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

Stand Alone Atoms
by Yasin Deep 13 Apr '23

13 Apr '23

Dear All, I want to calculate bond lengths of the SrFe2As2 parent compound for E//ab and E//c polarization with stand-alone atoms pack of the Demeter. How can I calculate bond lengths for these two different polarizations? There is a panel for polarization vector I guess that panel I should adjust. I should put (0,0,1) for E//c and E//ab (1,1,0) is this correct? What should I put let's say for 30 degrees of polarization? Thank you in advance, Dr. Yasin HACISALIHOGLU

2 1

Scattering paths in Artemis
by Jyoti Pandey 13 Apr '23

13 Apr '23

Hello everyone, I have a question regarding the scattering paths. Can we manually feed the scattering paths in artemis or it will only read from the feff input file. Thank you. With Best Regards Dr. Jyoti Pandey, Ph.D. Postdoctoral Researcher Department of Physics Central Michigan University, MI, USA Mobile No. +1-9282650599 .....................................

2 1

Exporting XANES data as a .csv file
by Kumar Jena 13 Apr '23

13 Apr '23

Dear, all, I am a new XAS user. I have done preprocessing of my data in Athena and have been trying to export the XANES data as a .csv file. I would like to fit the pre-peak region to pseudo-Voigt line shapes to extract approximate relative intensities of various transitions (A1, A2, A3, and B). Attached is a screenshot from an article for your reference ( https://doi.org/10.1021/jp981644k) Is it possible to do so in Athena? Any help would be appreciated. Kind regards, Kumar [image: image.png] -- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* *THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email.

3 4

Q2XAFS, Aug 17 and 18, Melbourne, Australia
by Matt Newville 05 Apr '23

05 Apr '23

Hi Folks, As a reminder to all interested, there Q2XAFS meeting will be August 17 and 18, 2023. See the attached flyer for details, and hope to see some of you there. --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

developer Zoom meeting
by Matt Newville 05 Apr '23

05 Apr '23

Hi Folks, As I mentioned a few weeks ago ( https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2023-March/010594.html) we are trying to start a monthly Zoom meeting to talk about the development of Larch and related tools. The first of these meetings will be this Friday, April 7 at 9 AM Chicago (1400 UTC, I believe). I'm reluctant to publish the Zoom link on this forum, but if anyone is interested, send me a direct email. I know this time is not convenient for many of you. If you would like to participate but cannot make this meeting, please let me know. I think the first order of business will be to work on a better day/time and organization. Thanks, --Matt Newville <newville at cars.uchicago.edu>

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 241, Issue 13
by van der Veer, Siebe 04 Apr '23

04 Apr '23

Dear Matt and Robert, Thanks for the feedback and information. I'll play around with the file and indeed think about what it means for what I'm trying to achieve. Best, Siebe On Fri, Mar 31, 2023 at 7:02 PM <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: Fortran runtime error when running feff on Hydrotalcite > cif (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Mar 2023 14:50:26 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Fortran runtime error when running feff on > Hydrotalcite cif > Message-ID: > < > CA+7ESbr_33qqQo4midvNcO3rQdrCu00KB9nNGY6WyeZhsc-NpQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Siebe, > > Sorry for the trouble. I agree with Robert's suggestion to check whether > "Wat" might be causing the problem. > > The CIF Browser and Feff runner in XAS Viewer does actually support > fractional occupancies, by randomly assigning atoms to match the partial > occupancy (but of course, not with great precision -- each X, Y, Z position > has exactly one actual atom of a determinant Z). That allows a lot CIF > files to "just work" that would otherwise need manual intervention. At the > moment (and possibly for the foreseeable future), the CIF Browser does not > support editing the CIF directly, but does support editing the result > Feff.inp file, but one can export a CIF, edit that elsewhere, and then > import it. > > What I see trying to run a calculation from that CIF file is that there are > many oxygen atoms that are too close together. Like Robert suggested, I > suspected these come from the "Wat", but when I removed those and the H > atoms, the prolem still happened. As Robert listed the atomic positions > for this structure, I think it might actually be the "C", "O2", as well as > the "Wat" with the low occupancy of "0.0833" that might be the problem. > > If I remove CO groups and Waters, these to generate the attached CIF (I > changed the ID number) that seems to run, though I don't know if it is then > the structure you actually are trying to model ;). > > --Matt > > > On Thu, Mar 30, 2023 at 6:51?AM van der Veer, Siebe <s.van.der.veer(a)rug.nl > > > wrote: > > > Dear all, > > > > I'm trying to run feff on the Hydrotalcite cif file as can be found in > the > > Larch Am Min CIF browser and I get the following error: > > > > > > *At line 125 of file ff2chi.f (unit = 1, file = 'list.dat')Fortran > runtime > > error: Bad real number in item 2 of list input* > > > > I've been able to gather that this means there is some unreadable input > in > > the file that is been used, but I don't know what file this is so I don't > > know what the actual bad input is and what has caused it. > > > > Any help is greatly appreciated! > > > > Kind regards, > > > > > > -- > > *Siebe van der Veer* | *PhD student* > > Nanostructures of Functional Oxides | Zernike Institute for Advanced > > Materials > > University of Groningen | Nijenborgh 4, 9747 AG Groningen | The > Netherlands > > Email: s.van.der.veer(a)rug.nl | > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > --Matt Newville <newville at cars.uchicago.edu> 630-327-7411 >

1 0

Save the date: XAFS short course at BNL and EXAFS-50 symposium
by Anatoly Frenkel 31 Mar '23

31 Mar '23

Dear subscribers, Please save the date for the two back-to-back, *in-person*, events: EXAFS-50 symposium (Oct. 30-31) and annual EXAFS short course (Nov. 1-3, 2023), both to be run at Brookhaven National Laboratory. While the usual format of our short courses is Wednesday through Friday, this year we will mark the 50th anniversary of discovery of EXAFS by organizing a two-day symposium on Monday-Tuesday to celebrate it. The short course participants will benefit from attending the symposium as well because they will be able to learn from, and interact with, leading experts in the field, credited for developing the foundations of the EXAFS experiments, theory, data analysis and modeling. Brookhaven shares with other synchrotron facilities good memories of developing new techniques and applications of EXAFS, and other labs, as well as the International X-ray Absorption Society (IXAS), are planning their own efforts to commemorate the 50th anniversary in the coming years. Regarding the short course: following up on the feedback we received after the 2022 course, we are planning to teach advanced topics in 2023. They will include but not limited to: Reverse Monte Carlo EXAFS, Molecular Dynamics EXAFS, Machine Learning EXAFS, MCR-ALS and others. More information will soon appear on the web site of the Synchrotron Catalysis Consortium that co-sponsors the short course. The other sponsors are National Laboratory and the Users Executive Committee at the National Synchrotron Light Source-II (to be confirmed). We are grateful to BNL and Stony Brook University, as well as NSLS-II UEC (to be confirmed) for the support of the EXAFS-50 symposium that will enable participants to attend it registration fee-free. Stay tuned for further updates. Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) Stony Brook University Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

1 0

Fortran runtime error when running feff on Hydrotalcite cif
by van der Veer, Siebe 30 Mar '23

30 Mar '23

Dear all, I'm trying to run feff on the Hydrotalcite cif file as can be found in the Larch Am Min CIF browser and I get the following error: *At line 125 of file ff2chi.f (unit = 1, file = 'list.dat')Fortran runtime error: Bad real number in item 2 of list input* I've been able to gather that this means there is some unreadable input in the file that is been used, but I don't know what file this is so I don't know what the actual bad input is and what has caused it. Any help is greatly appreciated! Kind regards, -- *Siebe van der Veer* | *PhD student* Nanostructures of Functional Oxides | Zernike Institute for Advanced Materials University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands Email: s.van.der.veer(a)rug.nl |

3 2

Problem with cif file in larch
by Otal Eugenio 25 Mar '23

25 Mar '23

Hi all, In November I was generating the feff-path in Larch using the .cif file I attached. Now I am generating additional paths from another absorbing atom and I am getting the error message "Error opening .cif file" using the same .cif file. Any ideas? Best regards. (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Dept. of Materials Chemistry Shinshu University 4-17-1 Wakasato, Nagano 380-8553, JAPAN eugenio_otal(a)shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates

2 2

monthly xraylarch developer zoom meeting
by Matt Newville 17 Mar '23

17 Mar '23

Hi All, A few of us would like to start having regular (or somewhat regular) Zoom meetings to discuss planning and development goals for the xraylarch project. We would like to eventually settle on a stable-ish time for the monthly meeting. A doodle poll for the time of the initial meeting is at: https://doodle.com/meeting/participate/id/e99lKPze I will send out an announcement by March 27th of when the first meeting will be. There are many potential topics to discuss. A few that are on my mind as topics for the next months/year might include: a) supporting (and perhaps working on design) of an XAS schema for NeXuS/HDF5 b) better support for using xraylarch from Jupyter, especially plotting routines. c) creating inputs, launching, and reading of outputs for XANES calculations with Feff and/or FDMNES. d) MCR-ALS or related additional linear algebra methods. e) improvement to XRF / XRF mapping schemas, formats, and analysis. These discussions will sort of focus on what these codes and programs should do, so anyone interested in working with Larch from Python or other tools is definitely most welcome. Having input from knowledgeable "power users" or experts in the field would be great. I think we don't want this to be a support forum, but if people would also like to see "virtual office hours" (say, 1 hour per month for support questions), please let me know. Thanks, --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

Looking for candidates for a PhD Thesis on the application of XAS to radioecology at the University of Nice (France)
by Lorenzo Stievano 16 Mar '23

16 Mar '23

Hi everybody, my colleague Christophe Den Auwer from the university of Nice is currently looking for candidates for a PhD Thesis on the application of XAS to radioecology. If anybody is interested, please do not hesitate to contact him. A description of the PhD project (in French and English) is joined. Have a nice day, Lorenzo Lorenzo STIEVANO Professeur Tél : +33 (0)4 48 79 21 00 <tel:+33 (0)4 48 79 21 00> Lorenzo.Stievano(a)umontpellier.fr <http://www.umontpellier.fr/> <http://www.umontpellier.fr> Institut Charles Gerhardt Montpellier UMR 5253 CNRS-UM-ENSCM D4 - Pôle Chimie Balard Recherche - 1919, route de Mende 34293 Montpellier cedex 5 - France www.icgm.fr <http://www.aime.icgm.fr> www.umontpellier.fr <http://www.umontpellier.fr>

1 0

Re: [Ifeffit] Looking for XANES Cr(II) carbide standard (Anna Wade)
by Paktunc, Dogan 03 Mar '23

03 Mar '23

Please check Ifeffit archives. I'd posted a spectrum of Cr3C2 several months ago. Dogan Dogan Paktunc, PhD Senior Research Scientist - CanmetMINING Natural Resources Canada / Government of Canada 555 Booth Street Ottawa, Ontario, K1A 0G1 Canada Chercheur principal - MINESCanmet Ressources naturelles Canada / Gouvernement du Canada 555 Rue, rue Booth Ottawa, Ontario, K1A 0G1 Canada Cell: (343) 543-9864 dogan.paktunc(a)nrcan-rncan.gc.ca -----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 2, 2023 8:43 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 241, Issue 5 ***Caution - email originated from outside of NRCan. Read the warning below / Attention- Ce courriel provient de l'extérieur des RNCan. Voir la mise en garde ci-dessous*** Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… 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. Looking for XANES Cr(II) carbide standard (Anna Wade) 2. Re: [External] Re: XAS viewer unit detection during data reading (Edmund Welter) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Mar 2023 16:33:32 -0500 From: Anna Wade <awade91(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Looking for XANES Cr(II) carbide standard Message-ID: <CAL9RWR4oO_+1yQbUDtBZYjpbTX4En9t+FeNr2rXq3m-jdXA8Xw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Good afternoon, Does anyone have a Cr2C3 standard scan they could share? I'm looking at stainless steel powder and know that Cr carbide can be used as an additive to combat corrosion. Thanks! Anna Wade

1 0

XAS viewer unit detection during data reading
by van der Veer, Siebe 02 Mar '23

02 Mar '23

Dear all, I am not sure if this mailing list is the correct medium for this question. Apologies, if not. I am looking to import files in XAS viewer, which worked fine in ATHENA, but in XAS viewer the correct units of the data are not detected and I cannot manually change them. I can get a plot of the data, but the data is not recognized by the software as XAS data, i.e. a lot of plotting/conversion options do not show. I hope the following screenshots provide sufficient information to illustrate my issue. Reading in a .dat file of fluorescence data. I can't change the units in the marked area. [image: image.png] The data can be read into the XAS viewer, but I don't have the regular plotting options in these dropdown menus. [image: image.png] Any advice would be much appreciated. Kind regards, -- *Siebe van der Veer* | *PhD student* Nanostructures of Functional Oxides | Zernike Institute for Advanced Materials University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands Email: s.van.der.veer(a)rug.nl |

6 9

Looking for XANES Cr(II) carbide standard
by Anna Wade 01 Mar '23

01 Mar '23

Good afternoon, Does anyone have a Cr2C3 standard scan they could share? I'm looking at stainless steel powder and know that Cr carbide can be used as an additive to combat corrosion. Thanks! Anna Wade

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 240, Issue 14
by van der Veer, Siebe 28 Feb '23

28 Feb '23

Dear Edmund, Thank you for the prompt reply. That did work. Cheers, Siebe On Tue, Feb 28, 2023 at 1:39 PM <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: XAS viewer unit detection during data reading (Welter, Edmund) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 28 Feb 2023 13:37:03 +0100 (CET) > From: "Welter, Edmund" <edmund.welter(a)desy.de> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XAS viewer unit detection during data reading > Message-ID: > <1505460518.63098920.1677587823196.JavaMail.zimbra(a)desy.de> > Content-Type: text/plain; charset="utf-8" > > Dear Siebe, > > did you try to change the data type from "raw" to XAS. If you click on the > small arrow on the right you should have the choice between xas and raw. On > my computer that works and after that I can choose the unit for the X-axis. > For some reason "raw" seems to be the preset choice. Maybe Matt could > change that, I fell into this trap several times. > > Cheers, > Edmund > > > From: "van der Veer, Siebe" <s.van.der.veer(a)rug.nl> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Tuesday, 28 February, 2023 13:16:18 > Subject: [Ifeffit] XAS viewer unit detection during data reading > > Dear all, > I am not sure if this mailing list is the correct medium for this > question. Apologies, if not. > > I am looking to import files in XAS viewer, which worked fine in ATHENA, > but in XAS viewer the correct units of the data are not detected and I > cannot manually change them. I can get a plot of the data, but the data is > not recognized by the software as XAS data, i.e. a lot of > plotting/conversion options do not show. > > I hope the following screenshots provide sufficient information to > illustrate my issue. > > Reading in a .dat file of fluorescence data. I can't change the units in > the marked area. > > > > The data can be read into the XAS viewer, but I don't have the regular > plotting options in these dropdown menus. > > > > Any advice would be much appreciated. > > Kind regards, > > > -- > Siebe van der Veer | PhD student > Nanostructures of Functional Oxides | Zernike Institute for Advanced > Materials > University of Groningen | Nijenborgh 4, 9747 AG Groningen | The > Netherlands > Email: [ mailto:s.van.der.veer@rug.nl | s.van.der.veer(a)rug.nl ] | > > _______________________________________________ > 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 >

1 0

Dumb question
by Roberta Candela 17 Feb '23

17 Feb '23

Hi all, I am attempting to graph a simple plot of intensity vs time for some supplemental info on a paper (from XAFS data from beamtime). I thought it should be simple enough since I can export I0 and If from Athena and I know the run time and time per data point but I can’t get anything that looks remotely like the logarithmic graph it should be. Am I missing some big fundamental point for why this isn’t possible? My apologies if this is way too vague!/I feel like I’m missing something super obvious Thank you for your time!Sincerely -B Sent from Yahoo Mail for iPhone

3 5

Error importing CIF files using Larch/ XAS Viewer
by Jack Geary 15 Feb '23

15 Feb '23

Hello, I have encountered an issue recently where any CIF file I attempt to open in XAS Viewer for Feff calculations returns an error that the file cannot be imported. This occurs with any CIF I have tried (all downloaded from CCDC). Is there a workaround for this? Thanks ---- Jack Geary Pronouns: he/him PhD Candidate, Xiao Group <https://xiaolab.org/> University of Washington

2 1

Y2O3 E0
by Otal Eugenio 14 Feb '23

14 Feb '23

Hi all, I am aligning in energy Y substituted sample but using Zr foil as a reference, no Y metal is available at the BL. Does anyone have well-calibrated in-energy Y2O3 spectra? Best regards. (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Dept. of Materials Chemistry Shinshu University 4-17-1 Wakasato, Nagano 380-8553, JAPAN eugenio_otal(a)shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates

1 0

Zr K edge EXAFS analysis of amorphous materials
by Angshuman Gupta 11 Feb '23

11 Feb '23

Dear everyone, I am working on alumina based amorphous materials containing ZrO2. I am interested in finding the bond length between Zr and O atoms and coordination number (N). Zr K edge spectra were collected at room temperature at 300K along with Zr foil as reference. Extracted So2 from reference (Zr foil) spectra was used to find N in the amorphous material. Local environment around Zr was modelled with harmonic and quasi harmonic models using a third cumulant of the distributions. Theoretical spectra fit well using quasi-harmonic models with large bond length (2.21 A) while harmonic models without third cumulants do not fit the spectra properly and calculating higher N value with 2.16 A as Zr-O bond length. I will be thankful if you kindly let me know what else we can do to improve the fitting and get some meaningful outcome. Any relevant journal articles are also helpful. I have attached the Artemis files. Thanking you Angshuman Gupta PhD research scholar IIT Bombay, Mumbai

2 2

Parameters for parent function in wavelet transform analysis
by Scott Calvin 08 Feb '23

08 Feb '23

Hi all, I’ve never actually tried wavelet transform analysis before, so I’m trying to understand it better, but there’s one aspect that’s puzzling me: The Morlet wavelet has two parameters, eta and sigma. Eta controls how fast it wiggles, and sigma how quickly the function dies out. (Essentially, it’s like the basis function for a Fourier transform multiplied by a Gaussian envelope.) In wavelet analysis we pick a parent function, which is often a Morlet wavelet with particular values of eta and sigma that we have chosen. We then create a set of child functions from the parent function by shifting and dilating the function in k-space. Each child function is then used as a basis function for a transform of chi(k) calculated by integrating over a range of k-values, much like what is done to calculate a Fourier transform. Since the Morlet wavelet is localized in k-space, and the child functions are shifted to focus on different regions of k-space, our wavelet transform produces plots which are a function of k. But since dilating the parent function by different amounts yields child functions with different frequencies, the plots are also a function of R. Therefore the result is a two-dimensional (k and R) contour plot. So far, so good. But what I’m wondering about is the effect of the initial choice of eta and sigma for the parent function. The dimensionless product of eta and sigma has a clear effect. If (eta)(sigma) is small, the parent function will not have very many oscillations of significant size; it it’s large, it will have a lot of oscillations. So if we want good resolution in R (and thus relatively poor resolution in k), we want a big value of (eta)(sigma). In the limit as (eta)(sigma) becomes arbitrarily large, we recover the Fourier transform. If we want good resolution in k, we use a small value for (eta)(sigma). In the limit as (eta)(sigma) becomes arbitrarily small we recover chi(k). That still makes sense to me! But what difference do sigma and eta make individually? In other words, how is sigma = 0.5 and eta = 10.0 different from sigma = 1.0 and eta = 5.0? Since we end up creating child functions that dilate the parent function anyway, I can’t see that it should have any effect at all. And if those two parameters don’t make an independent effect, why do we pretend there are two independent-looking parameters? I’ve seen at least one early paper that suggests choosing eta so that it’s close to the path length you’re most interested in probing, but I can’t see how that actually makes any difference, given the dilation. I expect there’s a good chance I’m missing something obvious, or have a fundamental misunderstanding of part of the process, and look forward to learning more! Best, Scott Calvin Lehman College of the City University of New York

2 2

Upcoming symposium on spectroscopy at large-scale facilities
by Dugan Hayes 08 Feb '23

08 Feb '23

Dear colleagues, The 76th International Symposium on Molecular Spectroscopy to be held June 19-23, 2023 at the University of Illinois Urbana-Champaign is now open for registration. The conference is highly student-oriented, aiming to give any student the opportunity to give an oral contribution. Each year, the ISMS spotlights topics of special interest in mini-symposia, typically lasting three or four half-day sessions. This year, Renske van der Veen, Joost Bakker, and I are organizing a mini-symposium entitled “Spectroscopy at Large-Scale Facilities: from Steady-State to Ultrafast.” The aim is to showcase how spectroscopy at large-scale facilities is practiced and what types of scientific questions can be addressed using the unique capabilities such facilities provide. Below is a short description of the mini-symposium, and more information on ISMS is available at the conference website: https://isms.illinois.edu/ The deadline for abstract submission is *March 1st*. We hope you would be willing to bring ISMS, and in particular our mini-symposium, to the attention of your Ph.D. students and postdocs - and of course urge them to come! Please also pass this announcement along to any other group leaders at your institute and beyond who may be interested. Regards, Dugan Hayes (University of Rhode Island) Joost Bakker (Radboud University, HFML-FELIX) Renske van der Veen (Helmholtz-Zentrum Berlin, BESSY) --------------------------------------------------------- *Spectroscopy at Large-Scale Facilities: from Steady-State to Ultrafast* The general topic of the symposium is IR/XUV/X-ray spectroscopy at synchrotrons and free-electron lasers, applied to, but not limited to the following topics: - Ion/gas-phase/cluster chemistry - Astro- and atmospheric chemistry - Molecules for catalysis and solar energy - Reaction dynamics - Photophysics of organic molecules and transition-metal complexes Symposium description: Large-scale facilities offer unique capabilities for spectroscopic investigations of, e.g., dilute solution-phase samples, clusters, or time-resolved molecular dynamics. With the recent advent of free-electron laser (FEL) facilities, yet a new era of molecular spectroscopy has begun. The goal of this symposium is to bring together the lab-based molecular spectroscopy community (historically largely represented at ISMS) with people from recently emerged fields such as (ultrafast) IR/XUV/X-ray spectroscopy at synchrotrons and FEL facilities. -- Dugan Hayes Assistant Professor | Department of Chemistry | University of Rhode Island Beaupre 374E | 140 Flagg Road | Kingston, RI 02881 (401) 874-5516 | (*he/him*) http://www.chm.uri.edu/hayesgroup/

1 0

FDMNES Simulation for ZnO
by Chen, Danting 06 Feb '23

06 Feb '23

Dear All, I tried to run some simulations through FDMNES about XANES of ZnO with the absorber of Zn, and there are the results for simulated ZnO (red) compared with the experimental one (Green curve). The white line matches well but the two additional peaks are not shown in the spectrum of simulated ZnO. I attached the input file for FDMNES here. Do you have any idea to improve it? I am quite new to running the simulation and would appreciate if you can give me some directions to modify it. Best Wishes, Danting [cid:image001.png@01D937EA.4B65FBB0]

4 3

FEFF simulation of DFT optimized structure at Fe K-edge
by Harry Zhang 25 Jan '23

25 Jan '23

Dear all, Thank you very much for answering many questions related to XAS! I am working on Fe modified zeolites and trying to simulate the Fe K-edge XANES using DFT optimized structures by FEFF10. I found the shape of simulated results are quite similar to the experimental data. However, there is an around 1.4 eV difference between the edge positions of the experimental data and the simulated results. I have calibrated the experimental spectra using reference sample (Fe foil) measured at the same time at synchrotron. I wonder if there are some methods to calibrate the edge energy of the simulated results. Thanks a lot for your help! Best regards, Harry

1 0

Logical range for Amplitude Reduction Factor in EXAFS fitting results
by Esmael Balaghi 24 Jan '23

24 Jan '23

Dear All, I noticed that some published works have reported extremely large values for the amplitude reduction factor. This seems a bit unusual, as the amplitude reduction factor is typically expected to be in the range of 0 to 1. I am curious to know what could be the reasons behind it to get such large values for the amplitude reduction factor during EXAFS fitting. Thank you in advance for your insights. Esmael

2 1

Yttrium standars for oxidation state
by Otal Eugenio 17 Jan '23

17 Jan '23

Hi all, I need to confirm the oxidation state of Y in a sample. I found some reports about Y(II), does someone have something like it? I was looking in the databases and had no luck. Best regards. (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Dept. of Materials Chemistry Shinshu University 4-17-1 Wakasato, Nagano 380-8553, JAPAN eugenio_otal(a)shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates

1 0

FEFF10 simulation of Pt alloy
by Andy Zhang 16 Jan '23

16 Jan '23

Dear all, I tried to use FEFF10 to simulate the XANES of Pt alloy (Pt L3 edge), and the simulation results fit the XANES collected using TFY mode. However, the white line intensity of the simulated XANES is much lower than the experiential spectra collected using HERFD mode. I wonder if there is way to fit the HERFD XANES results through simulation (in other words, to increase the white line intensity of the simulated XANES). Thanks a lot in advance! Best, Harry

5 5

Positions posts “PostDoc”, “PhD students” in the field of synchrotron-assisted investigations
by Tetyana MILOJEVIC 12 Jan '23

12 Jan '23

Dear colleagues, we announce several positions in the XAS & X-ray crystallography related fields: https://euraxess.ec.europa.eu/jobs/45514 I also attached here a pdf file of the posts. Could you perhaps spread it among your XAS community via your mailing list? Thank you very much in advance! Kind regards Tetyana Milojevic -- ****************************************** Prof. Milojevic Tetyana, PhD Chair of Exobiology at the University of Orléans CNRS, Centre de Biophysique Moléculaire, UPR 4301  3 Av. de la Recherche Scientifique, CS80054 45071 Orléans Cedex 2, France tel:+33 2 38 25 55 48 tetyana.milojevic(a)cnrs-orleans.fr ******************************************

