Run OctaDist

OctaDist supports both a graphical user interface (GUI) and a command line interface (CLI).

Run OctaDist GUI using EXE

If you have a standalone executable (.exe) of OctaDist GUI on your system, run OctaDist by double-clicking the .exe file as if you open other program.

Note

OctaDist can take time to launch the application, usually 5 - 10 seconds. However, if the program does not start, please restart your system and run it again.

Run OctaDist GUI on the terminal

Moreover, OctaDist can be called on the terminal such as CMD, PowerShell, and Terminal as long as it is added to environment variable, like this:

octadist

Run OctaDist CLI

You can execute command-line OctaDist interface by typing octadist_cli on the terminal. If it is executed without argument, the help docs will show by default.

(py37) user@Linux:~$ octadist_cli

# output
usage: octadist_cli [-h] [-i INPUT] [-f] [-r REF_CENTER_ATOM] [-c CUTOFF_DIST] [-s OUTPUT] [-p PARAMETER [PARAMETER ...]] [--show MOL [MOL ...]] [-g] [-a] [-v]

Octahedral Distortion Calculator:
A tool for computing octahedral distortion parameters in coordination complex.
For more details, please visit https://octadist.github.io.

optional arguments:
-h, --help            show this help message and exit
-i INPUT, --inp INPUT
                        Input structure in .xyz format
-f, --format          Show formatted output summary
-r REF_CENTER_ATOM, --ref-index REF_CENTER_ATOM
                        Index of the reference center atom. Default to 0
-c CUTOFF_DIST, --cutoff CUTOFF_DIST
                        Cutoff distance (in Angstroms) for determining octahedron. Default to 2.8
-s OUTPUT, --save OUTPUT
                        Save formatted output to text file, please specify name of OUTPUT file without '.txt' extension
-p PARAMETER [PARAMETER ...], --par PARAMETER [PARAMETER ...]
                        Select which the parameter (zeta, delta, sigma, theta) to show
--show MOL [MOL ...]  Show atomic symbol (atom) and atomic coordinate (coord) of octahedral structure
-g, --gui             launch OctaDist GUI (this option is the same as 'octadist' command
-a, --about           Show program info
-v, --version         show program's version number and exit

Rangsiman Ketkaew       Updated on 2024 E-mail: rangsiman1993@gmail.com

Using OctaDist to calculate the distortion of structure can be done as follows:

# Compute parameters
octadist_cli -i INPUT.xyz

# Compute parameters and show formatted output
octadist_cli -i INPUT.xyz -o

# Compute parameters and save output as file
octadist_cli -i INPUT.xyz -s OUTPUT

Tip

On Windows, you can check whether OctaDist is added to environment variables by using where command:

where octadist

For Linux and macOS, use which command instead:

which octadist

or

type -P "octadist" && echo "It's in path" || echo "It's not in path"