options[10] = {"-ex56_dm_refine 0",
                                    "-ex56_dm_refine 1",
                                    "-ex56_dm_refine 2",
                                    "-ex56_dm_refine 3",
                                    "-ex56_dm_refine 4",
                                    "-ex56_dm_refine 5",
                                    "-ex56_dm_refine 6",
                                    "-ex56_dm_refine 7",
                                    "-ex56_dm_refine 8",
                                    "-ex56_dm_refine 9"};
  PetscFunctionBeginUser;
  ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
  comm = PETSC_COMM_WORLD;
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &npe);CHKERRQ(ierr);
  /* options */
  ierr = PetscOptionsBegin(comm,NULL,"3D bilinear Q1 elasticity options","");CHKERRQ(ierr);
  {
    i = 3;
    ierr = PetscOptionsIntArray("-cells", "Number of (flux tube) processor in each dimension", "ex56.c", cells, &i, NULL);CHKERRQ(ierr);

    Lx = 1.; /* or ne for rod */
    max_conv_its = 3;
    ierr = PetscOptionsInt("-max_conv_its","Number of iterations in convergence study","",max_conv_its,&max_conv_its,NULL);CHKERRQ(ierr);
    if (max_conv_its<=0 || max_conv_its>7) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_USER, "Bad number of iterations for convergence test (%D)",max_conv_its);
    ierr = PetscOptionsReal("-lx","Length of domain","",Lx,&Lx,NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-alpha","material coefficient inside circle","",s_soft_alpha,&s_soft_alpha,NULL);CHKERRQ(ierr);
    ierr = PetscOptionsBool("-test_nonzero_cols","nonzero test","",test_nonzero_cols,&test_nonzero_cols,NULL);CHKERRQ(ierr);
    ierr = PetscOptionsBool("-use_mat_nearnullspace","MatNearNullSpace API test","",use_nearnullspace,&use_nearnullspace,NULL);CHKERRQ(ierr);
    ierr = PetscOptionsInt("-run_type","0: twisting load on cantalever, 1: 3rd order accurate convergence test","",run_type,&run_type,NULL);CHKERRQ(ierr);
    i = 3;
    ierr = PetscOptionsInt("-mat_block_size","","",i,&i,&flg);CHKERRQ(ierr);
    if (!flg || i!=3) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_USER, "'-mat_block_size 3' must be set (%D) and = 3 (%D)",flg,flg? i : 3);
  }
  ierr = PetscOptionsEnd();CHKERRQ(ierr);
  ierr = PetscLogStageRegister("Mesh Setup", &stage[6]);CHKERRQ(ierr);
  ierr = PetscLogStageRegister("1st Setup", &stage[0]);CHKERRQ(ierr);
  ierr = PetscLogStageRegister("1st Solve", &stage[1]);CHKERRQ(ierr);

  /* create DM, Plex calls DMSetup */
  ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
  ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr);
  {
    DMLabel         label;
    IS              is;
    ierr = DMCreateLabel(dm, "boundary");CHKERRQ(ierr);
    ierr = DMGetLabel(dm, "boundary", &label);CHKERRQ(ierr);
    ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr);
    if (run_type==0) {
      ierr = DMGetStratumIS(dm, "boundary", 1,  &is);CHKERRQ(ierr);
      ierr = DMCreateLabel(dm,"Faces");CHKERRQ(ierr);
      if (is) {
        PetscInt        d, f, Nf;
        const PetscInt *faces;
        PetscInt        csize;
        PetscSection    cs;
        Vec             coordinates ;
        DM              cdm;
        ierr = ISGetLocalSize(is, &Nf);CHKERRQ(ierr);
        ierr = ISGetIndices(is, &faces);CHKERRQ(ierr);
        ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
        ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
        ierr = DMGetDefaultSection(cdm, &cs);CHKERRQ(ierr);
        /* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */
        for (f = 0; f < Nf; ++f) {
          PetscReal   faceCoord;
          PetscInt    b,v;
          PetscScalar *coords = NULL;
          PetscInt    Nv;
          ierr = DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
          Nv   = csize/dim; /* Calculate mean coordinate vector */
          for (d = 0; d < dim; ++d) {
            faceCoord = 0.0;
            for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]);
            faceCoord /= Nv;
            for (b = 0; b < 2; ++b) {
              if (PetscAbs(faceCoord - b) < PETSC_SMALL) { /* domain have not been set yet, still [0,1]^3 */
                ierr = DMSetLabelValue(dm, "Faces", faces[f], d*2+b+1);CHKERRQ(ierr);
              }
            }
          }
          ierr = DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
        }
        ierr = ISRestoreIndices(is, &faces);CHKERRQ(ierr);
      }
      ierr = ISDestroy(&is);CHKERRQ(ierr);
      ierr = DMGetLabel(dm, "Faces", &label);CHKERRQ(ierr);
      ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr);
    }
  }
  {
    PetscInt dimEmbed, i;
    PetscInt nCoords;
    PetscScalar *coords,bounds[] = {0,Lx,-.5,.5,-.5,.5,}; /* x_min,x_max,y_min,y_max */
    Vec coordinates;
    if (run_type==1) {
      for (i = 0; i < 2*dim; i++) bounds[i] = (i%2) ? 1 : 0;
    }
    ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr);
    ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr);
    if (dimEmbed != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"dimEmbed != dim %D",dimEmbed);CHKERRQ(ierr);
    ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr);
    if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");CHKERRQ(ierr);
    ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr);
    for (i = 0; i < nCoords; i += dimEmbed) {
      PetscInt j;
      PetscScalar *coord = &coords[i];
      for (j = 0; j < dimEmbed; j++) {
        coord[j] = bounds[2 * j] + coord[j] * (bounds[2 * j + 1] - bounds[2 * j]);
      }
    }
    ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr);
    ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr);
  }