1 0

Gas-phase time-resolved x-ray photoelectron spectroscopy
by Dooshaye Moonshiram 11 Jan '23

11 Jan '23

Dear Colleagues, We are looking for a postdoctoral appointee funded over 2 years in “Gas-phase time-resolved photoelectron spectroscopy in biological and chemical catalysis” at the Instituto de Ciencia de Materiales de Madrid in collaboration with the small quantum systems (SQS) group at the European XFEL facility. The project description and more details can be found in attached call. Many thanks and Best Regards, Dooshaye Moonshiram Ramon y Cajal Group Leader Instituto de Ciencia de Materiales de Madrid 28049, Spain https://moonshiram.wordpress.com/

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 239, Issue 1 - Cr K-edge spectrum of Cr3C2
by Paktunc, Dogan 07 Jan '23

07 Jan '23

Anna - Please find attached the Cr K-edge spectrum of Cr3C2. It is based on 3 spectra collected at 20BM (APS, PNC-CAT). It has not yet been published but it was referenced to as "ferrochrome" in the following publication: Berryman & Paktunc (2022) Cr(VI) formation in ferrochrome-smelter dusts. J.Hazardous Mat. https://doi.org/10.1016/j.jhazmat.2021.126873 Dogan Dogan Paktunc, PhD Senior Research Scientist - CanmetMINING Natural Resources Canada / Government of Canada 555 Booth Street Ottawa, Ontario, K1A 0G1 Canada Chercheur principal - MINESCanmet Ressources naturelles Canada / Gouvernement du Canada 555 Rue, rue Booth Ottawa, Ontario, K1A 0G1 Canada Cell: (343) 543-9864 dogan.paktunc(a)nrcan-rncan.gc.ca -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: January 6, 2023 13:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 239, Issue 1 ***Caution - email originated from outside of NRCan. Read the warning below / Attention- Ce courriel provient de l'extérieur des RNCan. Voir la mise en garde ci-dessous*** Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… 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. Cr3C2 chromium carbide spectrum (Wade, Anna) ---------------------------------------------------------------------- Message: 1 Date: Fri, 6 Jan 2023 17:24:45 +0000 From: "Wade, Anna" <Wade.Anna(a)epa.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Cr3C2 chromium carbide spectrum Message-ID: <DM8PR09MB648534519B6B904F100ABF00E7FB9(a)DM8PR09MB6485.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Dear XAFS community, Does anyone have a spectrum of Cr3C2, chromium (II) carbide standard? Thanks in advance. Sincerely, Anna Wade EPA ORISE Postdoctoral Fellow ORD Land Remediation & Tech. Division 5995 Center Hill Ave Cincinnati, OH 45224 p: 513-569-7815

1 0

Cr3C2 chromium carbide spectrum
by Wade, Anna 06 Jan '23

06 Jan '23

Dear XAFS community, Does anyone have a spectrum of Cr3C2, chromium (II) carbide standard? Thanks in advance. Sincerely, Anna Wade EPA ORISE Postdoctoral Fellow ORD Land Remediation & Tech. Division 5995 Center Hill Ave Cincinnati, OH 45224 p: 513-569-7815

1 0

Using 3 or more CIF file for fitting in Artemis
by Esmael Balaghi 16 Dec '22

16 Dec '22

Dear all, Following the previous discussion ( https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg07118.html ) on using more than one CIF file for fitting, as Scott Calvin and Matthew Marcus suggested, we can fold the molar ratio into the amp parameter for each CIF. Does it mean that the overall S02 for all phases (all used CIF files in the fitting) is "set" to 1? Typically, for the regular fitting with one model (cif file or any simulated feff file), we take the S02 value from the known metal foil that has been measured simultaneously with the unknown sample. So if we used the mentioned method and folded the molar ratio into the amp, does it mean in Artemis we use the following terms? "in Artemis: S02= abs(amp) for one phase and for another one: S02= abs(1-abs(amp)" and leave “amp” parameter to “guess” Also if we are using X, Y, Z,.... CIF files, does it mean the summation of all S02 for all X,Y,Z,... cif models would be equal to 1? Im not sure, but I guess in this work ( https://www.sciencedirect.com/science/article/pii/S0016703702008888 ), the authors used this way and fixed the overall S02 for all phases to 1. I would appreciate having your comment on this method or if you have any suggestion on how to deal with the S02 value in Artemis when we are using more than 2 or 3 phases (cif files) for the fitting process. Thank you in advance, Bests, Esmael -- Linkedin: www.linkedin.com/in/esmael-balaghi <https://www.linkedin.com/in/esmael-balaghi/>i

2 1

Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with
by Mosselmans, Fred (DLSLtd,RAL,SCI) 14 Dec '22

14 Dec '22

Dear Matt and Carlo and Liam, I agree with Matt and Carlo that phase corrected plots are not a great idea, I think they lead people to forget that they are not looking at a radial distribution function and encourages people to think they can read distances off a plot of the amplitude of the FT of overlapping sine waves reliably. Thanks Fred J F W Mosselmans Principal Beamline Scientist I20 Diamond Light Source Harwell Campus Didcot OX11 0DE 01235 778568 Fred.mosselmans(a)diamond.ac.uk 07419362123 Message: 1 Date: Tue, 13 Dec 2022 16:53:03 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction Message-ID: <CA+7ESbr+dCT8hfwNtm2T+ToNyHQW4iqwfBbBJoECN4ESE+iscg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Liam, Yes, this is not currently available. It would not be hard to enable, but I am not sure it is a great thing to do. I admit that I sort of find that phase-correction plots need a lot of explanation, and so are prone to causing confusion. They might be useful for Pt metal, but they cannot really be correct for multi-atomic systems. Well, I guess "correct" is not the only consideration ;). I guess I would ask if there are suggestions and input from people teaching XAFS on whether phase corrections (and probably a handful of other "tricks" or analysis variations) are actually useful or just confusing. On Tue, Dec 13, 2022 at 7:58 AM Liam Nagle-Cocco <lavn2(a)cam.ac.uk> wrote: > Dear all, > > In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase > corrected - i.e. bond length corrected for deltaR. This is shown in > this screenshot below ("Use this path for phase corrected plotting"). > Is this possible in XAS Viewer? > > > Liam Nagle-Cocco *(he/his)* > > PhD Student in Condensed Matter Physics | Cavendish Laboratory > > Welfare Officer 2022-2023 | Jesus College MCR > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction
by Liam Nagle-Cocco 13 Dec '22

13 Dec '22

Dear all, In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase corrected - i.e. bond length corrected for deltaR. This is shown in this screenshot below ("Use this path for phase corrected plotting"). Is this possible in XAS Viewer? [cid:b58a0f44-1946-4c60-a12e-c1e0bfa50100] Liam Nagle-Cocco (he/his) PhD Student in Condensed Matter Physics | Cavendish Laboratory Welfare Officer 2022-2023 | Jesus College MCR

3 2

Re: [Ifeffit] Ifeffit Digest, Vol 238, Issue 13
by Liam Nagle-Cocco 13 Dec '22

13 Dec '22

Hi Matt, Thanks for your prompt response and explanation. Liam Nagle-Cocco (he/his) PhD Student in Condensed Matter Physics | Cavendish Laboratory Welfare Officer 2022-2023 | Jesus College MCR ________________________________ 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: 13 December 2022 22:53 To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 238, 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 https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… 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: Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 13 Dec 2022 16:53:03 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction Message-ID: <CA+7ESbr+dCT8hfwNtm2T+ToNyHQW4iqwfBbBJoECN4ESE+iscg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Liam, Yes, this is not currently available. It would not be hard to enable, but I am not sure it is a great thing to do. I admit that I sort of find that phase-correction plots need a lot of explanation, and so are prone to causing confusion. They might be useful for Pt metal, but they cannot really be correct for multi-atomic systems. Well, I guess "correct" is not the only consideration ;). I guess I would ask if there are suggestions and input from people teaching XAFS on whether phase corrections (and probably a handful of other "tricks" or analysis variations) are actually useful or just confusing. On Tue, Dec 13, 2022 at 7:58 AM Liam Nagle-Cocco <lavn2(a)cam.ac.uk> wrote: > Dear all, > > In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase > corrected - i.e. bond length corrected for deltaR. This is shown in this > screenshot below ("Use this path for phase corrected plotting"). Is this > possible in XAS Viewer? > > > Liam Nagle-Cocco *(he/his)* > > PhD Student in Condensed Matter Physics | Cavendish Laboratory > > Welfare Officer 2022-2023 | Jesus College MCR > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… > Unsubscribe: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

Installing Larch without installing Anaconda
by TRANCHANT Laurent 13 Dec '22

13 Dec '22

Dear Mr or Mrs, I am Laurent Tranchant, post-doctoral researcher working at the IPANEMA laboratory at the SOLEIL synchrotron in France. I would like to install Larch (especially to use XAS Viewer to treat my XAS data) without installing Anaconda on MacOS. Do you know if it is possible or not ? For example by using MacPorts instead of Anaconda... It seems that all the solutions proposed online to install Larch on MacOS require the installation of Anaconda Python environment. I thank you in advance for your help. Best regards, Laurent Tranchant

4 6

Re: [Ifeffit] Installing Demeter on macOS Ventura
by Ryuichi Shimogawa 07 Dec '22

07 Dec '22

Hi Yasin, I am a visiting scientist in Prof. Frenkel’s group at Stonybrook University. I am an Athena user on M1 Mac, and I might be able to give some information that might be useful. I am now using MacOS Monterey instead of Ventura, but there would be many things in common. I have a personal note for installing Demeter on M1 Mac. And you may try it if you want to use dathena on M1 Mac. https://github.com/Ameyanagi/Install_Demeter/blob/main/M1_Mac_native.md However, dartemis and dhephaestus does not work because for the following reasons. There is some incompatibility issue with the SDK of MacOSX11 and wxwidgets3.0, and it crashes with a segment fault. I can give a full crash report, but it is basically the same as the issue reported on GitHub of wxwidget 3.0 https://github.com/wxWidgets/wxWidgets/issues/19005 This is fixed with wxwidget3.1, but the wrapper for Perl (wxperl) doesn't work with the new version of wxwidgets, so I haven’t been able to fix it. wxperl has not been maintained for the past 5 years. Regards, Ryuichi Ryuichi Shimogawa, Ph.D. Visiting Scientist Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794 Visiting Scientist Structure and Dynamics of Applied Nanomaterials Group Chemistry Division Brookhaven National Laboratory On Dec 7, 2022, 1:00 PM -0500, 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: Installing Demeter on macOS Ventura (Yasin Deep) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 7 Dec 2022 01:35:03 +0300 > From: Yasin Deep <yasindeep(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Installing Demeter on macOS Ventura > Message-ID: > <CA+xwDbVFVV1a=gbx_jw41vewjDTdXwKZ5BLyMbJ7=wdbng6YEA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Matt, > > Thank you for your kind interest. After writing to you I have realized some > points. On my first trial I missed some of the steps in Macports > installation, even if demeter installation went well but I couldn't reach > Athena. On my second trial with reinstalling all macports steps I faced > with the error I wrote in the mail. After a while I have uninstalled all > macports and reinstalled demeter it seems it is installed again Commands > didn't functioning. Within a couple of days I will try your advices. But > I'm also interested in larch and its viewer or using virtual Machine of > Windows. > > Thank you for your kind interest. > > Best Regards > > Yasin > > > 5 Ara 2022 Pzt, saat 20:48 tarihinde Matt Newville < > newville(a)cars.uchicago.edu> ?unu yazd?: > > > Hi Yasin, > > > > > > On Sun, Dec 4, 2022 at 11:46 AM Yasin Deep <yasindeep(a)gmail.com> wrote: > > > > > Hi Dear All, > > > > > > I'm very new on MacOs and I'm trying to install demeter on MacOs Ventura. > > > > > > > > > 1. I have Installed Xcode from MacOS App Store and, > > > 2. Agreed Xcode license in Terminal: sudo xcodebuild -license > > > 3. I have Installed MacPorts for my Mac operating system: > > > - macOS Ventura v1 > > > <https://github.com/macports/macports-base/releases/download/v2.8.0/MacPorts…> > > > 3 > > > > > > Later while I applied sudo port install xorg-server demeter I get > > > attached error message. What should I do from now on Could you please help? > > > > > > Best Regards, > > > > > > Dr. Yasin HACISALIHOGLU > > > > > > > > > > I think that you probably need to do both > > > > xcodebuild -license > > xcode-select --install > > > > and it would probably help to install XQuartz (link on the MacPorts page). > > > > But, I just tried this too, on macOS 13.0 (Ventura). It looks like > > MacPorts does not yet have binaries for Ventura, and so will build > > everything (including compilers and system-level libraries) from source > > kits. That could easily take 6 hours and might be much more. I've had > > poor luck with MacPorts especially with trying to get GUI apps to run, but > > I'll see how it goes (currently compiling libgcc12!). If you have the > > patience to try this too, please let us know how it goes! > > > > If you are interested, Larch and its XAS Viewer GUI App have many of the > > features of Athena and Artemis and do install and run on macOS. > > > > > > _______________________________________________ > > 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 > > >

1 0

Installing Demeter on macOS Ventura
by Yasin Deep 06 Dec '22

06 Dec '22

Hi Dear All, I'm very new on MacOs and I'm trying to install demeter on MacOs Ventura. 1. I have Installed Xcode from MacOS App Store and, 2. Agreed Xcode license in Terminal: sudo xcodebuild -license 3. I have Installed MacPorts for my Mac operating system: - macOS Ventura v1 <https://github.com/macports/macports-base/releases/download/v2.8.0/MacPorts…> 3 Later while I applied sudo port install xorg-server demeter I get attached error message. What should I do from now on Could you please help? Best Regards, Dr. Yasin HACISALIHOGLU

2 2

Installing Demeter on Mac (Apple M1)
by agironda 05 Dec '22

05 Dec '22

Hi, I’m a graduate student in Gerald Seidler’s group at University of Washington. I’ve gone through the process of installing Demeter on my M1 mac using macports. I believe it has completed successfully and all dependencies have been installed/established. However, calling “athena” or other commands do nothing -here’s a screenshot from my terminal. [cid:image001.png@01D907FD.C1FC2D70] Transcription: anthonygironda@Anthonys-MacBook-Air-4 ~ % sudo port install xorg-server demeter Password: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Cleaning demeter ---> Scanning binaries for linking errors ---> No broken files found. ---> No broken ports found. anthonygironda@Anthonys-MacBook-Air-4 ~ % athena zsh: command not found: athena anthonygironda@Anthonys-MacBook-Air-4 ~ % I understand Demeter compatibility on Mac is not largely supported, but has someone encountered this and found a workaround? I’m a bit of a novice at command line, so I appreciate your consideration and help. Sincerely, Anthony Gironda

2 1

Re: [Ifeffit] Installing Demeter on Mac (Apple M1)
by Fowler, Joseph W. (Assoc) 05 Dec '22

05 Dec '22

Dear Anthony, I’m the official MacPorts maintainer of Demeter. Although I have an M1 mac, I have not even tried to install it there. This fact might give you an idea of how active my efforts have been lately. (Sorry about that, community. Volunteers who use Demeter in their daily life on a Mac would be most welcome to take over or share the load here!) I suspect your immediate problem is with your shell’s path. Can you… 1. Make sure demeter installed what you expect it to install? Try “port contents demeter | less”. I expect to find /opt/local/bin/athena in the list of contents. 2. Make sure the directory where athena is installed is “in your path”. Specifically, try “echo $PATH” and make sure that /opt/local/bin is in the colon-separated list of path elements. 3. If athena is installed, but not in the path, you can do “/opt/local/bin/athena” to start it. For future convenience, you can read up on how to add to your PATH variable via zsh startup files. However, even after all that, you might still have a problem. The root of the bigger problem is that ifeffit is no longer actively maintained, but it’s required for Demeter. The authors of the two packages have discussed the problem with me, but we have not come up with any satisfactory solution. You might investigate whether Larch (ifeffit’s successor) could help solve your problems outside of Athena? (That’s available in a port named py-xraylarch, which we added earlier in 2022. Or you can use pypi/pip to install Larch using Python’s package management outside of the MacPorts framework.) In principle, Larch might be capable of being mixed in to Demeter as a replacement for ifeffit, but in practice it would take some real work. (Or so the authors think.) Bruce, Matt: please correct any misunderstandings I’ve expressed in the previous paragraph! Best wishes, Joe Fowler NIST Boulder Labs On Dec 4, 2022, at 6:22 PM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov<mailto:ifeffit-owner@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. Installing Demeter on Mac (Apple M1) (agironda) From: agironda <agironda(a)uw.edu<mailto:agironda@uw.edu>> Subject: [Ifeffit] Installing Demeter on Mac (Apple M1) Date: December 4, 2022 at 5:33:43 PM MST To: "ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>" <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Hi, I’m a graduate student in Gerald Seidler’s group at University of Washington. I’ve gone through the process of installing Demeter on my M1 mac using macports. I believe it has completed successfully and all dependencies have been installed/established. However, calling “athena” or other commands do nothing -here’s a screenshot from my terminal. <image001.png> Transcription: anthonygironda@Anthonys-MacBook-Air-4 ~ % sudo port install xorg-server demeter Password: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Cleaning demeter ---> Scanning binaries for linking errors ---> No broken files found. ---> No broken ports found. anthonygironda@Anthonys-MacBook-Air-4 ~ % athena zsh: command not found: athena anthonygironda@Anthonys-MacBook-Air-4 ~ % I understand Demeter compatibility on Mac is not largely supported, but has someone encountered this and found a workaround? I’m a bit of a novice at command line, so I appreciate your consideration and help. Sincerely, Anthony Gironda _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

1 0

Artemis: Importing VPaths Crash Error
by Ryan Parmenter 03 Dec '22

03 Dec '22

Hello, I'm having an issue with opening a data file in Artemis. As usual, I started by importing an Athena data file and a CIF. The paths were calculated and plotted (all worked ok). Then, I opened a second Athena data file and attempted to copy over the paths to check the fit; however, transferring the path parameters from the first data set to the second crashed the programme and will no longer open that data file. I have replicated the problem by using a new data file with fewer paths. Again, when exporting the path parameters to a second data set causes the file to crash and no longer open. I have tried both versions, 0.9.26 and 0.9.25, on two different laptops - one with windows 10 and the other with Windows 11. The same issue occurs. Opening the .fpj file directly from the desktop opens Artemis, but it soon crashes and closes; however, opening Artemis and loading the file causes Artemis to get stuck on 'importing VPaths'. (see image). I have left this open for a couple of hours, and its remains on importing v paths. Checking the dartemis file log, it states: Can't call method "parent" without a package or object reference at C:/Users/rap/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/Fit.pm line 1717. '-q' is not recognized as an internal or external command, operable program or batch file. %PGPLOT, Unable to read font file: grfont.dat %PGPLOT, Use environment variable PGPLOT_FONT to specify the location of the PGPLOT grfont.dat file. I had a look in visual studio to look at line 1716 - 1719 in fit.pm This is: my $path = $this -> mo -> fetch(['Path','SSPath'], $pg); $path->parent(Demeter->mo->fetch("Feff", $path->parentgroup)) if not $path->parent; ##print $path->name, "|", $path->group, "|", $path->parent, $/; $this->push_paths($path); I could not debug due to being a newbie with visual studio and unable to debug without the 'Perl' language installed. I have tried to install this language, but that's a separate issue. Thanks, Ryan

1 0

PosDoc position at KIT
by Zimina, Anna (IKFT) 30 Nov '22

30 Nov '22

Dear all, Postdoc position for operando X-ray absorption studies on Fischer-Tropsch catalysts for the CARE-O-SENE Project is open now in our group at IKFT/KIT: https://www.pse.kit.edu/karriere/joboffer.php?id=91688 <https://www.pse.kit.edu/karriere/joboffer.php?id=91688&new=true> &new=true https://care-o-sene.com/en/ Feel free to apply and distribute the information further. Best regards, Anna Zimina ____________________________________________________________________________ __________ Karlsruhe Institute of Technology (KIT) Institute of Catalysis Research and Technology (IKFT) Dr. Anna Zimina Senior scientist Hermann-von-Helmholtz-Platz 1 Building 345 Office 304 76344 Eggenstein-Leopoldshafen Phone: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail <mailto:anna.zimina@kit.edu> anna.zimina(a)kit.edu

1 0

Re: [Ifeffit] XANES temperature estimation (Robert Gordon)
by Gabriele Garofalo 21 Nov '22

21 Nov '22

Hi Gordon, I have just one spectrum per sample, all taken at different T (unknown, due to technical problems) and P (known). I'd like to find T and using an EoS is not a viable option. I was thinking that maybe, assuming that the Debye-Waller term is explained only by thermal disorder, the Debye temperature is P independent, and there are no structural or electronic transformations, I could retrieve T by fitting the Debye-Waller term and using the reference spectra. Is this possible? Best regards Gabriele > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 21 Nov 2022 16:16:50 +0100 > From: Gabriele GAROFALO <gabriele.garofalo(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] XANES temperature estimation > Message-ID: <0ce690cc-ca47-5507-76b3-848bba8d7db8(a)esrf.fr> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi everyone, > > I'd like to estimate the temperature of some samples from some XANES > spectra, is there a way to do that? I couldn't find an answer in the > mailing list archive. > > Thanks! > > > > ------------------------------ > > Message: 2 > Date: Mon, 21 Nov 2022 10:23:10 -0500 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XANES temperature estimation > Message-ID: <B288F5DB-33C3-4F6C-A4A3-D41D713157B1(a)stonybrook.edu> > Content-Type: text/plain; charset=utf-8 > > Only evaporation temperature, when XANES spectrum disappears?:) > > Anatoly > >> On Nov 21, 2022, at 10:20 AM, Gabriele GAROFALO >> <gabriele.garofalo(a)esrf.fr> wrote: >> >> ?Hi everyone, >> >> I'd like to estimate the temperature of some samples from some XANES >> spectra, is there a way to do that? I couldn't find an answer in the >> mailing list archive. >> >> Thanks! >> >> _______________________________________________ >> 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 > > > > ------------------------------ > > Message: 3 > Date: Mon, 21 Nov 2022 09:13:19 -0800 > From: Robert Gordon <ragordon(a)alumni.sfu.ca> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XANES temperature estimation > Message-ID: > <CA+FiM0EvUpbWH2=WzqjKTRMwZsw2w-DSgJ-2J9XgAVAScbiSTg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Gabriele, > > To qualify Anatoly's cheerful, pre-morning coffee response, if your > samples > are part of a sequence of measurements > of a material whose XANES has been measured at different temperatures, > and > said XANES does have some changes > owing to changes in physical or electronic behavior with temperature > (i.e. > a phase transition), then you could estimate > where your samples fit within that determined behavior. > > Are you familiar with how temperature dependence manifests in a typical > XAFS measurement? > ...through the Debye-Waller term..the effects of which become less > pronounced at lower k... > > Temperature is more typically a controlled parameter during > measurements. > > So no, not really...unless there is a known behavior for comparison. > > -R.

2 1

XANES temperature estimation
by Gabriele GAROFALO 21 Nov '22

21 Nov '22

Hi everyone, I'd like to estimate the temperature of some samples from some XANES spectra, is there a way to do that? I couldn't find an answer in the mailing list archive. Thanks!

3 2

How to normalize tens of thousands of XAS data?
by 张驰 15 Nov '22

15 Nov '22

How to normalize tens of thousands of XAS data? I measured a series of the spectra of sample over time by in situ XAS, the results contained tens of thousands of sets of XAS data, and it was impossible to normalize each set of data individually.I would like to ask where to find the normalized source code of Athena, I can modify the code so I can use my computer to achieve a large number of processing.Thanks!

