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

Fri May 26 02:06:01 CDT 2023

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 at millenia.cars.aps.anl.gov>
wrote:

> Send Ifeffit mailing list submissions to
>         ifeffit at 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 at millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
>         ifeffit-owner at 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 <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Problems with FEFF calculation using CIF file
> Message-ID:
>         <CA+7ESbpH97zi+-xbK2R62m8ND-MG+6OgMB=
> R16zSqXE2za7yCA at 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 at 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
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20230524/90ae40d2/attachment-0001.htm
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
> ------------------------------
>
> End of Ifeffit Digest, Vol 243, Issue 17
> ****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20230526/42908579/attachment.htm>