PETScDMDAMesh.C File Reference

Go to the source code of this file.

Functions
	registerMooseObject ("ExternalPetscSolverApp", PETScDMDAMesh)
template<>
InputParameters	validParams< PETScDMDAMesh > ()
dof_id_type	node_id_Quad4 (const ElemType, const dof_id_type nx, const dof_id_type, const dof_id_type i, const dof_id_type j, const dof_id_type)
void	add_element_Quad4 (DM da, const dof_id_type nx, const dof_id_type ny, const dof_id_type i, const dof_id_type j, const dof_id_type elem_id, const processor_id_type pid, const ElemType type, MeshBase &mesh)
void	set_boundary_names_Quad4 (BoundaryInfo &boundary_info)
void	get_indices_Quad4 (const dof_id_type nx, const dof_id_type, const dof_id_type elem_id, dof_id_type &i, dof_id_type &j)
dof_id_type	elem_id_Quad4 (const dof_id_type nx, const dof_id_type, const dof_id_type i, const dof_id_type j, const dof_id_type)
void	get_neighbors_Quad4 (const dof_id_type nx, const dof_id_type ny, const dof_id_type i, const dof_id_type j, std::vector< dof_id_type > &neighbors)
void	get_ghost_neighbors_Quad4 (const dof_id_type nx, const dof_id_type ny, const MeshBase &mesh, std::set< dof_id_type > &ghost_elems)
void	add_node_Qua4 (dof_id_type nx, dof_id_type ny, dof_id_type i, dof_id_type j, processor_id_type pid, ElemType type, MeshBase &mesh)
void	build_cube_Quad4 (UnstructuredMesh &mesh, DM da, const ElemType type)

Function Documentation

add_element_Quad4()

void add_element_Quad4	(	DM	da,
		const dof_id_type	nx,
		const dof_id_type	ny,
		const dof_id_type	i,
		const dof_id_type	j,
		const dof_id_type	elem_id,
		const processor_id_type	pid,
		const ElemType	type,
		MeshBase &	mesh
	)

Definition at line 185 of file PETScDMDAMesh.C.

Referenced by build_cube_Quad4().

{
  BoundaryInfo & boundary_info = mesh.get_boundary_info();

#if LIBMESH_HAVE_PETSC
  // Mx: number of grid points in x direction for all processors
  // My: number of grid points in y direction for all processors
  // xp: number of processors in x direction
  // yp: number of processors in y direction
  PetscInt Mx, My, xp, yp;
  DMDAGetInfo(da,
              PETSC_IGNORE,
              &Mx,
              &My,
              PETSC_IGNORE,
              &xp,
              &yp,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE);

  const PetscInt *lx, *ly;
  PetscInt *lxo, *lyo;
  // PETSc-3.8.x or older use PetscDataType
#if PETSC_VERSION_LESS_THAN(3, 9, 0)
  DMGetWorkArray(da, xp + yp + 2, PETSC_INT, &lxo);
#else
  // PETSc-3.9.x or newer use MPI_DataType
  DMGetWorkArray(da, xp + yp + 2, MPIU_INT, &lxo);
#endif
  // Gets the ranges of indices in the x, y and z direction that are owned by each process
  // Ranges here are different from what we have in Mat and Vec.
  // It means how many points each processor holds
  DMDAGetOwnershipRanges(da, &lx, &ly, NULL);
  lxo[0] = 0;
  for (PetscInt i = 0; i < xp; i++)
    lxo[i + 1] = lxo[i] + lx[i];

  lyo = lxo + xp + 1;
  lyo[0] = 0;
  for (PetscInt i = 0; i < yp; i++)
    lyo[i + 1] = lyo[i] + ly[i];

  // Try to calculate processor-grid coordinate (xpid, ypid)
  PetscInt xpid, ypid, xpidplus, ypidplus;
  // Finds integer in a sorted array of integers
  // Loc:  the location if found, otherwise -(slot+1)
  // where slot is the place the value would go
  PetscFindInt(i, xp + 1, lxo, &xpid);

  xpid = xpid < 0 ? -xpid - 1 - 1 : xpid;

  PetscFindInt(i + 1, xp + 1, lxo, &xpidplus);

  xpidplus = xpidplus < 0 ? -xpidplus - 1 - 1 : xpidplus;

