Codes for identifying polyhedral units in grain boundary structures

Python Codes

The python codes are in the py_codes folder. The python codes perform the following tasks:

1. Reads all the dump files one-by-one.
   • Change the path to find the dump files.
2. Call the analyze_gb_atoms function in the pum_util_funcs module. This function reads the data in the dump file and creates a matlab data file (.mat).

The following steps are followed in the analyze_gb_atoms function:

1. Read the dump file using ovito.
2. Identify the indices of the grain boundary atoms.
3. Determine all the atoms within a certain cut-off radius of grain boundary atoms (e.g. rCut = 3*lat_par).
4. Create enough periodic images such that there are enough atoms sorrounding the grain boundary atoms in the unit cell (within rCut).
5. Save the atoms (with images), and grain boundary indices in the matlab data file (.mat file).

Matlab Codes

1. plot_poly_units: Reads the .mat files created by the python codes.
   • Calls the cc_coors_analysis(mat_name) function.
2. cc_coors_analysis: Reads the mat_file, which contains the atoms positions and indices of the grain boundary atoms.
   • Calls the following functions:
     • identify_gb_vv
     • get_polyhedra
     • get_polyhedra_attributes
     • find_sim_box_poly
     • plot_gb_poly