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

XAFS short course in BNL on Nov 5-7
by Anatoly I Frenkel 14 Oct '15

14 Oct '15

Dear subscribers, As a follow up to my previous message, the web page for the XAFS short course at Brookhaven and the application form are live: http://workshops.ps.bnl.gov/?w=XAFS2015 Please note the application deadline, September 20. Best regards, Anatoly Anatoly Frenkel, Ph.D. Professor and Chair, Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu<mailto:anatoly.frenkel@yu.edu>

1 2

Problems importing larch plugins to python
by Johan Nilsson 05 Oct '15

05 Oct '15

Hello everyone, I recently installed the latest development version of larch from github and now I'm having some problems importing larch plugins to my python scripts. I read in the documentation that there is a new method for doing this but that the old way should still work, this is what happens if I try to do it the way I've done it before: johan@johan-Latitude-E6430:~$ python Python 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from larch import use_plugin_path >>> use_plugin_path('xafs') >>> from pre_edge import pre_edge Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/johan/.larch/plugins/xafs/pre_edge.py", line 13, in <module> from larch_plugins.std import parse_group_args ImportError: No module named larch_plugins.std >>> I also tried the new method described in the docs: johan@johan-Latitude-E6430:~$ python Python 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import larch >>> from larch_plugins.xafs import autobk Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named larch_plugins.xafs >>> I'm running ubuntu 14.04. Any ideas of what is going on here? Best regards, Johan

3 10

Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)
by Jana Padeznik Gomilsek 29 Sep '15

29 Sep '15

It is very hard to measure or to calculate absolute absorption data, especially in the vicinity of the absorption edges and especially in the soft x-ray region. Therefore there are significant differences between the tables and I think nobody knows which are better. Chantler, for example, says the expected uncertainties of the tables in your region are 50 % to 100 % (http://physics.nist.gov/PhysRefData/FFast/Text2000/sec06.html#tab2) I would doubt the Chantler's L3+.1 number, all other numbers look ok - this is what you can get. jana padeznik gomilsek > Message: 3 > Date: Wed, 23 Sep 2015 18:02:08 -0700 > From: Matthew Marcus<mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Problem with Hephaestus at Ca L-edges > Message-ID:<56034B90.70405(a)lbl.gov> > Content-Type: text/plain; charset=utf-8; format=flowed > > I wanted to work out the edge-jump ratio between the L3 and L2 edges of Ca using Hephaestus. I ran into two problems: > > 1. The ratio implied by what it says for the unit-edge-step thickness does not agree with that derived by computing the absorption (cm^2/gm) above and below each edge and > dividing the difference (L3+ - L3-)/(L2+ - L2-). > > 2. The results differ wildly depending on which resource I use: > > L3-.1 L3+.1 L2-.1 L2+.1 (L1+ - L1-)/(L2+ - L2-) > Elam 4759.796 27837.796 27478.018 38434.277 2.106375908 > Chantler 4322.6 6547.121 32827.61 35436.543 0.852655473 > Cromer-Leiberman 4288.524 33471.375 32786.294 47072.991 2.042659055 > > The Henke table doesn't yield an L2 edge jump at all, while the Shaltout yields the same results as Cromer-Leiberman. Which one should I trust and why? > > This is old-style H. (V0.18), not Demeter. > mam > >

4 11

Problems during copper (II) oxide data treatment
by Pedro F B D Martins 24 Sep '15

24 Sep '15

Hi everyone, I’m having problems during the data treatment. The two samples (please find the project attached with the as-obtained data only, not with the following treatment) are of CuO (copper (II) oxide) were measured in a row and both were measured together with a reference (Cu foil). I have some doubts: 1) The first thing that I did was to calibrate the Reference of the first measurement (peak at maximum of first derivative). Next, I aligned the second Reference keeping the first reference as standard. Did I do correctly until now? 2) I removed the glitches that appeared in the pre-edge (1 glitch) and the EXAFS region (3 glitches) in both measurements. 3) Next, I set the E0 for both samples in the background removal session to set the 0 (zero) point in chi(k). However, when I plot chi(k) the samples profile in high k values differ. I think that they should be at least very close considering that both are the same copper oxide standard and measured in sequence. Am I correct? 4) I've also noticed that the first measurement (Cu_o_2), when plot in chi(R) has a small (but significant) peak positioned at R = 1, which seems not be right, as bond distances are bigger (> 1.5, for example). Is there anything wrong or missing at background removal treatment? I know that it seems novice doubts but as I’m new to XAFS, it really intrigues me. Best regards, Pedro Martins

