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"