March 2021 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Artemis fit error - chi-square and R-factors are always equal to 0
by Ava Rajh 27 Mar '21

27 Mar '21

HI, I hope I am replying to the thread correctly. Thank you for your insights, I have spent a lot of time tinkering with installation and I have a partial solution. To first answer your questions: - yes, the fit ran ok and comparing it to the same fit using ifeffit (done by a a machine using ifeffit that works correctly), the calculated parameters are almost the same, with slight differences of 10-5 order of magnitude. The plot after the fit also looks fine. -the log I attached was from the example Cu data set, but the issue happens on every fit I try to run. -I'm not sure about the feff.dat file used, I haven't been able to locate it in my installation. - Feff6 (or Feff6l if I set it in preferences) are able to run as far as I can tell -I have run the example larch scripts to which you pointed me, and most of them were able to run ok, with no obvious issues (the parameters looked ok and reduced chi-square and R vales were reported). There was an error in running a few of the tests something to do with PlotDisplay, but I'm pretty sure these aren't related issues. To me, all of this points to some trouble Artemis has communicating with larch. I have tried downgrading the installation from 0.9.50 (that installs with pip) to 0.9.49 (that the website says is the current) and an even older ones but no luck. The solution war disappointingly trivial: If I completely removed larch and demeter suite along with everything else I installed in the last few days, from my computer and tried to compile it again, this time with ifeffit, I finally managed to get the reduced-chi square and R values. I have no idea why it didn't work when I tried it a few times before before but now I am able to get the fit and all required parameters. It still doesn't work with larch, but for now, at least I'm able to get the results. I'll re-install Larch and tinker with it a bit more to try to figure out where the error was coming from and report back if I find anything that might help someone else facing the same issue. Thanks again for the help Best, Ava

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Unable to load Demeter modules with Perl
by Tyler Valentine 27 Mar '21

27 Mar '21

Hello, I am learning how to use a perl script to structure a fit with Demeter. However, when I input the 'use Demeter;' command into my script, I receive the following error: Can't load 'C:/Users/Tyler/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:The specified module could not be found at C:/Users/Tyler/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 193. I have changed the @INC to include all the directories where Demeter modules should be located, so I am not sure why I am receiving this error. I would appreciate hearing back from you about ways I could resolve this. Thank you for your time, Tyler

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Artemis fit error - chi-square and R-factors are always equal to 0
by Ava Rajh 26 Mar '21

26 Mar '21

Hello, I have recently installed Demeter suite on my LinuxMint 20 machine with all required dependencies met. Athena works well and Demeter passed all tests during installation. When running Artemis however, there is an issue with fits that persists with provided examples any any other projects I open (including the ones done by colleagues and just re-run on my machine). After the fit (which completes fine and returns expected fit that looks ok when comparing it to experiment), when inspecting the log file, chi-square, reduced chi-square and R values are equal to 0 (example log file attached bellow). No errors accompany the fit. I am using Larch installed with anaconda, and Artemis uses Feff6 executable. I have re-installed Demeter and tried to get it to work with Ifeffit but the error persists. I have found an existing git hub thread dealing with similar issue (https://github.com/bruceravel/demeter/issues/62) but no solution that I could discern. Could it be an issue with my perl version (5.30.0)? If someone has any ideas what the issue could be and how to fix it, I would appreciate the help. Please let me know if I can provide any additional information, and I apologize if there is something obvious I may have missed. Sincerely, Ava -- Ava Rajh

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FW: Postdoc position at BNL for studying molten salts using synchrotron methods
by Gill, Simerjeet 24 Mar '21

24 Mar '21

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 postdoctoral Research Associate position within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments. The position requires 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. You can find the detailed description of the position requirements and apply online, go to https://jobs.bnl.gov<https://jobs.bnl.gov/> under Job ID 2335 (https://jobs.bnl.gov/job/upton/post-doc-synchrotron-studies-of-molten-salts…) The postdoc will investigate molten salt systems using NSLS-II beamline facilities at Brookhaven National Laboratory, with X-ray absorption fine structure along with x-ray scattering techniques. 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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Cobalt carbide EXAFS spectrum
by Antonio Aguilar 18 Mar '21

