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

Hi Matthias, On Tue, Mar 10, 2015 at 10:43 AM, Matthias Filez 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 like to adjust the o

Re: [Ifeffit] Question about statistics

Olga, On Sat, Mar 7, 2015 at 12:26 AM, Olga Kashurnikova wrote: > I'm very sorry that I'm long. That is because I didn't suppose to explain the > approach > itself, but to understand what is with formulae of statistics in IFEFFIT. > I understood that you say that k-space is a problem because you

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 so

Re: [Ifeffit] Question about statistics

Hi Olga, It's a bit hard for me to tell what here is actually a question and what is an assertion of preconceived ideas, or a description of what you want (or think you want). You might find it more useful to ask questions in smaller units, and aim for more clarity. On Wed, Mar 4, 2015 at 3:51 P

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 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 fairly heur

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 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 corresponding > feff.inp file,

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 = loadtxt(open('citrate_003_log_0_

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 in

Re: [Ifeffit] S XANES question

s. >> aps.anl.gov> >> http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit < >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> >> >> >> >> ___ >> Ifeffit mailing list &g

Re: [Ifeffit] S XANES question

ever seen that? Yes, we checked calibration. > mam > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- --Matt Newville 630-252-0431 _

Re: [Ifeffit] Larch-0.9.24 with Python2

90660816e-04 1.42033309e-04 7.11215401e-05 > -4.54097265e-05 -3.46351385e-05 -3.10631849e-05 -9.24403309e-05 > -1.47993095e-04 -2.10994331e-04 -2.82751339e-04 -2.75720314e-04 > -2.00919076e-04 -1.47717375e-04 -6.51029766e-05 -3.22735306e-05 > -1.15212367e-04 -1.80394605e-04 -1.

Re: [Ifeffit] Larch-0.9.24 with Python2

version 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.ed

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] Larch-0.9.24 with Python2

On Tue, Nov 4, 2014 at 4:39 AM, Matthias Filez 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 > autobk(xafsdat.energy, xafsdat.mu, rbkg=1.0, _larch=my

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 vary

Re: [Ifeffit] Mac support for Demeter

On Tue, Oct 28, 2014 at 4:00 PM, Bruce Ravel 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 that do

Re: [Ifeffit] Question about using a proper model

Pushkar, On Mon, Oct 27, 2014 at 7:57 PM, pushkar shejwalkar 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 into .inp file, the form

Re: [Ifeffit] Question about using a proper model

On Mon, Oct 27, 2014 at 1:14 AM, pushkar shejwalkar 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 XAFS analysis as such but

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] XAFS Analysis using Ifeffit

Measuring U XAFS for UO2 in fluorescence is likely to not work well no matter how much you dilute it. There will greatly suppressed amplitudes of the XAFS amplitudes. For XANES, the fluorescence intensity will also be reduced quite a bit, giving and apparent edge shift to lower energy. A sample

Re: [Ifeffit] FEff

On Mon, Sep 29, 2014 at 11:48 AM, Bruce Ravel 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 su

Re: [Ifeffit] FEff

t;%2B46%20018%20471%203144> > e-mail:carlos.tri...@angstrom.uu.se > web:http://www.uu.se/ <http://www.uu.se/>* > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mai

Re: [Ifeffit] Inconsistency of the amplitude reduction factor

Changes in sample morphology could definitely be seen in S02, but I would think the main effect of a change in sample morphology for transmission data would be a change in data quality: glitches and so on in chi(k). So: Does the data quality get worse as you change the charging? How well harr

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

On Aug 29, 2014 9:32 AM, "Bruce Ravel" 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 qu

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 r

Re: [Ifeffit] Questions for Artemis fit

On Tue, Aug 19, 2014 at 9:55 AM, 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 doped atoms are > fillin

Re: [Ifeffit] Questions for Artemis fit

On Mon, Aug 18, 2014 at 7:45 PM, 이국승 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 http://cars9.uchi

