Re: [Ifeffit] Fitting mechanism of Artemis

2023-10-06 Thread Matt Newville
Hi Konstantin, On Fri, Oct 6, 2023 at 3:11 AM wrote: > Dear all, > I have a general question regarding the mechanism employed in the fitting > procedures implemented in Artemis. > How exactly is performed a fit? That is a pretty open-ended question to be able to answer with precision. Is

Re: [Ifeffit] Fitting mechanism of Artemis

2023-10-06 Thread Edmund Welter
Dear Konstantin, why would you want to do that? If you change the distance between A-B you the distance between B-A changes by the same amount. If you move the absorber away from let's say the centre of an octaeder you would split the (next) nearest neighbours shell into different shells with

[Ifeffit] Fitting mechanism of Artemis

2023-10-06 Thread bikov
Dear all, I have a general question regarding the mechanism employed in the fitting procedures implemented in Artemis. How exactly is performed a fit? Do we have a fixed central atom (absorbing/emitting atom) and only the distances to the neighbors included in the probed pathways are varied, i.e.

Re: [Ifeffit] Fitting multiple spectra simultaneously with Larch

2022-09-12 Thread Matt Newville
Hi Casey, Sorry for the late reply - I see that you asked this question 2 weeks ago - I think I got the same question from someone else by private email the same day I have had this question several times this summer. Anyway, sorry for missing this. Larch can definitely fit multiple

Re: [Ifeffit] Fitting multiple spectra simultaneously with Larch

2022-09-12 Thread Andy Zhang
Hi Casey, You can find some examples on the webpage https://xraypy.github.io/xraylarch/xafs_feffit.html#example-1-simple-fit-with-1-path . Have a nice evening! Best, Harry -- Harry Zhang Eindhoven University of Technology 5612 AZ, Eindhoven, The Netherlands On Mon, Sep 12, 2022 at 6:30

[Ifeffit] Fitting multiple spectra simultaneously with Larch

2022-09-12 Thread Van Stappen, Casey M
Dear Ifeffit team, I’d like to fit multiple EXAFS spectra simultaneously in Larch using several common parameters/relative restraints, but have not found a way to do so (yet). I’ve gone through Dr. Matt Newville’s youtube tutorials (generally very helpful), but this topic doesn’t seem to have

Re: [Ifeffit] Fitting in Wavelet transform space ?

2019-07-10 Thread Matt Newville
Hi Samy, On Wed, Jul 10, 2019 at 2:08 AM Samy Ould-Chikh wrote: > Dear colleagues, > > I have been using more and more wavelet transform in parallel of EXAFS > fitting. > In addition of the statistical parameters provided after the fit, I try > also to compare the wavelet transform of

[Ifeffit] Fitting in Wavelet transform space ?

2019-07-10 Thread Samy Ould-Chikh
Dear colleagues, I have been using more and more wavelet transform in parallel of EXAFS fitting. In addition of the statistical parameters provided after the fit, I try also to compare the wavelet transform of experimental data against various structural models to choose the best. Absolutely

Re: [Ifeffit] Fitting Problems in Artemis version 0.9.26

2018-06-29 Thread Scott Calvin
Dear Huan, Neither of those sound like a flaw in Artemis to me. 1) Fitting with a range that goes below Rbkg means fitting to a part of the data’s Fourier transform that has been suppressed by background subtraction, even though the theory’s Fourier transform has not been similarly

[Ifeffit] Fitting Problems in Artemis version 0.9.26

2018-06-28 Thread LIU HUAN
Dear Dr. Ravel, I want to ask you that when I use the new version "Artemis 0.9.26" I have two problems. (1) The fitting Range was reported to be a error that the Rmin should be larger than the Rkbg value. It makes that the fitting range cannot be smaller than 0.9 (the Rkbg value is 0.9). (2)