18 Mar '21

Dear community, I'm struggling with the data analysis of some Co samples, i think it might be some cobalt carbide. I was wondering if someone would be willing to share the spectrum of the Co2C reference please? That would be very helpful. Thank you in advance! Cheers, Antonio Aguilar -- Postdoctoral fellow Beamlines CRG FAME (BM30B) & FAME-UHD (BM16) | ESRF ESRF - The European Synchrotron 71 Avenue des Martyrs, 38043 Grenoble, France Tel: +33 (0)4 76 88 25 46 - Bureau : LOB 2-50

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Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)
by Mangold, Stefan (IPS) 16 Mar '21

16 Mar '21

Dear all, I tried to reinstall; before I updated and couldn’t open larch anymore conda install -yc GSECARS xraylarch Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: The following specifications were found to be incompatible with each other:

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Normalization of LCF coefficients when fitting experimental spectra with theoretical spectra
by Patricia Poths 11 Mar '21

11 Mar '21

Hi, I am a theoretical chemistry PhD student working on fitting experimental spectra with computed spectra in order to get a better understanding of the composition. In the LCF process with athena, I have found that when I allow "sum coefficients to 1", I get an unphysical negative coefficient of the last standard- after reading through the mailing list I understood why, and so no longer use that. The sum of my coefficients during the fitting now is close to 1- generally within the range of 0.95-1.1 at the absolute extremes, but more often around ~0.98- ~1.05. In order to compare these coefficients, I renormalize them to 1, so they can represent the fractions of each component present. However, to test this I took the new normalized coefficients and summed up the standards with their respective weights to create this normalized "fit", and found that it is worse than the initial one. Is this something I should be concerned about when reporting the qualitative trends in how the composition changes? And if so, is there a better way to do the fits in a more normalized way? Many thanks, Patricia

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Re: [Ifeffit] Ifeffit Digest, Vol 217, Issue 6
by Clark Adam Hugh (PSI) 10 Mar '21

10 Mar '21

Dear Valerie Sorry! I don't know where I got the idea that it was Fe, I was probably working on Fe data at the time of writing. Having looked back I can see Mo. "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." For Mo I also have some standards, maybe these would be helpful for you. These are all calibrated with the first derivative of the Mo foil and so are consistent with each other. Although measured on a different monochromator, the likely would serve well to compare the edge position to make sure the calibration is done consistently for the standards you have from the canadian light source to give some idea of if things are reliable. Si(111): Mo MoO2 MoO3 Fe2Mo3O12 Mo2C NiMoO4 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 ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Tuesday, March 9, 2021 7:00:01 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 6 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: Re. Larch Energy Calibration (Mangold, Stefan (IPS)) 2. Re: Larch Energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Mar 2021 11:20:38 +0000 From: "Mangold, Stefan (IPS)" <stefan.mangold(a)kit.edu> To: "Schoepfer, Valerie" <valerie.schoepfer(a)usask.ca> Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Re. Larch Energy Calibration Message-ID: <45116D6C-9314-4822-8E1B-7FB929333D72(a)kit.edu> Content-Type: text/plain; charset="utf-8" Dear Valerie, The reason why I'm currently not using Larch for my data-evaluation chain is, that I didn?t found some features (like energy calibration; not as I use it; like Calibration of references, absorption and fluorescence spectra in one group) in Larch, which I need for my data evaluation process. They might be there, but I didn?t found them. for the XANES data evaluation your energy region might be a bit to short to fit a good background to the data. Anyway you have to fine-tune the parameters to reach a good background fit in the XANES region. While the automatic process in Athena produces quite good results for a lot of absorption edges, one has to be careful not add artefacts to the data in the XANES. Best regards Stefan > Am 08.03.2021 um 14:17 schrieb Schoepfer, Valerie <valerie.schoepfer(a)usask.ca>: > > 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] 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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