Problem to import cif/xyz file for calculations

[Pikesh Pal]

Hi, 

I am having following problem during import of cif file for calculations!

Please have a look!

>>> Program started
>>> OctaDist 3.1.0 2024
Exception in Tkinter callback
Traceback (most recent call last):
  File "C:\ProgramData\anaconda3\Lib\tkinter\__init__.py", line 2068, in __call__
    return self.func(*args)
           ~~~~~~~~~^^^^^^^
  File "C:\ProgramData\anaconda3\Lib\site-packages\octadist\main.py", line 483, in open_file
    self.search_coord()
    ~~~~~~~~~~~~~~~~~^^
  File "C:\ProgramData\anaconda3\Lib\site-packages\octadist\main.py", line 508, in search_coord
    atom_full, coord_full = io.extract_coord(self.file_list[i])
                            ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\anaconda3\Lib\site-packages\octadist\src\io.py", line 790, in extract_coord
    atom, coord = get_coord_cif(file)
                  ~~~~~~~~~~~~~^^^^^^
  File "C:\ProgramData\anaconda3\Lib\site-packages\octadist\src\io.py", line 131, in get_coord_cif
    structure = pymatgen.Structure.from_file(f)
                ^^^^^^^^^^^^^^^^^^
AttributeError: module 'pymatgen' has no attribute 'Structure'

Thank you in advance for support!

Regards,

Pikesh

[Rangsiman Ketkaew]

Hi Pikesh,

Have you solved the problem?

Best,

Rangsiman

[Rangsiman Ketkaew]

It seems that Pymatgen is outdated, and the Structure method has already been moved to be under the core module in a new version of Pymatgen. I have fixed the bug and updated it in the nightly-build branch of OctaDist. https://github.com/OctaDist/OctaDist/commit/b81709ab693b7501e4f50f8647f36375bba6ab2e

To make it work, please try uninstalling the current OctaDist and install a new one from the nightly-build branch using the following command:

> pip uninstall octadist

> pip3 uninstall octadist

> pip3 install git+https://github.com/OctaDist/OctaDist.git@nightly-build

> octadist

Once the program started, it should be able to load and read CIF structure.

Hope this helps and let me know if you're struggling with the problem.

Best,

Rangsiman