Re: [Ifeffit] Fitting sorption EXAFS data in Artemis

2017-02-08 Thread Gemma Woodward [ee11glw]
From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Alexey Boubnov Sent: 08 February 2017 12:49 To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Fitting sorption EXAFS data in Artemis Dear Gemma, you indeed want

Re: [Ifeffit] Fitting sorption EXAFS data in Artemis

2017-02-08 Thread Alexey Boubnov
Dear Gemma, you indeed want a feff-input with a central Co on/in a kaolinite matrix. You should define the location of the Co ion - the simplest assumptions would be substitution of an Al or Si. Import the cif and run ATOMS to create the kaolinite structure. Then replace either Al or Si with Co

[Ifeffit] Fitting sorption EXAFS data in Artemis

2017-02-08 Thread Gemma Woodward [ee11glw]
Hi all I have EXAFS data for Co sorbed to kaolinite and want to fit this using artemis. I have a kaolinite cif file but am unsure where to go from here to include the Co so I get Co-Al/Si pathways. In the atoms window do I add a Co into the table at the bottom and make it the core atom?

Re: [Ifeffit] fitting of S XANES with arctans and gaussians

2016-07-19 Thread Bruce Ravel
On 07/18/2016 11:10 PM, Matthew Marcus wrote: I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using the method discussed in the paper by Manceau and Nagy "Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy", Geochimica et

[Ifeffit] fitting of S XANES with arctans and gaussians

2016-07-18 Thread Matthew Marcus
I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using the method discussed in the paper by Manceau and Nagy "Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy", Geochimica et Cosmochimica Acta 99 (2012) 206–223. In this paper,

Re: [Ifeffit] Fitting parameters corrleations between variables

2015-11-24 Thread Matt Newville
Hi Pushkar, On Mon, Nov 23, 2015 at 11:28 PM, pushkar shejwalkar < pshejwalkar2...@gmail.com> wrote: > Dear Matt, > Thank you very much for your response. One more question. What value of > corelation is acceptable/publishable? > A correlation > 0.999 is probably an indication of duplicate

Re: [Ifeffit] Fitting parameters corrleations between variables

2015-11-23 Thread Matt Newville
Pushkar, On Mon, Nov 23, 2015 at 8:59 PM, pushkar shejwalkar < pshejwalkar2...@gmail.com> wrote: > Dear All, > I am trying to fit in Pd compound and the fit that I obtained looks > kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These > standards were collected and fitted

Re: [Ifeffit] Fitting parameters corrleations between variables

2015-11-23 Thread pushkar shejwalkar
Dear Matt, Thank you very much for your response. One more question. What value of corelation is acceptable/publishable? also having a correlation number means the fit is not finished and I should change the values of variable that are correlated? is that so? Best Pushkar On Tue, Nov 24, 2015

[Ifeffit] Fitting parameters corrleations between variables

2015-11-23 Thread pushkar shejwalkar
Dear All, I am trying to fit in Pd compound and the fit that I obtained looks kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These standards were collected and fitted simultaneously and I got the SO2 value there as 0.67 with Pd foil coordination number as 12 which is correct when

Re: [Ifeffit] fitting mixture

2014-10-06 Thread Bruce Ravel
On 10/05/2014 10:42 AM, kaziz sameh wrote: hi, i want to fit Pd2Au36 in KPd edge with artemis. from the data spectrum and think there is a mixture of Pd in staple and in centre. could you help me how to do the fitting mixture. I have the same advice for you that I had for this person:

[Ifeffit] fitting mixture

2014-10-05 Thread kaziz sameh
hi, i want to fit Pd2Au36 in KPd edge with artemis. from the data spectrum and think there is a mixture of Pd in staple and in centre. could you help me how to do the fitting mixture.___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Scott Calvin
Hi Carl, I'm not sure what level you were asking your question from. Bruce provided an answer to one interpretation of the question. If the question is, however, has anyone written an automated script that allows the user to choose parameters given to ATOMS as fitting parameters for all space

