Re: [Ifeffit] problem with E0 (enot) parameters

2009-06-20 Thread Matt Newville
Hi Dariusz, Just to follow up on Stefan's request to not post large attachments to email: The ifeffit web page is a wiki, and would be an ideal place for posting the data (feff inputs, project files, images of plots) for such questions. You can read up on the wiki page for how to do create

Re: [Ifeffit] Interpolating in feff - the Lead Titanate example

2009-06-22 Thread Matt Newville
Hi Joseph, I think this thread may have gone under-noticed, so sorry for not responding. This seems like a really strange situation (how could Feff be getting path distances wrong??), but I suspect from your message that you may have been deliberately playing with the intermediate Feff files and

Re: [Ifeffit] Interpolating in feff - the Lead Titanate example

2009-06-22 Thread Matt Newville
Hi Joseph, On Mon, Jun 22, 2009 at 8:15 PM, joseph washington wrote: > Hi Matt, > Thanks for your reply. I actually did not diliberately modify the > intermediate FEFF files. I think you should probably post the input file. > Up to this point, I beleive that I've been > following Bruce's

Re: [Ifeffit] running diffkk and deltaf

2009-07-09 Thread Matt Newville
gt; built diffkk.inp and deltaf.inp files following the instructions given by > Matt Newville and Julie O. Cross in the Diffkk tutorial. Then, I begin to > run diffkk in ifeffit 1.2.11c as follows: > > ifeffit> run diffkk > ifeffit> read diffkk.inp > > or >  ifeffit>

[Ifeffit] post-doc position

2009-07-16 Thread Matt Newville
Hi Folks, A Post-Doctoral position using XAFS in Earth Sciences is open at St. Francis Xavier University, working with Alan Anderson. More details are at http://xafs.org/Jobs --Matt ___ Ifeffit mailing list [email protected]

Re: [Ifeffit] Is it legitimate to merge transmission data with fluorescence data?

2009-08-10 Thread Matt Newville
Dear Fiona, I think it would be pretty unusual for transmission and fluorescence data measured at the same time to be of comparable quality and both be "noisy-but-good-enough" that merging would actually help. Are you sure that the data a similar enough (no pinhole or self-absorption effects)

Re: [Ifeffit] Athena User Guide—FCFS

2009-08-11 Thread Matt Newville
I never got one --Matt On Tue, Aug 11, 2009 at 1:47 PM, Julie Olmsted Cross wrote: > I have ten copies of the Athena User Guide leftover from the 2009 APS XAFS > School. If you want one, send me your mailing address. First come, first > served. > > ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ > Dr. Julie

Re: [Ifeffit] Chi in arthemis

2009-08-18 Thread Matt Newville
Dear Eugenio, > I see that the R-factor is pretty good, 1.74%, amp is high cause is > correlated with the coordination number and always have big errors., delr > has the error of the total distance, so it is ok, but ss and enot have a a > really big error, is this normal? What leads you to

Re: [Ifeffit] Chi in arthemis

2009-08-19 Thread Matt Newville
Hi Scott, > Is this the most recent IXAS report on error reporting standards? > > http://www.i-x-s.org/OLD/subcommittee_reports/sc/err-rep.pdf Yes. To be clear, the main value of reduced chi-square is that it can be used (even if with some inherent uncertainty) to compare two models with

Re: [Ifeffit] Principle Component Analysis

2009-08-22 Thread Matt Newville
Hi Abhijeet, > I am trying to understand the method of Principal Component Analysis. What > is PCA, On what principle it works, How it can be applied to system and to > what type of system it can be applied. I am trying to find the answers of > these questions. If someone can please tell me

Re: [Ifeffit] Using Ifeffit in Perl

2009-08-24 Thread Matt Newville
Hi Jan, You probably need to install the entire Ifeffit perl module (not just Ifeffit.pm) which should be in a zip file in C:\Program Files\Ifeffit\build\wrappers\perl I think you have to unzip this into C:\Perl\, but I'm away from a machine I can test this on right now (hopefully someone will

[Ifeffit] job postings

2009-09-22 Thread Matt Newville
Hi Folks, There have been two post-doc positions posted at http://xafs.org/Jobs recently. If you know of anyone who might be interested, please pass these along. Cheers, --Matt Newville ___ Ifeffit mailing list [email protected] http

