Re: [Ifeffit] Help for EXAFS fitting

2022-09-14 Thread Matt Newville
Hi Dien, When I look at your project, I find that I have to add Parameters to the GDS page for the "P1.1" path. When I include that in the fit, the coordination number for that Path goes to 0 (0.07 +/- 0.3) and that "ss_P11" is -0.03 +/- 0.04. Both "P1.1" and "P1.4" show values for "delr" that

Re: [Ifeffit] Larch: Fitting error of the objective/model function

2022-09-14 Thread Matt Newville
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-what-can-i-do > for more inf

Re: [Ifeffit] Fitting multiple spectra simultaneously with Larch

2022-09-12 Thread Matt Newville
2350 Speedway > > Austin, TX 78705 > > USA > > > > Phone: +1 (512) 775-2658 > > E-mail: casey.vanstap...@austin.utexas.edu > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit &g

Re: [Ifeffit] Icon Resolution issue in 14 inch

2022-09-11 Thread Matt Newville
Hi Mohamad, On Sun, Sep 11, 2022 at 8:17 AM Mohamad Numan wrote: > 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

Re: [Ifeffit] Question related to an example of EXAFS fitting using Larch

2022-08-29 Thread Matt Newville
Hi Harry, On Mon, Aug 29, 2022 at 2:43 PM Andy Zhang wrote: > 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 >

Re: [Ifeffit] third cumulant in Larch

2022-08-19 Thread Matt Newville
Hi Harry, On Fri, Aug 19, 2022 at 9:10 AM Andy Zhang wrote: > 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:

Re: [Ifeffit] Standardized Spectra

2022-08-07 Thread Matt Newville
Hi Kyle, On Sun, Aug 7, 2022 at 8:15 PM Kyle Draim wrote: > 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

Re: [Ifeffit] xraylarch

2022-08-06 Thread Matt Newville
Hi Paul, On Fri, Aug 5, 2022 at 8:41 AM Paul Fons wrote: > 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

Re: [Ifeffit] Athena: the R factor for normalized mu(E)

2022-07-13 Thread Matt Newville
Hi Jon Petter, On Tue, Jul 12, 2022 at 12:46 AM Jon-Petter Gustafsson < jon-petter.gustafs...@slu.se> wrote: > 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

Re: [Ifeffit] Larch 0.9.61 and 60

2022-05-31 Thread Matt Newville
feffit@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 630-327-7411 ___ Ifeffit mailing list 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] Larch 0.9.61

2022-05-26 Thread Matt Newville
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

[Ifeffit] Larch 0.9.60

2022-05-23 Thread Matt Newville
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

Re: [Ifeffit] structure for reference Mn foil

2022-05-14 Thread Matt Newville
Hi Yang, On Thu, May 12, 2022 at 1:29 PM Hu, Yang (HIU) wrote: > Dear IFEFFIT members, > > > > I have been trying to obtain the S02 value from metal reference foils > measured at the beamline. > How was your sample Mn metal prepared? Do you have verification that it is metallic? When you

Re: [Ifeffit] Larch 0.9.59, problems with PCA

2022-05-10 Thread Matt Newville
; > Best regards > > Stefan Mangold > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov

[Ifeffit] XAFS 2022 reminders

2022-04-21 Thread Matt Newville
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

Re: [Ifeffit] [Ext] Larch 0.9.59

2022-04-04 Thread Matt Newville
Hi Carlo, On Sat, Apr 2, 2022 at 5:51 PM Carlo Segre wrote: > Hi Matt: > > My installation is a mix of Debian packages and pip3 installations. This > allows for more recent packages that are not in Debian. The trick is to > know which ones are needed. I can try the Linux install with one of

Re: [Ifeffit] Path output with feff8l

2022-04-04 Thread Matt Newville
Hi Shinichi, Make sure your feff.inp file for Feff8 has CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 EXAFS 20.0 and it will calculate the classic Feff.dat files. On Sun, Apr 3, 2022 at 11:25 PM 西村 真一 wrote: > Dear all, > > I have used Larch ver 0.9.59/0.9.58 on Linux for XAFS

