Re: [Ifeffit] Artemis\Plot mismatch\Artemis[Plot] [Feff] Atoms and Feff

Question 1: As explained here: https://bruceravel.github.io/demeter/documents/Artemis/feff/paths.html#path-plotting-and-path-geometry the plot made form the paths tab of the Feff window make no effort to set parameters like S02 and sigma^2 to sensible values. The plots made from the Data

Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data

Likeliest reason: https://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units Make sure "xmu" is selected in the indicated menu. Good luck, B On 12/7/20 10:26 AM, Deka, N. wrote: > Dear all > > I am a new student trying to work with Athena for

Re: [Ifeffit] Athena error on Linux mint

I would guess the problem is that Mint 20 uses a different version of perl than Mint 19. Either downgrade to the same version of perl or reinstall. Making it work as is, if even possible, would require A LOT of fiddling. B On 10/26/20 6:27 PM, Kyle Kluherz wrote: > I recently

Re: [Ifeffit] Requesting guidance in understanding results from Athena

You should read this: https://bruceravel.github.io/demeter/documents/Athena/bkg/rbkg.html B On 9/13/20 1:45 PM, Deepak Varanasi wrote: > Good afternoon > > I hope that you are doing well and are healthy. My name is Deepak > > Varanasi and ii am an undergraduate student at Middle Tennessee

Re: [Ifeffit] Unable to Import Data In Athena

Aha! Attached log file. Sorry. Didn't notice that on my phone :( I concur with Matt about Larch. And at the risk of irking Matt, you could try forcing the use of Ifeffit. While maybe not the best choice, it would isolate problems with Demeter from problems with Larch and your python

Re: [Ifeffit] Unable to Import Data In Athena

I do not recognize that error message. I would need to see what is written underneath the details button and/or what is written in green text in the terminal window behind Athena. B On 9/3/20 9:56 AM, Angshuman Gupta wrote: > Dear sir, > I am new to this mailing list and excuse me if the

[Ifeffit] interesting job posting at NSLS-II

Hi all, A colleague of mine here at NSLS-II has an interesting post-doc position open right now. https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-in-total-scattering-and-machine-learning/3437/14611841 This position is for a person doing total scattering (aka PDF). Strictly

Re: [Ifeffit] Trouble with energy spacing in .nor files Athena

This bug is explained here: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06572.html and in the next message by thread. Executive summary: the problem is a bug in Athena interpreting an energy column expressed in keV. It has since been fixed at GitHub. I am struggling

Re: [Ifeffit] no plot window with Demeter on Ubuntu 18.04

Hi Joseph, You did the first few troubleshooting steps. Good to know that gnuplot works by itself. What is the value of preferences->gnuplot->program ? On a linux machine, this parameter should simply be set to "gnuplot". That means that gnuplot needs to be in the execution path.

Re: [Ifeffit] about WebAoms

On 11/20/19 7:49 PM, Park Gyuchul wrote: > I appreciate for your precious comments. Your suggestion makes my life > easier!  Is "distance" column is not required information in feff.inp > format? (please find the part of the feff file attached. This is what I > got from WebAtoms (typical cif

Re: [Ifeffit] about WebAoms

Hi, I am wondering whether you are thinking about your problem in the most straight-forward way. Atoms is a tool to expand crystal data into a cluster. From lammps, you already have a cluster, you just don't have your cluster expressed in a form that Feff knows how to read. Unless I am

Re: [Ifeffit] Installation problems for Demeter on Ubuntu 16.04

Hi Jo, I am sorry this is proving so difficult. Just the other day, I installed everything on a machine with Ubuntu 19.10 and saw none of these problems. The problem you are seeing is not one I have ever run into, so it;s a bit hard to comment on. It is clearly a Wx problem. Your

Re: [Ifeffit] Solved concatenation bug Arrays.pm line 115

I'm glad you found a solution. I wish that Athena played better with languages that use unicode text. I imagine that there are plenty of places where I make -- intentionally or not -- that kind of assumption about user-supplied text. So there are probably other places where Athena might

