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

Re: [Ifeffit] Larch Energy calibration
by Schoepfer, Valerie 09 Mar '21

09 Mar '21

Hi Matt, The backstory is that I'm trying to find which standards will define my samples, so I am pulling standards from different beamlines and years to get a basic linear combination fit, to run new standards myself when I have more beamtime. I'm able to do it in Athena- where you more or less: 1. Assign E0 to the first peak in the first derivative of your standard reference foil. 2. Calibrate one standard reference foil to the theoretical edge energy. 3. Ensure E0 is right/adjust E0 for all samples and sample foils. 4. Align reference foils to the standard reference foil, because the foil will pull the sample with it. But in Larch, maybe I'm unsure about the groups function? I'm not convinced the reference foils 'follow' the sample spectra. If the reference and samples aren't tied together, how do you align samples when your energies are off because of different beamlines or years or people not as careful to calibrate the beamline energy? My first thought was using the first derivative peak of your sample, but if your edge energy shifts because of oxidation state changes, what do you use then? I'm still trying to form my question, so let me know if this still doesn't make much sense. Thanks! Valerie -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, March 4, 2021 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 3 CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing(a)usask.ca 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 energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 3 Mar 2021 18:38:24 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch energy calibration Message-ID: <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Valerie, On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer(a)usask.ca> wrote: > Hi, > > > > I am using Larch XAS Viewer for the first time to analyze some Mo > XANES data. It is fairly straightforward, however I am running into > problems with energy calibration, which leads to problems with Linear > Combination Fitting. > > > > Right now, which is likely wrong, I?m calibrating the energy of a > standard to the theoretical edge, then auto-aligning the samples to the standard. > But how do reference foils fit in here? Reference foils don?t seem to > be tied to the sample like they are in Athena. Should I be manually aligning? > > > > Is there a general guidance or work flow? > It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question. For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime. If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every measurement - that would indicate a serious problem. So, I think you should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable? I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead of time. I'm sure that leads to a bias in the software. I guess I forgot that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration. Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient? --Matt

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Re. Larch Energy Calibration
by Schoepfer, Valerie 09 Mar '21

09 Mar '21

Hi Chris and Adam, I'm actually looking at Mo, so the energy range is from about 19800 through 20200 eV on a Si(220) monochromator. (But thank you for your Fe offer!) The standards seem to be all from the Canadian Light Source, but going as far back as 2013... I'm not looking to make the LCF perfect at this point, but it does seem like the deeper I go, the less confident I am that I have the correct standards. I'm doing alright in Athena with respect to the process, its just that I can't get Larch to align properly. I'll probably just use Athena for data prep, Larch just seemed nice to learn. But then in Athena I run into trouble with incorrect standards. One thing after another, you know? Thanks- Valerie -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, March 4, 2021 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 3 CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing(a)usask.ca 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 energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 3 Mar 2021 18:38:24 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch energy calibration Message-ID: <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Valerie, On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer(a)usask.ca> wrote: > Hi, > > > > I am using Larch XAS Viewer for the first time to analyze some Mo > XANES data. It is fairly straightforward, however I am running into > problems with energy calibration, which leads to problems with Linear > Combination Fitting. > > > > Right now, which is likely wrong, I?m calibrating the energy of a > standard to the theoretical edge, then auto-aligning the samples to the standard. > But how do reference foils fit in here? Reference foils don?t seem to > be tied to the sample like they are in Athena. Should I be manually aligning? > > > > Is there a general guidance or work flow? > It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question. For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime. If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every measurement - that would indicate a serious problem. So, I think you should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable? I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead of time. I'm sure that leads to a bias in the software. I guess I forgot that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration. Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient? --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 217, Issue 4
by Clark Adam Hugh (PSI) 08 Mar '21

