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

Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10
by Dien.Li＠srnl.doe.gov 15 Sep '22

15 Sep '22

Hi, Matt and EXAFS experts Thank you so much. Our sample is porous silica + PO4 ligand on surface/pore, then react with LaNO3 in solution. The model is that La is bonding with PO4 through both mono- (corner-sharing) and di-dentate (edge sharing) modes. Please see the attachment. The first three fits in history are fits with increasing paths, with fixed CN for the La-P11 and La-P14 path, the ss parameters are reasonable, but to fix CN at 3 for La-P14 is unreasonable, which requires La to bind with three different PO4 groups. The last three fits are fits with increasing paths, in which CN was fitted, the fitted parameters are reasonable, EXCEPT for the negative ss parameters for the path La-P11 (edge sharing) and La-P14 (corner sharing). By the way, the length for La-P14 is +0.3 A, it is large, but not completely unreasonable, because the bond distances of La-O polyhedron may change from 2.4 to 3.1 A. Is it possible to constrain ss parameter? If so, how to set up this constrain? Thank you so much for your further instruction. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, September 14, 2022 4:03 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 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. Re: Larch: Fitting error of the objective/model function (Matt Newville) 2. Re: Help for EXAFS fitting (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Sep 2022 13:28:38 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch: Fitting error of the objective/model function Message-ID: <CA+7ESbodGVSNHuzTHZoeb3iL-jUsWFpeYM7TqLQPkkSyMyE2DA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Fan, Sorry for the trouble. That seems like a strange error to me - I don't see why changing those expressions for E0s (even if they are "slightly complicated"!) should generate NaNs or Infinities. I don't think I've seen that happen with "feffit" fittings. Can you send me a Larch Session File with this fit in it? One suggestion is to place bounds (say +/- 20 eV) on those Parameters, say pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr', min=-20, max=20) But I'm not certain whether that would solve this problem. On Wed, Sep 14, 2022 at 7:53 AM <dxfan(a)post.kek.jp> wrote: > 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-w… > 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 > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

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

Re: [Ifeffit] XAFS fitting in xas_viewer and reset of customized
by juejing.liu＠gmail.com 28 Aug '22

28 Aug '22

Hi Matt, Here is the session file for the UO2 fitting. The screenshot blow shows what the customized variables look like right before saving this session. Please feel free to let me know if you need any extra information. 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

1 0

Re: [Ifeffit] XAFS fitting in xas_viewer and reset of customized variables after save & load cycle
by Liu, Juejing 28 Aug '22

28 Aug '22

Hi Matt, Thanks for the quick response. I just noticed that the data in the screenshot is unpublished data so I may not be able to send you that one. But I will send you a typical UO2 fitting later today (in the larch session) so that you can look. 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

1 0

Quick Absorption and Scattering (QAS) beamline scientist position at NSLS II
by Stavitski, Eli 26 Aug '22

26 Aug '22

Dear all, We are looking for a beamline scientist for Quick Absorption and Scattering (QAS) beamline (https://www.bnl.gov/nsls2/beamlines/beamline.php?r=7-BM) The full job description is available here https://jobs.bnl.gov/job/upton/beamline-scientist-quick-x-ray-absorption-an… ____________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov> https://www.bnl.gov/ps/beamlines/beamline.php?r=8-ID

1 0

third cumulant in Larch
by Andy Zhang 19 Aug '22

19 Aug '22

Dear all, I have a quick question related to EXAFS fitting using Larch. I wonder how to include the third cumulant in the fitting. I tried to add "third" in the "pars" section, but it seems it did not work. [image: image.png] Thanks a lot for your help! Have a nice day! Best, Harry

2 2

Environmental geochemist position at DOE-National Energy Technology Laboratory
by Mengling Stuckman 18 Aug '22

18 Aug '22

Dear ifeffit members, Recently we are interested in hiring an environmental geochemist for our critical mineral sustainability program at NETL, Pittsburgh, PA. Synchrotron experience is a plus. U.S. citizens are strongly preferred. Here is the specific job posting. https://leidos.wd5.myworkdayjobs.com/External/job/Pittsburgh-PA/Environment… Feel free to pass along this information to your students who are interested. If you have any questions related to the post, feel free to contact me at mengling.stuckman(a)netl.doe.gov Thanks and have a nice day, Mengling -- Mengling Stuckman Leidos Technical Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

1 0

Using larch for feff Fitting -> simple 4 parameter fit
by Mangold, Stefan (IPS) 18 Aug '22

18 Aug '22

Dear all, I try to use larch for Feff Fitting. For a first start, I liked the option of Artemis with the „simple 4 parameter fit“. Larch produces for every path an independent dear and sigma2. Is there a simple way to make this simple 4 parameter fit also in larch? best regards Stefan Mangold