Re: [Ifeffit] Cementite EXAFS - thanks

2009-09-24 Thread Matt Newville
Hi Bhoopesh, It's amazing to me how many people have asked about this data set. I did not prepare the sample of Fe3C measured for the data in the model compound library. Basically, a user interested in reduced iron phases and with good knowledge of carbides showed up at the beamline with a

[Ifeffit] mailing list outages

2009-10-12 Thread Matt Newville
gh to notice. But don't be too surprised if mail to the mailing list takes a bit longer than usual this afternoon. Cheers, --Matt Newville ___ Ifeffit mailing list [email protected] http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Normalization in Athena

2009-10-26 Thread Matt Newville
Lisa, I think the issue you're seeing is most likely due to telling athena to fit the data between E0+199 and E0+200 with a constant. I'd recommend expanding that range some to give Athena a chance -- if there isn't any data between E=E0+199 and E0+200, Athena won't be able to figure out what

Re: [Ifeffit] Rbkg value

2009-10-26 Thread Matt Newville
Hi Chris, There is nothing sacred about Rbkg=1.0 Ang. It was chosen as a reasonable default. If you know you have atoms much closer than 2Ang, lowering Rbkg to half the first neighbor distance is a fine place to start. You may have to play with this value (and the k-weight used in the

Re: [Ifeffit] suppressing the stdout of FEFF

2009-10-26 Thread Matt Newville
Hi Jochen, Just to follow up on Bruce's response The short answer is No. Feff8 is hardwired to write to stdout. Changing that would be a large task. It sounds like you are writing a script to loop around running Feff8. If so, you can use system level redirects feff8 > output.txt

Re: [Ifeffit] SrSO4 (Celestite) and SrCO3

2009-10-27 Thread Matt Newville
Hi Peter, Attached is an athena project file with some Sr model compounds. All data is from SSRL from the mid 1990s, and most uses SrCO3 as a reference. Some of the data sets are from different runs, and I have not tried to align the data or standards for these -- these are as measured.

Re: [Ifeffit] Normalization in Athena

2009-10-27 Thread Matt Newville
Hi Lisa, On Mon, Oct 26, 2009 at 9:12 PM, Gudrun Lisa Bovenkamp wrote: > I am sure that Athena was tested a lot, but as Jeremy pointed out, which I > think now is the answer: If the > background is substracted before the fitting of the post edge. That is > actually how we are normalizing >

Re: [Ifeffit] consultation

2009-11-09 Thread Matt Newville
Hi Mingliang, Sorry for the trouble. It's a little hard to tell what's gone wrong, but here are some hints: The icon to run athena (and others) simply runs the program "runner.exe" in the Ifeffit "bin" folder (usually C:\Program Files\Ifeffit\bin). This program sets the path and other

Re: [Ifeffit] probem with run Athena

2009-11-11 Thread Matt Newville
Mingliang, ... but you still have not answered the questions I asked earlier. I'm willing to try to help, but you are not helping me. Answer those questions, and try to explain more precisely what you mean by "When open SixPack" and "open Athena". --Matt 2009/11/11 康明亮 : > Dear Matt, > Many

Re: [Ifeffit] Reply

2009-11-11 Thread Matt Newville
> would you pls open the enclosure > and help me to process it? It is only a little workload(Four reference and > three samples). I just want to know which chemical attribute to the samples, > FeSe, Se(0), FeSe2 or Se(IV). No. --Matt ___ Ifeffit

Re: [Ifeffit] Reply

2009-11-11 Thread Matt Newville
> I am not mean you need to help me to process them, I just don't know why > these data can't open in Sixpack or other programm. Is there any problem > with the raw data? Wish to obtain guidance from you. I have not looked at the data you sent. Did you expect I would? You have not answered to

Re: [Ifeffit] Reply

2009-11-13 Thread Matt Newville
Mingliang, It's not exactly how I would have liked the answers, but the screenshots of the steps you performed does actually (at least implicitly) answer to some of the questions: 1) how are you starting Athena and Sixpack? You never actually said this, before, bbut you are using

Re: [Ifeffit] Bug in Athena?

2009-11-19 Thread Matt Newville
Is there ever a case where a merged reference channel is useful? I thought the only possible use for a reference channel was for comparing individual scans. That is, prior to merging. --Matt On Thu, Nov 19, 2009 at 6:45 AM, Zajac, Dariusz A. wrote: > Dear Bruce, Dear All, > maybe it is a

Re: [Ifeffit] Bug in Athena?

