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Developed and written by:
Johannes J. Möller (johannes.moeller@fau.de),
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).
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!
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
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.py -c CONFIG
where 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.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.
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
Then run the BDA and start OVITO thereafter:
$> /path/to/ovito/bin/ovitos /path/to/bda/ovitos_bcc-defect-analysis.py -c example.chkpt -b 0 0 0 -p Men-II
$> /path/to/ovito/bin/ovito example.chkpt.bda &
To change the color scheme to the recommended color scheme for the BDA in OVITO, do the following:
- enable the 'color coding' modifier in the modification pipeline on the right;
- change the color scheme by selecting 'Load custom color map' in 'Color gradient:';
- navigate to the image 'colorbar_cubehelix_0-6.png' in the root directory of the BDA repository;
- adjust the range of the color map such that it contains the numbers from 0 to 6.
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
The author greatfully acknowledges the supervision and support by Prof. Dr. Erik Bitzek.