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

Plotting flattened feffit simulation results
by FonsPaul 28 Jan '19

28 Jan '19

Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions!

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Job posting: Lead Beamline Scientist at NSLS-II, Brookhaven National Lab
by Matt Newville 27 Jan '19

27 Jan '19

Hi Folks, I was asked to forward this job posting: There is an opening for a Lead Beamline Scientist position at the National Synchrotron Light Source-II, Brookhaven National Laboratory. The candidate will assume leadership of the Inner-Shell Spectroscopy (ISS) Beamline, a high-flux, fast-scanning, damping wiggler spectroscopy beamline, with in-situ and operando instrumentation capabilities. The candidate will also be expected to develop an independent research program that utilizes the beamline capabilities. See https://jobs.bnl.gov/job/upton/lead-beamline-scientist-inner-shell-spectros… for details. --Matt

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Question about parameters of principle components analysis (PCA)
by 雷思聪 26 Jan '19

26 Jan '19

Hello, I see in many publications the indicator values (IND) numbers used to evaluate how many components are included, and SPOIL value used to evaluate quality of target transform in principle components analysis (PCA). However, they are obtained from PCA performed on SIXpack, rather than Athena (version 0.9.26). Hence, I wonder if I can get similar parameters after running of PCA in Athena? If not, how do I evaluate the PCA results? Thanks for your help!

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Larch flattening
by Kirill Lomachenko 25 Jan '19

25 Jan '19

Dear Matt, I have a question and a comment regarding Larch. I would appreciate if you could have a look. 1) The flattening algorithm for XAS in Larch works differently with respect to Athena when linear post-edge function is used for normalization. In Larch the normalized spectrum is always fitted by a parabola for flattening, no matter which function was used for normalization. It works fine when the post-edge function is also a parabola, but when it is a straight line, the resulting flattened spectrum does not stick to Y=1, as it is expected to do (and as it does in Athena). My question is: is it a bug or a feature? Just in case, I made some minor modifications in the pre_edge.py file that allow to get the same results as in Athena when linear post-edge is used. Maybe these corrections are a bit clumsy, but it seems to work. If anyone needs, I can share. 2) There is a typo in the larch web-manual in the description of the nnorm parameter of the pre_edge() function. It is stated that it is the number of terms in the fitting polynomial (i.e., 1+degree) whereas it seems that it is just its degree. So, nnorm=1 corresponds to a linear function and nnorm=2 to quadratic. In the gui help it is partially corrected, but the phrase "Default=3 (quadratic)" stays. It is not critical at all, but may be misleading for beginners... Using the possibility, I would like to thank you for all the great work you are doing on Larch. It really helps for large datasets! All the best, Kirill -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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Re: [Ifeffit] Dynamic XAFS Simulations?
by Gentle, Cecilia M 23 Jan '19

23 Jan '19

Dear Hunter, I also recommend you to join the mailing list for the ultrafast laser community: dyna(a)listes.epfl.ch [to subscribe: dyna-subscribe(a)listes.epfl.ch] Best, Cecilia Gentle PhD Candidate, Department of Chemistry University of Illinois at Urbana-Champaign https://www.vanderveen-lab.com/ -----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, January 23, 2019 4:54 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 191, Issue 13 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. Dynamic XAFS Simulations? (Hunter Allison) 2. Re: Dynamic XAFS Simulations? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 23 Jan 2019 13:26:21 -0800 From: Hunter Allison <hgalliso(a)uci.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Dynamic XAFS Simulations? Message-ID: <CAH6J0e_vk1n4viX8H5A4vX=SRL0e5NQHmSZGEQ43wVxBzpwo5Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, I'm a graduate student at the University of California, Irvine. Firstly, thank you for all the copious resources. It is a treasure trove of information and a beacon of light for someone just starting out. Let's begin with some brief background. In my research group, we intend to perform pump-probe spectroscopy with attosecond x-ray probes. The Professor says that we can use XAFS to study how the electrons move on these very short timescales. While the system is being setup and other experiments are being conducted, my Professor wants me to figure out how to do simulations of XAFS. This is a bit of a daunting order, since I've never simulated anything before and only have basic programming knowledge. The only direction I have is, "Try Google.". So, today, I've been "trying Google" and found my way to here. Since, I don't really know what I'm doing, I thought I try asking and finding out if anyone else does this sort of thing: How/where does one do simulations of dynamic XAFS? Where would I get started? (Please forgive me if this question has been answered somewhere else or if it seems profoundly dumb or too broad. I'm really just looking for some more direction. Perhaps, it could be that nobody does this and, in that case, I need to figure out how to model this myself. Wow! That thought seems daunting.) For example, let's say I want to find out how the x-ray adsorption of a carbon foil like Graphene would change on attosecond time scales as it's heated by a femtosecond laser and electrons move. Is there a program or code out there that people use to model this sort of thing?

