January 2019 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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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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