- Ifeffit - millenia.cars.aps.anl.gov

Help for EXAFS fitting
by Dien.Li＠srnl.doe.gov 14 Sep '22

14 Sep '22

Hi, Matt and Carlo and other EXAFS experts Attached please find a fpj data file. The basic system is silica + PO4 ligand on surfaces, which was used for adsorption of La. We collected La L3-edge EAXFS data and did this fitting. I used two models of La binding as monodentate and bidentate. I saw the negative ss parameter. I saw this in some of my other EXAFS data fitting samples as well. I have two questions for help: 1. What might cause the negative ss parameters and how I may improve this, is this caused by incorrect structure models 2. If we can do some "stress" test to make sure the fitting is valid and meaningful. Please you can help look at and play this data set and direct me on how to do this correctly, thank you so much. Dien Li Savannah River National Laboratory

2 1

Larch: Fitting error of the objective/model function
by dxfan＠post.kek.jp 14 Sep '22

14 Sep '22

Dear All I am doing Temperature-dependent EXAFS experiment with a lot of data. Usually, we do these kinds of data fitting by several steps, like below: First, put every parameter free, and obtain the averaged value of amp. Second, set the amp to the averaged value, put other parameters free, and then obtain the averaged value of del_e0. Third, set the amp and del_e0 to the averaged value, and fit again. In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 (1995): 151-153. The fitting parameters of Cubic model is this: setattr(pars, f'alpha', param(0, vary=True)) setattr(pars, f'amp', param(0, vary=True)) setattr(pars, f'del_e0_O', param(0, vary=True)) setattr(pars, f'del_e0_Sr', param(0, vary=True)) setattr(pars, f'del_e0_Ti', param(0, vary=True)) setattr(pars, f'sig2_O', param(.002, vary=True)) setattr(pars, f'sig2_Sr', param(.002, vary=True)) setattr(pars, f'sig2_Ti', param(.002, vary=True)) setattr(pars, f'sig2_Tr1', param(.002, vary=True)) setattr(pars, f'sig2_p', param(.002, vary=True)) setattr(pars, f'sig2_Tr2', param(.002, vary=True)) #del_e0 for each path pars.del_e0_1=param(expr='del_e0_O') pars.del_e0_2=param(expr='del_e0_O') pars.del_e0_3=param(expr='del_e0_Sr') pars.del_e0_4=param(expr='del_e0_Ti') pars.del_e0_5=param(expr='del_e0_O') pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') In the first step, the fitting is fine, I obtained the averaged amp. However, in the second step, when I set amp to the averaged value, Error happens for "some" of the data. When I use different averaged amp value, the data that happens error is different. The error is: Traceback (most recent call last): File "STO16_C_2.py", line 250, in <module> out = feffit(pars, dset) File "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line 557, in feffit result = fit.leastsq() File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 1689, in leastsq lsout = scipy_leastsq(self.__residual, variables, **lskws) File "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", line 423, in leastsq retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 601, in __residual return _nan_policy(np.asarray(out).ravel(), File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 2436, in _nan_policy raise ValueError(msg) ValueError: NaN values detected in your input data or the output of your objective/model function - fitting algorithms cannot handle this! Please read https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-wh at-can-i-do for more information. I don't know what happened, can somebody help me figure this out? PS: when I use only one del_e0 for every path, no such error happens. Best regards Fan

2 1

FW: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 3
by Dien.Li＠srnl.doe.gov 13 Sep '22

13 Sep '22

Hi Matt and all I sent this and an attachment before. I hope you can help figure out why I often get negative ss parameter from fitting? For this specific example, if I fit the CN, it yields CN of ~1, the monodendate structure is reasonable, but I got negative ss. However, if I fixed CN at 3, the ss is reasonable, but it needs to bind with three different PO4 on the surfaces, this is interesting but I am uncertain. Thank you so much for your any advice. Dien Li Savannah River National Laboratory -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Friday, September 9, 2022 12:32 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 3 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Help for EXAFS fitting (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 9 Sep 2022 16:31:38 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help for EXAFS fitting Message-ID: <DM8PR09MB62323624C91F0A43DC7CB6D1C4439(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, Matt and Carlo and other EXAFS experts Attached please find a fpj data file. The basic system is silica + PO4 ligand on surfaces, which was used for adsorption of La. We collected La L3-edge EAXFS data and did this fitting. I used two models of La binding as monodentate and bidentate. I saw the negative ss parameter. I saw this in some of my other EXAFS data fitting samples as well. I have two questions for help: 1. What might cause the negative ss parameters and how I may improve this, is this caused by incorrect structure models 2. If we can do some "stress" test to make sure the fitting is valid and meaningful. Please you can help look at and play this data set and direct me on how to do this correctly, thank you so much. Dien Li Savannah River National Laboratory

1 0

Fitting multiple spectra simultaneously with Larch
by Van Stappen, Casey M 12 Sep '22

