Octahedral distortion calculator for coordination complexes
Project description
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
- 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
Project details
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