Hi
Matt, thank you! It works! I appreciate your support. I checked the FEFF console, and, indeed, I found that every "too close" alarm was pointing to the H atom.As a non-crystallographer and non-programmer, it's almost magical to me that this hurdle can be overcome by simply removing H atoms!
I'm very grateful for the help with this CIF file;)
Xinyu
-----Original Messages-----
From:"Matt Newville"
Sent Time:2022-02-10 12:59:17 (Thursday)
To: "XAFS Analysis using Ifeffit"
Cc:
Subject: Re: [Ifeffit] Artemis warning after FEFF calculation---can't close GLOB filehandle
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 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
