Re: [Ifeffit] Multi-electron peak in Yb

Hi Matthew, On Thu, Aug 4, 2016 at 2:24 PM, Matthew Marcus wrote: > Does anyone know of data on multi-electron peaks at the Yb L3 edge? One > of the users here was just running Yb and finds on every spectrum a bump at > the same > energy. It's not a Bragg glitch from the

Re: [Ifeffit] demeter installation in OSX El Capitan

Demeter 0.9.24 does work for me on El Capitan (10.11.5). In fact, I did a sudo port upgrade outdated and many packages updated, and and Demeter still lauches and seems to run. Yuan, you say you upgraded to 10.11. Does that mean you had Macports / Demeter working on 10.10 and it failed to

Re: [Ifeffit] Artemis (FEFF) question

Louis, On Tue, Jul 12, 2016 at 4:13 AM, Louis Forto wrote: > Dear All, > > I am trying to run a FEFF calculations on a quaternary glass , when I > import crystalline data obtained from ICSD website and try to run FEFF to > calculate the scattering paths of nearest neighbour

Re: [Ifeffit] How to input atoms in solid solution for Artemis

on numbers separately for Ni-Ni, Ni-Fe, Fe-Fe, and Fe-Ni to be very, very hard. My recollection (could be wrong) is that the nominal near-neighbor distances for fcc Ni and bcc Fe are both around 2.48 Ang. With Z different by only 2, I would not expect these to be distinguishable

Re: [Ifeffit] How to input atoms in solid solution for Artemis

Hi Fuxiang, On Thu, Jun 23, 2016 at 11:38 AM, Fuxiang Zhang wrote: > Hi, All, > I am new in using EXAFS techniques. Just wondering how to input atomic > structure of NiFe solid solution to Artemis. It has a simple Ni-structure, > but both Ni and Fe occupy the same site. If I

Re: [Ifeffit] Sorbed complex in Atoms

Gnu, First, we prefer people to use their real names here, because we are all adults discussing science. On Thu, Jun 9, 2016 at 11:12 AM, Gnu script wrote: > Hi Bruce, > Thanks for your reply. I am familiar with outer-sphere complexation and > how it works but I am much

Re: [Ifeffit] Atoms on the WEB

Searching the collection of atoms.inpt files to retrieve atoms.inp files that can be run with Artemis does work: http://cars9.uchicago.edu/~newville/adb/search.html Running Atoms on the server does not work.The old server had been running the pre-Demeter perl code that's no longer

Re: [Ifeffit] PGPLOT installation error!

That's not enough to go on. Please send a more detailed report, including what you typed, and the complete output. On Thu, May 26, 2016 at 12:15 PM, Ernesto wrote: > Dear all, > after running the PGPLOT_install script, I'm trying to continue the > installation using

Re: [Ifeffit] N independent variables

Jesus, On Mon, May 23, 2016 at 2:07 PM, Jesús Eduardo Vega Castillo < jeve...@gmail.com> wrote: > Dear list, > > I made an EXAFS analysis in Artemis (in Demeter 0.9.22) using all the > available variables. This is a fragment of the .log file I got: > > Independent points : 17.7666016 >

Re: [Ifeffit] Consultation on Reduced Chi2

Jesus, On Mon, May 23, 2016 at 7:08 AM, Jesús Eduardo Vega Castillo < jeve...@gmail.com> wrote: > Dear list, > > I am back with a new consultation on EXAFS fitting within Artemis. > > I have made a fit and obtained a reduced Chi2 value of 391 and R-factor of > 0.014 using 9 variables. Then I

[Ifeffit] XASLIB (was Re: data availability)

a, with the same web-based interface. This is not very well documented at the moment, but if anyone is interested in trying to set such a database at their home institution, let me know. --Matt Newville ___ Ifeffit mailing list Ifeffit@millenia.c

Re: [Ifeffit] how to use the data in the XAN library to estimate the transmission of an x-ray filter