Re: [Ifeffit] [Ext] Larch 0.9.59

2022-04-01 Thread Matt Newville
Hi Carlo, On Fri, Apr 1, 2022 at 5:39 PM Carlo Segre wrote: > Hi Matt: > > I have managed to figure out an installation procedure using Debian Linux > that installs Larch for all users on the system to use. If this is useful > for you , I can write it up. > > Yes - I think that would be very

Re: [Ifeffit] XAFS 2022: important deadlines

2022-04-01 Thread Matt Newville
On Fri, Apr 1, 2022 at 4:47 PM Robert Gordon wrote: > Matt's idea of an April Fool's joke no doubt... > > The XAFS2022 website indicates that the abstract deadline is April 17. > Thanks, Robert! And, just a regular fool ;). --Matt ___ Ifeffit

[Ifeffit] XAFS 2022: important deadlines

2022-04-01 Thread Matt Newville
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

[Ifeffit] Larch 0.9.59

2022-04-01 Thread Matt Newville
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

Re: [Ifeffit] Question related to save fitting results in Larch

2022-03-24 Thread Matt Newville
Hi Harry, On Thu, Mar 24, 2022 at 11:30 AM Andy Zhang wrote: > 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

Re: [Ifeffit] Larch install error on MacOS 12.2

2022-02-10 Thread Matt Newville
conda install -y pymatgen > conda install -y cython > > # Install lmfits and Xraylarch using Pip > pip install lmfit peakutils pyepics pyshortcuts termcolor sphinx dill > pycifrw xraydb wxmplot wxutils > pip install xraylarch > > larch -m > > &g

Re: [Ifeffit] Larch install error on MacOS 12.2

2022-02-09 Thread Matt Newville
led building wheel for fabio > Failed to build fabio > > also no director with XAS viewer created. > > > best regards > > Stefan Mangold -- --Matt Newville 630-327-7411 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov

[Ifeffit] post-doc opportunity

2022-01-24 Thread Matt Newville
January 25, 2022. UIUC is an Equal Opportunity/Affirmative Action employer, and applications from women and under-represented minorities are particularly encouraged.-- --Matt Newville ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http

Re: [Ifeffit] FEFF calculation on ferri-/ferrocyanide materials

2022-01-23 Thread Matt Newville
Hi Yang, On Sun, Jan 23, 2022 at 11:30 AM Hu, Yang (HIU) wrote: > 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

Re: [Ifeffit] Question_Demeter installation on Mac with Apple Silicon M1

2022-01-22 Thread Matt Newville
Hi Maolin, On Thu, Jan 20, 2022 at 11:13 PM 王茂林 wrote: > 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.html >

[Ifeffit] Larch 0.9.58

2022-01-16 Thread Matt Newville
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

Re: [Ifeffit] How do I launch Larch GUIs?

2022-01-12 Thread Matt Newville
Hi Betsy, Very sorry for the trouble and delay. I feel like my email signature should be "Sorry for the late reply. Zoom Meetings, Proposal Writing, and doom scrolling the NY Times Covid Page have prevented me from doing real work for the past year" On Mon, Jan 10, 2022 at 2:59 PM Swanner,

Re: [Ifeffit] Problem in xrayLarch installation

2021-12-15 Thread Matt Newville
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

[Ifeffit] Larch 0.9.57

2021-12-02 Thread Matt Newville
conversations here or on Github. Cheers, --Matt Newville ___ Ifeffit mailing list 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

Re: [Ifeffit] Fe and Ni carbide XAS reference spectra?

2021-11-15 Thread Matt Newville
Hi Valentijn, For Fe3C, see https://xaslib.xrayabsorption.org/spectrum//105/ I'm not sure what "does not contain the Energy values of the spectrum" means. On Mon, Nov 15, 2021 at 3:10 AM Valentijn De Coster < valentijn.decos...@ugent.be> wrote: > Dear ifeffit mailing list, > > > > My name is

Re: [Ifeffit] MacPorts XAFS software: announcing a Port for Larch; and do we actually need Demeter on Macs?