2 1

found some issues found in larch (read-in issues)
by Mangold, Stefan (IPS) 26 Oct '22

26 Oct '22

Dear All, dear Matt, all tests were done on Macs (one M1 & one Intel) with the latest version your software & latest OS. 1. Read-In of spec files works, but only one file at once. Even if multiple files are selected 2. If one tries to load text-files it is possible to load data form multiple files as long as you don’t try to load also the reference spectra. If you load the reference also the read-in stopps at the transmission/fluorescence spectrum of the second file selected. 3. Trouble, that I sometimes can’t unmount network volumes after reading from them, larch saved on local discs. MacOS claims that python has files open; no other python program running 4. unable to save the data of one XAS-viewer while having two xas-viewer open. best regards Stefan Mangold

3 3

Xraylarch installation
by Dien.Li＠srnl.doe.gov 14 Oct '22

14 Oct '22

Dear Matt With help of our IT folk, we downloaded Larch for windows binary installer file and installed the xraylarch 9.65 on my computer, however, the LARCH subdirectory with the five application platforms (e.g., XAS viewer) were NOT generated automatically. We tried to uninstall and install three times, it is still the same, could you please suggest what we may do to correct this? Thank you so much. Dien Li Savannah River National Laboratory

1 0

[Larch] S02 value larger than 1
by dxfan＠post.kek.jp 04 Oct '22

04 Oct '22

Dear All, � I have a very common question, which is already asked many times: the S02 value is larger than 1. I measure the Sr K-edge EXAFS of SrTiO3 with temperature dependence. The S02 value is larger than 1. I check the book of “XAFS for everyone”, in which say maybe because of the distorted data or wrong structure model. I check the data measured by other beamline with the same sample, the S02 value still is larger than 1. I change the background reduction parameters, same result. I also modify the model, still same result. � I am very confused with these results. I attached the data, FEFF paths, and the fitting python Code the package. Can anyone help me check my fitting procedure. � Best regards, Fan

1 0

Co2P spectrum
by Christian Wittee Lopes 21 Sep '22

21 Sep '22

Dear XAFS community, Does anyone have a spectrum of Co2P sample or standard? Thank you in advance. Best, Christian Wittee Lopes -- Christian Wittee Lopes Visiting Researcher - ANP/FINEP - PRH 50.1 Institute of Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS) chriswittee(a)gmail.com LinkedIn <https://www.linkedin.com/in/christian-wittee-lopes-561855219/> | ORCID <https://orcid.org/my-orcid?orcid=0000-0001-8420-1958> | Lattes <http://lattes.cnpq.br/4953371870936050>

3 3

Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 12
by Dien.Li＠srnl.doe.gov 15 Sep '22

15 Sep '22

HI, Matt Attached please find the raw data in Athena, could you please also look at this as well as the Artemis file. Due to limited by L1,2 edge, the EXAFS data may just go up to K 9. Anyhow, thank you so much for your any directions. Dien Li -----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, September 15, 2022 2:09 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 12 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: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11 (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Sep 2022 18:04:42 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11 Message-ID: <DM8PR09MB6232238674FEDB80096B6498C4499(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Please see this attachment. Thank you so much. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, September 15, 2022 1:42 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11 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: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Sep 2022 17:41:19 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Message-ID: <DM8PR09MB6232C4DEDD6CCE2CF3984655C4499(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, Matt and EXAFS experts Thank you so much. Our sample is porous silica + PO4 ligand on surface/pore, then react with LaNO3 in solution. The model is that La is bonding with PO4 through both mono- (corner-sharing) and di-dentate (edge sharing) modes. Please see the attachment. The first three fits in history are fits with increasing paths, with fixed CN for the La-P11 and La-P14 path, the ss parameters are reasonable, but to fix CN at 3 for La-P14 is unreasonable, which requires La to bind with three different PO4 groups. The last three fits are fits with increasing paths, in which CN was fitted, the fitted parameters are reasonable, EXCEPT for the negative ss parameters for the path La-P11 (edge sharing) and La-P14 (corner sharing). By the way, the length for La-P14 is +0.3 A, it is large, but not completely unreasonable, because the bond distances of La-O polyhedron may change from 2.4 to 3.1 A. Is it possible to constrain ss parameter? If so, how to set up this constrain? Thank you so much for your further instruction. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, September 14, 2022 4:03 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch: Fitting error of the objective/model function (Matt Newville) 2. Re: Help for EXAFS fitting (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Sep 2022 13:28:38 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch: Fitting error of the objective/model function Message-ID: <CA+7ESbodGVSNHuzTHZoeb3iL-jUsWFpeYM7TqLQPkkSyMyE2DA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Fan, Sorry for the trouble. That seems like a strange error to me - I don't see why changing those expressions for E0s (even if they are "slightly complicated"!) should generate NaNs or Infinities. I don't think I've seen that happen with "feffit" fittings. Can you send me a Larch Session File with this fit in it? One suggestion is to place bounds (say +/- 20 eV) on those Parameters, say pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr', min=-20, max=20) But I'm not certain whether that would solve this problem. On Wed, Sep 14, 2022 at 7:53 AM <dxfan(a)post.kek.jp> wrote: > Dear All > > > > I am doing Temperature-dependent EXAFS experiment with a lot of data. > > > > Usually, we do these kinds of data fitting by several steps, like below: > > First, put every parameter free, and obtain the averaged value of amp. > > Second, set the amp to the averaged value, put other parameters free, and > then obtain the averaged value of del_e0. > > Third, set the amp and del_e0 to the averaged value, and fit again. > > > > In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). > > To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as > suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 > (1995): 151-153. > > The fitting parameters of Cubic model is this: > > setattr(pars, f'alpha', param(0, vary=True)) > > setattr(pars, f'amp', param(0, vary=True)) > > setattr(pars, f'del_e0_O', param(0, vary=True)) > > setattr(pars, f'del_e0_Sr', param(0, vary=True)) > > setattr(pars, f'del_e0_Ti', param(0, vary=True)) > > setattr(pars, f'sig2_O', param(.002, vary=True)) > > setattr(pars, f'sig2_Sr', param(.002, vary=True)) > > setattr(pars, f'sig2_Ti', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr1', param(.002, vary=True)) > > setattr(pars, f'sig2_p', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr2', param(.002, vary=True)) > > > > #del_e0 for each path > > pars.del_e0_1=param(expr='del_e0_O') > > pars.del_e0_2=param(expr='del_e0_O') > > pars.del_e0_3=param(expr='del_e0_Sr') > > pars.del_e0_4=param(expr='del_e0_Ti') > > pars.del_e0_5=param(expr='del_e0_O') > > pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') > > pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') > > > > In the first step, the fitting is fine, I obtained the averaged amp. > > However, in the second step, when I set amp to the averaged value, Error > happens for ?some? of the data. > > When I use different averaged amp value, the data that happens error is > different. > > The error is: > > Traceback (most recent call last): > > File "STO16_C_2.py", line 250, in <module> > > out = feffit(pars, dset) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line > 557, in feffit > > result = fit.leastsq() > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 1689, in leastsq > > lsout = scipy_leastsq(self.__residual, variables, **lskws) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", > line 423, in leastsq > > retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 601, in __residual > > return _nan_policy(np.asarray(out).ravel(), > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 2436, in _nan_policy > > raise ValueError(msg) > > ValueError: NaN values detected in your input data or the output of your > objective/model function - fitting algorithms cannot handle this! Please > read > https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-w… > for more information. > > > > I don?t know what happened, can somebody help me figure this out? > > > > PS: when I use only one del_e0 for every path, no such error happens. > > > > Best regards > > Fan > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11
by Dien.Li＠srnl.doe.gov 15 Sep '22

15 Sep '22

Please see this attachment. Thank you so much. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, September 15, 2022 1:42 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11 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: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Sep 2022 17:41:19 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Message-ID: <DM8PR09MB6232C4DEDD6CCE2CF3984655C4499(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, Matt and EXAFS experts Thank you so much. Our sample is porous silica + PO4 ligand on surface/pore, then react with LaNO3 in solution. The model is that La is bonding with PO4 through both mono- (corner-sharing) and di-dentate (edge sharing) modes. Please see the attachment. The first three fits in history are fits with increasing paths, with fixed CN for the La-P11 and La-P14 path, the ss parameters are reasonable, but to fix CN at 3 for La-P14 is unreasonable, which requires La to bind with three different PO4 groups. The last three fits are fits with increasing paths, in which CN was fitted, the fitted parameters are reasonable, EXCEPT for the negative ss parameters for the path La-P11 (edge sharing) and La-P14 (corner sharing). By the way, the length for La-P14 is +0.3 A, it is large, but not completely unreasonable, because the bond distances of La-O polyhedron may change from 2.4 to 3.1 A. Is it possible to constrain ss parameter? If so, how to set up this constrain? Thank you so much for your further instruction. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, September 14, 2022 4:03 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch: Fitting error of the objective/model function (Matt Newville) 2. Re: Help for EXAFS fitting (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Sep 2022 13:28:38 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch: Fitting error of the objective/model function Message-ID: <CA+7ESbodGVSNHuzTHZoeb3iL-jUsWFpeYM7TqLQPkkSyMyE2DA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Fan, Sorry for the trouble. That seems like a strange error to me - I don't see why changing those expressions for E0s (even if they are "slightly complicated"!) should generate NaNs or Infinities. I don't think I've seen that happen with "feffit" fittings. Can you send me a Larch Session File with this fit in it? One suggestion is to place bounds (say +/- 20 eV) on those Parameters, say pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr', min=-20, max=20) But I'm not certain whether that would solve this problem. On Wed, Sep 14, 2022 at 7:53 AM <dxfan(a)post.kek.jp> wrote: > Dear All > > > > I am doing Temperature-dependent EXAFS experiment with a lot of data. > > > > Usually, we do these kinds of data fitting by several steps, like below: > > First, put every parameter free, and obtain the averaged value of amp. > > Second, set the amp to the averaged value, put other parameters free, and > then obtain the averaged value of del_e0. > > Third, set the amp and del_e0 to the averaged value, and fit again. > > > > In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). > > To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as > suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 > (1995): 151-153. > > The fitting parameters of Cubic model is this: > > setattr(pars, f'alpha', param(0, vary=True)) > > setattr(pars, f'amp', param(0, vary=True)) > > setattr(pars, f'del_e0_O', param(0, vary=True)) > > setattr(pars, f'del_e0_Sr', param(0, vary=True)) > > setattr(pars, f'del_e0_Ti', param(0, vary=True)) > > setattr(pars, f'sig2_O', param(.002, vary=True)) > > setattr(pars, f'sig2_Sr', param(.002, vary=True)) > > setattr(pars, f'sig2_Ti', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr1', param(.002, vary=True)) > > setattr(pars, f'sig2_p', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr2', param(.002, vary=True)) > > > > #del_e0 for each path > > pars.del_e0_1=param(expr='del_e0_O') > > pars.del_e0_2=param(expr='del_e0_O') > > pars.del_e0_3=param(expr='del_e0_Sr') > > pars.del_e0_4=param(expr='del_e0_Ti') > > pars.del_e0_5=param(expr='del_e0_O') > > pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') > > pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') > > > > In the first step, the fitting is fine, I obtained the averaged amp. > > However, in the second step, when I set amp to the averaged value, Error > happens for ?some? of the data. > > When I use different averaged amp value, the data that happens error is > different. > > The error is: > > Traceback (most recent call last): > > File "STO16_C_2.py", line 250, in <module> > > out = feffit(pars, dset) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line > 557, in feffit > > result = fit.leastsq() > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 1689, in leastsq > > lsout = scipy_leastsq(self.__residual, variables, **lskws) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", > line 423, in leastsq > > retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 601, in __residual > > return _nan_policy(np.asarray(out).ravel(), > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 2436, in _nan_policy > > raise ValueError(msg) > > ValueError: NaN values detected in your input data or the output of your > objective/model function - fitting algorithms cannot handle this! Please > read > https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-w… > for more information. > > > > I don?t know what happened, can somebody help me figure this out? > > > > PS: when I use only one del_e0 for every path, no such error happens. > > > > Best regards > > Fan > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

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

15 Sep '22

Hi, Matt and EXAFS experts Thank you so much. Our sample is porous silica + PO4 ligand on surface/pore, then react with LaNO3 in solution. The model is that La is bonding with PO4 through both mono- (corner-sharing) and di-dentate (edge sharing) modes. Please see the attachment. The first three fits in history are fits with increasing paths, with fixed CN for the La-P11 and La-P14 path, the ss parameters are reasonable, but to fix CN at 3 for La-P14 is unreasonable, which requires La to bind with three different PO4 groups. The last three fits are fits with increasing paths, in which CN was fitted, the fitted parameters are reasonable, EXCEPT for the negative ss parameters for the path La-P11 (edge sharing) and La-P14 (corner sharing). By the way, the length for La-P14 is +0.3 A, it is large, but not completely unreasonable, because the bond distances of La-O polyhedron may change from 2.4 to 3.1 A. Is it possible to constrain ss parameter? If so, how to set up this constrain? Thank you so much for your further instruction. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, September 14, 2022 4:03 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch: Fitting error of the objective/model function (Matt Newville) 2. Re: Help for EXAFS fitting (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Sep 2022 13:28:38 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch: Fitting error of the objective/model function Message-ID: <CA+7ESbodGVSNHuzTHZoeb3iL-jUsWFpeYM7TqLQPkkSyMyE2DA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Fan, Sorry for the trouble. That seems like a strange error to me - I don't see why changing those expressions for E0s (even if they are "slightly complicated"!) should generate NaNs or Infinities. I don't think I've seen that happen with "feffit" fittings. Can you send me a Larch Session File with this fit in it? One suggestion is to place bounds (say +/- 20 eV) on those Parameters, say pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr', min=-20, max=20) But I'm not certain whether that would solve this problem. On Wed, Sep 14, 2022 at 7:53 AM <dxfan(a)post.kek.jp> wrote: > Dear All > > > > I am doing Temperature-dependent EXAFS experiment with a lot of data. > > > > Usually, we do these kinds of data fitting by several steps, like below: > > First, put every parameter free, and obtain the averaged value of amp. > > Second, set the amp to the averaged value, put other parameters free, and > then obtain the averaged value of del_e0. > > Third, set the amp and del_e0 to the averaged value, and fit again. > > > > In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). > > To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as > suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 > (1995): 151-153. > > The fitting parameters of Cubic model is this: > > setattr(pars, f'alpha', param(0, vary=True)) > > setattr(pars, f'amp', param(0, vary=True)) > > setattr(pars, f'del_e0_O', param(0, vary=True)) > > setattr(pars, f'del_e0_Sr', param(0, vary=True)) > > setattr(pars, f'del_e0_Ti', param(0, vary=True)) > > setattr(pars, f'sig2_O', param(.002, vary=True)) > > setattr(pars, f'sig2_Sr', param(.002, vary=True)) > > setattr(pars, f'sig2_Ti', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr1', param(.002, vary=True)) > > setattr(pars, f'sig2_p', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr2', param(.002, vary=True)) > > > > #del_e0 for each path > > pars.del_e0_1=param(expr='del_e0_O') > > pars.del_e0_2=param(expr='del_e0_O') > > pars.del_e0_3=param(expr='del_e0_Sr') > > pars.del_e0_4=param(expr='del_e0_Ti') > > pars.del_e0_5=param(expr='del_e0_O') > > pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') > > pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') > > > > In the first step, the fitting is fine, I obtained the averaged amp. > > However, in the second step, when I set amp to the averaged value, Error > happens for ?some? of the data. > > When I use different averaged amp value, the data that happens error is > different. > > The error is: > > Traceback (most recent call last): > > File "STO16_C_2.py", line 250, in <module> > > out = feffit(pars, dset) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line > 557, in feffit > > result = fit.leastsq() > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 1689, in leastsq > > lsout = scipy_leastsq(self.__residual, variables, **lskws) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", > line 423, in leastsq > > retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 601, in __residual > > return _nan_policy(np.asarray(out).ravel(), > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 2436, in _nan_policy > > raise ValueError(msg) > > ValueError: NaN values detected in your input data or the output of your > objective/model function - fitting algorithms cannot handle this! Please > read > https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-w… > for more information. > > > > I don?t know what happened, can somebody help me figure this out? > > > > PS: when I use only one del_e0 for every path, no such error happens. > > > > Best regards > > Fan > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

Help for EXAFS fitting
by Dien.Li＠srnl.doe.gov 14 Sep '22

14 Sep '22

Hi, Matt and Carlo and other EXAFS experts Attached please find a fpj data file. The basic system is silica + PO4 ligand on surfaces, which was used for adsorption of La. We collected La L3-edge EAXFS data and did this fitting. I used two models of La binding as monodentate and bidentate. I saw the negative ss parameter. I saw this in some of my other EXAFS data fitting samples as well. I have two questions for help: 1. What might cause the negative ss parameters and how I may improve this, is this caused by incorrect structure models 2. If we can do some "stress" test to make sure the fitting is valid and meaningful. Please you can help look at and play this data set and direct me on how to do this correctly, thank you so much. Dien Li Savannah River National Laboratory

2 1

Larch: Fitting error of the objective/model function
by dxfan＠post.kek.jp 14 Sep '22

14 Sep '22

Dear All I am doing Temperature-dependent EXAFS experiment with a lot of data. Usually, we do these kinds of data fitting by several steps, like below: First, put every parameter free, and obtain the averaged value of amp. Second, set the amp to the averaged value, put other parameters free, and then obtain the averaged value of del_e0. Third, set the amp and del_e0 to the averaged value, and fit again. In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 (1995): 151-153. The fitting parameters of Cubic model is this: setattr(pars, f'alpha', param(0, vary=True)) setattr(pars, f'amp', param(0, vary=True)) setattr(pars, f'del_e0_O', param(0, vary=True)) setattr(pars, f'del_e0_Sr', param(0, vary=True)) setattr(pars, f'del_e0_Ti', param(0, vary=True)) setattr(pars, f'sig2_O', param(.002, vary=True)) setattr(pars, f'sig2_Sr', param(.002, vary=True)) setattr(pars, f'sig2_Ti', param(.002, vary=True)) setattr(pars, f'sig2_Tr1', param(.002, vary=True)) setattr(pars, f'sig2_p', param(.002, vary=True)) setattr(pars, f'sig2_Tr2', param(.002, vary=True)) #del_e0 for each path pars.del_e0_1=param(expr='del_e0_O') pars.del_e0_2=param(expr='del_e0_O') pars.del_e0_3=param(expr='del_e0_Sr') pars.del_e0_4=param(expr='del_e0_Ti') pars.del_e0_5=param(expr='del_e0_O') pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') In the first step, the fitting is fine, I obtained the averaged amp. However, in the second step, when I set amp to the averaged value, Error happens for "some" of the data. When I use different averaged amp value, the data that happens error is different. The error is: Traceback (most recent call last): File "STO16_C_2.py", line 250, in <module> out = feffit(pars, dset) File "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line 557, in feffit result = fit.leastsq() File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 1689, in leastsq lsout = scipy_leastsq(self.__residual, variables, **lskws) File "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", line 423, in leastsq retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 601, in __residual return _nan_policy(np.asarray(out).ravel(), File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 2436, in _nan_policy raise ValueError(msg) ValueError: NaN values detected in your input data or the output of your objective/model function - fitting algorithms cannot handle this! Please read https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-wh at-can-i-do for more information. I don't know what happened, can somebody help me figure this out? PS: when I use only one del_e0 for every path, no such error happens. Best regards Fan

2 1

FW: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 3
by Dien.Li＠srnl.doe.gov 13 Sep '22

13 Sep '22

Hi Matt and all I sent this and an attachment before. I hope you can help figure out why I often get negative ss parameter from fitting? For this specific example, if I fit the CN, it yields CN of ~1, the monodendate structure is reasonable, but I got negative ss. However, if I fixed CN at 3, the ss is reasonable, but it needs to bind with three different PO4 on the surfaces, this is interesting but I am uncertain. Thank you so much for your any advice. Dien Li Savannah River National Laboratory -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Friday, September 9, 2022 12:32 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 3 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Help for EXAFS fitting (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 9 Sep 2022 16:31:38 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help for EXAFS fitting Message-ID: <DM8PR09MB62323624C91F0A43DC7CB6D1C4439(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, Matt and Carlo and other EXAFS experts Attached please find a fpj data file. The basic system is silica + PO4 ligand on surfaces, which was used for adsorption of La. We collected La L3-edge EAXFS data and did this fitting. I used two models of La binding as monodentate and bidentate. I saw the negative ss parameter. I saw this in some of my other EXAFS data fitting samples as well. I have two questions for help: 1. What might cause the negative ss parameters and how I may improve this, is this caused by incorrect structure models 2. If we can do some "stress" test to make sure the fitting is valid and meaningful. Please you can help look at and play this data set and direct me on how to do this correctly, thank you so much. Dien Li Savannah River National Laboratory

1 0

Fitting multiple spectra simultaneously with Larch
by Van Stappen, Casey M 12 Sep '22

12 Sep '22

Dear Ifeffit team, I’d like to fit multiple EXAFS spectra simultaneously in Larch using several common parameters/relative restraints, but have not found a way to do so (yet). I’ve gone through Dr. Matt Newville’s youtube tutorials (generally very helpful), but this topic doesn’t seem to have been covered. Any suggestions? Thanks! Best, Casey Van Stappen ------------------------------------------------------------------------ Dr. Casey Van Stappen University of Texas at Austin Robert A. Welch Hall, 4.318 2350 Speedway Austin, TX 78705 USA Phone: +1 (512) 775-2658 E-mail: casey.vanstappen(a)austin.utexas.edu

3 2

Icon Resolution issue in 14 inch
by Mohamad Numan 11 Sep '22

11 Sep '22

Dear Developers, I am using the Demeter package on my windows 11 laptop. I am facing some resolution issues in the icons of Athena and Artemis. The icons look pretty dull and very distressing to the eyes. Attaching a screenshot for your reference. I will be happy to hear an update from you. Thanks & Regards Mohamad Numan Ph.D. Student, IACS

2 1

Virtual SSRL Summer School on Synchrotron X-Ray Absorption Spectroscopy and Imaging Oct 25-28, 2022
by Ritimukta Sarangi 06 Sep '22

06 Sep '22

Hello EXAFS enthusiasts, We are hosting the SSRL "not quite summer" summer school at the end of October this year (Oct 25-28). We wanted to include real experiments and deferred the school to the start of operations at SSRL. The event is virtual and all information (including registration details) can be found at: https://conf.slac.stanford.edu/exafs-2022/ We recognize that there are several really good online resources for learning about EXAFS and it has proved to be quite beneficial to the new and experienced learners alike. We have changed our summer school format to include additional teaching modules that can help participants learn aspects of EXAFS data analysis that are beyond what we have typically taught in the past. These new modules are especially helpful to the novice user and include: 1) Opportunity to write a 1 to 1.5 page proposal to compete for experimental time during the school. 2) A complete 1-day remote data measurement and hands-on demonstration of beamline optimization and experiment setup during the live session. 3) Insights into becoming a user at SSRL, proposal writing and its review process with examples of past successful proposals. Looking forward to seeing some of you at the school. Best Regards, Riti Sarangi

1 0

XAFS fitting in xas_viewer and reset of customized variables after save & load cycle
by juejing.liu＠gmail.com 04 Sep '22

04 Sep '22

Hi all, I am using xas_viewer, version 0.9.65, to fit some XAFS data. In a typical situation I will also fit the coordination numbers of atoms by add customized variables in the amplitude boxes (image below). It works fine during my fitting. However, when I save my result as a larch session and load it later, all my customized parameters are disappeared, and the amplitude boxes are reset. Therefore, I need to refill all the variables after each save & load cycle. This becomes increasingly tedious when dealing with about 20 different paths. Is there any workaround of this problem? Best, Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304

3 2

Simultaneous multispectral fitting in Larch?
by Van Stappen, Casey M 30 Aug '22

30 Aug '22

To whom it concerns, I wanted to inquire regarding how best to perform multispectral fitting (i.e. fitting several EXAFS spectra simultaneously with shared parameters) in Larch? This was something that could be done with (relative) ease in Artemis, but I was hoping to perform this at a larger scale (6 spectra, >10 restrictions) in Larch. I’ve hunted through Dr. Newville’s excellent Youtube tutorials, but didn’t find this specific information. Thank you for your help! Best, Casey Van Stappen ------------------------------------------------------------------------ Dr. Casey Van Stappen University of Texas at Austin Robert A. Welch Hall, 4.318 2350 Speedway Austin, TX 78705 USA Phone: +1 (512) 775-2658 E-mail: casey.vanstappen(a)austin.utexas.edu

1 0

XAFS short course at BNL: November 2-4
by Anatoly Frenkel 29 Aug '22

29 Aug '22

Dear subscribers, This is a reminder about the annual XAFS short course at BNL. The dates are: November 2-4. It will be virtual. The level will be intermediate to advanced As in the past, lectures, discussions and software demonstration sessions will be on Wednesday and Thursday, and the full day data analysis practicum will be on Friday. The course agenda and the link to the application form are available at the BNL web site: https://www.bnl.gov/xafscourse/index.php and at the web site of the Synchrotron Catalysis Consortium: https://you.stonybrook.edu/scc2/xafs-workshops/ Registration deadline is September 11. Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

1 0

Question related to an example of EXAFS fitting using Larch
by Andy Zhang 29 Aug '22

29 Aug '22

Dear all, I am learning Larch and read the manual of Larch online. In the "13.8.10. Example 3: Fit 3 datasets with 1 Path" of the webpage https://xraypy.github.io/xraylarch/xafs_feffit.html#example-3-fit-3-dataset…, it shows an example that fitting Cu at different temperatures. Einstein model was used to simulate the sigma2, as shown in the figure below. [image: image.png] However, in some papers (eg. Radiation Physicsand Chemistry137 (2017) 93–98) that model EXAFS at elevated temperatures, they separates the total sigma2 to static and thermo components (Sigma^2 = Sigma_static^2 + Sigma_thermo^2), which is different from the above Larch example. I am a little confused about the utilization of Einstein model. I wonder if the Sigma2 obtained by Einstein model can reflect the total sigma2 or can only reflect the thermo part. Many thanks for your help! Best regards, Harry

2 1

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

28 Aug '22

Hi Matt, Here is the session file for the UO2 fitting. The screenshot blow shows what the customized variables look like right before saving this session. Please feel free to let me know if you need any extra information. Best, Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304

1 0

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

28 Aug '22

Hi Matt, Thanks for the quick response. I just noticed that the data in the screenshot is unpublished data so I may not be able to send you that one. But I will send you a typical UO2 fitting later today (in the larch session) so that you can look. Best, Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304

1 0

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

26 Aug '22

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

1 0

third cumulant in Larch
by Andy Zhang 19 Aug '22

19 Aug '22

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

2 2

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

18 Aug '22

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

1 0

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

18 Aug '22

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

2 2

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

09 Aug '22

Dear subscribers: Please spread the word to those who may be interested in our next annual short course at BNL on X-ray absorption fine structure. The dates are: November 2-4. It will be virtual. The level will be intermediate to advance (last year it was a beginner level). As in the past, lectures, discussions and software demonstration sessions will be on Wednesday and Thursday, and the full day data analysis practicum will be on Friday. More information about the course and the link to the application form will appear soon on BNL web site, and on the web site of the Synchrotron Catalysis Consortium (SCC). Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

