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 publicati

[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 Wo

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 issues

[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
its" or "license" for more information. > > > Any suggestions anyone has to offer will be appreciated. > > Wishing you all the best, > > Don > > > -- > > Melting rocks today for a better tomorrow . . . > Don R. Baker, Professor of Geochemistry, McGil

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

2021-06-10 Thread Matt Newville
gy > > Callinstr. 3, Room 325 > > 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 >

Re: [Ifeffit] Analyzing EXAFS data on Artemis

2021-05-27 Thread Matt Newville
gt; question 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 &

[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, a

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 d

[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 rea

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
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

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 you

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

2021-03-16 Thread Matt Newville
lib/python3.8/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 > ModuleNotFou

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
ches above it would 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 (n

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

2021-03-13 Thread Matt Newville
illenia.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@millenia.cars.aps

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 basic

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 leads

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 am

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 literatur

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
___ > 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 _

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 particular

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 > > life

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

2020-09-28 Thread Matt Newville
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
lenia.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 > >

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
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 proble

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` module

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 htt

Re: [Ifeffit] Jupyter/python question for Larch

2020-08-04 Thread Matt Newville
r time! > Garret > > -- > Garret Bland > PhD Student > Carnegie Mellon University > Civil and Environmental Engineering > Porter Hall 201 > Pittsburgh, PA, 15213 > ___ > Ifeffit mailing list > Ifeffi

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 go

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

2020-05-07 Thread Matt Newville
ue...) 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 > wrote: > >  > Hi Simon, > > This is definitely a t

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 base

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" butt

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:

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

2020-04-29 Thread Matt Newville
nExportFitResult > 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'

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
> 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 ___ 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 sh

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 t

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
anl.gov/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.a

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

2020-03-09 Thread Matt Newville
millenia 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 htt

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 (curr

Re: [Ifeffit] Larch 0.9.47

2020-03-02 Thread Matt Newville
ed anymore. 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

[Ifeffit] Larch 0.9.47

2020-02-28 Thread Matt Newville
tly 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 > an

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

Re: [Ifeffit] what happened to the website?

2020-01-29 Thread Matt Newville
2020, 5:54 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 Ma

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 ap

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
cPtr): > TypeError: item 1 in _argtypes_ passes 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, >

Re: [Ifeffit] Download Demeter in Ubuntu 18.04

2019-12-13 Thread Matt Newville
7;t > 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

Re: [Ifeffit] Download Demeter in Ubuntu 18.04

2019-12-13 Thread Matt Newville
Hi Sri, On Wed, Dec 11, 2019 at 3:17 PM sri tapaswi wrote: > Hi all, > > I am using the following link to install Demeter from the source > code. > http://bruceravel.github.io/demeter/documents/SinglePage/installation.html > > In step-1, when I do "./configure", it gives an error th

Re: [Ifeffit] selection of pixels by criteria

2019-11-22 Thread Matt Newville
retty easy to add, and it makes sense to be able to save those selections. So, I will add that. Thanks for the suggestion! Sincerely, > Matthew Marcus > > On 11/21/2019 12:26 PM, Matt Newville wrote: > > HI Troy, > > > > Sorry for the late reply -- I think this s

Re: [Ifeffit] selection of pixels by criteria

2019-11-21 Thread Matt Newville
HI Troy, Sorry for the late reply -- I think this sort of slipped off my radar screen. On Sat, Nov 16, 2019 at 2:09 PM E. Rasbury wrote: > I have used larch some for XRF maps. I like the feature for defining ROI's > and then looking at the statistics of the data. I have some samples that > are

Re: [Ifeffit] about WebAoms

2019-11-20 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 ___ Ifeffit mailing list Ifeffi

Re: [Ifeffit] Mac problems

2019-10-04 Thread Matt Newville
On Thu, Oct 3, 2019 at 2:10 PM Enrico Tusini wrote: > Hey there, I have this problem with the installation of Athena package on > Mac Mojave : > > Failed to build pgplot: command execution failed > Error: See > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macpor