08 Mar '21

Dear Valerie Which Fe standards are you looking to compare? I have a large collection of Fe references collected from the SuperXAS beamline all relatively recently and are all calibrated using Fe reference foil measured simultaneously. Using a Si(111) monochromator: Fe2O3 Fe3C Fe5C2 Fe3O4 FeO Ferrihydrite Goethite Lepidrocrite FeCl3.xH2O FeCl2 FeSO4 FeAmmoniumSulfate Fe_Nitrate Using Si(311) monochromator: FeO Fe2O3 Geothite Lepidrocrite Ferrihydrite FeIII_Hexacyanoferrate Fephthalocyanine Fetetraohenylporphyrine FePhenanthroline Fephthalocyanine chloride FeII_Hexacyanoferrate FeBisglycinate FeAmmoniumSulfate Fe2EDTA Fe3EDTA The monochromator crystal choice affects the shape of the XANES due to the relative energy resolution of the crystal. Regards Adam __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Freitag, 5. März 2021 17:58 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 4 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 Energy calibration (Schoepfer, Valerie) 2. Re: Larch Energy calibration (Christopher Patridge) ---------------------------------------------------------------------- Message: 1 Date: Fri, 5 Mar 2021 16:06:22 +0000 From: "Schoepfer, Valerie" <valerie.schoepfer(a)usask.ca> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch Energy calibration Message-ID: <YTBPR01MB27659005C1015912348BA93894969(a)YTBPR01MB2765.CANPRD01.PROD.OUTLOOK.COM> Content-Type: text/plain; charset="us-ascii" Hi Matt, The backstory is that I'm trying to find which standards will define my samples, so I am pulling standards from different beamlines and years to get a basic linear combination fit, to run new standards myself when I have more beamtime. I'm able to do it in Athena- where you more or less: 1. Assign E0 to the first peak in the first derivative of your standard reference foil. 2. Calibrate one standard reference foil to the theoretical edge energy. 3. Ensure E0 is right/adjust E0 for all samples and sample foils. 4. Align reference foils to the standard reference foil, because the foil will pull the sample with it. But in Larch, maybe I'm unsure about the groups function? I'm not convinced the reference foils 'follow' the sample spectra. If the reference and samples aren't tied together, how do you align samples when your energies are off because of different beamlines or years or people not as careful to calibrate the beamline energy? My first thought was using the first derivative peak of your sample, but if your edge energy shifts because of oxidation state changes, what do you use then? I'm still trying to form my question, so let me know if this still doesn't make much sense. Thanks! Valerie -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, March 4, 2021 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 3 CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing(a)usask.ca 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 energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 3 Mar 2021 18:38:24 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch energy calibration Message-ID: <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Valerie, On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer(a)usask.ca> wrote: > Hi, > > > > I am using Larch XAS Viewer for the first time to analyze some Mo > XANES data. It is fairly straightforward, however I am running into > problems with energy calibration, which leads to problems with Linear > Combination Fitting. > > > > Right now, which is likely wrong, I?m calibrating the energy of a > standard to the theoretical edge, then auto-aligning the samples to the standard. > But how do reference foils fit in here? Reference foils don?t seem to > be tied to the sample like they are in Athena. Should I be manually aligning? > > > > Is there a general guidance or work flow? > It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question. For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime. If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every measurement - that would indicate a serious problem. So, I think you should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable? I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead of time. I'm sure that leads to a bias in the software. I guess I forgot that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration. Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient? --Matt

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Larch energy calibration
by Schoepfer, Valerie 04 Mar '21

04 Mar '21

Hi, I am using Larch XAS Viewer for the first time to analyze some Mo XANES data. It is fairly straightforward, however I am running into problems with energy calibration, which leads to problems with Linear Combination Fitting. Right now, which is likely wrong, I'm calibrating the energy of a standard to the theoretical edge, then auto-aligning the samples to the standard. But how do reference foils fit in here? Reference foils don't seem to be tied to the sample like they are in Athena. Should I be manually aligning? Is there a general guidance or work flow? Thank you- Valerie Valerie Schoepfer, PhD Postdoctoral Fellow Department of Geological Sciences [cid:image001.jpg@01D5CBC1.8203C730]

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Athena plugin for synchrotrons in Japan
by Yohei Uemura 01 Mar '21

