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

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite
by Raimundo Lora Serrano 22 Sep '15

22 Sep '15

Dear all, I have the same problems installing Athena/Demeter on Yosemite (10.10.5) as Remi. Also in my case (as for Rémi) - I use the Rémi’s message edited as required to my softwares’ versions: > Athena launches well from the Terminal, I have the > main window (perl5.22), I can import data or load former athena projects > etc, but there is no plot window. No error message shows up in the > terminal. > I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode Version 7.0 (7A220), > agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. > I runned the "sudo port -v selfupdate" command > Then "sudo port install demeter-devel” > And port upgrade outdated to ensure everything is up to date > Plus, I have XQuartz 2.7.7 installed. I also uninstalled and reinstalled macports (and Xcode, xquartz) but the problem remains. By typing echo $DISPLAY /private/tmp/com.apple.launchd.RgzrDheMAp/org.macosforge.xquartz:0 Any guess? Many thanks in advance. Raimundo > Em 21/09/2015, à(s) 14:00, ifeffit-request(a)millenia.cars.aps.anl.gov escreveu: > > 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. No plot window in Athena/Demeter on Mac OS X Yosemite > (R?mi BELISSONT) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 21 Sep 2015 14:57:34 +0200 > From: R?mi BELISSONT <remi.belissont(a)univ-lorraine.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] No plot window in Athena/Demeter on Mac OS X > Yosemite > Message-ID: <6D35429A-8B4F-42FA-BA4D-92407447F7A9(a)univ-lorraine.fr> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I?m currently using Athena using the iXAFS 3.0.3 application, which is ? if I?ve well understood ? an old version no longer updated (http://cars9.uchicago.edu/ifeffit/Downloads <http://cars9.uchicago.edu/ifeffit/Downloads>). > > So, today I tried to install the current version by installing Demeter, following the procedure detailed at http://bruceravel.github.io/demeter/ <http://bruceravel.github.io/demeter/>. > > I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. > I runned the sudo port -v self update command > Then sudo port install xorg-server demeter > And port upgrade outdated to ensure everything is up to date > Plus, I have XQuartz 2.7.7 installed. > > Here is my problem. > Athena launches well from the Terminal (in home directory), I have the main window (pearl5.22), I can import data or load former athena projects etc, but there is no plot window. No error message shows up in the terminal. However I can still produce a PNG of the plot I?m desperately trying to see via Plots/Save last plot as... > > I?ve seen a similar thread concerning such an issue in OS X Mavericks but couldn?t solve it from what was explained there (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html>). I guess the issue comes from the DISPLAY environment but I don?t have any clue to solve that. > > Thank you in advance for your help, > I think it may be useful for other users, > > Kind regards, > > R?mi > > > ??????????????????????????????????????? > R?mi Belissont > Ph.D. Student | Universit? de Lorraine ? Labex R21 > > GeoRessources > CNRS-UMR 7359, Facult? des Sciences > BP 70239, 54506 Vandoeuvre-l?s-Nancy Cedex, France > Phone +33 (0)3 83 68 47 14 > > Centre de Recherches P?trographiques et G?ochimiques > CNRS-UMR 7358, 15 Rue Notre Dame des Pauvres > BP 20, 54501 Vandeuvre-l?s-Nancy Cedex, France > >

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No plot window in Athena/Demeter on Mac OS X Yosemite
by Rémi BELISSONT 21 Sep '15

21 Sep '15

Hello, I’m currently using Athena using the iXAFS 3.0.3 application, which is – if I’ve well understood – an old version no longer updated (http://cars9.uchicago.edu/ifeffit/Downloads <http://cars9.uchicago.edu/ifeffit/Downloads>). So, today I tried to install the current version by installing Demeter, following the procedure detailed at http://bruceravel.github.io/demeter/ <http://bruceravel.github.io/demeter/>. I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. I runned the sudo port -v self update command Then sudo port install xorg-server demeter And port upgrade outdated to ensure everything is up to date Plus, I have XQuartz 2.7.7 installed. Here is my problem. Athena launches well from the Terminal (in home directory), I have the main window (pearl5.22), I can import data or load former athena projects etc, but there is no plot window. No error message shows up in the terminal. However I can still produce a PNG of the plot I’m desperately trying to see via Plots/Save last plot as... I’ve seen a similar thread concerning such an issue in OS X Mavericks but couldn’t solve it from what was explained there (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html>). I guess the issue comes from the DISPLAY environment but I don’t have any clue to solve that. Thank you in advance for your help, I think it may be useful for other users, Kind regards, Rémi ––––––––––––––––––––––––––––––––––––––– Rémi Belissont Ph.D. Student | Université de Lorraine – Labex R21 GeoRessources CNRS-UMR 7359, Faculté des Sciences BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex, France Phone +33 (0)3 83 68 47 14 Centre de Recherches Pétrographiques et Géochimiques CNRS-UMR 7358, 15 Rue Notre Dame des Pauvres BP 20, 54501 Vandeuvre-lès-Nancy Cedex, France

