However, after FEFF calculation, they become C1.1 C2.1 C3.1, so do the other atoms like nitrogen and hydrogen. The VESTA GUI shows that there are C1, C2, and C3 carbons in a unit cell. I GOT SOME QUESTIONS when I imported the CIF File into the FEFF calculation.ġ) I’m confused with the atom label. I’m practicing EXAFS fitting with some standard crystal data. 主题: Question-FEFF calclulated atom coordinates and labels Sorry for the trouble, I forgot to register this email. The second occurrence from the absorbing atom of the O1 atom will be denoted at O1.2. 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. Each of them are denoted by the number following the letter, i.e. 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 Path-column on the paths-page shows symbol for the scattering atom. 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. In this way, the eight degeneracies of C1.1 and N1.1 C1.1 can be satisfied. 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. I want to chime in here and add my question. See that C1 and C2 are very close to the same distance from Zn. Here is a picture of where those atoms are and their distances from Zn. 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. But then you can have the photoelectron travel in two different ways between these atoms like this: or so there are two paths for each of the 4 atom groups. The degeneracy of path 5 is 8 because there are 4 groups of N1 atoms and C1 atoms (giving 4 paths). Here is the output with the margin set to zero. 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. The Path denotation C1 is just one representation of the path. The Margin parameter is used to reduce the number of paths that have very similar bond lengths. Maybe your questions will be answered if you rerun the feff calculation and set the Margin parameter to zero as shown here: Subject: Re: Question-FEFF calclulated atom coordinates and labels Thank you very very much for the patient and detailed answer!Ĭarlo, I appreciate your additional suggestion thank you! Next message (by thread): Question-FEFF calclulated atom coordinates and labels.Previous message (by thread): Re: Question-FEFF calclulated atom coordinates and labels.Question-FEFF calclulated atom coordinates and labels Xinyu Luo xinyuluo at Question-FEFF calclulated atom coordinates and labels
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