01 Mar '21

Dear Bruce, This is Yohei Uemura. We are using the Athena plugin to read the data format used in synchrotrons in Japan. It is very helpful to read XAFS data directly into Athena. We appreciate the plugin. Recently, we realised that the plugin does not work properly for some data sets. When the data is like below (I0 and I are integers), the plugin works fine. Step scan (or QXAFS) using a counter device [image: image.png] However, if the data is like below (I0 and I are decimal fractions), the outputs of I0 and I are 4digit such as 0.345. QXAFS: I0 and I are decimal fractions [image: image.png] I found the problem was at l. 63. my $pattern = " %9.3f %9.3f %10.6f" . " %12.3f" x $ndet . $/; The output data is terminated by 3 digits after a decimal point. If the plugin is modified as the attached file, both the files were read correctly. The modification is: my $pattern = " %9.3f %9.3f %10.6f" . " %12.3f" x $ndet . $/; *$pattern = " %9.3f %9.3f %10.6f" . " %12.6f" x $ndet . $/ if $list[2+$ndet] =~ m/\d*\.\d+/;* I added the bolded line in order not to truncate the I0 and I by 3 digits. Could you modify the plugin which is provided with the demeter package? Best regards, Yohei -- ================================================ Yohei Uemura (Ph.D) Affiliation : Paul Scherrer Institut (PSI), Laboratory for Environmental Chemistry (LUC) Address : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland Phone: +41 (0)5-6310-4571 上村洋平所属 : Paul Scherrer Institut (PSI), Laboratory for Environmental Chemistry (LUC) 住所 : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland 電話 : +41 (0)5-6310-4571 ================================================

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postdoc opportunity at LANL
by Hickam, Sarah Margaret 03 Feb '21

03 Feb '21

Dear all, Los Alamos National Laboratory currently has a postdoc position open for xafs studies of actinide materials. The posting can be found at the following link: https://lanl.jobs/los-alamos-nm/nuclear-forensicsactinide-research-postdoc/… Please feel free to forward this to anyone who might be interested or contact me with any questions. Best regards, Sarah Sarah Hickam Postdoctoral Research Associate Los Alamos National Laboratory MST-16 (505) 695-3515

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Nanocrystalline NiO
by Christian Wittee Lopes 18 Jan '21

18 Jan '21

Dear all, Firstly I would like to wish you a much better year than in 2020. Does anyone have some spectra of nanocrystalline NiO (not bulk standards)? I have a spectrum of a mixed compound and would like to get more insights into what I really have in this sample. Thank you in advance!!! Kind regards, -- *Christian Wittee Lopes* *Visiting Researcher* ANP/FINEP - PRH50 Institute of Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS) Phone: +55 54 992430264

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Larch: AttributeError
by Rachita Rana 13 Jan '21

13 Jan '21

Hi Everyone, I am using Larch for reading and fitting EXAFS data and I get the autobk and Fourier transforms working. But when I try to generate the fefffpaths and fit the data I get an error from the feffit function. I am using the developer version of Larch on MC OS Catalina. Below is the error and the sample script- runfile('/Users/rachita/Box/Larch/Feff_Try2/001.py', wdir='/Users/rachita/Box/Larch/Feff_Try2') Traceback (most recent call last): File "/Users/rachita/Box/Larch/Feff_Try2/001.py", line 27, in <module> fit = feffit(params, dset) File "/Users/rachita/opt/anaconda3/lib/python3.8/site-packages/xraylarch-0.9.50-py3.8.egg/larch/xafs/feffit.py", line 534, in feffit ds.prepare_fit(params=params) File "/Users/rachita/opt/anaconda3/lib/python3.8/site-packages/xraylarch-0.9.50-py3.8.egg/larch/xafs/feffit.py", line 265, in prepare_fit ikmax = int(1.01 + max(self.data.k)/trans.kstep) AttributeError: 'AthenaGroup' object has no attribute ‘k’ #tried this with xdi format data and got the same error Below is the script - #!/usr/bin/env python3 # -*- coding: utf-8 -*- from larch.fitting import param_group, Parameter from larch.io <http://larch.io/> import read_xdi from larch.xafs import feffpath, feffit_dataset, feffit_transform, feffit, feffit_report data = read_xdi('cu_metal_rt.xdi’) #I tried importing Athena project file too path1 = feffpath('feff0001.dat', s02='amplitude', e0='del_e0', sigma2='sigma2', deltar='del_r') trans = feffit_transform(kmin=3, kmax=16, kw=(2,1,3), dk=1, window='hanning', rmin=1.7, rmax=3.1) params = param_group(amplitude= Parameter(1, vary=True), del_e0 = Parameter(1e-7, vary=True), del_r = Parameter(1e-7, vary=True), sigma2 = Parameter(0.003, vary=True)) dset = feffit_dataset(data=data, pathlist=[path1], transform=trans) fit = feffit(params, dset) print(feffit_report(fit)) By printing path groups and transform fit, I confirmed that the data is read correctly. Please let me know if there are ways to fix this or if there is an error in my script. Thank You! Rachita

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Artemis\Plot mismatch\Artemis[Plot]&Artemis [Feff] Atoms and Feff
by Huaming 12 Jan '21

