June 2015 - Ifeffit - millenia.cars.aps.anl.gov

Linear Combination Fitting problem
by Iuliia Mikulska 13 Sep '15

13 Sep '15

Hello, I'm using Demeter 0.9.21 on Windows 7 (32 bit). I encountering a few problems with Athena. So I wonder if it can be solved in future releases. 1. The names of my spectra are quite long (around 40 characters). The first problem is when I try to import data from Athena project file: appears "Import from Athena project file" window. In this window I can see the name of the spectra only partially and this window can not be resized. So my first question is if the "Import from Athena project file" window can be done resizable? 2. I'm using Athena to perform Linear Combination Fits of my spectra. As I said, the names of my spectra are quite long, so to see the full name in the Athena I need to resize the window. The resizing works fine, but if I change the "Main Window" to "Linear Combination Fitting" then the window of the program resizes back to the standard size and I need again to resize it to see the full name of the spectra. It happens each time when I'm using "Data menu" to access different data processing features. 3. When I performing Linear Combination fits, the results of the fits can not be saved into project. This option was perfectly working in old Athena. Here are steps how to reproduce this problem: 1. I chose the spectrum which I would like to fit with standards. 2. Then I chose a few Standards. 3. Then I press button "Fit this group". 4. Now in "Fit results" tab you can see the results of the fit. Up to this step everything works fine. Now I need to fit next spectra. So I choose next spectra in group list and then I repeat 2-4 aforementioned steps. I again get the proper fit. The problem comes when I would like to check the fit which I did for previous spectrum. So in group list I simply choose the previous spectrum, but "Fit results" tab is empty. "Standards" tab shows the standards used for fit of second spectrum. So you can access the results of the Linear Combination Fitting only immediately after fitting. As soon as you move to another spectrum, fit results for previous spectrum are lost. If you need more information, please let me know. Best regards, Iuliia Mikulska

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Bug report - autosave on mac
by Jean-Baptiste ABBE 16 Jul '15

16 Jul '15

Hi everybody, I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days. Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue. Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens : 1) athena launch, a little bit longer than usual 2) a box appear to give me choice to recover data by importing it from autosave or not 3) I can’t select anaything and the rainbow wheel of death appears. After a few hours, nothing changes… and I have to terminate the programm manually. So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions : https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html> https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.h… <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html> I tried to find the autosave file : nothing I tried to uninstall and reinstall macports : nothing I tried to uninstall macports and install the demeter-devel : nothing In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment. I will try again other solutions, but I will gladly accept any kind of help to solve my issues. Thank you ABBE J-Baptiste

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Be EXAFS and publication
by Joshua Kas 07 Jul '15

07 Jul '15

Hi, This may be a long shot, but I was wondering if anyone is aware of EXAFS data on HCP Be. In particular we are looking for Debye-Waller Factors, so a publication would be great, but just data might work as well. Thanks, Josh Kas

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Question about deglitching EXAFS data
by Francesco Marafatto 07 Jul '15

07 Jul '15

Hello All, I have enjoyed this digest in the past and found it very helpful! I hope it may provide an answer to my question. I am collecting Mn EXAFS data out to k of 15 Å-1, and the data look fine. However, the monochromator (Si 111) has 5 strong 2-point glitches and 3 minor 1-point glitches in one of the regions that I am most interested in (k between 5 and 9 Å-1). My question relates to how many data points I can remove before influencing the data. In my previous experience I have removed 2 or 3 points but never more. I have read through the deglitching section of “XAFS for Everyone”, and think that I could oversample the EXAFS (with k steps of 0.03 Å-1 vs 0.05 Å-1), but most of the data have already been collected. Is there a rule of thumb about deglitching? In other words, is there a limit to the number of bad points I can eliminate for an EXAFS scan to k of 15 Å-1? Thanks and looking forward to hearing your thoughts, Francesco Francesco Femi Marafatto francesco.marafatto(a)unil.ch FNS PhD student, Environmental Geochemistry Laboratory IDyST - FGSE Bureau 3233 Gèopolis Université de Lausanne CH-1015 Lausanne T. +41 (0)21 692 4451