[Ifeffit] Fwd: 32 bit package for install

http://bruceravel.github.io/demeter/#old Forwarded Message Subject:32 bit package for install Date: Mon, 28 Oct 2019 20:30:40 +0200 From: Margaret Blazhynska To: ifeffit-ow...@millenia.cars.aps.anl.gov To whom it may concern, Could you please send me the

Re: [Ifeffit] Issue with the Athena software - Athena Warning: redundant argument in sprintf

Hi, It's hard for me to really troubleshoot the problem without seeing the data. It looks like the fit ran to completion, that is, the plot looks OK. A couple of your standards don't actually seem to be represented in your fit. Augite has a negative weight and Olivine is barely outside its

Re: [Ifeffit] software installation

By a very long stretch, the most common explanation for problems on Windows is that your anti-virus software is blocking something that the software needs. You might try digging through the AV log files to see if a file installed with Demeter shows up. If you are your administrator can

Re: [Ifeffit] Install for Mac error

Here's one time recently that question was answered: https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-June/009822.html The archives of this mailing list are quite useful: https://millenia.cars.aps.anl.gov/pipermail/ifeffit/ B On 10/2/19 6:04 PM, Wu Xiaohan wrote: > Hello

Re: [Ifeffit] Athena data uploading: Fourier transform parameters are not showing

http://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units On 9/30/19 2:42 AM, Pankaj Singh Rawat wrote: > Hey There, Do anyone have idea about following problem: > > I uploaded C-k edge on Athena but fourier transform parameters are not > showing/open

[Ifeffit] Fwd: 64-bit Demeter not able to use on Windows computer

Brittany, In your first post to the mailing list, you said you could not get the software to run on "a Windows computer". That you are looking for a 32 bit installer seems like extremely relevant information. I no longer have the capacity to build 32 bit versions of the installer, but I

Re: [Ifeffit] Unable to use 64-bit Demeter on Windows computer

I am always suspicious of anti-virus in this situation. I have seen many times where AV is flagging one of the libraries used by the software. Definitely my first guess ofr troubleshooting. The AV software should have a log that reports what it's unhappy with. The administrator can then put

Re: [Ifeffit] Trouble with MacOS 10.14 Mojave

Fun fact: our mailing lists has an archive of previous posts. https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-June/009821.html and https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-June/009822.html On 7/25/19 5:03 AM, christophe den auwer wrote: > Hi all, > > I have to

Re: [Ifeffit] averaging data

http://bruceravel.github.io/demeter/documents/Athena/process/merge.html On 7/18/19 2:15 PM, Danielle Brown wrote: > How do I average two data sets in Athena? > > Thanks! > — > > Danielle Brown > Office: CSE L180 > Cell: 317-605-9311 > IIT '20 - BS Physics > IIT ID: A20417782 >

Re: [Ifeffit] How to install Demeter on ubuntu 18.04

William, I'm a bit confused by the information you've given, but it seems that the installation location of Athena is not in perl's path. Try this: At the command line type export PERL5LIB=/home/opd30/demeter Then perl should find the "missing" module. If that does the trick on your

Re: [Ifeffit] Problem with Demeter installation on mac OS Mojave

A frequently asked question on this mailing list Here's one solution to the problem: Find the file Demeter.pm where ever it is installed on your computer. Open it in a text editor (not a word processor, if you use Word, you will make more problems for yourself) and scroll down to about

Re: [Ifeffit] Athena labels

Not easily (*). The plotting in Athena is pretty proscriptive. The user does not have a much freedom to change what gets plotted. That was by design. On one hand, I didn't want to write a support a full featured plotting tool. On the other hand, I didn't want the user to spend time

Re: [Ifeffit] Pseudo Voigt crash Athena

On 05/01/2019 10:57 PM, Matt Newville wrote: > Larch (and the lmfit library it uses) and the XAS Viewer GUI are all > supported. Peak-fitting of XANES is one feature which I am confident to > say is definitely better than Athena. I'm willing to take 100% of the > blame for this, but

