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 <ifeffit-request@millenia.cars.aps.anl.gov> wrote:

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Today's Topics:

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


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Message: 1
Date: Wed, 24 May 2023 12:29:01 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Problems with FEFF calculation using CIF file
Message-ID:
        <CA+7ESbpH97zi+-xbK2R62m8ND-MG+6OgMB=R16zSqXE2za7yCA@mail.gmail.com>
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 <a.volker@student.rug.nl>
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
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--
--Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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