1 1

Standardized Spectra
by Kyle Draim 08 Aug '22

08 Aug '22

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

4 3

xraylarch
by Paul Fons 06 Aug '22

06 Aug '22

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

2 1

VC and V(CO)6 data to share
by Ismael Graff 05 Aug '22

05 Aug '22

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

3 4

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

04 Aug '22

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

1 0

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

03 Aug '22

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

1 0

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

02 Aug '22

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

1 0

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

13 Jul '22

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

2 1

Literature question---FEFF-based wavelet
by Xinyu Luo 29 Jun '22

29 Jun '22

Hi everyone, I'm a graduate student interested in using wt-EXAFS to analyze LDH compounds. I've surfed the ESRF website, tried Continuous Cauchy and Morlet as mother wavelets, and am aware of their limitations. I'm inspired by previous work by Funke et al. [J. Synchrotron Radiat. 2007, 14 (5), 426–432.], that customizing the mother wavelet can strengthen the sensitivity to the path of interest. I have some questions as follows. 1)Can the FEFF-Morlet wavelet be manipulated through parameters like the Morlet or Cauchy wavelet to reach the desired Heisenberg box? 2)How to practically execute the as-mentioned four steps to construct the FEFF-Morlet wavelet? Could you suggest some software toolkit to start, perhaps Matlab? 3)I'm also curious about the 2D contour generated by FEFF-Morlet which didn't show up in the paper. Will the overview wt figure gain better general resolution simply by choosing an appropriate mother wavelet? Regards Xinyu

1 0

data plotting
by Ofierska Weronika Lucja 28 Jun '22

28 Jun '22

Dear all, I am a new user of Athena and encountered some issues with data plotting. While plotting the uXAS data for Fe K pre-edge the quality of plotting is somehow less sharp compared to the actual data I plotted using other graphical tool (see below) [cid:4465cab9-2ae8-49e7-8253-e54ac3d22bb7] vs what I get from Athena [cid:4db817c1-78d0-4ac8-b094-12d37d055466] As you can see the resolution of the pre-edge in Athena is so poor I cannot resolve the Fe2+/Fe3+ ratio as the peak for Fe3+ is not visible. (I plotted Bruce's data from lepidocrocite to see if it's a common problem and it seems that his data look much better than mine). During my time on synchrotron we actually spent a lot of time to resolve best resolution on the pre edge, so it's not a acquisition problem. Does anyone have any idea how to fix this? I am attaching the project file and txt file (plot FluoRT2 column) with the original data. Thank you for your help, Weronika Ofierska

5 4

new opening for high resolution X-ray spectroscopic studies of spent nuclear fuel
by Vitova, Tonya (INE) 15 Jun '22

15 Jun '22

Dear all, Please see this new job opportunity: https://www.pse.kit.edu/english/karriere/joboffer.php?id=155626 I hope that many of you will apply! Best regards, Tonya -----Ursprüngliche Nachricht----- Von: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Im Auftrag von ifeffit-request(a)millenia.cars.aps.anl.gov Gesendet: Dienstag, 31. Mai 2022 19:00 An: ifeffit(a)millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 231, Issue 22 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 0.9.61 and 60 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 31 May 2022 07:10:28 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch 0.9.61 and 60 Message-ID: <CA+7ESbpx-dFvXkNkL0EFXPPxsi8d3oO4vO3T3xTWeVKYNKXNzA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Kathy, Thanks and sorry for the trouble. I think I can reproduce this: changing the definitions of Path Parameters is being ignored. I have a theory of what is going wrong, but I'll have to investigate this a bit... On Tue, May 31, 2022 at 6:12 AM Kathy Dardenne <kathy.dardenne(a)kit.edu> wrote: > Hello, > > > > I was trying to use Larch 0.9.59 to fit EXAFS Data. There was no > possibility to save work in progress but it was possible to do fit, > change name of the variable used and define the expression for > amplitude (default defined as ?n*s02? in Larch where n is taken from the feff calculation). > > I have 6 slightly different Cf-O distances in my model structure and > took only one path, changing the amplitude definition ?1.0 * s02? by ?NO * s02? > . this worked perfectly. > > > > However in Larch 60 and 61 where, thanks a lot!!!, we can now save our > work, it is not possible any more to change anything in the path > parameter (neither name or expression). The added variable is not any > more varied and not taken into account. Independently of the amplitude > definition s02 get the same value as default definition and new > variables stay by start value having no influence on the fit. > > > > I join some screenshot as well ?Path parameters? and ?Fit script?. > Looking at the Path parameter I saw that the amplitude is still by > default definition so no wonder that it acts without taking into account changes. > This is the same for name changes. > > > > Am I the only one having trouble now? I worked till now with artemis, > ifeffit and previously feffit soI do not have a big experience with Larch. > The old feffit based versions stop all by Pu (Z=94) and I need Z=98 so > I changed to Larch but need to get used to. > > I am using Larch in anaconda3 on a Win10 Computer. > > > > Thanks a lot for your help. > > > > Kind regards > > > > Kathy > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

Larch 0.9.61 and 60
by Kathy Dardenne 31 May '22

31 May '22

Hello, I was trying to use Larch 0.9.59 to fit EXAFS Data. There was no possibility to save work in progress but it was possible to do fit, change name of the variable used and define the expression for amplitude (default defined as "n*s02" in Larch where n is taken from the feff calculation). I have 6 slightly different Cf-O distances in my model structure and took only one path, changing the amplitude definition "1.0 * s02" by "NO * s02" . this worked perfectly. However in Larch 60 and 61 where, thanks a lot!!!, we can now save our work, it is not possible any more to change anything in the path parameter (neither name or expression). The added variable is not any more varied and not taken into account. Independently of the amplitude definition s02 get the same value as default definition and new variables stay by start value having no influence on the fit. I join some screenshot as well "Path parameters" and "Fit script". Looking at the Path parameter I saw that the amplitude is still by default definition so no wonder that it acts without taking into account changes. This is the same for name changes. Am I the only one having trouble now? I worked till now with artemis, ifeffit and previously feffit soI do not have a big experience with Larch. The old feffit based versions stop all by Pu (Z=94) and I need Z=98 so I changed to Larch but need to get used to. I am using Larch in anaconda3 on a Win10 Computer. Thanks a lot for your help. Kind regards Kathy

2 1

PostDoc position at BM23/ID24 beamlines of ESRF
by Kirill LOMACHENKO 30 May '22

30 May '22

Dear all, we are looking for an outstanding postdoc to do research in chemistry at BM23 and ID24 XAS beamlines of the ESRF. The prioritized fields are catalysis and electrochemistry. We expect a postdoc to run their own research exploiting their collaboration network. The ideal candidate would be a link between our cutting-edge XAS facilities and leading academic groups in the field. More details and the Apply button are here: https://esrf.gestmax.eu/1592/1/post-doc-id24-bm23/en_US Thank you for spreading the news! All the best, Kirill Lomachenko -- 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

1 0

Larch 0.9.61
by Matt Newville 26 May '22

26 May '22

Hi Folks, It's only been a few days, but there were some fairly important bugs and misfeatures found with Larch 0.9.60. Rather than wait, these have mostly been fixed (details at https://github.com/xraypy/xraylarch/releases/tag/0.9.61) You can either update the code yourself with `pip install --upgrade xraylarch`, with the binary installer, or by allowing XAS Viewer to run its updater. Bug reports, comments, and suggestions are always welcome. --Matt

1 0

Larch 0.9.60
by Matt Newville 23 May '22

23 May '22

Hi Folks, Larch version 0.9.60 has been released. It should now be installed by default using all installation mechanisms, and you should see a notice to update, perhaps the next time you run XAS Viewer. There are several bug fixes and feature improvements in XAS Viewer. This version also adds some important new features to XAS Viewer and Larch. These are described in a bit more detail at https://github.com/xraypy/xraylarch/releases/tag/0.9.60 Briefly, the new features for XAS Viewer are: 1. Each data "Group" has a processing Journal, with a time-stamped history of processing events. This will document the main processing steps. 2. Many preferences for XAS Viewer can now be set program-wide and saved for future sessions. Copying processing parameters between groups now works better. 3. A Session or Project file can now be saved at any time. This will contain all the arrays for a Group and also include fitting models and per-group fit histories for Pre-edge Peaks, Linear-Combination analyses, Feff-fitting (including Feff Paths), and so on. These Session files can be read back in and fit models and histories are restored in XAS Viewer. That is, these files are intended to be suitable for exchanging by email and archiving, etc. Session files are also "auto-saved" periodically and can be used to recover the last session on startup. There are several changes here. I'm confident with the basic functionality and have been testing myself on all platforms. But GUI actions are hard to test thoroughly, so it is reasonable to expect some new bugs or misfeatures. With upcoming workshops in July, I expect to need a release focused on bug and feature fixes in about a month. So, I hope you will be able to test and make any suggestions, comments, or error reports. Cheers, --Matt PS: For Python users, all of Python 3.7, 3.8, 3.9, and 3.10 should work, though the main installers are still using either Python 3.8 or Python 3.9.

1 0

Simulated XANES spectra does not match with experimental spectra in the white line region
by Monica Bairagi 23 May '22

23 May '22

Dear IFEFFIT members, Using FEFF10, I am simulating XANES spectra of copper complexes in which aspartic and glutamic acid are primary ligands. The experimental XANES spectra show a broadened peak with two weak humps, in the white line as shown in the accompanying figure. In the simulated spectra I am not getting a broadened white line, it shows a peak-like structure. My question is whether FEFF10 can show in the simulated spectra a broadened white line. As is known the white line structure is due to molecular orbital of 4p orbitals. Does FEFF10 takes into account of the molecular orbital also, if so, then why I am not able to reproduce the white line structure as is obtained in the experimental spectra. Please find attached screenshots of Experimental and theoretical spectra of copper complex (in which asp is ligand). Kind regards. Monica Bairagi, Ph.D. Student, India.

1 0

Save and load XAFS fittings in xas_viewer, Larch
by Liu, Juejing 21 May '22

21 May '22

Hi all, I have another quick question about saving & loading Feff fittings. Let's say I have a good Feff fitting for my XAFS spectrum. How to save my fitting project for the future refinement? I checked the xas_viewer document in the Larch site. It only mentioned how to save a pre-edge peak fitting, and there is no content about saving and loading about Feff fittings. The file bottom at the tool bar of the Feffit Result window seems saves everything (e.g., paths used, fitting parameters, and even fitting plots). But there is no "load" bottom at that window, therefore the saved fittings are not recoverable. Best, Juejing Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304 [cid:image001.png@01D86D1D.2A250CE0]

1 0

Re: [Ifeffit] Using Larch to analyze uranium compounds
by juejing.liu＠gmail.com 21 May '22

21 May '22

Hi All, Thank you for the information. I double-checked my Feff calculation and noticed that I did not change the uranium edge from K (default, but not reasonable for uranium) to L3 (what I used in experiment). After using the correct uranium edge to run the Feff calculation, the fitting result looks good. I previously used Artemis. The Feff function in this software would automatically pick the common edge for the absorbing elements (in my case, L3-edge for uranium or thorium). That makes me ignore the edge box in Larch. Best, Juejing -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Saturday, May 21, 2022 12:26 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 231, Issue 14 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: Using Larch to analyze uranium compounds (John J Rehr) ---------------------------------------------------------------------- Message: 1 Date: Sat, 21 May 2022 12:25:21 -0700 From: John J Rehr <jjr(a)uw.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Using Larch to analyze uranium compounds Message-ID: <CAMw-=E-W8=7eksBMTkFkftn_8fbLo=RSPpPLBR11r5J0sO+PZw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Juejing, It also wasn't clear to me which edge you were measuring, but U XAFS are interesting. The large size of Uranium atoms typically improves convergence of XAFSs calculations, so FEFF calculations often work well for L-edge XAFS spectra with 17 keV x-rays. On the other hand, K-edge XAFS of U compounds is often not useful due to the large core-hole broadening of U which limits the XAFS to short near neighbor distances, and the large > 100 keV K-edge energy is not available at many synchrotron sources. I'll be interested to hear what source you used to measure the XAFS. Thanks. With best wishes, John On Sat, May 21, 2022 at 10:13 AM Matt Newville <newville(a)cars.uchicago.edu> wrote: > Hi Juejing, > > Sorry for the trouble. It's hard to guess from the screenshots alone - > if only we had a Project file you could send (soon, soon). > > One thing I see is it looks like the Feff calculation you're using was > done at the U K-edge. Is that correct? Is the data U K-edge too? > > I don't know if that would completely explain the difference, and > Mike's suggestion of looking at the coordination number is a good idea. > > XAS Viewer writes a "feffit script" in your user folder > (C:\Users\jiuju\larch\xas_viewer\feffit_script.lar). Compared to the > GUI form, that's a little bit cryptic and formal, but it is also what > the program is really doing. If the suggestions above don't help > clarify the problem, can you post that? > > > > On Fri, May 20, 2022 at 7:35 PM <juejing.liu(a)gmail.com> wrote: > >> Hi, >> >> >> >> I am recently trying to use Larch to fit XAS spectra of uranium >> compounds (e.g., UO2, using an existing CIF file). I did not achieve >> a good fit and the amplitude of the model is way lower than the data. >> Then I tried to plot the uranium oxygen 1st path with all 8 atoms a >> sigma2=0.001 by using the plot model function. The resulting >> scattering peak is still far lower than it should be (images below). Did I do something strange with the program? >> >> >> >> The Larch version I used was 0.9.59. I can send the cif file and the >> UO2 data I used if necessary. >> >> >> >> Best, >> >> >> >> Juejing >> >> >> >> >> >> >> >> >> >> *Juejing Liu* >> >> Guo Group >> >> Materials Science and Engineering program >> >> Alexandra Navrotsky Institute for Experimental Thermodynamics >> >> Washington State University >> Pullman, WA 99164-4630 >> Office: Fulmer Hall, Room 630 >> Phone: 208-206-7304 >> >> >> >> >> _______________________________________________ >> 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 > _______________________________________________ > 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 >

1 0

Using Larch to analyze uranium compounds
by juejing.liu＠gmail.com 21 May '22

21 May '22

Hi, I am recently trying to use Larch to fit XAS spectra of uranium compounds (e.g., UO2, using an existing CIF file). I did not achieve a good fit and the amplitude of the model is way lower than the data. Then I tried to plot the uranium oxygen 1st path with all 8 atoms a sigma2=0.001 by using the plot model function. The resulting scattering peak is still far lower than it should be (images below). Did I do something strange with the program? The Larch version I used was 0.9.59. I can send the cif file and the UO2 data I used if necessary. Best, Juejing Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304

4 3

Error Larch installation
by Christian Wittee Lopes 17 May '22

17 May '22

Dear Matt and members of the XAFS community. I'm trying to install Larch and after the installation process, I'm not able to run the program. It doesn't open. I am trying the Binary Installer File for Windows (64 bit). The error I get when running Larch GUI can be seen in the attachment. Am I doing something wrong? [image: image.png] Thank you in advance. Christian Wittee -- Christian Wittee Lopes Visiting Researcher - ANP/FINEP - PRH 50.1 Institute of Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS) chriswittee(a)gmail.com LinkedIn <https://www.linkedin.com/in/christian-wittee-lopes-561855219/> | ORCID <https://orcid.org/my-orcid?orcid=0000-0001-8420-1958> | Lattes <http://lattes.cnpq.br/4953371870936050>

2 3

structure for reference Mn foil
by Hu, Yang (HIU) 17 May '22

17 May '22

Dear IFEFFIT members, I have been trying to obtain the S02 value from metal reference foils measured at the beamline. However, I constantly got a very low S02 value, such as 0.2 or 0.3 using Mn alpha or gamma cif file (first shell of 12 Mn). Only Mn-beta (4 subshell * 3 Mn) could give a S02 in the range 0.8 ~ 1, depending on whether I constrained sigam2 for all the 12 Mn or whether I fixed the CN for each subshell. But the uncertainty is very high. I also fitted the MnO measured together leaving S02 variable, and it resulted in a S02 close to 1. So I am guessing I didn't use the correct structure file for Mn foil . I appreciate if someone could help on this! Best regards, Yang Hu

3 4

1. structure for reference Mn foil (Hu, Yang (HIU))
by Pierre Lecante 13 May '22

13 May '22

Dear Yang Hu, Your experience rings à bell in my mind: several times we got weird data from Co and Fe NPs, with S02 close to 0.2, much smaller than expected for a simple size effect. The point is that PDF studies were consistent with the so called Co Epsilon structure... based on the Mn beta phase, very disordered. By the way, I'd be very interested to check hypothesis on my side : I'd be very glad if you could provide me à data set. Sincerely, Pierre Lecante Le 13 mai 2022 19:00:01 GMT+02:00, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : >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. structure for reference Mn foil (Hu, Yang (HIU)) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 12 May 2022 18:29:19 +0000 >From: "Hu, Yang (HIU)" <yang.hu(a)kit.edu> >To: "Ifeffit(a)millenia.cars.aps.anl.gov" > <Ifeffit(a)millenia.cars.aps.anl.gov> >Subject: [Ifeffit] structure for reference Mn foil >Message-ID: <999901d0ad3743f59182feca823a08bd(a)kit.edu> >Content-Type: text/plain; charset="us-ascii" > >Dear IFEFFIT members, > > > >I have been trying to obtain the S02 value from metal reference foils >measured at the beamline. > > > >However, I constantly got a very low S02 value, such as 0.2 or 0.3 using Mn >alpha or gamma cif file (first shell of 12 Mn). Only Mn-beta (4 subshell * 3 >Mn) could give a S02 in the range 0.8 ~ 1, depending on whether I >constrained sigam2 for all the 12 Mn or whether I fixed the CN for each >subshell. But the uncertainty is very high. > > > >I also fitted the MnO measured together leaving S02 variable, and it >resulted in a S02 close to 1. So I am guessing I didn't use the correct >structure file for Mn foil . > > > >I appreciate if someone could help on this! > > > >Best regards, > >Yang Hu > > > > > >

1 0

Larch 0.9.59, problems with PCA
by Mangold, Stefan (IPS) 10 May '22

10 May '22

Dear all, on 2 computers (Mac, Intel and ARM, newest version operating system) the PCA does not work. If I press "Build Model with selected groups“ on both computers and several different datasets, I only get „training model“ and nothing else happens. Absolutely nothing else changes within this tab inside XAS viewer. Best regards Stefan Mangold

2 1

Question about an EXAFS analysis of C60-Cu/SiO2
by 王茂林 05 May '22

05 May '22

Dear IFEFFIT members, Recently I have read a paper <ambient-pressure synthesis of ethylene glycol catalyzed by C60-buffered Cu/SiO2> (https://www.science.org/doi/10.1126/science.abm9257) I have a question about the EXAFS analysis: the wavelet transform of C60-Cu/SiO2 (Figure S15B) has 2 peaks at (k, R) = (1.4, 2.2) and (3.8, 1.5), the author assigned them to Cu-C and Cu-O, respectively. And they think Cu-C is derived from d-\pi interactions between Cu and C60. However, Cu-C and Cu-O paths can hardly be separated since the f(k) and \phi(k) are nearly identical for C and O. Besides, the Cu-C distance is ~2 angstrom (according to the ref. 30: S.-Z. Zhan et al., J. Am. Chem. Soc. 2020, 142, 5943-5947.), why it can have a peak at R = 2.2 angstrom? (with Cu-O R = 1.5 angstrom) Thanks you advance for you time! Best regards, Maolin Wang

1 0

2022 APS/IIT XAFS Summer School
by Matt Newville 24 Apr '22

24 Apr '22

Hi Folks, The APS/IIT XAFS Summer School will be July 24-29, 2022 at the Illinois Institute of Technology. The school will be in-person but limited to 40 students due to continuing concerns about COVID. See the attached flyer for details. For even more information, and to apply, please email bunker(a)iit.edu with the subject line “2022 XAFS School”. --Matt Newville

1 0

XAFS 2022 reminders
by Matt Newville 21 Apr '22

21 Apr '22

Hi Folks, Another reminder for XAFS 2022: The abstract deadline has been extended to Monday, April 25th, but with a deadline of midnight Sydney time: https://xafs2022.org And, nominations for the IXAS awards are due May 1: https://xrayabsorption.org/ixas-awards-2022/ Cheers, --Matt

1 0

a Windows GUI for wavelet transformation of EXAFS
by Peng Liu 11 Apr '22

11 Apr '22

Dear XAS community, I would like to share a Windows GUI for wavelet transformation of EXAFS. It is written in Python by my student Zhihang Ye. There are also other applications developed by different groups. This one may be more user-friendly. The GUI, instructions, code, references, and other related information are in GITHUB. https://github.com/Himmelspol/wtEXAFS If you find any problems or have any suggestions, please let us know. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 230, Issue 6
by Vitova, Tonya (INE) 08 Apr '22

08 Apr '22

Dear XAS/XES community, I would like to share with you our new opening for a postdoc/scientist with strong background in synchrotron radiation instrumentation, XAS/XES spectroscopy and ideally with experience in developing and building XES spectrometers. https://www.pse.kit.edu/karriere/joboffer.php?id=61306&new=true&language=de The description is only in German. In case you have questions, please do not hesitate to write me: Tonya.Vitova(a)kit.edu Best regards, Tonya -----Ursprüngliche Nachricht----- Von: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Im Auftrag von ifeffit-request(a)millenia.cars.aps.anl.gov Gesendet: Donnerstag, 7. April 2022 07:53 An: ifeffit(a)millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 230, 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. PhD at LPG, IMN in Nantes and SOLEIL Synchrotron (morizet-y) ---------------------------------------------------------------------- Message: 1 Date: Thu, 7 Apr 2022 07:53:05 +0200 From: morizet-y <yann.morizet(a)univ-nantes.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Cc: TRCERA Nicolas <nicolas.trcera(a)synchrotron-soleil.fr>, Michael Paris <Michael.Paris(a)cnrs-imn.fr> Subject: [Ifeffit] PhD at LPG, IMN in Nantes and SOLEIL Synchrotron Message-ID: <d04b284c-2517-9b28-5c7b-c683c3a9ff98(a)univ-nantes.fr> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear all, Please find attached a PhD position to be circulated and starting in october 2022. The PhD involves the LPG and IMN laboratories in Nantes as well as the SOLEIL Synchrotron near Paris. Best regards, Yann Morizet -- ___________________________________________ Dr Yann Morizet Ma?tre de Conf?rence Laboratoire de Plan?tologie et G?osciences Nantes (LPG) UMR-CNRS 6112 Universit? de Nantes 2 rue de la Houssini?re 44322 Nantes Cedex (FRANCE) t?l: +33 (0) 2 5112 5491 fax: +33 (0) 2 5112 5268 ___________________________________________

1 0

PhD at LPG, IMN in Nantes and SOLEIL Synchrotron
by morizet-y 07 Apr '22

07 Apr '22

Dear all, Please find attached a PhD position to be circulated and starting in october 2022. The PhD involves the LPG and IMN laboratories in Nantes as well as the SOLEIL Synchrotron near Paris. Best regards, Yann Morizet -- ___________________________________________ Dr Yann Morizet Maître de Conférence Laboratoire de Planétologie et Géosciences Nantes (LPG) UMR-CNRS 6112 Université de Nantes 2 rue de la Houssinière 44322 Nantes Cedex (FRANCE) tél: +33 (0) 2 5112 5491 fax: +33 (0) 2 5112 5268 ___________________________________________

1 0

Path output with feff8l
by 西村真一 04 Apr '22

04 Apr '22

Dear all, I have used Larch ver 0.9.59/0.9.58 on Linux for XAFS data processing and analysis. The scripting features are pretty helpful in our study. In the EXAFS analysis, I met a strange behavior of a function. The feff8l function does not generate the "feffNNNN.dat" files like Feff6l. This behavior is different from that in the web document (13.7.1.2). What is the best way to import the paths from the output of feff8l? Or is there any way to generate the "feffNNNN.dat" files with feff8l? I will appreciate your help. Best wishes, Shinichi ——————————————————— Shin-ichi NISHIMURA, Ph.D nishimura(a)chemsys.t.u-tokyo.ac.jp Atsuo YAMADA Group, Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo Yamada Lab., Engineering Bldg.#3-5C08, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan

3 2

Larch 0.9.59
by Matt Newville 04 Apr '22

04 Apr '22

Hi Folks, Larch version 0.9.59 has been released. It should now be installed by default using all installation mechanisms, and you may see a notice to update if running xas_viewer. This is mostly bug fixes, but some are important enough to warrant pushing out now. Changes are detailed at https://github.com/xraypy/xraylarch/releases/tag/0.9.59 For XAS Viewer use, the most important of these are a) "energy reference" and "energy shifting" of spectra work much better. b) the action of the "pin icon to select points on the graph" has now changed (by popular opinion) to be: click on pin icon, *and then* cliick on point of the graph. There are also new binary installers - the one for Linux might work for more people ;), and the installation might be faster for more people. We're hoping that there will be another release in a couple of months to give a more comprehensive "Project File" concept. But, as always, suggestions or comments are welcome. Cheers, --Matt

2 4

XAFS 2022: important deadlines
by Matt Newville 01 Apr '22

01 Apr '22

Hi Folks, ... and some reminders: Abstracts for XAFS 2022 are due April 19. Please submit a presentation for your work! https://xafs2022.org Nominations for the International X-ray Absorption Society Awards are due May 1. See https://xrayabsorption.org/ixas-awards-2022/ for details. --Matt

2 2

Question related to save fitting results in Larch
by Andy Zhang 24 Mar '22

24 Mar '22

Dear Sir/Madam, I have a question related to saving fitting results in Larch. I wonder if it is possible to save the project file with fitting results, just like the .fpj file in Artemis. In this way, I could save the partially finished work and do it later. Thanks a lot! Best, Harry

2 1

Open postdoc position in the APS Spectroscopy Group
by Sterbinsky, George E. 24 Mar '22

24 Mar '22

Hello all, The Advanced Photon Source Spectroscopy Group currently has an opening for a Postdoctoral Research Associate in the area of x-ray absorption spectroscopy. Interested candidates can view the full position description and apply at https://argonne.wd1.myworkdayjobs.com/Argonne_Careers/job/Argonne-National-…. Best, George George E. Sterbinsky, PhD X-ray Science Division Advanced Photon Source Argonne National Laboratory sterbinsky(a)anl.gov