12 Jan '21

Dear all, I am using Artemis for EXAFS data fitting and found that the |χ(R)| plot shown in "Artemis [Plot]" and "Artemis [Feff] Atoms and Feff" are in great difference for a same scattering path. However, the |χ(k)| plots shown in the above two windows is the same. For the plot shown in "Artemis [Feff] Atoms and Feff" window, one path is selected and 'Plot path' is clicked. For the plot shown in "Artemis [Plot]", the same path is dragged into the "Artemis window" and then transfered path and plot in R by click "Action" menu. I would like to know what is the difference of data shown in the two windows. BTW, whether it is possible to have two peaks in the |chi(R)| plot for a single scattering path? For some scatters with high-Z, the f(k) may feature multiple peaks. Thanks, All bests, Huaming Hou

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How do I create a histogram based on R-space values
by Deepak Varanasi 10 Dec '20

10 Dec '20

4 6

How to perform normalisation and background removal of data containing L3 and L2 edges
by Deka, N. 07 Dec '20

07 Dec '20

Dear all I am a student trying to learn Athena for XAS data processing. Attached is a data file which contains L3 and L2 edge of Ru. What should be the right parameters for background removal and normalization of this data set? In the videos from Bruce Ravel, I could not find any example for such a data set containing two edges. Thank you Best Regards, Nipon Deka Leiden University

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Unable to see background and "k", "q", "R" plots for imported data
by Deka, N. 07 Dec '20

07 Dec '20

Dear all I am a new student trying to work with Athena for XAS data processing. Attached is a data file which when I import does not show the background and also Athena cannot plot "k" , "q" , "R" plots for the data. Please suggest me a possible solution. Thank you Best Regards, Nipon Deka Leiden University

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Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported
by Mosselmans, Fred (DLSLtd,RAL,SCI) 07 Dec '20

07 Dec '20

Dear Nipon, I suspect you have read the spectrum in as XANEs if you change the data type to mu(e)(e) it should give you what you want Thanks Fred Mosslemans Message: 2 Date: Mon, 7 Dec 2020 15:26:19 +0000 From: "Deka, N." <n.deka(a)lic.leidenuniv.nl> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data Message-ID: <3088c35cdc4c4e488b2782623526d7bb(a)lic.leidenuniv.nl> Content-Type: text/plain; charset="us-ascii" Dear all I am a new student trying to work with Athena for XAS data processing. Attached is a data file which when I import does not show the background and also Athena cannot plot "k" , "q" , "R" plots for the data. Please suggest me a possible solution. Thank you Best Regards, Nipon Deka Leiden University

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Postdoctoral research opportunity in photocatalysis and x-ray spectroscopy
by Sokaras, Dimosthenis 06 Dec '20

06 Dec '20

Hello XAFS Community, We have a new postdoctoral research opportunity in the field of photocatalysis, aiming to study photocatalytic conversion of CO2 to liquid fuels. The selected candidate will be performing time-resolved and operando x-rays characterizations of photocatalytic materials in order to extract fundamental electronic-structure insights that can correlate and guide catalytic activity and photocatalysts material’s properties. An extensive part of the research will take place at LBNL/SLAC where the candidate will be developing and performing novel x-ray spectroscopy methodologies. Applicants interested in this opportunity may reach out to Junko Yano (LBNL, jyano(a)lbl.gov) and Dimosthenis Sokaras (SLAC, dsokaras(a)slac.stanford.edu) Thank you, Junko Yano and Dimosthenis Sokaras

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LARCH- XRF- fitting the spectrum
by Ana Mijo 04 Dec '20

04 Dec '20

Hello, I have images from GSECARS. I am trying to improve the background reduction by fitting the spectrum and getting new ROIs. I did a fit but I don’t manage to update the ROI’s. I tried saving to a .mca file and uploading again but I don’ t see a change. Since I come from other software I may have pre-concepts, maybe the first question is: can a new fit be done and get new (maybe cleaner) images? or Can I only work with the ROI’s from the experiment? If it can be done, how should I proceed after doing the fit to update ROI’s? I have emailed this question to Matt also (before finding this mailing list). Thanks in advance, Best regards, Ana Ana Mijovilovich Czech Republic ana_mijo(a)yahoo.com

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Pd nanoparticle K-edge XANES
by Eva Bajnoczi 30 Nov '20

