Re: [Ifeffit] Problems with FEFF calculation using CIF file (Matt Newville)

Dear Matt, Thank you for the quick response. The first error gets indeed resolved by removing the atoms labeled with a B. I was not very clear in my first post that I had to do this to have the ATOMS window run properly in Artemis. The problem I am stuck on is that when I have them removed and then run the FEFF window, it seems to all work fine, until I try and drag the paths into the Path window in Artemis. At that point the paths seem to no longer exist. I hope this clears up my question a bit more. Kind regards, Anouk On Thu, May 25, 2023 at 7:02 PM wrote:

Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov

To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov

You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov

When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..."

Today's Topics:

1. Re: Problems with FEFF calculation using CIF file (Matt Newville)

----------------------------------------------------------------------

Message: 1 Date: Wed, 24 May 2023 12:29:01 -0500 From: Matt Newville To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with FEFF calculation using CIF file Message-ID: Content-Type: text/plain; charset="utf-8"

Hi Anouk,

I am not sure what is happening with that CIF file. When I try to read that with pymatgen, I get

...

...

...

from pymatgen.io.cif import CifParser structs = CifParser('VOXZAJ.cif') structs.get_structures() .../site-packages/pymatgen/io/cif.py:1145: UserWarning: Error is Species occupancies sum to more than 1!. warnings.warn(f"Error is {str(exc)}.") .../site-packages/pymatgen/io/cif.py:1148: UserWarning: Issues encountered while parsing CIF: Some occupancies ([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]) sum to > 1! If they are within the occupancy_tolerance, they will be rescaled. The current occupancy_tolerance is set to: 1.0 Species occupancies sum to more than 1! warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings)) Traceback (most recent call last): File "<stdin>", line 1, in <module> .../site-packages/pymatgen/io/cif.py", line 1150, in get_structures raise ValueError("Invalid cif file with no structures!") ValueError: Invalid cif file with no structures!

If you remove all the atomic sites that have a "B" in their name, that gets resolved, but I do not know if that is still the correct structure - or what the "B" means.

CIF is complicated, but just from a practical point of view, I think we are going to take `pymatgen` as the arbitrator of "valid CIF".

On Wed, May 24, 2023 at 11:30?AM Volker, Anouk wrote:

...

Dear all,

I hope this email finds you well. I have encountered a problem that I have not been able to fix on my own. I have a specific CIF file (from the CCDC database) that is attached to the e-mail. After removing the duplicate atoms in the file, the ATOMS window seems fine. The FEFF calculation will run without any errors and within the FEFF window the paths are displayed and can be plotted. The problem arises when I try to take some of the paths from the FEFF window and drag them into the Path window. Now the paths can no longer be plotted and when trying to use them to fit, it seems like the paths are non-existent as well.

Is there something wrong with the CIF file that causes this to happen and if so, what can be done to fix it? I have already tried to make a feff.inp file from the xyz data (after opening the CIF file in any viewer), but this gives the same problem.

Thank you in advance,

Kind regards, Anouk Volker

Master student, Browne Group Stratingh Institute, University of Groningen _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411