1 0

Conduction band energy and deltae0
by Melike Babucci 12 Mar '22

12 Mar '22

Dear all, For a reliable comparison of two EXAFS data sets (lets say before and after Cu-doping), which parameters should be kept consant in the first model? I understand that sigma^2 values should be the same in two fittings, and I would see a change in coordination numbers and deltaE0 and deltar after Cu doping. Is that a good approach? Does the new deltaE0 indicate a change in the conduction band energy? Thanks in advance. Best regards, Melike N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

2 1

Open postdoc position at DESY XAFS beamline
by Edmund Welter 10 Mar '22

10 Mar '22

Dear colleagues, in case you are interested in a post doc position as beamline scientist at a XAFS beamline at DESY in Hamburg (a place with notoriously good weather!) please have a look at the following job offer: https://v22.desy.de/e67416/records155637/index_eng.html If you know of a colleague who might be interested please forward this mail to her/him. For any questions concerning the advertised position please do not hesitate to contact me via e-mail but please take care that you do not send your reply to the mail list. The job offer is open till we hired a suited candidate. Best regards, Edmund Welter

1 0

[ifeffit] Intensity difference in XANES
by Chen, Danting 07 Mar '22

07 Mar '22

Dear All, I have been studied Zn XANES and EXAFS for my environmental samples. Due to the unknow Zn speciation in my samples, called ‘A’, I do not have adequate Zn reference materials. I found some Zn reference materials from others work, called ‘B’, and extracted the data from their paper. I found quite similar features, e.g., the location of each peak and bottom. However, the intensity of these peaks or bottoms does not correspond very well. I am guessing that the features of XANES is mainly decided by the bond lengths, ligands and oxidation states of the core atom. The intensity of these features may be influenced by the multiple scattering from the neighbouring atoms beyond the first coordination. Can I conclude that the Zn speciation in my sample ‘A’ has a similar first coordination as other work ‘B’, but the coordination environment beyond the first coordination may be different. I compare their Fourier Transform ‘B’ with my samples ‘A’, and found each peak location correspond well but the intensity is different. I am guessing that their surrounding atoms are heavier than my samples. I am unsure if my explanation. Would you mind providing some suggestions regarding the factors influencing the intensity and also the references for this explanation? I will appreciate your help and many thanks. Best Wishes, Danting Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 2

fully funded PhD position at ESRF
by Marius Retegan 24 Feb '22

24 Feb '22

Dear IFEFFIT members, We are looking for a PhD student to develop and apply machine learning techniques to analyse X-ray spectroscopy data. The PhD is funded by the Marie Skłodowska-Curie COFUND project ENGAGE. Additional details about the offer can be found at https://esrf.gestmax.eu/1575/1/phd-student-engage-05/en_US <https://esrf.gestmax.eu/1575/1/phd-student-engage-05/en_US>. Applications should be made via the ENGAGE website (https://engage.cyi.ac.cy/?page_id=36 <https://engage.cyi.ac.cy/?page_id=36>), and the application deadline is 15 March 2022. The applicants must not have resided or carried out their main activity (work, studies, etc.) in France for more than 12 months in the three years immediately before the call deadline. Please feel free to forward this offer to any potentially interested candidates. Thank you in advance! Best regards, Marius -- Dr. Marius Retegan European Synchrotron Radiation Facility (ESRF) 71 Avenue des Martyrs 38000 Grenoble phone: +33 4 38 88 19 29 email: marius.retegan(a)esrf.fr

1 0

Larch install error on MacOS 12.2
by Mangold, Stefan (IPS) 11 Feb '22

11 Feb '22

Dear all, I upgraded a machine to 12.2 (MacPro), Larch was installed via binary installer. Afterwards Larch didn’t launch. I did a re-install with the binary installer and this didn’t work, because already installed. deleted it, but this also didn’t work tried pip install xraylarch stopped with ERROR: Failed building wheel for fabio Failed to build fabio also no director with XAS viewer created. best regards Stefan Mangold

3 5

Artemis warning after FEFF calculation---can't close GLOB filehandle
by Xinyu Luo 10 Feb '22

10 Feb '22

Dear ifeffit memebers, I received an Artemis warning after importing a CIF file into FEFF calculation as usual, which said, “Can’t close GLOB(…) filehandle at …” I first assumed it might be caused by some system errors. So I tried this CIF file on another PC and received a similar warning---can’t close a GLOB() filehandle. Also, I tried FEFF8 using Webatoms, but this still didn't work... Is that due to the CIF file itself or the software bug on my PC? I never met this situation before because it's always been very smooth to import a CIF file and generate atomic coordinates and paths before fitting... I don’t know how to handle this. The CIF file is attached. I appreciate any suggestions that might be helpful. Thank you for your time! Xinyu Luo

3 4

Re: [Ifeffit] [Ext] Larch install error on MacOS 12.2
by Jeffrey Terry 09 Feb '22

09 Feb '22

Hi Stefan, We recently updated our EXAFS Neo analysis package to work with the new version of Larch. I installed Larch using the detailed instructions on our GitHub site on a number of Macs* running OS X 12.x this weekend. https://github.com/laumiulun/EXAFS-Neo-Public If you want to use the Larch GUIs, you need to take the additional step of: larch -m Which puts links to the GUIs on the desktop. Our code calls uses larch Python routines so we have developed a fairly robust procedure for making sure larch installs correctly on all operating systems. Hope that helps. Jeff *all M1 machines but I don’t expect it will make a difference Jeff Terry Interim Chair, Department of Social Sciences Professor of Physics Professor of Mechanical, Materials, and Aerospace Engineering Editor, Applied Surface Science Illinois Institute of Technology 3101 S. Dearborn St. Chicago IL 60616 630-252-9708 Sent from my iPhone > On Feb 9, 2022, at 2:05 AM, Mangold, Stefan (IPS) <stefan.mangold(a)kit.edu> wrote: > Dear all, > > I upgraded a machine to 12.2 (MacPro), Larch was installed via binary installer. Afterwards Larch didn’t launch. I did a re-install with the binary installer and this didn’t work, because already installed. deleted it, but this also didn’t work > > tried > > pip install xraylarch > > stopped > with > ERROR: Failed building wheel for fabio > Failed to build fabio > > also no director with XAS viewer created. > > > best regards > > Stefan Mangold > > _______________________________________________ > 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

1 0

Postdoc position in X-ray spectroscopy at NSLS-II
by Stavitski, Eli 08 Feb '22

08 Feb '22

NSLS-II is seeking exceptional candidates for a research associate position in the Hard X-ray Scattering and Spectroscopy program. The successful candidate will work collaboratively with the ISS team and supporting technical, engineering and controls staff. They will be involved in developing, commissioning, and testing custom sample environments for catalysis experiments, including high pressure gas and integration of the high energy resolution spectrometers in the ISS operando catalysis research infrastructure. They will also be involved in the support of the users at the beamline, including industrial partners. Leveraging the technical developments, the successful candidate will conduct mechanistic studies of catalytic carbon dioxide hydrogenation at high pressures in collaboration with ISS scientists. See full posting at https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-catalysis-an… ____________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov> https://www.bnl.gov/ps/beamlines/beamline.php?r=8-ID

1 0

Research scientist position at DOE-NETL
by Mengling Stuckman 07 Feb '22

07 Feb '22

Dear ifeffit members, We are looking for talented environmental scientist/engineer familiar with soil science and synchrotron application experiences at Leidos working for US Department of Energy - National Energy Technology Laboratory, Pittsburgh, PA: Environmental Scientist / Engineer (myworkdayjobs.com) <https://leidos.wd5.myworkdayjobs.com/External/job/Pittsburgh-PA/Environment…> This is a full-time research scientist position that will help with the following projects: (1) converting oil and gas drilling wastes to soil supplements; (2) synchrotron microprobe and bulk XAS studies on critical mineral characterization in different coal byproducts (e.g., REE in fly ash). If you have any related questions, feel free to let me know at mengling.stuckman(a)netl.doe.gov. Thank you, Mengling -- Mengling Stuckman Leidos Technical Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

1 0

Fwd: Position at USDOE-NETL
by Mengling Stuckman 07 Feb '22

07 Feb '22

Dear ifeffit members, We are looking for talented environmental scientist/engineer familiar with soil science and synchrotron application experiences at Leidos working for US Department of Energy - National Energy Technology Laboratory, Pittsburgh, PA: Environmental Scientist / Engineer (myworkdayjobs.com) <https://leidos.wd5.myworkdayjobs.com/External/job/Pittsburgh-PA/Environment…> This is a full-time research scientist position that will help with the following projects: (1) converting oil and gas drilling wastes to soil supplements; (2) synchrotron microprobe and bulk XAS studies on critical mineral characterization in different coal byproducts (e.g., REE in fly ash). If you have any related questions, feel free to let me know at mengling.stuckman(a)netl.doe.gov. Thank you, Mengling -- Mengling Stuckman Leidos Technical Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

1 0

Re: [Ifeffit] Postdoctoral position for Synchrotron Studies of Molten Salts, Solutes and Interfaces
by Gill, Simerjeet 07 Feb '22

07 Feb '22

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 2921(https://jobs.bnl.gov/job/upton/post-doc-synchrotron-studies-of-molten-… 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

1 2

Postdoc position available at PAL
by 이국승(에너지환경소재연구팀) 27 Jan '22

27 Jan '22

Dear ifeffit members, I would like to let you know a postdoc position available at 8C Nano-XAFS beamline of PAL. Please refer to the following posting. Postdoctoral Research Associate - Pohang Accelerator Laboratory Post details: Full time / Annual contract Application deadline: until the recruitment is completed Job description - In-situ XAFS analysis of electrocatalysts (experience of XAFS analysis preferred) Requirements - PhD degree in physics, chemistry, materials science, or chemical engineering - Excellent writing and communication skills in english. Offered - USD 30,000 - 40,000 according to career If you are interested in this position, please send your CV (including list of publications) to lks3006(a)postch.ac.kr. * Additional documents can be required, for example, two letters of reference, representative publications, etc. Kind regards, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Scopus : https://www.scopus.com/authid/detail.uri?authorId=56953635300 Google Scholar : ?<https://scholar.google.co.kr/citations?hl=ko&user=CRS8vHkAAAAJ>?Kug-Seung Lee? - ?Google 학술 검색?<https://scholar.google.co.kr/citations?hl=ko&user=CRS8vHkAAAAJ>

1 0

Post-doc in catalysis at the ESRF
by Mauro ROVEZZI 27 Jan '22

27 Jan '22

Dear all, I'd like to advertise for a post-doc position in catalysis at the French CRG spectroscopy beamlines at the ESRF: https://bit.ly/32FaDCQ Please, feel free to diffuse it. Best, Mauro -- Mauro Rovezzi CNRS-OSUG | French CRG @ ESRF Beamlines FAME (BM30) & FAME-UHD (BM16) 71 Avenue des Martyrs, 38043 Grenoble, France Tel: +33(0)47688 2963 | Office: LOB-2-50

1 0

post-doc opportunity
by Matt Newville 24 Jan '22

24 Jan '22

Hi Folks, I'd like to pass on this advertisement for a post-doc position at U Illinois at Urbana Champaign: Post-doctoral researcher, Dept of Geology, University of Illinois Urbana Champaign: XAS study of molecular complexation of PGE sulfides in high temperature and pressure geological fluids Applications are invited for a postdoctoral researcher position in the Department of Geology (School of Earth, Society and the Environment) at the University of Illinois at Urbana Champaign. We seek a person with strong background in high-temperature hydrothermal/magmatic liquids and experimental geochemistry to perform EXAFS and XANES analyses on both glasses and solutions produced in high temperature and pressure laboratory experiments. The goal is to determine the solubilities and understand the molecular complexation of PdS and PtS in hydrous alkali silicate and carbonate liquids. Experience and knowledge of synchrotron XAS analyses are required. Skills in performing experiments at high pressure and temperature as well as advanced knowledge of chemical thermodynamics and computational geochemistry are all preferred qualifications. The postdoc will have opportunities to participate in interdisciplinary research involving aspects of geoscience, chemistry, and material science. Requirements and qualifications include: PhD in mineralogy, chemistry, material science, or closely related field. Prior experience with synchrotron X-ray spectroscopy/scattering/microscopy techniques is required. Familiarity with other analytical techniques such as SEM-EDS, XRD, and ICP-MS is highly favorable. Prior experience with high pressure experimental geochemistry is preferred. Excellent oral and written communication skills This position is part of a new collaborative project between UIUC (PI C. Lundstrom), Johns Hopkins University (Co-PI D. Sverjensky), and University of Chicago (Co-PI G. Gauli). This project is funded by the Department of Energy (DOE) Basic Energy Sciences under the critical minerals and materials program (https://www.energy.gov/articles/doe-awards- 30m-secure-domestic-supply-chain-critical-materials). The selected candidate would start in late Spring 2022 at UIUC. XAS analyses at Argonne/APS would likely start in summer 2022 and occur through April of 2023 when the APS beamline shuts down. For the remainder of 2023 and 2024, XAS work using a pressurized hydrothermal cell is planned to occur at Grenoble/European Union Synchrotron facility. The initial appointment is for one year with possible renewal for another 1.5 years upon mutual satisfaction. Interested individuals should submit a single pdf file that includes: 1) a cover letter that outlines the applicant's research, expertise match to the position, and career goals; 2) curriculum vitae; 3) copies of representative recent research publications; and 4) contact information of three references, electronically to Prof. Craig Lundstrom, lundstro(a)illinois.edu. Review of applications will begin January 25, 2022. UIUC is an Equal Opportunity/Affirmative Action employer, and applications from women and under-represented minorities are particularly encouraged.-- --Matt Newville

1 0

FEFF calculation on ferri-/ferrocyanide materials
by Hu, Yang (HIU) 23 Jan '22

23 Jan '22

Dear IFEFFIT members, I am trying to apply the FEFF calculation on Metal-[Fe(CN)6] type materials (in Larch). The calculations were successful with cif files from (K, Na)x(Cu, Ni) [Fe(CN)6] for both C-coordinated Fe and N-coordinated metals, and their results include higher-order paths. However, the calculation on NaxFe[Fe(CN)6] always gives the warning ".Two atoms very close together. Check input." and takes long time. The calculated results have some collinear 5- and 6-leg paths with several hundred or even thousand importance value. I am wondering if it is possible to limit the multiple scattering to a lower order in the calculation (such as suggested in Artemis user guide). Plus, if I only aim to model the nearest Fe-C and Fe-N for its Fe K-edge spectra, are there any alternative methods for the calculation? - I also would like to ask whether it is meaningful to do this while ignoring those multiple scatterings in this type of materials. Your help and comments are highly appreciated, Best regards, Yang

2 1

Question_Demeter installation on Mac with Apple Silicon M1
by 王茂林 22 Jan '22

22 Jan '22

Dear IFEFFIT members, Here I want to install Demeter in my Mac with M1 pro, I followed the processes in https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h… (First, install Xcode and Xcode command tool; Then install Macport). But when I type " sudo port install xorg-server demeter in the terminal and after agreeing to the terms, there came to a warning, shown in the attached figure. What should I do to install it on my mac? And the log file (also attached) seems like Demeter doesn't support the M1 with ARM architecture? I'm looking forward to your helpful reply! Best regards, Maolin Wang 确定

2 2

The possibility of the defect concentration estimation by feff
by Iraida N. Demchenko 16 Jan '22

16 Jan '22

Dear All, Do I understand correctly that using feff calculations it is impossible to calculate the concentration of defects in a sample? I'll try to explain my question with an example. Let us assume that we have a (Ga,Mn)As sample, where Mn is a dopant. Comparing the experimental curve (Mn K edge) with the theoretical spectrum, we see that the experimental one is well described by a linear combination of two theoretical ones, namely, substitutional manganese in the position of gallium (Mn_Ga) and interstitial manganese (Mn_i) in proportions of 65 and 35%, respectively. Is it possible to recalculate these phases weights (I mean Mn_Ga and Mn_i) to the real concentration of the mentioned above defects in the sample? For example, for the Mn_Ga model, ONE manganese atom was considered per cluster of 900 atoms (FMS 7A). Does it make sense to recalculate the stoichiometry (using cluster size) and, subsequently, the weights of this model when compared to the experimental curve, which will eventually give the selected defect concentration at the low level (like ~0.2%). Do I understand it correctly? I will be very grateful for your help in understanding. Best, Iraida.

2 1

Larch 0.9.58
by Matt Newville 16 Jan '22

16 Jan '22

Hi Folks, Larch version 0.9.58 has been released. It should now be installed by default using all installation mechanisms, and you may see a notice to update if running xas_viewer. Coming only 6 weeks after 0.9.57, and with the holidays in between, this is mostly a set of bug fixes, especially surrounding installation and errors associated with our use of deprecated features of silx and numpy. Thanks mostly to Mauro for this, and for updating the documentation for installation, especially for existing Anaconda Python users, and on Linux. FWIW, I checked that a fresh install works on Windows 10, MacOS 12, CentOS 7, CentOS 8 Stream, and that "auto-updates" work with "larch -u" or from XAS Viewer works on MacOS 12 and on Fedora 34. But, of course, let us know if you have suggestions, comments, or problems. There are a few fixes for reading some kinds of data files and with de-glitching XAS spectra. The plans discussed in the previous release message (see https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2021-December/010345.ht…) about saving more complex projects and how to think "reference spectra" have not had much work done on them. The request for suggestions and comments on these topics still stands. --Matt

1 0

Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels
by Ming Zhang 13 Jan '22

13 Jan '22

sorry for the trouble, I forgot to register this email. -----原始邮件----- 发件人:"Ming Zhang" <mzhang17(a)zju.edu.cn> 发送时间:2022-01-13 14:41:04 (星期四) 收件人: ifeffit(a)millenia.cars.aps.anl.gov 抄送: 主题: Question--FEFF calclulated atom coordinates and labels Dear IFEFFIT members, I’m practicing EXAFS fitting with some standard crystal data. I GOT SOME QUESTIONS when I imported the CIF File into the FEFF calculation. 1)I’m confused with the atom label. The VESTA GUI shows that there are C1, C2, and C3 carbons in a unit cell. However, after FEFF calculation, they become C1.1 C2.1 C3.1, so do the other atoms like nitrogen and hydrogen. Since I need to set some geometry constraints, I have to figure out the nomenclature of the atom coordinates calculated by FEFF and link those atoms to real physical images. 2)I’m also confused with the calculated degeneracy, like the path of @ C1.1 @ (I have no idea about the atom C1.1 stands for). It’s a zinc absorber placed in a tetrahedron coordinated by the N atom of imidazole. Very intuitively, the degeneracy of @ N1.1 @ (row 1) is 4, and YES IT IS. But how comes the single scattering path (row 2) of the C atom next to N become 8? Also in row 5, degeneracy of @ N1.1 C2.1 @ is 8. Notably, we only got 3 C atoms in a coordinated molecule, so even treating closely located C atoms into the same one couldn’t help explain this. FEFF calculation VESTA GUI The CIF file is attached. I would appreciate it very much if you could help me out. Best regards Ming Zhang

5 7

How do I launch Larch GUIs?
by Swanner, Elizabeth S [GE AT] 12 Jan '22

12 Jan '22

I use a Mac recently updated to Big Sur (11.6). I used the Binary Installer File for Larch and am a little stuck on what to do next. I was able to run the installer, and I have an xraylarch folder on my computer. However, I was hoping to use the XAS Viewer and do not see it within the folder. Should it be there? I had an old version of XAS Viewer I got while at APS but needed to replace that as it did not have all the modules. I did not check before removing that whether it was working on this OS. I am also not clear how to use Larch in general (i.e., the Basic Larch GUI). Do I need to install python? I see there is a python application in the folder but when I try to open that nothing happens. I’m not sure if these are issues with my OS or if I am missing something really basic about how to launch Larch. Best, Betsy Swanner

2 1

Issues reinstalling Larch, error creating desktop shortcut for macOS
by Lauren N. Pincus 04 Jan '22

04 Jan '22

Hi Matt, I'm having an issue with reinstalling Larch. I'm using macOS Catalina 10.15.7. I had Larch previously installed and it was working well, but found I was no longer able to open up XAS Viewer. The application would start and then quit. So, I removed Larch from my system and tried to reinstall it. I first used the mac installer but would get an error that the "Installation failed. The installer encountered an error that caused the installation to fail." I then tried the installation using the script in terminal. This appeared successful, but no desktop shortcut was created. I tried to create a desktop shortcut using larch -m but get the following error: (base) laurenpincus@lnp24mbp2020 ~ % larch -m Traceback (most recent call last): File "/Users/laurenpincus/xraylarch/bin/larch", line 5, in <module> from larch.apps import run_larch File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/builtins.py", line 22, in <module> from . import io File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/__init__.py", line 39, in <module> from .specfile_reader import (str2rng_larch, read_specfile, open_specfile, File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/specfile_reader.py", line 26, in <module> from silx.io.convert import write_to_h5, _is_commonh5_group ImportError: cannot import name '_is_commonh5_group' from 'silx.io.convert' (/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/silx/io/convert.py) (base) laurenpincus@lnp24mbp2020 ~ % Thanks, Lauren Lauren Pincus, PhD NSF Earth Sciences Postdoctoral Fellow Princeton University Department of Geosciences

2 1

Re: [Ifeffit] [Ext] Re: Problem in xrayLarch installation
by Jeffrey Terry 20 Dec '21

20 Dec '21

We’ve had to come up with a slightly different install plan for Windows users of our analysis package EXAFS Neo that is built on top of xrayLarch. We recommend a slightly different route using both conda and pip. You can read through out full recommended analysis route for xrayLarch in the Prerequisites section of our readme file at: https://github.com/laumiulun/EXAFS-Neo-Public We are pretty confident that the installation method given there works for xrayLarch installation on Mac, Windows, and Linux. Jeff Jeff Terry Interim Chair, Department of Social Sciences Professor of Physics Professor of Mechanical, Materials, and Aerospace Engineering Editor, Applied Surface Science Prairie Chapter Chair, AVS Illinois Institute of Technology 3101 S. Dearborn St. Chicago IL 60616 630-252-9708 Sent from my iPhone > On Dec 15, 2021, at 2:42 AM, Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> wrote: > Dear Latif, > > Thanks for reporting this. Unfortunately `pip` is not able to correctly install all dependencies of Larch. The way to go is to install those dependencies via `conda`. > > Under Windows, this is achieved by running the script `GetLarch.bat` (https://raw.githubusercontent.com/xraypy/xraylarch/master/installers/GetLar…) This script will download and install a minconda distribution, plus install Larch in it. > > Seen you already have Anaconda installed, you could simply run the following commands from your Anaconda prompt: > > conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw > pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch > > If this does not work, please, let me know. I have created a related Github issue in order to avoid such troubles in the future: > > https://github.com/xraypy/xraylarch/issues/333 > > Best, > Mauro > > On 2021-12-15 08:20, Latif Ullah Khan wrote: >> Dear Sir Madam, >> I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using “pip install xraylarch” . However, it is not installing and give me an following error: >> If you kindly help me in this regard, I will be grateful to you. >> Thank you in advance >> Best regards >> Latif >> _______________________________________________ >> 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 > > _______________________________________________ > 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

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 226, Issue 9_Problem in wavelet code
by Latif Ullah Khan 20 Dec '21

20 Dec '21

Dear Matt Newville and Mauro, Many thanks for the kind reply and great support in installation of the XrayLarch through window. Unfortunately, I could not install through Anaconda prompt using command " conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch" as suggested by Mauro. Fortunately I succeeded to install through window command prompt using the source code. Now I am using through VS Studio code. I just adopted the code for wavelet transformation written by Matt Newville, however, I faced some problem in plotting the 2D CCWT image, I am sharing the code with input data and also the code. Its showing some error in following syntax, probably "imopts" has problem: plt.imshow(f.wcauchy_mag, win=1, label='Wavelet Transform: Magnitude', **imopts) plt.imshow(f.wcauchy_re, win=2, label='Wavelet Transform: Real Part', **imopts) If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif -----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, December 15, 2021 6:08 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 226, Issue 9 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: Problem in xrayLarch installation (Matt Newville) 2. Re: Any coorelation about 'white line" in K-edge XAS with oxidation states? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2021 09:23:47 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "Ifeffit-request(a)millenia.cars.aps.anl.gov" <Ifeffit-request(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem in xrayLarch installation Message-ID: <CA+7ESbqCSsM+==XmUgzkjzjPHTOJjfLRGw8JRDqN5CGUxzJCuQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Latif, Sorry for the trouble. As Mauro said, some of the packages needed (and pymatgen is one of these) are not super-well supported for installing with pip. FWIW, I agree that the needed combination of conda and pip is sort of unfortunate. But most of the "problem packages" are either Windowing systems (wxPython: that have been challenging to have consistent binary support on Linux is very challenging) or packages of scientific code written by and for scientists, some with excellent engineering support and some (like us!) with "less" support. Conda is a popular option for many of these. We try to support the simpler / more ubiquitous pip where we can. Anyway, that's basically why we have the binary installers and installation scripts. But also: thanks for the report and we are trying to clean up or at least document some of these kinds of issues where we can: https://github.com/xraypy/xraylarch/issues/333 --Matt

1 0

Any coorelation about 'white line" in K-edge XAS with oxidation states?
by Marco Wang 16 Dec '21

16 Dec '21

Dear everyone: Ihave some questions about the interpretation of "white line", from anarticle (https://doi.org/10.1038/s41467-021-27116-8) and the figure was attached. In the article, it is said that “the sample was fully reduced to Ni (0) state at ~480 °C judging from the edge position and ‘white-line’ profiles”. First, we assumed that the metal was coordinated with the same anion. We all know that K-edge transition in 3d and 4d metalis' spin forbidden, so it may be inappropriate to conclude that the intensity of the "white line" is correlated with metals' oxidation states. But in other words, the probability for s→d transition may be proportional to thenumber of empty d orbitals, so it seems like if the the intensity of "white line" is higher, the oxidation state is higher. So, how should we correctly interpret the “white line” and edge energy from XAS spectrum of metals’ K-edge and L-edge? Thank you in advance for your time. Marco Wang

4 5

Problem in xrayLarch installation
by Latif Ullah Khan 15 Dec '21

15 Dec '21

Dear Sir Madam, I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using "pip install xraylarch" . However, it is not installing and give me an following error: If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif [cid:image001.png@01D7F194.F5C60C50]

3 2

Re: [Ifeffit] XEOL
by Eugenio Otal 06 Dec '21

06 Dec '21

Dear Robert, sorry for the late reply, life... Brilliant suggestion! I will let you know the results if the proposal is approved. Best regards, euG If you can move between Nd L3 and Br K, why not stop at Nd L1 if you want to see if a Nd s-type initial state has any influence on the XEOL? You should not need to go up to Nd K. Some references: https://aip.scitation.org/doi/abs/10.1063/1.477320?journalCode=jcp https://iopscience.iop.org/article/10.1149/1.3211180 and a book chapter https://www.worldscientific.com/doi/10.1142/9789812775757_0015 On 2021-11-25 5:50 p.m., Eugenio Otal wrote: > Hi all, > I am planning XEOL measurements and I have a doubt. > My system is Nd coordinated to Eosin, tetrabromofluorescein. I want to > measure XEOL exciting on the Br K-edge (13.4keV) and the Nd > L3-edge(6.2keV) and measure the emission spectra of the dye and the > Nd. I just measured the emission of the Nd exciting at 530nm and it > worked perfectly. > My question is, I have access to Nd K-edge, is it worthy?to measure > XEOL at the K-edge? I am in the time limit to?request an?extra shift. > I would appreciate some bibliography. > Best regards. > > _______________________________________________ > 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

1 0

Larch 0.9.57
by Matt Newville 02 Dec '21

02 Dec '21

Hi All, Larch version 0.9.57 has been released and is available on PyPI ( https://pypi.org/project/xraylarch) It should now be installed by default using most installation mechanisms, and you may see a notice to update if running xas_viewer. The updates are described in some at https://github.com/xraypy/xraylarch/releases/tag/0.9.57 and in the github commit history. This includes adding support for reading RIXS data files from ESRF BM16, better support for de-glitching in XAS_Viewer, and fixing of reading of many Athena Project Files that were saved in the "old style" and have non-ASCII characters (the code now correctly reads the 78 Project files at https://github.com/xraypy/xraylarch/tree/master/examples/xafsdata/AthenaPro… ). Much of the work for this release has come from Mauro Rovezzi. In a conversation we had yesterday about this release, we talked about several potential changes going forward, especially for XAS_Viewer, about saving processing history, how to improve the concept of "reference spectrum" for a measurement, and other topics related to keeping track of analysis history and provenance. Some of these ideas are encapsulated in Github Issues at https://github.com/xraypy/xraylarch/issues, and the plan is to work on this. One possibility would be to be able to read and export to Athena Project files but use a different format (probably HDF5) as a new default "Larch Project File" so that more complexly nested data and some sort of "journal" per data set could be saved, displayed, edited, and so on. If anyone here has some thoughts on how such topics could or should be handled, please let us know. If you have other ideas on what might be added or improved, also don't hesitate to speak up, either in conversations here or on Github. Cheers, --Matt Newville

1 0

XEOL
by Eugenio Otal 25 Nov '21

25 Nov '21

Hi all, I am planning XEOL measurements and I have a doubt. My system is Nd coordinated to Eosin, tetrabromofluorescein. I want to measure XEOL exciting on the Br K-edge (13.4keV) and the Nd L3-edge(6.2keV) and measure the emission spectra of the dye and the Nd. I just measured the emission of the Nd exciting at 530nm and it worked perfectly. My question is, I have access to Nd K-edge, is it worthy to measure XEOL at the K-edge? I am in the time limit to request an extra shift. I would appreciate some bibliography. Best regards.