  PetscFindInt(j, yp + 1, lyo, &ypid);

  ypid = ypid < 0 ? -ypid - 1 - 1 : ypid;

  PetscFindInt(j + 1, yp + 1, lyo, &ypidplus);

  ypidplus = ypidplus < 0 ? -ypidplus - 1 - 1 : ypidplus;
#if PETSC_VERSION_LESS_THAN(3, 9, 0)
  DMRestoreWorkArray(da, xp + yp + 2, PETSC_INT, &lxo);
#else
  DMRestoreWorkArray(da, xp + yp + 2, MPIU_INT, &lxo);
#endif
#endif
  // Bottom Left
  auto node0_ptr = mesh.add_point(Point(static_cast<Real>(i) / nx, static_cast<Real>(j) / ny, 0),
                                  node_id_Quad4(type, nx, 0, i, j, 0));
  node0_ptr->set_unique_id() = node_id_Quad4(type, nx, 0, i, j, 0);
  node0_ptr->set_id() = node0_ptr->unique_id();
  // xpid + ypid * xp is the global processor ID
  node0_ptr->processor_id() = xpid + ypid * xp;

  // Bottom Right
  auto node1_ptr =
      mesh.add_point(Point(static_cast<Real>(i + 1) / nx, static_cast<Real>(j) / ny, 0),
                     node_id_Quad4(type, nx, 0, i + 1, j, 0));
  node1_ptr->set_unique_id() = node_id_Quad4(type, nx, 0, i + 1, j, 0);
  node1_ptr->set_id() = node1_ptr->unique_id();
  node1_ptr->processor_id() = xpidplus + ypid * xp;

  // Top Right
  auto node2_ptr =
      mesh.add_point(Point(static_cast<Real>(i + 1) / nx, static_cast<Real>(j + 1) / ny, 0),
                     node_id_Quad4(type, nx, 0, i + 1, j + 1, 0));
  node2_ptr->set_unique_id() = node_id_Quad4(type, nx, 0, i + 1, j + 1, 0);
  node2_ptr->set_id() = node2_ptr->unique_id();
  node2_ptr->processor_id() = xpidplus + ypidplus * xp;

  // Top Left
  auto node3_ptr =
      mesh.add_point(Point(static_cast<Real>(i) / nx, static_cast<Real>(j + 1) / ny, 0),
                     node_id_Quad4(type, nx, 0, i, j + 1, 0));
  node3_ptr->set_unique_id() = node_id_Quad4(type, nx, 0, i, j + 1, 0);
  node3_ptr->set_id() = node3_ptr->unique_id();
  node3_ptr->processor_id() = xpid + ypidplus * xp;

  // New an element and attach four nodes to it
  Elem * elem = new Quad4;
  elem->set_id(elem_id);
  elem->processor_id() = pid;
  elem->set_unique_id() = elem_id;
  elem = mesh.add_elem(elem);
  elem->set_node(0) = node0_ptr;
  elem->set_node(1) = node1_ptr;
  elem->set_node(2) = node2_ptr;
  elem->set_node(3) = node3_ptr;

  // Bottom
  if (j == 0)
    boundary_info.add_side(elem, 0, 0);

  // Right
  if (i == nx - 1)
    boundary_info.add_side(elem, 1, 1);

  // Top
  if (j == ny - 1)
    boundary_info.add_side(elem, 2, 2);

  // Left
  if (i == 0)
    boundary_info.add_side(elem, 3, 3);
}

add_node_Qua4()

void add_node_Qua4	(	dof_id_type	nx,
		dof_id_type	ny,
		dof_id_type	i,
		dof_id_type	j,
		processor_id_type	pid,
		ElemType	type,
		MeshBase &	mesh
	)

Definition at line 418 of file PETScDMDAMesh.C.

Referenced by build_cube_Quad4().

{
  // Bottom Left
  auto node0_ptr = mesh.add_point(Point(static_cast<Real>(i) / nx, static_cast<Real>(j) / ny, 0),
                                  node_id_Quad4(type, nx, 0, i, j, 0));
  node0_ptr->set_unique_id() = node_id_Quad4(type, nx, 0, i, j, 0);
  node0_ptr->processor_id() = pid;
}

build_cube_Quad4()

void build_cube_Quad4	(	UnstructuredMesh &	mesh,
		DM	da,
		const ElemType	type
	)

Definition at line 435 of file PETScDMDAMesh.C.