Re: [Ifeffit] importing larch functionality

On Mon, Aug 18, 2014 at 1:22 PM, Bruce Ravel 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 plugin I

Re: [Ifeffit] Questions for Artemis fit

Hi On Mon, Aug 18, 2014 at 3:01 AM, 이국승 wrote: > Dear, > > I am a biginer in this area and I have two stupid questions. > > I met a problem while I was trying to fit a Au foil data using Artemis > following the process of 'Artemis instruction videos' which (I guess) was > made by Bruce. > > I f

Re: [Ifeffit] larch warning about epics plugin

Hi Johan, On Fri, Aug 1, 2014 at 10:30 AM, Johan Nilsson 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 install. Everything went

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 wrote: > Hi all, > > I searched the Farel Lytle Database

Re: [Ifeffit] Quick first shell fit - Artemis

Hi Karin, On Wed, Jul 30, 2014 at 8:04 AM, Karin Julius wrote: > Hello, > > I'm trying to do a quick first shell fit with Artemis for my EXAFS > measurement of 0.1 M auqeous solution of RbCl. > I'm especially interested in the first hydration shell of the Rb ion. > So I made an atoms input file

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

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

fs.org/BruceRavel > Software: https://github.com/bruceravel > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- --Matt Newville 630-252-0431 ___ 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

Hi Michael, On Mon, Jul 7, 2014 at 10:49 AM, Michael Weir 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 models. We

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 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 amp_bft and the

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] Demeter-devel MacPorts Athena issues & work-around

HI Scott, On Sun, Jul 6, 2014 at 6:48 PM, Scott Calvin wrote: > Hi all, > > This is probably as good a time as any to mention a miscommunication I've > seen come up a couple of times on the list that may have caused unnecessary > friction. It's a good time because it =isn't= what transpired in

Re: [Ifeffit] Demeter-devel MacPorts Athena issues & work-around

On Sun, Jul 6, 2014 at 5:24 PM, Bruce Ravel wrote: > > Matt, > > You're right. I was too grouchy. Margaret Anne, I apologize if I was too > mean-spirited in my emails over the weekend. > > > > On 07/06/2014 05:54 PM, Matt Newville wrote: > >> Wait, wha

Re: [Ifeffit] Demeter-devel MacPorts Athena issues & work-around

Hi, On Sat, Jul 5, 2014 at 2:06 PM, Bruce Ravel wrote: > On 07/04/2014 12:11 PM, Margaret Hinkle wrote: > >> Thanks for your help & your quick reply. I did not expect my altering >> one character in the code to fix the problem -- I had just hoped it >> would tell me if the Tip of the Day was in

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

Hi Zhanfei, Bruce, Scott, Sorry for jumping in to this conversation a bit late. Like Bruce said, there is no magic trick for determining whether a part of the R-space spectrum comes from one or more scatterers. And while XAFS is sensitive to Z, the sensitivity is weak. Because it's XAFS School

Re: [Ifeffit] 32 Windows installer for testing

All programs started for me on 32 bit Windows7. Including Atoms, which seemed to run just fine for me (only tried one input file, but it worked and ran feff). Haven't tested other things thoroughly. I did notice that the main Hephaestus window seemed a little short so that the "Element Data

Re: [Ifeffit] Exchange Dirac Hara on Artemis

The recommendation is to update to a more recent version of Artemis with a version of Feff6.02: http://s3.amazonaws.com/demeter4xas/Demeter_Updater_for_Windows_0_9_18_2.exe --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://milleni

Re: [Ifeffit] Exchange Dirac Hara on Artemis

keep and heap limits 0.000 0.000 Preparing neighbor table nfound nheap nheapx nscr 1000734 737 65.1542 2000938 946 65.5456 On Wed, Jun 25, 2014 at 2:45 PM, Siri V wrote: > > > Dear Dr. Matt Newville, > > Tha

