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BDA (BCC Defect Analysis)

A novel method for identifying defects in body-centered cubic crystals

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Developed and written by:
       Johannes J. Möller ([email protected]),
       Department of Materials Science and Engineering, Institute I,
       Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Germany.

In its current implementation, the BDA is a Python script that uses the scripting interface of OVITO (http://www.ovito.org).

System prerequisites

The BDA Python script only needs OVITO to be installed on the system. The current version of the BDA was tested with the following operating systems:

• openSuSE 13.1 Linux
• Mac OS X 10.10.5 Yosemite

I'm happy to receive your reports on how it works (or not) on other OS/distributions!

How to obtain the BDA

The BDA script can be either directly downloaded from this GitHub repository or cloned to a local git repository by, e.g.:

$> git clone https://github.com/jomoeller/bda.git /path/to/bda

Using the BDA

The usage of the BDA script is very simple. In the simplest case the BDA is invoked on Linux, as follows:

$> /path/to/ovito/bin/ovitos /path/to/bda/ovitos_bcc-defect-analysis_vX.py -c CONFIG

where vX is either v1 or v2 depending on the installed OVITO version, see above section on compatibility. Here, CONFIG stands for an arbitrary atomistic configuration, which is supported by OVITO. On Mac operating systems, the BDA is started as follows:

$> /Applications/Ovito.app/Contents/MacOS/ovitos /path/to/bda/ovitos_bcc-defect-analysis_vX.py -c CONFIG

The option -c (or --config) is the only argument that needs to be passed to the script. It can be either a single file or a list of files, e.g., *.xyz.

A complete list of arguments is printed if the BDA script is invoked with the -h or --help option:

-c CONFIG [CONFIG ...], --config CONFIG [CONFIG ...]
                    Atomistic configuration(s)

-b X Y Z, --boundary-conditions X Y Z
                    Boundary conditions (0:free|1:periodic)

-a LATTICE_PARAMETER, --lattice-parameter LATTICE_PARAMETER
                    BCC Lattice parameter

-p POTENTIAL, --potential POTENTIAL
                    Name of interatomic potential

-r BOUNDARY_REGION, --boundary-region BOUNDARY_REGION
                    Regions to cut away from non-periodic boundaries
                    (default: 5)

-i, --include-perfect
                    Include perfect lattice atoms in exported files

-k, --keep-unidentified
                    Keep unidentified and do no optimization loops

Note that the BDA script comes with a limited number of 0 K lattice parameters for certain interatomic EAM potentials (-p options, i.e. the Chiesa, Men-II, Chamati, Gordon, Marinica11, Rosato potentials for Fe). If the configuration's filename contains one of these strings, the -p option is not needed. If your potential is not among these, the lattice parameter has to be defined explicitly using the -a option.

Example

The BDA is distributed along with an application example in the example subfolder, which is also presented in the original publication. It is the penny-shaped crack on a (010) plane in Fe modelled with the Mendelev-II potential, click here for further details.

In the downloaded example folder, do the following to concatenate and unzip the example configuration:

$> cat example.chkpt.gz.part-* > example.chkpt.gz
$> gunzip example.chkpt.gz

Citing the BDA

If you used the BDA method to analyze your simulation results, please cite the BDA in your publications as follows:
       J.J. Möller and E. Bitzek
       BDA: A novel method for identifying defects in body-centered cubic crystals
       MethodsX 3 (2016), 279-288
       http://dx.doi.org/10.1016/j.mex.2016.03.013

Acknowledgements

The author greatfully acknowledges the supervision and support by Prof. Dr. Erik Bitzek.

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