2 2

XAFS short course at BNL: November 2-4
by Anatoly Frenkel 09 Aug '22

09 Aug '22

Dear subscribers: Please spread the word to those who may be interested in our next annual short course at BNL on X-ray absorption fine structure. The dates are: November 2-4. It will be virtual. The level will be intermediate to advance (last year it was a beginner level). 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. More information about the course and the link to the application form will appear soon on BNL web site, and on the web site of the Synchrotron Catalysis Consortium (SCC). 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 1

Standardized Spectra
by Kyle Draim 08 Aug '22

08 Aug '22

Hello! I don't have any X-Ray data to analyze in your app, I'm just seeking a visual display of each element's standardized/accepted X-Ray spectra (instead of a table of numbers). So far, I've downloaded the application, but I'm stuck on how to find this information. I would greatly appreciate it if you would be willing to provide the necessary steps to accessing this information or if you would be willing to direct me to the right source for that info. Thanks, Kyle

4 3

xraylarch
by Paul Fons 06 Aug '22

06 Aug '22

Hi. Due to the difficulties of getting demeter to work on the Apple M1 machines, I have started to use xraylarch and so far I like the interface as well as the possibility of scripting later on. I had a couple of observations and a question regarding xraylarch usage that I hope could be addressed here. First, one can load multiple spectra into the (feff) fitting window. It seems, however, that which paths are selected are universal (the selected paths are used for all exafs spectra). Does this mean that multiple edge fitting is not possible. If multiple edge fitting is possible, how is it done? In the fitting window, one can have several spectra loaded and one can select all or some of the spectra to be fit. The interface seems like it was designed for multiple edge fitting, but is it? Second, it is strange that whenever a parameter is changed that the fitting variable settings (fixed, vary, constrain) are reset. For complex fits, this generates a lot of unnecessary clicking (and the corresponding mistake possibilities) Third, when one reads in several different feff calculations, one would, in principle, like to have a different value of e0 (the origin of energy offset) for each feff calculation. By default when a feff calculation is read in the variable e0 is defined. When one defines alternative energy offset variables for the different feff calculations and deletes the original e0 value, something strange happens. Accessing the “Edit Parameters” window results in e0 reappearing (even though it has been manually deleted previously). Is this a feature? The same thing may happen for other “automatic” variables as well. Four. This is really a feature request. When a variable is unused (lets say some additional paths are introduced in the fitting process and a new fit without them is attempted), the choices in the parameter list are (fix, vary, and constrain). There is no option to “skip” like in Artemis. Obviously, one can choose fix, but in doing so the unused variable shows up in the fit result summary and is somewhat confusing. It would be subjectively better to have the option to “skip” a variable and not have it show up in the fit summary. Just some initial thoughts...

2 1

VC and V(CO)6 data to share
by Ismael Graff 06 Aug '22

06 Aug '22

Dear XAFS enthusiasts, would anyone have XAFS data of crystalline vanadium carbide (VC) and vanadium hexacarbonyl (V(CO)6) to share? In the case of V(CO)6 I´m having great trouble of finding any published measurement! I found papers for Cr(CO)6, but not V(CO)6. Bibliographical references are also welcome. All the best, Ismael. -- ************************************ * Ismael Graff * * * * Universidade Federal do Paraná * * Departamento de Física, CP 19044 * * 81531-980, Curitiba, Brazil. * * Tel (office): +55 41 3361 3093 * * Tel (Lab): +55 41 3361 3427 * * Fax: +55 41 3361 3418 * * http://fisica.ufpr.br/graff * * * * "DOCENDO DISCIMUS" * ************************************

3 4

Re: [Ifeffit] Exafs spectra Fitting of WO3 nanoparticles (Abdallah Nassereddine)
by Mosselmans, Fred (DLSLtd,RAL,SCI) 04 Aug '22

04 Aug '22

Dear Abdallah, It is often quite reasonable to fix two paths debye waller factors to be the same if they are the same atom at similar distances. However there is a slight problem with what you are trying to do. Because EXAFS is a sum of sine waves the minimum distance it can resolve between two paths of the same atom type is Pi/2*Kmax where kmax is the maximum k value in your data. Hence if you are trying to fit separate paths of the same atom type 0.06 A apart you need data out to about 26 k. I think and no one has ever told me this is completely Ok the only way to get two distances from such an analysis is to assert that the difference between the path is a fixed value and thus refine the two paths with the same delta R (and probably the same debye wller factor) this in my experience works in some cases Best regards Fred Mosselmans -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 03 August 2022 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 234, Issue 2 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. Exafs spectra Fitting of WO3 nanoparticles (Abdallah Nassereddine) ---------------------------------------------------------------------- Message: 1 Date: Wed, 03 Aug 2022 14:40:44 +0200 From: Abdallah Nassereddine <abdallah.nassereddine(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Exafs spectra Fitting of WO3 nanoparticles Message-ID: <ddfc8c51f227c914d472d4115733b956(a)esrf.fr> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear all, Good morning, I try to Fit EXAFS spectra of a sample composed of supported tungsten oxide ( WO3/ZSM-5) nanoparticles obtained by operando studies under gas (CH4, He) at 750 ?C. First, and after several trials, I analyzed the WO3 reference spectrum obtained at room temperature and I succeeded in determining the amplitude (S0) by using the monoclinic structure WO3 cif file. Then, I used the value of this amplitude obtained to be able to fit the structural parameters (coordination number N, Debye-waller Factor, Interatomic distance) of WO3/ZSM-5 nanoparticles under gas, but I can't. the best result I got was by selecting the first two shells (at 1.858 and 1.919 Angstrom) of the monoclinic structure. However, with all the optimizations, the Debye-waller factor obtained for the second W-O shell (1.919 Angstrom) is always negative, and if I don't take this shell into account, I completely lose my Fit. Have any of you ever worked on this type of sample and might have an idea that would help me improve my Fit? Thank you in advance, Best regards, Abdallah Nassereddine