2021-11-12 Thread Matt Newville
Hi Joseph, First, thanks very much for doing this. I know that it is a lot of work, and you really only hear when it doesn't work perfectly. So, thanks! Second, please keep working on those TES detectors! We need those too! On Demeter: I sort of think the reality is that it is just too

Re: [Ifeffit] Problem in installing Larch

2021-10-20 Thread Matt Newville
ity Park, PA > > > > > ___ > Ifeffit mailing list > 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 > -- --Ma

Re: [Ifeffit] Bug report: Athena, multiple data export

2021-10-10 Thread Matt Newville
Hi Soyoung, On Fri, Oct 8, 2021 at 5:29 PM Soyoung Kim wrote: > I see. Thank you for the quick reply. > > But would it be difficult to program it so that it will export properly, > e.g., with multiple energy axes? > Sorry for the slight delay, and I have two answers here: In general, it

Re: [Ifeffit] S02 selection from reviewer

2021-10-02 Thread Matt Newville
Hi Peng, On Sat, Oct 2, 2021 at 2:50 AM Peng Liu wrote: > 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.

Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matt Newville
k 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 > -- > *보낸 사람:* Matt Newville 대신 Ifeffit < > ifeffit-boun...@millenia.cars.aps.anl.gov> > *보낸 날짜:*

Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matt Newville
n/options/ifeffit__;!!JmPEgBY0HMszNaDT!_9MKQWuqA2MOuT45VXoI-3HKCOtMuCieGeTJVnN_NT2ZWYzBJuzUu-6yy1MIeXhr1XA$ > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe

Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matt Newville
Hi Shinhyo, Liane, On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo 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

Re: [Ifeffit] Manuscript comments regarding EXAFS modeling

2021-08-29 Thread Matt Newville
Hi Peng, This will echo much of what Matthew Marcus wrote: For comment 1 on S02, picking a value of 0.85 seems reasonable. I think the reviewer is asking you to explain how you got that value. Saying something like "we chose that value so that the data from a simple metal foil (or simple metal

Re: [Ifeffit] Problem Importing CIF files into Larch

2021-08-16 Thread Matt Newville
which would > then work with Larch. I believe that Pymatgen cleans up cifs in a way, so > that they become compatible. > > Vincent > > On Mon, Aug 16, 2021 at 1:22 PM Matt Newville > wrote: > >> Hi Amol, >> >> Sorry for the delay, I was offline most of last wee

Re: [Ifeffit] Problem Importing CIF files into Larch

2021-08-16 Thread Matt Newville
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

[Ifeffit] Larch 0.9.55

2021-07-18 Thread Matt Newville
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

Re: [Ifeffit] Another Mac OS install question

2021-07-07 Thread Matt Newville
Hi Tom, On Wed, Jul 7, 2021 at 10:36 AM Jilbert, Tom wrote: > 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

[Ifeffit] Larch 0.9.53

2021-07-03 Thread Matt Newville
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.

Re: [Ifeffit] Cannon start larch on ubuntu 20.04.2 LTS

2021-06-28 Thread Matt Newville
e" 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 > ___

Re: [Ifeffit] PCA Sixpack results compared to Athena (etc.)

2021-06-10 Thread Matt Newville
> > D-30167 Hannover, Germany > > > > Phone: +49 (0)511 762-8058 > > Email: t.zahoran...@mineralogie.uni-hannover.de > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/m

Re: [Ifeffit] Analyzing EXAFS data on Artemis

2021-05-27 Thread Matt Newville
uestion 1) > > Ph.D candidate, > Institute of Electronic Structure and Laser (IESL), > Foundation for Research and Technology - Hellas > (FORTH)___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > U

[Ifeffit] millenia.cars.aps.anl.gov outage starting April 29

2021-04-28 Thread Matt Newville
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,

Re: [Ifeffit] Larch 0.9.51

2021-04-27 Thread Matt Newville
Hi Stefan, On Tue, Apr 27, 2021 at 12:24 PM Mangold, Stefan (IPS) < stefan.mang...@kit.edu> wrote: > Dear all, > > tested the latest version on two Macs: > Sorry for the trouble. > M1 on Big Sur > XAS viewer starts up, but the open dialog doesn’t work, it doesn’t open at > all > Oh, I can