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

Or use one of the older releases from back when I still had a 32 bit computer on which to build installer packages. http://bruceravel.github.io/demeter/#old B On 04/23/2019 07:48 AM, Matt Newville wrote: > > > On Tue, Apr 23, 2019 at 6:24 AM m.rezaie > wrote: > >

Re: [Ifeffit] Demeter - Athena Warning, crashing

Hi, The Demeter problem that presents itself with error messages like: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, line 236. is one that comes up pretty often here on the mailing list. It is

Re: [Ifeffit] Import Error

'help' to > ifeffit-requ...@millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-ow...@millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific than "Re: > Contents of Ifeffit digest..

Re: [Ifeffit] [SUSPECTED SPAM] - How to use deconvolution function in larch using athena

There isn't any major functionality in Demeter that is not explained in the documentation. The thing you are asking for is not documented, thus it's not available. If you need larch's deconvolution function you might consider, you know, using larch B On 04/06/2019 08:56 AM,

Re: [Ifeffit] Data Import Bug (Athena 0.9.26)

Unfortunately, I don't observe what you are describing. Grasping at straws here, but are you inadvertently using this import feature? http://bruceravel.github.io/demeter/documents/Athena/import/preproc.html#rebinning-quick-scan-data B On 04/05/2019 07:33 AM, Clark Adam Hugh (PSI) wrote: >

Re: [Ifeffit] Export measured difference integrated areas

That would certainly be a good feature B On 04/04/2019 09:29 AM, Patridge, Christopher wrote: > Hello everyone, > > Is there an export option for the integrated areas found in difference > spectra from Athena?  It appears the only option is exporting the > picture of plotted values?  I

Re: [Ifeffit] how to best implement fitting u (oxygen parameter) in an spinel

The assumption we make when doing EXAFS analysis with Feff and any Feff-using tool (Artemis, for example, but there are others) is that a small change in local configuration affects the argument of the sin() in the EXAFS equation significantly, but the scattering function negligibly. To say

Re: [Ifeffit] ????Athena????32??????????????????

On 01/16/2019 06:41 AM, 2225295803 wrote: > 32?? > ??32EXAFSAthena?? With the help of Google Translate, I was able to understand that you are looking for a 32 bit version of my software. 32 bit

Re: [Ifeffit] Unwanted rescaling of energy axis when importing ascii file into Athena (Demeter 0.9.26)

Lukas, A mistake is made related to the keV units in the first column of your data file. This mistake is made only with the Ifeffit backend and only for data with keV energy units. The Larch backend does not suffer from this problem. Nor do data files with eV energy units. I just checked

Re: [Ifeffit] Extrating standard deviation value from merged dataset in Athena

That doesn't get exported by any of the export options. That's kind of a weird oversight. I am surprised no one has ever pointed that out and I am surprised that I never thought to put that into one of the export files. It's available and is saved to and restored from the project file.

Re: [Ifeffit] difference of feff interpretation generated by different version of artemis

As I have said before, that's a feature, not a bug. http://bruceravel.github.io/demeter/documents/Artemis/extended/fuzzy.html B On 10/17/2018 10:19 AM, woschangqi...@126.com wrote: > Hello, everyone. I recently ran into an issue in using Artemis software. > > I  used two versions of Artemis  

[Ifeffit] larch warning that I don't understand

Matt, When Larch starts, what is meant by warnings like this: No handlers could be found for logger "pyFAI.opencl.common" or No handlers could be found for logger "pyFAI.gui.matplotlib" The first one went away by installing python's opencl interface -- a rather sizable prerequisite! I

Re: [Ifeffit] determining reasonable fitting parameters

That's my understanding also. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:

Re: [Ifeffit] PGPLOT intallation error!

"Debutant". Thanks spell-check! I meant "debian" B On May 26, 2016, at 1:45 PM, "Ravel, Bruce" <bra...@bnl.gov> wrote: Ernesto, That cannot possibly be the entire screen output. If you don't know enough to interpret and troubleshoot the screen o

Re: [Ifeffit] PGPLOT intallation error!

