Re: [Ifeffit] Larch as python library

Hi Sean, On Tue, Nov 1, 2016 at 5:35 PM, Sean Fackler wrote: > Hi Matt, > > On Nov 1, 2016, at 2:00 PM, Matt Newville > wrote: > > Hi Sean, > > On Tue, Nov 1, 2016 at 1:39 PM, Sean Fackler wrote: > >> Dear Matt, >> >> I’ve been working to

Re: [Ifeffit] Larch as python library

Hi Sean, On Tue, Nov 1, 2016 at 1:39 PM, Sean Fackler wrote: > Dear Matt, > > I’ve been working to implement Larch functions as a Python library. During > the implementation I found a number of things I needed to do including: > > You can use Larch functions from Python, of course. Normally, y

Re: [Ifeffit] Larch mback error report

Hi Sean, On Wed, Oct 12, 2016 at 7:36 PM, Sean Fackler wrote: > Dear Larch developers (Matt), > > I believe I found an error in the mback function where I get a NameError > saying the name ‘f1_chantler’ is not defined. I found that simply adding > f1_chantler to the larch_plugins.xray import sec

Re: [Ifeffit] ifeffit on Mac OS X: fink package

efiles. But one step after the other. > Installing Demeter on Mac OSX has been a continuing struggle, at least partly due to continued maintainers, and also partly due to troubles building wxPerl on OSX with clang/llvm from wxPerl sources. Neither of those are actually problems with Demeter

Re: [Ifeffit] larch on Mac OS X: fink package

Hi Michael, Thanks for the earlier post on Fink vs MacPorts.I'll respond to that (out of order, I know) later today. On Fri, Oct 7, 2016 at 6:52 AM, Karl-Michael Schindler < karl-michael.schind...@physik.uni-halle.de> wrote: > Hi all. > > After fixing wxwidgets and wxpython, a first version

Re: [Ifeffit] ifeffit on Mac OS X: fink package

as successor and i am working on it as > well as on demeter, but i did not manage to build it so far. > > Michael. > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ife

Re: [Ifeffit] problem in data processing in athena

Arkaprava, On Sat, Sep 24, 2016 at 1:24 AM, Arkaprava Das wrote: > Respected Sir, > I am a research scholar in Inter university accelerator centre, new Delhi, > India. I am facing one peculiar problem in athena data processing. I have > attached the .xls file in the mail for Zr k edge which has

Re: [Ifeffit] Larch user base?

Hi Sean, On Wed, Aug 31, 2016 at 7:25 PM, Sean Fackler wrote: > Hi Matt, > > I do have wxPython installed and wxmplot. I use anaconda which should > handle the obvious dependencies. Is there a list of known dependencies I > should double check? > > if you're using Anaconda, the main dependencie

Re: [Ifeffit] pgplot and ifeffit installation on current linux systems

Hi Anselm, On Fri, Aug 26, 2016 at 6:33 AM, Loges, Anselm G wrote: > Dear all, > > > I hope this is the right platform for my question. If not, sorry to bother > anyone. The question: > > Has anyone successfully installed pgplot and ifeffit on a recent Arch > Linux system and could provide a qui

Re: [Ifeffit] Demeter Installation issues

Hi Gaurab, On Fri, Aug 19, 2016 at 12:26 PM, Gaurab Rimal wrote: > Hello, > I have been trying to install demeter in my archlinux machine but have > issues in the build process. I had issues installing pgplot from ifeffit > git source so I installed pgplot separately (as outlined in the ori

Re: [Ifeffit] Larch user base?

Hi Sean On Mon, Aug 15, 2016 at 12:23 PM, Sean Fackler wrote: > Thanks Matt for the thorough explanation. > > Actually it was Jamie Sethian who asked. I am working on using Larch as a > code basis for doing high-throughput NEXAFS analysis. You can imagine > automating just basic normalizing and

Re: [Ifeffit] Larch user base?

Hi Sean, On Sun, Aug 14, 2016 at 4:35 PM, Sean Fackler wrote: > Hello all! > > Do you have an idea of Larch user base or Larch package download stats? > Thanks for any information. > > Funny you should ask. It turns out that a kind and generous NSF Program Manager recently gave me a friendly r

Re: [Ifeffit] Ifeffit Digest, Vol 162, Issue 17

Hi Chris, On Fri, Aug 12, 2016 at 4:36 PM, Christopher Thomas Chantler < chant...@unimelb.edu.au> wrote: > Topic 1: We have a routine /edit within ifeffit (our modified version) > which propagates and fits uncertainty. > Working on a couple of minor details before passing it on to Matt and > Bruc

