Display option doesn't work

[Chamini Shammi Pathiraja Mudiyanselage]

Hello,

I have run octadist to calculate the distortion in CrI3. However, I have faced several issues;

1. I cannot upload .cif files. I could, however, upload a .xyz file and calculate the distortion.

2. The display of the complex and octahedra doesn't work.

How can I resolve these issues please?

Thank you,

Chamini

[Rangsiman Ketkaew]

Hi Chamini,

Please provide details on your machine and OctaDist.

1. What OS are you using (Windows, Linux (Ubuntu?), macOS)?

2. Version of Python

3. Version of OctaDist

4. How did you install OctaDist?

5. If you use Linux, how did you start OctaDist?

Best,

Rangsiman

[Chamini Shammi Pathiraja Mudiyanselage]

Hi Rangsiman,

I have installed Octadist on MacOS using the instructions in the website. I have the Python version 3.11.8 and Octadist version 2.6.1.

I tried to upgrade the Octadist, but I received an error message. 

When I attempt to upgrade Octadist to version 3.1.0, I receive the following error message.

ERROR: Ignored the following versions that require a different python version: 3.1.0 Requires-Python !=3.0.*,!=3.1.*,!=3.10.*,!=3.11.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=3

ERROR: Could not find a version that satisfies the requirement octadist==3.1.0 (from versions: 2.5.0, 2.5.1, 2.5.2, 2.5.3, 2.5.4, 2.5.4.5, 2.6.0, 2.6.1, 3.0.0)

ERROR: No matching distribution found for octadist==3.1.0

[Rangsiman Ketkaew]

OctaDist 3.1.0 doesn't support Python 3.11. So you need Python 3.12 or a newer version.

Try upgrading your Python to preferably version 3.13 with conda and install OctaDist again with the specific version 3.1.0:

$ conda install python=3.13

$ pip install octadist==3.1.0

If you haven't had conda installed on macOS, you can use brew to install conda first:

$ brew install anaconda

Best,

Rangsiman

[Chamini Shammi Pathiraja Mudiyanselage]

Hi Rangsiman,

I have installed Octadist version 3.1.0 in my macOS. However, I still get the error message when I attempt to display the complex and the octahedra.

Do you have any idea why that is?

Thank you,

Chamini

[Chamini Shammi Pathiraja Mudiyanselage]

Dear Rangsiman,

Do you have any updates on my question about the visualization of the distorted octahedra in Mac? 

I still could not get the display function to work properly. Neither the complex nor the octahedra are showing up.

Chamini

[Rangsiman Ketkaew]

Hi Chamini,

I am working on it. I will let you know when it is fixed. Could you share your example coordinates file to test?

Best,

Rangsiman

[Chamini Shammi Pathiraja Mudiyanselage]

Hi Rangsiman,

I have attached an example of coordinates below.

Atom                       Cartesian coordinate
 Cr         0.000000000     0.000000000     6.748956000
 Cl        -1.078695000    -1.622045000     5.417430000
 Cl         1.944080000    -0.123154000     5.417430000
 Cl        -0.865385000     1.745200000     5.417430000
 Cl         0.865385000     1.745374000     8.081144000
 Cl        -1.944231000    -0.123242000     8.081144000
 Cl         1.078846000    -1.622133000     8.081144000

Chamini

[Chamini Shammi Pathiraja Mudiyanselage]

Dear Rangsiman,

Do you have any updates on my question about the visualization of the distorted octahedra in Mac? 

I still could not get the display function to work properly. Neither the complex nor the octahedra are showing up.

I am working on a manuscript, and I would like to add the distortion calculations if possible. Please let me know if you can resolve the issue in the near future?

Thank you,

Chamini

[Rangsiman Ketkaew]

Hi Chamini,

Sorry for the delay. I have fixed the bug (the molecule is not properly displayed in the display area).

You can try the updated OctaDist version via pip install:

1. Open the terminal

2. Install the latest patch with pip using the following command

> pip install git+https://github.com/OctaDist/OctaDist.git

3. Launch OctaDist and try displaying your molecule

> octadist

Let me know if you still have an issue.

Best,

Rangsiman

[Chamini Shammi Pathiraja Mudiyanselage]

Quick question,

Which python package does it need? I have Python 3.11.8, but the update won't support it.

[Rangsiman Ketkaew]

It is not recommended to use Python 3.11 for the new version of OctaDist. I suggest Python 3.12 or a newer version.