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

FOLP error in Feff calculation
by Kewei Zhao 26 May '20

26 May '20

Dear colleagues, I'm using Feff to simulate the EXAFS of an aqueous Ca cluster. But I got this error when I tried to include Cl in the structure (potential type 0 is Ca, 1 is O, 2 is H, and 3 is Cl): Feff 8.50L Ca in water Calculating potentials ... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 initial state energy overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 muffin tin radii and interstitial parameters FOLP for POTENTIAL type 3 is too big. Reduce overlap using FOLP and rerun MOVRLP-1 If I change the type 3 atom to other elements or move its position, the error is gone. However, I do not want to change the input structure. Including FOLP or AFOLP cards in the input file did not work. Is there anyway to bypass this error? Please find my input file attached. Thanks, Kewei Zhao -- Kewei Zhao Ph.D. Student Myneni Lab Princeton University

1 0

Artemis crash upon empirical standard import.
by George Sterbinsky 22 May '20

22 May '20

Hello, I am trying to import an empirical standard (.es file created in Athena) into Artemis. Upon import, Artemis crashes. This occurs with both the latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I have attached an Athena project file containing the data used to generate the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have also attached the .es file. Following the instructions at https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.h…, I import Co1-57C-toFit into Artemis and the choose "import an empirical standard" in the data window. When I choose the .es file from the file selection dialog, Artemis crashes. Thank you, George

5 6

FEFF: problem with calculations of La and Eu XANES spectra with UNFREEZEF card
by Павел Засимов 15 May '20

15 May '20

Dear XAFS community, I have got a problem with FEFF9 calculations of La and Eu XANES spectra with UNFREEZEF card (The calculation don't converge, but it runs without any problems if I do not use UNFREEZEF card). This problem does not depend on the chemical form of the element (i.e. it occurs in La2O3, EuPO4, LaTp3, EuTp3, where Tp is trispyrazolylborate) and seems to be element-specific: the same feff.inp files where La/Eu are replaced with Ce or U are processed by FEFF program without the problem. To note, SCF settings were the same as recommended in the FEFF9.6 manual: SCF 3.7 0 30 0.05 10. Logfile (log1_er.dat), as well as an example of an input file (feff_er.inp), are attached to this mail. The fragment of logfile reporting about the error is shown below: Electronic configuration iph il N_el 0 0 1.683 Found bad counts. Occupation number in getorb is 4.000 Will repeat this iteration. 0 1 7.372 0 2 10.521 Found bad counts. Occupation number in getorb is 1.000 Will repeat this iteration. 0 3 0.727 ... 3 3 0.000 Core-valence separation Bad counts found repeatedly - pot will exit now. Did anyone notice anything similar? Thanks for any help, Zasimov Pavel

2 1

Change in fixed baseline after fit in XAS Viewer
by George Sterbinsky 11 May '20

11 May '20

Hello, I have observed changes in fixed parameters while running a pre-edge peak fit in XAS Viewer. I first run a baseline fit. This provides a good match to the data in the baseline fitting region. I would like to subtract the baseline from the data and then numerically integrate the data. In order to export the baseline fit and data, I fix all of the fitting parameters for bline and bpeak and then click "fit model". This generates a baseline and fit that no longer match the data well in the baseline fitting region. Additionally, in the "Fit Results" window, the reported best-fit values of the fixed parameters are slightly different from the values reported in the "Value" field after the baseline fit, to which they were fixed. This appears to be the result of rounding of the baseline fit parameters at some point after the baseline fit. For example bline_slope was fixed to "-0.0024752483" but the best-fit value is "-0.00247500". I realize I am using XAS Viewer in a way that it was not exactly designed for, and perhaps no one anticipated someone fixing a parameter out to 10 decimal places. However, what I am doing still seems reasonable, and I would greatly appreciate it if XAS Viewer could be updated so that all digits entered in the Value field for a fixed parameter will be maintained for the fit. I am happy to provide a project file and instructions to reproduce my observation if they would be helpful. Thank you, George

2 3

Reported W L3-edge and L2-edge energy
by Bare, Simon R 08 May '20

08 May '20

All: We are wondering if others agree that the reported values for the W L3 and W L2 edges are incorrect. We recently noticed the following: The "Edge" - defined by the inflection point of the absorption edge step When using the Ir L3 edge (11215.0 eV) as a calibration, the W L3- and L2-edges are 10203.4 eV and 11542.4 eV, respectively. When using the Pt L3 edge (11564.0 eV) as a calibration, the W L3- and L2-edges are 10203.3 eV and 11542.4 eV, respectively. These observations are thus different than the reported values of 10207.0 eV and 11544.0 eV for the L3 and L2 edges, respectively. Thanks in advance for the discussion and feedback. Simon R Bare Distinguished Scientist SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629 [co_access_logo_text]