Hi Nino, On Tue, Apr 12, 2016 at 9:08 PM, pereira wrote: > Hi All, > > new to this list and to the field, so please be patient and kind > and helpful in any response you may have. So far everyone I've > reached on this topic has been extraordinary good. I still have to

Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3

Hi Matthew, On Sun, Apr 3, 2016 at 8:13 PM, Matthew Marcus wrote: > > It shouldn't be called 'self-absorption'. That's a misnomer, which seems > to have come from a 1992 > paper (Troger, et. al."Full correction of the self-absorption in > soft-fluorescence extended

Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3

On Sun, Apr 3, 2016 at 6:56 PM, Matteo Busi wrote: > Hi Bruce, > Thanks for your help, it's really appreciated. > I was trying to keep it simple but it seems I'm just messing around. > > What I am trying to do is to perform a new developed self-absorption > correction using

Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 1

Matteo, On Fri, Apr 1, 2016 at 8:35 AM, Matteo Busi wrote: > Hi Bruce, > Now this is clear. > In my case the correction I have to perform requires these > measured/evaluated parameters: chi, mu (not sure if it's better to work > with normmu here) and the background

Re: [Ifeffit] Question about Io during data collection

Hi Todd, On Thu, Mar 31, 2016 at 9:27 AM, Luxton, Todd wrote: > All: > > > > Recently our group was at the APS collecting Pb L(III) spectra on an ID > line using quick XAFS. Data was collected from -200 to +800 eV for Pb > L(III) at 0.2 eV steps with a count rate of

Re: [Ifeffit] Running Examples for larch

Panagiotis, On Sat, Mar 19, 2016 at 2:38 PM, Panagiotis Mougkogiannis wrote: > Hello Dear all, > > > I am struggling to run the larch-0.9.27 examples. > > From previous email messages in IFEFFIT info page I managed to install > larch and the icons appeared in my desktop

Re: [Ifeffit] fluo_corr() script

Hi Gerome, (I'm CCing this to the Ifeffit mailing list) On Thu, Feb 25, 2016 at 9:30 PM, Gerome Melaet wrote: > Dear Dr. Newville, > I have tried to use the flu_corr() function to correct some of my recent > x-ray data on the cobalt K-edge. > Unfortunately, after multiple

Re: [Ifeffit] Athena with IOS "El Capitan"

Hi Manuel, On Mon, Feb 1, 2016 at 4:16 PM, Manuel Cossio Kohler wrote: > Hello, > > I am having some issues with the Athena software. After upgrading the OS > of the macbook pro to "El Capitan" Version 10.11.3, Athena stopped working > properly. Once the iXAFS icon was

Re: [Ifeffit] pi/2deltak

Hi Riti, On Sat, Jan 30, 2016 at 7:35 PM, Ritimukta Sarangi wrote: > Hello, > > I was recently asked about the accuracy of this formulation for obtaining > EXAFS resolution and I did not have a good answer. Can someone point to a > reference or explain here? > Thank you for

Re: [Ifeffit] XANES pre-edge vs. edge features

Aditya, The distinction between "edge" and "pre-edge" is not very clear, either when looking at a single spectrum or even conceptually. In broad terms, the main edge is at the energy where the unoccupied electron levels start - the Fermi energy. For 1s levels, the transition is to p levels

Re: [Ifeffit] DAFS calculation

Y, 11973 > > > > Homepage: http://bruceravel.github.io/home/ > > Software: https://github.com/bruceravel > > Demeter: http://bruceravel.github.io/demeter/ > > ___ > > Ifeffit mailing list > > Ifeff

[Ifeffit] Ifeffit Mailing List

either on this list or in private. --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] Solution to running Demeter on an ORNL computer

Hi Dave, The main reasoning for changing the installation location to the Users folder was so that installation doesn't require Admin permission to write to, say, C:\Program Files. In the new scheme, everything is being written to a folder that the unprivileged user has complete write access.