30 Nov '20

Dear Mailing List Readers, I wonder if there is anyone who has and also would be willing to provide a K-edge XANES spectrum measured on Pd nanoparticles. Or to point me to a source where I can find one. Our particles most probably around 5nm, so this size-range would be ideal, but anything would be very much appreciated, as that would be a better reference than metallic Pd foil. We have got some interesting reviewer questions on a paper and to answer them a Pd nanoparticle XANES would be highly useful, but under the circumstances, it is not possible to measure it on our own in the forseeable future. Thank you for any kind of help in advance! Best regards, Eva Bajnoczi -- Bajnóczi Éva / Éva Bajnóczi tudományos munkatárs / research fellow Wigner Fizikai Kutatóközpont / Wigner Research Centre for Physics 1121 Budapest, Konkoly-Thege Miklós út 29-33. Magyarország / Hungary

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Workshop Opportunity for XAS users in the field of Biogeochemistry.
by Ritimukta Sarangi 24 Nov '20

24 Nov '20

Hello, Apologies for the mass email. SSRL, in conjunction with EMSL is organizing a Workshop titled "Spectroscopy and Modeling for Molecular Insights into Environmental Processes" on 26, Jan 2021. The main focus is to encourage and provide help in getting started with the use of theory and modeling (such as DFT and MD) in the interpretation of EXAFS/XAS data. Please find more information in the event flyer below: https://www.dropbox.com/s/vvshxqpji4yok2s/SSRL_EMSL_Workshop_Flyer.pdf?dl=0 We encourage interested users and research groups to register and attend the workshop. Looking forward to your participation. Best regards, Riti Sarangi SSRL

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Two phases EXAFS fitting-help
by Chen, Danting 10 Nov '20

10 Nov '20

Hi Mr/Ms, I have a sample and get a two major phases result by linear combination analysis, one dominate 59.5% of hydrozincite( and another is 33.5% zinc phosphate (. I would like to use Artemis to fit the k-space and the first shell of R-space. For R-space, my idea is to fit the first Zn-O shell since both dominate phases are both tetrahedral and octahedral coordination and the first shell is the similar environment. For k-space, shall I fit each phase with the sample individually and then sum the different weight of fitting curve together to see how it fit finally? If it is right, may I ask how exactly it fits? I have no idea how the weight is set in Artemis or it can only be summed half by half? Also, since my sample numbers are only two, I am unable to use PCA to fit. Except the above mentioned, is there anything else that I can do? Sorry, I am a new learner of XAS and have many things to learn. Best Wishes, Danting Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Re: [Ifeffit] Postdoctoral positions in MSEE EFRC at Brookhaven National Lab
by Gill, Simerjeet 09 Nov '20

09 Nov '20

Hello XAFS Community, On behalf of Energy Frontier Research Center on Molten Salts in Extreme Environments (MSEE) at Brookhaven National Laboratory (BNL), I would like to bring your attention to two postdoctoral Research Associate positions within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments. The positions require a Ph.D. degree in chemistry, physics, materials science or a related field. The interdisciplinary research will focus on structural and spectroscopic investigation of molten salts, solutes in them, and liquid-solid interfaces. The positions are located in the BNL Nuclear Science and Technology Department (Job ID 2335) and Chemistry Department (Job ID 2341). Experiments will be performed at the National Synchrotron Light Source II (NSLS-II), BNL's new, state-of-the-art synchrotron, the BNL Chemistry Division and the BNL Center for Functional Nanomaterials. To find detailed descriptions of the position requirements and apply online, go to https://jobs.bnl.gov<https://jobs.bnl.gov/>. For Job ID 2335, hands-on experience in either X-ray scattering, spectroscopy and reflectivity is required. For Job ID 2341, demonstrated experience in electrochemical methods or working with molten salts is required. Experience with the chemical and physical properties of materials at high-temperature is highly desirable for both positions. If you have follow up questions, please don't hesitate to contact: Jim Wishart: wishart(a)bnl.gov<mailto:wishart@bnl.gov> or Simerjeet Gill: gills(a)bnl.gov<mailto:gills@bnl.gov>. For position 2335, postdoc will investigate molten salt systems using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Nuclear Science and Technology Department at Brookhaven National Lab, Under supervision of Dr. Simerjeet Gill. Responsibilities will include performing synchrotron experiments on molten salt systems with and without actinides and collaborating with other participants of MSEE-EFRC. For inquiries, please email me at gills(a)bnl.gov<mailto:gills@bnl.gov>. Thank you, Simerjeet K Gill, Group leader, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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Postdoctoral position in MSEE EFRC at Brookhaven National Lab
by Gill, Simerjeet 03 Nov '20