6 11

Re: [Ifeffit] Ifeffit Digest, Vol 207, Issue 14
by Christopher Chantler 07 May '20

07 May '20

Dear all This is an excellent thread. Just to give some background literature, you will be aware of the calibration of X-ray energies by diffraction (either like Kraft or better accuracy from the NIST group and Dick Deslattes, etc). This remains the best method for beamline calibration, though the mono is usually affected by heatload and detuning to shift the energies. [So you want either a 4-bounce or an analyser 'mono']. You will also be aware of the International Tables of Crystallography Volume C Section 4.2.2 [Not our XAFS one, Volume I, but the main Physical Tables Volume]. The old issue summarised a lot of details about current known and not-known accuracy of X-ray energies and is embedded in the NIST website, though the original publication[s] Deslattes et al. are in many ways superior. However, Volume C is coming out with a new edition [soon*] and the summary of the known and unknown accuracies and what to do about them is in the new section 4.2.2. It should be available this year, I understand. Secondly, by far the best edge energy determinations are those of Kraft et al., and these were based around the subset of transition metals and K edges. Most other edges have not been published with an absolute energy measurement, so they really do flop around in the literature. This is a major and important [urgent] task that maybe we can all help with. The issue of stability of lines, crystals etc. is a closely related and important issue. The issue is compounded at lower energies and for L edges. One of the best current examples is that of the recent Mendenhall et al. publication on copper... I hope this thread has emphasised the importance of this work and that we would all like more progress in this area Very best wishes Chris -------------------------------------------------------------------------------------- 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: Friday, 8 May 2020 8:55 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 207, 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: Reported W L3-edge and L2-edge energy (Matthew Marcus) 2. Re: Reported W L3-edge and L2-edge energy (Mike Massey) ---------------------------------------------------------------------- Message: 1 Date: Thu, 7 May 2020 15:17:20 -0700 From: Matthew Marcus <mamarcus(a)lbl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Reported W L3-edge and L2-edge energy Message-ID: <c838484f-6689-8a82-78f3-a6ef211d1068(a)lbl.gov> Content-Type: text/plain; charset=utf-8; format=flowed For elements like P and S, people often use the energies of peaks. These are more immune to noise, energy-resolution effects and overabsorption than inflection points are. For instance, on ALS 10.3.2, I used the sulfate peak of gypsum set at 2482.74eV. I forget where I got that number. Going down to soft X-rays, a common convention for the carbon edge is to use a pair of sharp peaks in CO2 gas at 292.74 and 294.96eV. mam On 5/7/2020 3:09 PM, Mike Massey wrote: > Hi Matt, > > > Indeed, in my experience (which is limited to one beamline at one > synchrotron facility for P XAS), once it is calibrated, the energy > selection tends to be quite stable, so I think you're on-target there. > > The trouble I still run into, though, is comparability of data between > studies. The difficulty is magnified by the fact that people tend to > identify certain near-edge features by the energy range at which they > occur. I do the same, of course, but I also try to carefully document > the material and energy I used to calibrate the monochromator. > > For the P K-edge, it doesn't really seem like people have settled on a > convention for calibrating the monochromator, unlike in the case of > iron, for example (where one just uses a foil and sets some feature of > that spectrum to their preferred value). If everyone was using the same > thing all would be happy, but most people use different materials and > different values. So datasets for P at the K-edge really aren't too > comparable just yet. > > Sorry to hijack the conversation, it's just an issue I've been mulling > over for a few years. The discussion of energy calibration values made > me think of it again. > > > Best, > > > > Mike > > > > >> On May 8, 2020, at 8:51 AM, Matt Newville <newville(a)cars.uchicago.edu> >> wrote: >> >> ? >> Hi Mike, >> >> >> On Tue, May 5, 2020 at 10:56 PM Mike Massey <mmassey(a)gmail.com >> <mailto:mmassey@gmail.com>> wrote: >> >> On a tangentially related topic, I find that phosphorus K-edge XAS >> energy calibration conventions are still in a bit of a "Wild West" >> state, with a wide variety of materials and values in use for >> energy calibration. As an extreme example, one or two frequently >> cited papers in my field from the 2000s don't even report the >> material or value used for energy calibration, and only show >> portions of the spectra on an