Re: [Ifeffit] Question about XAFS resolution

Hi Shoaib, On Wed, Jun 25, 2014 at 7:34 AM, Shoaib Muhammad wrote: > > Dear Matt Newville, > > Sorry to disturb you by asking one question, hopefully you will mind it. Asking on the ifeffit mailing list is generally better. I am CCing this reply to that list. > I often see

Re: [Ifeffit] Exchange Dirac Hara on Artemis

Hi Siri, Hmm, not sure -- running feff6L with exchange 1 works for me. The exchange card only takes 3 numbers (index v_real v_imag). If you're still having troubles, please send a complete input file, plain text format, or the complete project file. Sending the full plain text of the output y

Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

Hi Bruce, All, Sorry if I wasn't clear earlier: Version 0.9.20_pre5 does works for me on 64bit Windows7 to read in a project with a Feff calculation but without any fits in it. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://m

Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

> Here is an early look at the next release. Could you give it a try and let me know if it > solves the problem for you. (It works for me on your example project file.) > > https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_pre5.exe

Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

I'd guess that the empty fits/ folder is causing the restore_fit() function in Demeter/UI/Artemis/Project.pm to fail to restore any fits. It's easy enough to reproduce: Start Artemis, open any Feff input file, run feff, load no data. Save the project, and quit. The project cannot be reopene

Re: [Ifeffit] Exchange Dirac Hara on Artemis

Hi Siri, On Mon, Jun 23, 2014 at 2:21 PM, Siri V wrote: > Dear ifeffit members, > > I would like to inquire whether the Feff's Exchange card (Dirac Hara) is > supported on Artemis fitting program. > Yes. You can edit the feff input file and change the exchange card (or other cards) before r

Re: [Ifeffit] Use of the 3rd and 4th Parameter

roblems. > > Thanks a lot for your time and efford. > > Sincerly yours, > > Michael Kömm > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- --Matt

Re: [Ifeffit] Fitting EXAFS simulation to experimental

Hi Matthew, On Thu, May 29, 2014 at 11:18 AM, Matthew Marcus wrote: > I wonder if what he was asking about is an automated way of mapping the > position parameters for a given space group, that is, fractional atomic > coordinates as listed in a .cif, onto > the various path distances. As it i

Re: [Ifeffit] Fitting EXAFS simulation to experimental

Hi All, As Scott, Bruce, Anatoly have said, it is certainly possible to map certain crystallographic distortions to local structure, and so predict the effect on EXAFS, and model EXAFS in terms of those distortions. But to be clear for the original question, EXAFS is inherently a local structure

Re: [Ifeffit] Possible bug in fitting

Hi Ditty, On Wed, Apr 30, 2014 at 7:05 AM, Ditty Dixon wrote: > > Hello IFEFFIT users, > > > > I am working on LiNi0.5Mn1.5O4 cathode materials, I am pretty sure that > some of you already worked on it. On the first look, a multiple edge > analysis on both Ni and Mn is interesting; however it’

[Ifeffit] wavelet transforms for EXAFS

Hi Folks, It's been on my To-Do list for many years, and was one of the arguments for needing to be able to handle multi-dimensional arrays for EXAFS analysis. So I'm happy to say that the Continuous Cauchy Wavelet transform of Munuz, Argoul, and Farges (from American Mineralogist 2003) is now (on

Re: [Ifeffit] Demeter: Problem closing communication to gnuplot

That should probably be $data -> pause ; --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Dafs - DIFFKK

Hi Alessandro, On Wed, Apr 9, 2014 at 3:39 PM, Alessandro Lisboa wrote: > Dear, > > My name is Alessandro Lisboa. I am a phd student of physics in Brazil - > University of Brasilia. In the last February was held the first experiment > DAFS in the Laboratório Nacional de Luz Síncrotron of Brazil.