2009-11-19 Thread Matt Newville
Hi Scott On Thu, Nov 19, 2009 at 9:50 AM, Scott Calvin wrote: > Hi Matt, > > I'm the one who requested the merged reference channel. > > If the data is ideal, of course only one reference scan is needed. But there > are two common ways it can be nonideal that are relevant: > > 1) The

Re: [Ifeffit] Mackale's Table for backscattering amplitude

2009-12-03 Thread Matt Newville
Dear Mrs Parsai, Ifeffit includes tabularized scattering amplitudes and phase shifts from Feff6, which should be a more accurate than the McKale tables. I believe that M Vaarkamp, et al, Phys Rev B 50, 117872, 1994 showed this fairly convincingly. Admittedly, the format of the Feff tables

Re: [Ifeffit] Double crystal monochromator

2009-12-04 Thread Matt Newville
Just to follow up a little on Matthew's answer: The Darwin width is the angular width over which a particular reflection will diffract. A rocking curve measurement usually leaves one crystal at a fixed angle and rotates the second crystal. For a perfectly collimated beam, the resulting

Re: [Ifeffit] installing IFeffit, etc on user accounts

2009-12-22 Thread Matt Newville
Hi Elizabeth, If you can install as the user who will run athena/artemis, that should definitely help. As Bruce suggested, the most likely problem is that Athena/Artemis are trying to write files to a directory they do not have permission to write to (hope the grammar police are not reading

Re: [Ifeffit] Lattice parameters: EXAFS vs. XRD

2009-12-30 Thread Matt Newville
Hi Scott, I believe we had a conversation about this last January. XAFS is not sensitive to the crystallographic lattice constants. It measures the spacing between atoms. Because of thermal vibrations and other disorder terms, the average distance between atoms is larger than the distance

[Ifeffit] Job Posting: Post-Doc postion at Missouri State Univ, Material in Extreme Conditions

2010-01-15 Thread Matt Newville
Hi Folks, Prof. Robert Mayanovic at Missouri Sate University is searching for a post-doctoral associate to work on materials in extreme conditions. More details are at http://xafs.org/Jobs --Matt ___ Ifeffit mailing list

Re: [Ifeffit] Compiler cannot handle complex function properly

2010-01-15 Thread Matt Newville
Dear Ying, On Thu, Jan 14, 2010 at 1:00 PM, Ying Zou wrote: > Dear all, > One colleague of mine brought up this to my attention. He tried a > simple Fourier transformation C code on different machines (PowerPC > based MAC G4, Intel based MAC G5, and PCs). The computations yield > different

Re: [Ifeffit] consultation

2010-01-20 Thread Matt Newville
Bruce's guess is correct: Athena cannot open files with non-ASCII characters in the file or path name. --Matt ___ Ifeffit mailing list [email protected] http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Problem opening up project files

2010-01-20 Thread Matt Newville
Hi Bruce, Was the problem an ifeffit problem -- truncating strings and then not recognizing them?? If so, what happened? > P.S. While I am at it, I'll look into the issue of non-ascii > characters in filenames that Mingliang asked about earlier today. I think this is an Ifeffit problem.

Re: [Ifeffit] SIXPack : How to load data file

2010-01-22 Thread Matt Newville
Dear Rashmi, Vijay, Abhijeet, , Can you please ask this question more precisely? Asking for "guidance" is a bit too vague to expect a helpful answer. > I am doing some data analysis of XANES as well as EXAFS data using > data analysis software SIXPack. I am not able to load any data file.

Re: [Ifeffit] Ifeffit Digest, Vol 83, Issue 22

2010-01-23 Thread Matt Newville
> Thanks for your suggestions. Actually sometimes we are not > able to frame the question correctly, which is also one of the reason of not > getting a response. The issue is not so much framing a question correctly, but asking a question that can be answered. > To be

Re: [Ifeffit] Bruce ayuda, problemas con athena

2010-02-13 Thread Matt Newville
On Sat, Feb 13, 2010 at 10:38 AM, Frenkel, Anatoly wrote: > Can't wait for a question in Russian. > Anatoly Как объясните самопоглощение в русском? --Matt ___ Ifeffit mailing list [email protected]

Re: [Ifeffit] Bruce ayuda, problemas con athena

2010-02-13 Thread Matt Newville
On Sat, Feb 13, 2010 at 10:59 AM, Scott Calvin wrote: > You'll probably get Russian before I get Latin. Quam utor postulo notitia quinymo quam Feff ut a vexillum in Artemis? But you're right: Russian did come before Latin ;) --Matt ___ Ifeffit