[Ifeffit] Larch 0.9.51

2021-04-23 Thread Matt Newville
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

Re: [Ifeffit] Fourier transform parameters not saved in Larch XAS Viewer

2021-04-18 Thread Matt Newville
Hi Tyler, On Sun, Apr 18, 2021 at 5:28 PM Tyler Valentine wrote: > 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

[Ifeffit] XAFS 2021 Virtual Conference deadlines

2021-04-18 Thread Matt Newville
. 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 630-327-7411

Re: [Ifeffit] Artemis fit error - chi-square and R-factors are always equal to 0

2021-03-26 Thread Matt Newville
Hi Ava, Sorry for the trouble. It looks to me like the fit actually ran. Like, getting non-trivial and non-starting values and uncertainties for 'ss_Cu1', 'dr_Cu1', etc tells me that many parts of the fit and code worked. I'm not at all sure why Chi-square and R-factor would report 0. Do

Re: [Ifeffit] Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)

2021-03-16 Thread Matt Newville
3.8/site-packages/larch/wxxas/__init__.py", > line 1, in > from .taskpanel import TaskPanel, FONTSIZE > File > "/Users/myloginname/opt/anaconda3/lib/python3.8/site-packages/larch/wxxas/taskpanel.py", > line 10, in > import wx > ModuleNotFoundError: N

Re: [Ifeffit] Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)

2021-03-15 Thread Matt Newville
screen. Please run with a Framework build of python, and only when you are logged in on the main display of your Mac. then you need to make sure you're running with "pythonw", not "python". On Mon, Mar 15, 2021 at 5:32 PM Matt Newville wrote: > Hi Stefan, > >

Re: [Ifeffit] Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)

2021-03-15 Thread Matt Newville
ould help identify what the problem is. --Matt On Mon, Mar 15, 2021 at 7:59 AM Mangold, Stefan (IPS) < stefan.mang...@kit.edu> wrote: > Thanks Matt, > > installation worked. But still have the problem, that I can’t start XAS > Viewer. I executed also larch -m (no error message

Re: [Ifeffit] Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)

2021-03-13 Thread Matt Newville
.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http:/

Re: [Ifeffit] Larch Energy calibration

2021-03-09 Thread Matt Newville
Hi Valerie, Sorry for the delay. On Fri, Mar 5, 2021 at 10:06 AM Schoepfer, Valerie < valerie.schoep...@usask.ca> wrote: > 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

Re: [Ifeffit] Larch energy calibration

2021-03-03 Thread Matt Newville
Hi Valerie, On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoep...@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

Re: [Ifeffit] Larch: AttributeError

2021-01-13 Thread Matt Newville
Hi Rachita, On Wed, Jan 13, 2021 at 2:00 PM Rachita Rana wrote: > Hi Everyone, > > I am using Larch for reading and fitting EXAFS data and I get the autobk > and Fourier transforms working. But when I try to generate the fefffpaths > and fit the data I get an error from the feffit function. I

Re: [Ifeffit] How do I create a histogram based on R-space values

2020-12-10 Thread Matt Newville
Deepak, On Wed, Dec 9, 2020 at 9:27 PM Deepak Varanasi wrote: > Good evening > > May I also know how to calculate the necessary ingredients in building a > histogram such as R and N? > The analysis of EXAFS to extract structural parameters is slightly complex. There is quite a bit of

Re: [Ifeffit] How do I create a histogram based on R-space values

2020-12-09 Thread Matt Newville
Deepak, The data files you sent appear to be plots of XAFS |chi(R)|, including offsets for the plotting. That is certainly a reasonable visualization to make for EXAFS data and Demeter can make those easily. But |chi(R)| is not a histogram of the number of atoms as a function of distance. That

Re: [Ifeffit] Athena error on Linux mint

2020-10-26 Thread Matt Newville
gt; Ifeffit mailing list > 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 630-252-0431 ___ Ifeffi

