Running MASTODON

Input to MASTODON

MASTODON simulation models are defined by the user through a text file that defines the parameters of the run. This text file specifies the set of code objects that are composed together to simulate a physical problem, and provides parameters that control how those objects behave and interact with each other. This text file can be prepared using any text editor. The free and opensource Atom text editor has several packages that help with creating MOOSE and MASTODON input files. Please read this article about using Atom for writing MASTODON input files.

In addition to the text file describing the model parameters, MASTODON also requires a definition of the finite element mesh on which the physics equations are solved. The mesh can be generated internally by MASTODON using parameters defined in MASTODON's input file for very simple geometries, or can be read from a file as defined in the MASTODON input file. MASTODON supports the full set of mesh file formats supported by MOOSE, although the most common mesh format is the ExodusII format.

Basic Syntax

The input file used by MASTODON (or any MOOSE application) is broken into sections or blocks identified with square brackets. The type of input block is placed in the opening brackets, and empty brackets mark the end of the block.

[BlockName]
  block_lines_and_subblocks
[]

Each block may contain an arbitrary number of line commands to define parameters related to that block. They can also optionally contain one or more subblocks, which may in turn contain their own nested subblocks. Subblocks are opened and closed with the following syntax:

[./subblock_name]
  line_command1
  line_command2
[../]

Parameters are defined with line commands, and are given as key/value pairs separated by an equals sign (=). They specify parameters to be used by the object being described. The key is a string (no whitespace), and the value may be a string, an integer, a real number, or a list of strings, integers, or real numbers. Lists are given in single quotes and are separated by whitespace.

The following are examples of line commands for a single parameter and for a list of parameters:

single_parameter = 2.3
list_of_parameters = '1.0 2.3 3.7'

Blocks and subblocks at any level can contain line commands, which must be appropriate for the scope of the block containing them. Most of the time, blocks are used to create instances of MOOSE objects, and contain a `type = ` parameter to specify the type of MOOSE object to be created. The name of the MOOSE object specified in the parameter corresponds to the name of the class in the C++ source code.

Each object type has a unique set of input parameters that are valid for specifying the behavior of that object. Some parameters are required, and some are optional, and revert to default behavior if they are not specified. An error message is generated if a line command does not apply within the scope in which it is provided. Repeating a line within a block also results in an error. A full list of object types and the corresponding parameters valid for that object can be found in syntax.

The name of a subblock ([./name]) is arbitrary. However, these names should be chosen to be meaningful because they can be used to refer to those entities elsewhere in the input file. Not every created entity is referenced elsewhere, but a name must be created for every entity regardless.

Summary of MOOSE Object Types

MOOSE is an objected-oriented system with well-defined interfaces for applications to define their own physics-specific code modules. The following is a listing of the major types of MOOSE objects used by MASTODON:

• Variable

• Kernel

• AuxVariable

• AuxKernel

• Material

• BoundaryCondition

• Function

• Postprocessor

• VectorPostprocessor

• Constraint

• Damper

Specialized versions of these object types are implemented to provide the functionality needed to model physics of interest for MASTODON.

Input Syntax Page

A complete listing of all input syntax options in MOOSE is available on the MOOSE Documentation page. See the section on Input File Documentation, you can run

./mastodon-opt --dump

to get a list of valid input options for MASTODON.

Units

MASTODON can be run using any unit system preferred by the user.

Executing MASTODON

When first starting out with MASTODON, it is recommended to start from an example problem similar to the problem that you are trying to solve. Multiple examples can be found at mastodon/examples/. It may be worth running the example problems to see how the code works and modifying input parameters to see how the run time, results and convergence behavior change.

To demonstrate running MASTODON, consider the simple shear example problem included in the MASTODON example set:

cd ~/projects/mastodon/examples/ex01
# To run with one processor

~/projects/mastodon/mastodon-opt -i HYS_darendeli.i
# To run in parallel (2 processors)

mpiexec -n 2 ../../mastodon-opt -i HYS_darendeli.i

Post Processing

MASTODON typically writes solution data to an ExodusII file. Data may also be written in other formats, a simple comma separated file giving global data being the most common.

Several options exist for viewing ExodusII results files. These include commercial as well as open-source tools. One good choice is Paraview, which is also open-source.

Paraview is available on a variety of platforms. It is capable of displaying node and element data in several ways. It will also produce line plots of global data or data from a particular node or element.

Graphical User Interface

It is worth noting that a graphical user interface (GUI) exists for all MOOSE-based applications. This GUI is named Peacock. Information about Peacock and how to set it up for use may be found on the MOOSE wiki page.

Peacock may be used to generate a text input file. It is also capable of submitting the analysis. It also provides basic post processing capabilities.