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Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 26
by Nils Skoglund 27 Jun '15

27 Jun '15

Hello Everton, Matt and Pushkar, Thank you for your replies. I have tried both the 32-bit and 64-bit versions with uninstalling in between, to no avail. I'm curious if it is a priority issue between the dual GPU's on the laptop that gnuplot can't handle well; there's both a dedicated GPU and an integrated one. System temperatures look normal and none of the fans are revving up, so it shouldn't be heat-related. Other softwares handle plotting without issues so the suggestion about gnuplot being the culprit seems like the most reasonable one. If I narrow this issue down and find a way to work around it, I'll let you know. Until then I'll just find some other workstation for the evaluation work - thanks again! //Nils -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: den 26 juni 2015 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 148, Issue 26 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Issues with Athena on high-performance systems (pushkar shejwalkar) 2. Re: Issues with Athena on high-performance systems (ebonturim(a)usp.br) ---------------------------------------------------------------------- Message: 1 Date: Fri, 26 Jun 2015 10:05:23 +0900 From: pushkar shejwalkar <pshejwalkar2004(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Issues with Athena on high-performance systems Message-ID: <CAN0ZRcEm=2KRDeXO-=t60yDZHwT4Rp8Zzs6pwPSbt7ndiQBGCg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi all, I am not an expert in this. In fact , I am one of the very new user of athena. But have you tried uninstalling and then reinstalling the whole package again? ( I am sure you have but since you didnt mentioned just wondering?) Sometimes, that also helps. not sure why and how? but it did for me. Pushkar On Fri, Jun 26, 2015 at 5:00 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > 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. > Athena rarely makes a very big dent in the system resources (well, > comparable to a web browser, so a bit of a hog, but well under 1Gb RAM). > > Perhaps what you're seeing is related to the plotting with Gnuplot. > I'm not sure why that would be a problem... Any ideas? > > --Matt > > Hi, > > > > I?m curious if anyone else is experiencing issues with Athena in more > high-end systems running Windows 7? While I am used to having to wait > for the *first* plot to show up, the software is virtually unusable > to me now where any slight change (e.g. modifying range for the > spline) to already imported data takes up to over a minute to replot. > This didn?t use to be the case for me. The system is a laptop running > Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space > on the hard drives and a dedicated Intel HD 4600 graphics circuit. > > > > If anyone has a work-around for this problem or can suggest anything > to make Athena usable again, it would be most appreciated. Has anyone > noticed previous versions of Athena running more smoothly? > > > > Best regards, > > Nils > > > > *------------------------------------------------------------------* > > *Nils Skoglund, Ph.D.* > Post-doctoral researcher > > Energy Science > Department of Engineering Sciences and Mathematics Lule? University of > Technology > SE-971 87 Lule? > Sweden > > > > Cell : +46 (0)72 529 52 08 > > Web page: http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en > > Publications: http://www.researcherid.com/rid/D-3493-2011 > > *-------------------------------------------------------------------* > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Sapporo, Japan

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Issues with Athena on high-performance systems
by Nils Skoglund 25 Jun '15

25 Jun '15

Hi, Im curious if anyone else is experiencing issues with Athena in more high-end systems running Windows 7? While I am used to having to wait for the first plot to show up, the software is virtually unusable to me now where any slight change (e.g. modifying range for the spline) to already imported data takes up to over a minute to replot. This didnt use to be the case for me. The system is a laptop running Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space on the hard drives and a dedicated Intel HD 4600 graphics circuit. If anyone has a work-around for this problem or can suggest anything to make Athena usable again, it would be most appreciated. Has anyone noticed previous versions of Athena running more smoothly? Best regards, Nils ------------------------------------------------------------------ Nils Skoglund, Ph.D. Post-doctoral researcher Energy Science Department of Engineering Sciences and Mathematics Luleå University of Technology SE-971 87 Luleå Sweden Cell : +46 (0)72 529 52 08 Web page: <http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en> http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en Publications: <http://www.researcherid.com/rid/D-3493-2011> http://www.researcherid.com/rid/D-3493-2011 -------------------------------------------------------------------