[Ifeffit] [ANN] Larch 0.9.27

Hi Folks, Though I've resisted making an announcement about each minor release of Larch, I wanted to let everyone know about an important change starting with the latest release. As both Bruce and I (and Sam, and probably anyone who has tried) have experienced, and many of you have witnessed

Re: [Ifeffit] Fitting parameters corrleations between variables

Hi Pushkar, On Mon, Nov 23, 2015 at 11:28 PM, pushkar shejwalkar < pshejwalkar2...@gmail.com> wrote: > Dear Matt, > Thank you very much for your response. One more question. What value of > corelation is acceptable/publishable? > A correlation > 0.999 is probably an indication of duplicate

Re: [Ifeffit] Fitting parameters corrleations between variables

Pushkar, On Mon, Nov 23, 2015 at 8:59 PM, pushkar shejwalkar < pshejwalkar2...@gmail.com> wrote: > Dear All, > I am trying to fit in Pd compound and the fit that I obtained looks > kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These > standards were collected and fitted

Re: [Ifeffit] Hello

Hi Riti, On Fri, Nov 13, 2015 at 6:25 PM, Ritimukta Sarangi wrote: > Hi Bruce and Matt, > Are there any obvious examples of where Sterns criteria is shown to be > incorrect? Meaning that 2delkdelR/pi +2 has been shown to over predict the > number of available independent

Re: [Ifeffit] Demeter under El Capitan

Hi Joe, On Fri, Nov 13, 2015 at 12:54 PM, Fowler, Joseph W. wrote: > Dear Matt, > > I’m the official MacPorts maintainer for Demeter. I am an amateur at this > (i.e., at Ports), but I do have notes somewhere on how to update the port > file (and, indeed, where to find it in

Re: [Ifeffit] Demeter under El Capitan

Hi George, All, Some progress: The MacPorts folks fixed the problem with PDL so that a 'port selfupdate' will then allow PDL to build and then install. With that, Demeter then installs, though there are some warnings about missing dependencies (Heap, XMLRPC::Lite, File::Slurp::Tiny,

Re: [Ifeffit] Problem with Perl interpreter

Hi Wojciech, Bruce, Don't know if this is relevant, but I've definitely seen conflicts with Perl interpreters when trying to develop Epics applications on Windows, as Epics builds need Perl with Strawberry recommended for Windows. I've been able to have both C:\Strawberry and C:\Demeter as long

Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

On Thu, Nov 12, 2015 at 4:55 PM, Bruce Ravel wrote: > On 11/10/2015 05:54 PM, Carolyn Carr wrote: > >> Thanks so much for clarifying that for me! I have been basing my fitting >> in R-space off of >> >> XAFS spectroscopy; fundamental principles and data analysis DOI >>

Re: [Ifeffit] LCF, Sayers & Bunker, R and ATHENA

HI Florian, On Thu, Nov 12, 2015 at 11:06 AM, Florian Werner wrote: > Dear mailing list, > > we recently published a paper where we broke with the "Sayers & Bunker > 1988 - Paradigm" to apply normalization as consistently as possible between > samples and standards

Re: [Ifeffit] Demeter under El Capitan

Hi George, On Thu, Nov 12, 2015 at 7:59 PM, George Sterbinsky < georgesterbin...@u.northwestern.edu> wrote: > Hi Matt, > > I am just guessing here, but Zack and Manuel both mention installing > XQuartz, whereas you mention installing xorg-server. While Demeter should > work with either,

Re: [Ifeffit] Demeter under El Capitan

ke I said, I haven't looked into this in great detail, but MacPorts is not very transparent. I'm also trying to assess using Brew (which, conveniently installs binaries, but inconveniently uses /usr/local instead of its own folder) or other options for Larch. Suggestions on the best way to do these t

Re: [Ifeffit] Demeter under El Capitan

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 > Unsubscribe: http://millenia.cars.aps.anl.gov/

Re: [Ifeffit] Data Summation Bugs

Matteo, It sounds like this issue is really about reading in data from saved projects, not about summation of data. Is that correct or is there another problem too? One of the main features of the Athena project files is that you can send them in an email. Doing that would make it possible for

