octadist 3.0.0

OctaDist: A tool for calculating distortion parameters in molecule.

OctaDist

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

Register for OctaDist

To get notified when we release new version of OctaDist, please register at https://cutt.ly/regis-octadist.

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 for graphical analysis.
• implement OctaDist's module into your or other program.
• access the program core directly via an interactive scripting language.

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	Status
Windows
Linux
macOS
PyPI library
Anaconda cloud
Nightly build	Development build

Branch:

1. master
2. nightly-build

Git Clone

git clone https://github.com/OctaDist/OctaDist.git
git checkout nightly-build
git pull origin nightly-build

Documents

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

Reference manual :

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

Download and Install

For Windows users, we strongly suggest a standalone executable:

Click Here to Download OctaDist-3.0.0-Win-x86-64.exe

For Linux or macOS users and already have Python 3 installed on the system, the easiest way to install OctaDist is to use pip.

pip install octadist

or use conda for those who have Anaconda:

conda install -c rangsiman octadist

Starting OctaDist

Graphical User Interface (GUI)

To start GUI program:

octadist

Screenshots of program:

OctaDist GUI	XYZ coordinates	Computed distortion parameters

Command Line Interface (CLI)

To start program command line:

octadist_cli

To calculate distortion parameters:

octadist_cli --inp EXAMPLE_INPUT.xyz

To calculate distortion parameters and show formatted output:

octadist_cli --inp EXAMPLE_INPUT.xyz --out

Supporting input format

• CIF: *.cif
• XYZ: *.xyz
• Computational chemistry outputs: *.out and *.log
  • Gaussian
  • NWChem
  • ORCA
  • Q-Chem

Running the tests

Example 1: OctaDist as a package

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             # 0.228072561
delta = dist.delta           # 0.000476251
sigma = dist.sigma           # 47.92652837
theta = dist.theta           # 122.6889727

Example 2: Display 3D structure of molecule

import octadist as oc

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

atom_full, coord_full = oc.io.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, respectively.

Citation

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

Ketkaew, R.; Tantirungrotechai, Y.; Harding, P.; Chastanet, G.; Guionneau, P.; Marchivie, M.; Harding, D. J. 
OctaDist: A Tool for Calculating Distortion Parameters in Spin Crossover and Coordination Complexes. 
*Dalton Trans.*, **2021**,50, 1086-1096. https://doi.org/10.1039/D0DT03988H

BibTeX

@article{Ketkaew2021,
  doi = {10.1039/d0dt03988h},
  url = {https://doi.org/10.1039/d0dt03988h},
  year = {2021},
  publisher = {Royal Society of Chemistry ({RSC})},
  volume = {50},
  number = {3},
  pages = {1086--1096},
  author = {Rangsiman Ketkaew and Yuthana Tantirungrotechai and Phimphaka Harding and Guillaume Chastanet and Philippe Guionneau and Mathieu Marchivie and David J. Harding},
  title = {OctaDist: a tool for calculating distortion parameters in spin crossover and coordination complexes},
  journal = {Dalton Transactions}
}

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]
• Phimphaka Harding (Walailak University, Thailand)
  • E-mail: [e-mail]
• Guillaume Chastanet (University of Bordeaux, France)
  • E-mail: [e-mail]
• Philippe Guionneau (University of Bordeaux, France)
  • E-mail: [e-mail]
• Mathieu Marchivie (University of Bordeaux, France)
  • E-mail: [e-mail]
• David J. Harding (Walailak University, Thailand)
  • E-mail: [e-mail]