Re: [Ifeffit] Athena interpolation when removing mono glitches

Hi Michael, On Fri, Aug 12, 2016 at 6:56 AM, Michael Gaultois wrote: > Dear members of the Ifeffit list, > > I recently collected some EXAFS data with some significant monochromator > glitches that I am looking to remove. I have used a python script > graciously written by the beamline scientist

Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

On Tue, Aug 9, 2016 at 1:07 PM, Bruce Ravel wrote: > On 08/09/2016 01:50 PM, Matthew Marcus wrote: > >> This actually results in a bit of inconvenience - if you want to use >> ATOMS, you have to load some data into Artemis and pretend you want to >> analyze it. >> > > There is a "Stand-alone Atom

Re: [Ifeffit] Multi-electron peak in Yb

Hi Matthew, No one ever expects lutetium. --Matt ___ 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] Multi-electron peak in Yb

Hi Matthew, Attached is a file of Yb L3 edge on something that was labeled "Yb AC" and measured in fluorescence many years ago, almost certainly in solution. I suspect that "AC" means "acetate". This is a plain ASCII file (not XDI!). The data quality is not great. Does this have the feature yo

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 sample or an I0 glitc

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 wo

Re: [Ifeffit] fitting of S XANES with arctans and gaussians

On Tue, Jul 19, 2016 at 6:38 AM, Jon Wade wrote: > > I can’t recommend LMFIT in python enough (or Larch - never used it mind, > but see no reason why I haven’t). > > Its well documented, easy to use and, best of all, its FREE! :) > > > https://lmfit.github.io/lmfit-py/builtin_models.html#built

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 atoms relative to > a

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

ng distances and coordination 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

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 use partial occupanc

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 less familiar with Artem

Re: [Ifeffit] Heavy Scatterer Resonance

Pieter, Please use the ifeffit mailing list for questions about XAFS Analysis. I am CCing this reply to that list. On Thu, Jun 2, 2016 at 2:35 AM, Pieter Tack wrote: > Dear Dr. Newville, > > > During the analyses of some metallic Au EXAFS I noticed the Au-Au single > scatter first shell is cha

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 suppor

Re: [Ifeffit] Small larch bug

Hi Johan, On Fri, May 27, 2016 at 6:21 AM, Johan Nilsson wrote: > Hello, > > > I've found a small "bug" in larch when I tried to run the pre_edge > function for some spectra. It seems that find_e0 will not accept a 2d > 1-column array as input for energy or mu, and it gives a traceback which i

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 ./configure, and sudo make,

Re: [Ifeffit] Question about H scattering

Hi Riti, On Mon, May 23, 2016 at 1:50 PM, Ritimukta Sarangi wrote: > Hi Matt, > I have a question about FEFF and I hope you can shed some light on it. > Several references point to the high muffin tin radius of H (0.77) in FEFF > and say that it should be closer to 0.2. Is there a way of changi

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 ha

Re: [Ifeffit] How to assign measure unit to XAFS data

Hi Matteo, On Thu, May 12, 2016 at 7:11 PM, Matteo Busi wrote: > Hi Bruce, Matt, and mailing list readers, > > I have one question regarding the XAFS data. I have collected absorption > coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however > my question can be generalized

[Ifeffit] XASLIB (was Re: data availability)

XAS spectra, 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@

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 > learn the lore though.

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 x-ray-absorption fine stru

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 collected fluorescence

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 function. > Is it physically

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 0.025 seconds. Each scan

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 (see attached picture la

Re: [Ifeffit] Error in N (Number of Scatterers)

On Wed, Mar 9, 2016 at 2:06 PM, Carolyn Carr wrote: > Hello Mailing List, > > I have read papers describing that EXAFS has an error regarding N the > number of scatters of +/- 20%. To be clear, I think you mean an uncertainty of +/- 20%, not a systematic error in the value for N. > The only o

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 tryout I am unable to

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 clicked nothing happened.

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 your time, > Best, >

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 (and

Re: [Ifeffit] DAFS calculation

t; Building 535A > > Upton NY, 11973 > > > > Homepage: http://bruceravel.github.io/home/ > > Software: https://github.com/bruceravel > > Demeter: http://bruceravel.github.io/demeter/ > > ___ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.a

[Ifeffit] Ifeffit Mailing List

to send me an email 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. Yo

[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 fro

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 pa

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 simulta

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 parameters? I have ofte

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 the first place!). >

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 a

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, Encoding::Fi

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, perhaps

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 >> 10.1023/A:1019105310221 >>

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 when performing linear combina

Re: [Ifeffit] Demeter under El Capitan

cPorts Portfiles actually are. Like 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 La

Re: [Ifeffit] Demeter under El Capitan

ns/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/mailman/options/ifeffit > >

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 represent that the averag

[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 box. Below are speci

Re: [Ifeffit] Demeter 0.9.23 in multi-user environments

pton NY, 11973 > > Homepage:http://bruceravel.github.io/home/ > 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/i