2 2

Re: [Ifeffit] Demeter version 0.9.22 do not work properly in Windows 10
by Pedro F B D Martins 24 Sep '15

24 Sep '15

I would like to thank to Bruce Ravel and Guanghui Zhang for the suggestions. I've modified the restrictions of Demeter and all items related to it in Kaspersky, and also installed the new version of Demeter 0.9.23, which seems to be working just fine. The problem with selecting a point in the plot is resolved. Many thanks. Pedro F. B. D. Martins

3 2

Problem with Hephaestus at Ca L-edges
by Matthew Marcus 24 Sep '15

24 Sep '15

I wanted to work out the edge-jump ratio between the L3 and L2 edges of Ca using Hephaestus. I ran into two problems: 1. The ratio implied by what it says for the unit-edge-step thickness does not agree with that derived by computing the absorption (cm^2/gm) above and below each edge and dividing the difference (L3+ - L3-)/(L2+ - L2-). 2. The results differ wildly depending on which resource I use: L3-.1 L3+.1 L2-.1 L2+.1 (L1+ - L1-)/(L2+ - L2-) Elam 4759.796 27837.796 27478.018 38434.277 2.106375908 Chantler 4322.6 6547.121 32827.61 35436.543 0.852655473 Cromer-Leiberman 4288.524 33471.375 32786.294 47072.991 2.042659055 The Henke table doesn't yield an L2 edge jump at all, while the Shaltout yields the same results as Cromer-Leiberman. Which one should I trust and why? This is old-style H. (V0.18), not Demeter. mam

1 0

Demeter version 0.9.22 do not work properly in Windows 10
by Pedro F B D Martins 23 Sep '15

23 Sep '15

Hi Everyone, I'm having a lot of trouble in processing my XAS data at Demeter 0.9.22 (and also in ifeffit-1.2.11). Things like selecting points in the data (for example, selecting the point at maximum first derivative) is one of it. Moreover, when trying to work with a set of data (let say 5 spectra, which is not that much at all), the program crashes ("not responding" appears). I've attempted to install Windows XP together with my Windows 10, but I'm having problems with that, since windows 10 does not allow me to install a VirtualBox to boot Windows XP. What may I do? I'm new to XAS data treatment, and I would like to start practicing my analysis as soon as possible. Best regards, Pedro Martins

3 2

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite
by Raimundo Lora Serrano 23 Sep '15

23 Sep '15

Bruce, I did what you suggested. > * Can you run gnuplot from the command line? Yes. > > * If so, what is the default terminal? To find out, do this at the > gnuplot command line: "show terminal” “aqua” is the default terminal. > > * If the default terminal is something other than "X11", "wxt", or > "qt", can you reset it? That is done at the gnuplot command line > by, for instance, "set terminal wxt” I reset as suggested. gnuplot is working fine. The plot is generated. Even with “aqua”, the plot is visualized. > * Can you make a plot? To find out, plot a sine wave at the gnuplot > command line with "plot sin(x)” Yes. I just tested and left the gnuplot window opened and ran “athena” in another terminal, but there is no communication with gnuplot. Still, no data is plotted. > Em 22/09/2015, à(s) 16:53, 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. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (Raimundo Lora Serrano) > 2. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Sep 2015 16:38:40 -0300 > From: Raimundo Lora Serrano <rloraserrano(a)infis.ufu.br> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X > Yosemite > Message-ID: <1F27C0D9-A926-490A-A33B-2A46DB8FCEDD(a)infis.ufu.br> > Content-Type: text/plain; charset="utf-8" > > Hi again, > I just reinstalled ?xorg-server demeter?, now I get: > /private/tmp/com.apple.launchd.lXiE4HyZ2W/org.macports:0 > > but there is no plot window. The problem remains. > > >> Em 22/09/2015, ?(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. Re: No plot window in Athena/Demeter on Mac OS X Yosemite >> (George Sterbinsky) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 22 Sep 2015 10:05:29 -0500 >> From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >> Yosemite >> Message-ID: >> <CALoY8Yx1Y4dodQ7ywgUFX5wuLEnauF9ib9LjJQLyi_Awf-T1Kg(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi All, >> >> The result I get is >> /private/tmp/com.apple.launchd.a2i2wnuP2l/org.macosforge.xquartz:0 and >> Athena is working fine on my system. >> >> George >> >> On Tue, Sep 22, 2015 at 6:50 AM, Alison Tebo <agtebo(a)umich.edu> wrote: >> >>> Hi Raimundo (and R?mi), >>> >>> I'm not a pro here but, have you installed xorg-server? It seems like your >>> $DISPLAY variables are not being set correctly. The problem might be >>> XQuartz. The demeter build from Macports doesn't know to use that X windows >>> server (everything is installed in different places) and is looking for the >>> macports version. Your $DISPLAY variable should be something with >>> org.macports rather than org.macosforge.xquartz:0. FWIW, xorg-server is >>> maintained by and updated with XQuartz. >>> >>> Good luck, >>> >>> Alison >>> >>> On Mon, Sep 21, 2015 at 10:15 PM, Raimundo Lora Serrano < >>> rloraserrano(a)infis.ufu.br> wrote: >>> >>>> Dear all, >>>> >>>> I have the same problems installing Athena/Demeter on Yosemite (10.10.5) >>>> as Remi. >>>> Also in my case (as for R?mi) - I use the R?mi?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, ?(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 >>>> >>>>