03 Nov '20

Hi, I would like to post below message regarding postdoc positions in MSEE EFRC at BNL, with attached flyer to XAFS community. Thanks, Simer Hello XAFS Community, On behalf of Energy Frontier Research Center on Molten Salts in Extreme Environments (MSEE) at Brookhaven National Laboratory (BNL), I would like to bring your attention to two postdoctoral Research Associate positions within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments. Information about the positions is summarized in a flyer attached to this message. For position 2325, postdoc will investigate molten salt systems using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Nuclear Science and Technology Department at Brookhaven National Lab, Under supervision of Dr. Simerjeet Gill. Responsibilities will include performing synchrotron experiments on molten salt systems with and without actinides and collaborating with other participants of MSEE-EFRC. For inquiries, please email me at gills(a)bnl.gov<mailto:gills@bnl.gov>. Thank you, Simerjeet K Gill, Group leader, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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XAS question
by Chen, Danting 29 Oct '20

29 Oct '20

Hi Mr/Ms, I am a new learner of XAS and meet a problem like before and hope you can give me some hints. [cid:image001.png@01D6ADDA.9D016B40] [cid:image005.png@01D6ADDA.9D016B40] I have a data set after merged and alignment. But at 11-13 A-1, the amplitude of k is much higher than normal but there seems no weird points at XAS spectrum. I wonder how I could deal with this part? If I shorter kmax and it must lose some important information. Best Wishes, Danting Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Advanced XAS Workshop at CLS
by Gosia Korbas 27 Oct '20

27 Oct '20

Hi all, On behalf of the BioXAS team at the Canadian Light Source, I would like to invite you to participate in the virtual Advanced XAS Data Analysis and Modeling Workshop to be conducted in four half-day (8 AM to 1 PM, UTC-6, Saskatchewan Time) remote sessions through WebEX on November 10, 13, 20 and 24. The workshop is organized by the BioXAS-Spectroscopy senior scientist, Roman Chernikov. For more details and registration (free) please follow the link: https://bioxas-spectroscopy.lightsource.ca/advanced-spectroscopy-workshop-2… We hope to see you there! Gosia Korbas --------------------------------------------------------------------- Gosia Korbas, Ph.D. BioXAS-Imaging Senior Scientist BioXAS-Sector Responsible Canadian Light Source Phone: +1-306-657-3859 BioXAS-Imaging website<https://bioxas-imaging.lightsource.ca/> gosiakorbas.net<https://gosiakorbas.net/>

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Athena error on Linux mint
by Kyle Kluherz 27 Oct '20

27 Oct '20

I recently successfully installed the Demeter suite on my Linux Mint 19 machine. Last week, I updated to Linux Mint 20, and now I get the following error when trying to run athena from the command line: Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/local/bin/dathena line 7. BEGIN failed--compilation aborted at /usr/local/bin/dathena line 7. I was wondering if there was a relatively easy way to fix this, or if the best recourse is to simply reinstall Demeter? It took some fiddling to install initially, so I don't want to reinstall it unless that's the easiest way to fix the issue. Also, the mailing list link on the Demeter home page (http://cars9.uchicago.edu/mailman/listinfo/ifeffit/) times out. Fortunately I was able to get a working link (https://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) from a friend. Sincerely, Kyle Kluherz -- Kyle (Tk) Kluherz Graduate Student Gamelin & De Yoreo groups Department of Chemistry, UW Materials Science Division, PNNL

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Wyartite XAS spectrum?
by Mike Massey 17 Oct '20

17 Oct '20

Hi All, And now for something not-phosphorus... Does anyone happen to have a wyartite U L3-edge XAS spectrum laying around? If you do, and happened to be willing to talk with me about it, I would be most grateful. Kind Regards, Mike

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Re: [Ifeffit] P K-edge XANES spectrum question (Mangold, Stefan (IPS))- (Mike Massey); Re: Ifeffit Digest, Vol 212, Issue 7 (Luis Carlos Colocho Hurtarte)
by Ganga Hettiarachchi 16 Oct '20

16 Oct '20

Mike, Thanks, we will try diluted samples to make sure that this is not an issue due to concentration. Luis, Thanks for sharing those papers. We have plenty of OC in these systems, but Pb or other trace elements concentrations are very small (below 10 mg/kg). Best regards, Ganga -------------------- Ganga M. Hettiarachchi

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