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Artemis on IOS Yosemite 10.10.3
by ebonturim＠usp.br 25 Jun '15

25 Jun '15

Hi guys, Anyone know why Artemis don't work in IOS 10.10.3? I can use the Athenas and Hephaestus, but when I type artemis on Terminal screen, I see this message: _______________________________________________________ Evertons-MacBook-Pro:~ ebonturim$ artemis Can't locate Math/Round.pm in @INC (@INC contains: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter.pm line 306. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Artemis.pm line 26. Compilation failed in require at /opt/local/bin/artemis line 34. BEGIN failed--compilation aborted at /opt/local/bin/artemis line 34. Evertons -MacBook-Pro:~ ebonturim$ _______________________________________________________ Someone could help me? Thank you! Best, Everton.

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Hephaestus edge step calculation
by Guanghui Zhang 22 Jun '15

22 Jun '15

Hello, Bruce. Thanks very much for writing and keeping upgrading the amazing software. I was mainly doing homogeneous catalysis, so most of my samples were solution samples. I found that it was quite convienent to calculate the absoption length and edge step using the old version Hephaestus (ifeffit 1.2.11). Simply go to the Formulas tab, choose Molarity, type in the formula, molarity, and energy. The calculation results will show up after clicking the Compute button. For example, if I type in the Formula as Pt, molarity as 0.03 mol/L and Energy as 11564 eV (Pt L3 edge), the calculation results showed as follows: element number barns/atom cm^2/gm --------- ---------------------------------- Pt 1.000 63044.107 194.641 This weighs 195.090 amu. Absorbtion length = 0.878 cm at 11564.00 eV for a 0.03 molar sample. Unit edge step length at Pt L3 edge (11564.0 eV) is 15108.1 microns Remember that a molarity calculation only considers the absorption of the solute. The solvent also absorbs. The Elam database and the total cross-sections were used in the calculation. However, in the new version Hephaestus (Demeter 0.9.22, trial version 4, Windows 8 64 bit). It does not work. If I type the same informaiton, Pt, 0.03 mol/L, 11564 eV. The following results showed up. element number barns/atom cm^2/gm --------- ---------------------------------- Pt 1.000 63044.107 194.641 This weighs 195.090 amu. Absorption length = 0.0 micron at 11564 eV for a 0.03 molar sample. Unit edge step length at Pt L3 edge (11564.0 eV) is 0.0 microns Remember that a molarity calculation only considers the absorption of the solute. The solvent also absorbs. The Elam database and the full cross-sections were used in the calculation. If I do the calculation for the solid samples using "density" instead of "Molarity", the calculation worked fine. I am wondering if there is any problem with my softwar and/or laptop, or there is a missing function in the new version Hephaestus. Thanks Guanghui 2015-06-18

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Re: [Ifeffit] "Simple" question/s about fuzzy degeneracy
by Juan Manuel Conde Garrido 22 Jun '15