Re: [Ifeffit] a small question

Shaofeng, On Wed, Nov 4, 2015 at 6:29 AM, Shaofeng Wang wrote: > Dear all experts, > > I am processing two As K edge EXAFS data shown as following figure. The > first shell is As-O. The difference of the As-O peak btween sample As1 and > As2 is around 0.03A. Does this

[Ifeffit] *****SPAM*****Re: Athena and Artemis installation problem

Hi Wuhib, Sorry to jump in a little late. On Mon, Oct 26, 2015 at 4:42 AM, Wuhib Tamrat wrote: > Hi all, > This is with regard to an installation problem that I am facing at the > moment on my Mac. Sorry, if this is too basic a problem and the email is > spamming your mail

Re: [Ifeffit] larch xray plugin - incorrect chantler data at edges

this is > still better than the totally unphysical spline interpolation. > > Best regards, > > -- > Johannes > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > &

Re: [Ifeffit] Problems importing larch plugins to python

> Software:https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- --Matt Newvill

Re: [Ifeffit] Problems importing larch plugins to python

gt;>> from larch_plugins.xafs import autobk > Traceback (most recent call last): > File "", line 1, in > ImportError: No module named larch_plugins.xafs > >>> > > I'm running ubuntu 14.04. Any ideas of what is going on here? > > Best regards, > Johan

Re: [Ifeffit] Problems importing larch plugins to python

Hi Johan, On Wed, Sep 30, 2015 at 10:53 AM, Johan Nilsson wrote: > Hello Matt, > > I was able to import pre_edge, autobk, and xftf without problems. Is it > possible to import feff paths and do a fit to exafs data in a python > script? I was able to do > >

Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)

Hi Matthew, On Thu, Sep 24, 2015 at 12:47 PM, Matthew Marcus wrote: > OK, at least we've come to convergence about what 'edge jump' means in > this context. > > Do you think the Elam value for (mu(+)-mu(-))_L3/(mu(+)-mu(-))_L2 is > correct? > Well, I don't really know.

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite

Sorry for not keeping up with the "Athena on OS X" details. Here's my experience (OS X 10.10.5, up to date patches from Apple) which might be helpful to some. Athena from macports was working fine for me, but was many months old. This evening I did sudo port -v selfupdate sudo port install

Re: [Ifeffit] Binary SSRL Files crash upon import.

Hi Logan, On Wed, Sep 16, 2015 at 5:26 PM, Logan Giles wrote: > Hello everyone, > > I am running Demeter 0.9.22 and trying import recent SSRL Binary files. I > have the SSRL plugins enabled as well. The problem is when I try to import > binary files, the program

Re: [Ifeffit] Binary SSRL Files crash upon import.

> running the program in "run as administrator" as well. No luck. > > Any other suggestions? > > -Logan > > On Thu, Sep 17, 2015 at 5:14 AM, Matt Newville <newvi...@cars.uchicago.edu > > wrote: > >> Hi Logan, >> >> >> On Wed, Sep 16,

Re: [Ifeffit] Deglitching

Hi Bruce, Sorry for delay, took me a while to get around to trying out the new version. On Tue, Sep 8, 2015 at 1:12 PM, Bruce Ravel <bra...@bnl.gov> wrote: > On 09/08/2015 02:02 PM, Matt Newville wrote: > >> Any chance of trying out the suggestions in >> https://githu

Re: [Ifeffit] Error in running Artemis - Rmin too smaller than Rbkg

Marco, On Mon, Sep 7, 2015 at 9:53 PM, M.F.Bertuzzo wrote: > Dear all, > > I am facing this error when I try to run a fit. The file in question > required a larger than normal Rbkg value of 3.0. > > In what sense did this **require** Rbkg > 3.0?Normally (and for your data