Re: [Ifeffit] Larch: problems importing feff paths

Hi Johan, Sorry for the trouble. Apparently I haven't tested with a wide enough range of Feff files! For reference, this feff.dat file did not have labeled atoms, which is allowed in Feff but which I hadn't considered. The attached feffdat.py solves this problem (and fixed in the github reposit

Re: [Ifeffit] Problem with importing projects from ATHENA into ARTEMIS

905 > www.xfel.eu/de > > Postadresse: Notkestraße 85, 22607 Hamburg > Sitz: Albert-Einstein-Ring 19, 22761 Hamburg > > Geschäftsführer: Prof. Dr. Massimo Altarelli, Dr. Claudia Burger > Registriert als European X-Ray Free-Electron Laser Facility GmbH > beim Amtsgericht Hamburg, H

Re: [Ifeffit] Peaks in MCA spectra

Hi George, On Tue, Apr 1, 2014 at 11:56 AM, George Sterbinsky wrote: > Hi Matthew, > > Hephaestus shows the strength of the Ll emission to be about 10% of the La2 > emission. When fitting the spectrum as a sum of Gaussians, I find that the > area of of the Gaussian used to fit the Ll is 24% of th

Re: [Ifeffit] Peaks in MCA spectra

nyone know what these shoulders might result from if not > lower energy transitions? If they are low energy transitions, why would the > relative transition strengths differ from tabulated values? > > Thank you, > George > > > > > __

Re: [Ifeffit] Interest in more accurate theoretical standards

Hi Sam, On Tue, Mar 25, 2014 at 3:30 PM, Samuel T. Chill wrote: > Dear List, > > I have noticed that EXAFS fits to Au foils at 298 K underestimate the known > equilibrium bond length. According to the CRC Handbook the lattice constant > at 298 K is 4.0782 +/- 0.0002 Å. This is a bond length of 2.

Re: [Ifeffit] questions about ifeffit

Athena has pull down menus to export data to ASCII column files. 'nor' gives the normalized XAFS. See http://bruceravel.github.io/demeter/aug/output/index.html On Mon, Mar 24, 2014 at 7:27 AM, Artillery wrote: > Hi, > > I am a student from Shanghai. Now I am using IFEFFIT to do my thesis. Athen

Re: [Ifeffit] Ifeffit Digest, Vol 133, Issue 1

Hi Abhijeet, On Thu, Mar 13, 2014 at 9:52 AM, Abhijeet Gaur wrote: > Hi Matt, > Thanks for your suggestion. I will use this for the analysis of > my sample. > I have a query that what if I change the Mn by Zn at the Atoms > page calculation so that the feff.inp file has

Re: [Ifeffit] Analysis of EXAFS data of a Zn sample with the theoretical model of a similar Mn sample

Abhijeet, On Wed, Mar 12, 2014 at 8:52 AM, Abhijeet Gaur wrote: > Hi all, > I am trying to analyse the EXAFS data of Zn sample whose > structure is not available. > The crystallographic data is available for a Mn sample which is > likely to have same coordination environm

Re: [Ifeffit] EXAFS simulations - peak too high

Lisa, On Mon, Feb 3, 2014 at 12:27 PM, Lisa Bovenkamp wrote: > Hello. > > I am running some EXAFS simulations Au L3 on Au clusters with SR coating. > In the outer shell Au sits between 2 S atoms. 4 Au atoms are in the > neighborhood > up to 3.5 Angström. > Expecting two peaks in the chi(R) - o

Re: [Ifeffit] How can I fit the results obtained from FEFF9 to the experimental data using the ARTEMIS.

Hi Abhijeet, On Mon, Feb 3, 2014 at 1:33 AM, Abhijeet Gaur wrote: > Hi, > > I have started using FEFF9 recently. I am using it to generate > theoretical model for some copper compounds and complexes. As you have > mentioned in one of research article' Nuclear Instruments and Methods in > P

Re: [Ifeffit] MacPorts install of Demeter

Frank, All, Just to add my thanks and experience so far: Thank you so much for this! As Martha and others have seen, everything with Athena seems to work fine for me on 10.8.5, but Hephaestus and Artemis segfault on launching (after splash screen). Should I try installing demeter from the git re

Re: [Ifeffit] Absorption-coefficient data repository?