Re: [Ifeffit] Athena Freezing Desktop

2010-02-15 Thread Matt Newville
David, I suspect that you *should* get sensible error messages from Athena about running out of Ifeffit resources well before seeing a crash of X. Not in the sense of "Bruce ought to change Athena to report this", but in the sense of "Bruce already does report this". Generally, Ifeffit/Athena

Re: [Ifeffit] Athena Freezing Desktop

2010-02-16 Thread Matt Newville
Hi David, Do you (or can you) see such issues with other applications? I would probably first try /usr/bin/widget, the Perl/Tk demo code (I think that should be installed with the debian package), to see if that ever has the same problem. I might try re-installing (or even rebuilding from

Re: [Ifeffit] ifeffit OS X 10.6

2010-02-18 Thread Matt Newville
Hi Thorsten, Thorsten Bartels-Rausch wrote: > Hi Matt > >    thanks for the ifeffit software package that we also use here at the > Swiss Light Source (PSI SLS). May > I kindly ask, if you have a binary version of the package that runs under Os > X 10.6 Snow Leopard (64 bit)? > Or should I

Re: [Ifeffit] [OT] Ifeffit mailing-list available also on Gmane

2010-02-20 Thread Matt Newville
Thanks Mauro! --Matt On Sat, Feb 20, 2010 at 3:03 AM, Mauro Rovezzi wrote: > Dear all, > > A short off-topic message to inform you that I have subscribed (in > accord with Matt) the Ifeffit mailing-list to the http://gmane.org > archive. This will permit to follow this (traffic-growing)

Re: [Ifeffit] Is Athena NFS safe?

2010-03-23 Thread Matt Newville
Hi David, There is no explicit protection for disk access to prevent i/o conflicts between different applications (and nothing specific to NFS or other networked drives), but disk access is relatively rare and reasonably well encapsulated. So, yes there are "potential problems", though I don't

Re: [Ifeffit] No background subtraction in some cases?

2010-04-02 Thread Matt Newville
Hi Alexander, I see two issues with these data files that are probably tripping up Athena: First: the files end with an "END OF DATA" line. This is a fine choice for how to organize a data file, but it's not what Ifeffit is expecting. Second: a bigger issue is that there isn't a column for

Re: [Ifeffit] fitting simultaneously two different K-edges

2010-05-03 Thread Matt Newville
Dear Maria, If you haven't already done so, I would suggest that you begin by separately fitting the data for each edge on each sample. This will give you a good understanding of the local structure around each metal ion. Once you have this intimacy with the structural models, you will be able

[Ifeffit] expected network outage to millenia.cars.aps.anl.gov

2010-05-04 Thread Matt Newville
Hi Folks, The APS networking people will be doing some hardware work next week which means that millenia.cars.aps.anl.gov will be inaccessible to the outside world May 10,11,12, and 17. Because of this, xafs.org, the Ifeffit wiki, and this mailing list will all appear to be down on these days.

Re: [Ifeffit] Debye model on artemis

2010-05-11 Thread Matt Newville
Hi Kleber, > I'd like to use the third cumulant option in Artemis, but considering the > Debye model. Artemis has a Debye function for the second cumulant > (Debye-Waller factor) but not to the third. How could this be done in > Artemis? The debye and eins functions in Artemis/Ifeffit calculates

Re: [Ifeffit] the use of constraints

2010-05-28 Thread Matt Newville
ggested min/max idiom. > > I like better the idea of penalizing a fit when percap is outside of a > defined range and thus "encouraging" the fit to settle percap somewhere > inside this range. But in trying to use the restraint idea, including the > fix suggested by Matt Newvill

Re: [Ifeffit] Exporting derivative data

2010-05-31 Thread Matt Newville
> By default, Athena smooths derivative data three times before plotting it. > This is controlled by the plot->smoothderiv parameter (which can be set in > the preferences dialog under the Setting menu). > > When you export the derivative data, it is not smoothed. So, to reproduce > Athena's plot

Re: [Ifeffit] can sigma square ever be less than zero?