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Anatoly I Frenkel
...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Scott Calvin [scal...@sarahlawrence.edu] Sent: Thursday, May 29, 2014 10:40 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting EXAFS simulation to experimental Hi Carl, I'm not sure what level you were

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Matt Newville
Hi All, As Scott, Bruce, Anatoly have said, it is certainly possible to map certain crystallographic distortions to local structure, and so predict the effect on EXAFS, and model EXAFS in terms of those distortions. But to be clear for the original question, EXAFS is inherently a local structure

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Matthew Marcus
I wonder if what he was asking about is an automated way of mapping the position parameters for a given space group, that is, fractional atomic coordinates as listed in a .cif, onto the various path distances. As it is now, it's impractically hard to do it except for very simple cases. Maybe

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Scott Calvin
Dear Carl, The short answer is yes, but it takes a little bit of effort. One method is to actually figure out how stretching the c-axis impacts the lengths of each path geometrically, and then use the functions determine to express the delr's of each path in terms of the change in c. This

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Matt Newville
Hi Matthew, On Thu, May 29, 2014 at 11:18 AM, Matthew Marcus mamar...@lbl.gov wrote: I wonder if what he was asking about is an automated way of mapping the position parameters for a given space group, that is, fractional atomic coordinates as listed in a .cif, onto the various path

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Carl Brozek
Hi Scott, Thanks a lot for the insight. It seems like it'll take a bit of work, but I'm happy to hear it's doable. best, Carl On Thu, May 29, 2014 at 12:54 PM, Scott Calvin scal...@sarahlawrence.eduwrote: Dear Carl, The short answer is yes, but it takes a little bit of effort. One method

[Ifeffit] Fitting EXAFS simulation to experimental

2014-05-28 Thread Carl Brozek
Dear listhost, I'm using Artemis as a front end for ATOMS and FEFF and I would like to build a simulated EXAFS spectrum based on experimental data I have. I know how to generate a simulation based on a .cif or .xyz file, but is it possible to vary parameters in these input geometries to best

Re: [Ifeffit] fitting a specific k range

2013-12-06 Thread Scott Calvin
Hi Matt, Yes--we clearly disagree. The word complaining has come up a couple of times. I didn't think of it that way, although clearly it's coming off that way. I said it was my least favorite warning, and that usually one of the first things I tell students to do is to change the

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Bruce Ravel
Matt, At the risk of coming off sounding a bit mean, I don't think you are asking a very well-posed question. Examining the history of this project, I see that you are fitting in q space. Like Matt, this is not my favorite choice, but there is nothing horribly wrong about it, so long as you

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Chris Patridge
Matt, Outside of the question of fitting the data, can you collect absorption data on the additional 3+ metal you are adding the material? Chris *** Dr. Christopher Patridge Assistant Professor Department of Math and Natural Sciences D'youville

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Scott Calvin
First, a disclaimer--I haven't looked at the data Matt sent (it's a busy time of year!), but I disagree in a general sense with my reading of what Bruce wrote (perhaps I am reading it wrong). In particular, I disagree with this statement: Given that you are fitting in q-space, it is

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Bruce Ravel
On 12/05/2013 12:18 PM, Scott Calvin wrote: While I defend that principle as a very important one, I'm not claiming it applies in Matt's case--it probably doesn't. To reproduce features at high-R, it IS necessary to have a model (i.e. paths) that cover the high-R contribution, and it sounds like

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Chris Patridge
Bruce, Without those friendly warnings (reminders), beginners would likely fall down several rabbit holes before understanding many of the important steps necessary to get meaningful answers in EXAFS. I know I would have. Chris *** Dr. Christopher

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Jensen, Mark P.
Subject: Re: [Ifeffit] fitting a specific k range I object the use of hosannas of adoration. Other than the use of Greek mythology, I propose the mailing list to be religion-neutral and tautology-free. How about you should consider praise or adoration, instead of you should consider hosannas

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Anatoly I Frenkel
From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Bruce Ravel [bra...@bnl.gov] Sent: Thursday, December 05, 2013 1:19 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] fitting a specific k range On 12/05/2013 12:18 PM

