Python script for generating coherent C15 phases of arbitrary size in a base-centered cubic crystal with LAMMPS
The construction roughly follows the prescription outlined in M.-C. Marinica, F. Willaime, and J.-P. Crocombette, Phys. Rev. Lett. 108, 025501.
git clone https://github.com/mb4512/C15builder.git
The script requires LAMMPS to be built with the MANYBODY package to enable support for embedded atom model (EAM) potentials. LAMMPS must be compiled as a shared library linked to Python 3+ with the numpy, scipy, and mpi4py packages. See the LAMMPS documentation for more information on how to set this up.
The json/*.json files contains simulation settings such as box dimensions in x,y, and z, and paths to important files and directories, such as the EAM potential file and the data directory. Update the paths as appropriate for your system. The json file acts as the input file for the simulation, enabling the running of multiple similar simulations without having to manually edit the Python script.
To build an example C15 cluster containing 10 interstitials in iron from the terminal, first ensure that an iron EAM potential is available, for example M07_eam.fs by Malerba et al. (2010) available at the NIST Interatomic Potentials repository. To run the relaxation in parallel using 8 cores, run the script as follows:
mpirun -n 8 python3 icosa.py json/test.json 10
As the simulation runs, the structure is initialised and relaxed. The following output files are written:
data/test.ico.10.xyz: xyz file of interstitial and vacancy coordinates required to create the C15 phase inside the BCC crystaldata/test.unrelaxed.10.data: LAMMPS data file of the C15 phase before structural relaxationdata/test.relaxed.10.data: LAMMPS data file of the C15 phase after structural relaxation
In practice, the unrelaxed structure test.unrelaxed.10.data is constructed by inserting into and deleting atoms from the pristine BCC crystal following the prescription of test.ico.10.xyz. This repository already comes with the test.ico.*.xyz output files for sizes in the range between 2 and 100 interstitials. Note that these structures do not represent the global energy minimum of a C15 phase in BCC, as we do not optimise for the precise shape; for this purpose, some heuristic global minimisation scheme must be used, for example as outlined by Alexander et al. (2016). In principle, this script could be modified for this purpose.