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

Thu Jan 13 20:21:38 CST 2022

Dear ifeffit members,

I want to say a sincere thank you to all of you. Thanks for this discussion. It helps a lot.

Ming

-----原始邮件-----
发件人:"Xinyu Luo" <xinyuluo at zju.edu.cn>
发送时间:2022-01-14 07:19:15 (星期五)
收件人: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
抄送:
主题: Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels

Shelly, now I understand. Thank you very very much for the patient and detailed answer! 

Carlo, I appreciate your additional suggestion; thank you! 

Xinyu

-----Original Messages-----
From:"Kelly, Shelly D." <skelly at anl.gov>
Sent Time:2022-01-14 01:56:02 (Friday)
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Cc:
Subject: Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels

Hi Xinyu:

Maybe your questions will be answered if you rerun the feff calculation and set the Margin parameter to zero as shown here:

The Margin parameter is used to reduce the number of paths that have very similar bond lengths.

The Path denotation @ C1 @  is just one representation of the path.  The degeneracy counts for all of them.  So if the Margin is set to 0.03 and the C1 atom is close to the C2 atom in distance from Zn, they both will be included in the degeneracy, although only one is used for the path description.   Here is the output with the margin set to zero.

The degeneracy of path 5 is 8 because there are 4 groups of N1 atoms and  C1 atoms (giving 4 paths).  But then you can have the photoelectron travel in two different ways between these atoms like this: @-N1-C1-@ or @-C1-N1-@, so there are two paths for each of the 4 atom groups.

In addition:  You don’t get to decide which atoms are C1, C2 and C3 this is done based on the unit cell that goes as input into the feff calculation.

Here is a picture of where those atoms are and their distances from Zn.  I made these using crystalmaker.

See that C1 and C2 are very close to the same distance from Zn.

From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov> On Behalf Of Xinyu Luo
Sent: Thursday, January 13, 2022 10:49 AM
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels

Hello Ming, Shelly, and Chris

I want to chime in here and add my question. If I understand it correctly, C1 refers to the two C atoms next to the N atom, and C3 is on the methyl pendant group. In this way, the eight degeneracies of [@ C1.1 @] and [@ N1.1 C1.1 @] can be satisfied. However, the remaining C atom on the ring has then to be C2, but it seems it can't generate eight degeneracy of the path (raw 5, @ N1.1 C2.1 @). I don't know how to apportion C1 and C2 in that image then...

Kind regards

Xinyu

-----Original Messages-----
From:"Kelly, Shelly D." <skelly at anl.gov>
Sent Time:2022-01-13 22:48:27 (Thursday)
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Cc:
Subject: Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels

Hi Ming:

The Path-column on the paths-page shows @ symbol for the scattering atom.  A single scattering path is shown as “@ O1.1 @”  This can be understood as the photoelectron generated at the absorbing atom travels to the first occurrence of the first oxygen atom in the unit cell and then back to the adsorbing atom.  The unit cell may contain many O atoms.  Each of them are denoted by the number following the letter, i.e. O1, O2, O3.  When the unit cell is expanded to make the cluster the O1 atom may show up in the first path and then again at a longer distance in say the 4th path.  The second occurrence from the absorbing atom of the O1 atom will be denoted at O1.2.

Kind regards,

Shelly

From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov> On Behalf Of Ming Zhang
Sent: Thursday, January 13, 2022 6:20 AM
To:ifeffit at millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels

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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