  /* convert to p4est, and distribute */

  ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
  ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format (should not be Plex!)","ex56.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
  ierr = PetscOptionsEnd();
  if (flg) {
    DM newdm;
    ierr = DMConvert(dm,convType,&newdm);CHKERRQ(ierr);
    if (newdm) {
      const char *prefix;
      PetscBool isForest;
      ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
      ierr = PetscObjectSetOptionsPrefix((PetscObject)newdm,prefix);CHKERRQ(ierr);
      ierr = DMIsForest(newdm,&isForest);CHKERRQ(ierr);
      if (isForest) {
      } else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?");
      ierr = DMDestroy(&dm);CHKERRQ(ierr);
      dm   = newdm;
    } else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?");
  } else {
    /* Plex Distribute mesh over processes */
    ierr = DMPlexDistribute(dm, 0, NULL, &distdm);CHKERRQ(ierr);
    if (distdm) {
      const char *prefix;
      ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
      ierr = PetscObjectSetOptionsPrefix((PetscObject)distdm,prefix);CHKERRQ(ierr);
      ierr = DMDestroy(&dm);CHKERRQ(ierr);
      dm   = distdm;
    }
  }
  ierr = PetscLogStagePop();CHKERRQ(ierr);
  basedm = dm; dm = NULL;

  for (iter=0 ; iter<max_conv_its ; iter++) {
    ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
    /* make new DM */
    ierr = DMClone(basedm, &dm);CHKERRQ(ierr);
    ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, "ex56_");CHKERRQ(ierr);
    ierr = PetscObjectSetName( (PetscObject)dm,"Mesh");CHKERRQ(ierr);
    ierr = PetscOptionsClearValue(NULL,"-ex56_dm_refine");CHKERRQ(ierr);
    ierr = PetscOptionsInsertString(NULL,options[iter]);CHKERRQ(ierr);
    ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* refinement done here in Plex, p4est */
    /* snes */
    ierr = SNESCreate(comm, &snes);CHKERRQ(ierr);
    ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
    /* fem */
    {
      const PetscInt Ncomp = dim;
      const PetscInt components[] = {0,1,2};
      const PetscInt Nfid = 1, Npid = 1;
      const PetscInt fid[] = {1}; /* The fixed faces (x=0) */
      const PetscInt pid[] = {2}; /* The faces with loading (x=L_x) */
      PetscFE         fe;
      PetscDS         prob;
      DM              cdm = dm;

