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

Robert Gordon ragordon at alumni.sfu.ca
Fri May 26 03:42:09 CDT 2023 

Hi,

No paths showing up. I can reproduce that on my win10 pc.

I did a test with Fe foil and get no paths either...started from atoms and
bcc fe...
I compared the Feff input file in the screen:
[image: image.png]
with what is in the directory where Artemis runs the Feff calculation:
[image: image.png]
and the control and print values are different from what is in the above
interface window.
No feff####.dat files are being generated as a result.
If I edit the feff.inp in the folder, and run feff from Artemis again, it
overwrites the values
and I get no paths. If I edit and run feff directly in that folder, the
paths appear,
and then if I run Feff through Artemis, Artemis finds the paths:
[image: image.png]

But erases the feff####.dat files, and I have to replace the feff.inp and
run feff again
in the directory to have the files.

Hmmm...problem is more extensive than that. List.dat after running feff
(via Artemis or in folder):
[image: image.png]

List.dat after dragging path over to fitting setup screen:
[image: image.png]

which isn't found when I try to fit the 1st shell.

I am guessing a windows update has done something. Makes no difference
if I run legacy console versus win10 standard.

-R.












On Fri, May 26, 2023 at 12:06 AM Volker, Anouk <a.volker at student.rug.nl>
wrote:

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