Re: [Ifeffit] Larch install error

2019-10-03 Thread Matt Newville
Hi Stefan, On Wed, Oct 2, 2019 at 12:08 PM Mangold, Stefan (IPS) < stefan.mang...@kit.edu> wrote: > Dear Matt, > > > I tried to install larch via Anaconda. Install of Anaconda and larch seems > to work fine, but I couldn’t create the Links via > > larch -m > [numexpr.utils] INFO : NumExpr defau

Re: [Ifeffit] Larch single-file installers problem on Mac

2019-09-17 Thread Matt Newville
Hi Youchiuan, I believe you installed to /anaconda3 and then got prompted for an administrator password. Unfortunately, with the MacOS Package Installer this is the default. But you should remove /anaconda3 and /Users/willie/.larch (which will probably require Administrator privilege) and then

Re: [Ifeffit] Running FEFF 8 in Artemis

2019-09-16 Thread Matt Newville
Hi Jose, On Sat, Sep 14, 2019 at 1:53 PM José C. Conesa wrote: > Dear Matt, > > I exchanged with you on this matter some messages in September 2017, and > after that I exchanged also other messages with Bruce Ravel in December > 2017 and January 2018. He told me that he was very busy with its ne

[Ifeffit] Larch 0.9.46

2019-09-14 Thread Matt Newville
been made. These are still behind but will continue to be worked on over the next few months. If you having any questions or suggestions, please let us know. --Matt Newville ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.a

Re: [Ifeffit] Running FEFF 8 in Artemis

2019-09-14 Thread Matt Newville
Hi José, On Sat, Sep 14, 2019 at 1:51 AM José C. Conesa wrote: > Hi, > > As far as I know, Artemis can only work with the format files produced by > feff 6. > Artemis can definitely work with output of Feff8. Lots of people do this. > I tried months ago to urge the Artemis authors to make it w

Re: [Ifeffit] need version for 32 bit

2019-09-11 Thread Matt Newville
> or > changing and adjusting its content in any way. > > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millen

Re: [Ifeffit] Larch import error

2019-09-10 Thread Matt Newville
Hi Chris, On Tue, Sep 10, 2019 at 6:52 AM Patridge, Christopher wrote: > Good morning, > > I have OSX Larch installed and attempting to open XAS data files. It > cannot read the file and Larch returns an error: > > Error trying to read > '/Users/DrPatridge/Desktop/2019-03-21/CaVO_50-40-10_vs_Z

Re: [Ifeffit] QFS fit for Am

2019-08-22 Thread Matt Newville
; > Thank you > > -Daria > ___ > 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/optio

Re: [Ifeffit] Installation of Demeter on Mac Issue

2019-08-11 Thread Matt Newville
Hi Yimeng, I'm not sure this is really the best approach or an actual solution, but I put a copy of that version of the file at https://cars.uchicago.edu/gsecars/data/Larch/Demeter/Template.pm if that helps you or anyone else get Demeter working on MacOSX. Cheers,

Re: [Ifeffit] Trouble with MacOS 10.14 Mojave

2019-07-25 Thread Matt Newville
Hi Christophe, On Thu, Jul 25, 2019 at 4:04 AM christophe den auwer < christophe.denau...@univ-cotedazur.fr> wrote: > Hi all, > > I have to re-install Demeter on my Mojave MacBook (version 10.14.5). > X code version 10.2.1 > > Well it didn't totally worked out…. > > When I launch either Athena or

Re: [Ifeffit] Fitting in Wavelet transform space ?

2019-07-10 Thread Matt Newville
Hi Samy, On Wed, Jul 10, 2019 at 2:08 AM Samy Ould-Chikh wrote: > Dear colleagues, > > I have been using more and more wavelet transform in parallel of EXAFS > fitting. > In addition of the statistical parameters provided after the fit, I try > also to compare the wavelet transform of experiment

Re: [Ifeffit] Larch 0.9.43

2019-05-02 Thread Matt Newville
Hi Stefan, On Thu, May 2, 2019 at 12:20 PM Mangold, Stefan (IPS) < stefan.mang...@kit.edu> wrote: > Dear Matt, > > > conda update —all > does not help. I think re-install anaconda is the only option. I testet > this on a Mac (10.12.6). > > OK, thanks! It looks like `conda update --all` cannot u