Ernesto, That cannot possibly be the entire screen output. If you don't know enough to interpret and troubleshoot the screen output, then you cannot reliably edit it. Capture everything. Post everything. If you do not provide sufficient context, you cannot expect me to be able to help. It

Re: [Ifeffit] Bug report ATHENA (Demeter 0.9.24)

Sunil, You are correct. Athena does not save settings from the LCF tool. That's not so much a bug as it is a missing feature. It's on my to do list (there's a link to the to do list on the Demeter home page). I am hoping to make a new release next month ... I will try to address this

Re: [Ifeffit] low and negative ss2 and bug in the log file of fit history

Further i have found a small bug in the fit history window. After each fit, earlier data set in the log file of fit history is found to overwritten with the latest fitting parameters (like k range, dk, etc..). Here in my log file window, all fit data set contain the same data set value as

Re: [Ifeffit] Create Atoms input with just coordinates

Maryline, Vasiliy's is the correct answer. You don't have a crystal. Atoms is the right tool for interpreting crystal data, but not the right tool in your case. See page 7 and following in https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples and/or watch my Modelling non

Re: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED]

, and it doesn’t work by manually change them either. I’m happy to send you screen shots if necessary. Thanks again for your help. Zhaoming From: Ravel, Bruce [mailto:bra...@bnl.gov] Sent: Thursday, 2 April 2015 12:43 PM To: ZHANG, Zhaoming Subject: RE: [Ifeffit] Importing data

Re: [Ifeffit] Athena does not React after 2-4 steps

I need to see the C:\Users\Michael\AppData\Roaming\demeter\dathena.log file. You don't need to guess what information to send me. I explain it clearly here: http://bruceravel.github.io/demeter/pods/bugs.pod.html#The_basic_rules_to_good_bug_reportin B -- Bruce Ravel

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

I cannot solve a problem that I cannot reproduce on my own computer. Please read and follow these hints on submitting a useful bug report: http://bruceravel.github.io/demeter/pods/bugs.pod.html#The_basic_rules_to_good_bug_reportin In particular note the location of the error message --

Re: [Ifeffit] to use scattering path in different model or to construct a new model which is the combination of different simple compound

Chances, You should read this paper by Shelly Kelly: http://dx.doi.org/10.1016/S0016-7037(02)00947-X It shows an example that is, I think, similar to your question. She fits an unknown by combining paths from different FEFF calculations. B On June 29, 2014, at 2:19PM, ZHAN Fei wrote:

Re: [Ifeffit] to use scattering path in different model or to construct a new model which is the combination of different simple compound

Chances??? Damn autocorrect! Sorry about that Zhanfei. B On June 30, 2014, at 10:09AM, Ravel, Bruce wrote: Chances, You should read this paper by Shelly Kelly: http://dx.doi.org/10.1016/S0016-7037(02)00947-X It shows an example that is, I think, similar to your question. She fits

Re: [Ifeffit] Demeter on Ubuntu 14.04

I'm on vacation right now and only have my tablet, so typing a decent response is a challenge. From what you included, it looks as though you pulled or cloned the latest from within, but did not do the perl Build.pl or ./Build installdeps steps. If not starting from a clean install, it may

Re: [Ifeffit] XANES + EXAFS for light elements in diluted samples

Federico Boschirini's compilation of the world's XAFS beamlines should help: http://www.iucr.org/resources/commissions/xafs B On May 10, 2014, at 12:04PM, Marcelo Alves wrote: Dear all, I am interested in running some measurements of XANES and EXAFS K-edge spectra of elements such as Ca

Re: [Ifeffit] XANES + EXAFS for light elements in diluted samples

, Ravel, Bruce wrote: Federico Boschirini's compilation of the world's XAFS beamlines should help: http://www.iucr.org/resources/commissions/xafs B On May 10, 2014, at 12:04PM, Marcelo Alves wrote: Dear all, I am interested in running some measurements of XANES and EXAFS K-edge spectra