Hi Damon, On Mon, Jan 27, 2014 at 12:30 PM, Damon Turney wrote: > Dear XAFS Community, > > I'm looking for values of absorption coefficient (or mass absorption > coefficient) of ZnO in the XANES region of the Zn edge, but all the > publications give XANES plots in "arbitrary units", so I have no

Re: [Ifeffit] "Save marked groups as..." command

Hi Danilo, On Wed, Jan 22, 2014 at 9:40 AM, Danilo Oliveira de Souza wrote: > Dear list, > > I have a big collection of data from a catalytic reaction. > I tried to export all the spectra (about 200) to a unique file containing > the normalized ones. I used the "File>Save marked groups as>norm(E)

Re: [Ifeffit] Demeter not working on Windows 8.1 64bit

Hi Shoaib, On Tue, Jan 14, 2014 at 10:46 AM, Shoaib Muhammad wrote: > Hi, > > > > I have recently upgraded my computer to Windows 8.1 Pro x64 and after this > upgrade I can’t run Athena and Artemis. The problem symptoms are: > > > > 1- If I use Demeter version 0.9.13, Athena opens but when I

Re: [Ifeffit] Connecting Artemis to FEFF9.6.4

Hi Kevin, On Sat, Jan 11, 2014 at 11:01 PM, Kevin Jorissen wrote: > Hi Bao and Bruce, > > There has indeed been progress since FEFF6 -- the newer versions of the > program have new input options that the old program will not recognize. > E.g., as described in the post Bruce linked to, we now gen

Re: [Ifeffit] Demeter 0.9.19

Hi Frank, On Fri, Jan 10, 2014 at 12:33 PM, Schima, Frank wrote: > > On Jan 9, 2014, at 8:33 PM, Matt Newville wrote: > >> Hi Frank, >> >> On Thu, Jan 9, 2014 at 10:47 AM, Schima, Frank wrote: >>> Hi all, >>> >>> On Jan 9, 2014, at 8:26 AM,

Re: [Ifeffit] Demeter 0.9.19

Hi Kevin, On Thu, Jan 9, 2014 at 11:37 PM, Kevin Jorissen wrote: > I can concur with others here that making something work on Mac can be a > miserable experience. Sometimes you have to admit defeat and change the > approach. > > Anyway, I tried "sudo port install p5.16-ifeffit" and failed: > >

Re: [Ifeffit] Demeter 0.9.19

Hi Frank, On Thu, Jan 9, 2014 at 10:47 AM, Schima, Frank wrote: > Hi all, > > On Jan 9, 2014, at 8:26 AM, Matt Newville > wrote: > > On Thu, Jan 9, 2014 at 8:04 AM, Bruce Ravel wrote: > > On 01/09/2014 08:24 AM, Stefano Luciano Ciurli wrote: > > > Hello Bruce

Re: [Ifeffit] Demeter 0.9.19

Hi Bruce, On Thu, Jan 9, 2014 at 8:04 AM, Bruce Ravel wrote: > On 01/09/2014 08:24 AM, Stefano Luciano Ciurli wrote: >> >> Hello Bruce and thank you for your hard work! >> instructions to install on OS X 10.6.8? > > > There is not a Mac package. I do not own a Mac and and so do not have > the ab

Re: [Ifeffit] Athena deglitch problem

Hi, On Mon, Dec 16, 2013 at 12:42 PM, Sathish Mayanna wrote: > Dear Matt > >> > >> > Now it seems working well except some minor things, I can remove the >> > points >> > from the data, the random point selection by software works better for >> > rebinned data. I think the only problem I have n