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Pain of SSRL file formats
by Webb, Samuel M. 17 Sep '15

17 Sep '15

I do agree with many of the previous comments on the state of SSRL binary XAS formats and I certainly won't defend them -- they are horrid and it took me quite a long time to figure out the format so that SIXPACK and others could read them. Tragically, the format goes way back to the VMS days and is essentially in my view under to unsupported. From my past experience, most of the problems I have had with the binary files is transferring them across FTP sites, where a bad choice of data transfer formats (non-explicit binary transfer) has been chosen. That tends to forever corrupt the file and it needs to be reFTP'd to be at all useable. This in itself is the main reason why I never use the binary data format. The only real program that appears actually want to deal with SSRL binaries is EXAFSPAK. Many people who like the VMS data collector still use the old data collection system, and that's a fine user preference. In those instances, those users will need to deal with their data in that preferred format, and if they chose to use that old collector, then I would normally presume that they know how to deal with that data. However, there is no need for any user from SSRL to need to use the antiquated binary data formats. All the beam lines that have that somewhat ancient data collector all have an ASCII transfer utility and users (should) be told about that utility when they arrive. Thus, there is no excuse for someone to have to deal with data in a binary format if they don't want to. As for other beam lines (as well as XAS beam lines that are not on VMS anymore), there are newer XAS data collectors that collect data only in ASCII formats. Granted, it is the slightly screwy SSRL ASCII still, in some effort to be backward compatible, but it is at least readable and manageable. On a separate note, I find that many users (and sometimes support personnel) will edit the standard beam line detector definitions to a point where many data analysis programs that I use (read SIXPACK) cannot read the data either. That said, the newer data collectors at the beam line should (and do) produce readable data that should (and is) easily managed by both Athena as well as many other programs (at least SIXPACK). I haven't always followed the current trend in data file formats for XAS - has anyone ever decided on a common data format, or at least an interchange format? Sam

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Binary SSRL Files crash upon import.
by Logan Giles 17 Sep '15

17 Sep '15

Hello everyone, I am running Demeter 0.9.22 and trying import recent SSRL Binary files. I have the SSRL plugins enabled as well. The problem is when I try to import binary files, the program crashes. It seems that something might have changed recently in SSRL BL 7-3 files because I can import July 2013 files but not July 2015. I have attached a NaMoO4 sweep at the Mo K-edge from each run for your testing. Immediately after trying to import the binary July 2015 files, the program immediately crashes and exits. The July 2013 binary opens right up. When I look at the dathena.log file for the "2015 crash", everything looks normal until the end: "Demeter version 0.9.22 At line 316 of file iff_rddata.fFortran runtime error: End of record" Also, when I try to import the ascii files of the July 2013 or July 2015 data, I get an error as well, but the same error. I can fix this by changing two of the blank rows, which are the column labels for the data, to "BLANK" or something. I have attached these unedited ascii files as well, but I am more concerned with my binary problem. The reason for this is that I was recently sent some other SSRL binary files without their corresponding ascii files that also crash. Let me know that you think, or if you can reproduce the error in trying to import the binary files. Thanks for your assistance and best regards, -Logan

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EXAFS signal from dopant atoms
by Eugenio Paris 17 Sep '15

17 Sep '15

Dear all, I have a very general question about EXAFS analysis. Let's take as example a binary system AB in which i am substituting the atom B with another atom C so that we have AB(1-x)C(x). Let us imagine that we know the structure of binaries AB and AC with Rab and Rac atomic distances and we know that in AB(1-x)C(x) the substitutional site will be 100% the B-site. If I measure the EXAFS spectrum of atom C as a function of "x" what can I expect for the EXAFS oscillations? My idea is that when "x" is very small the EXAFS will be highly noisy and damped, while as "x" increases the oscillations will become more evident above the noise level. How to model this situation to get information on C-A bond? In Athena I can start with the .cif file of AC structure with full occupancy and obtain the distance and the DWF for the A-C bond but.. how to treat the signal-to-noise ratio? I mean, as "x" decreases I think there must be a leaking out of the EXAFS signal, should this effect be introduced in S0^2? Or can it affect the effective number of neighbors? Hope I explained myself, thank you! Eugenio Paris PhD student, University of Rome (Italy)