Re: [Ifeffit] Ifeffit Question

2020-10-07 Thread Matt Newville
Hi Nicholas, On Wed, Oct 7, 2020 at 10:02 PM Nicholas Weingartz < nicholasweingartz2...@u.northwestern.edu> wrote: > Hello List, > > I'm having a strange problem with my EXAFS fits in Artemis in which they > seem to fly off at higher k. I was having trouble with background fitting > a

Re: [Ifeffit] Core-hole Lifetimes in Hephaestus 0.9.26

2020-09-28 Thread Matt Newville
Hi Daniel, On Mon, Sep 28, 2020 at 2:15 PM Daniel Przyrembel < daniel.przyrem...@fu-berlin.de> wrote: > Hi Matt, > > Well, independent of what Krause et al. have done, the correct uncertainty > relation between core-hole widths as FWHM (full width at half maximum) and > the lifetime is > >

Re: [Ifeffit] Core-hole Lifetimes in Hephaestus 0.9.26

2020-09-28 Thread Matt Newville
at https://xraydb.xrayabsorption.org/ On Mon, Sep 28, 2020 at 1:37 PM Matt Newville wrote: > I believe it is using (or intends to use) > > lifetime = hbar /gamma > > which is what Krause et al give. With gamma = 0.2 eV, and hbar ~= > 4.13567e-15 eVs, then lifetime is ~20fs. &

Re: [Ifeffit] Core-hole Lifetimes in Hephaestus 0.9.26

2020-09-28 Thread Matt Newville
; Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > >> > > ___ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit &g

Re: [Ifeffit] Core-hole Lifetimes in Hephaestus 0.9.26

2020-09-28 Thread Matt Newville
Hi Daniel, Thanks - that does seem wrong. FWIW, Larch uses XrayDB which uses corehole widths from Krause and Oliver for Z>10 and Keski-Rahkoken nand Krause for Z<10. For the F K edge, this give 0.2089 eV. For this or other core-hole widths, and assuming you have Python installed, try: ~> pip

[Ifeffit] mailing list / webserver outage for upgrade

2020-09-09 Thread Matt Newville
. In addition, I have not yet been able to get the Webatoms program running on the new server yet. I will try to solve this over the next few days. --Matt Newville ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov

Re: [Ifeffit] Unable to Import Data In Athena

2020-09-03 Thread Matt Newville
On Thu, Sep 3, 2020 at 10:11 AM Ravel, Bruce wrote: > > Aha! Attached log file. Sorry. Didn't notice that on my phone :( > > I concur with Matt about Larch. > > And at the risk of irking Matt, you could try forcing the use of > Ifeffit. While maybe not the best choice, it would isolate

Re: [Ifeffit] Unable to Import Data In Athena

2020-09-03 Thread Matt Newville
Hi Angshuman, The logfile you attached says that Athena is using Larch and that is where the error is coming from. A few comments on that: a) it looks like it is using Python 2.7 which actually has not been supported for xraylarch for some time now (well over a year) b) that the `pyfai`

Re: [Ifeffit] web apps for X-ray data and XAS library

2020-08-14 Thread Matt Newville
Hi Carlo, Oops, that link for the XAS Data library should be https://xaslib.xrayabsorption.org/elem/ On Fri, Aug 14, 2020 at 9:39 AM Matt Newville wrote: > Hi Folks, > > I was fortunate enough to have a summer student this crazy summer and had > them work (from home, of cou

[Ifeffit] web apps for X-ray data and XAS library

2020-08-14 Thread Matt Newville
Hi Folks, I was fortunate enough to have a summer student this crazy summer and had them work (from home, of course!) on web applications for X-ray data resources, including absorption calculations for materials. The result is a bit like a web version of Hephaestus and is currently at both

Re: [Ifeffit] Jupyter/python question for Larch

2020-08-04 Thread Matt Newville
> PhD Student > Carnegie Mellon University > Civil and Environmental Engineering > Porter Hall 201 > Pittsburgh, PA, 15213 > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.c