      ierr = PetscFECreateDefault(dm, dim, dim, PETSC_FALSE, NULL, PETSC_DECIDE, &fe);CHKERRQ(ierr); /* elasticity */
      ierr = PetscObjectSetName((PetscObject) fe, "deformation");CHKERRQ(ierr);
      /* FEM prob */
      ierr = DMGetDS(dm, &prob);CHKERRQ(ierr);
      ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr);
      /* setup problem */
      if (run_type==1) {
        ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d);CHKERRQ(ierr);
        ierr = PetscDSSetResidual(prob, 0, f0_u_x4, f1_u_3d);CHKERRQ(ierr);
      } else {
        ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d_alpha);CHKERRQ(ierr);
        ierr = PetscDSSetResidual(prob, 0, f0_u, f1_u_3d_alpha);CHKERRQ(ierr);
        ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u_3d, f1_bd_u);CHKERRQ(ierr);
      }
      /* bcs */
      if (run_type==1) {
        PetscInt id = 1;
        ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "boundary", 0, 0, NULL, (void (*)()) zero, 1, &id, NULL);CHKERRQ(ierr);
      } else {
        ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "fixed", "Faces", 0, Ncomp, components, (void (*)()) zero, Nfid, fid, NULL);CHKERRQ(ierr);
        ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "traction", "Faces", 0, Ncomp, components, NULL, Npid, pid, NULL);CHKERRQ(ierr);
      }
      while (cdm) {
        ierr = DMSetDS(cdm,prob);CHKERRQ(ierr);
        ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
      }
      ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
    }
    /* vecs & mat */
    ierr = DMCreateGlobalVector(dm,&xx);CHKERRQ(ierr);
    ierr = VecDuplicate(xx, &bb);CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject) bb, "b");CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject) xx, "u");CHKERRQ(ierr);
    ierr = DMCreateMatrix(dm, &Amat);CHKERRQ(ierr);
    ierr = VecGetSize(bb,&N);CHKERRQ(ierr);
    local_sizes[iter] = N;
    ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d global equations, %d vertices\n",rank,PETSC_FUNCTION_NAME,N,N/dim);CHKERRQ(ierr);
    if (use_nearnullspace && N/dim > 1) {
      /* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */
      DM           subdm;
      MatNullSpace nearNullSpace;
      PetscInt     fields = 0;
      PetscObject  deformation;
      ierr = DMCreateSubDM(dm, 1, &fields, NULL, &subdm);CHKERRQ(ierr);
      ierr = DMPlexCreateRigidBody(subdm, &nearNullSpace);CHKERRQ(ierr);
      ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr);
      ierr = PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);CHKERRQ(ierr);
      ierr = DMDestroy(&subdm);CHKERRQ(ierr);
      ierr = MatNullSpaceDestroy(&nearNullSpace);CHKERRQ(ierr); /* created by DM and destroyed by Mat */
    }
    ierr = DMPlexSetSNESLocalFEM(dm,NULL,NULL,NULL);CHKERRQ(ierr);
    ierr = SNESSetJacobian(snes, Amat, Amat, NULL, NULL);CHKERRQ(ierr);
    ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
    ierr = DMSetUp(dm);CHKERRQ(ierr);
    ierr = PetscLogStagePop();CHKERRQ(ierr);
    ierr = PetscLogStagePush(stage[0]);CHKERRQ(ierr);
    /* ksp */
    ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr);
    ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
    /* test BCs */
    ierr = VecZeroEntries(xx);CHKERRQ(ierr);
    if (test_nonzero_cols) {
      if (rank==0) ierr = VecSetValue(xx,0,1.0,INSERT_VALUES);CHKERRQ(ierr);
      ierr = VecAssemblyBegin(xx);CHKERRQ(ierr);
      ierr = VecAssemblyEnd(xx);CHKERRQ(ierr);
    }
    ierr = VecZeroEntries(bb);CHKERRQ(ierr);
    ierr = VecGetSize(bb,&i);CHKERRQ(ierr);
    local_sizes[iter] = i;
    ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d equations in vector, %d vertices\n",rank,PETSC_FUNCTION_NAME,i,i/dim);CHKERRQ(ierr);
    /* setup solver, dummy solve to really setup */
    if (0) {
      ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1);CHKERRQ(ierr);
      ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
      ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,50);CHKERRQ(ierr);
      ierr = VecZeroEntries(xx);CHKERRQ(ierr);
    }
    ierr = PetscLogStagePop();CHKERRQ(ierr);
    /* solve */
    ierr = PetscLogStagePush(stage[1]);CHKERRQ(ierr);
    ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
    ierr = PetscLogStagePop();CHKERRQ(ierr);
    ierr = VecNorm(xx,NORM_INFINITY,&mdisp[iter]);CHKERRQ(ierr);
    ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
    {
      PetscViewer       viewer = NULL;
      PetscViewerFormat fmt;
      ierr = PetscOptionsGetViewer(comm,"ex56_","-vec_view",&viewer,&fmt,&flg);CHKERRQ(ierr);
      if (flg) {
        ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr);
        ierr = VecView(xx,viewer);CHKERRQ(ierr);
        ierr = VecView(bb,viewer);CHKERRQ(ierr);
        ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
      }
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }
    /* Free work space */
    ierr = DMDestroy(&dm);CHKERRQ(ierr);
    ierr = SNESDestroy(&snes);CHKERRQ(ierr);
    ierr = VecDestroy(&xx);CHKERRQ(ierr);
    ierr = VecDestroy(&bb);CHKERRQ(ierr);
    ierr = MatDestroy(&Amat);CHKERRQ(ierr);
  }
  ierr = DMDestroy(&basedm);CHKERRQ(ierr);
  if (run_type==1) {
    err[0] = 59.975208 - mdisp[0]; /* error with what I think is the exact solution */
  } else {
    err[0] = 171.038 - mdisp[0];
  }
  for (iter=1 ; iter<max_conv_its ; iter++) {
    if (run_type==1) {
      err[iter] = 59.975208 - mdisp[iter];
    } else {
      err[iter] = 171.038 - mdisp[iter];
    }
    PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %D) N=%12D, max displ=%9.7e, disp diff=%9.2e, error=%4.3e, rate=%3.2g\n",
                rank,PETSC_FUNCTION_NAME,iter,local_sizes[iter],mdisp[iter],
                mdisp[iter]-mdisp[iter-1],err[iter],log(err[iter-1]/err[iter])/log(2.));
  }

  ierr = PetscFinalize();
  return ierr;
}
Exemple #4
0
int main(int argc, char **argv)
{
  DM             dm;
  PetscSection   s;
  Vec            u;
  AppCtx         user;
  PetscInt       cells[3] = {2, 2, 2};
  PetscInt       size = 0, cStart, cEnd, cell, c, f, i, j;
  PetscErrorCode ierr;

  ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
  ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
  ierr = DMPlexCreateHexBoxMesh(PETSC_COMM_WORLD, user.dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr);
  ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
  /* Create a section for SEM order k */
  {
    PetscInt *numDof, d;

    ierr = PetscMalloc1(user.Nf*(user.dim+1), &numDof);CHKERRQ(ierr);
    for (f = 0; f < user.Nf; ++f) {
      for (d = 0; d <= user.dim; ++d) numDof[f*(user.dim+1)+d] = PetscPowInt(user.k[f]-1, d)*user.Nc[f];
      size += PetscPowInt(user.k[f]+1, d)*user.Nc[f];
    }
    ierr = DMPlexCreateSection(dm, user.dim, user.Nf, user.Nc, numDof, 0, NULL, NULL, NULL, NULL, &s);CHKERRQ(ierr);
    ierr = SetSymmetries(dm, s, &user);CHKERRQ(ierr);
    ierr = PetscFree(numDof);CHKERRQ(ierr);
  }
  ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
  /* Create spectral ordering and load in data */
  ierr = DMPlexCreateSpectralClosurePermutation(dm, NULL);CHKERRQ(ierr);
  ierr = DMGetLocalVector(dm, &u);CHKERRQ(ierr);
  switch (user.dim) {
  case 2: ierr = LoadData2D(dm, 2, 2, size, u, &user);CHKERRQ(ierr);break;
  case 3: ierr = LoadData3D(dm, 2, 2, 2, size, u, &user);CHKERRQ(ierr);break;
  }
  /* Remove ordering and check some values */
  ierr = PetscSectionSetClosurePermutation(s, (PetscObject) dm, NULL);CHKERRQ(ierr);
  switch (user.dim) {
  case 2:
    ierr = CheckPoint(dm, u,  0, &user);CHKERRQ(ierr);
    ierr = CheckPoint(dm, u, 13, &user);CHKERRQ(ierr);
    ierr = CheckPoint(dm, u, 15, &user);CHKERRQ(ierr);
    ierr = CheckPoint(dm, u, 19, &user);CHKERRQ(ierr);
    break;
  case 3:
    ierr = CheckPoint(dm, u,  0, &user);CHKERRQ(ierr);
    ierr = CheckPoint(dm, u, 13, &user);CHKERRQ(ierr);
    ierr = CheckPoint(dm, u, 15, &user);CHKERRQ(ierr);
    ierr = CheckPoint(dm, u, 19, &user);CHKERRQ(ierr);
    break;
  }
  /* Recreate spectral ordering and read out data */
  ierr = DMPlexCreateSpectralClosurePermutation(dm, s);CHKERRQ(ierr);
  switch (user.dim) {
  case 2: ierr = ReadData2D(dm, u, &user);CHKERRQ(ierr);break;
  case 3: ierr = ReadData3D(dm, u, &user);CHKERRQ(ierr);break;
  }
  ierr = DMRestoreLocalVector(dm, &u);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
  ierr = DMDestroy(&dm);CHKERRQ(ierr);
  ierr = PetscFree(user.Nc);CHKERRQ(ierr);
  ierr = PetscFree(user.k);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Exemple #5
0
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
  DM             dmDist      = NULL;
  PetscInt       dim         = user->dim;
  PetscBool      cellSimplex = user->cellSimplex;
  const char    *filename    = user->filename;
  const PetscInt cells[3]    = {2, 2, 2};
  size_t         len;
  PetscErrorCode ierr;

  PetscFunctionBeginUser;
  ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
  if (len)              {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);}
  else if (cellSimplex) {ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, dm);CHKERRQ(ierr);}
  else                  {ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);CHKERRQ(ierr);}
  if (user->testPartition) {
    PetscPartitioner part;
    const PetscInt  *sizes  = NULL;
    const PetscInt  *points = NULL;
    PetscMPIInt      rank, numProcs;

    ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
    ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
    if (!rank) {
      if (dim == 2 && cellSimplex && numProcs == 2) {
        switch (user->testNum) {
        case 0: {
          PetscInt triSizes_p2[2]  = {4, 4};
          PetscInt triPoints_p2[8] = {3, 5, 6, 7, 0, 1, 2, 4};

          sizes = triSizes_p2; points = triPoints_p2;break;}
        case 1: {
          PetscInt triSizes_p2[2]  = {6, 2};
          PetscInt triPoints_p2[8] = {1, 2, 3, 4, 6, 7, 0, 5};

          sizes = triSizes_p2; points = triPoints_p2;break;}
        default:
          SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for triangular mesh on 2 procs", user->testNum);
        }
      } else if (dim == 2 && cellSimplex && numProcs == 3) {
        PetscInt triSizes_p3[3]  = {3, 3, 2};
        PetscInt triPoints_p3[8] = {1, 2, 4, 3, 6, 7, 0, 5};

        sizes = triSizes_p3; points = triPoints_p3;
      } else if (dim == 2 && !cellSimplex && numProcs == 2) {
        PetscInt quadSizes_p2[2]  = {2, 2};
        PetscInt quadPoints_p2[4] = {2, 3, 0, 1};

        sizes = quadSizes_p2; points = quadPoints_p2;
      } else SETERRQ3(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test partition dim: %D simplex: %D numProcs: %D", dim, (PetscInt) cellSimplex, (PetscInt) numProcs);
    }
    ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
    ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr);
    ierr = PetscPartitionerShellSetPartition(part, numProcs, sizes, points);CHKERRQ(ierr);
  }
  ierr = DMPlexDistribute(*dm, 0, NULL, &dmDist);CHKERRQ(ierr);
  if (dmDist) {
    ierr = DMDestroy(dm);CHKERRQ(ierr);
    *dm  = dmDist;
  }
  ierr = PetscObjectSetName((PetscObject) *dm, cellSimplex ? "Simplicial Mesh" : "Tensor Product Mesh");CHKERRQ(ierr);
  ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Exemple #6
0
PetscErrorCode CreateMesh(MPI_Comm comm, PetscInt testNum, AppCtx *user, DM *dm)
{
  PetscInt       dim          = user->dim;
  PetscBool      cellSimplex  = user->cellSimplex;
  PetscBool      useGenerator = user->useGenerator;
  const char    *filename     = user->filename;
  size_t         len;
  PetscMPIInt    rank;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
  if (len) {
    ierr = DMPlexCreateFromFile(comm, filename, PETSC_FALSE, dm);CHKERRQ(ierr);
    ierr = DMGetDimension(*dm, &dim);CHKERRQ(ierr);
  } else if (useGenerator) {
    if (cellSimplex) {
      ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_FALSE, dm);CHKERRQ(ierr);
    } else {
      const PetscInt cells[3] = {2, 2, 2};

      ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, PETSC_FALSE, PETSC_FALSE, PETSC_FALSE, dm);CHKERRQ(ierr);
    }
  } else {
    ierr = DMCreate(comm, dm);CHKERRQ(ierr);
    ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
    ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
    switch (dim) {
    case 2:
      if (cellSimplex) {
        ierr = CreateSimplex_2D(comm, *dm);CHKERRQ(ierr);
      } else {
        ierr = CreateQuad_2D(comm, testNum, *dm);CHKERRQ(ierr);
      }
      break;
    case 3:
      if (cellSimplex) {
        ierr = CreateSimplex_3D(comm, *dm);CHKERRQ(ierr);
      } else {
        ierr = CreateHex_3D(comm, *dm);CHKERRQ(ierr);
      }
      break;
    default:
      SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
    }
  }
  {
    DM interpolatedMesh = NULL;

    ierr = CheckMesh(*dm, user);CHKERRQ(ierr);
    ierr = DMPlexInterpolate(*dm, &interpolatedMesh);CHKERRQ(ierr);
    ierr = DMPlexCopyCoordinates(*dm, interpolatedMesh);CHKERRQ(ierr);
    ierr = CompareCones(*dm, interpolatedMesh);CHKERRQ(ierr);
    ierr = DMDestroy(dm);CHKERRQ(ierr);
    *dm  = interpolatedMesh;
  }
  {
    DM distributedMesh = NULL;

    /* Distribute mesh over processes */
    ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
    if (distributedMesh) {
      ierr = DMViewFromOptions(distributedMesh, NULL, "-dm_view");CHKERRQ(ierr);
      ierr = DMDestroy(dm);CHKERRQ(ierr);
      *dm  = distributedMesh;
    }
  }
  ierr = PetscObjectSetName((PetscObject) *dm, "Interpolated Mesh");CHKERRQ(ierr);
  ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
  user->dm = *dm;
  PetscFunctionReturn(0);
}
Exemple #7
0
int main(int argc, char **argv)
{
  MPI_Comm       comm;
  DM             base, preForest, postForest;
  PetscInt       dim = 2;
  PetscInt       preCount, postCount;
  Vec            preVec, postVecTransfer, postVecExact;
  PetscErrorCode (*funcs[1]) (PetscInt,PetscReal,const PetscReal [],PetscInt,PetscScalar [], void *) = {MultiaffineFunction};
  void           *ctxs[1] = {NULL};
  const PetscInt cells[] = {3, 3, 3};
  PetscReal      diff, tol = PETSC_SMALL;
  PetscBool      linear = PETSC_FALSE;
  PetscBool      useFV = PETSC_FALSE;
  PetscDS        ds;
  bc_func_ctx    bcCtx;
  DMLabel        adaptLabel;
  PetscErrorCode ierr;

  ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
  comm = PETSC_COMM_WORLD;
  ierr = PetscOptionsBegin(comm, "", "DMForestTransferVec() Test Options", "DMFOREST");CHKERRQ(ierr);
  ierr = PetscOptionsInt("-dim", "The dimension (2 or 3)", "ex2.c", dim, &dim, NULL);CHKERRQ(ierr);
  ierr = PetscOptionsBool("-linear","Transfer a simple linear function", "ex2.c", linear, &linear, NULL);CHKERRQ(ierr);
  ierr = PetscOptionsBool("-use_fv","Use a finite volume approximation", "ex2.c", useFV, &useFV, NULL);CHKERRQ(ierr);
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  if (linear) {
    funcs[0] = LinearFunction;
  }

  bcCtx.func = funcs[0];
  bcCtx.dim  = dim;
  bcCtx.Nf   = 1;
  bcCtx.ctx  = NULL;

  /* the base mesh */
  ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &base);CHKERRQ(ierr);
  if (useFV) {
    PetscFV      fv;
    PetscLimiter limiter;
    DM           baseFV;

    ierr = DMPlexConstructGhostCells(base,NULL,NULL,&baseFV);CHKERRQ(ierr);
    ierr = DMDestroy(&base);CHKERRQ(ierr);
    base = baseFV;
    ierr = PetscFVCreate(comm, &fv);CHKERRQ(ierr);
    ierr = PetscFVSetSpatialDimension(fv,dim);CHKERRQ(ierr);
    ierr = PetscFVSetType(fv,PETSCFVLEASTSQUARES);CHKERRQ(ierr);
    ierr = PetscFVSetNumComponents(fv,1);CHKERRQ(ierr);
    ierr = PetscLimiterCreate(comm,&limiter);CHKERRQ(ierr);
    ierr = PetscLimiterSetType(limiter,PETSCLIMITERNONE);CHKERRQ(ierr);
    ierr = PetscFVSetLimiter(fv,limiter);CHKERRQ(ierr);
    ierr = PetscLimiterDestroy(&limiter);CHKERRQ(ierr);
    ierr = PetscFVSetFromOptions(fv);CHKERRQ(ierr);
    ierr = DMSetField(base,0,(PetscObject)fv);CHKERRQ(ierr);
    ierr = PetscFVDestroy(&fv);CHKERRQ(ierr);
  } else {
    PetscFE fe;
    ierr = PetscFECreateDefault(base,dim,1,PETSC_FALSE,NULL,PETSC_DEFAULT,&fe);CHKERRQ(ierr);
    ierr = DMSetField(base,0,(PetscObject)fe);CHKERRQ(ierr);
    ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
  }
  {
    PetscDS  prob;
    PetscInt comps[] = {0};
    PetscInt ids[]   = {1, 2, 3, 4, 5, 6};

    ierr = DMGetDS(base,&prob);CHKERRQ(ierr);
    ierr = PetscDSAddBoundary(prob,PETSC_TRUE, "bc", "marker", 0, 1, comps, useFV ? (void(*)()) bc_func_fv : (void(*)()) funcs[0], 2 * dim, ids, useFV ? (void *) &bcCtx : NULL);CHKERRQ(ierr);
  }
  ierr = AddIdentityLabel(base);CHKERRQ(ierr);
  ierr = DMViewFromOptions(base,NULL,"-dm_base_view");CHKERRQ(ierr);

  /* the pre adaptivity forest */
  ierr = DMCreate(comm,&preForest);CHKERRQ(ierr);
  ierr = DMSetType(preForest,(dim == 2) ? DMP4EST : DMP8EST);CHKERRQ(ierr);
  ierr = DMGetDS(base,&ds);CHKERRQ(ierr);
  ierr = DMSetDS(preForest,ds);CHKERRQ(ierr);
  ierr = DMForestSetBaseDM(preForest,base);CHKERRQ(ierr);
  ierr = DMForestSetMinimumRefinement(preForest,1);CHKERRQ(ierr);
  ierr = DMForestSetInitialRefinement(preForest,1);CHKERRQ(ierr);
  ierr = DMSetFromOptions(preForest);CHKERRQ(ierr);
  ierr = DMSetUp(preForest);CHKERRQ(ierr);
  ierr = DMViewFromOptions(preForest,NULL,"-dm_pre_view");CHKERRQ(ierr);