2 1

PostDoc position at Northeastern University
by NUCRET 23 Nov '21

23 Nov '21

Northeastern University Center for Renewable Energy Technology is currently looking for highly qualified candidate to fill a Post-Doctoral Research Associate position with hands-on experience in the area of in situ and operando XAS, XANES, EXAFS spectroscopy, high-energy XRD as applicable to batteries (especially solid-state), fuel cells and electrolyzers. Familiarity with Brookhaven synchrotron facility (or other US-based light source facilities, e.g. ANL, SLAC) is a plus. Candidates should be in the US and authorized to work in the US (visa is _not_ offered). To apply, please use Northeastern University Career Portal: https://careers.hrm.northeastern.edu/cw/en-us/job/508477/postdoctoral-resea…

1 0

Postdoctoral beamline scientist position at Illinois Tech/MRCAT
by Carlo Segre 22 Nov '21

22 Nov '21

Please find attached the advertisement for a postdoctoral position at MRCAT (Sector 10) at the Advanced Photon Source. The position is with Illinois Institute of Technology, which operates MRCAT for its institutional membership. Feel free to share this with any appropriate individuals. Carlo -- Carlo U. Segre (he/him) -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

1 0

SSRL post-doctoral position
by Ritimukta Sarangi 17 Nov '21

17 Nov '21

Hi, I would like to bring this unique opportunity to the EXAFS user community. I am looking to hire a post-doctoral fellow who will apply spectroscopy tools to the Ni-Fe containing active site in Carbon Monoxide dehydrogenase, which is part of a pathway that biologically captures CO2 and converts it into acetate. This project is funded by the Department of Energy and is extremely relevant to our understanding and remediation of CO2 in the atmosphere. You will work with a diverse team of postdocs working on a variety of X-ray spectroscopy projects and will get the experience of working in a national laboratory setting. See the attached posting for more information. Kind regards, Riti Sarangi

1 0

Fe and Ni carbide XAS reference spectra?
by Valentijn De Coster 17 Nov '21

17 Nov '21

Dear ifeffit mailing list, My name is Valentijn De Coster. I am a PhD student at Ghent University, Belgium, working on Ni and Fe materials for CO2 utilization. I am currently looking for Fe and Ni carbide (Fe3C, Ni3C) reference XAS spectra, at the respective Fe K and Ni K edges, for fingerprinting purposes. As such, I was wondering whether anyone would have such data available. On a side note, I checked the CARS database, and while this has an Fe3C (Fe K edge) reference, the data file does not contain the Energy values of the spectrum. Thank you in advance for your time. Kind regards, Valentijn De Coster [Image result for ghent university logo] Valentijn De Coster PhD Student Laboratory for Chemical Technology (LCT) Department of Materials, Textiles and Chemical Engineering Technologiepark 125, 9052 Ghent, Belgium T: +32 9 331 17 M: +32 (0) 331 17 10 https://www.lct.ugent.be<https://www.lct.ugent.be/> https://helpdesk.UGent.be/e-maildisclaimer.php<https://helpdesk.ugent.be/e-maildisclaimer.php> Member of CSC: https://www.csc.ugent.be<https://www.csc.ugent.be/>

3 3

MacPorts XAFS software: announcing a Port for Larch; and do we actually need Demeter on Macs?
by Fowler, Joseph W. (Assoc) 12 Nov '21

12 Nov '21

Hello XAFS fans: This note is about the Demeter package on MacPorts. If you don’t use Demeter through MacPorts on a Mac, skip this note. I’m the MacPorts “maintainer” of the ports demeter and ifeffit. They have been not installable or upgradeable for something like a year, because of new releases of … something? Probably either Mac OS X, and/or Apple's Xcode development system. I’ve made a ton of progress on my big goal of restoring demeter to life, but I cannot get all the way to finish the project. I have to say here that I’m a poor choice to maintain these ports. I barely understand how MacPorts works, and I don’t understand or use Perl at all. I am not even really an x-ray scientist—I develop superconducting x-ray sensors in a team at NIST, and I happened to be a collaborator of the previous maintainer when he left the field 6 or 8 years ago. I worked on the problem in two parallel paths. One was to create an official port for the Python package Larch. Late last month this was complete, so you can do a “sudo port install py39-xraylarch” and have it. (Replace “py39” with “py38” or “py37” if you use Python 3.8/3.7.) This required creating about a dozen new ports for Larch’s dependencies. (Actually, I know a ton more about how MacPorts works than I did six weeks ago.) Some new ports that might be of interest to this community include: * py39-pymatgen * py39-peakutils * py39-xraydb * py39-spglib * py39-xraylarch My other path was to track down and fix the problem that prevented ifeffit from compiling. (Recall that this package is unmaintained since 2014. See https://github.com/newville/ifeffit/) It looks like Xcode’s C compiler recently turned the “implicit function warning” into an error. A few hours ago, MacPorts accepted my proposed patches, so at least ifeffit should be installable as a port again. Unfortunately, demeter still won’t install completely, owing to problems in certain Perl-based ports that it depends upon, like p5.30-wx. That problem is so far from my expertise that I am completely stuck. I had hoped that if I got ifeffit to work, demeter would follow, but I was wrong. There are four strategies I can imagine from here: 1. Declare the ports ifeffit and demeter to be obsolete. Mac users will need to figure out other ways to do what Athena and Artemis do. 2. Wait until Perl experts fix the Perl dependencies (expect it to take months or more), then I fix demeter. 3. Modify/migrate Demeter so that Athena and Artemis rely completely on Larch and not at all on ifeffit. 4. Ask this mailing list for advice. I don’t know what strategy #3 would entail—again, I know zero Perl and don’t use this software. Demeter’s author told me he doesn’t have much interest in this upgrade. All I can really support alone is strategy #1 or #2: obsoleting or waiting. And that’s why I’m writing. On one side, does anyone care if Athena/Artemis become unavailable through MacPorts? So, does anyone object to path #1? On the other, does anyone here have better ideas? Best wishes, Joe Fowler NIST Boulder Labs

2 1

how to learn wavelet analysis
by 罗昕宇 10 Nov '21

10 Nov '21

Dear IFEFFIT members, I'm a fresh graduate student majoring in chemical engineering. I began to learn XAFS by myself one month ago. I bought and read the book XAFS for Everyone written by Dr. Calvin. I think I have got a clear image of how EXAFS works. Recently, I am attracted by the technique called Wavelet Analysis from literatures. It seems pretty powerful to correlate both temporal and frequency information, but something just went probably beyond my current knowledge base. I understand that a changeable window should be adapted to a make a trade-off between time and frequency, but I don't understand the logic that good time-resolution in high frequency is preferred while in low frequency a good frequency-resolution is better. I would appreciate it very much if you could answer my half-baked question and offer me with some learning material. Best regards Xinyu

3 2

iodine L-edge spectra
by Enyuan Hu 26 Oct '21

26 Oct '21

Hi, Does anybody happen to have the iodine element L-edge spectra (L1 preferred, but L2 and L3 are also okay) and is willing to share? thanks! Enyuan

1 0

Larch R plot
by Christopher Patridge 25 Oct '21

25 Oct '21

Hello, I am using Larch and Athena together and I just have a question about the magnitude plots and its effect (if any) on EXAFS modeling. Below are plots of the same merged samples using the same setting values. I noted that the plot in Larch begins below 0 and just want to make sure this is not a setting I missed in Larch? Thank you, Chris ********************************************** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patridgc(a)dyc.edu www.dyc.edu <http://www.dyc.edu/> Social: Twitter <http://www.twitter.com/drpatridgc>

3 4

Re: [Ifeffit] Ifeffit Digest, Vol 224, Issue 12
by Lisa Langlois 25 Oct '21

25 Oct '21

XAS Library? Dear Bruce. I was wondering how the XAS library is coming along. I have not seen too much update on that in Hephaestus. Best wishes, Lisa On Wed, Oct 20, 2021 at 9:33 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: [Ext] FW: Problem in installing Larch (Jeffrey Terry) > 2. Re: Problem in installing Larch (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Oct 2021 09:31:56 -0500 > From: Jeffrey Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] [Ext] FW: Problem in installing Larch > Message-ID: <8D09051C-F118-4DFB-BF91-221C63110D54(a)iit.edu> > Content-Type: text/plain; charset="utf-8" > > ?Hi Raheleh, > > We have submitted a bug fix for this. Expect a new version of Larch to be > released shortly. > > We rely heavily on Larch for our EXAFS Neo analysis package and this has > broken our code as well. > > Jeff > > Jeff Terry > Interim Chair, Department of Social Sciences > Professor of Physics > Professor of Mechanical, Materials, and Aerospace Engineering > Editor, Applied Surface Science > Prairie Chapter Chair, AVS > Illinois Institute of Technology > 3101 S. Dearborn St. > Chicago IL 60616 > 630-252-9708 > > > Sent from my iPhone > > > On Oct 20, 2021, at 9:12 AM, Daneshpour, Raheleh <rmd5926(a)psu.edu> > wrote: > > ? > > > > Hello! > > > > I am Raheleh a PhD student at Penn State working in FeNi catalysis and > using XAS. I am trying to install the Larch, but I constantly get an error > message on different computers and using different installation methods. > The attached file is a screenshot of the error message I got. Could you > please help me to figure out how to solve the problem? > > Thanks, > > Raheleh > > > > <image001.png> > > Raheleh Daneshpour (She/Her) > > Ph.d. student > > > > Email: rmd5926(a)psu.edu > > > > Chemical engineering department > > The Pennsylvania State University > > University Park, PA > > > > > > <Capture-larch.PNG> > > _______________________________________________ > > 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 >

3 2

Larch 0.9.56
by Matthew Newville 21 Oct '21

21 Oct '21

Hi Folks, Larch version 0.9.56 is now available on PyPI ( https://pypi.org/project/xraylarch) and should now be installed by default using most installation mechanisms. This really represents a collection of small improvements and bug fixes but includes one emergency bug fix that many people have seen with the latest version of `lmfit` (which was released recently). I believe that this will now work, but please let me know if you continue to have installation problems. Cheers, --Matt Newville

2 2

Re: [Ifeffit] [Ext] FW: Problem in installing Larch
by Jeffrey Terry 20 Oct '21

20 Oct '21

Hi Raheleh, We have submitted a bug fix for this. Expect a new version of Larch to be released shortly. We rely heavily on Larch for our EXAFS Neo analysis package and this has broken our code as well. Jeff Jeff Terry Interim Chair, Department of Social Sciences Professor of Physics Professor of Mechanical, Materials, and Aerospace Engineering Editor, Applied Surface Science Prairie Chapter Chair, AVS Illinois Institute of Technology 3101 S. Dearborn St. Chicago IL 60616 630-252-9708 Sent from my iPhone > On Oct 20, 2021, at 9:12 AM, Daneshpour, Raheleh <rmd5926(a)psu.edu> wrote: > > > Hello! > > I am Raheleh a PhD student at Penn State working in FeNi catalysis and using XAS. I am trying to install the Larch, but I constantly get an error message on different computers and using different installation methods. The attached file is a screenshot of the error message I got. Could you please help me to figure out how to solve the problem? > Thanks, > Raheleh > > <image001.png> > Raheleh Daneshpour (She/Her) > Ph.d. student > > Email: rmd5926(a)psu.edu > > Chemical engineering department > The Pennsylvania State University > University Park, PA > > > <Capture-larch.PNG> > _______________________________________________ > 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

1 0

Problem in installing Larch
by Daneshpour, Raheleh 20 Oct '21

20 Oct '21

Hello! I am Raheleh a PhD student at Penn State working in FeNi catalysis and using XAS. I am trying to install the Larch, but I constantly get an error message on different computers and using different installation methods. The attached file is a screenshot of the error message I got. Could you please help me to figure out how to solve the problem? Thanks, Raheleh [cid:image001.png@01D7C4CE.9ECA8AE0] Raheleh Daneshpour (She/Her) Ph.d. student Email: rmd5926(a)psu.edu<mailto:rmd5926@psu.edu> Chemical engineering department The Pennsylvania State University University Park, PA

2 2

Fit in R or k
by LIMA DA SILVA, WILL (PGR) 12 Oct '21

12 Oct '21

Dear IFEFFIT members, I have been fitting some EXAFS data, and my supervisor and I are having doubts if it's better to fit in k or R space. What are the main differences between the two approaches? I have learnt that R space is the right approach, but I am not sure how to explain it. Much appreciated, Will Silva

2 1

Bug report: Athena, multiple data export
by Soyoung Kim 10 Oct '21

10 Oct '21

Dear Bruce and IFEFFIT community, Hope all is well. I found a bug with Athena's file export function. I had two normalized mu(E) data with very similar spectra but different x-axis values (collected with different energy step settings). [image: image.png] When I batch exported them to a .dat file using the purple E button while "Save next plot to a file" was turned on, the resulting data only had a single x-axis column, which was taken from the first data. Hence, when I plot the two spectra from this .dat file, they now look different: [image: image.png] If I export each data individually to .dat files, then they are correct. [image: image.png] I'm attaching the Athena project file containing the two data and the .dat files I exported, both together and individually. Please let me know if anything is unclear. Thank you in advance for your help. Best, Soyoung Kim

3 4

Open postdoc position in the APS Spectroscopy Group
by Sterbinsky, George E. 04 Oct '21

04 Oct '21

Hello all, The Advanced Photon Source Spectroscopy Group currently has an opening for a Postdoctoral Research Associate in the area of x-ray absorption spectroscopy. Interested candidates can view the full position description and apply at https://argonne.wd1.myworkdayjobs.com/en-US/Argonne_Careers/job/Argonne-Nat…. Best, George George E. Sterbinsky, PhD X-ray Science Division Advanced Photon Source Argonne National Laboratory sterbinsky(a)anl.gov

1 0

S02 selection from reviewer
by Peng Liu 03 Oct '21

03 Oct '21

Dear IFEFFIT members, I am sorry to bother you again. I asked about S02 selection for the first major revision. I just received the second revision. The reviewer is not satisfied with one S02 value for all our samples. " 1. I am still not satisfied with selected SO2 value (it is set to 0.85). SO2 is not transferable between different samples and detection methods. It is not possible to use a value obtained from different compound using transmission measurement mode to completely different other compound measured using fluorescence mode. One method to fix SO2 value is to measure diluted solution (to avoid self-absorption) of reference material in fluorescence mode. Other is to use multiple spectra fitting for all samples of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2 parameter is the same for all samples. At the same time I am confident that CN values 5.6, 7.1 and 6.9 correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for measurements in fluorescence mode. " We do get the S02 from a similar reference material measured in transmission mode, and our samples were all measured in fluorescence mode. It is not possible to measure the diluted reference material in fluorescence mode in one or two months. If you could give me some suggestions, that would be great. -- Best Regards, Peng Liu

7 7

Open postdoc position at SSRL for theorist (DFT)
by Bone, Sharon 17 Sep '21

17 Sep '21

Hello Everyone, SSRL has an open postdoc position for a researcher with expertise in DFT, especially in application of DFT to X-ray absorption spectroscopy analysis. Please see the listing here if you are interested: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/SSR… Thanks! Sharon Sharon Bone, PhD Beamline Scientist Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory (650) 926-3104

1 0

SSRL User Meeting Sept 20-24: Session on XAS +Theory for Environmental Systems
by Bone, Sharon 17 Sep '21

17 Sep '21

Hi All, The annual SSR:/LCLS User Meeting is coming up Sept 20-24th. I am advertising a session on Thursday, Sept. 23rd, titled: "Enhancing X-ray Spectroscopy with ab initio and classical computational tools to understand environmental processes" Agenda: https://events.bizzabo.com/SLAC-UsersMeeting-2021/agenda/session/565625 In this workshop, we will examine how theoretical tools, such as DFT and MD, can be used to aid interpretation of XAS data and enhance understanding of chemical structure and reactivity in environmental systems (e.g., for biogeochemical and geochemical applications). The User Meeting will be held virtually this year and registration is free. You can find the registration link here: https://events.bizzabo.com/SLAC-UsersMeeting-2021/home We hope to see you there! Best, Sharon Bone, Ritimukta Sarangi and Jocelyn Richardson Sharon Bone, PhD Beamline Scientist Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory (650) 926-3104

1 0

EXAFS Fitting with 2 CIF files
by Zihao Yan 12 Sep '21

12 Sep '21

Dear Ifeffit members: I have a sample which is a mixture of PtFe and PtO2. In order to do the EXAFS fitting, I imported 2 CIF files on Artemis and generated the following 3 paths: >From PtO2: Pt-O @ 2.07 nm >From Pt3Fe: Pt-Pt @ 2.736 nm, Pt-Fe @ 2.736 nm Then, I used these 3 bonds to do the fitting as in the online tutorial (which used 1 CIF file). The fitting result is good in terms of R^2 but it is not scientifically correct. I think I didn't set up a parameter which determines the ratio between CIF(PtO2) and CIF(Pt3Fe). I mean there should be a parameter that regulates how much each CIF contributes to the fitting or the molar ratio between PtO2 and Pt3Fe in my system. Could someone please give me some suggestions on how to do EXAFS fitting with 2 CIF files? Is there anywhere I can set up the molar ratio between PtO2 and Pt3Fe? Yours sincerely, Zihao Yan

5 6

Re: [Ifeffit] Ifeffit Digest, Vol 223, Issue 9
by Moreau, Liane Michelle 07 Sep '21

07 Sep '21

Dear Matts, Thank you for helping Shinhyo sort out his saving problem. Now we can do science! I appreciate your help (as someone who is less technologically inclined I was pretty lost as to suggestions). It was kind of you to take the time to work with him. Thank you, Liane Liane Moreau, PhD Assistant Professor Department of Chemistry Washington State University 509-335-6073 ________________________________ 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, September 7, 2021 7:26 PM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 223, Issue 9 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… 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: IFEFFIT file saving issue (Bang, Shinhyo) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Sep 2021 02:25:50 +0000 From: "Bang, Shinhyo" <shinhyo.bang(a)wsu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] IFEFFIT file saving issue Message-ID: <DM6PR01MB48596919474C38ED6664E81F97D49(a)DM6PR01MB4859.prod.exchangelabs.com> Content-Type: text/plain; charset="euc-kr" Dear Matthew, I can certainly save the files onto a folder directly under the C: (although I have to point out that I had/have only English alphabets in the folder names). Thank you very much. I appreciate your support. Best, Shinhyo ________________________________ ?? ??: Matthew Marcus <mamarcus(a)lbl.gov> ?? Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> ?? ??: 2021? 9? 7? ??? ?? 7:14 ?? ??: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> ??: Re: [Ifeffit] IFEFFIT file saving issue This probably isn't relevant, but Desktop is actually a folder under c:. On my computer, it's C:\Users\MAMarcus. I see that 'other Matt' concurs with this and seems to be suggesting that your username may have non-ASCII characters. I'm guessing Korean. Try making a new folder under C:\ with only ASCII characters in the name. mam On 9/7/2021 6:25 PM, Bang, Shinhyo wrote: > Dear Matthew, > > I tried to save a project to "Desktop" which had no parent folder, but > the same problem occurred. I think the non-ASCII character is not the > only problem. > Still, I can save onto a usb from now on. Thank you very much. > > Best, > Shinhyo > ------------------------------------------------------------------------ > *?? ??:* Matt Newville <newville(a)cars.uchicago.edu> ?? Ifeffit > <ifeffit-bounces(a)millenia.cars.aps.anl.gov> > *?? ??:* 2021? 9? 7? ??? ?? 6:06 > *?? ??:* XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > *??:* Re: [Ifeffit] IFEFFIT file saving issue > Hi Shinhyo, > > Again, I would ask to check that the folder you are having trouble > saving to has any non-ASCII characters. For sure, ifeffit and demeter > are not going to be able to handle folder or file names with non-ASCII > characters. > > Larch is slightly better at this - it can work with files with names in > non-ASCII text encodings. To be clear, the situation with Larch is > still not ideal, especially on Windows, because > a) the base installation folder can contain only ASCII characters, > and cannot contain any spaces (apparently this is some problem > with other libraries or possibly some other variation on point b). > b) the concept of "localization" on Windows machines is sort of a > mess and many libraries (at least, from Python) don't handle this very > well. For Larch, we recently had to explicitly set locale to be "simple > C / ASCII". That sort (or should!?) mean that you can read/write files > and folders with non-ASCII characters, though I'm not certain that will > work for all character encoding sets. It's possible this will get > better with time, but it's not something that we can solve. > > For ifeffit / demeter there is simply no hope for non-ASCII text to ever > be handled. > > > On Tue, Sep 7, 2021 at 7:45 PM Bang, Shinhyo <shinhyo.bang(a)wsu.edu > <mailto:shinhyo.bang@wsu.edu>> wrote: > > Dear Matthew, > > I tried to save the project onto a usb, and it WORKed! Thank you so > much for your help. > > Best, > Shinhyo > ------------------------------------------------------------------------ > *?? ??:* Matthew Marcus <mamarcus(a)lbl.gov > <mailto:mamarcus@lbl.gov>> ?? Ifeffit > <ifeffit-bounces(a)millenia.cars.aps.anl.gov > <mailto:ifeffit-bounces@millenia.cars.aps.anl.gov>> > *?? ??:* 2021? 9? 7? ??? ?? 4:11 > *?? ??:* ifeffit(a)millenia.cars.aps.anl.gov > <mailto:ifeffit@millenia.cars.aps.anl.gov> > <ifeffit(a)millenia.cars.aps.anl.gov > <mailto:ifeffit@millenia.cars.aps.anl.gov>> > *??:* Re: [Ifeffit] IFEFFIT file saving issue > There are other characters that Windoze doesn't like in filenames: > |\/*":<>? > mam > > On 9/7/2021 3:58 PM, Matt Newville wrote: > > Hi Shinhyo, Liane, > > > > On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo <shinhyo.bang(a)wsu.edu <mailto:shinhyo.bang@wsu.edu> > > <mailto:shinhyo.bang@wsu.edu <mailto:shinhyo.bang@wsu.edu>>> wrote: > > > > Thank you for the response. > > The OS is Windows 10. > > In addition to the symptom that was described aforehand, Athena > > freezes when I try to save the file. > > > > > > Is it possible that the folder or file you are saving to has a space or > > other non-ASCII character in it? I believe that non-ASCII characters > > are known to cause problems. > > Can you check whether you can save a file anywhere (maybe even the > > top-level "C:\" folder)? > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > > > Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > > Unsubscribe: > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > Unsubscribe: > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > > > -- > --Matt Newville <newville at cars.uchicago.edu > <https://urldefense.com/v3/__http://cars.uchicago.edu__;!!JmPEgBY0HMszNaDT!9…>> > 630-327-7411 > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…