12 Sep '22

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 been covered. Any suggestions? Thanks! Best, Casey Van Stappen ------------------------------------------------------------------------ Dr. Casey Van Stappen University of Texas at Austin Robert A. Welch Hall, 4.318 2350 Speedway Austin, TX 78705 USA Phone: +1 (512) 775-2658 E-mail: casey.vanstappen(a)austin.utexas.edu

3 2

Icon Resolution issue in 14 inch
by Mohamad Numan 12 Sep '22

12 Sep '22

Dear Developers, I am using the Demeter package on my windows 11 laptop. I am facing some resolution issues in the icons of Athena and Artemis. The icons look pretty dull and very distressing to the eyes. Attaching a screenshot for your reference. I will be happy to hear an update from you. Thanks & Regards Mohamad Numan Ph.D. Student, IACS

2 1

Virtual SSRL Summer School on Synchrotron X-Ray Absorption Spectroscopy and Imaging Oct 25-28, 2022
by Ritimukta Sarangi 06 Sep '22

06 Sep '22

Hello EXAFS enthusiasts, We are hosting the SSRL "not quite summer" summer school at the end of October this year (Oct 25-28). We wanted to include real experiments and deferred the school to the start of operations at SSRL. The event is virtual and all information (including registration details) can be found at: https://conf.slac.stanford.edu/exafs-2022/ We recognize that there are several really good online resources for learning about EXAFS and it has proved to be quite beneficial to the new and experienced learners alike. We have changed our summer school format to include additional teaching modules that can help participants learn aspects of EXAFS data analysis that are beyond what we have typically taught in the past. These new modules are especially helpful to the novice user and include: 1) Opportunity to write a 1 to 1.5 page proposal to compete for experimental time during the school. 2) A complete 1-day remote data measurement and hands-on demonstration of beamline optimization and experiment setup during the live session. 3) Insights into becoming a user at SSRL, proposal writing and its review process with examples of past successful proposals. Looking forward to seeing some of you at the school. Best Regards, Riti Sarangi

1 0

XAFS fitting in xas_viewer and reset of customized variables after save & load cycle
by juejing.liu＠gmail.com 04 Sep '22

04 Sep '22

Hi all, I am using xas_viewer, version 0.9.65, to fit some XAFS data. In a typical situation I will also fit the coordination numbers of atoms by add customized variables in the amplitude boxes (image below). It works fine during my fitting. However, when I save my result as a larch session and load it later, all my customized parameters are disappeared, and the amplitude boxes are reset. Therefore, I need to refill all the variables after each save & load cycle. This becomes increasingly tedious when dealing with about 20 different paths. Is there any workaround of this problem? Best, Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304

3 2

Simultaneous multispectral fitting in Larch?
by Van Stappen, Casey M 30 Aug '22

30 Aug '22

To whom it concerns, I wanted to inquire regarding how best to perform multispectral fitting (i.e. fitting several EXAFS spectra simultaneously with shared parameters) in Larch? This was something that could be done with (relative) ease in Artemis, but I was hoping to perform this at a larger scale (6 spectra, >10 restrictions) in Larch. I’ve hunted through Dr. Newville’s excellent Youtube tutorials, but didn’t find this specific information. Thank you for your help! Best, Casey Van Stappen ------------------------------------------------------------------------ Dr. Casey Van Stappen University of Texas at Austin Robert A. Welch Hall, 4.318 2350 Speedway Austin, TX 78705 USA Phone: +1 (512) 775-2658 E-mail: casey.vanstappen(a)austin.utexas.edu

1 0

XAFS short course at BNL: November 2-4
by Anatoly Frenkel 29 Aug '22

29 Aug '22

Dear subscribers, This is a reminder about the annual XAFS short course at BNL. The dates are: November 2-4. It will be virtual. The level will be intermediate to advanced As in the past, lectures, discussions and software demonstration sessions will be on Wednesday and Thursday, and the full day data analysis practicum will be on Friday. The course agenda and the link to the application form are available at the BNL web site: https://www.bnl.gov/xafscourse/index.php and at the web site of the Synchrotron Catalysis Consortium: https://you.stonybrook.edu/scc2/xafs-workshops/ Registration deadline is September 11. Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

1 0

Question related to an example of EXAFS fitting using Larch
by Andy Zhang 29 Aug '22

29 Aug '22

Dear all, I am learning Larch and read the manual of Larch online. In the "13.8.10. Example 3: Fit 3 datasets with 1 Path" of the webpage https://xraypy.github.io/xraylarch/xafs_feffit.html#example-3-fit-3-dataset…, it shows an example that fitting Cu at different temperatures. Einstein model was used to simulate the sigma2, as shown in the figure below. [image: image.png] However, in some papers (eg. Radiation Physicsand Chemistry137 (2017) 93–98) that model EXAFS at elevated temperatures, they separates the total sigma2 to static and thermo components (Sigma^2 = Sigma_static^2 + Sigma_thermo^2), which is different from the above Larch example. I am a little confused about the utilization of Einstein model. I wonder if the Sigma2 obtained by Einstein model can reflect the total sigma2 or can only reflect the thermo part. Many thanks for your help! Best regards, Harry

2 1