Re: [Ifeffit] Reported W L3-edge and L2-edge energy

2020-05-07 Thread Matt Newville
Hi Mike, Matthew, On Thu, May 7, 2020 at 5:55 PM Mike Massey wrote: > 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

Re: [Ifeffit] Reported W L3-edge and L2-edge energy

2020-05-07 Thread Matt Newville
iate 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 > wrote: > >  > Hi Simon, > > This is definitely a timely discussion for me,

Re: [Ifeffit] Change in fixed baseline after fit in XAS Viewer

2020-05-04 Thread Matt Newville
Hi George, On Mon, May 4, 2020 at 12:25 PM George Sterbinsky < georgesterbin...@u.northwestern.edu> wrote: > 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

Re: [Ifeffit] Problem with XAS Viewer

2020-05-04 Thread Matt Newville
On Mon, May 4, 2020 at 12:55 PM Xinyue Wang wrote: > Hi Matt, > > I am trying to fit the main peak. So, to do the general peak fitting, > should I use the pre-edge peak tab in XAS viewer or other tab? > Thanks for your help. > > What sort of model do you want to use to fit the main peak? If you

Re: [Ifeffit] Problem with XAS Viewer

2020-05-03 Thread Matt Newville
On Sat, May 2, 2020 at 3:18 PM Xinyue Wang wrote: > Hi Matt, > > Thanks for your detailed instructions. I am just trying to follow the > steps and see how it works. I am not trying to do complicated things. > My issue is I would expect the grey vertical lines after press the "Fit > Baseline"

Re: [Ifeffit] Problem with XAS Viewer

2020-05-02 Thread Matt Newville
Hi Xinyue, On Fri, May 1, 2020 at 9:16 PM Xinyue Wang wrote: > 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 >

Re: [Ifeffit] unable to export xdi file in xas viewer

2020-05-01 Thread Matt Newville
it could not do this calculation because, for some reason, it did not have those uncertainties. So, what I meant was that the code should not be trying to estimate that `delta_fit` if it doesn't have uncertainties in the parameters. --Matt George > > On Wed, Apr 29, 2020 at 12:05 PM Matt

Re: [Ifeffit] unable to export xdi file in xas viewer

2020-04-29 Thread Matt Newville
rtFitResult > yerr=yerr, x=x) > File > "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py", > line 59, in export_modelresult > delta_fit = 0.0*result_best_fit > NameError: name 'result_best_fit' is not define

Re: [Ifeffit] How Artemis handle crystal structure data with partial occupancy in vorlanite (cubic CaUO4)

2020-04-28 Thread Matt Newville
Hi Dien, Yes, basically Artemis / Atoms cannot handle partial occupancy for crystallographic sites because partial occupancy is not readily translated to a cluster of atoms. So, what you have to do is start with a CIF without fractional occupancy, say that has only Ca or only U in that site, and

Re: [Ifeffit] unable to export xdi file in xas viewer

2020-04-21 Thread Matt Newville
s.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville 630-252-0431 ___ Ifeffit mailing list 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

Re: [Ifeffit] Larch 0.9.47

2020-04-18 Thread Matt Newville
Hi George, Sorry for the trouble. I think a fresh install is not the only option, but it might be the simplest ;). It seems there were some challenges with using conda to update, including that it sometimes just seems to take forever. I'm not sure what to do about that. I think pip install

Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 206, Issue 8

2020-04-13 Thread Matt Newville
Hi Dien, On Mon, Apr 13, 2020 at 2:02 PM dien...@srnl.doe.gov wrote: > Hi, all > > I fitted my Cr EXAFS data, but E0 was -2.5. I calibrated the spectrum in > energy space by +10 eV, the spectra in K and R space were identical before > and after this calibration, in contract to my understanding

Re: [Ifeffit] errors in bond lengths

2020-04-12 Thread Matt Newville
Hi George, I think this will not be a different answer from Matthew's or Anatoly's answers, but just reiterate their points. The Purans et al 2008 PRL from 2008 appears to use both non-linear fitting with Feff and EDA (which should give basically the same results as Artemis/Ifeffit/Larch, though