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Matt Newville
Scott, On Thu, Dec 5, 2013 at 11:18 AM, Scott Calvin scal...@sarahlawrence.edu wrote: First, a disclaimer--I haven't looked at the data Matt sent (it's a busy time of year!), but I disagree in a general sense with my reading of what Bruce wrote (perhaps I am reading it wrong). In particular,

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread fred.mosselmans
What I find reassuring about Bruce's warnings is they allow you to think properly about what you are doing. Fortunately, unlike Chris, I am not of a size where I have to worry about falling down rabbit holes, unless American rabbits are much bigger than English ones. I would commend Matt's

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Matt Newville
Hi Anatoly, On Thu, Dec 5, 2013 at 12:28 PM, Anatoly I Frenkel afren...@yu.edu wrote: I object the use of hosannas of adoration. Other than the use of Greek mythology, I propose the mailing list to be religion-neutral and tautology-free. Is Down the rabbit hole OK? I'm not sure it usually

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Matthew Marcus
It must be a slow day in the EXAFS world. Does the term 'topic drift' mean anything? :-) The Wikipedia entry http://en.wikipedia.org/wiki/Hosanna has some examples of secular use of the word, FWIW, which I admit isn't much. mam On 12/5/2013 2:02 PM, Matt Newville wrote: Hi Anatoly,

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Scott Calvin
I love the warnings Artemis gives! They're not just for novices--they often catch when I've made a dumb mistake somewhere. I praise them, defend them, and generally think Bruce has done a wonderful thing by having them. The out of range default warning, however, I find counterproductive and

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Matt Newville
Hi Scott, On Thu, Dec 5, 2013 at 4:56 PM, Scott Calvin scal...@sarahlawrence.edu wrote: I love the warnings Artemis gives! They're not just for novices--they often catch when I've made a dumb mistake somewhere. I praise them, defend them, and generally think Bruce has done a wonderful thing

Re: [Ifeffit] fitting a specific k range

2013-12-04 Thread Matt Newville
Hi Matt, On Wed, Dec 4, 2013 at 1:17 PM, Matt Frith matt.fr...@gmail.com wrote: Dear All, I need some help in fitting an amorphous iron oxyhydoxide sample. I am having difficulty producing a good fit, particularly in the k=4-6 range. Fitting this region well is very important for me,

[Ifeffit] questions related to ifeffit fitting

2013-03-14 Thread davood dar
Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1.What is the ideal value of R- factor for any fit. 2. ** Can we use (fit) the theoretical model generated from

[Ifeffit] questions regarding to ifeffit fitting

2013-03-13 Thread davood dar
Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. What is the ideal value of R- factor for any fit. 2. * * Can we use (fit) the theoretical model generated from

Re: [Ifeffit] Fitting XANES spectrun with standards (Adrien Couet)

2012-07-03 Thread adrien couet
Thanks for the answer Bruce! I think one thing I did not understand about the single fit is that it tries to use all standards (although some of the standard's weights can be equal to 0 in the results), which can be detrimental to the fitting. Thanks a lot for the precisions, things are clearer

Re: [Ifeffit] Fitting XANES spectrun with standards

2012-06-29 Thread Bruce Ravel
Adrien, For starters, I am not very happy with your data. With such short pre- and post-edge ranges, I really doubt that you can reliably normalize any of your data. Without relilable normalization, I would doubt any result you get from LCF. In fact, if presented with data of such limited

Re: [Ifeffit] Fitting XANES spectrun with standards (Adrien Couet)

2012-06-29 Thread Bruce Ravel
On Friday, June 29, 2012 03:56:24 PM adrien couet wrote: Going back to the original question, I did select 8 standards for both cases (single fit with fit this group and combination of fits with fit all combinations), which gives me 247 combinations (see Excel file attached). In the case of