2010-06-28 Thread Matt Newville
Hi Chris, On Mon, Jun 28, 2010 at 3:10 PM, Chris Patridge wrote: > Hello all, > > I am working on W L3 edge data.  W is acting as a substitution dopant in > vanadium dioxide at rather low concentration.  In a past mailing > conversation discussing Feff6 overestimation of E0 for heavier elements

Re: [Ifeffit] Clarification needed on the structured 2nn peak

2010-07-06 Thread Matt Newville
Dear Varadarian, I didn't look at your attachments, but have you considered that there might be some Cd-Ca in the second shell? I didn't see what value of x you had in Cd(1-x)CaxO, but if the oxides form a solid solution one might naively expect the second shell to have (1-x) Cd and x Ca

Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of absorbing atoms"

2010-07-28 Thread Matt Newville
Dear Rana, Delta E0 is a shift in the Energy origin of k, that is where k=0. For the experimental data, this was chosen empirically (and so somewhat arbitrarily) from the measured data. For the FEFF calculation, it was chosen at the calculated absorption threshold (lowest available electronic

Re: [Ifeffit] updating Athena in Windows 7

2010-07-28 Thread Matt Newville
Hi Todd, On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd wrote: > On Saturday, while starting up Athena, I was informed that there was an > update to Athena available.  I tried installing the update but failed.  I am > afraid this is due to some user permission issue in windows 7.  How can I > try

Re: [Ifeffit] updating Athena in Windows 7 (Matt Newville)

2010-08-11 Thread Matt Newville
Hi Todd, That sounds like a permissions problem to me. Some account needs to be able to write to that file If updating the updater.ini file is not working, and Laurent's suggestions don't let you edit that file, you could also try downloading and installing the update zip files by hand.

Re: [Ifeffit] Fwd: Windows 7?

2010-08-12 Thread Matt Newville
Yes, Athena, Artemis, Hephaestus, Artemis, and SixPack all run fine on Windows 7. Even 64bit Windows7. Even on a Mac running Parallels. --Matt ___ Ifeffit mailing list [email protected]

Re: [Ifeffit] PYTHON scripting on MacOS & XP

2010-08-12 Thread Matt Newville
Hi Joel, Sorry that Python scripting is not currently included in the iXAFS installation or easily available on Mac OS X. I'll work on this and post it as soon as possible. I am just getting back to having a Mac with a build system, so it might take me a little time. For windows, there is

Re: [Ifeffit] PYTHON scripting on MacOS & XP

2010-08-13 Thread Matt Newville
Hi Joel, I updated the Ifeffit-Python extension for Windows, and have put it at: http://cars9.uchicago.edu/ifeffit/Python This requires a working windows installation of Ifeffit+, but it does work on a Mac running Parallels. I've only tested the Python extension with Python2.6, but I

Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 7

2010-08-16 Thread Matt Newville
Hi Aranwela, Thanks for the report. I do think this is a permissions problem. That's not to say it's not a real problem, just that it should be solvable. I just tested this by resetting the "update level" in config/current.dat, and forcing the updater to run. It worked fine to download and

Re: [Ifeffit] incorporating feff 8 into Artemis

2010-08-17 Thread Matt Newville
Rana, Yes, see http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-September/007204.html for details. --Matt ___ Ifeffit mailing list [email protected] http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] PYTHON scripting on MacOS & XP (Joel Brugger)

2010-08-17 Thread Matt Newville
quot;credits" or "license" for more information. >>> import Ifeffit >>> iff = Ifeffit.Ifeffit() >>> iff.ifeffit('show $&build') $&build= 1.2.11c Copyright (c) 2008 Matt Newville, Univ of Chicago 0 >>> import numpy >>> x = nu

Re: [Ifeffit] Manual update to iXAFS

2010-08-31 Thread Matt Newville
Hi, I have made a little progress understanding and getting Ken McIvor's iXAFS build scripts to run on my Macbook Pro. I have not yet tackled a full 64-bit version, but have managed to get it to compile ifeffit 1.2.11c and everything up to horae, including Tk and PGPLOT. I could not get

Re: [Ifeffit] Manual update to iXAFS

2010-08-31 Thread Matt Newville
op me complaining about perl. OK, that was a half a day Now back to OS X and trying to build perl and horae there... --Matt On Tue, Aug 31, 2010 at 10:07 AM, Bruce Ravel wrote: > On Tuesday 31 August 2010 10:42:02 am Matt Newville wrote: >> I could also not get horae-070 to bui

[Ifeffit] iXAFS for Mac OS X

2010-09-03 Thread Matt Newville
Hi Folks, With help from Ken McIvor and Jeff Terry, I've built a new version of iXAFS for Mac OS X. This version should be considered experimental, but for the brave and/or foolhardy please try it out and let us know how it works. This version offers the latest versions of Athena, Artemis, and