Re: [Ifeffit] Deglitching

Hi Bruce, Any chance of trying out the suggestions in https://github.com/bruceravel/demeter/issues/24 to try to avoid PATH issues, and allow Demeter to be installed in the users directory (sans admin privilege)? On Tue, Sep 8, 2015 at 12:34 PM, Bruce Ravel wrote: > On

Re: [Ifeffit] Deglitching

Hi Martina, On Sep 3, 2015 12:58 PM, "Martina Ralle" wrote: > Hi Matt, > > > > I have a quick question. When I try to deglitch in Athena it won't let me > pick a point for deglitching. No matter where I double click it always > chooses 8990. > > > > Have others encountered this

Re: [Ifeffit] Demeter installation on partition d on Windows 7 32 bit -- programs do not start

Hi Bruce, A gentle reminder that this and related PATH problems on Windows have been reported several times. Please see https://github.com/bruceravel/demeter/issues/24 https://github.com/bruceravel/demeter/issues/24Sorry I don't have a PR for this, but it looks to be not too difficult. In

Re: [Ifeffit] Vanadium-Chromium Prussian Blue Analog XANES fitting

Adora, On Thu, Jul 30, 2015 at 6:38 PM, Adora Graham abaldwin2...@gmail.com wrote: Hello, First of all, I am still very new to XAS analysis, so please excuse any misunderstandings I may have. I have a series of compounds nominally consisting of KxVx[Cr(CN)6] Prussian blue analogs (where x

Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)

Le-Rang, On Wed, Jul 29, 2015 at 2:11 PM, Ie-Rang Jeon j...@northwestern.edu wrote: Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? 10.6.8 is pretty

Re: [Ifeffit] Setting ranges in peak fitting Athena

I thought maybe Ken was asking about having box constraints or min/max constraints on parameter values. But that is kind of a guess. Hi Ken, I'm sorry, but I don't quite understand your question. And I have no idea what casaXPS is, so that reference doesn't help me. Are you asking whether

Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

I think Ellen wants to first do a linear combination fit with chi(k) data and then look at what that combination of spectral components would look like for the XANES region. It seems like a fine idea to me. Off the top of my head I don't know the easiest way to do this. I don't think there is

Re: [Ifeffit] Demeter won't start in Windows 7

Hi Bruce, On Sun, Jul 12, 2015 at 12:33 PM, Bruce Ravel bra...@bnl.gov wrote: I'll add that something seems kind of broken on your computer: PATH: t Shared\Windows Live;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program

Re: [Ifeffit] Demeter won't start in Windows 7

Hi William, As with the recent message about Demeter on Mac-with-Parallels, I suspect this is an issue with how the PATH is set. It looks to me like you don't have all the path locations set correctly, though it also appears that it is finding the DLL, just not recognizing it as a Win32 DLL

Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp

/listinfo/ifeffit -- --Matt Newville newville at cars.uchicago.edu 630-252-0431 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Issues with Athena on high-performance systems

Nils, We run Athena on non-wimpy Windows 7 systems at our beamline computers all the time, using both 64- and 32-bit Windows, and typically on multi-core machines with at least 16 Gb RAM and multiple screens. Like Robert, we don't see any real performance problems with a handful (50) spectra.

Re: [Ifeffit] polarization in Artemis

On Sun, May 24, 2015 at 1:50 PM, Bruce Ravel bra...@bnl.gov wrote: Hi, Everything in the discussion between Eugenio and Matt is stuff I agree with, except ... When I rewrote Artemis, one of the motivations was that I wanted to write my own pathfinder rather than to continue using the one

Re: [Ifeffit] Ca EXAFS with Ge220 or InSb111 (Lisa Bovenkamp)

Hi Lisa, Just to second Matthew's suggestion, Si(111) should work fine for Ca K edge. In my experience, using high angle makes it much more challenging to keep a stable beam -- roll errors become more important, and thermal load can also be worse (power density on 1st crystal, heating from

Re: [Ifeffit] Ca EXAFS with Ge220 or InSb111 (Lisa Bovenkamp)

Hi Robert, Lisa, On Mon, May 11, 2015 at 3:51 PM, Robert Gordon ragor...@alumni.sfu.ca wrote: Another possibility is that the L-edges of In and Sb are giving considerable energy-dependence to the beam in the EXAFS region...any non-linearity between detectors will make extraction of the

Re: [Ifeffit] Demeter Package for mac

Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- --Matt Newville newville at cars.uchicago.edu 630-252-0431 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov

Re: [Ifeffit] Incomplete source tarballs for larch?