Re: [Ifeffit] Demeter deglitch problem

Hi Sathish, On Sat, Dec 14, 2013 at 2:35 PM, Sathish Mayanna wrote: > Dear Matt and Bruce > > Thanks a lot for your help, > > I noticed your suggestions, regarding the deglitch problem, I installed the > Demeter in another drive than in drive C. > > Now it seems working well except some minor t

Re: [Ifeffit] Fwd: Re: Demeter deglitch problem

Sathish, Bruce, On Thu, Dec 12, 2013 at 12:51 PM, Bruce Ravel wrote: > > Sathish, > > I'm sorry, Sathish, but I simply don't see this behavior, on any of > the computers I have tried. > > I have no trouble putting the cursor on the point in question. It can > be a little tricky getting the curso

Re: [Ifeffit] Ifeffit Digest, Vol 130, Issue 13

Hi Sathish, On Tue, Dec 10, 2013 at 4:06 AM, Sathish Mayanna wrote: > Dear Matt and Bruce > > Thanks, I thought its a common problem, i will be more specific in this > message. > > I am using windows 7, 64 bits and/or 32 bits Operating System, installed > with updating 0.9.18.2 Demeter, its in th

Re: [Ifeffit] Athena 0.9.18.2 deglitch option

On Mon, Dec 9, 2013 at 12:24 PM, Sathish Mayanna wrote: > Dear all > > I wondering, if anyone has problem with the option deglitch in Athena > especially for 32 or 64 bits Windows system? > > Would be really great, if anyone could help me to solve the problem, I have > a EXAFS data with huge glitc

Re: [Ifeffit] Itinerant vs localized XAFS

On Mon, Dec 9, 2013 at 9:02 AM, Maurits Boeije wrote: > Dear XAFS specialists, > > > > We’ve performed an experiment at the ESRF in Grenoble to find experimental > evidence of an electronic change in our system. We suspect, from ab initio > calculations, that there is a change in how electrons are

Re: [Ifeffit] fitting a specific k range

Hi Scott, On Thu, Dec 5, 2013 at 4:56 PM, Scott Calvin wrote: > I love the warnings Artemis gives! They're not just for novices--they often > catch when I've made a dumb mistake somewhere. I praise them, defend them, > and generally think Bruce has done a wonderful thing by having them. > > The

Re: [Ifeffit] fitting a specific k range

Hi Anatoly, On Thu, Dec 5, 2013 at 12:28 PM, Anatoly I Frenkel wrote: > I object the use of "hosannas of adoration". Other than the use of Greek > mythology, I propose the mailing list to be religion-neutral and > tautology-free. Is "Down the rabbit hole" OK? I'm not sure it usually counts a

Re: [Ifeffit] fitting a specific k range

Scott, On Thu, Dec 5, 2013 at 11:18 AM, Scott Calvin wrote: > First, a disclaimer--I haven't looked at the data Matt sent (it's a busy time > of year!), but I disagree in a general sense with my reading of what Bruce > wrote (perhaps I am reading it wrong). In particular, I disagree with this

Re: [Ifeffit] fitting a specific k range

Hi Matt, On Wed, Dec 4, 2013 at 1:17 PM, Matt Frith wrote: > Dear All, > > > I need some help in fitting an amorphous iron oxyhydoxide sample. I am > having difficulty producing a good fit, particularly in the k=4-6 range. > Fitting this region well is very important for me, because if I add ano

Re: [Ifeffit] Is it possible to use ATOMS to solve this problem?

Hi Aderson, On Tue, Nov 5, 2013 at 8:16 AM, Áderson Miranda wrote: > Dear Prof. Newville, > I am a PhD. student from Brazil and I am trying to use ATOMS to a solve a > particular problem in my thesis. I would like to generate a big cubic > unitary cell with a S2O3 molecule surrounded by six wat

Re: [Ifeffit] Fwd: problem compiling ifeffit

Hi Rene, Bruce, I pulled this merge request. With the fixed code, I verified on Fedora 15 x86_64 that I could install PGPLOT and ifeffit with sudo sh ./PGPLOT_install ./configure make sudo make install This is with gcc 4-6 series for x86_64. That is, I think this should work for you now.