Re: [Ifeffit] iXAFS for Mac OS X

2010-09-03 Thread Matt Newville
Sorry for the typo. The download is at http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg --Matt On Fri, Sep 3, 2010 at 10:08 PM, Matt Newville wrote: > Hi Folks, > > With help from Ken McIvor and Jeff Terry,  I've built a new version of > iXAFS for Mac OS X.  This

Re: [Ifeffit] iXAFS3.0 - not much luck so far

2010-09-06 Thread Matt Newville
Hi Joel, All, Yes, sorry for that. I'm still learning how to do this. Here's the latest news (some progress, incomplete): With Jeff's earlier message I looked into and solved at least one of the problems: that /Users/Newville/Codes/ifeffit/local/bin/perl was all over the place and expected.

[Ifeffit] iXAFS3.0.2

2010-09-07 Thread Matt Newville
appreciated. Cheers, --Matt On Mon, Sep 6, 2010 at 11:06 AM, Jeff Terry wrote: > Hi All, > > Looks like it works now on intel machines.. > I can run ifeffit from the iXAFS shell. > > The iXAFS app is not universal though, it is Intel only. > > Nice job Matt. > > Jef

Re: [Ifeffit] iXAFS3.0.2

2010-09-08 Thread Matt Newville
For kicks I also tried 'arch -x86_64 ifeffit' and got the error > 'arch: posix_spawnp: ifeffit: Bad CPU type in executable'.  Let me know if > there is any other information that I can provide you with. > > Thanks again > Brandon > > On Tue, Sep 7, 2010 at 2

Re: [Ifeffit] IXAFS3.0.2 and python scripting

2010-09-09 Thread Matt Newville
till have '. > /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh' in my > '.profile'. Do I need to keep this? If so, it would be nice to fix > iff_init.sh too :-) > > Thanks, > > Joel + Barb > > ____ &

Re: [Ifeffit] atoms input file

2010-09-09 Thread Matt Newville
Hi Mohamed, I'm not certain I understand what you're trying to do, but to add a "dopant" or partial occupancy of an atom at a particular lattice site, run atoms on the "pure" structure (UO2) and then replace some of the "solvant" (U) with the "solute" (Ce) in the feff.inp. See

Re: [Ifeffit] (Reposted) K-space vs R-spce fitting

2010-09-10 Thread Matt Newville
Hi Juan, On Fri, Sep 10, 2010 at 7:29 PM, Lezama Pacheco, Juan Salvador wrote: > Reposting, just notice no line breaks, sorry! > Juan > Dear All: > First of all, nicely done you guys! This is indeed > a set great of tools the community really appreciates > it and I have been putting into heavy

Re: [Ifeffit] (Reposted) K-space vs R-spce fitting

2010-09-11 Thread Matt Newville
Hi Juan, The data and model are k-weighted and multiplied by the chosen window function before the least-squares fit. So yes, as you see, the choice of dk will change a k-space fit. I wouldn't expect it to change the results by a huge amount no matter how the fit was done. I would suspect

Re: [Ifeffit] XasPerlBundle problems

2010-09-17 Thread Matt Newville
Hi Josh, That cpan command should be done from the horae install directory. Saying perl -MCPAN -e 'install Bundle::XXX' is looking for the file named XXX.pm (which simply contains a list of Perl modules) in the directory Bundle/. I think that if it can't find that, then it goes to look

[Ifeffit] iXAFS 3.0.3 for Mac OS X

2010-09-19 Thread Matt Newville
Hi All, OK, sorry for the delay, but I think that http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.3.dmg should now work well for both Mac OS X 10.6 and 10.5. That is, all the applications launch for me on a 10.6.5 machine and a 10.5.8 machine, and seem to work as expected. I'll try this on

Re: [Ifeffit] XasPerlBundle problems

2010-09-19 Thread Matt Newville
Hi Josh, > Hi Matt, > Thanks for the quick response. I did run the command from within the horae > install directory, and the file XasPerlBundle.pm is in the Bundle directory, > i.e., > > verrocchio.phys #] pwd > /tmp/horae-070 > verrocchio.phys #] ls > . Bundle INSTALL aug

Re: [Ifeffit] iXAFS 3.0.3 for Mac OS X (Brandon Reese)

2010-09-23 Thread Matt Newville
Type "help", "copyright", "credits" or "license" for more information. >>> import Ifeffit >>> i = Ifeffit.Ifeffit() >>> i.ifeffit("show $&build") $&build= 1.2.12 Copyright (c) 2005 Matt Newville, Uni