  /* the pre adaptivity field */
  ierr = DMCreateGlobalVector(preForest,&preVec);CHKERRQ(ierr);
  ierr = DMProjectFunction(preForest,0.,funcs,ctxs,INSERT_VALUES,preVec);CHKERRQ(ierr);
  ierr = VecViewFromOptions(preVec,NULL,"-vec_pre_view");CHKERRQ(ierr);

  ierr = PetscObjectGetReference((PetscObject)preForest,&preCount);CHKERRQ(ierr);

  /* adapt */
  ierr = CreateAdaptivityLabel(preForest,&adaptLabel);CHKERRQ(ierr);
  ierr = DMForestTemplate(preForest,comm,&postForest);CHKERRQ(ierr);
  ierr = DMForestSetMinimumRefinement(postForest,0);CHKERRQ(ierr);
  ierr = DMForestSetInitialRefinement(postForest,0);CHKERRQ(ierr);
  ierr = DMForestSetAdaptivityLabel(postForest,adaptLabel);CHKERRQ(ierr);
  ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr);
  ierr = DMSetUp(postForest);CHKERRQ(ierr);
  ierr = DMViewFromOptions(postForest,NULL,"-dm_post_view");CHKERRQ(ierr);

  /* transfer */
  ierr = DMCreateGlobalVector(postForest,&postVecTransfer);CHKERRQ(ierr);
  ierr = DMForestTransferVec(preForest,preVec,postForest,postVecTransfer,PETSC_TRUE,0.0);CHKERRQ(ierr);
  ierr = VecViewFromOptions(postVecTransfer,NULL,"-vec_post_transfer_view");CHKERRQ(ierr);

  /* the exact post adaptivity field */
  ierr = DMCreateGlobalVector(postForest,&postVecExact);CHKERRQ(ierr);
  ierr = DMProjectFunction(postForest,0.,funcs,ctxs,INSERT_VALUES,postVecExact);CHKERRQ(ierr);
  ierr = VecViewFromOptions(postVecExact,NULL,"-vec_post_exact_view");CHKERRQ(ierr);

  /* compare */
  ierr = VecAXPY(postVecTransfer,-1.,postVecExact);CHKERRQ(ierr);
  ierr = VecViewFromOptions(postVecTransfer,NULL,"-vec_diff_view");CHKERRQ(ierr);
  ierr = VecNorm(postVecTransfer,NORM_2,&diff);CHKERRQ(ierr);

  /* output */
  if (diff < tol) {
    ierr = PetscPrintf(comm,"DMForestTransferVec() passes.\n");CHKERRQ(ierr);
  } else {
    ierr = PetscPrintf(comm,"DMForestTransferVec() fails with error %g and tolerance %g\n",diff,tol);CHKERRQ(ierr);
  }

  /* disconnect preForest from postForest */
  ierr = DMForestSetAdaptivityForest(postForest,NULL);CHKERRQ(ierr);
  ierr = PetscObjectGetReference((PetscObject)preForest,&postCount);CHKERRQ(ierr);
  if (postCount != preCount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Adaptation not memory neutral: reference count increase from %d to %d\n",preCount,postCount);

  /* cleanup */
  ierr = VecDestroy(&postVecExact);CHKERRQ(ierr);
  ierr = VecDestroy(&postVecTransfer);CHKERRQ(ierr);
  ierr = DMDestroy(&postForest);CHKERRQ(ierr);
  ierr = VecDestroy(&preVec);CHKERRQ(ierr);
  ierr = DMDestroy(&preForest);CHKERRQ(ierr);
  ierr = DMDestroy(&base);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Exemple #8
0
PetscErrorCode CreateMesh(MPI_Comm comm, PetscInt testNum, AppCtx *user, DM *dm)
{
  PetscInt       dim          = user->dim;
  PetscBool      cellSimplex  = user->cellSimplex;
  PetscBool      useGenerator = user->useGenerator;
  const char    *filename     = user->filename;
  const char    *partitioner  = "chaco";
  size_t         len;
  PetscMPIInt    rank;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
  if (len) {
#if defined(PETSC_HAVE_EXODUSII)
    int   CPU_word_size = 0, IO_word_size = 0, exoid = -1;
    float version;