Re: [Ifeffit] Fitting pre-edge feature in Fe XANES

2012-06-11 Thread Erik Farquhar
Subject: [Ifeffit] Fitting pre-edge feature in Fe XANES Dear All: I would like to attempt fits to the pre-edge features of a set of Fe K-edge XANES spectra for Fe(II) samples that show partial oxidation with the goal of determining whether Fe(III) exists in octahedral or tetrahedral coordination

[Ifeffit] Fitting pre-edge feature in Fe XANES

2012-06-08 Thread shbone
Dear All: I would like to attempt fits to the pre-edge features of a set of Fe K-edge XANES spectra for Fe(II) samples that show partial oxidation with the goal of determining whether Fe(III) exists in octahedral or tetrahedral coordination (e.g. Wilke et al., American Mineralogist, 2001).

Re: [Ifeffit] fitting sulphur using standards by Athena

2012-02-14 Thread Bruce Ravel
On Tuesday, February 14, 2012 07:55:54 am 陈娟 wrote: As I known, the spectra for standard diluted with BN and non-diluted are different. The peak of the non-diluted is low due to self-absorption, as shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur to about 3%. For

Re: [Ifeffit] fitting sulphur using standards by Athena

2012-02-14 Thread Matthew Marcus
- From: Bruce Ravel bra...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Tuesday, February 14, 2012 6:07 AM Subject: Re: [Ifeffit] fitting sulphur using standards by Athena On Tuesday, February 14, 2012 07:55:54 am 陈娟 wrote: As I known, the spectra for standard

Re: [Ifeffit] Fitting on Athena

2011-09-08 Thread Bruce Ravel
On Wednesday, September 07, 2011 07:52:38 pm Niken Wijaya wrote: I think I have to clarify that I used MBACK to do the normalization instead of ATHENA. This might as well explain why I got such a high value of y-axis offset, why you think I did not choose the right parameters for the

Re: [Ifeffit] Fitting on Athena

2011-09-08 Thread Matt Newville
Niken, Have you compared MBACK to using the 'CLnorm' normalization in Athena (found under Background Removal Additional Parameters)? The algorithms are not identical, but have a lot in common, and would probably make it easier to compare with other data in Athena. If I understand correctly,

Re: [Ifeffit] Fitting on Athena

2011-09-07 Thread Niken Wijaya
On 7/09/2011 7:24 AM, Bruce Ravel wrote: On Sunday, September 04, 2011 08:52:30 pm Niken Wijaya wrote: 1. As you can see on the figure (i.e. filename: ifeffitlist-sample1 fitting), the intensity of the fitting spectra is higher than the actual sample. This is I believe due to the higher

Re: [Ifeffit] Fitting on Athena

2011-09-06 Thread Bruce Ravel
On Sunday, September 04, 2011 08:52:30 pm Niken Wijaya wrote: 1. As you can see on the figure (i.e. filename: ifeffitlist-sample1 fitting), the intensity of the fitting spectra is higher than the actual sample. This is I believe due to the higher intensity of the individual standard

[Ifeffit] Fitting bond lengths without a known FEFF file

2011-07-01 Thread Hana
Dear list experts, Here is another challenging question for me; can someone help? I have soil samples, trying to fit the first shell, I have 3 different optional bond lengths, which might give a lot of information. Now I have two questions: 1. If I do not know of specific structure (XRD implies

[Ifeffit] fitting

2010-05-26 Thread mohamed sobhy
- Forwarded Message From: mohamed sobhy bakhshwan1...@yahoo.com To: ifeffit@millenia.cars.aps.anl.gov Sent: Thu, May 20, 2010 4:14:18 PM Subject: [Ifeffit] fitting Dear all thanks for your help and explanation about the background I fitted my data after removing the background

[Ifeffit] fitting

2010-05-20 Thread mohamed sobhy
Dear all thanks for your help and explanation about the background I fitted my data after removing the background and in the attached file I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. So

