Mesh

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 section).

  • If you have a specific mesh format 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.

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 for having names for blocks 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

  • Calculation 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 the code if you have a pure Lagrangian formulation.