[Ifeffit] Ifeffit Digest, Vol 241, Issue 13

Tue Apr 4 02:23:13 CDT 2023

Dear Matt and Robert,

Thanks for the feedback and information. I'll play around with the file and
indeed think about what it means for what I'm trying to achieve.

Best,

Siebe

On Fri, Mar 31, 2023 at 7:02 PM <ifeffit-request at millenia.cars.aps.anl.gov>
wrote:

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> Today's Topics:
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>    1. Re: Fortran runtime error when running feff on Hydrotalcite
>       cif (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 30 Mar 2023 14:50:26 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Fortran runtime error when running feff on
>         Hydrotalcite cif
> Message-ID:
>         <
> CA+7ESbr_33qqQo4midvNcO3rQdrCu00KB9nNGY6WyeZhsc-NpQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Siebe,
>
> Sorry for the trouble.   I agree with Robert's suggestion to check whether
> "Wat" might be causing the problem.
>
> The CIF Browser and Feff runner in XAS Viewer does actually support
> fractional occupancies, by randomly assigning atoms to match the partial
> occupancy (but of course, not with great precision -- each X, Y, Z position
> has exactly one actual atom of a determinant Z).  That allows a lot CIF
> files to "just work" that would otherwise need manual intervention.  At the
> moment (and possibly for the foreseeable future),  the CIF Browser does not
> support editing the CIF directly, but does support editing the result
> Feff.inp file, but one can export a CIF, edit that elsewhere, and then
> import it.
>
> What I see trying to run a calculation from that CIF file is that there are
> many oxygen atoms that are too close together.  Like Robert suggested, I
> suspected these come from the "Wat", but when I removed those and the H
> atoms, the prolem still happened.  As Robert listed the atomic positions
> for this structure, I think it might actually be the "C", "O2", as well as
> the "Wat" with the low occupancy of "0.0833" that might be the problem.
>
> If I remove CO groups and Waters, these to generate the attached CIF (I
> changed the ID number) that seems to run, though I don't know if it is then
> the structure you actually are trying to model ;).
>
> --Matt
>
>
> On Thu, Mar 30, 2023 at 6:51?AM van der Veer, Siebe <s.van.der.veer at rug.nl
> >
> wrote:
>
> > Dear all,
> >
> > I'm trying to run feff on the Hydrotalcite cif file as can be found in
> the
> > Larch Am Min CIF browser and I get the following error:
> >
> >
> > *At line 125 of file ff2chi.f (unit = 1, file = 'list.dat')Fortran
> runtime
> > error: Bad real number in item 2 of list input*
> >
> > I've been able to gather that this means there is some unreadable input
> in
> > the file that is been used, but I don't know what file this is so I don't
> > know what the actual bad input is and what has caused it.
> >
> > Any help is greatly appreciated!
> >
> > Kind regards,
> >
> >
> > --
> > *Siebe van der Veer* | *PhD student*
> > Nanostructures of Functional Oxides | Zernike Institute for Advanced
> > Materials
> > University of Groningen | Nijenborgh 4, 9747 AG Groningen | The
> Netherlands
> > Email: s.van.der.veer at rug.nl |
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>
>
> --
> --Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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> End of Ifeffit Digest, Vol 241, Issue 13
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