22 Jun '15

Thanks again!I'm so sorry, I had missed the "Aggregate" button (I think I pushed it once, but got deterred by the warning message).I got the path list that I wanted now and thanks to your explanation, I understood how the math works.Sorry for my silly newbie mistake and thanks again!Juan El Lunes, 22 de junio, 2015 8:30:39, Bruce Ravel <bravel(a)bnl.gov> escribió: On 06/20/2015 09:19 AM, Juan Manuel Conde Garrido wrote: > Thanks Bruce for the quick response! > I understood perfectly how to get from table 1 to table 2. > I'm still a little lost on how to use that in Artemis. > You said: "Artemis has compressed the three Feff calculations you would > normally have to do into a single fuzzily degenerate path list." > That's the thing I don't know how to do. > How do I use Artemis to get the scattering paths listed in table 2 (Reff > and degeneracy) > What would be the step by step procedure in Artemis to get those paths > so I can move them to the Path page? So, I concur that this page of the document http://bruceravel.github.io/demeter/artug/feff/aggregate.html is somewhat terse, but it seems clear to me. I don't understand what's confusing to you. You press the button, Artemis does some stuff, Artemis displays a bunch of paths. It works just like a normal Feff calculation. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ El Lunes, 22 de junio, 2015 8:30:39, Bruce Ravel <bravel(a)bnl.gov> escribió: On 06/20/2015 09:19 AM, Juan Manuel Conde Garrido wrote: > Thanks Bruce for the quick response! > I understood perfectly how to get from table 1 to table 2. > I'm still a little lost on how to use that in Artemis. > You said: "Artemis has compressed the three Feff calculations you would > normally have to do into a single fuzzily degenerate path list." > That's the thing I don't know how to do. > How do I use Artemis to get the scattering paths listed in table 2 (Reff > and degeneracy) > What would be the step by step procedure in Artemis to get those paths > so I can move them to the Path page? So, I concur that this page of the document http://bruceravel.github.io/demeter/artug/feff/aggregate.html is somewhat terse, but it seems clear to me. I don't understand what's confusing to you. You press the button, Artemis does some stuff, Artemis displays a bunch of paths. It works just like a normal Feff calculation. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ El Lunes, 22 de junio, 2015 8:30:39, Bruce Ravel <bravel(a)bnl.gov> escribió: On 06/20/2015 09:19 AM, Juan Manuel Conde Garrido wrote: > Thanks Bruce for the quick response! > I understood perfectly how to get from table 1 to table 2. > I'm still a little lost on how to use that in Artemis. > You said: "Artemis has compressed the three Feff calculations you would > normally have to do into a single fuzzily degenerate path list." > That's the thing I don't know how to do. > How do I use Artemis to get the scattering paths listed in table 2 (Reff > and degeneracy) > What would be the step by step procedure in Artemis to get those paths > so I can move them to the Path page? So, I concur that this page of the document http://bruceravel.github.io/demeter/artug/feff/aggregate.html is somewhat terse, but it seems clear to me. I don't understand what's confusing to you. You press the button, Artemis does some stuff, Artemis displays a bunch of paths. It works just like a normal Feff calculation. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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"Simple" question/s about fuzzy degeneracy
by Juan Manuel Conde Garrido 20 Jun '15

20 Jun '15

Hi everyone, I'm somewhat new to EXAFS and this is my first question for the Ifeffit mailing list (which is a great source of information by the way).I was reading the excellent paper: "Path degeneracy and EXAFS analysis of disordered materials" and I have a "simple" question to ask:How do I get from table 1 to table 2? Specifically, I think I know how to use fuzzy degeneracy in Artemis for the paths in one FEFF calculation, but in this case there are 3 sites for Ti, and that means 3 FEFF calculations (rigth?). So how do I use fuzzy degeneracy for paths from different FEFF calculations? And by the way, is it right if I imagine the material as having only 1 "fuzzy"/average site for Ti? Thanks in advance Juan ****************************** ****************************** ****************************** *********Dr. Juan Manuel Conde GarridoLaboratorio de Sólidos AmorfosDepartameno de Física, Facultad de Ingeniería, Universidad de Buenos Aires INTECIN (UBA-CONICET) Av. Paseo Colón 850 C1063ACV - Ciudad de Buenos Aires ARGENTINA Tel: +54 (11) 4343-0893/4343-0092 (Int. 1101) http://intecin.fi.uba.ar ****************************** ****************************** ****************************** *********

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