Artemis warning after FEFF calculation---can't close GLOB filehandle
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
Dear Luo,
A quick look at your attached figures tells me that you have several pairs of atom that are too close to each other.
For example, pair #1: atom #144 and atom #160, and pair #2: atom #145 and atom #161, as in the output console.
This trouble usually happens when one uses a CIF file which is an output from a Rietveld refinement software like Fullprof.
I now present here one way to solve this issue.
1. Attached, please find the CIF file that I have simplified for you.
2. Please open it with Demeter.
3. Now at the Shift vector, please input 1/4 0 0.
4. "Run Atoms".
5. "Run feff" and wait for some seconds.
Attached, please also see two other figure files for your reference.
I wish you luck.
Sincerely yours,
Duc-Chau Nguyen, PhD.
A postdoc at IoP-AS, Taiwan.
-----Original message-----
From:Xinyu Luo
Hello Duc-Chau,
Thank you very much for the timely help! I followed your guideline, and the FEFF calculation was completed successfully. Could you please tell me more about how you fixed my CIF file? Or just throw me some references? I did receive warnings about atoms too close in other CIF files, but they were just fine, unlike this situation.
And, about the shift vector, frankly, I don't have much background knowledge and I haven't edited it before. I tried another value, say, 1/8, and got a successful FEFF calculation but with totally different REFFs. Surprisingly, 1/4 0 0 shift vector also works on the original CIF file and can generate a PATH column same to the one in your attached figure. Could you kindly provide me with more information to help me understand?
Thank you again!
Xinyu Luo
-----Original Messages-----
From:dcnguyen
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
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 _______________________________________________ Ifeffit mailing list Ifeffit@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
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"
participants (3)
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dcnguyen -
Matt Newville -
Xinyu Luo