How to use "OVERLAP" card?
I have read some references of Kelly Shelly, and I have got some idea of how to construct a structure without difinite crystalline structure. But when I try to apply to my own question, meet some difficulties. In my case, four nitrogen atoms is surrounding a iron atom. So I use OVERLAP and SS card as to define such system as described in the FEFF manual: -------------------------------------------------- POTENTIALS * ipot Z element 0 26 Fe 1 7 N * Determine approximate overlap for central and 1st nn in Cu OVERLAP 0 *determine overlap for central atom of Fe *iphovr novr rovr * ipot, number in shell, distance 1 4 2.15 OVERLAP 1 *determine approximate overlap for 1st shell N *iphovr novr rovr * ipot, number in shell, distance 0 1 2.15 *SS index ipot deg rss SS 1 1 4 2.15 -------------------------------------------------- but feff8 stopped and said: Absorbing atom coords not specified. Cannot find multiple scattering paths. since the OVERLAP does't need ATOMES card, where can I define the coordination of absorbing atom? Is there any other CARD needed for such situation? ========================================= Hi Jun, That keyword is explained here: http://feff.phys.washington.edu/feff/wiki/index.php?title=OVERLAP I think the problem is that you have not specified the SS keyword: http://feff.phys.washington.edu/feff/wiki/index.php?title=SS I use the overlap/ss thing in feff very infrequently. My preference is to start from a known structure that is somehow similar to the material I am investigating. For example, if I were to look at amorphous germanium, I would use crystalline germanium as my starting point. I would then construct the model in such a way that I parameterize the differences between the starting structure and what I expect to find in the data. I'd recommend reading papers by Scott Calvin or Anatoly Frenkel on nanoparticles or by Shelly Kelly on uranium in biogeochemical systems for excellent examples of how that sort of analysis is done. Hope that helps, B -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800
Hi, Below is an old but working example. See the comment about the units (Bohr's units in SS card v. Angstrom in Overlap card) - it used to be a bug in FEFF6 - and it may still be unless Bruce/Matt changed the code in the recent distribution. If rescaling the distances in your SS card does not help, swap the SS and the OVERLAP cards (in my example SS preceeds OVERLAP - may be it matters). Let me know if it helped, Anatoly TITLE Cu metal in aqueous solution TITLE Structure is from Beagley et al, J. Phys.: Cond. Matt. 1, 2395 (1989) TITLE Distance units are in Angstroms in OVERLAP cards TITLE Distance units are in Angstroms/0.529177249 in SS cards HOLE 1 1.0 Cu K edge ( 8.979 keV), s0^2=1.0 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 POTENTIALS * ipot z label 0 29 Cu 1 8 O 2 8 O 3 1 H 4 8 O SS 1 1 4 3.760555 SS 2 2 2 4.327473 SS 3 4 11 7.464418 * note that the distances above correspond to the three shells: *1.99, 2.29 and 3.95 A. However, because of the bug in FEFF6, *these distances should are used in FEFF6 in the units of Bohr's radius. *Therefore, for the program to work properly, you should divide the true *shell distance by a0 = 0.529177249 to enter in SS cards, as in the example above *The overlap distances below stay in Angstroms, as they should. OVERLAP 0 * Cu - O_eq 1 4 1.99 * Cu - O_ax 2 2 2.29 OVERLAP 1 * O_eq - H 3 2 0.957 * O_eq - Cu 0 1 1.99 OVERLAP 2 * O_ax - H 3 2 0.957 * O_ax - Cu 0 1 2.29 OVERLAP 3 * H - O_eq 1 1 0.957 * H - H 3 1 1.513 * H - O_2sh 4 1 0.957 OVERLAP 4 * O_2sh - H 3 2 0.957 -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Jun Lin Sent: Tuesday, May 08, 2007 10:07 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] How to use "OVERLAP" card? I have read some references of Kelly Shelly, and I have got some idea of how to construct a structure without difinite crystalline structure. But when I try toapply to my own question, meet some difficulties. In my case, four nitrogen atoms is surrounding a iron atom. So I use OVERLAP and SS card as to define such system as described in the FEFF manual:--------------------------------------------------POTENTIALS * ipot Z element 0 26 Fe 1 7 N * Determine approximate overlap for central and 1st nn in CuOVERLAP 0 *determine overlap for central atom of Fe *iphovr novr rovr * ipot, number in shell, distance 1 4 2.15OVERLAP 1 *determine approximate overlap for 1st shell N *iphovr novr rovr * ipot, number in shell, distance 0 1 2.15 *SS index ipot deg rssSS 1 1 4 2.15--------------------------------------------------but feff8 stopped and said: Absorbing atom coords not specified. Cannot find multiple scattering paths. since the OVERLAP does't need ATOMES card, where can I define the coordination of absorbing atom?Is there any other CARD needed for such situation?========================================= Hi Jun, That keyword is explained here: http://feff.phys.washington.edu/feff/wiki/index.php?title=OVERLAPI think the problem is that you have not specified the SS keyword: http://feff.phys.washington.edu/feff/wiki/index.php?title=SSI use the overlap/ss thing in feff very infrequently. My preference is to start from a known structure that is somehow similar to thematerial I am investigating. For example, if I were to look atamorphous germanium, I would use crystalline germanium as my startingpoint. I would then construct the model in such a way that I parameterize the differences between the starting structure and what Iexpect to find in the data.I'd recommend reading papers by Scott Calvin or Anatoly Frenkel onnanoparticles or by Shelly Kelly on uranium in biogeochemical systems for excellent examples of how that sort of analysis is done.Hope that helps,B -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800
On Tuesday 08 May 2007, Jun Lin wrote:
I have read some references of Kelly Shelly, and I have got some idea of how to construct a structure without difinite crystalline structure. But when I try to apply to my own question, meet some difficulties.
In my case, four nitrogen atoms is surrounding a iron atom. So I use OVERLAP and SS card as to define such system as described in the FEFF manual:
Jun, Just to reiterate, neither I nor Shelly would advocate your approach. (I think I can speak for her on this topic. I'm sure she'll let me know if I am mistaken! ;-) ) In my earlier email I was trying to suggest that you use the ATOMS list in Feff on a related compound and attempt to model your data in terms of that related compound. That is certainly what Shelly has done in any of her papers that you might have read. There are a number of reasons I suggest this, mostly having to do with approaching the problem with as much flexibility as possible. For instance, the OVERLAP/SS use of Feff means that you cannot (easily) consider multiple scattering contributions in your fit. It is also considerably harder to interpret your fitting parameters in terms of the 3D structure of the material you are analyzing when you use the OVERLAP/SS approach in Feff. The main reason I recommend against the OVERLAP/SS approach is that that's not how Artemis works. Artemis expects you to use an ATOMS list. Scott Calvin's Artemis tutorial at http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib is a good way to learn how Artemis works. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
participants (3)
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Anatoly Frenkel -
Bruce Ravel -
Jun Lin