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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!

Compatibility with OVITO versions

Since there was a minor change in how the simulation box dimensions are accessed via the Python interface in OVITO version 2.6.0, two different versions of the BDA are available here:

• Version 1.0 for OVITO versions earlier than 2.6.0
• Version 2.0 for OVITO versions after 2.6.0 I would be very pleased if you report any compatibility problems!

How to obtain the BDA

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. Here, CONFIG stands for an arbitrary atomistic configuration, which is supported by OVITO. On Mac, 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) in IMD format

-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
                    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

Example

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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