Referenced by PETScDMDAMesh::buildMesh().

{
  const auto pid = mesh.comm().rank();

  BoundaryInfo & boundary_info = mesh.get_boundary_info();
  // xs: start grid point (not element) index on local in x direction
  // ys: start grid point index on local in y direction
  // xm: number of grid points owned by the local processor in x direction
  // ym: number of grid points owned by the local processor in y direction
  // Mx: number of grid points on all processors in x direction
  // My: number of grid points on all processors in y direction
  // xp: number of processor cores in x direction
  // yp: number of processor cores in y direction
  PetscInt xs, ys, xm, ym, Mx, My, xp, yp;

  /* Get local grid boundaries */
  DMDAGetCorners(da, &xs, &ys, PETSC_IGNORE, &xm, &ym, PETSC_IGNORE);
  DMDAGetInfo(da,
              PETSC_IGNORE,
              &Mx,
              &My,
              PETSC_IGNORE,
              &xp,
              &yp,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE,
              PETSC_IGNORE);

  for (PetscInt j = ys; j < ys + ym; j++)
    for (PetscInt i = xs; i < xs + xm; i++)
    {
      // We loop over grid points, but we are
      // here building elements. So that we just
      // simply skip the first x and y points since the
      // number of grid ponts is one more than
      // the number of grid elements
      if (!i || !j)
        continue;

      dof_id_type ele_id = (i - 1) + (j - 1) * (Mx - 1);

      add_element_Quad4(da, Mx - 1, My - 1, i - 1, j - 1, ele_id, pid, type, mesh);
    }

  // If there is no element at the given processor
  // We need to manually add all mesh nodes
  if ((ys == 0 && ym == 1) || (xs == 0 && xm == 1))
    for (PetscInt j = ys; j < ys + ym; j++)
      for (PetscInt i = xs; i < xs + xm; i++)
        add_node_Qua4(Mx, My, i, j, pid, type, mesh);

  // Need to link up the local elements before we can know what's missing
  mesh.find_neighbors();

  mesh.find_neighbors(true);

  // Set RemoteElem neighbors
  for (auto & elem_ptr : mesh.element_ptr_range())
    for (unsigned int s = 0; s < elem_ptr->n_sides(); s++)
      if (!elem_ptr->neighbor_ptr(s) && !boundary_info.n_boundary_ids(elem_ptr, s))
        elem_ptr->set_neighbor(s, const_cast<RemoteElem *>(remote_elem));

  set_boundary_names_Quad4(boundary_info);
  // Already partitioned!
  mesh.skip_partitioning(true);

  // No need to renumber or find neighbors - done did it.
  // Avoid deprecation message/error by _also_ setting
  // allow_renumbering(false). This is a bit silly, but we want to
  // catch cases where people are purely using the old "skip"
  // interface and not the new flag setting one.
  mesh.allow_renumbering(false);
  mesh.prepare_for_use(/*skip_renumber (ignored!) = */ false,
                       /*skip_find_neighbors = */ true);
}

elem_id_Quad4()

dof_id_type elem_id_Quad4	(	const dof_id_type	nx,
		const dof_id_type	,
		const dof_id_type	i,
		const dof_id_type	j,
		const dof_id_type
	)

Definition at line 347 of file PETScDMDAMesh.C.

Referenced by get_neighbors_Quad4().

{
  return (j * nx) + i;
}

get_ghost_neighbors_Quad4()

void get_ghost_neighbors_Quad4	(	const dof_id_type	nx,
		const dof_id_type	ny,
		const MeshBase &	mesh,
		std::set< dof_id_type > &	ghost_elems
	)

Definition at line 383 of file PETScDMDAMesh.C.

{
  auto & boundary_info = mesh.get_boundary_info();

  dof_id_type i, j;

  std::vector<dof_id_type> neighbors(4);

  for (auto elem_ptr : mesh.element_ptr_range())
  {
    for (unsigned int s = 0; s < elem_ptr->n_sides(); s++)
    {
      // No current neighbor
      if (!elem_ptr->neighbor_ptr(s))
      {
        // Not on a boundary
        if (!boundary_info.n_boundary_ids(elem_ptr, s))
        {
          auto elem_id = elem_ptr->id();

          get_indices_Quad4(nx, 0, elem_id, i, j);

          get_neighbors_Quad4(nx, ny, i, j, neighbors);

          ghost_elems.insert(neighbors[s]);
        }
      }
    }
  }
}

get_indices_Quad4()

void get_indices_Quad4	(	const dof_id_type	nx,
		const dof_id_type	,
		const dof_id_type	elem_id,
		dof_id_type &	i,
		dof_id_type &	j
	)

Definition at line 336 of file PETScDMDAMesh.C.

