May 2018 - Ifeffit - millenia.cars.aps.anl.gov

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

05 Aug '20

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

5 7

Demeter on Windows 10 does not work
by sikolen 11 Jun '18

11 Jun '18

Dear all, I've just changed my loving Windows-7 to the new Windows-10. I've installed Demeter (v.0.9.26, 64-bit), but it does not work: cmd-Windows appears for the a couple of seconds and disappears forever. Is it already known problem of the OS? Sorry, may be this question already appeared here, I just missed it. Vadim -- *********************************** Dr. Vadim Sikolenko Senior Scientist Frank Laboratory of Neutron Physics Vadim.Sikolenko(a)jinr.ru Skype: svadimm **********************************

3 3

Different Enot for different shells
by Abdul Ahad 30 May '18

30 May '18

Hi all, Again i have a question to experts. Suppose i have bond length information via first shell fitting. And by symmetry of crystal structure i know that higher shell should be double of that bond length .....like lattice parameter that is just double of particular bond length (Metal to metal distance which should double of Metal to oxygen which is observable via first shell). I would like to know that in this case my Enot will be same or different as in first shell or i have to Guess another enot, Then how can i control all these parameters. Thanks in advance

2 1

Amplitude and sigma square
by Abdul Ahad 29 May '18

29 May '18

Hi all, Thanks to Professor Pierre, Prof. Segre and Prof. Scott, for make some beautiful comments. One thing i wish to mention here that i have both Fluorescence and Transmission data, with the same model transmission data give Amplitude around 0.72 but Fluorescence gives 0.15, Is this self absorption problem, as prof. Segre suggested. Also i have tried with one shell with N=6 and then 4 and 2 and i got the genuine trend on average under limit of error. But the for N=2 the sigma goes to 0.0001 order while for N=4 it is usual 0.001 order (this both have simultaneously taken in a one fit). Also N=6 gives all variable fine. thanks

2 1

Amplitude and sigma square
by Abdul Ahad 29 May '18

29 May '18

Hi all, I have couple of questions. 1. I found in many tutorials that the value of amp should lie between 0.7 and 1. But when I refined it goes to 0.15, what's wrong with it. 2. The value of sigma2. Some time at high k, value, it turns to negative but small. What I suppose to do? 3. If I need to know the behavior of octahedra distortion with temperature, and it is lies within the first shell. So what is the need of higher shell fitting.??? Thanks in advance

3 2

Amplitude and sigma square (Abdul Ahad)
by Pierre Lecante 28 May '18

28 May '18

Hi Abdul, In my opinion, the short answer is that your model is wrong; amplitude, coordination number and sigma square are strongly correlated; if your model is not adequate or if values are too far from the convergence zone, non physical effects appear; usually, very small or negative values for sigma2 mean coordination number too low, but very small amplitude means the reverse! I suggest to start with a plain simulation (all parameters locked to expected values) and check that there is not something weird in different k zones, which might eventually indicate unexpected species close to the central atom; my 2 cents, Pierre Le 28/05/2018 à 19:00, 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. Amplitude and sigma square (Abdul Ahad) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 May 2018 14:16:39 +0530 > From: Abdul Ahad <matrixabdulahad(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Amplitude and sigma square > Message-ID: > <CAEFSGt6r3xbjc2zPk1fc2bGmKwgb_AVVcfrWa198kmY8QkpMJA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I have couple of questions. > 1. I found in many tutorials that the value of amp should lie between 0.7 > and 1. But when I refined it goes to 0.15, what's wrong with it. > > 2. The value of sigma2. Some time at high k, value, it turns to negative > but small. What I suppose to do? > > 3. If I need to know the behavior of octahedra distortion with temperature, > and it is lies within the first shell. So what is the need of higher shell > fitting.??? > > Thanks in advance >

1 0

Re: [Ifeffit] S02
by Matt Newville 25 May '18

25 May '18

Julian, On Fri, May 25, 2018 at 9:01 AM Julian Ehwald <jehwald(a)gmail.com> wrote: > Dear Matt, > > > > Thank you for your superfast answer. I obtained new data from the people > at the beamline today, and the set contains both Total electron Yield and > Total fluorescence yield. As far as I understand, they both tell us > something about the absorption. Which is usually used for analysis? If I > process them with Athena I get considerable differences… > > > Please use the mailing list. Either or both of total electron yied and total fluorescence yield can be used for XAFS. That is, total emission of high-energy electrons and emission of fluorescence X-rays are both proportional to the absorption cross-section for an atom, at least to first approximation. There are complications in using these. For X-ray fluorescence the main complication is "over absorption" which happens in materials in which the element of interest is high concentration (effects can be noticeable at ~1% and are usually significant-but-correctable up to ~10%, and are nearly impossible to correct above ~50% concentration). For electron yield, the main complication is that the electron escape depth is shallow enough that the measurement may be more sensitive to the surface than the bulk of the sample. That sort of depends on how you define "surface" (the electrons escape from 10s to 100s of Angstroms), but can be seen as an advantage if surface sensitivity is what you want. For both, using the data as XAFS means using mu ~ EmissionIntensity / I0. That's very different from transmission data, which often trips people up when importing the data into Athena: DO NOT use the log( EmissionIntensity / I0), use EmissionIntensity/I0. --Matt

