[Ifeffit] Question--FEFF calclulated atom coordinates and labels

Christopher Patridge patridge at buffalo.edu
Thu Jan 13 07:04:00 CST 2022


Without venturing in too far to the structure, there are two C off of each N and that would generate 8 degenerate paths to explain one of your questions. 

Hope that helps,
Chris 

*********************************************
Dr. Chris Patridge
Assistant Professor
Department of Chemistry 
SASE 315
D’Youville College 
320 Porter Ave
Buffalo, NY 14201
716-829-8096
patridgc at dyc.edu


> On Jan 13, 2022, at 7:20 AM, Ming Zhang <mzhang17 at zju.edu.cn> wrote:
> 
> 
> sorry for the trouble, I forgot to register this email.
> 
> -----原始邮件-----
> 发件人:"Ming Zhang" <mzhang17 at zju.edu.cn>
> 发送时间:2022-01-13 14:41:04 (星期四)
> 收件人: ifeffit at millenia.cars.aps.anl.gov
> 抄送: 
> 主题: Question--FEFF calclulated atom coordinates and labels
> 
> Dear IFEFFIT members,
> 
>  
> 
> I’m practicing EXAFS fitting with some standard crystal data. I GOT SOME QUESTIONS when I imported the CIF File into the FEFF calculation.
> 
> 1) I’m confused with the atom label. The VESTA GUI shows that there are C1, C2, and C3 carbons in a unit cell. However, after FEFF calculation, they become C1.1 C2.1 C3.1, so do the other atoms like nitrogen and hydrogen. Since I need to set some geometry constraints, I have to figure out the nomenclature of the atom coordinates calculated by FEFF and link those atoms to real physical images.
> 
> 2) I’m also confused with the calculated degeneracy, like the path of @ C1.1 @ (I have no idea about the atom C1.1 stands for). It’s a zinc absorber placed in a tetrahedron coordinated by the N atom of imidazole. Very intuitively, the degeneracy of @ N1.1 @ (row 1) is 4, and YES IT IS. But how comes the single scattering path (row 2) of the C atom next to N become 8? Also in row 5, degeneracy of @ N1.1 C2.1 @ is 8. Notably, we only got 3 C atoms in a coordinated molecule, so even treating closely located C atoms into the same one couldn’t help explain this.
> 
> 
> 
> FEFF calculation 
> 
> 
> 
> 
> 
> VESTA GUI
> 
>  
> 
> The CIF file is attached. I would appreciate it very much if you could help me out.
> 
> 
> 
> Best regards
> 
> Ming Zhang
> 
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