Re: [Ifeffit] Aligning Energy scales

2010-09-28 Thread Matt Newville
Dear Elsa, It sounds like you want to adjust the data chi(k) so that deltaE0 is 0 in a fit. Is that correct, or are you trying to do something else (say, align the XANES)?If that assumption is correct, you want to change the E0 used to extract chi(k) from the experimental spectra -- the E0

Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28

2010-09-30 Thread Matt Newville
Hi Elsa, On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo wrote: > > Dear Matt, > > I have to perform EXAFS analysis, and when I tried to fit the first > shell, I found deltaE0 values of about 8 eV. Following the paper of > Kelly et al (Analysis of soils and minerals using X-ray absorption >

Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths

2010-10-08 Thread Matt Newville
Dear Jatin, I tried to answer both of these question in chapter 3 of http://xafs.org/Tutorials?action=AttachFile&do=view&target=Newville_xas_fundamentals.pdf Does the explanation there help? If not, do you have any suggestions for making it clearer? The basic physics is that an absorbed

Re: [Ifeffit] calibration/alignment

2010-10-14 Thread Matt Newville
Dear Ornel, Alignment here means to make sure that the energy scale has not drifted between different scans. At many (especially older) facilities, it is not too unusual to have the apparent energy scale drift around a bit over time. Sometimes a reference sample is measured simultaneously

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-25 Thread Matt Newville
Hi Scott, That's a pretty amazing use case. But I'm not sure I understand the issue exactly right. I would have thought the volume (r**3) was the important physical parameter, and that a 1000nm particle would dominate the spectra over 3nm particles. Or is it that you are trying to

Re: [Ifeffit] feff question

2010-10-27 Thread Matt Newville
Hi George, Feff6 comes built in with the Mac distributions of Ifeffit (iXAFS.app), and is at /Applications/iXAFS.app/Contents/Resources/local/bin/feff6. Is that OK or do you really need Feff7? There's not much in Feff7 that's not in Feff6 (or a whole lot better in Feff8). FWIW, that version was

Re: [Ifeffit] Scripting - Python

2010-11-01 Thread Matt Newville
Hi Andrew, On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda wrote: > I'm looking to introduce some scripting routines to some of my EXAFS > fitting work. Looking around I ran across the Python module and > downloaded that. The shell works fine, as does enter commands directly > into Ifeffit,

Re: [Ifeffit] feff question

2010-11-03 Thread Matt Newville
Hi George, On Wed, Nov 3, 2010 at 2:07 PM, George Sterbinsky wrote: > Is it possible that I need to download and install the gfortran-4.2.3.dmg > file in addition to gfortran-42-5577.pkg file? Any suggestions as to what to > try would be appreciated. I doubt it. >> It took me some time to

Re: [Ifeffit] feff question

2010-11-03 Thread Matt Newville
Hi George, On Wed, Nov 3, 2010 at 2:37 PM, George Sterbinsky wrote: > I've also noticed that there is not a file or directory called gfortran in > '/usr/local/bin'. This is what made me think I may also need to install the > gfortran-4.2.3.dmg file. If I do not see a file or directory called

Re: [Ifeffit] help

2010-11-12 Thread Matt Newville
Hi Aaron, If you're having troubles with the updater, I would suggest: re-installing and then say No to the automated "shall I update for you?".See http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/RunnerProgram and http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater

Re: [Ifeffit] Origin of terminology "self-absorption"

2010-11-16 Thread Matt Newville
It's a term taken from x-ray fluorescence spectroscopy, or probably really any fluorescence spectroscopy, where it has very sensible meaning: the attenuation of the fluorescence signal by the sample itself. I would even say it is used "mostly correctly" in XAFS, or at least with a similar intent

Re: [Ifeffit] Transmission EXAFS sample

2010-11-19 Thread Matt Newville
Dear Jatin, The idea that the optimum absorption length (mu*t) for transmission experiments is 2.3 assumes that the errors in the measurement are due to counting statistics of the x-rays. For any synchrotron experiment, the number of x-rays in the transmission chamber is high enough that the

Re: [Ifeffit] Distortion of transmission spectra due to particle size

2010-11-22 Thread Matt Newville
Scott, I agree with Jeremy and Matthew. Layering very small (compared to an absorption length) spheres is exactly what "powder on tape" and mixing with a low-Z binder do, and that's why these are the preferred methods for turning a powder into a sample of uniform thickness. If the spheres are