1 0

IFEFFIT file saving issue
by Moreau, Liane Michelle 07 Sep '21

07 Sep '21

Dear fellow XAFS enthusiasts, My student is running into some trouble in that he can't seem to get any files from IFEFFIT (be it project or exported data files) to save on his computer. When he saves, no files show up in the folder he has saved to. I watched him do this myself to confirm this is indeed the case. I have never run into this issue, nor have I heard of anyone else having this issue previously, but has anyone else run into this issue, and, if so, how did they solve it? I imagine there might be something incompatible with the student's computer settings somehow, although he is able to use the software just fine, it is just that nothing will save. He tried uninstalling and reinstalling Demeter, but unfortunately that did not fix the problem. I appreciate any experience anyone can share that might be helpful. Thank you! Liane Liane Moreau, PhD Assistant Professor Department of Chemistry Washington State University 509-335-6073

4 11

EXAFS fitting - noisy data
by Hu, Yang (HIU) 01 Sep '21

01 Sep '21

Dear Ifeffit members, I have some fundamental questions regarding noisy data, and I am wondering how to tell whether the data quality worth doing Fourier transformation/EXAFS fitting or not. For example, the attached MnO chi(k) data becomes noisy from 7 Å-1 when it was measured up to 12 Å-1. The deglitching (left: red -> blue) mitigated the strong dips but the high-k end still has too much noise. I practiced the FT and fitting the 1st and 2nd shells by using the lower part. But My questions here are: 1) How noisy would be too noisy? Like the data between 8 and 10 Å-1 in the attached file, can they still be included for the FT? 2) We can choose the high-k end based on the signal-to-noise ratio, but to what extend? With data being noisy from even 5 or 6 Å-1, can they still be used? 3) For fitting the 1st and 2nd shells, I still lack of clear understanding how the high-k portion can influence. If I measure a set of samples, and one of them has much noisy data so a shorter k-range is picked up for background subtraction and FT. In this case, can I still consider the change or evolution in the fitted parameters systematic? Thank you in advance, Best regards, Yang

3 2

Manuscript comments regarding EXAFS modeling
by Peng Liu 29 Aug '21

29 Aug '21

Dear Ifeffit members, I received the following two comments. " Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a fixed value (0.85). This factor is specific to particular chemical compound and sample preparation and quality (mostly homogeneity), measurement method (e.g. absorption, fluorescence). Authors can find in literature [e.g. Rehr2000] that SO2 for ideal samples (having no other effects) represent multielectron effects, which by definition depend on valence and ligands. Even more, SO2 is correlated with Debye-Waller factor (σ²) and coordination number (CN), so any chosen value will be compensated by CN and σ². As coordination numbers are used as quantitative indicators in discussion and following conclusions. I would request to clarify the selection criteria for SO2 values and advise to revise this approach (i.e. not to fix SO2 as the same value for all samples). I do not expect drastic changes in obtained CN values, but this should be tested. Comment 2: As I mentioned previously, coordination number (CN) is correlated with Debye-Waller factor (σ²). My question is: how this correlation is managed (eliminated)? Most probably (in FEFFIT) this is done by using 3 separate values for n (1,2,3), where n is a power in expression chi(k)*(k^n). " I used Artemis for the calculation. 1) Because S02 and CN are multiplication relations in the EXAFS equation, as we usually do, we fixed S02 to obtain CN for unknown samples. 2) there are outputs regarding the correlation between different fitting parameters from Artemis. Is there a way to manage or eliminate the correlation as the reviewer mentioned using Artemis or Larch? If you also could give me some suggestions to answer the comments, that would also be greatly appreciated. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm

3 2

Re: [Ifeffit] [EXT] Ifeffit Digest, Vol 222, Issue 6
by Christopher Chantler 28 Aug '21

28 Aug '21

Just a little comment. If you propagate uncertainties, there is mathematically no difference between the weightings and expected fits for k powers times chi, so differences will mainly be in correlated parameters. Without propagating uncertainties you can get different answers in different regions of k fitting but the differences do not reflect physical parameters. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ 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: Sunday, 29 August 2021 3:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [EXT] Ifeffit Digest, Vol 222, Issue 6 External email: Please exercise caution 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. Manuscript comments regarding EXAFS modeling (Peng Liu) 2. Re: Manuscript comments regarding EXAFS modeling (Matthew Marcus) ---------------------------------------------------------------------- Message: 1 Date: Sat, 28 Aug 2021 10:40:37 +0800 From: Peng Liu <liupeng5182(a)gmail.com> To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Manuscript comments regarding EXAFS modeling Message-ID: <CAJniE5J7VBPfTkKjU01fWUUzYoFR-DqarJmwNuLuDfK5GO2Niw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Ifeffit members, I received the following two comments. " Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a fixed value (0.85). This factor is specific to particular chemical compound and sample preparation and quality (mostly homogeneity), measurement method (e.g. absorption, fluorescence). Authors can find in literature [e.g. Rehr2000] that SO2 for ideal samples (having no other effects) represent multielectron effects, which by definition depend on valence and ligands. Even more, SO2 is correlated with Debye-Waller factor (??) and coordination number (CN), so any chosen value will be compensated by CN and ??. As coordination numbers are used as quantitative indicators in discussion and following conclusions. I would request to clarify the selection criteria for SO2 values and advise to revise this approach (i.e. not to fix SO2 as the same value for all samples). I do not expect drastic changes in obtained CN values, but this should be tested. Comment 2: As I mentioned previously, coordination number (CN) is correlated with Debye-Waller factor (??). My question is: how this correlation is managed (eliminated)? Most probably (in FEFFIT) this is done by using 3 separate values for n (1,2,3), where n is a power in expression chi(k)*(k^n). " I used Artemis for the calculation. 1) Because S02 and CN are multiplication relations in the EXAFS equation, as we usually do, we fixed S02 to obtain CN for unknown samples. 2) there are outputs regarding the correlation between different fitting parameters from Artemis. Is there a way to manage or eliminate the correlation as the reviewer mentioned using Artemis or Larch? If you also could give me some suggestions to answer the comments, that would also be greatly appreciated. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm

1 0

Global XAS seminar on Thursday: Ultrafast x-rays...
by Gerald T. Seidler 23 Aug '21

23 Aug '21

Dear ifeffit mailing list recipients, See seminar details below, and please send recommendations for speakers. Jerry Seidler (seidler(a)uw.edu) ------------------------------------ *Deciphering the Dynamics of the Ferrous Cytochrome c Photodissociative State Using Ultrafast X-ray Spectroscopy and Scattering Methods* Prof. Michael Mara (Northwestern University) Thursday August 26: 9 am Seattle (PDT), 12 noon NY, 5 pm London, 6 pm Berlin, 7 pm Moscow link: https://washington.zoom.us/j/92742942089 password: EXAFS *Abstract*: The femtosecond X-ray pulses provided by X-ray free electron lasers enable tracking of electronic and structural dynamics in metalloprotein active sites immediately following photoexcitation. Here, we decipher the evolution of the photodissociated state of ferrous cytochrome c using Fe K-edge X-ray absorption and emission spectroscopies, as well as X-ray solution scattering. By absorption and emission methods, we track the rebinding of the cleaved ligand and identify an electronic intermediate state involved in ligand dissociation. X-ray scattering further defines the early-time active site structure while following heat dissipation from the hot ground state of the active site into the solvent. By relating the active site temperature to the kinetics of ligand recombination, we quantify the protein bulk contribution to stabilizing the protein iron-methionine bond; this is the first direct measurement of the protein entatic state, whereby the protein regulates activity through modest tuning of the energetics of the active site. *Suggested reading:* [1] Mara, M. W. et al., Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy, Science, 2017, 356, 1276-1280. https://science.sciencemag.org/content/356/6344/1276.full [2] Reinhard, M. E. et al, Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c, Nature Communications, 2021, 12, 1086. https://doi.org/10.1038/s41467-021-21423-w -- *Gerald Seidler* *Professor, Physics Department* *University of Washington* *http://faculty.washington.edu/seidler/index.html <http://faculty.washington.edu/seidler/index.html>* *seidler(a)uw.edu <seidler(a)uw.edu>*

1 0

XAS/MEX workshop at the Australian Synchrotron 26-27 August - Registrations closing soon! [SEC=OFFICIAL]
by MITCHELL, Valerie 22 Aug '21

22 Aug '21

[https://mcusercontent.com/50e44d7c99f0bcbe3f66cb4e9/images/3527f043-2633-a6…] Registrations closing soon! XAS & MEX Workshop [https://cdn-images.mailchimp.com/template_images/gallery/ribbon_bottom.png] [https://cdn-images.mailchimp.com/template_images/gallery/icon_clock2.gif] Thursday 26 & Friday 27 August, 2021 [https://cdn-images.mailchimp.com/template_images/gallery/icon_info2.gif] [https://mcusercontent.com/50e44d7c99f0bcbe3f66cb4e9/images/da939b82-7a45-84…] The Australian Synchrotron will be hosting a two day workshop designed for new XAS users and those interested in the capabilities of the soon-to-come MEX beamline. Registrations close at 24:00 AEST, 24 August, 2021. Program: Day 1 On the first day, talks from beamline scientists and experts in the field will highlight the capabilities of the XAS and MEX beamlines, discuss how to get the most out of beamtime, and present case studies illustrating how these techniques can help solve questions in earth, biological and chemical sciences. Day 2 Day two will feature a hands-on tutorial in XANES data analysis led by Dr. Ryo Sekine of the University of the Sunshine Coast. Opportunities will be available to discuss common data issues with beamline scientists. Presenters Dr. Niloofar Karimian, Southern Cross University Assoc. Prof. Neeraj Sharma, University of New South Wales Prof. Peter Kopittke, University of Queensland Dr. Mark Hackett, Curtin University Dr. Rosalie Hocking, Swinburne University of Technology Dr. Ryo Sekine, University of the Sunshine Coast XAS Beamline Scientists: Dr. Bernt Johannessen, Dr. Valerie Mitchell, Dr. Jessica Hamilton MEX Beamline Scientists: Dr. Chris Glover, Dr. Jeremy Wykes, Dr. Simon James, Dr. Emily Finch, Dr. Krystina Lamb Program<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [https://cdn-images.mailchimp.com/template_images/gallery/icon_locator2.gif] Free Virtual Event [https://cdn-images.mailchimp.com/template_images/gallery/icon_share2.png] Registration is essential Click to register <https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Facebook]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Facebook<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Twitter]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Twitter<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Website]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Website<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [YouTube]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> YouTube<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> You are receiving this email because you are an ANSTO User. Edit Subscription Preferences<https://ansto.us17.list-manage.com/profile?u=50e44d7c99f0bcbe3f66cb4e9&id=0…> Unsubscribe<https://ansto.us17.list-manage.com/unsubscribe?u=50e44d7c99f0bcbe3f66cb4e9&…> [https://cdn-images.mailchimp.com/template_images/gallery/icon_contact2.gif] ANSTO New Illawarra Rd LUCAS HEIGHTS, NSW 2234 Australia [Email Marketing Powered by Mailchimp]<http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…> OFFICIAL

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 222, Issue 2
by Vitova, Tonya (INE) 17 Aug '21

17 Aug '21

Hi everybody, I would like to draw your attention to the following postdoc position: https://www.pse.kit.edu/karriere/joboffer.php?id=85889&language=en It will be great if you forward it to suitable candidates. Thank you in advance and best from me, Tonya -----Ursprüngliche Nachricht----- Von: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Im Auftrag von ifeffit-request(a)millenia.cars.aps.anl.gov Gesendet: Montag, 16. August 2021 23:46 An: ifeffit(a)millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 222, Issue 2 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Problem Importing CIF files into Larch (Matt Newville) 2. Re: Problem Importing CIF files into Larch (Vincent Wu) 3. Re: Problem Importing CIF files into Larch (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Mon, 16 Aug 2021 15:21:13 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem Importing CIF files into Larch Message-ID: <CA+7ESbrWMTGYTa+T+2u+++Qz92JQyTJFDqsFkhVZCCqMQfiXhw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Amol, Sorry for the delay, I was offline most of last week. Thanks for posting these CIF files. I think these should be usable -- the basic "cif2feffinp()" function works on these to generate a valid Feff.inp, but the GUI CIF Browser is currently expecting additional fields such as publication information. I guess those fields should be optional. I think there is another issue with using multi-site CIF structures that I want to look into. So, I hope to get this fixed soon, but I also want to tackle a few other issues before posting a completely new version. --Matt On Tue, Aug 10, 2021 at 4:12 PM <amolagarwal2025(a)u.northwestern.edu> wrote: > Hi, > > I hope you are doing well. I am writing regarding some issues that I > am having with opening my CIF files in Larch. I have used these same > CIF files in the past in Artemis to run feff calculations. When I open > these files in the Larch open feff tab, it shows a dialog box saying > that there is an error opening the CIF file. This is happening with > all my CIF files and I am not sure why. I am attaching a couple of > these CIF files. I would really appreciate some help on this. > > > > Amol Agarwal > > PhD Student > > Materials Science & Engineering | Northwestern University > > > _______________________________________________ > 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 >

1 0

Problem Importing CIF files into Larch
by amolagarwal2025＠u.northwestern.edu 16 Aug '21

16 Aug '21

Hi, I hope you are doing well. I am writing regarding some issues that I am having with opening my CIF files in Larch. I have used these same CIF files in the past in Artemis to run feff calculations. When I open these files in the Larch open feff tab, it shows a dialog box saying that there is an error opening the CIF file. This is happening with all my CIF files and I am not sure why. I am attaching a couple of these CIF files. I would really appreciate some help on this. Amol Agarwal PhD Student Materials Science & Engineering | Northwestern University

3 3

XAFS short course at BNL: Nov. 17-19
by Anatoly Frenkel 30 Jul '21

30 Jul '21

Dear subscribers: As it does every year in the Fall, Synchrotron Catalysis Consortium at Brookhaven National Laboratory will run a short course from November 17 to 19 at BNL. As in the last year, when it gathered 80 participants, it will be virtual, and the course will be limited to 80 registered participants again. The course application deadline is August 15. It will be an introductory course, gearing at the beginner level. The link with the course information and application instructions is here: https://www.bnl.gov/xafs2021/ Please share this information with your group members and anyone else who may be interested. Thank you very much, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

1 0

Larch 0.9.55
by Matt Newville 18 Jul '21

18 Jul '21

Hi Folks, Larch 0.9.55 is now available for download. This comes only two weeks after the announcement for 0.9.53, but there have been several important improvements especially for Windows users outside of the US, and based on bugs found or features requested during the Larch for XAFS Analysis Workshop at the Virtual XAFS 2021 conference (there was a 0.9.54, but a few things were fixed since then too!). If you have installed a recent version of Larch and are on a machine connected to the internet, you should see a notice that version 0.9.55 is available, and can use that notice to automatically install the update. That will be much faster than installing from the full installer. A series of instructional videos made for this workshop on using Larch's XAS Viewer application for various aspects of XANES and EXAFS analysis are now publicly available at https://www.youtube.com/playlist?list=PLgNIl_xwV_vK4V6CmrsEsahNCAsjt8_Be. Comments, questions, suggestions on these are most welcome, either on youtube or here. For folks without access to youtube.com, these videos are also at https://millenia.cars.aps.anl.gov/videos/XrayLarch/ The changes here are relatively minor compared to the changes made in 0.9.53 (see https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2021-July/010251.html) The most important changes and fixes since 0.9.53 are: - Larch's GUI applications should again work without problems on non-US Windows 10 machines. There was a serious bug (possibly since Larch 0.9.52) for using wxPython applications with Python>=3.8 and wxPython>=4.1.0. I believe we have a workaround, at least for now. - Fixes for turning CIF structures into Feff inputs and running Feff: -- more external CIF files from Crystallography Open Database and Materials Project can be converted to Feff.inp. -- external Feff.inp files can be loaded and run. -- the name of the folder created for any Feff calculation can be renamed before running Feff. - the plot selection choice in the XAS normalization panel for "one group" and "selected groups" are no longer reset each time a data set is selected. - A reference spectrum can now be set for any XAFS spectrum. When aligning or energy-shifting XAFS data, you can now easily select all of the spectra that share a reference and apply the same energy shift to those spectra. You can also easily select a reference group for one XAS spectrum and copy that to a set of other "selected spectra". There is not (yet?) a way to select a reference channel from a file when importing data, so these must be read separately and assigned. - a bug was fixed on the EXAFS / background subtraction panel on "copied groups" to ensure that processing parameters (kweight, rbkg, etc) are kept separate. - For linear combination fitting, a single energy shift can be varied during the fit, shifting the unknown data to match the combination of a (presumably aligned) set of standards. - For pre-edge peak fitting and Feff Path fitting, entries in the "fit history" can have user-specified labels which can be more meaningful than the default "Fit #1", "Fit #2", etc. - testing is now done only with Github Actions, not with the appveyor service. I want to thank all the people who took part in the workshop and gave feedback -- XAS Viewer is a lot better than it was a week ago. Thanks to Monica Bairagi and Nengchuan Tian for help, and special thanks to Klemen Bucar for helping track down and solving the Locale issue and working on the testing tools. And also thanks to Mauro Rovezzi for continued suggestions and fixes. If you have any questions, problems, or suggestions, please let me know. --Matt

1 0

Position available: Postdoc (f/m/d) specialization in chemistry or physics
by Zimina, Anna (IKFT) 15 Jul '21

15 Jul '21

Dear all, we are looking for a chemist or physicist with a doctorate and several years of experience in the fields of catalysis, laboratory support, synchrotron radiation source, commissioning of in situ cells for X-ray absorption spectroscopy, material characterization, modelling of spectra and detailed EXAFS analysis. The main tasks include the scientific supervision of a beamline for X-ray absorption spectroscopy at the Karlsruhe synchrotron (CAT-ACT) and structural investigations of mono- and bimetallic nanoparticles for various catalytic processes. Further information can be found here: https://www.pse.kit.edu/karriere/joboffer.php?id=86224&language=en ______________________________________________________________________________________ Karlsruhe Institute of Technology (KIT) Institute of Catalysis Research and Technology (IKFT) Dr. Anna Zimina Beamline scientist Hermann-von-Helmholtz-Platz 1 Building 345 Office 304 76344 Eggenstein-Leopoldshafen Phone: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail <mailto:anna.zimina@kit.edu> anna.zimina(a)kit.edu

1 0

Position available: NSLS-II Quick Absorption and Scattering (QAS) Lead Beamline Scientist
by Stavitski, Eli 14 Jul '21

14 Jul '21

Dear all, NSLS-II is seeking high-profile candidates for the lead scientist position of the QAS beamline. The lead beamline scientist has a vision, defines the strategy to advance the science program, enhances the beamline capabilities and proposes facility improvements and upgrades. The lead beamline scientist develops, monitors, and maintains safe operating conditions at the beamline and provides oversight of all staff and users of the beamline. The lead beamline scientist is responsible for the operation of the beamline in support of the NSLS-II facility users, supervises a group of scientific and technical staff, reaches out effectively to the relevant scientific and industrial user communities, develops collaborative programs, and liaises with vendors. The lead beamline scientist works closely with users, oversees the design, implementation, maintenance and upgrade of the beamline equipment, provides guidance and oversees progress in advanced data management and analysis. https://jobs.bnl.gov/job/upton/lead-beamline-scientist-quick-x-ray-absorpti… ____________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov>

1 0

July 15 seminar: X-ray Spectroscopy of Light-induced Chemical Reactions -- A New Universal Probe of Photoexcited Molecular Dynamics
by Gerald T. Seidler 12 Jul '21

12 Jul '21

Dear Colleagues, The Global XAS Journal club is an ongoing virtual seminar series. The seminar for this week in the Americas/Europe time window is below -- you can forward this to interested persons in the XAS community but *please do not make any public posting *(we've had problems with zoom-bombing). Please email me seidler(a)uw.edu to be added to the direct mailing list, where you would get this information for both the Americas/Europe and also Asia-Oceania/Europe timed seminars. About 70 prior lectures are available at the youtube channel https://www.youtube.com/channel/UCwtkyiTV4BltKTQ7tS0CltQ/videos Looking to August and the autumn term I am particularly interested in finding: (1) XAS speakers who are early career scientists, such as postdocs, assistant professors, or new staff scientists at facilities and national labs, and (2) beamline scientists to speak about capabilities and science outcomes/goals at their beamlines. Please send suggestions! Cheers, Jerry Seidler (seidler(a)uw.edu) ---------------------------------------------------------------------------------- *X-ray Spectroscopy of Light-induced Chemical Reactions -- A New Universal Probe of Photoexcited Molecular Dynamics * Prof. Aditi Bhattacherjee (University of Iowa) Thursday July 15: 9 am Seattle (PDT), 12 noon NY, 5 pm London, 6 pm Berlin, 7 pm Moscow link: https://washington.zoom.us/j/96246359168 password: EXAFS *Abstract*: Photochemical reactions of small organic molecules are prevalent in the atmosphere, in biological machineries and photocatalytic materials. Recent laboratory breakthroughs have enabled access to ultrafast X-ray spectroscopy at the carbon K-edge (1s absorption edge of carbon, at 284 electron volts). This has opened new avenues to explore ultrafast reaction mechanisms in a host of photochemical reactions in small molecules with high temporal resolution.[1] In this talk, I will discuss experiments that show how the excitation of 1s-core electrons of the constituent carbon atoms in organic molecules is a key spectroscopic probe of photoinduced molecular dynamics. First, I will present the mechanistic details that emerge in the ultrafast ring-opening reactions of hydrocarbon as well as heteronuclear organic molecules from the direct orbital sensitivity of time-resolved X-ray absorption spectroscopy at the near edge.[2,3] Second, I will also show that in favorable cases, ultrafast intersystem crossing in molecules can be identified even though X-ray absorption spectroscopy is not directly sensitive to spin states.[4] Our work reveals that future chemical applications of this method at multiple absorption edges may provide new universal spectroscopic probes of photoinduced molecular dynamics. *Suggested reading*: [1] Bhattacherjee and Leone AccChemRes 21, 3203, 2018. https://pubs.acs.org/doi/10.1021/acs.accounts.8b00462 [2] Attar, Bhattacherjee, Das, Schnorr, Closser, Prendergast, and Leone Science 356, 54, 2017. https://science.sciencemag.org/content/356/6333/54 [3] Bhattacherjee, Schnorr, Oesterling, Yang, Xue, Vivie-Riedle and Leone JAmChemSoc 140, 39, 12538, 2018. https://pubs.acs.org/doi/10.1021/jacs.8b07155 [4] Bhattacherjee, Das, Schnorr, Attar and Leone JAmChemSoc 139, 46, 2017. https://pubs.acs.org/doi/abs/10.1021/jacs.7b07532 -- *Gerald Seidler* *Professor, Physics Department* *University of Washington* *http://faculty.washington.edu/seidler/index.html <http://faculty.washington.edu/seidler/index.html>* *seidler(a)uw.edu <seidler(a)uw.edu>*

1 0

Another Mac OS install question
by Jilbert, Tom 07 Jul '21

07 Jul '21

Hi Ifeffit folks, I am attempting installation via macports on Mac OS Big Sur, and there are problems to build demeter. Before I send around a log file, I wanted to check if anyone is still maintaining/solving macports issues (Joe Fowler?). ie is it worth it to keep trying. From the archive it seems that installing a virtual machine is a recommended alternative. Cheers, Tom

2 1

Farrel Lytle database
by Monica Bairagi 06 Jul '21

06 Jul '21

Hello all: I am looking forward to standard metal foil data of titanium. I downloaded the data from the Farrel Lytle database but I can not import it into Athena. I looked into the data, it looked wired for me. As Athena expects data to be in columns of energy but this data is not recorded by energy but by steps of the monochromator rotation stage. I am wondering if anyone has any idea how to import or transfer the data. I am attached herewith the data file. Thanks Monica Bairagi Ph.D. Student, Ujjain, India

4 3

Larch 0.9.53
by Matt Newville 03 Jul '21

03 Jul '21

Hi Folks, Larch 0.9.53 is now available for download and use. Although the last announcement here was in April for version 0.9.51, there have been several improvements especially to the XAS Viewer application since the last release, mostly in anticipation of upcoming workshops and short courses. - There are important fixes for reading Spec/Bliss HDF5 files from ESRF - thanks to Mauro Rovezzi for this. You can now import multiple XAS spectra from Spec/HDF5 files. - XAS Viewer now supports doing Feff6l or Feff8l calculations and has a GUI interface for doing a Feffit fit to a sum of Feff paths. In the current GUI frame, this is limited to analyzing one dataset at a time. This brings up a related feature: - A database (sqlite3) of CIF structures from the American Mineralogist Crystal Structure Database (http://rruff.geo.arizona.edu/AMS/amcsd.php) is included. The version of this database in the source code contains about 9000 structures. If your machine is well-connected to the internet and can reach https:/millenia.cars.aps.anl.gov, a more complete version (~30 Mb) with 20,000 structures will be downloaded and used. To be clear, the 9000 structures in the smaller set are probably sufficient -- what is removed is some CIFs from publications with many similar structures (T or P dependence) or structures so large and complex that they will be hard to make into single Feff files. - The CIF files from this DB or other CIF files (well, CIF is notoriously variable!) can be automatically converted to Feff input files (using python tools from the Materials Project, modified a bit). Because many of these CIF structures contain fractional occupancy, that is handled (probably poorly, but at least not failing) by randomly selecting atoms based on the site occupancy. - XAS Viewer has a CIF Browser (from the Feff menu) where you can browse by mineral name, included atoms, etc. From that you can generate a Feff6l or Feff8l input file, potentially edit that input file, and run Feff to generate path files. These will be organized in your home folder (C:\Users\Name\larch\feff for most Windows users, $HOME/.larch/feff for Linux/MacOS). There is also a Feff browser to select Feffnnnn.dat files from your previous Feff runs and bring them into the "Feffit" tab in XAS Viewer to use in the sum of paths fitting of EXAFS spectra. Of course, all of this Feff and Feff fitting interface should be viewed as "initial release" and comments, suggestions, and bug reports are welcome. The notes above are approximately the extent of the documentation, though some videos of using this will be publicly available in a few weeks. There are updated binary installers for Windows, MacOSX, and Linux. There are also updated "GetLarch.sh" and "GetLarch.bat" scripts that also hopefully fix any earlier problems. If you have any questions, problems, or suggestions, please let me know. --Matt