1 0

Exafs spectra Fitting of WO3 nanoparticles
by Abdallah Nassereddine 03 Aug '22

03 Aug '22

Dear all, Good morning, I try to Fit EXAFS spectra of a sample composed of supported tungsten oxide ( WO3/ZSM-5) nanoparticles obtained by operando studies under gas (CH4, He) at 750 °C. First, and after several trials, I analyzed the WO3 reference spectrum obtained at room temperature and I succeeded in determining the amplitude (S0) by using the monoclinic structure WO3 cif file. Then, I used the value of this amplitude obtained to be able to fit the structural parameters (coordination number N, Debye-waller Factor, Interatomic distance) of WO3/ZSM-5 nanoparticles under gas, but I can't. the best result I got was by selecting the first two shells (at 1.858 and 1.919 Angstrom) of the monoclinic structure. However, with all the optimizations, the Debye-waller factor obtained for the second W-O shell (1.919 Angstrom) is always negative, and if I don't take this shell into account, I completely lose my Fit. Have any of you ever worked on this type of sample and might have an idea that would help me improve my Fit? Thank you in advance, Best regards, Abdallah Nassereddine

1 0

Synchrotron geochemist position at DOE-National Energy Technology Laboratory
by Mengling Stuckman 02 Aug '22

02 Aug '22

Dear ifeffit members, Recently we are interested in hiring a synchrotron geochemist for our critical mineral sustainability program at NETL. U.S. citizens are strongly preferred. Here is the specific job posting. https://careers.leidos.com/jobs/9878648-synchrotron-geochemist Feel free to pass along this information to your coworkers or postdocs who are interested. If you have any questions related to the post, feel free to contact me at mengling.stuckman(a)netl.doe.gov Thanks and have a nice day, Mengling -- Mengling Stuckman Leidos Technical Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

1 0

Athena: the R factor for normalized mu(E)
by Jon-Petter Gustafsson 13 Jul '22

13 Jul '22

Hello all, I have been a frequent user of Athena for many years, mostly for interpreting P K-edge XANES spectra. Until last week I thought that the R factor in Athena was always defined as: sum( [data_i - fit_i]^2 ) ------------------------------- sum( data_i^2 ] This is also the definition given in the online manual, and it has been stated by me and by other colleagues in a number of papers dealing with P K-edge XANES. But well, this is not true when dealing with normalized XANES spectra! I realized this when I played around with a number of my old LC fits in Excel. While the chi-square value (or maybe more precisely, the sum of squared residuals) was reproduced perfectly, I always got "R factors" (i.e. with the above definition) between 2 and 3 times lower than what Athena gives. After that I consulted the Demeter programming documentation (https://bruceravel.github.io/demeter/pods/Demeter/LCF.pm.html) to find that, for normalized mu(E), "Demeter thus scales the R-factor to make it somewhat closer to 10^-2". However, the equation stated on this page actually reproduces the R factor even more poorly, and therefore I won't reiterate it here. After inspecting the Perl code, and trying out different alternatives in Excel, I now believe that the following equation provides a more accurate definition of the R factor (correct me if I'm wrong!): sum( [data_i - fit_i]^2 ) ------------------------------- sum( [data_i - avg data]^2 ) where "avg data" is the arithmetic mean of the data in the LC fitting range. It would be great if others could confirm this. As far as I understand, this won't affect the interpretations that any of us have made over the years, it only affects the understanding of what the R factor actually is... Kind regards, Jon Petter Jon Petter Gustafsson, Professor in Soil Chemistry Department of Soil and Environment Swedish University of Agricultural Sciences (SLU) Box 7014 750 07 Uppsala, Sweden Phone: 018-671284; e-mail: jon-petter.gustafsson(a)slu.se<mailto:jon-petter.gustafsson@slu.se> --- N?r du skickar e-post till SLU s? inneb?r detta att SLU behandlar dina personuppgifter. F?r att l?sa mer om hur detta g?r till, klicka h?r <https://www.slu.se/om-slu/kontakta-slu/personuppgifter/> E-mailing SLU will result in SLU processing your personal data. For more information on how this is done, click here <https://www.slu.se/en/about-slu/contact-slu/personal-data/>

2 1