Referenced by get_ghost_neighbors_Quad4().

{
  i = elem_id % nx;
  j = (elem_id - i) / nx;
}

get_neighbors_Quad4()

void get_neighbors_Quad4 ( const dof_id_type  nx, const dof_id_type  ny, const dof_id_type  i, const dof_id_type  j, std::vector< dof_id_type > &  neighbors  )

inline

Definition at line 357 of file PETScDMDAMesh.C.

Referenced by get_ghost_neighbors_Quad4().

{
  std::fill(neighbors.begin(), neighbors.end(), Elem::invalid_id);

  // Bottom
  if (j != 0)
    neighbors[0] = elem_id_Quad4(nx, 0, i, j - 1, 0);

  // Right
  if (i != nx - 1)
    neighbors[1] = elem_id_Quad4(nx, 0, i + 1, j, 0);

  // Top
  if (j != ny - 1)
    neighbors[2] = elem_id_Quad4(nx, 0, i, j + 1, 0);

  // Left
  if (i != 0)
    neighbors[3] = elem_id_Quad4(nx, 0, i - 1, j, 0);
}

node_id_Quad4()

dof_id_type node_id_Quad4 ( const ElemType  , const dof_id_type  nx, const dof_id_type  , const dof_id_type  i, const dof_id_type  j, const dof_id_type    )

inline

Definition at line 171 of file PETScDMDAMesh.C.

Referenced by add_element_Quad4(), and add_node_Qua4().

{
  // Transform a grid coordinate (i, j) to its global node ID
  // This match what PETSc does
  return i + j * (nx + 1);
}

registerMooseObject()

registerMooseObject	(	"ExternalPetscSolverApp"	,
		PETScDMDAMesh
	)

set_boundary_names_Quad4()

void set_boundary_names_Quad4

(

BoundaryInfo &

boundary_info

)

Definition at line 327 of file PETScDMDAMesh.C.

Referenced by build_cube_Quad4().

{
  boundary_info.sideset_name(0) = "bottom";
  boundary_info.sideset_name(1) = "right";
  boundary_info.sideset_name(2) = "top";
  boundary_info.sideset_name(3) = "left";
}

validParams< PETScDMDAMesh >()

template<>

InputParameters validParams< PETScDMDAMesh >

(

)

Definition at line 36 of file PETScDMDAMesh.C.

{
  InputParameters params = validParams<MooseMesh>();

  MooseEnum elem_types("EDGE2  QUAD4  HEX8"); // no default

  MooseEnum dims("1=1 2 3", "2");
  params.addRequiredParam<MooseEnum>(
      "dim", dims, "The dimension of the mesh to be generated"); // Make this parameter required

  params.addParam<dof_id_type>("nx", 11, "Number of elements in the X direction");
  params.addParam<dof_id_type>("ny", 11, "Number of elements in the Y direction");
  params.addParam<dof_id_type>("nz", 11, "Number of elements in the Z direction");
  params.addParam<Real>("xmin", 0.0, "Lower X Coordinate of the generated mesh");
  params.addParam<Real>("ymin", 0.0, "Lower Y Coordinate of the generated mesh");
  params.addParam<Real>("zmin", 0.0, "Lower Z Coordinate of the generated mesh");
  params.addParam<Real>("xmax", 1.0, "Upper X Coordinate of the generated mesh");
  params.addParam<Real>("ymax", 1.0, "Upper Y Coordinate of the generated mesh");
  params.addParam<Real>("zmax", 1.0, "Upper Z Coordinate of the generated mesh");
  params.addParam<MooseEnum>("elem_type",
                             elem_types,
                             "The type of element from libMesh to "
                             "generate (default: linear element for "
                             "requested dimension)");

  params.addParamNamesToGroup("dim", "Main");

  params.addClassDescription(
      "Create a line, square, or cube mesh with uniformly spaced memsh using PETSc DMDA.");

  // This mesh is always distributed
  params.set<MooseEnum>("parallel_type") = "DISTRIBUTED";

  return params;
}