    if (!rank) {
      exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version);
      if (exoid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open(\"%s\",...) did not return a valid file ID", filename);
    }
    ierr = DMPlexCreateExodus(comm, exoid, PETSC_FALSE, dm);CHKERRQ(ierr);
    if (!rank) {ierr = ex_close(exoid);CHKERRQ(ierr);}
    ierr = DMPlexGetDimension(*dm, &dim);CHKERRQ(ierr);
#else
    SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires ExodusII support. Reconfigure using --download-exodusii");
#endif
  } else if (useGenerator) {
    if (cellSimplex) {
      ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, dm);CHKERRQ(ierr);
    } else {
      ierr = DMPlexCreateHexBoxMesh(comm, dim, PETSC_FALSE, dm);CHKERRQ(ierr);
    }
  } else {
    ierr = DMCreate(comm, dm);CHKERRQ(ierr);
    ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
    ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr);
    switch (dim) {
    case 2:
      if (cellSimplex) {
        ierr = CreateSimplex_2D(comm, *dm);CHKERRQ(ierr);
      } else {
        ierr = CreateQuad_2D(comm, testNum, *dm);CHKERRQ(ierr);
      }
      break;
    case 3:
      if (cellSimplex) {
        ierr = CreateSimplex_3D(comm, *dm);CHKERRQ(ierr);
      } else {
        ierr = CreateHex_3D(comm, *dm);CHKERRQ(ierr);
      }
      break;
    default:
      SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
    }
  }
  {
    DM interpolatedMesh = NULL;

    ierr = CheckMesh(*dm);CHKERRQ(ierr);
    ierr = DMPlexInterpolate(*dm, &interpolatedMesh);CHKERRQ(ierr);
    ierr = DMPlexCopyCoordinates(*dm, interpolatedMesh);CHKERRQ(ierr);
    ierr = CompareCones(*dm, interpolatedMesh);CHKERRQ(ierr);
    ierr = DMDestroy(dm);CHKERRQ(ierr);
    *dm  = interpolatedMesh;
  }
  {
    DM distributedMesh = NULL;

    /* Distribute mesh over processes */
    ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr);
    if (distributedMesh) {
      ierr = DMDestroy(dm);CHKERRQ(ierr);
      *dm  = distributedMesh;
    }
  }
  ierr     = PetscObjectSetName((PetscObject) *dm, "Interpolated Mesh");CHKERRQ(ierr);
  ierr     = DMSetFromOptions(*dm);CHKERRQ(ierr);
  user->dm = *dm;
  PetscFunctionReturn(0);
}
Exemple #9
0
PETSC_EXTERN void PETSC_STDCALL  dmplexcreatehexboxmesh_(MPI_Fint * comm,PetscInt *dim, PetscInt cells[],DMBoundaryType *periodicX,DMBoundaryType *periodicY,DMBoundaryType *periodicZ,DM *dm, int *__ierr ){
*__ierr = DMPlexCreateHexBoxMesh(
	MPI_Comm_f2c( *(comm) ),*dim,cells,*periodicX,*periodicY,*periodicZ,dm);
}
Exemple #10
0
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
  PetscInt       dim               = user->dim;
  PetscBool      interpolate       = user->interpolate;
  PetscBool      refinementUniform = user->refinementUniform;
  PetscReal      refinementLimit   = user->refinementLimit;
  PetscBool      cellSimplex       = user->cellSimplex;
  const char    *filename          = user->filename;
  const char    *partitioner       = "chaco";
  size_t         len;
  PetscMPIInt    rank;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
  if (len) {
#if defined(PETSC_HAVE_CGNS)
    int cgid = -1;

    if (!rank) {
      ierr = cg_open(filename, CG_MODE_READ, &cgid);CHKERRQ(ierr);
      if (cgid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename);
    }
    ierr = DMPlexCreateCGNS(comm, cgid, interpolate, dm);CHKERRQ(ierr);
    if (!rank) {ierr = cg_close(cgid);CHKERRQ(ierr);}
#else
    SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir");
#endif
  } else if (cellSimplex) {
    ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);
  } else {
    const PetscInt cells[3] = {2, 2, 2};

    ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, dm);CHKERRQ(ierr);
  }
  {
    DM refinedMesh     = NULL;
    DM distributedMesh = NULL;

    /* Refine mesh using a volume constraint */
    ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
    ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
    ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
    if (refinedMesh) {
      ierr = DMDestroy(dm);CHKERRQ(ierr);
      *dm  = refinedMesh;
    }
    /* Distribute mesh over processes */
    ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr);
    if (distributedMesh) {
      ierr = DMDestroy(dm);CHKERRQ(ierr);
      *dm  = distributedMesh;
    }
    if (refinementUniform) {
      ierr = DMPlexSetRefinementUniform(*dm, refinementUniform);CHKERRQ(ierr);
      ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
      if (refinedMesh) {
        ierr = DMDestroy(dm);CHKERRQ(ierr);
        *dm  = refinedMesh;
      }
    }
  }
  ierr     = PetscObjectSetName((PetscObject) *dm, "Simplical Mesh");CHKERRQ(ierr);
  ierr     = DMSetFromOptions(*dm);CHKERRQ(ierr);
  ierr     = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
  user->dm = *dm;
  PetscFunctionReturn(0);
}