How to keep enot,delr, and ss within acceptable limits
Dear All, I am currently using ARTEMIS to fit Zn-O, Zn-Zn paths to first and second shells, respectively. Many times I would get unacceptable values for enot, ss, and delr. My question is: is there a way to tell ARTEMIS that I want these parameters to be within acceptable limits? For example, you cannot have negative ss, so how can I avoid any fit result that produces negative values for ss? Or high extremely high values for enot and delr? I appreciate your assistance and guidance. Regards, Hashem Stietiya School of plant, Environmental and Soil Sciences Louisiana State University
Hi Hashem, Yes, there is, sort of. Use a restraint of this form: Penalty(enot,-10,10)*1000 This adds a penalty to chi-square when enot is outside of the range -10 to 10. The *1000 part just makes it a very steep penalty; you can make it smaller (or larger) to allow it to drift a little outside the targeted range. Having said that, I find that it usually doesn't work as desired. Most of the time the fit just goes to the edge of wherever you set the penalty and sits there. That means there's an underlying problem in the model or the data which really needs to be addressed. Once in a while, though, the penalty function will keep you out of a false minimum and put you in the right one. --Scott Calvin Sarah Lawrence College On Jan 9, 2009, at 12:34 PM, Hashem Stietiya wrote:
Dear All,
I am currently using ARTEMIS to fit Zn-O, Zn-Zn paths to first and second shells, respectively. Many times I would get unacceptable values for enot, ss, and delr. My question is: is there a way to tell ARTEMIS that I want these parameters to be within acceptable limits? For example, you cannot have negative ss, so how can I avoid any fit result that produces negative values for ss? Or high extremely high values for enot and delr?
I appreciate your assistance and guidance.
Regards, Hashem Stietiya School of plant, Environmental and Soil Sciences Louisiana State University
On Friday 09 January 2009 12:34:01 pm Hashem Stietiya wrote:
I am currently using ARTEMIS to fit Zn-O, Zn-Zn paths to first and second shells, respectively. Many times I would get unacceptable values for enot, ss, and delr. My question is: is there a way to tell ARTEMIS that I want these parameters to be within acceptable limits? For example, you cannot have negative ss, so how can I avoid any fit result that produces negative values for ss? Or high extremely high values for enot and delr?
Hashem, There are two possible answers to your question -- the one you are probably looking for and the one that involves me getting up on my soapbox and lecturing. So.... in that order.... You are probably looking to use restraints. If you search the mailing list archives, you'll find some discussion of that topic. You might also find my explanation in this presentation useful: http://xafs.org/Workshops/APS2008?action=AttachFile&do=get&target=Ravel_Advanced.pdf In short, a restraint is a term that you add to the evaluation of the fitting metric which imposes a penalty on the fit when a parameter wanders away from a value that you have prior knowledge about. The next to last slide in that talk shows a screen shot that should make it clear how they get implemented in Artemis. I would caution you, though, against disregarding a fit that results in unphysical parameter values. That a parameter takes on an unphysical value is usually telling you something about your fitting model. If your delta R parameter is really large, perhaps your starting structure is not a very good representation of your real sample. If your sigma^2 parameter is negative, perhaps you have too much structural disorder in your model and the fit is compensating by inflating those paths with a negative sigma^2. Ifeffit and Artemis do not report things like negative sigma^2 parameters just to mess with your head. (Although that *would* be fun...!) The parameters reported are the parameters required to minimize the fit. Ifeffit doesn't know anything about science -- it just does what it can to make the fitting metric as small as possible. It's kinda stupid that way and Artemis isn't any smarter. Fortunately, _you_ are smarter. When a physically unreasonable parameter is reported, you can examine the assumptions made in your fitting model. If parameters are coming back in an unphysical state, it is almost certain that there is something unphysical about your fitting model. Thus, wonky values for the parameters of a bad fit are full of information that you need to interpret and use to refine your fitting model. Hope that helps, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hello If delr has higher than 0.2, Check your model in atoms.inp. I think that the enot considerably correlates with the bonding length from my experience. You can control the bonding length, as you change lattice constant or oxygen position on c-axis in atoms.inp with wurtzite structure. From: mstiet2@lsu.eduTo: ifeffit@millenia.cars.aps.anl.govDate: Fri, 9 Jan 2009 11:34:01 -0600Subject: [Ifeffit] How to keep enot,delr, and ss within acceptable limits Dear All, I am currently using ARTEMIS to fit Zn-O, Zn-Zn paths to first and second shells, respectively. Many times I would get unacceptable values for enot, ss, and delr. My question is: is there a way to tell ARTEMIS that I want these parameters to be within acceptable limits? For example, you cannot have negative ss, so how can I avoid any fit result that produces negative values for ss? Or high extremely high values for enot and delr? I appreciate your assistance and guidance. Regards, Hashem Stietiya School of plant, Environmental and Soil Sciences Louisiana State University _________________________________________________________________ 클릭 한번으로 전세계 이미지가 검색된다. http://www.live.com/?scope=images
