Program allows you to process Mayer bond orders MBO 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:
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
py main.py
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: 10
pairs_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-O
calculations:
q_i:
calc: true
bond_id: P-O
cn: true
connections: true
bond_length: true
covalence: true
If you would like to cite the program in your work. The information below is provided.