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.

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 = DirichletBC
    preset = true
    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 = DirichletBC
    preset = true
    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:

  
  InputParameters
  SomeKernel::validParams()
  {
    InputParameters params = Kernel::validParams();
    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.