Creating a Mesh

  • For complicated geometries, we generally use CUBIT from Sandia National Laboratories.
  • CUBIT can be licensed from CSimSoft for a fee depending on the type of organization you work for.
  • Other mesh generators can work as long as they output a file format that libMesh reads (next slide).
  • If you have a specific mesh format that you like, we can take a look at adding support for it to libMesh.

FileMesh

  • FileMesh is the default type.
  • MOOSE supports reading and writing a large number of formats and could be extended to read more.

Extension Description
.dat Tecplot ASCII file
.e, .exd Sandia's ExodusII format
.fro ACDL's surface triangulation file
.gmv LANL's GMV (General Mesh Viewer) format
.mat Matlab triangular ASCII file (read only)
.msh GMSH ASCII file
.n, .nem Sandia's Nemesis format
.plt Tecplot binary file (write only)
.node, .ele; .poly TetGen ASCII file (read; write)
.inp Abaqus .inp format (read only)
.ucd AVS's ASCII UCD format
.unv I-deas Universal format
.xda, .xdr libMesh formats
.vtk, .pvtu Visualization Toolkit

GeneratedMesh

  • type = GeneratedMesh
  • Built-in mesh generation is implemented for lines, rectangles, and rectangular prisms ("boxes") but could be extended.
  • The sides are named in a logical way and are numbered:
    • In 1D, left = 0, right = 1
    • In 2D, bottom = 0, right = 1, top = 2, left = 3
    • In 3D, back = 0, bottom = 1, right = 2, top = 3, left = 4, front = 5
  • The length, width, and height of the domain, and the number of elements in each direction can be specified independently.

Named Entity Support

  • Human-readable names can be assigned to blocks, sidesets, and nodesets
  • These names will be automatically read in and can be used throughout the input file.
    • This is typically done inside of Cubit.
  • Any parameter that takes entity IDs in the input file will accept either numbers or "names".
  • Names can also be assigned to IDs on-the-fly in existing meshes to ease input file maintenance (see example).
  • On-the-fly names will also be written to Exodus/XDA/XDR files.
  • An illustration for mesh in exodus file format.

[Mesh]
  file = three_block.e

  #These names will be applied on the
  #fly to the mesh so that they can be
  #used in the input file. In addition
  #they will be written to the output
  #file
  block_id = '1 2 3'
  block_name = 'wood steel copper'

  boundary_id = '1 2'
  boundary_name = 'left right'
[]

Example Name Support

  • An illustration for mesh in UNV file format having names for block and boundaries.
[Mesh]
  file = three_block.unv
  #If the names wood, steel, copper, left and right
  #are generated via Salome software in the UNV mesh
  #then they can be read directly by MOOSE
  #which is illustrated here by commenting(#) the numbers
  #block_id = '1 2 3'
  block_name = 'wood steel copper'
  #boundary_id = '1 2'
  boundary_name = 'left right'
[]
...
[BCs]
  [./left_bc] #Temperature on left edge is fixed at 800K
    type = PresetBC
    variable = T
    #boundary = '1'
    boundary = 'left'
    value = 800
  [../]
  [./right_x] #Temperature in the right sideset is fixed at 298 K
    type = DirichletBC
    variable = T
    #boundary = '2'
    boundary = 'right'
    value = 298.0
  [../]
[]

[](---)
  • An illustration for mesh in UNV file format and requirement of on-the-fly names of block and boundaries in moose input file.
[Mesh]
  file = three_block.unv
  #the numbers should be verified from the 
  #unv mesh format to be represented for a 
  #particular block and boundary of the geometry
  #The random BC ids 7 and 48 are written here
  #to highlight the role of verification from within
  #the file
  #That is the numbers 1, 2 ,3 , 7 and 48 are obtained from the mesh
  block_id = '1 2 3'
  block_name = 'wood steel copper'
  boundary_id = '7 48'
  boundary_name = 'left right'
[]
...
[BCs]
  [./left_bc] #Temperature on left edge is fixed at 800K
    type = PresetBC
    variable = T
    #boundary = '7'
    boundary = 'left'
    value = 800
  [../]
  [./right_x] #Temperature in the right sideset is fixed at 298 K
    type = DirichletBC
    variable = T
    #boundary = '48'
    boundary = 'right'
    value = 298.0
  [../]
[]

Parallel Mesh

  • Useful when the mesh data structure dominates memory usage.
  • Only the pieces of the mesh "owned" by processor $$$N$$$ are actually stored by processor $$$N$$$.
  • If the mesh is too large to read in on a single processor, it can be split prior to the simulation.
  • Copy the mesh to a large memory machine.
  • Use a tool to split the mesh into $$$n$$$ pieces (SEACAS, loadbal).
  • Copy the pieces to your working directory on the cluster.
  • Use the Nemesis reader to read the mesh using $$$n$$$ processors.

Displaced Mesh

  • Calculations can take place in either the initial mesh configuration or, when requested, the "displaced" configuration.
  • To enable displacements, provide a vector of displacement variable names for each spatial dimension in the section, e.g.:
displacements = 'disp_x disp_y disp_z'
  • Once enabled, the parameter can be set on individual MooseObjects which will enable them to use displaced coordinates during calculations:
template<>
InputParameters validParams<SomeKernel>()
{
  InputParameters params = validParams<Kernel>();
  params.set<bool>("use_displaced_mesh") = true;
  return params;
}
  • This can also be set in the input file, but it is a good idea to do it in code if you have a pure Lagrangian formulation.