octadist 2.5.2

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/

This program is written entirely in Python 3 and tested on PyCharm (Community Edition).

Features

OctaDist is designed as a smart tool used for studying the structural distortion in coordinate complexes. With the abilities of OctaDist, you can:

• identify the type of octahedral coordination complexes.
• compute octahedral distortion parameters.
• display 3D molecule and other stuff.
• implement its functionality in your or other program.

Getting started

All details of OctaDist is available at user manual on the website.

Installing

• Install the latest version:

  pip install octadist
  

• Upgrade/downgrade to a specific version:

  pip install --upgrade octadist==2.5.1
  

Running the test

Prepare two lists of atomic symbols and atomic coordinates, the latter can be stored in array:

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

coor = [[2.298354000, 5.161785000, 7.971898000],  # <- Metal center 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]]

Import necessary module for computing the octahedral distortion parameters, called calc:

from octadist import calc

Then calculate all parameters separately, for example:

d_bond = octadist.calc_d_bond(coor)         # Bond distance
d_mean = octadist.calc_d_mean(coor)         # Mean distance
zeta = octadist.calc_zeta(coor)             # Zeta
delta = octadist.calc_delta(coor)           # Delta
angle = octadist.calc_bond_angle(coor)      # Bond angle
sigma = octadist.calc_sigma(coor)           # Sigma
theta = octadist.calc_theta(atom, coor)     # Theta

or calculate them at once:

zeta, delta, sigma, theta = calc.calc_all(coor)

Then print all computed parameters:

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

Example scripts and coordinate files are available at example-py and at example-input.

Citation

Please cite this project when you have used 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 us at here.

Project team

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