1 0

Beamline Scientist position
by Kelly, Shelly D. 01 Jul '21

01 Jul '21

Hello XAFS community: I'm excited to let you know that we have an opening for beamline scientist within the Spectroscopy group at the Advanced Photon Source. Please help spread the word. https://bit.ly/3iN7Ehe Kind Regards, Shelly Kelly Spectroscopy Group Leader Advanced Photon Source

1 0

Question about CsNO3 L3 edge
by 田能全 01 Jul '21

01 Jul '21

Hi everyone, My colleague sent me data of liquid CsNO3 sample measured using fluorescence model. According to the attached figure, I don't understand why mu(E) increased with increasing energy before and after the L3 edge. Does it make sense for cesium? Thanks. Nengchuan [image: image.png]

5 7

Postdoc position for XAFS analysis
by 이국승(에너지환경소재연구팀) 30 Jun '21

30 Jun '21

Dear Ifeffit members, We are looking for a postdoc candidate for XAFS analysis in PAL. Tasks will be 1. XAFS analysis of electrochemical energy materials 2. Beamline management at Nano-probe XAFS beamline (BL8C) 3. One's own research The position requires PhD degree in Electrochemistry, Chemistry, Materials science or Physics, Excellent writing and communication skills in English, Experience in XAFS analysis. The position begins at any time in this year but earlier is better. If you are interested in this position, please send your CV including list of publications to Dr. Kug-Seung Lee. (lks3006(a)postech.ac.kr) Additional documents can be required including references. Kind regards, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Scopus : https://www.scopus.com/authid/detail.uri?authorId=56953635300 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

1 0

Bi L3 standards
by Schlesinger, Danielle R. 29 Jun '21

29 Jun '21

Hi everyone, Does anyone have a set of Bi L3 edge standards that they would be willing to share? Thank you! Danielle Danielle R. Schlesinger, Ph.D. Post Doctoral Fellow – AOS/QPC Johns Hopkins University – Applied Physics Laboratory Tel: (240) 592-5243

2 2

Cannon start larch on ubuntu 20.04.2 LTS
by Don Baker, Dr. 29 Jun '21

29 Jun '21

Hi Folks, I think I am missing something obvious and am hoping that you can quickly tell me my mistake, so let me begin my story: I downloaded xraylarch-2021-060Linux-x86_64.sh into downloads on a Asus Zenbook using ubuntu 20.04.2 LTS I ran the command bash ./xraylarch-2021-060Linux-x86_64.sh Larch appears to have been correctly installed, but because I am using a gnome desktop no shortcuts appeared on my desktop (as promised) and there were no files that I could identify as shortcuts in my Downloads directory (which was set to display hidden files) I then moved to the /xraylarch/bin and tried to launch larch using python and this is what happened: python larch Traceback (most recent call last): File "larch", line 5, in <module> from larch.apps import run_larch File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/builtins.py", line 27, in <module> from . import xrd File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/__init__.py", line 25, in <module> from .amscifdb import CifStructure, get_amscifdb, get_cif, find_cifs File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/amscifdb.py", line 40, in <module> from pymatgen.io.cif import CifParser File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/io/cif.py", line 25, in <module> from pymatgen.core.composition import Composition File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/__init__.py", line 21, in <module> from .lattice import Lattice # noqa File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/lattice.py", line 23, in <module> from pymatgen.util.coord import pbc_shortest_vectors File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/util/coord.py", line 17, in <module> from . import coord_cython as cuc File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject I also tried to use python to start larch_server and xas_viewer and had the same results. I also have the same results if I try to launch larch using ./larch This is the information on the version of Python that I am running: Python 3.8.10 (default, Jun 4 2021, 15:09:15) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. Any suggestions anyone has to offer will be appreciated. Wishing you all the best, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, McGill University

2 2

Cannot start larch on ubuntu 20.04.2 LTS
by Don Baker, Dr. 28 Jun '21

28 Jun '21

Hi Folks, I think I am missing something obvious and am hoping that you can quickly tell me my mistake, so let me begin my story: I downloaded xraylarch-2021-060Linux-x86_64.sh into downloads on a Asus Zenbook using ubuntu 20.04.2 LTS I ran the command bash ./xraylarch-2021-060Linux-x86_64.sh Larch appears to have been correctly installed, but because I am using a gnome desktop no shortcuts appeared on my desktop (as promised) ,and there were no files that I could identify as shortcuts in my Downloads directory (which was set to display hidden files) I then moved to the /xraylarch/bin and tried to launch larch using python and this is what happened: python larch Traceback (most recent call last): File "larch", line 5, in <module> from larch.apps import run_larch File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/builtins.py", line 27, in <module> from . import xrd File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/__init__.py", line 25, in <module> from .amscifdb import CifStructure, get_amscifdb, get_cif, find_cifs File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/amscifdb.py", line 40, in <module> from pymatgen.io.cif import CifParser File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/io/cif.py", line 25, in <module> from pymatgen.core.composition import Composition File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/__init__.py", line 21, in <module> from .lattice import Lattice # noqa File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/lattice.py", line 23, in <module> from pymatgen.util.coord import pbc_shortest_vectors File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/util/coord.py", line 17, in <module> from . import coord_cython as cuc File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject I also tried to use python to start larch_server and xas_viewer and had the same results. I also have the same results if I try to launch larch using ./larch This is the information on the version of Python that I am running: Python 3.8.10 (default, Jun 4 2021, 15:09:15) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. Any suggestions anyone has to offer will be appreciated. Wishing you all the best, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, McGill University

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 220, Issue 2
by Danilo Oliveira de Souza 15 Jun '21

15 Jun '21

Hi Teresa and Matt, Concerning the SPOIL function, some months ago I digged on that and I found the first paper (I guess) on this topic, which is from Edmund R. Malinowski in an Analytical Chimica Acta, 1978 ( 10.1016/S0003-2670(01)83099-3 <https://doi.org/10.1016/S0003-2670(01)83099-3> ). Instead of reproducing this paper here (it is not just a couple of lines), I let to you read the precise definition of such a function. I have the copy on pdf of the paper if any of you is interested in it. Cheers, Danilo *Danilo OLIVEIRA DE SOUZA* *Research Fellow @ ELETTRA Sincrotrone, XAFS beamline* * Strada Statale 14 - km 163,5 in AREA Science Park* * 34149 Basovizza, Trieste ITALY* *http://www.elettra.trieste.it/elettra-beamlines/xafs.html <http://www.elettra.trieste.it/elettra-beamlines/xafs.html>* * e-mail: danilo.oliveiradesouza(a)elettra.eu <danilo.oliveiradesouza(a)elettra.eu> * * mobile: (+39) 351 50.30.731 bureau: (+39) 040-375-8604* Em qui., 10 de jun. de 2021 às 19:00, < ifeffit-request(a)millenia.cars.aps.anl.gov> escreveu: > 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: PCA Sixpack results compared to Athena (etc.) (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 10 Jun 2021 07:08:19 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] PCA Sixpack results compared to Athena (etc.) > Message-ID: > <CA+7ESbq= > J9fZ3Y0PPuyjShk+XNFOGjOTktX4m7oyu6PFfTwM5w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Teresa, > > I'm sorry that I cannot give you a definitive answer. I should admit that > when adding PCA methods to Larch and XAS Viewer (which I invite you to try > out), I tried to follow the scikit-learn approach but also to follow the > Athena implementation. I think I never tried to test against the results > from SixPack. FWIW, Larch only does (easily) PCA on normalized mu(E) or > its derivative. I suppose PCA on chi(k) could be added, but I'm a bit sort > of skeptical of this. > > In fact, the code at > https://github.com/xraypy/xraylarch/blob/master/larch/math/pca.py (and, > just to be clear, having this both in Python and publicly available is > motivated by having these conversations of "what does it do?") has a few > different methods to train a PCA set: one directly from scikit-learn, one > basically reproducing Demeter's PCA.pm (modulo slight differences in > underlying math libraries, which should be insignificant), one that aims to > use only non-negative components (not really worth in my opinion), and one > that is sort of hand-coded and including the IND statistic. I don't know > what SixPack does. > > I cannot really explain why, but the default "readily exposed in Larch XAS > Viewer" is to use the hand-coded version of `pca_train`. In fact, they > should be all more or less interchangeable. I did some tests with these > but that was now several years ago, but it might be worth trying that > again. If you're up for that, please do try. If not and would like to > send your project and an outline of what you get, I might be able to look > at this too. > > For "target transformation", this is implemented as `pca_fit`: how well can > a data set be explained by the first N components of a training model? > > For fit statistics: I have seen "SPOIL" used several places in the EXAFS > literature but am afraid I do not actually know of a definition for this. > If anyone can explain what these are, that would be helpful. Larch can > calculate the F1 and IND statistics that are more common in the PCA > literature. XAS Viewer exposes and automatically plots IND - it's a very > useful way to select how many components are significant. > > I'm pretty sure that does not answer your actual question, but maybe it > will be helpful. If you or anyone else has suggestions for additions, > improvements, or other optional methods or statistics for PCA and/or > related methods, please let me know. > > --Matt > > > On Tue, Jun 8, 2021 at 7:43 AM <t.zahoransky(a)mineralogie.uni-hannover.de> > wrote: > > > > > Dear XAS Community, > > > > I stumbled over the issue that a PCA on 20 EXAFS spectra (k?, k = > > 2.0-11.0 ?-1) perfomed in Sixpack does not give the same results > > (Eigenvalues, variance) as in Athena. However, when I use other > > statistical programs (i.e., TIBCO Statistica or SPSS), I get the same > > results as reported in Athena. I tested this with another EXAFS > > dataset of over 30 samples and the problem persited. > > > > An old entry from 2017 in the ifeffit mailing list ("[Ifeffit] > > Calculation of SPOIL value for the reconstruction of standard > > spectra"), told me that as of Sixpack version 1.4 on, a new/different > > PCA algorithm from the scikit-learn Python package is used. > > > > So I downloaded older versions of Sixpack (i.e. 1.3) and used "Use Old > > PCA"-selection in the "Rotation" menu bar, which actually gave > > different results. However, they are still different from the > > Athena/Statistical program results. > > > > My question is: What is behind this? Is there some sort of > > normalization or axis rotation, that leads to the different values? Is > > there any way to change this so that the results are comparable to > > other programs? > > > > As I need to use the Target Transform option after PCA, which is not > > yet possible in Athena, I am at a loss as to how to deal with these > > different results and where they come from. > > > > > > Thank you very much for your help, > > > > Teresa > > > > > > -- > > Teresa Zahoransky > > > > Soil Mineralogy > > > > Gottfried Wilhelm Leibniz Universit?t Hannover > > > > Institute of Mineralogy > > > > Callinstr. 3, Room 325 > > > > D-30167 Hannover, Germany > > > > > > > > Phone: +49 (0)511 762-8058 > > > > Email: t.zahoransky(a)mineralogie.uni-hannover.de > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > --Matt Newville <newville at cars.uchicago.edu> 630-327-7411 >

1 0

TiFe EXELFS Two Phase Co-Refinement Question
by Wilson, Catrina 10 Jun '21

10 Jun '21

Hello, I am using Artemis to fit EXELFS data on a TiFe alloy. There are multiple interfaces between two phases (Im-3m, and P63/mmc) present in the data. I am attempting to co-refine using both phases to create a path list and using paths from both phases in the fit. My understanding of this process is that the software uses a linear combination of each path. However, that would imply that there is a weighting factor applied to each phase that would be correlated to the phase weight for that region. I was wondering if there is a way to determine what the weighting factors during a co-refinement to multiple phases are in Artemis, assuming my initial understanding of the co-refinement process is correct? Thanks for your time, Catrina Wilson Ph.D. Candidate The Ohio State University Doan-Nguyen Group and McComb Group Materials Science and Engineering Center for Electron Microscopy, 1305 Kinnear Rd., Columbus, OH 43212 (614) 643-3110 Office wilson.3981(a)osu.edu<mailto:wilson.3981@osu.edu> / osu.edu<http://osu.edu/> Pronouns: she/her/hers

2 1

PCA Sixpack results compared to Athena (etc.)
by t.zahoransky＠mineralogie.uni-hannover.de 10 Jun '21

10 Jun '21

Dear XAS Community, I stumbled over the issue that a PCA on 20 EXAFS spectra (k², k = 2.0-11.0 Å-1) perfomed in Sixpack does not give the same results (Eigenvalues, variance) as in Athena. However, when I use other statistical programs (i.e., TIBCO Statistica or SPSS), I get the same results as reported in Athena. I tested this with another EXAFS dataset of over 30 samples and the problem persited. An old entry from 2017 in the ifeffit mailing list ("[Ifeffit] Calculation of SPOIL value for the reconstruction of standard spectra"), told me that as of Sixpack version 1.4 on, a new/different PCA algorithm from the scikit-learn Python package is used. So I downloaded older versions of Sixpack (i.e. 1.3) and used "Use Old PCA"-selection in the "Rotation" menu bar, which actually gave different results. However, they are still different from the Athena/Statistical program results. My question is: What is behind this? Is there some sort of normalization or axis rotation, that leads to the different values? Is there any way to change this so that the results are comparable to other programs? As I need to use the Target Transform option after PCA, which is not yet possible in Athena, I am at a loss as to how to deal with these different results and where they come from. Thank you very much for your help, Teresa -- Teresa Zahoransky Soil Mineralogy Gottfried Wilhelm Leibniz Universität Hannover Institute of Mineralogy Callinstr. 3, Room 325 D-30167 Hannover, Germany Phone: +49 (0)511 762-8058 Email: t.zahoransky(a)mineralogie.uni-hannover.de

2 1

Analyzing EXAFS data on Artemis
by Alexandros Deltsidis 28 May '21

28 May '21

Dear mailing list, I am currently analyzing some EXAFS data. I am studying a Lix(C5H5N)FeSe system in a temperature grid that extends from 20 K to 300 K and I have 4 such datasets which correspond to different amount of doping (x). Right now, im focusing on fitting the 1st coordination cell, in Artemis for the Se K-edge. My starting model is the simple P4/nmm FeSe. So, in my system the 1st coordination cell, in the Se K-edge, corresponds to the Se (absorber) - Fe (backscatterer) pair. I have 2 questions: 1) I realize now, that I have a certain impurity in the high doping range on my system, namely Li2Se. I try to include a scattering path from the respective Li2Se crystal model in my fits, since a Se (absorber) - Li (backscatterer) pair is present in the R-range of my fit in the Forward Fourier Transform. My question here is if this makes sense since Li is much smaller scatterer compared to Se. In other words, does it make sense to look for physical parameters (Li-Se bond length and DW factor respectively) of a signal (Se-Li) that is "tucked" in below the main peak coming from the "majority" Se-Fe signal in the FFT? 2)Also, I'm attempting to extract an Einstein temperature for each of those datasets, by utilizing the "eins(T, thetae)" function implemented in Artemis. What is the equation that is parametrized here? Does it include the s0^2 offset term that accounts for the overall configuration disorder in the system? And if that is the case is there same way to separate it from the temperature dependent s^2 term? Thank you in advance, Deltsidis Alexandros PS:I am attaching a png. file exported from Artemis that is relative to my question 1) Ph.D candidate, Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology - Hellas (FORTH)

4 4

Free Oxford Ion Chambers Available [SEC=OFFICIAL]
by MITCHELL, Valerie 25 May '21

25 May '21

Dear All, The XAS beamline at the Australian Synchrotron has four Oxford IC SPEC ion chambers available for free (picture attached). If interested please let me know, and I'm happy to answer any questions. Kind regards, Valerie Mitchell OFFICIAL

1 0

APS/IIT EXAFS Summer School
by Carlo Segre 19 May '21

19 May '21

Hello All: I am attaching the announcement for the 2021 APS/IIT EXAFS Summer School which will be held virtually this year from August 1-4, 2021. Please see the attached for more detail. To register, please send email to Grant Bunker <bunker(a)iit.edu> Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

1 0

IMP: Inquiry for a postdoc position
by Nirmalendu Patra 18 May '21

18 May '21

Dear XAS group Members, I apologize in advance for spamming everyone with this posting. I am Nirmalendu Patra (Ph.D). I have been working as a postdoc in Dr. Simon R. Bare’s group at Stanford Synchrotron Radiation Light Source (SSRL), SLAC National Accelerator Laboratory, California, USA since June of 2020. My current role in the group is to support the team effort to broaden the experimental capabilities by conducting the in-situ XAS (XANES / EXAFS) experimental plan, data acquisition and analysis using IFEFFIT software package (Athena and Artemis) and finally preparing the manuscript. I am also working on the Principal component analysis (PCA) and clustering using TXM XANES Wizard to visualize the unidentified chemical species and the pattern in a large dataset. Before my current postdoc position, I graduated with a Ph.D. in Physics, working on the X-ray Absorption Spectroscopy studies on magnetic thin films and bulk materials at the Indus-2 Synchrotron, RRCAT, Indore, India under the guidance of Dr. Dibyendu Bhattacharyya, BARC, Mumbai, India. The title of my thesis was “Investigation on local structures of various thin film Heusler alloys by XAS and XMCD measurements”. The main objective of my thesis study the local atomic structure, surface morphology and elemental composition of the PLD deposited Heusler alloy thin ﬁlms and correlate their atomic structure with their magnetic properties. My postdoctoral fellowship with Dr. Bare is ending on June 25th, 2021. I am looking for a new postdoctoral position that will enable me to study materials for energy conversion and storage. I am also interested in studying electronic, structural, physio-chemical properties and morphology of materials using advanced spectroscopy techniques. XAS study on metallic alloys or metal oxide thin ﬁlms for spintronic applications are also a part of my research interest. My resume is attached here, and more details can be found from my LinkedIn profile (www.linkedin.com/in/nirmalendu-patra-82701365) If any group has an opening for a postdoc position, kindly respond to my email. Because of the COVID situation in India, I don't want to return now. So trying hard to find a new position. I am available for hiring and will appreciate your help to find a postdoc position. Thank you. With kind regards, *Nirmalendu Patra*

1 0

Illinois Tech Synchrotron Radiation Course
by Carlo Segre 09 May '21

09 May '21

Hello All: Illinois Tech is offering the graduate Introduction to Synchrotron Radiation course once again in Fall 2021. Please see the attached course summary. The course is offered online and it is very straightforward to apply as a non-degree graduate student as late as the second week of classes in September. The online course will be a one (1) credit course instead of the three (3) credits taken by degree-seeking Illinois Tech students. If you are interested or have interested students please contact me for more details on the course or how to apply and register. Cheers, Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

2 1

Postdoc positon in synchrotron characterization of lithium-ion batteries available at SOLEIL
by BELIN Stephanie 06 May '21

06 May '21

Dear All, I would like to share information about one funded Postdoc positions at SOLEIL synchrotron. We are looking for a Postdoc candidate on advanced synchrotron characterization of lithium-ion batteries within the framework of the Battery Interface Genome Materials Accelerated Platform (BIG-MAP<http://www.big-map.eu>, www.big-map.eu<http://www.big-map.eu>). The Postdoc position is dedicated to the development of versatile electrochemical cells and set-ups for operando experiments using spectroscopic and scattering techniques such as synchrotron X-ray absorption spectroscopy (XAS), X-ray emission spectroscopy (XES), X-ray diffraction (XRD), and small-angle X-ray scattering (SAXS), combined with conventional laboratory techniques, such as Raman scattering. Please find the advertisement in the attachment. https://www.synchrotron-soleil.fr/en/job-offers/post-doctoral-position-adva… Please pass on to suitable candidates you are aware of and disseminate to relevant networks! Thank you for your help. With kind regards, Stéphanie &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Dr Stéphanie BELIN ROCK beamline scientist tel. (0033) 01 69 35 96 45 ROCK (0033) 01 69 35 81 46 Fax (0033) 01 69 35 94 57 Email : stephanie.belin(a)synchrotron-soleil.fr<mailto:stephanie.belin@synchrotron-soleil.fr> Synchrotron SOLEIL - Division Expériences L'orme des Merisiers - Saint Aubin BP48 91192 GIF sur YVETTE [cid:image002.png@01D105CE.75C2FD50] http://www.synchrotron-soleil.fr<http://www.synchrotron-soleil.fr/> &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&

1 0

millenia.cars.aps.anl.gov outage starting April 29
by Matt Newville 29 Apr '21

29 Apr '21

Hi Folks, The server millenia.cars.aps.anl.gov that hosts this mailing list and related services including Webatoms and the binary installers for Larch will be offline due to a planned power outage at the APS. We'll gracefully shut down this server on the afternoon (Chicago time) of April 29th, a bit more than 24 hours from now. The estimate for restoring power is May 4th, but it is possible that the outage will go for another day or so. During that time, any messages sent to this list are likely to be lost. In the meantime, please do consider submitting an abstract for the Virtual XAFS Conference! --Matt PS: if you need to contact me directly by email that will (or should) still work during the APS power outage.

2 1

Larch 0.9.51
by Matt Newville 27 Apr '21

27 Apr '21

Hi Folks, Larch 0.9.51 is now available for download and use. It's been several months since the last release, and there have been some important improvements to XAFS data processing and to the XAS Viewer application: - Parameters saved in an Athena Project File are now correctly saved and read into XAS Viewer (thanks Tyler Valentine!) - There is now a simple "Apply to all marked groups" feature for pre-edge peak fitting. That is, you can define a pre-edge peak model with one data set and then apply it to many others, either inspecting the individual fits or saving a CSV file with all the parameters and uncertainties for each fit to each data set. - XAS Viewer can now import multiple scans from a Spec file (thanks Mauro Rovezzi for help with this). It may seem that Specfiles are "legacy", but the reader should also be able to handle the ESRF Bliss HDF5 files (as read in with the silx package, from ESRF), which is their way of efficiently stacking multiple scans into a single binary file. While support for this here should be considered "beta" (or maybe "alpha"!), it is also reasonable to expect that this or a similar HDF5 format file will become a common way to collect and store XAFS data. - There are binary installers for Windows, MacOSX, and Linux. There are also now "GetLarch.sh" and "GetLarch.bat" scripts (that are very short) that can be run to do the download and install, essentially mimicking what the binary installer does. This may be useful for folks wanting to install Larch on multi-user servers or in existing (or "other") Python environments. This might also be useful for those who run into permissions issues, especially on MacOS, where installing a package from an untrusted source is often blocked by default. With the installer script, the unprivileged user is simply running a script that downloads a bunch of files and places them in the home folder. These scripts might also be useful for those who run into problems downloading very large files from millenia.cars.aps.anl.gov, as the installer scripts will use Anaconda and PyPI resources that are better distributed throughout the world. ... which brings me to a final note (I'll send out another message next week): The APS will have a planned power outage from April 30 to May 4 . This will take millenia.cars.aps.anl.gov off-line for those 5 +/- 1 days. That machine hosts the binary installers and also this mailing list. Mail sent to this list during that time will likely be lost (email routing servers can handle destination servers being down for a few hours, but not days). So, if you're planning on sending announcements here, either do it before April 29 or wait until May 5. If you have any questions, problems, or suggestions, please let me know. --Matt

2 2

Fourier transform parameters not saved in Larch XAS Viewer
by Tyler Valentine 18 Apr '21

18 Apr '21

Hello, I am using Larch XAS Viewer. I noticed that when I save my work to an Athena project file (.prj) and reopen it later, the Fourier transform parameters are reset. It seems to be correctly saving other values that I set such as the pre-edge and normalization ranges, so I am unsure why it does not also save the transform parameters. Is it possible to have these values saved? Thank you, Tyler

2 1

XAFS 2021 Virtual Conference deadlines
by Matt Newville 18 Apr '21

18 Apr '21

Hi Folks, I hope most of you have seen information about the 2021 Virtual XAFS Conference this summer: https://xafs2021.org/ There will be an in-person conference in the summer of 2022 in Sydney and a briefer, virtual conference this summer: 11-13 July 2021. I especially want to draw your attention to the Virtual Poster session for students and early-career scientists. The abstract deadline is 1 May, a little less than two weeks from now: see https://xafs2021.org/call-for-abstracts.php for details. Please consider submitting a poster or encouraging your colleagues to do so. There will also be a Virtual Workshop on Data Analysis with Larch: I'll be pre-recording lectures, and then going over some of the finer details of using XAS Viewer and doing simple XAFS analysis during the workshop. Hope to see you there, --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

1 0

Looking for the XAS of Zn3P2
by Madeleine Han 16 Apr '21

16 Apr '21

Dear Ifeffit community, I am looking for the X-ray absorption spectrum of Zn3P2 to use as a reference to determine the composition of an unknown compound. Does anyone know if it has already been recorded? If so, where can I find it? Thank you in advance for your help, Yours sincerely Madeleine Han

2 1

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

1 0

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

1 0

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

3 2

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

1 0

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

1 0

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:

3 7

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

3 2

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 >

1 0

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

3 2

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

2 1

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

1 0

Larch energy calibration
by Schoepfer, Valerie 03 Mar '21

03 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]

2 1

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 ================================================

1 0

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

1 0

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

2 1