octadist 3.1.0

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/

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.

Documents

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

Reference manual :

Version	Status	Docs
Latest		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-2.6.1-Win-x86-64.exe (104 MB)

Click Here to Download OctaDist-3.0.0-Win-x86-64.exe (320 MB)

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

Note that OctaDist supports up to Python 3.9.

pip install octadist

or use conda for those who have Anaconda:

conda install -c rangsiman octadist

Starting OctaDist

The following commands can be used to start OctaDist in different ways:

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 --format

Supporting input format

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

Running the tests: OctaDist as a package

Example 1: Explicitly define atomic label and coordinates

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: Load external Cartesian coordinates file

import os
import octadist as oc

# You can also import your input file, like this:

file = "Multiple-metals.xyz"

# Then use coord.extract_file to extract all atomic symbols and coordinates,
# and then use coord.extract_octa for taking the octahedral structure.

atom_full, coord_full = oc.io.extract_coord(file)
atom, coord = oc.io.extract_octa(atom_full, coord_full)

dist = oc.CalcDistortion(coord)
zeta = dist.zeta              # 0.0030146365519487794
delta = dist.delta            # 1.3695007180404868e-07
sigma = dist.sigma            # 147.3168033970211
theta = dist.theta            # 520.6407679851042

Example 3: Display 3D structure of molecule

import os
import octadist as oc

file = "Multiple-metals.xyz"

atom_full, coord_full = oc.io.extract_coord(file)

my_plot = oc.draw.DrawComplex_Matplotlib(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.

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
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

Register for OctaDist

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

OctaDist Forum

The users can post questions in our Google Groups: OctaDist Forum

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]