Re: [Ifeffit] fitting

2010-05-14 Thread Iztok Arčon
Dear Mohamed, There is an example of CeO2 EXAFS analysis, taking into account background problems, in the following paper: *J. Padežnik Gomilšek, I. Kozjek-Škofic, N. Bukovec, A. Kodre */X-ray absorption study of CeO2 and Ce/V mixed oxide thin films obtained by sol-gel deposition. /* *Thin

[Ifeffit] fitting

2010-05-13 Thread mohamed sobhy
Dear all I am trying to use artemis to do fitting to CeO2. But really I cant get the right way to do that. During the fitting, I am using amp as set and change in N degeneracy of the path. attached is the best fit i got but it still not good and the chi-square is 41.109065479 so can you

Re: [Ifeffit] fitting

2010-05-13 Thread Frenkel, Anatoly
sobhy Sent: Thu 5/13/2010 5:21 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] fitting Dear all I am trying to use artemis to do fitting to CeO2. But really I cant get the right way to do that. During the fitting, I am using amp as set and change in N degeneracy of the path

Re: [Ifeffit] fitting

2010-05-13 Thread María Elena Montero Cabrera
To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] fitting Dear all I am trying to use artemis to do fitting to CeO2. But really I cant get the right way to do that. During the fitting, I am using amp as set and change in N degeneracy of the path. attached is the best fit i got but it still

Re: [Ifeffit] fitting

2010-05-13 Thread Frenkel, Anatoly
Then what I wrote is an overkill... Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of María Elena Montero Cabrera Sent: Thu 5/13/2010 5:34 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] fitting I don't know anything about CeO2

Re: [Ifeffit] fitting

2010-05-13 Thread Stefan Mangold
: [Ifeffit] fitting Dear all I am trying to use artemis to do fitting to CeO2. But really I cant get the right way to do that. During the fitting, I am using amp as set and change in N degeneracy of the path. attached is the best fit i got but it still not good and the chi-square

Re: [Ifeffit] fitting

2010-05-13 Thread Bruce Ravel
On Thursday 13 May 2010, 05:21:02 pm, mohamed sobhy wrote: Dear all I am trying to use artemis to do fitting to CeO2. But really I cant get the right way to do that. During the fitting, I am using amp as set and change in N degeneracy of the path. attached is the best fit i got but it still

[Ifeffit] fitting simultaneously two different K-edges

2010-05-01 Thread María Elena Montero Cabrera
Dear friends, Sam Webb, Bruce Ravel or any other, I have XAFS measurements, performed at SSRL at room temperature, of three compounds. All compounds have multielemental character and I have K-edge XAFS of two elements in each compound. It is desirable to make IFEFFIT fitting of both edges

[Ifeffit] fitting

2010-04-22 Thread mohamed sobhy
Dear all I am trying to fit some data of coordination number 8, but I always find the fitting of the first shell give the coordination number only about 0.5. I do not know what is wrong. Do I need to fit first and second and third shells altogether, and if that is right how Can I do that??

Re: [Ifeffit] fitting

2010-04-22 Thread Shelly Kelly
Hi Mohamed: It is hard to help you without some more information. The coordination number (CN) is a little bit complicated by the high correlation it has with the value for S02, degeneracy, and the normalization edge step. You have to have all of those things correct to get the CN correct. If you

Re: [Ifeffit] Fitting results

2010-01-21 Thread Shelly Kelly
Hi Abhijeet, I think that there is a problem with you structure for Cu2O. Each Cu atoms must be coordinated by more than just two O atoms in the first shell. Shelly On Thu, Jan 21, 2010 at 1:28 AM, Abhijeet Gaur abhijeetga...@gmail.com wrote: Hello Sir,    I had done fitting of a

Re: [Ifeffit] Fitting using Experimental standard

2010-01-05 Thread Bruce Ravel
On Monday 04 January 2010 10:16:15 pm you wrote: Dear all, Can somebody please explain to me what is theoretical standard and what is experimental standard. My understanding of theoretical standard is the crystallographic data. However, it is first time I heard experimental standard. Thanks