Re: [Ifeffit] Larch 0.9.43

2019-05-02 Thread Matt Newville
3.7.3 and I was able to > update to the current version. And thanks for fixing up the import > statements! Can't wait to use larch on jupyter notebook :). > Great, I'd be interested to see what you use these for. That is, it might be nice to have some example notebooks. --Matt Newvi

Re: [Ifeffit] Pseudo Voigt crash Athena

2019-05-01 Thread Matt Newville
Hi Craig, On Wed, May 1, 2019 at 10:51 AM Lawley Craig Richard (PSI) < craig.law...@psi.ch> wrote: > Dear Mailing list, > > > > I have run into an issue with the peak fitting section included in Athena. > If I include a peak that is a Pseudo-Voigt and then save the project file. > Upon trying to

[Ifeffit] Larch 0.9.43

2019-05-01 Thread Matt Newville
upyter notebooks. I should note that the documentation and examples are definitely lagging behind the code especially regarding the most recent developments, but this will be worked on. If you having any questions, trouble, or suggestions on any part of Larch, plea

Re: [Ifeffit] Question about PCA

2019-04-25 Thread Matt Newville
7;s IND and perhaps F would be fine statistics, but I only see how to do that if `s=c` (that is the total number of spectra). --Matt On Wed, Apr 24, 2019 at 10:59 PM Matt Newville wrote: > Hi Joselaine, > > > On Wed, Apr 24, 2019 at 8:40 PM Joselaine Cáceres gonzalez < > josela

Re: [Ifeffit] Question about PCA

2019-04-24 Thread Matt Newville
Hi Joselaine, On Wed, Apr 24, 2019 at 8:40 PM Joselaine Cáceres gonzalez < joselainecace...@gmail.com> wrote: > Hi Matt, thank you for your answer!. The references I have about > Malinowski´s work and some applications are: > > Malinowski, E.R., *Theory of error in factor analysis.* Analytical >

Re: [Ifeffit] Question about PCA

2019-04-23 Thread Matt Newville
Hi Joselaine, On Tue, Apr 23, 2019 at 2:35 PM Joselaine Cáceres gonzalez < joselainecace...@gmail.com> wrote: > Dear all, > > I performed PCA in a set of 11 XANES spectra and I was trying to use some > of the functions and tests developed by Malinowski to extract the number of > primary component

Re: [Ifeffit] can't open Athena 0.9.26!

2019-04-23 Thread Matt Newville
On Tue, Apr 23, 2019 at 6:24 AM m.rezaie wrote: > Hi, > > I upgraded my DEMETER to DEMETER 0.9.26 but I can't open it on my computer > which is Win 7, 32 bit. How can I solve this problem? > > > I believe the installer for Demeter 0.9.26 works only with 64-bit machines. You (or someone else) mig

Re: [Ifeffit] Energy resolution issue [DLM=For-Official-Use-Only]

2019-04-11 Thread Matt Newville
Hi Bernt, Sorry for the trouble. We've had a few similar questions here over the past few months, and some very recently. Is the Energy channel for your raw data in keV? If so, and if you're converting it to Athena-friendly ASCII-readable anyway, try putting the Energy in eV. On Thu, Apr 11,

Re: [Ifeffit] Demeter question and Larch

2019-03-27 Thread Matt Newville
stry > SASE 315 > D’Youville College > 320 Porter Ave. > Buffalo, NY 14201 > 716-829-8096 / 315-529-0501 > patri...@dyc.edu > > > > On Mar 27, 2019, at 9:08 AM, Matt Newville > wrote: > > Hi Chris, > > On Tue, Mar 26, 2019 at 1:57 PM Patridge, Chri

Re: [Ifeffit] Demeter question and Larch

2019-03-27 Thread Matt Newville
Hi Chris, On Tue, Mar 26, 2019 at 1:57 PM Patridge, Christopher wrote: > Hi everyone, > > A Demeter question - Is the memory limit hard set in Athena? > It is really set by the Ifeffit library, not by Athena itself. It should be lifted if using Larch as a backend for Athena. That *ought* to w

Re: [Ifeffit] Larch - LCF error

2019-03-15 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 ___ 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] How to use Larch as function server

