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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 26 Jun '15

26 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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Questions on Correlated Debye in FEFF6
by Bennett, Doran (D) 19 Jun '15

19 Jun '15

Hi Everyone, I have just recently begun learning about EXAFS and running EXAFS simulations using FEFF6. I have a few very basic questions about the underlying calculations for the correlated Debye model implemented in FEFF6 (called by "DEBYE" keyword). For the questions below, I am assuming I input a single crystallographic structure and want the correlated Debye model to simulate the influence of a thermal distribution on the EXAFS spectrum. I would appreciate any insight you can give me into the questions below. I would also welcome any and all references for the original papers where that is appropriate. 1. Are the Debye-Waller factors calculated for each path individually? (It seems like they should be since the paths will have different levels of influence from the thermal distribution of atomic positions) 2. Assuming the DW factors are calculated path-by-path, is the magnitude of the DW factor determined by assuming the total path length R is the appropriate length to use for the correlation term in the Debye spectral density? It seems like it would not be reasonable to treat all paths of the same R as having the same Debye-Waller factor since a single scattering path and multiple scattering paths are perturbed by a different set of relative atomic motion that are likely to have different correlations. I couldn't locate a clear statement about how this calculations is actually done within the code. 3. Is the C1 shift that results from the vibrational motion normal to the bond axis along a path incorporated in the calculation? (Presumably using \Delta C1 = sigma_perp^2/(2<r>)) And is this formula still appropriate in multiple-scattering paths? 4. Assuming the C1 shift is incorporated, does the correlated Debye model assume that the perpendicular and parallel displacements have the same spectral density? Thank you for the assistance! Doran Doran I. G. Bennett The Dow Chemical Company Core R&D, Inorganic Material and Heterogeneous Catalysis Phone: (610)-244-7062 Alternate Phone: (630)-222-2906

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Reference for Setting k range in EXAFS analysis
by Navneet Singh 19 Jun '15

19 Jun '15

Dear All Can I get some study material mentioning how to set the K-range for EXAFS analysis. With best regards Navneet Singh

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Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 13
by M. Janeth LOZANO RODRIGUEZ 11 Jun '15

11 Jun '15

Dear all, It's true and precise your remark Fred. With Demeter 9.21, the Feff 8.2 is running properly in Demeter Atoms or well in Artemis, but at the moment to get the paths they are not present. But if you right click with the mouse, you can READ the geometry for the paths but with a error message : Demeter:UI:Artemi Error Couldn't retrieve information about list control item -1 ... from my eyes it seems to be something related with Demeter's pathfinder but I'm not an expert Anyway, also thanks Guanghui for your comments that help us to understand where is coming from this problematic. Could be great if in the future someone could find/propose a solution Kind regards Janeth On 10/06/2015 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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. how to manage Demeter with a newer FEFF version ? > (fred.mosselmans(a)diamond.ac.uk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 10 Jun 2015 07:42:35 +0000 > From: <fred.mosselmans(a)diamond.ac.uk> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] how to manage Demeter with a newer FEFF version ? > Message-ID: > <CF65047C5B0562499EAFF9FBBC542D649FB4EBBF(a)EXCHMBX01.fed.cclrc.ac.uk> > Content-Type: text/plain; charset=us-ascii > > Dear Janeth, > > Feff8.5L (and presumably 8.4) works in some fashion in Demeter version 18.2 , in later versions it doesnt. : It runs through atoms and gives fits that seems sensible for transuranic elements in the times I and some of my collaborators have used it. > > Thus in the short term if you want to use something higher than FEFF6 in your exafs calculations and want to use Demeter that's your option, > > If you need to use FeFF9 and want to use Demeter: I think your best option is to have a go at persuading some of the software guys at your facility to collaborate with Bruce and Matt in adding a FEFF9 option to larch and in turn then Demeter. > > Best wishes > Fred > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 08 Jun 2015 11:13:33 +0200 > From: "M. Janeth LOZANO RODRIGUEZ" <janeth.lozano-rodriguez(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] how to manage Demeter with a newer FEFF version ? > Message-ID: <55755CBD.6010007(a)esrf.fr> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear XAFS community, > > I wondering about the availability to use a newer FEFF version in > Demeter. Since my knowledge only I can run FEFF6. In my case I found > different discrepancies using FEFF6 and FEFF9 in the determination of > bond length distances for instance. In terms of review of papers, > reviewers ask to use a newer version instead FEFF6. These points > strongly suggest me coming back to the obsolete Athena/Artemis version. > > On this obsolete version, you can download the paths generated by FEFF8, > FEFF9. This issue is really useful when we have access to FEFF 9, for > example. Is there any option to implement this nice feature in Demeter? > Does anyone have an idea how to do it? > > Kind regards > Janeth Lozano > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 148, Issue 10 > **************************************** >

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new build of the Demeter installer for Windows
by Bruce Ravel 11 Jun '15

11 Jun '15

Hi all, I have made quite a few changes to my analysis software in recent weeks in response to comments on the mailing list. I think that everything from recent weeks is in the latest build in some form. I am not quite ready to declare this a proper release with a new version number, so it can be found at http://bruceravel.github.io/demeter/#windows as "Pre-release trial version #4". Among other things, this corrects the recent deglitching problem, adds support for linear polarization in the Feff calculation, and attempts to streamline the plotting of a sum of paths (see the top of the Actions menu in the data window). I would be grateful if the two people who recently asked about polarization (Shaoib Muhammad and Anna Wolska) could try Artemis and let me know if you think it is working correctly. I have done quite a bit of testing, but one never knows.... I am not 100% confident that everything is implemented quite right. I could easily have missed something... See the change log at https://github.com/bruceravel/demeter/blob/master/Changes.org for the changes that are in this trial version. Cheers, 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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