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

[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 <dcnguyen at gate.sinica.edu.tw>
Sent Time:2022-02-09 22:16:00 (Wednesday)
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Cc:
Subject: Re: [Ifeffit] Artemis warning after FEFF calculation---can't close GLOB filehandle


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<xinyuluo at zju.edu.cn>
To:ifeffit<ifeffit at millenia.cars.aps.anl.gov>
Date: Wed, 09 Feb 2022 20:38:09
Subject: [Ifeffit] 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


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