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ATOMS for XANES simulation by FEFF8.4
by María Elena Montero Cabrera 16 Sep '15

16 Sep '15

Dear all, I am trying to "produce" a new feff.inp using the space group, the asymmetric unit and related data of a compound, for simulating XANES by using FEFF8.4. Long time ago I have used the program "WebAtoms" for obtaining the file, and afterwards I used to edit it, as you have to "uncomment" some lines and "comment" others to run FEFF for XANES. However, in the "Artemis-Demeter" program you have ATOMS also, and Bruce explicitly tells you that the old WebAtoms is not "supported". When I run my data from my compound in Artemis the feff.inp file I have obtained looks, at least for me, different from that I have expected for running XANES in FEFF. Please, tell me what I have to do. Should I use the old Atoms, or I have to tell Atoms in Artemis that I want a "XANES" feff.inp? How can I do it? Thanks a lot in advance María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123 http://redtuls.org/

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[Resolved] Issues with Athena, first posted 2015-06-25 - Kaspersky antivirus caused the problems
by Nils Skoglund 16 Sep '15

16 Sep '15

Hi, I finally figured out what was causing the horrible performance of Athena on my system; as in all too many cases the antivirus policies of enforced by system managers was the culprit. Every time a change was made in Athena (e.g. using a drop-down menu) the shell would freeze for several seconds while the Kaspersky antivirus scanned whatever function was called, what Athena had stored in RAM and such before allowing the function call to proceed. The same was repeated for the renewing of plots in gnuplot, which is why I initially thought it was related to gnuplot. Once I managed to persuade our IT-staff that my user should have the permission to kill off that process, everything in Athena was working like a charm. In short, beware Kaspersky if you are not permitted to set exceptions for certain software due to local security policies at your university or institute. Best regards, Nils Skoglund -----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 27 juni 2015 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 148, Issue 27 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: Ifeffit Digest, Vol 148, Issue 26 (Nils Skoglund) ---------------------------------------------------------------------- Message: 1 Date: Sat, 27 Jun 2015 09:59:01 +0200 From: "Nils Skoglund" <nils.skoglund(a)ltu.se> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 26 Message-ID: <005901d0b0af$220d5990$66280cb0$(a)ltu.se> Content-Type: text/plain; charset="us-ascii" 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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Linear Combination Fitting problem
by Iuliia Mikulska 14 Sep '15

14 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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No plot window in Athena/Demeter on Mac OS X Yosemite
by Rémi BELISSONT 10 Sep '15

10 Sep '15

Hello, I’m currently using Athena using the iXAFS 3.0.3 application, which is – if I’ve well understood – an old version no longer updated (http://cars9.uchicago.edu/ifeffit/Downloads) So, today I tried to install the current version by installing Demeter, following the procedure detailed at http://bruceravel.github.io/demeter/. I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. I runned the sudo port -v self update command Then sudo port install xorg-server demeter And port upgrade outdated to ensure everything is up to date Plus, I have XQuartz 2.7.7 installed. Here is my problem. Athena launches well from the Terminal (in home directory), I have the main window (pearl5.22), I can import data or load former athena projects etc, but there is no plot window. No error message shows up in the terminal. However I can still produce a PNG of the plot I’m desperately trying to see via Plots/Save last plot as... I’ve seen a similar thread concerning such an issue in OS X Mavericks but couldn’t solve it from what was explained there (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html) I guess the issue comes from the DISPLAY environment but I don’t have any clue to solve that. Thank you in advance for your help, I think it may be useful for other users, Kind regards, Rémi

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Re: [Ifeffit] Deglitching
by Bruce Ravel 10 Sep '15

10 Sep '15

On 09/04/2015 01:37 PM, Robert Gordon wrote: > > I can confirm something funny is happening here. In 0.9.21, the deglitch > menu would not display > points. I upgraded to 0.9.22 today and deglitch now displays points, but > when I choose a point > in a test data file (As2O3) and double-click, the energy point removed > is 11804.228, regardless of where > I double-click. I reverted back to 0.9.21 and with the same dataset, > this did not occur. In 0.9.21, > double-click removed the closest point to where I clicked. > > I have win10pro x64 and installed the 64-bit versions of 0.9.21, .22 Can we *please* use the mailing list for these things. It is helpful to the next person who runs into these issues if a discoverable record is left behind. Using the preference tool, can you tell me what the value for gnuplot->terminal is? If it is something other than "wxt", try changing it to "wxt". The interaction with the cursor does not work correctly on some terminals. If that's not the problem, then I am at a loss. I don't see this behavior on any of my computers. 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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