energy axis with values relative to >> an unknown E0. >> >> >> I have never measured a P K edge, or indeed any edge lower in energy >> than the S K edge (ignoring some X-ray raman work).? But if one is >> using a Si(111) double-crystal monochromator where P or S is >> approximately the low-energy (high-angle) limit, then it really should >> be that the calibration does not drift much and cannot be too wrong at >> low energies. >> >> That is, a mono calibration is controlled by a d-spacing and angular >> offset. Normally (or perhaps, in my experience), "re-calibrating" is >> done by changing the angular offset, leaving the d-spacing alone. >> That is, the d-spacing is presumably known, at least to within some >> thermal drift. >> If that is the case that the d-spacing really is not changing and what >> needs to be refined is the angular?offset, then setting the offset at >> relatively high energy edges will be much more sensitive, and changing >> the angular offset to that a high-energy edge is correct should move >> lower energy edges by a smaller amount.? ?The corollary is that you >> have to move the offset a lot to move the P? K edge around, and that >> would have a larger (and ever-increasing) impact on higher energy >> edges such as Ca, Fe, Cu or Mo. >> >> The counter-argument is also true:? d-spacing has a bigger effect on >> the high-angle / low-energy edges. >> >> So, if you believe the mono d-spacing (or you believe the beamline >> scientist who believes it ;)) then calibrate at the highest energy you >> can.? ?The Kraft values don't go very low in energy. >> >> All that said, if using a different mono crystal such as InSb or more >> exotic crystals, I have no idea how stable those are. >> >> >> I too have picked my own material and value, and will be the first >> to acknowledge that I did so out of necessity and ease of >> comparison to other available data, rather than because I thought >> it was correct. >> >> The issue of calibration conventions and values definitely seems >> to be one that merits continued discussion. It has been >> interesting to watch things evolve over time in the case of iron, >> for example (it's good to know that 7110.75 is a candidate >> calibration value...) I appreciate Matt's detailed thoughts, and >> the data that he's been working with. Thanks Matt! >> >> >> Cheers, >> >> >> >> Mike >> >> >> >> >> >>> On May 6, 2020, at 3:32 PM, Matt Newville >>> <newville(a)cars.uchicago.edu <mailto:newville@cars.uchicago.edu>> >>> wrote: >>> >>> ? >>> Hi Simon, >>> >>> This is definitely a timely discussion for me, as I've been >>> spending part of the quartine?working on collating data and >>> expanding datasets for an XAFS spectral database.? I'm hoping to >>> have something ready for public comment and to start asking for >>> contributions of data in a few weeks, but I'll be happy to have >>> more discussion about that sooner too. >>> >>> I generally believe that the monochromator I use at GSECARS is >>> both well-calibrated and reasonably accurate.? That is, with 2 >>> angular encoders with a resolution of >130,000 lines per degree >>> and an air-bearing, I believe the angular accuracy and >>> repeatability are very good.? I believe there are equally good >>> moons in existence.? ?As Matthew Marcus pointed to the Kraft >>> paper (which used an older source but 4-bounce mono to improve >>> resolution), we find that Fe foil is definitely?better defined as >>> 7110.75 and Cu foil is between 8980.0 and 8980.5 eV.? That is, >>> we've measured multiple foils, found their first derivatives, and >>> refined the d-spacing and angular offset.? We do this about once >>> per run, and the offsets tend to be very consistent.? ?For sure, >>> there is some question about whether the Kraft numbers are >>> perfect.? ?For sure, putting Fe foil at 7110.75?+/- 0.25 eV >>> appears to be "most right" to us. >>> >>> I also believe that we should probably re-measure these metal >>> foils (and other compounds) with a single calibration set for >>> both Si(111) and Si(311).? We will probably have time to do that >>> this summer in the time between "beamline staff can get back to >>> the beamline" and "open for outside users". >>> >>> What I can tell you now is:? I have some data on W metal, WO2, >>> and WO3 measured all at the same time on our bending magnet line, >>> with Si(111).? An Athena project for this is attached (W.prj). >>> ?I cannot vouch for the absolute calibration. >>> >>> I also attach a set of foils (V, Fe, Cu, Mo) measured with the >>> same calibration (and Si(111) on our ID line), after adjusting >>> d-space and offset?to be close to the Kraft values >>> (CalibratedFoils2013.prj). >>> >>> I also attach a set of foils (Fe, Cu, Au L3, Au L2, Au L1, Pb L3, >>> Pb L2, Pb L1 edges) measured in 2016 (again, using Si(111) on our >>> ID line), also with the same calibration values >>> (FeCu_Au_Pb.prj).? I'm pretty certain these use the same >>> d-spacing as the 2013 Foils to?at