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

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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Fwd: FEFF trouble help me please !!!!
by Bruce Ravel 07 Jul '15

07 Jul '15

Hi, I want to remind everyone that it is important to use the mailing list. I do not feel that I am obligated to answer questions about the software that come to me by any other channel, particularly when I do not have a personal relationship with the person asking the question. That said, I am forwarding this fellow's question to the mailing list and providing an answer. Thitipong, this is a case of GIGO. According to Acta Cryst. (1972). B28, 3102-3103 (the reference I found for Cr23C6): The crystal structure of chromium carbide, C r 2 3 C 6 , has been described as cubic, space group Fm3m, 4Cr (I) in (a) (000), 8Cr (II) in (c) (l-lq:), 48Cr (III) in (h) (Oxx), x= 0.165, 32Cr (IV) in (f) (xxx), x=0.385, 24C in (e) (x00), x=0-275 (Westgren, 1933) on the basis of X-ray single crystal and powder diffraction data. We have confirmed this structure and determined the atom positions more precisely by a neutron diffraction study of a powder sample. Using those coordinates, I have no problem running atoms and feff. The structure is a bit strange -- I guess this is more like a metal than a carbide -- but it seems consistent with the paper after a cursory inspection. According to http://www.crystallography.net/cod/1009019.html, the space group for Cr7C3 is P M C N. Atoms and feff run fine with this input data. Some hints on asking questions that so you'll get the answers you are looking for: http://bruceravel.github.com/demeter/pods/bugs.pod.html http://bruceravel.github.com/demeter/pods/help.pod.html B -------- Forwarded Message -------- Subject: FEFF trouble help me please !!!! Resent-Date: Fri, 3 Jul 2015 04:25:57 +0000 Resent-From: bruce.ravel(a)nist.gov Date: Fri, 3 Jul 2015 11:33:12 +0700 From: Thitipong Po-Kloy <thitipong_37(a)hotmail.com> To: bruce.ravel(a)nist.gov <bruce.ravel(a)nist.gov> Hi Bruce , My name is Thitipong . I have trouble about FEFF program and believes you can help me. Now I am doing "XANES simulation" Cr23C6 and Cr7C3 . So , when I run FEFF program - it report TWO ATOMS VERY CLOSE TOGETHER . How can I fix it ? This it Data of atom Cr23C6 title name : Cr23C6 title formula : Cr23C6 space F M 3 M a=10.6599 b=10.6599 c=10.6599 rmax = 10 core=Cr1 atom Cr 0 0 0 Cr1 Cr 0.25 0.25 0.25 Cr2 Cr 0.385 0.385 0.385 Cr3 Cr 0 0 0.340 Cr4 C 0.276 0.276 0.276 C1 and Cr7C3 title name : Cr7C3 title formula : Cr7C3 space P M C M a=7.0149 b=12.1530 c=4.5320 rmax = 10 rpath=6 core=Cr1 atom Cr 0.064 0.811 0.056 Cr1 Cr 0.250 0.626 0.057 Cr2 Cr 0.250 0.206 0.250 Cr3 Cr 0.250 0.416 0.261 Cr4 Cr 0.065 0.021 0.250 Cr5 C 0.250 0.562 0.459 C1 C 0.029 0.342 0.028 C2 If there is any other way please let me know. Thank You , Thitipong -- 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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Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 07 Jul '15

07 Jul '15

Sorry for not noticing. The log files are attached now. It is pretty much the same for all three cases of Athena, Artemis and Hephaestus. Ganesh > > Message: 2 > Date: Mon, 06 Jul 2015 08:18:08 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp > Message-ID: <559A7200.9050207(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 07/04/2015 06:10 PM, Ganesh Subramanian wrote: > > Hi. > > > > This is Ganesh and I am a first time user of the Demeter accessories. > > > > I downloaded and installed the files from the github site using the > > 0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7 > > on my Macbook Pro (2012). It seemed to have installed fine, but the > > moment I click on the icons to open any of Athena, Artemis or > > Hephaestus, all of them show a command window, thats empty, and in a few > > seconds crash and close. No error windows or command line error prompts. > > > > Any idea on what might be wrong ? > > > It is basically impossible to answer a question like this without a look > at the log file, as explained here: > > http://bruceravel.github.io/demeter/pods/bugs.pod.html > > 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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Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 06 Jul '15

06 Jul '15

Hi. This is Ganesh and I am a first time user of the Demeter accessories. I downloaded and installed the files from the github site using the 0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7 on my Macbook Pro (2012). It seemed to have installed fine, but the moment I click on the icons to open any of Athena, Artemis or Hephaestus, all of them show a command window, thats empty, and in a few seconds crash and close. No error windows or command line error prompts. Any idea on what might be wrong ? Thanks, Ganesh

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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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