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

7;s data, but 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/

Re: [Ifeffit] Problems importing larch plugins to python

me/ > 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 Newville

[Ifeffit] mailing list / web page downtime

Hi Folks, The machine that hosts this mailing list, the ifeffit web pages, and xafs.org (millenia.cars.aps.anl.gov) is going to be replaced with a new machine today. I think everything should work, but there may be some outages over the next two days. If you have any troubles past that, let me k

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 > >larch.enable_plugins() >from la

Re: [Ifeffit] Problems importing larch plugins to python

rom 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,

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. "Around 2" seems somewh

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 x

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

e program in "run as administrator" as well. No luck. > > Any other suggestions? > > -Logan > > On Thu, Sep 17, 2015 at 5:14 AM, Matt Newville > wrote: > >> Hi Logan, >> >> >> On Wed, Sep 16, 2015 at 5:26 PM, Logan Giles >> wrote:

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 crashes. > > It seems that somet

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 wrote: > On 09/08/2015 02:02 PM, Matt Newville wrote: > >> Any chance of trying out the suggestions in >> https://github.com/bruceravel/demete

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 09/04/2015 02:54 PM, Rober

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 as well), Rbkg arou

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 error? I am runni

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 Sorry I don't have a PR for this, but it looks to be not too difficult. In shor

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

Adora, On Thu, Jul 30, 2015 at 6:38 PM, Adora Graham 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 is ~1) with Cr(

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 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 old for a Mac OS

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 you

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 a

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

Hi Bruce, On Sun, Jul 12, 2015 at 12:33 PM, Bruce Ravel 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 > Files\In

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 Tha

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

t;> *** >> > > > ___ > 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] Demeter Crashes on opening in Windows Bootcamp

Ganesh -- gnuplot.exe is not being found in your PATH.Can you find it? Any ideas why it might be missing? --Matt On Mon, Jul 6, 2015 at 6:58 PM, Ganesh Subramanian wrote: > Sorry for not noticing. The log files are attached now. It is pretty much > the same for all three cases of Athena, Ar

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. A

Re: [Ifeffit] Questions on Correlated Debye in FEFF6

Hi Doran, Bruce, Sorry for not responding earlier, and thanks Bruce for giving links. I'll make a few comments, which might suggest why I was hesitant to respond earlier. On Thu, Jun 11, 2015 at 2:18 PM, Bennett, Doran (D) wrote: > Hi Everyone, > > > > I have just recently begun learning abou

Re: [Ifeffit] polarization in Artemis

On Sun, May 24, 2015 at 1:50 PM, Bruce Ravel 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 in Feff

Re: [Ifeffit] polarization on FEFF calculation

Hi Eugenio, On Sun, May 24, 2015 at 7:30 AM, Eugenio Paris wrote: > Thank you for the answer, now things are more clear. > > Now the question is: how to go further on the fitting procedure? > > If the Artemis software is weighting the contribution of different paths > using the "Rank" value it

Re: [Ifeffit] polarization on FEFF calculation

Eugenio, On Sun, May 24, 2015 at 5:26 AM, Eugenio Paris wrote: > Dear all, > > i have a question about polarization vector in performing the FEFF > calculation in Artemis. > I am studying the system CeOBiS2 using Bi L3-edge EXAFS. Starting from > *.cif file i'm creating the *.inp file which ato

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

Hi Robert, Lisa, On Mon, May 11, 2015 at 3:51 PM, Robert Gordon 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 EXAFS > problematic. Lo

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 sc

Re: [Ifeffit] Demeter Package for mac

> 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] Incomplete source tarballs for larch?

ramework/Versions/2.7/bin or where ever macports or brew decide to place python binaries. 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 wi

Re: [Ifeffit] amplitude parameter S02 larger than 1

On Mon, Mar 23, 2015 at 9:45 PM, Scott Calvin wrote: > Hi Anatoly, > > The method Ifeffit uses to compute uncertainties in fitted parameters is > independent of noise in the data because it, in essence, assumes the fit is > statistically good and rescales accordingly. This means that the estimate

Re: [Ifeffit] Breaking down correlationships between parameters

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

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

HI Jatin, On Sat, Mar 21, 2015 at 8:06 AM, Rana, Jatinkumar Kantilal < jatinkumar.r...@helmholtz-berlin.de> wrote: > Dear All, > > I have stumbled upon a question regarding correlationships between > various parameters in EXAFS fitting. As we know, the parameters S02*N and > sigma2 are highly

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

On Wed, Mar 11, 2015 at 2:07 PM, Kathy Dardenne 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 inc

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

e-so...@ed.univ-lille1.fr > tel: +33 06.63.55.86.12 > > ___ > 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

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