Re: [Ifeffit] Artemis Software Issue

I think the most direct answer would be > Is there some kind of patch I can download? No. See below. > The updates don't seem to work when I startup the software. Can you elaborate? > Is there a newer version of the software I could use? Please let me know how > to fix the problem. Yes. http

Re: [Ifeffit] Problem opening Demeter in Windows - doesn't work at all

Arjen, On Tue, Oct 22, 2013 at 11:04 AM, Arjen van Veelen wrote: > Dear Bruce, >> >> I reinstalled Demeter today, since it didn’t want to start up (it worked >> before as far as I know). I >> re-installed it and still does not start up. >> >> I see a window appearing and disappearing, but not Ath

Re: [Ifeffit] problem with Demeter on non-unicode machine

Hi Andrei, All On Sat, Sep 7, 2013 at 1:58 PM, Andrei Shiryaev wrote: > Dear Matt, > > Thank you very much, the recipe apparently works! > > Sincerely, > Andrei > Great! Now we can help Bruce (and many others) out, with pretty simple steps 0. Get an account on Github 1. Go to https://gith

Re: [Ifeffit] problem with Demeter on non-unicode machine

t; Andrei > > -- > > -- > Andrei Shiryaev > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- --Matt Newville 630-252-0431 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] amorphous metal alloys EXAFS spectra to be fitted with Artemis

Hi Piotr, On Aug 24, 2013 4:19 PM, Piotr J. Bardziński wrote: > > Dear Sir or Madam, > > I got a normalized Fe K-edge EXAFS spectrum for my amorphous 7-component alloy sample, for which I know its atomic percent composition. > > I need to find out the interatomic distances between the Fe and the

Re: [Ifeffit] crystal analyzer and microprobe

Hi Matthew, On Aug 16, 2013 11:53 AM, "Matthew Marcus" wrote: > > I know that this is somewhat off-topic, but the list reaches all the right people. I have some collaborators who are looking to measure > the Ni/Fe ratio is particles of Fe-rich material. This ratio is << 1, and they need a non-d

Re: [Ifeffit] Unable to import data from HXMA beamline at CLS into Athena

On Jun 26, 2013 12:11 PM, "Bruce Ravel" wrote: > > > Athena clearly needs FAQ. This is a question that gets answered over > and over on this list. I think it might be HXMA that needs the FAQ. Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl

Re: [Ifeffit] normalization methods

Hi Matthew, George, Zach, Thanks for the discussion! On Wed, May 15, 2013 at 5:41 PM, Matthew Marcus wrote: > I'm not sure what 'flattening' means. Does that mean dividing by a linear > or other polynomial function, fitted to the post-edge? > mam Sorry, I should have been clearer. "St

Re: [Ifeffit] normalization methods

Hi Matthew, On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus wrote: > What I typically do for XANES is divide mu-mu_pre_edge_line by a linear > function which goes through the post-edge oscillations. > This division goes over the whole data range, including pre-edge. If the > data has obvious cur

[Ifeffit] normalization methods

Hi Folks, Over on the github pages for larch, Mauro and Bruce raised an issue about the "flattening" in Athena. See https://github.com/xraypy/xraylarch/issues/44 I've added a "flattened output" from Larch's pre_edge() function, but the question has been raised of whether this is "better" than the

Re: [Ifeffit] Installing on Mac OSX Lion

Hi Nate, On Thu, May 9, 2013 at 7:31 PM, Nate Turner wrote: > Hello, > > I believe I have successfully installed PGPLOT, Ifeffit, and the horae suite > of programs onto my mac OSX and have constructed executable files for > artemis, athena, atoms, and hephaestus. I am now at a loss however, as wh

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