Re: [Ifeffit] larch can not deconvolve my data

2020-04-09 Thread Matt Newville
ov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville 630-252-0431 S_Wang.prj Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.an

Re: [Ifeffit] Unable to access content on millenia.cars.aps.anl.gov website

2020-03-09 Thread Matt Newville
nia itself!) But also: it seems that most browsers will usually know to auto-magically translate links once you have gone to the "https" version. hope that helps, --Matt Newville ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://m

Re: [Ifeffit] Larch 0.9.47

2020-03-03 Thread Matt Newville
Hi Garret, On Tue, Mar 3, 2020 at 8:01 AM Garret Bland wrote: > Hi All, > I tried to reinstall anaconda (Windows 10) and create a new environment to > install the newest version of larch. It gave me the following error: > > conda install -yc GSECARS xraylarch > Collecting package metadata

Re: [Ifeffit] Larch 0.9.47

2020-03-02 Thread Matt Newville
ymore. It worked again after a complete delete and > re-install of the actual version of anaconda3 > > Best regards > > Stefan Mangold > > Am 28.02.2020 um 21:53 schrieb Matt Newville : > > Hi Everyone, > > Larch 0.9.47 is now available, with installers and source code

[Ifeffit] Larch 0.9.47

2020-02-28 Thread Matt Newville
reatly be appreciated. If you or your students have time to work through the larch examples and/or documentation and make improvements or even suggestions for improvements in readability or completeness, it would be greatly appreciated. Thanks, --Matt Newville __

Re: [Ifeffit] XAFS detection limit

2020-02-09 Thread Matt Newville
Hi Christian, On Thu, Feb 6, 2020, 8:40 PM Christian Wittee Lopes wrote: > Dear all, > > Recently I was questioned about the EXAFS detection limit when describing > different metal species in a bimetallic sample. > > By checking Pd and Cu K-edges, for example, I found Pd metal nanoparticles >

Re: [Ifeffit] XAFS.ORG WEBSITE??

2020-01-30 Thread Matt Newville
Ifeffit mailing list > 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 630-252-0431 ___ If

Re: [Ifeffit] what happened to the website?

2020-01-29 Thread Matt Newville
PM Matthew Marcus wrote: > OK, thanks. I figured that you removed it because it's obsolete. > > Are you sure the server isn't running Windows 7? :-) > > Sincerely, > Matthew Marcus > > On 1/29/2020 3:48 PM, Matt Newville wrote: > > Hi Matthew, > > >

Re: [Ifeffit] what happened to the website?

2020-01-29 Thread Matt Newville
Hi Matthew, On Wed, Jan 29, 2020 at 4:39 PM Matthew Marcus wrote: > The http://millenia.cars.aps.anl.gov/ website seems to have gone > off-line, which means that WebAtoms doesn't work anymore. Is there a > replacement? > Of course, I can use the stand-alone Atoms in Demeter. > The webpages

Re: [Ifeffit] Larch Mac OS X 10.15 Catalina

2020-01-10 Thread Matt Newville
ts==1.5 and then `larch -m` should work. I will try to get out a release of larch 0.9.47 by the end of the month that fixes all this. And, FWIW, the pyepics vd Py3.7.6 problem is now resolved. Thanks, > > Jeff > > > > On Jan 9, 2020, at 9:36 AM, Matt Newville > wrote:

Re: [Ifeffit] Larch Mac OS X 10.15 Catalina

2020-01-09 Thread Matt Newville
a struct/union with a bitfield by > value, which is unsupported. > > > > I think that line 11 is: load_entry_point('xraylarch==0.9.46', > 'console_scripts', 'larch')() > > Any ideas on how to address this issue? > > Thanks, > > Jeff > > Jeff Terry > Professor of Physics, Illinois Institute of

Re: [Ifeffit] Download Demeter in Ubuntu 18.04

2019-12-13 Thread Matt Newville
gt; plotting properly, however I was able to successfully install it on my > colleagues computer running Ubuntu 16.04. Matt Newville is correct. > Installing PGPlot from source would be a huge headache and wouldn't work. > There is, however, a pgplot5 package available for Ubuntu, which yo

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