. I'm open for suggestions on this, especially on Mac / Windows. It's completely reasonable to say that we need a standalone package for Mac (and for Windows) that does interact with any other software. For Mac, creating a Macports or brew script might be OK too. -- --Matt Newville

Re: [Ifeffit] Breaking down correlationships between parameters

Hi Jatin, On Sat, Mar 21, 2015 at 10:41 AM, Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de wrote: Hi Matt, Thanks a lot for your prompt reply. The method I am referring to is not the multiple k-weight fits by constraining N*S02. My apologies for not being clear enough.

Re: [Ifeffit] Breaking down correlationships between parameters

On Sun, Mar 22, 2015 at 12:44 PM, Scott Calvin scal...@sarahlawrence.edu wrote: One side-comment from me: On Mar 22, 2015, at 12:52 PM, Matt Newville newvi...@cars.uchicago.edu wrote: N and S02 are always 100% correlated (mathematically, not merely by the finite k range). Matt is saying

Re: [Ifeffit] wavelet transformed XAS in Larch-0.9.24

://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- --Matt Newville newville at cars.uchicago.edu 630-252-0431 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] wavelet transformed XAS in Larch-0.9.24

On Wed, Mar 11, 2015 at 2:07 PM, Kathy Dardenne kathy.darde...@kit.edu wrote: Hi, There is already something written in python availble. http://www.esrf.eu/UsersAndScience/Experiments/CRG/BM20/Software/Wavelets/Python Regards Kathy I may be mistaken, but I think this does not

Re: [Ifeffit] wavelet transformed XAS in Larch-0.9.24

Hi Matthias, On Tue, Mar 10, 2015 at 10:43 AM, Matthias Filez matthias.fi...@ugent.be wrote: Dear mailing list user, I am currently trying to use the cauchy_wavelet.py plugin of Larch-0.9.24 to wavelet transform some k-space EXAFS data. In principle, everything works properly, but I would

Re: [Ifeffit] Question about statistics

Olga, I'm having a very difficult time understanding what you are trying to say and do. Lengthy emails aren't necessarily helpful. Please try to state simple questions and post simple examples. Please understand that you want us to read your messages, understand them, and respond to them with

Re: [Ifeffit] SSRL-data

Hi Syed, If any beamline is giving you data in a non-standard binary format and not providing software to deal with the data, either complain very loudly (and not to the people at the beamline -- complain to the people *paying* the people who are running the beamline), or use another beamline.

Re: [Ifeffit] Exploring XANES data for getting EXAFS results

On Fri, Jan 16, 2015 at 9:21 AM, Marcelo Alves meal...@gmail.com wrote: Hi all, I wonder if it is possible from XANES unusual data treatment to get information such as number and distances of neigbhors in the first and second shells. There is an old-ish (like, from the 1950's I think) and

Re: [Ifeffit] is there any ongoing effort to integrate feff and larch?

Hi Angel, On Tue, Dec 30, 2014 at 10:46 PM, Angel Yanguas-Gil angel.yang...@gmail.com wrote: So far it seems from the sphinx doc that feff cannot be called from larch. Is there any ongoing effort to implement that? The simplest way would be to create a python module to generate the

Re: [Ifeffit] Handling large data sets in Athena (and energy dispersive calibration)

Ian, This would be a perfect example for why Larch exists With it, you can read this file, and even make sense of it, even if Ifeffit (and so by extension, current versions of Athena) cannot. With Larch (essentially, Python), it is as simple as: larch data =

