December 2022 - Ifeffit - millenia.cars.aps.anl.gov

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

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