2019-03-14 Thread Matt Newville
Hi, On Wed, Mar 13, 2019 at 10:26 PM ASAKURA, Hiroyuki < asak...@moleng.kyoto-u.ac.jp> wrote: > Dear Matt, > > Thank you for your prompt response. > > If I understand correctly, Athena works with Larch by making command > strings (Text::Template?) and submitting it to Larch via XML-RPC. > So, it

Re: [Ifeffit] How to use Larch as function server

2019-03-03 Thread Matt Newville
Hi Hiroyuki, On Sat, Mar 2, 2019 at 11:40 PM ASAKURA, Hiroyuki < asak...@moleng.kyoto-u.ac.jp> wrote: > Dear all, > > I would like to use Larch as an external function server. > I'm a Python novice, but if I understand correctly, the present server > (larch -r) provides access to a Larch process

[Ifeffit] Larch 0.9.42

2019-02-26 Thread Matt Newville
uggestions. --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] Problem with using lincomb_fit function in the Larch

2019-02-26 Thread Matt Newville
Hi Ahkil, On Tue, Feb 26, 2019 at 3:51 AM Tayal, Akhil wrote: > Hello Matt, > > I could not be able to perform LCA using the lincomb_fit function in the > Larch software. I am getting the error message from line number 80 in > the lincombo_fitting.py script. I expect the function has some bug w

[Ifeffit] Larch 0.9.41

2019-02-07 Thread Matt Newville
ing any questions or trouble. 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] Problems Opening a larch saved athena Project in Athena

2019-02-05 Thread Matt Newville
Hi Luis, On Tue, Feb 5, 2019 at 9:09 AM Luis Carlos Colocho Hurtarte < luis.colo...@wzw.tum.de> wrote: > Hi all, > > > > I have a some data from CLS, using the plug-in in Athena I could open most > of them except a couple. I managed to open the rest using Larch (no Problem > there), my interest

Re: [Ifeffit] Problem with running mback algorithm in the newer version of Larch

2019-02-04 Thread Matt Newville
Hi Akhil, I think this will be fixed in 0.9.41, which I hope to release in the next few days. But, if you can supply an example, I'll make sure to test that before releasing it. --Matt On Mon, Feb 4, 2019 at 5:18 AM Tayal, Akhil wrote: > Hello Matt, > > I found that while running the 'mback'

Re: [Ifeffit] Plotting flattened feffit simulation results

2019-01-28 Thread Matt Newville
Hi Paul, On Mon, Jan 28, 2019 at 2:57 AM FonsPaul wrote: > Hi All, > I have a rather simple question and a reply for either Larch or athena > would be welcome. I have calculated a number of structures using DFT and > have run feff on each of the appropriate sites and have then averaged the

[Ifeffit] Job posting: Lead Beamline Scientist at NSLS-II, Brookhaven National Lab

2019-01-27 Thread Matt Newville
Hi Folks, I was asked to forward this job posting: There is an opening for a Lead Beamline Scientist position at the National Synchrotron Light Source-II, Brookhaven National Laboratory. The candidate will assume leadership of the Inner-Shell Spectroscopy (ISS) Beamline, a high-flux, fast-scanni

Re: [Ifeffit] Question about parameters of principle components analysis (PCA)

2019-01-26 Thread Matt Newville
arer definitions of these sort of terms that are often reported in the literature. --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] Larch flattening

2019-01-25 Thread Matt Newville
pparently not that well-defined. I either learned it wrong long ago or mis-remembered. I'm in the process of trying to release the next version, so I'll make these changes soon. > > Using the possibility, I would like to thank you for al

Re: [Ifeffit] Standard deviation of R value

2019-01-11 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 ___ Ifeffit mailing list Ife

Re: [Ifeffit] Question about k-weighting real-world practice and outcomes

2018-12-16 Thread Matt Newville
Hi John, On Fri, Dec 14, 2018 at 7:56 PM John Ferre wrote: > Dear EXAFS folk, > > I'm a graduate student in Jerry Seidler's group at the University of > Washington, Seattle. I've been doing a numerical and experimental study on > how to optimize k-weighting for EXAFS when the total experimental

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