Dear all, I have the same problem with Hashem. My sample is nanocrystal Wurtzite InN (XRD and AFM results). I do the absorption experiment at In L3-edge at room temperature. After an data processing process, I get 2 broad peaks in FT. When i try to fitting a Wurtzite InN model to the EXAFS spectra for the first and second shells, I always get unacceptable parameters. First of all, I try to change my WZ InN model (changing lattice constant a and c, u-parameter) but it is inefficiently. How could I do? This figure 1 shown a FT of In-L3 EXAFS spectra, the Blue line is my 2 broad peaks and red line is calculate with my WZ InN model which set all parameter to initial value (not guess any thing). figure 1 >> http://nanotech.sytes.net/kaswat/01.emf After I have read Bruce's mail ("If your sigma^2 parameter is negative, perhaps you have too much structural disorder in your model and the fit is compensating by inflating those paths with a negative sigma^2."). How do I construct a WZ InN model which have too many structural disorder. P.S. I have read some papers, they have use model of nanocrystalline alloy which containing amorphous model. How to construct an amorphous model like they. -- Mr. Kittiphong Amnuyswat [kaswat] Post Graduate student College of KMITL Nanotechnology Contact : kaswat@gmail.com, nakz_zz@hotmail.com [MSN Available]
Hi I saw your figure. The second peak of Nanocrystal in wurtzite generally is week or not, because there is an amount of disorder in second shell. The second peak in your fitting may make a problem. First, Fit your data in first shell with 4 nitrogen atoms, not with second shell. After that, you can fit second shell with 'set first shell varables'. To fit second shell is not easy. when you fit second shell, check the number of second shell atoms. I think there are not 12 In around probe atom. Date: Mon, 12 Jan 2009 15:30:52 +0700From: kaswat@gmail.comTo: ifeffit@millenia.cars.aps.anl.govSubject: Re: [Ifeffit] How to keep enot, delr, and ss within acceptable limits Dear all, I have the same problem with Hashem. My sample is nanocrystal Wurtzite InN (XRD and AFM results). I do the absorption experiment at In L3-edge at room temperature. After an data processing process, I get 2 broad peaks in FT. When i try to fitting a Wurtzite InN model to the EXAFS spectra for the first and second shells, I always get unacceptable parameters. First of all, I try to change my WZ InN model (changing lattice constant a and c, u-parameter) but it is inefficiently. How could I do? This figure 1 shown a FT of In-L3 EXAFS spectra, the Blue line is my 2 broad peaks and red line is calculate with my WZ InN model which set all parameter to initial value (not guess any thing). figure 1 >> http://nanotech.sytes.net/kaswat/01.emf After I have read Bruce's mail ("If your sigma^2 parameter is negative, perhaps you have too much structural disorder in your model and the fit is compensating by inflating those paths with a negative sigma^2."). How do I construct a WZ InN model which have too many structural disorder. P.S. I have read some papers, they have use model of nanocrystalline alloy which containing amorphous model. How to construct an amorphous model like they.-- Mr. Kittiphong Amnuyswat [kaswat]Post Graduate student College of KMITL NanotechnologyContact : kaswat@gmail.com, nakz_zz@hotmail.com [MSN Available] _________________________________________________________________ 클릭 한번으로 전세계 이미지가 검색된다. http://www.live.com/?scope=images
THank JeongEunSuk , Thank you for your suggestion, I will try to fitting it again. I just recheck the XRD result. I got a only 1 sharp peak at 002 (31.311 degree) which represent a WZ structure, but you are talking about atomic disorder. Could you describe about this difference. -- Mr. Kittiphong Amnuyswat [kaswat] Post Graduate student College of KMITL Nanotechnology Contact : kaswat@gmail.com, nakz_zz@hotmail.com [MSN Available]
I saw second peak with some In atoms in your figure. Second shell usually means that your sample is crystalized. But the peak of second shell in your figure is low and broaden, which means that there are some disorder or small number of atoms around probe atom. If you compare your sample with perfect crystal InN in XRD, you can check how much your sample have disorder. Date: Wed, 14 Jan 2009 10:15:44 +0700From: kaswat@gmail.comTo: ifeffit@millenia.cars.aps.anl.govSubject: Re: [Ifeffit] How to keep enot, delr, and ss within acceptable limits THank JeongEunSuk , Thank you for your suggestion, I will try to fitting it again. I just recheck the XRD result. I got a only 1 sharp peak at 002 (31.311 degree) which represent a WZ structure, but you are talking about atomic disorder. Could you describe about this difference. -- Mr. Kittiphong Amnuyswat [kaswat]Post Graduate student College of KMITL NanotechnologyContact : kaswat@gmail.com, nakz_zz@hotmail.com [MSN Available] _________________________________________________________________ 간편하고 정확한 나만의 맞춤 검색, Live Search! http://search.live.com
participants (5)
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Bruce Ravel -
Hashem Stietiya -
JeongEunSuk -
K.A. Swat -
Scott Calvin