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Dynamic XAFS Simulations?
by Hunter Allison 23 Jan '19

23 Jan '19

Hi, I'm a graduate student at the University of California, Irvine. Firstly, thank you for all the copious resources. It is a treasure trove of information and a beacon of light for someone just starting out. Let's begin with some brief background. In my research group, we intend to perform pump-probe spectroscopy with attosecond x-ray probes. The Professor says that we can use XAFS to study how the electrons move on these very short timescales. While the system is being setup and other experiments are being conducted, my Professor wants me to figure out how to do simulations of XAFS. This is a bit of a daunting order, since I've never simulated anything before and only have basic programming knowledge. The only direction I have is, "Try Google.". So, today, I've been "trying Google" and found my way to here. Since, I don't really know what I'm doing, I thought I try asking and finding out if anyone else does this sort of thing: How/where does one do simulations of dynamic XAFS? Where would I get started? (Please forgive me if this question has been answered somewhere else or if it seems profoundly dumb or too broad. I'm really just looking for some more direction. Perhaps, it could be that nobody does this and, in that case, I need to figure out how to model this myself. Wow! That thought seems daunting.) For example, let's say I want to find out how the x-ray adsorption of a carbon foil like Graphene would change on attosecond time scales as it's heated by a femtosecond laser and electrons move. Is there a program or code out there that people use to model this sort of thing?

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XAS data for Nickel Chloride
by Gill, Simerjeet 18 Jan '19

18 Jan '19

Hi, I am working with a molten salt system with Nickel Chloride as one of the components. If you have measured XAS data on anhydrous and hydrated Nickel Chloride at RT and elevated temperature, I would appreciate you sharing your data. Thanks in advance for your help! Simer Simerjeet K Gill, Materials Scientist, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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求助Athena软件32位电脑安装包，谢谢
by 2225295803 16 Jan '19

16 Jan '19

你好，我是天津大学马新宾课题组的硕士研究生袭雨杉，我的电脑是32位的，请问有32位的EXAFS分析软件Athena吗？可以发给我吗？谢谢

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Advice on using Athena for XANES LCF on spectra with a small edge step?
by Mike Massey 15 Jan '19

15 Jan '19

Hi All, Does anyone have advice for LCF of spectra with a small edge step? I've recently found myself with more and more issues fitting spectra like the one shown in the attached photo, where the spectrum is of good quality, but the fits end up not working out due to normalization (as far as I can tell). Sadly, I have so far ended up just throwing these fits out, but I'm hoping there is a better solution out there that someone might be able to recommend. One solution is "get more of the element of interest," as a beamline scientist recently told me. I'm just reluctant to really load it up in the data collection, because at 2 keV I get nervous about artifacts like self-absorption. Is there a better way? What am I missing? Thanks for your thoughts, Mike

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Nickel Chloride XAS data at RT and 320C
by Gill, Simerjeet 15 Jan '19

15 Jan '19

Hi, I am working with a molten salt system with Nickel Chloride as one of the components. If you have measured XAS data on anhydrous and hydrated Nickel Chloride at RT and 320C, I would really appreciate if you could share the raw data with me. Thanks in advance for your help! Simer Simerjeet K Gill, Materials Scientist, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973 -----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, January 11, 2019 12:20 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 191, Issue 7 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: Standard deviation of R value (Matt Newville) 2. Re: Standard deviation of R value (Anatoly Frenkel) 3. Re: Standard deviation of R value (Erin Finley) ---------------------------------------------------------------------- Message: 1 Date: Fri, 11 Jan 2019 10:04:49 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Standard deviation of R value Message-ID: <CA+7ESbo=kOiHZx9skxwv6qzHADH9q5Rh2u=Y8np+5AB-XqRyiA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Erin, On Fri, Jan 11, 2019 at 8:19 AM Erin Finley <efinley9033(a)gmail.com> wrote: > Hello, I see in many publications the R value reported with a standard > deviation. However, when I look at my resulting data from a fit I > don't see one listed. I am still new to EXAFS research and so I am > wondering where I can get this information. I am assuming I need to > calculate it from another parameter I am just not sure which one. > > The uncertainties in R are typically in the fit report. But also, we typically refine a "delR" parameter that is R - Reff, where Reff is the distance (half path-lengh) for the scattering path. So, if you don't see an uncertainty reported for R but do see an uncertainty for delR (or whatever parameter name you used), use that. The uncertainty in R will (normally) be the uncertainty in delR. If I'm misunderstanding the question, pleas give more details about what you are doing. --Matt Thanks for your help! > Cheers, > > -- > Erin Finley > PhD Candidate > Brgoch Research Group > Department of Chemistry > University of Houston > _______________________________________________ > 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> 630-252-0431

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