Re: [Ifeffit] LCF fitting marked groups in Athena

Thanks as always for the bug report, Fred. I am on travel right now, but I am hoping to make a new release in the next few weeks. I will put this on the to do list. The work-around is, as I am sure you know, rather obvious. You'll have to do the fits one-by-one. B Bruce Ravel

Re: [Ifeffit] Problem with Demeter 0.9.18 pluck tool

Denis, I have a question. What gnuplot terminal do you use? That is, what's the value of the gnuplot-terminal configuration parameter? It seems that the way I do the pluck buttons does not work with the X11 terminal, but it should work with the wxt terminal. So if that parameter is set to

Re: [Ifeffit] Problem with Demeter 0.9.18 pluck tool

Hi Denis, The plucking thing is odd. Both the X11 and wxt terminals seem to interact with the clipboard in the same way, but my code only successfully retrieves the point from the clipboard when I use the wxt terminal. B Bruce Ravel bra...@bnl.gov

Re: [Ifeffit] Athena- Demeter 0.9.14 importing data

As I have said many, many, many times on this mailing list, there is nothing I can do to fix -- much less understand -- a problem without being able to reproduce it on my own computer. Atul, the reason you have not gotten a response to your post is because you did not provide an example of

Re: [Ifeffit] Problem with running Demeter

Amitava, It is very difficult for me to take your email seriously. In fact, I just wrote an extremely sarcastic email, then thought better of it. Looking up the web page of the cleaning tool you used, it seems that one of the purposes of that thing is to target third party applications (like

Re: [Ifeffit] artemis can not use a cif file

Shaofeng, What have you tried so far to address your problem? B From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Shaofeng Wang [wangshaof...@iae.ac.cn] Sent: Monday, April 22, 2013 10:54 PM To: XAFS

Re: [Ifeffit] problem with importing data between version of artemis

Georges, Thanks for the bug report. I'll look into it soon, although it may have to wait until next week. Things are pretty busy at the beamline this week. Cheers, B From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov]

Re: [Ifeffit] generating high res figures

As others said, it is not my intention that AA be used for publication quality plots, although part of the motivation to make Demeter, as compared to the earlier version, was not make prettier plots. I, in fact, use screen captures of the plot window regularly in presentations and posters.

Re: [Ifeffit] demeter windows download

Darren, Erik's answer was the right one. I updated that wiki page. Thanks for reporting the documentation bug. Cheers, B From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Darren Dale

Re: [Ifeffit] Hephaestus crash

Darren, This is fixed at github. You can git pull and reinstall. Since I am working on integrating Matt's larch with Demeter, I have instrumented one of the main choke points in Demeter with a useful (to me) screen message that helps me track the flow through the parts of the program

Re: [Ifeffit] Athena doesn't start - Larch server not running

I'm really sorry. I left Demeter in a broken state on github. I am currently at work getting Demeter to use Larch, but it is most certainly not ready for prime-time. I will disable the use of larch in Demeter and push that to github. I am currently at the beamline, so it will be an hour or

Re: [Ifeffit] Basic question in normalization and background removal

Cyril, My favorite answer is don't measure data that way. At the very least, add a few widely spaced points in the pre- and post edge regions so that normalization can be done. If you added 10 points spaced 20 volts apart to the data on the right, then normalization would be much less

Re: [Ifeffit] Problem downloading windows installer for Demeter

From: Javier Alonso [jalonsom...@gmail.com] Sent: Sunday, January 06, 2013 7:59 AM To: Ravel, Bruce Subject: Problem downloading windows installer for Demeter Dear Dr. Ravel, Firts, I'd like to personally thank you for Demeter: it really helps me a lot with my

[Ifeffit] Using this mailing list effectively

I think you are really right, I am in too great a hurry that I lost my patience to set a time to learn basics quietly. Thanks for reminding. And for my second question, could you give me some suggestion too? Mr. Tian, Asking questions is an art. Anyone can barf out sentences that end with

Re: [Ifeffit] The degeneracy and the coordination number

Go the archives for this mailing list: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/index.html Enter the words coordination and degeneracy in the box at the top of the page, then click the button labeled Search. I suspect the answers from the many times this question has been