least 5 digits.? ?For >>> completeness, all of the raw data files are also under >>> https://github.com/XraySpectroscopy/XASDataLibrary/tree/master/data >>> >>> In my experience, the Pb L3 edge value has the biggest variation >>> in the literature, with values ranging from 13035 to 13055 eV >>> (possibly a typo somewhere along the line).? Fortunately, the >>> Kraft-based calibration splits the difference and puts the value >>> at 13040 eV. >>> >>> For W in particular, I will look if I have measured this recently >>> on our ID line.? I can tell you that I use CdWO4 as a phosphor >>> and use that to focus our X-ray beam.? ?I use this trick all the >>> time: any tail from the beam penetrating the phosphor is shortest >>> at the peak of the white-line and for CdWO4 that is always >>> between 10210 and 10215 eV. >>> >>> I hope that helps.? I am interested in trying to get all these >>> values as accurately as possible, so any comments or suggestions >>> would be most welcome. >>> >>> --Matt >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On Tue, May 5, 2020 at 5:14 PM Bare, Simon R >>> <srbare(a)slac.stanford.edu <mailto:srbare@slac.stanford.edu>> wrote: >>> >>> All:____ >>> >>> __ __ >>> >>> We are wondering if others agree that the reported values for >>> the W L3 and W L2 edges are *incorrect*. We recently noticed >>> the following:____ >>> >>> __ __ >>> >>> The ?Edge? ? defined by the inflection point of the >>> absorption edge step____ >>> >>> __ __ >>> >>> When using the Ir L_3 edge (11215.0 eV) as a calibration, the >>> W L_3 - and L_2 -edges are *10203.4 eV* and *11542.4 eV*, >>> respectively. ____ >>> >>> __ __ >>> >>> When using the Pt L_3 edge (11564.0 eV) as a calibration, the >>> W L_3 - and L_2 -edges are *10203.3 eV* and *11542.4 eV*, >>> respectively.____ >>> >>> __ __ >>> >>> These observations are thus different than the reported >>> values of *10207.0 eV* and *11544.0 eV* for the L_3 and L_2 >>> edges, respectively.____ >>> >>> __ __ >>> >>> Thanks in advance for the discussion and feedback.____ >>> >>> __ __ >>> >>> __ __ >>> >>> Simon R Bare____ >>> >>> /Distinguished Scientist____/ >>> >>> /SSRL, MS69____/ >>> >>> /SLAC National Accelerator Lab____/ >>> >>> /2575 Sand Hill Road____/ >>> >>> /Menlo Park CA 94025____/ >>> >>> __ __ >>> >>> simon.bare(a)slac.stanford.edu >>> <mailto:simon.bare@slac.stanford.edu>____ >>> >>> Ph: 650-926-2629____ >>> >>> __ __ >>> >>> <image001.png> >>> ____ >>> >>> __ __ >>> >>> _______________________________________________ >>> 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 >>> >>> >>> >>> -- >>> --Matt Newville <newville at cars.uchicago.edu >>> <http://cars.uchicago.edu>> 630-252-0431 >>> <W.prj> >>> <CalibratedFoils2013.prj> >>> <FeCu_AuPb.prj> >>> _______________________________________________ >>> 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 >> _______________________________________________ >> 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 >> >> >> >> -- >> --Matt Newville <newville at cars.uchicago.edu >> <http://cars.uchicago.edu>> 630-252-0431 >> _______________________________________________ >> 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 > ------------------------------ Message: 2 Date: Fri, 8 May 2020 10:54:07 +1200 From: Mike Massey <mmassey(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Reported W L3-edge and L2-edge energy Message-ID: <CC4875F1-C227-4726-8D25-CD597ED4592D(a)gmail.com> Content-Type: text/plain; charset=utf-8 I agree Matthew, I also tend to use the primary K-edge peak for P calibration, but one issue to be wary of is attenuation/flattening of the primary peak (if one is using a concentrated sample). Gypsum sounds like a good material to use for S, since it is commonly available and probably not too variable. My material of choice for P (lazulite) might fail on both counts, so it might be a poor choice. Mike > On May 8, 2020, at 10:19 AM, Matthew Marcus <mamarcus(a)lbl.gov> wrote: > > ?For elements like P and S, people often use the energies of peaks. These are more immune to noise, energy-resolution effects and overabsorption than inflection points are. For instance, on ALS 10.3.2, I used the sulfate peak of gypsum set at 2482.74eV. I forget where I got that number. Going down to soft X-rays, a common convention for the carbon edge is to use a pair of sharp peaks in CO2 gas at 292.74 and 294.96eV. > mam > >> On 5/7/2020 3:09 PM, Mike Massey wrote: >> Hi Matt, >> Indeed, in my experience (which is limited to one beamline at one synchrotron facility for P XAS), once it is calibrated, the energy selection tends to be quite stable, so I think you're on-target there. >> The trouble I still run into, though, is comparability of data between studies. The difficulty is magnified by the fact that people tend to identify certain near-edge features by the energy range at which they occur. I do the same, of course, but I also try to carefully document the material and energy I used to