[Ifeffit] Artemis warning after FEFF calculation---can't close GLOB filehandle

[Matt Newville]

Hi,

I suspect that the calculation would work much better if you removed the H
atoms. When trying to use this CIF file in Larch, I noticed 3 challenges:

a) the label of
       _chemical_formula_moiety         ' C8 H8 F6 N4 Ni Si, 2(O) '

doesn't parse correctly in Larch.  Apparently, it does in Artemis.  I
changed it to  ' C8 H8 F6 N4 Ni Si O2 '.

b) the hydrogen atoms cause overlap problems.  I removed these from the
`atoms` loop.  This is not an uncommon problem.

c) the unit cell is large enough that one could run into a problem of not
having an atom of the same species as the central atom
(I guess Ni is what you're looking at).   Artemis might not require this,
but I found that the cluster had to be at least 7.02 Ang to
make sure that a Ni scatterer was in the cluster.

Hope this helps,




On Wed, Feb 9, 2022 at 6:40 AM Xinyu Luo <xinyuluo at zju.edu.cn> wrote:

> Dear ifeffit memebers,
>
>
>
> I received an Artemis warning after importing a CIF file into FEFF
> calculation as usual, which said, “Can’t close GLOB(…) filehandle at …” I
> first assumed it might be caused by some system errors. So I tried this CIF
> file on another PC and received a similar warning---can’t close a GLOB()
> filehandle. Also, I tried FEFF8 using Webatoms, but this still didn't
> work... Is that due to the CIF file itself or the software bug on my PC? I
> never met this situation before because it's always been very smooth to
> import a CIF file and generate atomic coordinates and paths before
> fitting... I don’t know how to handle this.
>
> The CIF file is attached. I appreciate any suggestions that might be
> helpful. Thank you for your time!
>
> Xinyu Luo
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-- 
--Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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