Re: [Ifeffit] Fit a mixture

Kaziz, I think that the reason you haven't received an answer might be that no one really understands what your question is. For example. I don't know any details of what you're working on and cannot tell if the question is about the mechanics of performing a fit with mixed sites or about the

Re: [Ifeffit] S XANES question

checked calibration. mam ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- --Matt Newville newville at cars.uchicago.edu 630-252-0431

Re: [Ifeffit] S XANES question

://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- --Matt Newville newville at cars.uchicago.edu 630-252-0431

Re: [Ifeffit] Larch-0.9.24 with Python2

is 1.6.1. What versions are required? Thanks a lot! Matthias Van: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] namens Matt Newville [newvi...@cars.uchicago.edu] Verzonden: dinsdag 4 november 2014 18:59 Aan

Re: [Ifeffit] Larch-0.9.24 with Python2

-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] namens Matt Newville [newvi...@cars.uchicago.edu] Verzonden: woensdag 5 november 2014 14:23 Aan: XAFS Analysis using Ifeffit Onderwerp: Re: [Ifeffit] Larch-0.9.24 with Python2 Hi Matthias, OK, having scipy

Re: [Ifeffit] Reporting the fitting data (uncertainty associated with N)

The amplitude parameter is N*S02, so that S02 and N are completely correlated. If you set N = 2 guess S02 = 0.8 and the fit returns S02 = 0.75 +/- 0.05 Then the correct interpretation is that N*S02 = 2*(0.75 +/- 0.05) = 1.5 +/- 0.10 If you had asserted that S02 = 0.75 and

Re: [Ifeffit] Larch-0.9.24 with Python2

On Tue, Nov 4, 2014 at 4:39 AM, Matthias Filez matthias.fi...@ugent.be wrote: Dear mailing list user, When running an example file of Larch-0.9.24 with Python2 on Ubuntu x86_64, the following error was reported. File Py_usinglarch.py, line 32, in module autobk(xafsdat.energy,

Re: [Ifeffit] Larch-0.9.24 with Python2

Hi Matthias, Hmm, looking at this more closely, my guess is that you're using an older version scipy than I am. Can you verify what scipy version you have? That is, I do see that the return value for this call did change sometime in the past 2 years, though I'm not sure exactly which version.

Re: [Ifeffit] Mac support for Demeter

On Tue, Oct 28, 2014 at 4:00 PM, Bruce Ravel bra...@bnl.gov wrote: Hi gang, I just heard from Frank Schima, the fellow who kindly provided packaging of Demeter via MacPorts. Frank is moving to a new position at NIST Boulder and will no longer be providing IT support for the group out there

Re: [Ifeffit] Question about using a proper model

On Mon, Oct 27, 2014 at 1:14 AM, pushkar shejwalkar pshejwalkar2...@gmail.com wrote: Dear All, I am new to XAFS data analysis and have very limited knowledge about using modelling structures for XAS analysis. I am not sure as to if this question is directly related to Demter or

Re: [Ifeffit] Question about using a proper model

Pushkar, On Mon, Oct 27, 2014 at 7:57 PM, pushkar shejwalkar pshejwalkar2...@gmail.com wrote: Dear Matt, Thank you very much for your reply. Yes it generates list of XYZ cordinates. I am wondering if its ok to use such information. The reason is that while converting the XYZ file

Re: [Ifeffit] Artemis closes when I try to open a project file or import data

Kurinji, Could this be similar to the conversation discussed at http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-August/012075.html ? It does appear quite possible to break an Artemis project file in such a way that it cannot be re-opened by Artemis.This can happen if one does a fit

Re: [Ifeffit] FEff

/* ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- --Matt Newville newville at cars.uchicago.edu 630-252-0431 ___ Ifeffit mailing list

Re: [Ifeffit] FEff

On Mon, Sep 29, 2014 at 11:48 AM, Bruce Ravel bra...@bnl.gov wrote: On 09/29/2014 11:44 AM, Carlos Triana Estupinan wrote: Dear Feff group I am Carlos Triana, and I want ask you the following. I am trying to calculate the feff.inp file for a theoretical amorphous structure composed by a