calibrate the monochromator. >> For the P K-edge, it doesn't really seem like people have settled on a convention for calibrating the monochromator, unlike in the case of iron, for example (where one just uses a foil and sets some feature of that spectrum to their preferred value). If everyone was using the same thing all would be happy, but most people use different materials and different values. So datasets for P at the K-edge really aren't too comparable just yet. >> Sorry to hijack the conversation, it's just an issue I've been mulling over for a few years. The discussion of energy calibration values made me think of it again. >> Best, >> Mike >>>> On May 8, 2020, at 8:51 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: >>> >>> ? >>> Hi Mike, >>> >>> >>>> On Tue, May 5, 2020 at 10:56 PM Mike Massey <mmassey(a)gmail.com <mailto:mmassey@gmail.com>> wrote: >>> >>> On a tangentially related topic, I find that phosphorus K-edge XAS >>> energy calibration conventions are still in a bit of a "Wild West" >>> state, with a wide variety of materials and values in use for >>> energy calibration. As an extreme example, one or two frequently >>> cited papers in my field from the 2000s don't even report the >>> material or value used for energy calibration, and only show >>> portions of the spectra on an energy axis with values relative to >>> an unknown E0. >>> >>> >>> I have never measured a P K edge, or indeed any edge lower in energy than the S K edge (ignoring some X-ray raman work). But if one is using a Si(111) double-crystal monochromator where P or S is approximately the low-energy (high-angle) limit, then it really should be that the calibration does not drift much and cannot be too wrong at low energies. >>> >>> That is, a mono calibration is controlled by a d-spacing and angular offset. Normally (or perhaps, in my experience), "re-calibrating" is done by changing the angular offset, leaving the d-spacing alone. That is, the d-spacing is presumably known, at least to within some thermal drift. >>> If that is the case that the d-spacing really is not changing and what needs to be refined is the angular offset, then setting the offset at relatively high energy edges will be much more sensitive, and changing the angular offset to that a high-energy edge is correct should move lower energy edges by a smaller amount. The corollary is that you have to move the offset a lot to move the P K edge around, and that would have a larger (and ever-increasing) impact on higher energy edges such as Ca, Fe, Cu or Mo. >>> >>> The counter-argument is also true: d-spacing has a bigger effect on the high-angle / low-energy edges. >>> >>> So, if you believe the mono d-spacing (or you believe the beamline scientist who believes it ;)) then calibrate at the highest energy you can. The Kraft values don't go very low in energy. >>> >>> All that said, if using a different mono crystal such as InSb or more exotic crystals, I have no idea how stable those are. >>> >>> >>> I too have picked my own material and value, and will be the first >>> to acknowledge that I did so out of necessity and ease of >>> comparison to other available data, rather than because I thought >>> it was correct. >>> >>> The issue of calibration conventions and values definitely seems >>> to be one that merits continued discussion. It has been >>> interesting to watch things evolve over time in the case of iron, >>> for example (it's good to know that 7110.75 is a candidate >>> calibration value...) I appreciate Matt's detailed thoughts, and >>> the data that he's been working with. Thanks Matt! >>> >>> >>> Cheers, >>> >>> >>> >>> Mike >>> >>> >>> >>> >>> >>>> On May 6, 2020, at 3:32 PM, Matt Newville >>>> <newville(a)cars.uchicago.edu <mailto:newville@cars.uchicago.edu>> >>>> wrote: >>>> >>>> ? >>>> Hi Simon, >>>> >>>> This is definitely a timely discussion for me, as I've been >>>> spending part of the quartine working on collating data and >>>> expanding datasets for an XAFS spectral database. I'm hoping to >>>> have something ready for public comment and to start asking for >>>> contributions of data in a few weeks, but I'll be happy to have >>>> more discussion about that sooner too. >>>> >>>> I generally believe that the monochromator I use at GSECARS is >>>> both well-calibrated and reasonably accurate. That is, with 2 >>>> angular encoders with a resolution of >130,000 lines per degree >>>> and an air-bearing, I believe the angular accuracy and >>>> repeatability are very good. I believe there are equally good >>>> moons in existence. As Matthew Marcus pointed to the Kraft >>>> paper (which used an older source but 4-bounce mono to improve >>>> resolution), we find that Fe foil is definitely better defined as >>>> 7110.75 and Cu foil is between 8980.0 and 8980.5 eV. That is, >>>> we've measured multiple foils, found their first derivatives, and >>>> refined the d-spacing and angular offset. We do this about once >>>> per run, and the