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