octadist 2.5.1

OctaDist

Octahedral distortion calculator: A program for determining the structural distortion of the octahedral complexes. https://octadist.github.io/

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

Installation

• Install the latest version: pip install octadist
• Upgrade to the latest version: pip install --upgrade octadist
• Upgrade/downgrade to a specific version: pip install --upgrade octadist==2.5.0

Sample usage

Example scripts are available at here.

First of all, you have to import necessary modules for computing the octahedral distortion parameters, called calc:

from octadist import calc

Prepare list (or array) for atomic labels and coordinates:

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

coor = [[2.298354000, 5.161785000, 7.971898000],
        [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]]

or you can open input file and extract the octahedral structure from input metal complex using a module called coord:

from octadist import coord, calc

For example, input file full\path\of\your\input\file\Multiple-metals.xyz (other example input files are available at here):

file = r"full\path\of\your\input\file\Multiple-metals.xyz"

atom, coor = coord.extract_octa(file)

Then calculate all octahedral parameters

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

and print all computed parameters:

All computed parameters
-----------------------
Zeta  = 0.22807256171728651
Delta = 0.0004762517834704151
Sigma = 47.926528379270124
Theta = 122.688972774546

Citation

Please cite this project when you have used OctaDist for scientific publication.

Bug report

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

Project team

• Rangsiman Ketkaew (Thammasat University)
  
  • E-mail: rangsiman1993@gmail.com
    
• Yuthana Tantirungrotechai (Thammasat University)
  • E-mail: yt203y@gmail.com
• David J. Harding (Walailak University)
  • E-mail: hdavid@mail.wu.ac.th
• Phimphaka Harding (Walailak University, Thailand)
  • E-mail: kphimpha@mail.wu.ac.th
• Mathieu Marchivie (Université de Bordeaux, France)
  • E-mail: mathieu.marchivie@icmcb.cnrs.fr