offsets tend to be very consistent. For sure, >>>> there is some question about whether the Kraft numbers are >>>> perfect. For sure, putting Fe foil at 7110.75 +/- 0.25 eV >>>> appears to be "most right" to us. >>>> >>>> I also believe that we should probably re-measure these metal >>>> foils (and other compounds) with a single calibration set for >>>> both Si(111) and Si(311). We will probably have time to do that >>>> this summer in the time between "beamline staff can get back to >>>> the beamline" and "open for outside users". >>>> >>>> What I can tell you now is: I have some data on W metal, WO2, >>>> and WO3 measured all at the same time on our bending magnet line, >>>> with Si(111). An Athena project for this is attached (W.prj). I cannot vouch for the absolute calibration. >>>> >>>> I also attach a set of foils (V, Fe, Cu, Mo) measured with the >>>> same calibration (and Si(111) on our ID line), after adjusting >>>> d-space and offset to be close to the Kraft values >>>> (CalibratedFoils2013.prj). >>>> >>>> I also attach a set of foils (Fe, Cu, Au L3, Au L2, Au L1, Pb L3, >>>> Pb L2, Pb L1 edges) measured in 2016 (again, using Si(111) on our >>>> ID line), also with the same calibration values >>>> (FeCu_Au_Pb.prj). I'm pretty certain these use the same >>>> d-spacing as the 2013 Foils to at least 5 digits. For >>>> completeness, all of the raw data files are also under >>>> https://github.com/XraySpectroscopy/XASDataLibrary/tree/master/data >>>> >>>> In my experience, the Pb L3 edge value has the biggest variation >>>> in the literature, with values ranging from 13035 to 13055 eV >>>> (possibly a typo somewhere along the line). Fortunately, the >>>> Kraft-based calibration splits the difference and puts the value >>>> at 13040 eV. >>>> >>>> For W in particular, I will look if I have measured this recently >>>> on our ID line. I can tell you that I use CdWO4 as a phosphor >>>> and use that to focus our X-ray beam. I use this trick all the >>>> time: any tail from the beam penetrating the phosphor is shortest >>>> at the peak of the white-line and for CdWO4 that is always >>>> between 10210 and 10215 eV. >>>> >>>> I hope that helps. I am interested in trying to get all these >>>> values as accurately as possible, so any comments or suggestions >>>> would be most welcome. >>>> >>>> --Matt >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Tue, May 5, 2020 at 5:14 PM Bare, Simon R >>>> <srbare(a)slac.stanford.edu <mailto:srbare@slac.stanford.edu>> wrote: >>>> >>>> All:____ >>>> >>>> __ __ >>>> >>>> We are wondering if others agree that the reported values for >>>> the W L3 and W L2 edges are *incorrect*. We recently noticed >>>> the following:____ >>>> >>>> __ __ >>>> >>>> The ?Edge? ? defined by the inflection point of the >>>> absorption edge step____ >>>> >>>> __ __ >>>> >>>> When using the Ir L_3 edge (11215.0 eV) as a calibration, the >>>> W L_3 - and L_2 -edges are *10203.4 eV* and *11542.4 eV*, >>>> respectively. ____ >>>> >>>> __ __ >>>> >>>> When using the Pt L_3 edge (11564.0 eV) as a calibration, the >>>> W L_3 - and L_2 -edges are *10203.3 eV* and *11542.4 eV*, >>>> respectively.____ >>>> >>>> __ __ >>>> >>>> These observations are thus different than the reported >>>> values of *10207.0 eV* and *11544.0 eV* for the L_3 and L_2 >>>> edges, respectively.____ >>>> >>>> __ __ >>>> >>>> Thanks in advance for the discussion and feedback.____ >>>> >>>> __ __ >>>> >>>> __ __ >>>> >>>> Simon R Bare____ >>>> >>>> /Distinguished Scientist____/ >>>> >>>> /SSRL, MS69____/ >>>> >>>> /SLAC National Accelerator Lab____/ >>>> >>>> /2575 Sand Hill Road____/ >>>> >>>> /Menlo Park CA 94025____/ >>>> >>>> __ __ >>>> >>>> simon.bare(a)slac.stanford.edu >>>> <mailto:simon.bare@slac.stanford.edu>____ >>>> >>>> Ph: 650-926-2629____ >>>> >>>> __ __ >>>> >>>> <image001.png> >>>> ____ >>>> >>>> __ __ >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>>> >>>> -- --Matt Newville <newville at cars.uchicago.edu >>>> <http://cars.uchicago.edu>> 630-252-0431 >>>> <W.prj> >>>> <CalibratedFoils2013.prj> >>>> <FeCu_AuPb.prj> >>>> _______________________________________________ >>>> 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 >>> _______________________________________________ >>> 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 >>> >>> >>> >>> -- >>> --Matt Newville <newville at cars.uchicago.edu <http://cars.uchicago.edu>> 630-252-0431 >>> _______________________________________________ >>> 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 > _______________________________________________ > 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 ------------------------------ Subject: Digest Footer _______________________________________________ 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 ------------------------------ End of Ifeffit Digest, Vol 207, Issue 14 ****************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 207, Issue 10
by Caliebe, Wolfgang 06 May '20