Re: [Ifeffit] Plot multiple fits in (D)Artemis and statistical errors

Hi, I am aware of both of these problems. The tool for overplotting fits from the fit history is currently broken. So is the tool for restoring an old fit. Fixing both of those is on my list of things to do. Sorry for the inconvenience. B From:

Re: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos

Ku-Ding, I don't know what to tell you. On the computer I am sitting in front of right now, I opened your two project files and hit the fit buttons, I get the same fit with only numerical differences. Here I am cutting and pasting from the two log files: old artemis: Chi-square

Re: [Ifeffit] path averaging in Artemis

Hi Simon, That's not a problem. Quite the contrary. It is by design and is something that I consider to be one of the compelling new features in Artemis. In the new versions of Atoms and Artemis, I introduced a concept called fuzzy degeneracy whose purpose is explicitly to combine together

Re: [Ifeffit] Importing Multiple Data Sets into Athena

I feel I should weigh in here. There were two separate issues in the files Dan sent the other day -- one was the issue he intended to report, the other was a problem of his own creation. The intended issue was a problem importing data for which the reference spectrum was of a different

Re: [Ifeffit] Problem with Demeter Artemis 0.9.10

Hi Matt, Thanks for the report. I'll look into it and let you know what I find. Clearly the only work-around right now is to recreate your fitting model from scratch in the new Athena. Admittedly not a very satisfying answer,... B From:

Re: [Ifeffit] Importing data to Athena crashes on WinXP

Hi Bradley, This appears to be an example of a problem that I thought I had fixed some time ago. The thing making Athena unhappy is the length of the line of column labels in your file. This triggers a mistake in how Athena communicates with Ifeffit. I will fix this for the next release.

Re: [Ifeffit] first official relezse of my new software

Thanks a lot also to Matt Newville for IFEFFIT. Ismael, Thank you for mentioning that. I neglected to do so in my email. Obviously, there wouldn't be an Athena or an Artemis without an Ifeffit. Matt does a lot for all of us. B PS: Did everyone notice how I misspelled release in the

Re: [Ifeffit] Artemis: How to treat Neglected? DS path

Hi Takahide, See the first full paragraph below equation A.1 in Zabinski et al, Phys. Rev. B 52, 2995–3009 (1995), http://dx.doi.org/10.1103/PhysRevB.52.2995 Regards, B From: ifeffit-boun...@millenia.cars.aps.anl.gov

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

I think you are correct in principle that more layers can reduce the thickness effect problem. If harmonics were not an issue, eventually if you pile up enough random layers, the thickness will be uniform. Whether this is useful in practice is another matter, but suspect it may not be when

Re: [Ifeffit] Primitive unit cell from .cif file

I don't really understand what you are driving at, but it seems as though you want to express Diamond as a simple cubic cell with a two atom basis? Isn't that Pm3m with atoms at 0,0,0 and 1/4,1/4,1/4, or some such. I don't really understand how that will save you time in abinit, but, of

Re: [Ifeffit] Primitive unit cell from .cif file

Hi Josh, If I understand your question, I think that Atoms does what you want. Running the command line tool as atoms -p turns the attached cif file into the attached p1.inp file. You can do the same thing inside of Artemis using write special output in the Theory menu. B -- Bruce Ravel

Re: [Ifeffit] about wolframite crystallographic file

Yordy, I'll look into this when I get a chance, but that might not be until later in the week (I am on travel at the moment). B -- Bruce Ravel --- [EMAIL PROTECTED] National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven

Re: [Ifeffit] Athena can not open any file

Gilberto, Great to hear!! I'll fix the instuctions for installing from source on my web page as soon as I can. Thanks, B -- Bruce Ravel --- [EMAIL PROTECTED] National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National

Re: [Ifeffit] X-ray absorption measurements for Fluorescence detection.

