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Program allows you to process Mayer bond ordersMBO from the CPMD software (https://github.com/CPMD-code) output file. It is planned to add the ability of the program to work with other software output files having the ability to calculate MBO.

You can calculate from Mayer bond orders:

• coordination numbers,
• Qi units,
• Connections between atoms,
• Relation between bond order and length
• Covalence (The sum of the bond orders of a given atom. This value is close to the valence if atom have only purely covalent bonds)

• Application works fine with python 3.10. The application has not been tested on other python versions.

• Before you run app, install dependencies by pip from requirements.txt

• After installing requirements install "matplotlib" flower from kivy garden. Below cmd command:

  garden install garden.matplotlib

• If you ues windows you can install app, download "pyMayCoor.zip" (find it in Releases). Unpack it and run installer "pyMayCoor.exe".

• launching the application gui:

py main.py

• launching the application in cmd:

py main.py -i <input_file_from_CPMD> -s <settings.yaml> -o <output_file>

Command flags:

-i - set path to input file

-s - set path to settings file

-o - set path for output file

Settings file is in yaml format. You can specify what calculations you want to perform. It should also be specified for which pairs of atoms they are to be made.

histogram:  calc: true  nr_bars: 10pairs_atoms_list:  - atom_1: P    atom_2: O    mbo_min: 1.2    mbo_max: 2    id: P=O  - atom_1: P    atom_2: O    mbo_min: 0.1    mbo_max: INF    id: P-O  - atom_1: Al    atom_2: O    mbo_min: 0.1    mbo_max: INF    id: Al-O  - atom_1: Fe    atom_2: O    mbo_min: 0.1    mbo_max: INF    id: Fe-Ocalculations:  q_i:    calc: true    bond_id: P-O  cn: true  connections: true  bond_length: true  covalence: true

• https://github.com/pawelgoj/pyMayCoor/tree/master/main/BondOrderProcessing

• Documentation page

• python 3.10
• kivy
• kivyMD
• multiprocessing
• regex
• numpy
• pytest
• player
• mypy
• yaml
• PyYAML
• pdoc
• github actions
• plyer
• matplotlib
• seaborn
• pyinstaller
• Inno Setup Compiler
• Google Fonts

If you would like to cite the program in your work. The information below is provided.

1. P. Stoch, P. Goj, M. Ciecińska, P. Jeleń, A. Błachowski, A. Stoch, I. Krakowiak, Influence of aluminum on structural properties of iron-polyphosphate glasses, Ceram. Int. 46 (2020) 19146–19157. doi:10.1016/j.ceramint.2020.04.250.