Re: [Ifeffit] Fitting using Experimental standard

2010-01-05 Thread Matthew
The very valid question whenever the topic of empirical standards comes up is Why do you think you need it? I am unconvinced that empirical standards are ever needed. Of course, I am also unconvinced that I am right in saying that! So who knows...? There is some evidence that empirical

[Ifeffit] Fitting using Experimental standard

2010-01-04 Thread abhijeet gaur
A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Bruce Ravel
On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote: Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Frenkel, Anatoly
of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Scott Calvin
Hi Fiona, An experimental standard is a spectrum of a known material (the term is also often used for the known material itself, in addition to its spectrum). If you use Athena to do a linear combination fit, you are most commonly using experimental standards to do it. A theoretical

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Matthew
: Fiona R. Kizewski jrkiz...@ncsu.edu To: bra...@bnl.gov; XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Monday, January 04, 2010 7:16 PM Subject: Re: [Ifeffit] Fitting using Experimental standard Dear all, Can somebody please explain to me what is theoretical standard

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Frenkel, Anatoly
-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Mon Jan 04 22:34:56 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard You're describing the way many of us, including me, used to analyze data before FEFF became as reliable

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Matthew
Re: [Ifeffit] Fitting using Experimental standardAh, I see. I think Artemis has some way of putting in experimental phase and amp, but that may be just to make a corrected FT. Is that so? Otherwise, I suppose it should be possible to write a fake FEFF path file and read it in. I guess that's

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Frenkel, Anatoly
). A. From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Mon Jan 04 22:54:30 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard Ah, I

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Matthew Marcus
@millenia.cars.aps.anl.gov *Sent*: Mon Jan 04 22:54:30 2010 *Subject*: Re: [Ifeffit] Fitting using Experimental standard Ah, I see. I think Artemis has some way of putting in experimental phase and amp, but that may be just to make a corrected FT. Is that so? Otherwise, I suppose it should be possible

Re: [Ifeffit] Fitting Cu2O

2009-07-04 Thread umesh palikundwar
Hi all, I am fitting Cu2O data. But when I fit the first shell using the first path, I got the guess value for SS parameter negative which is around -0.0028 and also the guessed value for SO2 parameter comes out to be around 0.52. Are these values logically correct as I am getting a nice

[Ifeffit] Fitting procedure

2009-04-24 Thread abhijeet gaur
Hello Matt Sir, Thanks a lot for your valuable sugestions. I had fitted the Cu foil spectra as you suggested. I had taken same SO2 value for all the paths and after fitting the first shell , making its parameter fix when fitting second shell I changed the fit R range 2.9- 3.7

Re: [Ifeffit] Fitting procedure

2009-04-24 Thread Matt Newville
Hi Abhijeet, On Fri, Apr 24, 2009 at 7:09 AM, abhijeet gaur abhijeetga...@gmail.com wrote: Hello Matt Sir, Thanks a lot for your valuable sugestions. I had fitted the Cu foil spectra as you suggested. I had taken same SO2 value for all the paths and after fitting the

Re: [Ifeffit] Fitting procedure

2009-04-20 Thread Matt Newville
HI Abhijeet, I think there is a lot of confusion over the method that i used for fitting, So I should make it clear here. In this method I fit the first shell by taking into account only first shell R range i.e. 1.5 - 2.7. Then after getting a nice fit for the first shell, I

[Ifeffit] Fitting procedure

2009-04-19 Thread abhijeet gaur
I want to add some more things I have done 1) E0 is kept same for all the shells 2) All other parameters like SO2 , del r , SS2 are calculated separately for different shells. So. is there problem with taking different SO2 for different shells. Surely del r and SO2 will be different for different

Re: [Ifeffit] Fitting procedure

2009-04-18 Thread Matt Newville
Hi Adam, I am confused by this thread too! As you say, the original issue involved using S02 for individual shells of data on Cu foil. Of course, having separate S02 for each shell is not usually necessary to model Cu foil -- in fact I can't think of a case where it is needed. But since S02