The sotfware is certanly capable of dealing with fluorescence and tranmission equally. You need tomake sure to import your data correctly into Athena: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/columns.html Regards, B -- Bruce Ravel

Re: [Ifeffit] sorting files in Athena

if I can suggest, whould be useful the posibility of move marked groups in Athena, like copy and paste... Ctrl-y copies a group and places it at the end of the list. I haven't implemented cut and paste or other ways of moving groups around in the list, but inertia is the only reason. I'll

Re: [Ifeffit] sorting files in Athena

but then you have to ask every beamline owner to change the file names, at each synchrotron... Not necessarily, it really only applies to those generating 10's or 100's of scans such as scanning in QEXAFS mode. Not to mention that it is already implemented in many beamlines that had the

Re: [Ifeffit] sorting files in Athena

Hi, I can not find one small thing - sorting files in Athena - it makes me crazy ;) I work with QEXAFS data - usualy few tens of files or even more. Files are named in such way: file_namerXX.fio where XX is next file number (1, 2, 3, ... ,10, 11, 12, ... , 20, 21, etc.). I use Iffefit

Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?

Hi Bruce I have spent 1 month to learn the Athena by using your ATHENA User's Guide updated at Aug. 31,2007. I am very satisfied with it and thank you very much. Now I am learning the ARTEMIS. However, till now I can not find a suitable guide for a beginner. The PPT wrote by Shelly is not

Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?

What would be really useful is to make a searchable database with links to original publications (many of them are more than 20 years old but are still the best resources on many issues) on many subjects discussed in this list. Anatoly, This seems like an awfully good start:

[Ifeffit] two issues with Athena on Windows and one with Artemis

Hi, For the last few weeks, I have been doing experiments at beamlines with Windows machines. This has afforded me more time than normal using my programs under Windows. I am appreciating my linux machines more than normal, but that is not the point of this email ;-) I have found a few

Re: [Ifeffit] different edge step by linux and window vista

Hi Shanshan, A few questions: 1. Are the normalization orders the same? (Click the Show additional parameters button in the background removal section to see that parameter.) 2. Are the values of spline clamps the same. (Also visible among the additional parameters.) 3. Are the

Re: [Ifeffit] Graphics Problems in ATHENA

Hi Sola, This is the sort of question that should go to the Ifeffit mailing list, so I am taking the liberty of CCing my answer there. I recently encountered a problem with a .prj file in ATHENA. The first issue was the notification that ATHENA may be out of memory and when I checked the

Re: [Ifeffit] phase shift correction

Hi Bindu, Why the peak in the Fourier transform of the experimental spectrum is less than the actual one. The EXAFS equation is: N S02 F(K) chi(k) = --- exp(-2k^2 sigma^2) sin(2kR + phi(k)) 2kR^2 In the oscillatory term, there is a piece

Re: [Ifeffit] excuse me!

Hi Yuzhiguo, This chapter of the Athena manual explains in some detail how to move data into Athena. http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/index.html As you can see there, Athena is capable of importing data without modification from many different beamlines. If

Re: [Ifeffit] space group C-1

Nan, You haven't quite given me enough information to actually help. In this case, I'd need to see the crystallographic reference, or at least the input data, for the problem at hand. This is point #5 at http://cars9.uchicago.edu/~ravel/software/bugs.html. B -- Bruce Ravel

Re: [Ifeffit] The common question!

Hi Pei-chang, Regarding questions 1 and 2: Go to http://xafs.org/Tutorials and read Matt Newville's The Fundamentals of XAFS. Regarding question 3 - 5: On that same page, Matt's and Shelly's tutorials cover that information. This part of the Athena document is also relevant:

Re: [Ifeffit] Using windows apj files on linux

Hi all, I spent some time on an airplane this morning fixing this problem that Josh reported. It should be fixed in the next release. In light of this being a linux-only problem, I will probably make a source code release before the new windows executables are ready. B P.S. In case you

RE: [Ifeffit] Problems with the flatten option in Athena

Flattening involves removing from the data the difference in slope and quadrature between the pre-and post-edge lines. Because this does not make sense in the pre-edge, Athena multiplies this difference array by a step function centered at E0. If your E0 is not somewhere sensible (i.e. in the