Re: [Ifeffit] Transmission EXAFS sample

2010-11-22 Thread Matt Newville
Hi Edmund, Thanks for that post... I'd never seen the UV-vis literature on this and didn't know what a Ringbom plot was. A google search led to Ramirez-Munoz 1967 (doi:10.1016/0026-265X(67)90042-2) on Atomic-Absorption Photometry, which shows a very nice result that significant distortions

Re: [Ifeffit] Distortion of transmission spectra due to particle size

2010-11-22 Thread Matt Newville
On Mon, Nov 22, 2010 at 4:55 PM, Scott Calvin wrote: > Some follow-up. > This, for example, is from an excellent workshop presentation by Rob > Scarrow: > > Errors from large particles are independent of thickness Yes... one can have a sample that is uniform, or made of small particles, and

Re: [Ifeffit] maximum number of paths in Artemis

2010-11-22 Thread Matt Newville
Hi Yuan, Bruce, It looks like I need to make a dll with more than 512 paths. I'm on this, but it might take me a day or so. --Matt On Mon, Nov 22, 2010 at 5:09 PM, Bruce Ravel wrote: > > Yuan, > > It seems unwise to post a new question at the end of a long and active > thread.  Presumably

Re: [Ifeffit] maximum number of paths in Artemis

2010-11-22 Thread Matt Newville
Yuan, All, I put several Windows dlls for Ifeffit at http://cars9.uchicago.edu/~ifeffit/src/Win32_dlls/1.2.12/ There are versions there with 256, 512, 1024, and 2048 paths.I have not tested these beyond loading them, and running a trivial python script. Please let me know if there are

Re: [Ifeffit] Distortion of transmission spectra due to particle size

2010-11-24 Thread Matt Newville
Scott, > OK, I've got it straight now. The answer is yes, the distortion from > nonuniformity is as bad for four strips stacked as for the single strip. I don't think that's correct. > This is surprising to me, but the mathematics is fairly clear. Stacking > multiple layers of tape rather than

Re: [Ifeffit] Distortion of transmission spectra due to particle size

2010-11-24 Thread Matt Newville
Scott, You said: > the distortion from nonuniformity is as bad for four strips > stacked as for the single strip. As I showed earlier, a four layer sample is more uniform than a one layer sample, whether the total thickness is preserved or the thickness per layer is preserved. > For 1%

Re: [Ifeffit] Distortion of transmission spectra due to particlesize

2010-11-24 Thread Matt Newville
  0.099  | >> # 5    |   1.0  |    4.950  |    0.225  | >> #    25    |   1.0  |    24.750  |    0.500    | >> >> As before, the standard deviation increases as square root of >> N. Using a cumulant expansion (admittedly slightly funky

Re: [Ifeffit] Distortion of transmission spectra due to particlesize

2010-11-24 Thread Matt Newville
Hi Jeremy, Anatoly, Thanks, you're absolutely right -- I got the parentheses wrong. Anatoly, > However, thickness is present in mu*t only because of the total number of > absorbers. There are 1/2 absorbers in > the foil with 50% holes, and thus (t*mu)_measured is equal to (1/2) * >

Re: [Ifeffit] Distortion of transmission spectra due to particle size

2010-11-25 Thread Matt Newville
Scott, > Let me try again. I think I understand you now, and I think I agree completely. > First of all, perhaps you missed that after my first post, I acknowledged > that my statement in the first post was mistaken? In fact, I later said: > >> So there's nothing wrong with the arguments in Lu

Re: [Ifeffit] iXAFS

2010-11-29 Thread Matt Newville
Hi George, The 'About' screen didn't get changed. I did very little to Jeff and Ken's "outer Cocoa layer". I'll try to fix that, but it's probably not worth a new install. The main thing to check is whether Athena is the right version (0.8.061). Like Jeff said, iXAFS 2 and 3 do nothing to

Re: [Ifeffit] RE : Ifeffit Digest, Vol 94, Issue 2

2010-12-17 Thread Matt Newville
Dear Qingyu, I haven't analyzed this data carefully, but attached is an Athena Project File of some room temperature data on W metal from a powder-on-tape sample, Si(111) mono, W L3 edge, APS bending magnet line. I don't have ready details on the absolute calibration, but the edge energy is

Re: [Ifeffit] Ifeffit Digest, Vol 94, Issue 4

2010-12-18 Thread Matt Newville
fit > or, via email, send a message with subject or body 'help' to >[email protected] > > You can reach the person managing the list at >[email protected] > > When replying, please edit your Subje

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