06 May '20

Dear All, there is another publication about high precision measurements of X-Ray Absorption Edges from the early 90ies from the same group: Measurement of the Energy of X‐Ray Absorption Edges J. Stümpel P. Becker St. Joksch R. Frahm G. Materlik First published: 16 April 1991 https://doi.org/10.1002/pssa.2211240224 The trick is that the authors don't use the monochromator in order to determine the energy of the edge, but instead an analyzer-crystal on a rotary stage with an encoder. This analyzer-crystal can be rotated to two different angles, where it fulfills the Bragg condition. Instead of measuring an absolute angle, they measure a difference of two angles, which is twice the Bragg-angle. This is more precise. They also measure the temperature of the crystal, which is essential to determine the lattice constant and to calculate the correct energy. More than 15 years ago, Syed Khalid used the values from the PTB-publications to calibrate the monochromator at X18b, and he used these values to determine the temperature of the monochromator crystal. All energies of the edges of the 3d-metals could be nicely reproduced, and the deviations from the PTB-values were rather small and not jumping by several eV as the Bearden-values from the yellow book. Unfortunately, the web-page got lost after NSLS was shut-down (at least, I cannot find it again). Syed tried to convince his users to use the PTB-values for calibration, but they all refused since they had used the old values for decades and did not want to switch. There might have been also users from UOP. Those, who listen to Jerry Seidler's Global XAFS Journal Club might remember the lecture by Joe Fowler: The tabulated values for the energies of fluorescence lines are ancient, some were still measured with photographic paper, and it is not much different for absorption edges. I agree with Matt that new values are required, and we should compare our results! With best regards, Wolfgang ----- Original Message ----- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Wednesday, 6 May, 2020 05:32:08 Subject: Ifeffit Digest, Vol 207, 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: Reported W L3-edge and L2-edge energy (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 5 May 2020 22:31:27 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Reported W L3-edge and L2-edge energy Message-ID: <CA+7ESbpcjj0QNkTNFTax9W2e=SB4JeezJ2Lmfb-KMEKsQotCAw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Simon, This is definitely a timely discussion for me, as I've been spending part of the quartine working on collating data and expanding datasets for an XAFS spectral database. I'm hoping to have something ready for public comment and to start asking for contributions of data in a few weeks, but I'll be happy to have more discussion about that sooner too. I generally believe that the monochromator I use at GSECARS is both well-calibrated and reasonably accurate. That is, with 2 angular encoders with a resolution of >130,000 lines per degree and an air-bearing, I believe the angular accuracy and repeatability are very good. I believe there are equally good moons in existence. As Matthew Marcus pointed to the Kraft paper (which used an older source but 4-bounce mono to improve resolution), we find that Fe foil is definitely better defined as 7110.75 and Cu foil is between 8980.0 and 8980.5 eV. That is, we've measured multiple foils, found their first derivatives, and refined the d-spacing and angular offset. We do this about once per run, and the offsets tend to be very consistent. For sure, there is some question about whether the Kraft numbers are perfect. For sure, putting Fe foil at 7110.75 +/- 0.25 eV appears to be "most right" to us. I also believe that we should probably re-measure these metal foils (and other compounds) with a single calibration set for both Si(111) and Si(311). We will probably have time to do that this summer in the time between "beamline staff can get back to the beamline" and "open for outside users". What I can tell you now is: I have some data on W metal, WO2, and WO3 measured all at the same time on our bending magnet line, with Si(111). An Athena project for this is attached (W.prj). I cannot vouch for the absolute calibration. I also attach a set of foils (V, Fe, Cu, Mo) measured with the same calibration (and Si(111) on our ID line), after adjusting d-space and offset to be close to the Kraft values (CalibratedFoils2013.prj). I also attach a set of foils (Fe, Cu, Au L3, Au L2, Au L1, Pb L3, Pb L2, Pb L1 edges) measured in 2016 (again, using Si(111) on our ID line), also with the same calibration values (FeCu_Au_Pb.prj). I'm pretty certain these use the same d-spacing as the 2013 Foils to at least 5 digits. For completeness, all of the raw data files are also under https://github.com/XraySpectroscopy/XASDataLibrary/tree/master/data In my experience, the Pb L3 edge value has the biggest variation in the literature, with values ranging from 13035 to 13055 eV (possibly a typo somewhere along the line). Fortunately, the Kraft-based calibration splits the difference and puts the value at 13040 eV. For W in particular, I will look if I have measured this recently on our ID line. I can tell you that I use CdWO4 as a phosphor and use that to focus our X-ray beam. I use this trick all the time: any tail from the beam penetrating the phosphor is shortest at the peak of the white-line and for CdWO4 that is always between 10210 and 10215 eV. I hope that helps. I am interested in trying to get all these values as accurately as possible, so any comments or suggestions would be most welcome. --Matt On Tue, May 5, 2020 at 5:14 PM Bare, Simon R <srbare(a)slac.stanford.edu> wrote: > All: > > > > We are wondering if others agree that the reported values for the W L3 and > W L2 edges are *incorrect*. We recently noticed the following: > > > > The ?Edge? ? defined by the inflection point of the absorption edge step > > > > When using the Ir L3 edge (11215.0 eV) as a calibration, the W L3- and L2-edges > are *10203.4 eV* and *11542.4 eV*, respectively. > > > > When using the Pt L3 edge (11564.0 eV) as a calibration, the W L3- and L2-edges > are *10203.3 eV* and *11542.4 eV*, respectively. > > > > These observations are thus different than the reported values of *10207.0 > eV* and *11544.0 eV* for the L3 and L2 edges, respectively. > > > > Thanks in advance for the discussion and feedback. > > > > > > Simon R Bare > > *Distinguished Scientist* > > *SSRL, MS69* > > *SLAC National Accelerator Lab* > > *2575 Sand Hill Road* > > *Menlo Park CA 94025* > > > > simon.bare(a)slac.stanford.edu > > Ph: 650-926-2629 > > > > [image: co_access_logo_text] > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-252-0431