Re: [Ifeffit] spline fitting

Hi Matthias, I don't see a problem with this background removal (using Rbkg=1.0 and kweight=3 as in your project file). The mu0 spline does shoot up (to perhaps a value of 3 for the normalized XAFS) whereas the data goes to about 1.8 (again, for normalized XAFS).Mu0 then drops down into the

Re: [Ifeffit] save Artemis project and cannot find Path List information when reopen

On Aug 29, 2014 9:32 AM, Bruce Ravel bra...@bnl.gov wrote: On 08/29/2014 10:20 AM, huyan...@physics.utoronto.ca wrote: Hi Bruce, Thank you for your help. Yes, it happens consistently to me, but sometimes I did the same thing and it won't happen. So I was confused. I'm afraid I don't

Re: [Ifeffit] Questions for Artemis fit

On Tue, Aug 19, 2014 at 9:55 AM, huyan...@physics.utoronto.ca wrote: Hi Dr. Newville, I had similar situation and questions as with choosing Path Parameters. My goal is to identify the occupancy sites for a doped element in my sample. We have a rough guess of two possible sites, part of the

Re: [Ifeffit] importing larch functionality

On Mon, Aug 18, 2014 at 1:22 PM, Bruce Ravel bra...@bnl.gov wrote: This: use_plugin_path('xafs') from feffdat import feffpath works as expected. It adds the path to larch's xafs plugins into the search path and imports feffdat such that it can be used in the namespace of the

Re: [Ifeffit] Questions for Artemis fit

On Mon, Aug 18, 2014 at 7:45 PM, 이국승 lks3...@postech.ac.kr wrote: Dr Newville, Thank you for your reply. My first question is that I did not find the atoms.inp file in the demeter installer. If that is true, where can I get the atoms.inp file? You might find what you're looking for at

Re: [Ifeffit] larch warning about epics plugin

Hi Johan, On Fri, Aug 1, 2014 at 10:30 AM, Johan Nilsson johan.nils...@chalmers.se wrote: Hello, Today I reinstalled larch after upgrading my computer to Ubuntu 14.04. I downloaded the latest source and installed all the recommended dependencies except PyEpics and then continued with the

Re: [Ifeffit] Import XAFS Data from Farrel Lytle Database (http://ixs.iit.edu/database/)

Hi Peng, See http://cars9.uchicago.edu/ifeffit/FAQ/Data_Handling#How_can_I_read_data_file_from_Farrel_Lytle_database.3F I believe there is a plugin for reading these files in (D)Athena. --Matt On Wed, Jul 30, 2014 at 9:54 PM, Peng Liu p26...@uwaterloo.ca wrote: Hi all, I searched the

Re: [Ifeffit] trial release #9 for Windows for Demeter 0.9.20 (Bruce Ravel)

Hi Kathy, Thanks, but the automated link shown in the email reader wasn't actually the problem. Badari's report showed the full url (ending with pre9.exe) and the result was not file not found but access denied. Looking for the 0.9.20 pre9 exe now gives a file not found error -- Bruce must have

Re: [Ifeffit] Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7

Send a file for which this happens (for each of these two almost certainly separate problems). --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] How to distinguish whether the coordination element is heavy or light

Hi Zhan, On Mon, Jul 7, 2014 at 3:40 AM, ZHAN Fei zhan...@ihep.ac.cn wrote: Hi Matti， Thanks for your attention and patience. The back fourier transform of the specific peak (use window)of Chi(R) gives the amplitude,donated by amp_bft。As in previous mails,I ask whether the compare the

Re: [Ifeffit] How to distinguish whether the coordination

Hi Michael, On Mon, Jul 7, 2014 at 10:49 AM, Michael Weir mgw...@udel.edu wrote: Hi Matt and Zhan, I think this is the point where adding another approach would be very useful. In my limited experience, XAFS was much more powerful when combined with other techniques to eliminate potential

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