Re: [Ifeffit] Fitting procedure

2009-04-18 Thread Scott Calvin
Hi all, Well, I'm understanding my own views on this more clearly as the conversation continues, so it's been helpful to me! There are several different issues that have floated through this thread, but let me focus on one aspect. One possible fitting strategy is a shell-by-shell method, in

Re: [Ifeffit] Fitting procedure

2009-04-18 Thread Chappell, Mark A ERDC-EL-MS
: [Ifeffit] Fitting procedure They're on theur way back to Vicksburg. I yried to guide them from home but couldn't figure out where she was. By 230, she hung it up and turned back - Message sent via my BlackBerry Wireless Device - Original Message - From: ifeffit-boun

[Ifeffit] Fitting procedure

2009-04-17 Thread abhijeet gaur
Hi all, Thanks to all the concerned persons for having such a wonderful discussion over fitting procedure. I am able to understand the things better by going through these discussions. But what I am trying to say is that I had first applied the fitting procedure in which I make the

Re: [Ifeffit] Fitting procedure

2009-04-17 Thread Kelly, Shelly
, April 17, 2009 2:29 AM To: ifeffit Subject: [Ifeffit] Fitting procedure Hi all, Thanks to all the concerned persons for having such a wonderful discussion over fitting procedure. I am able to understand the things better by going through these discussions. But what I am trying to say

Re: [Ifeffit] Fitting procedure

2009-04-17 Thread Matt Newville
Shelly wrote: ….and what we are trying to say is that your method is not generally accepted as the best way to model data. We are? If I understand Abhijeet's approach (first fit the first shell, then fix those parameters, change the R-range to the second shell and fit that), it is exactly

Re: [Ifeffit] Fitting procedure

2009-04-17 Thread Kelly, Shelly
- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit- boun...@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville Sent: Friday, April 17, 2009 9:23 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting procedure Shelly wrote: and what we are trying

Re: [Ifeffit] Fitting procedure

2009-04-17 Thread Adam Webb
] On Behalf Of Matt Newville Sent: Friday, April 17, 2009 9:23 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting procedure Shelly wrote: and what we are trying to say is that your method is not generally accepted as the best way to model data. We are? If I understand

Re: [Ifeffit] fitting ReO2

2008-12-10 Thread Zajac, Dariusz
PROTECTED] On Behalf Of Edward L. Kunkes Sent: Wednesday, December 10, 2008 4:23 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] fitting ReO2 Hi everyone, I am trying to do a first shell fit of ReO2 - where there are 2 different Re-O distances in the first coordination shell. Does

Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

2007-03-30 Thread E. Bosman
etc... are the cause. Ciao, Eckhard PS: sorry for the off-topic spam ;-) Original-Nachricht Datum: Wed, 28 Mar 2007 16:43:35 -0400 Von: Anatoly Frenkel [EMAIL PROTECTED] An: \'XAFS Analysis using Ifeffit\' ifeffit@millenia.cars.aps.anl.gov Betreff: Re: [Ifeffit] Fitting EXAFS

Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

2007-03-28 Thread Scott Calvin
Hi Mario, There are a couple of different ways to approach the kind of problem you describe, although you must be willing to guess at what the local environment looks like. For example, maybe the chemical composition tells you that you have an iron oxide. At a minimum, you could use Atoms to

Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

2007-03-28 Thread Bruce Ravel
On Wednesday 28 March 2007 13:15, Mario Gomez wrote: Hi Bruce my name is Mario and I was just wondering if your program can fir the EXAFS spectra without any atomic positions. Obviously the answer is no if you use atoms to create the FEFF file but what does one do when we have a

Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

2007-03-28 Thread Anatoly Frenkel
: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Ravel Sent: Wednesday, March 28, 2007 3:41 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates? On Wednesday 28 March 2007 13:15, Mario Gomez wrote: Hi Bruce my name is Mario and I

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