octadist 2.5.4

OctaDist: A tool for calculating distortion parameters in coordination complexes.

OctaDist

Octahedral distortion calculator: A tool for calculating distortion parameters in coordination complexes. https://octadist.github.io/

Standard abilities

OctaDist is computer software for inorganic chemistry and crystallography program. OctaDist can be used for studying the structural distortion in coordination complexes. With the abilities of OctaDist, you can:

• analyze the structure and conformation of coordination complexes.
• compute the octahedral distortion parameters.
• explore tilting distortion in perovskite and metal-organic framework.
• display 3D molecule and other graphical analysis.
• upgrade your and other program with OctaDist abilities.

Development and Release

OctaDist is written entirely in Python 3 binding to Tkinter GUI toolkit. It is cross-platform program which can work on multiple operating systems. The stable version and development build of OctaDist are released at here. A standalone executable for graphical user interface (GUI) and source code for command line interface (CLI) are available for as follows:

Platform	Description	Usability	Status
Windows	A standalone executable	GUI
Linux	Source code as a Python package	GUI & CLI
macOS	Source code as a Python package	CLI
PyPI library		CLI
Anaconda cloud		CLI
Nightly build	Development build	GUI & CLI

Documents

User manual : https://octadist.github.io/manual.html.

Reference manual :

Version	Status	Docs
Stable		HTML / PDF / Epub
Dev Build		HTML / PDF / Epub

Installing

The easiest way to install OctaDist is to use pip.

pip install octadist

or use conda for those who have Anaconda installed on your system.

conda install -c rangsiman octadist

To execute OctaDist package, use the following command:

python -m octadist.Run

Note that you have to stay at the top-level directory (outside octadist).

Running the tests

Graphical User Interface (GUI)

Just download a standalone executable to your system.

OctaDist GUI	XYZ coordinates	Computed distortion parameters

Command Line Interface (CLI)

Example 1

import octadist as oc

# Prepare list of atomic coordinates of octahedral structure:

atom = ['Fe', 'O', 'O', 'N', 'N', 'N', 'N']

coord = [[2.298354000, 5.161785000, 7.971898000],  # <- Metal atom
         [1.885657000, 4.804777000, 6.183726000],
         [1.747515000, 6.960963000, 7.932784000],
         [4.094380000, 5.807257000, 7.588689000],
         [0.539005000, 4.482809000, 8.460004000],
         [2.812425000, 3.266553000, 8.131637000],
         [2.886404000, 5.392925000, 9.848966000]]

dist = oc.CalcDistortion(coord)
zeta = dist.zeta             # Zeta
delta = dist.delta           # Delta
sigma = dist.sigma           # Sigma
theta = dist.theta           # Theta

Example of output for computed parameters:

Computed parameters
-------------------
Zeta  = 0.228072561
Delta = 0.000476251
Sigma = 47.92652837
Theta = 122.6889727

Example 2

OctaDist can display the 3D structure of molecule.

import octadist as oc

file = r"../example-input/Multiple-metals.xyz"

atom_full, coord_full = oc.molecule.extract_coord(file)

my_plot = oc.draw.DrawComplex(atom=atom_full, coord=coord_full)
my_plot.add_atom()
my_plot.add_bond()
my_plot.add_legend()
my_plot.save_img()
my_plot.show_plot()

# Figure will be saved as Complex_saved_by_OctaDist.png by default.

Other example scripts and octahedral complexes are available at example-py and example-input.

Citation

Please cite this project when you use OctaDist for scientific publication.

OctaDist - A tool for calculating distortion parameters in coordination complexes.
https://octadist.github.io

Bug report

If you found issues in OctaDist, please report it to us at here.

Project team

• Rangsiman Ketkaew (Thammasat University, Thailand)
  
  • E-mail: [e-mail]
    
• Yuthana Tantirungrotechai (Thammasat University, Thailand)
  • E-mail: [e-mail]
• David J. Harding (Walailak University, Thailand)
  • E-mail: [e-mail]
• Phimphaka Harding (Walailak University, Thailand)
  • E-mail: [e-mail]
• Mathieu Marchivie (University of Bordeaux, France)
  • E-mail: [e-mail]