Hi Iraida, Hm, neither pycifrw nor the pymatgen CIF Parser can read the CIF file you posted because the first line data_Structure 2 cannot be interpreted. Changing that to “data_Structure2” (no space) works for `pycifrw`. Pymatgen still fails,
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.
 
ZjQcmQRYFpfptBannerEnd

Hi Iraida,

Hm, neither pycifrw nor the pymatgen CIF Parser can read the CIF file you posted because the first line

   data_Structure 2

 

cannot be interpreted.  Changing that to “data_Structure2” (no space) works for `pycifrw`.  Pymatgen still fails, as `?` is not a valid number.  I guess `pycifrw` thinks ‘?’ are OK, but it is not trying to do any numerical work with these values.

 

So, I’m not sure pymatgen is correct to fail with ‘?’, but it seems forgivable. CIF is just obnoxious.

 

Changing ‘?’ to 0 and removing some of the unused data gives a file that pymatgen can use, see

       https://larixite.seescience.org/cifs/K-Ga2O3-diamond.cif

 

But, when using this, pymatgen also says Ga1, Ga2, and Ga3 have 6 oxygen neighbors, while Ga4 has 4.    

Are you sure that Crystal Impact really did what you think it did?    

 

--Matt

 

 

From: I. D. via Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Date: Saturday, August 30, 2025 at 10:36 AM
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Cc: I. D. <indemchenko2@gmail.com>
Subject: [Ifeffit] Re: Issue with AtomS reporting CIF file created in Diamond

Dear All, I am experiencing a problem with AtomS reporting a CIF file generated in Diamond. Please find the CIF file attached. Diamond correctly displays the coordination of each gallium atom in this structure (space group Pna2₁): Ga1 has tetrahedral

ZjQcmQRYFpfptBannerStart

This Message Is From an External Sender

This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd

Dear All,

 

I am experiencing a problem with AtomS reporting a CIF file generated in Diamond. Please find the CIF file attached.

Diamond correctly displays the coordination of each gallium atom in this structure (space group Pna2₁):

·         Ga1 has tetrahedral coordination,

·         Ga2 has octahedral coordination,

·         Ga3 has pentahedral coordination,

·         Ga4 has tetrahedral coordination.

However, when I load the CIF file into AtomS, only Ga4 shows the correct coordination. The other three Ga atoms are all reported with coordination 6 instead of 4, 6, and 5, respectively.

Could you please advise on how to resolve this issue?

Thank you in advance for your help.

Best regards,

Iraida

PS: A similar problem occurs if the *.cif file is generated by the Vesta program.