1 0

Re: [Ifeffit] S02
by Matt Newville 25 May '18

25 May '18

On Fri, May 25, 2018 at 5:11 AM Julian Ehwald <jehwald(a)gmail.com> wrote: > Dear Matt, > > > > I still have questions about Artemis concerning the S0^2. In your > book/summary called XAFS-Fundamentals there is a section at the beginning > of chapter six that says: > > > > “Starting with this structure, we can calculate the scattering amplitude > and phaseshifts > > and theoretically. The complete calculation is beyond the scope of this > treatment, > > but don’t worry too much by that phrase “we’ll calculate these > theoretically”! These > > functions are actually fairly easy to calculate using one of a few > different computer > > programs – for the calculations here, the FEFF program was used. The > results of the > > FEFF calculation are stored in simple files containing the scattering > factors and meanfree- > > path for a given coordination shell. The calculations in these files can > be used > > directly in a number of analysis programs.” > > > > Are these somewhere listed in Artemis? > The calculations stored in the feffNNNN.dat files can be accessed from Larch, but I think they're not readily exposed by Artemis. The point is that you don't have to worry about these scattering factors, but only about the Path Parameters (S02, E0, deltaR, sigma2, etc) that modify these scattering terms. > Because if I start fitting the value in GDS is always guessed to be one, > for any element in the sample. If I go and look at the FEFF calculation it > tells me: > > > > > > TITLE LiPF6 > > > > HOLE 1 1.0 * FYI: (F K edge @ 696.7 eV, 2nd number is S0^2) > > * mphase,mpath,mfeff,mchi > > CONTROL 1 1 1 1 > > PRINT 1 0 0 0 > > > > I don’t really understand which is the second number and why all S0^2 then > are either 0 or 1. > > > > Best, Julian > One can set an S02 value during the Feff calculation. That is what goes as the second number in the HOLE entry in feff.inp (The first value is an integer indicating the edge type -- 1 for 'K', and so on). Setting that value will apply the S02 value to all paths calculated by that run of Feff. You can also set values for sigma2 from Feff too, Artemis/Ifeffit/Larch etc use the Feff calculations stored in feffNNNN.dat (or equivalent) and build a model from a collection of paths from Feff. If S02 or sigma2 is set in the original Feff calculation(s), it is difficult to track during the analysis (neither S02 nor sigma2 are written to the individual feffNNNN.dat files). In some sense Artemis/Ifeffit/Larch etc only use part of Feff -- the calculation of the EXAFS contribution of a single, idealized path. They do not use the sum-of-paths module(s) of Feff, but instead replace that with its own sum-of-paths implementation that is richer (allowing feffNNNN.dat from different feff runs, allowing parameters like S02, sigma2, E0, deltaR, etc to be varied, etc). So, the recommendation (more like an expectation, really) is to NOT set S02 to any value except 1.0 and to NOT set any parameters that will calculate sigma2 in feff.inp if the intention is to use those paths for fitting. Let the fitting program adjust S02 and/or disorder terms. Hope that helps, --Matt

1 0

EXAFS above 5 angstroms
by Daniel Sneed 23 May '18

23 May '18

Hello, This is my first time posting to the mailing list, so please forgive me if I did not do it correctly. I am currently working on EXAFS of tin(IV) oxide, and I have what appears to be high quality data out to 9 angstroms or so, but I am having some issues in fitting the data above 4 angstroms. I am attempting to verify a crystal structure with a= ~6 angstroms, and another structure with a=~9 angstroms. I know that there is some inhibiting physics at such long distances, such as inelastic scattering, and core-hole lifetime issues that can effect the data. My question for the group is, is there any methodical way to deal with these issues, other than incorporating Ei and the higher cumulants? Or is it even possible to get results from such large R? Thank you for your time. regards, Daniel Sneed

4 3

temperature dependency of amp parameter
by Abdul Ahad 21 May '18

21 May '18

Hi all, I have little confusion that do i fix or change S2 for each data set measured at different temperature. The compound is not monoatomic so i used Einstein model for sigma2. What about amplitude S2. thanks *A. Ahad*

2 1