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Re: [Ifeffit] Ifeffit Digest, Vol 207, Issue 8
by Christopher Chantler 05 May '20

05 May '20

Dear Simon, good work Currently most synchrotron beamlines will report calibrations of the edge according to the inflection point, or first peak in the derivative spectrum. As we know, this changes with experimental resolution, monochromation pre-edge structure and bandwidth, so is neither a fixed definition nor fully portable. However, apart from direct [powder or single crystal] diffraction measurement post monochromation, this is one of the best markers we have to date. The discrepancy you mention is quite large prima facie to be just the above, so more likely is a calibration error or even monochromation calibration error [of one or the other]. These studies are very important to make progress in the field and to cross-calibrate, and to question theoretical predictions based around the edge structure, which are ongoing. [PS I did not directly answer your question!] Best wishes Chris -------------------------------------------------------------------------------------- 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: Wednesday, 6 May 2020 8:14 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 207, Issue 8 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. Reported W L3-edge and L2-edge energy (Bare, Simon R) ---------------------------------------------------------------------- Message: 1 Date: Tue, 5 May 2020 22:14:12 +0000 From: "Bare, Simon R" <srbare(a)slac.stanford.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Reported W L3-edge and L2-edge energy Message-ID: <MWHPR07MB38690FD1A9915311AC5859A491A70(a)MWHPR07MB3869.namprd07.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" All: We are wondering if others agree that the reported values for the W L3 and W L2 edges are incorrect. We recently noticed the following: The "Edge" - defined by the inflection point of the absorption edge step When using the Ir L3 edge (11215.0 eV) as a calibration, the W L3- and L2-edges are 10203.4 eV and 11542.4 eV, respectively. When using the Pt L3 edge (11564.0 eV) as a calibration, the W L3- and L2-edges are 10203.3 eV and 11542.4 eV, respectively. These observations are thus different than the reported values of 10207.0 eV and 11544.0 eV for the L3 and L2 edges, respectively. Thanks in advance for the discussion and feedback. Simon R Bare Distinguished Scientist SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629 [co_access_logo_text]

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Problem with XAS Viewer
by Xinyue Wang 04 May '20

04 May '20

Hi, I am Xinyue, a student who interested in using XAS Viewer. My issue is when I tried baseline fitting, I followed the document. But there was no region, no centroid, and no fitting line shown. Here is a screenshot of my work. Could you please help me with this? Thanks for your help. Thanks, Xinyue

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unable to export xdi file in xas viewer
by George Sterbinsky 04 May '20

04 May '20

Hello, When attempting to export an xdi file for a pre-edge peak fit in XAS viewer, the error message below prints to the terminal and the xdi file is not generated. I can provide the project file and instructions for generating the error message if that would be helpful. Thank you, George Traceback (most recent call last): File "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line 369, in onExportFitResult yerr=yerr, x=x) File "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", line 60, in export_modelresult delta_fit = result.eval_uncertainty(result.params, **kwargs) File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line 1488, in eval_uncertainty dval = pars[pname].stderr/3.0 TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'

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