4 4

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite
by Raimundo Lora Serrano 23 Sep '15

23 Sep '15

Thank you George! Problem solved! :) > Em 22/09/2015, à(s) 19:13, 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. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (Raimundo Lora Serrano) > 2. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (Bruce Ravel) > 3. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (George Sterbinsky) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Sep 2015 18:03:14 -0300 > From: Raimundo Lora Serrano <rloraserrano(a)infis.ufu.br> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X > Yosemite > Message-ID: <C6750595-EFDF-4F4B-A1B4-065B3DBC5C7D(a)infis.ufu.br> > Content-Type: text/plain; charset=utf-8 > > Bruce, > I did what you suggested. > >> * Can you run gnuplot from the command line? > > Yes. > >> >> * If so, what is the default terminal? To find out, do this at the >> gnuplot command line: "show terminal? > > ?aqua? is the default terminal. > >> >> * If the default terminal is something other than "X11", "wxt", or >> "qt", can you reset it? That is done at the gnuplot command line >> by, for instance, "set terminal wxt? > > I reset as suggested. gnuplot is working fine. The plot is generated. Even with ?aqua?, the plot is visualized. > >> * Can you make a plot? To find out, plot a sine wave at the gnuplot >> command line with "plot sin(x)? > > Yes. I just tested and left the gnuplot window opened and ran ?athena? in another terminal, but there is no communication with gnuplot. Still, no data is plotted. > > >> Em 22/09/2015, ?(s) 16:53, 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. Re: No plot window in Athena/Demeter on Mac OS X Yosemite >> (Raimundo Lora Serrano) >> 2. Re: No plot window in Athena/Demeter on Mac OS X Yosemite >> (Bruce Ravel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 22 Sep 2015 16:38:40 -0300 >> From: Raimundo Lora Serrano <rloraserrano(a)infis.ufu.br> >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >> Yosemite >> Message-ID: <1F27C0D9-A926-490A-A33B-2A46DB8FCEDD(a)infis.ufu.br> >> Content-Type: text/plain; charset="utf-8" >> >> Hi again, >> I just reinstalled ?xorg-server demeter?, now I get: >> /private/tmp/com.apple.launchd.lXiE4HyZ2W/org.macports:0 >> >> but there is no plot window. The problem remains. >> >> >>> Em 22/09/2015, ?(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. Re: No plot window in Athena/Demeter on Mac OS X Yosemite >>> (George Sterbinsky) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Tue, 22 Sep 2015 10:05:29 -0500 >>> From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> >>> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >>> Yosemite >>> Message-ID: >>> <CALoY8Yx1Y4dodQ7ywgUFX5wuLEnauF9ib9LjJQLyi_Awf-T1Kg(a)mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi All, >>> >>> The result I get is >>> /private/tmp/com.apple.launchd.a2i2wnuP2l/org.macosforge.xquartz:0 and >>> Athena is working fine on my system. >>> >>> George >>> >>> On Tue, Sep 22, 2015 at 6:50 AM, Alison Tebo <agtebo(a)umich.edu> wrote: >>> >>>> Hi Raimundo (and R?mi), >>>> >>>> I'm not a pro here but, have you installed xorg-server? It seems like your >>>> $DISPLAY variables are not being set correctly. The problem might be >>>> XQuartz. The demeter build from Macports doesn't know to use that X windows >>>> server (everything is installed in different places) and is looking for the >>>> macports version. Your $DISPLAY variable should be something with >>>> org.macports rather than org.macosforge.xquartz:0. FWIW, xorg-server is >>>> maintained by and updated with XQuartz. >>>> >>>> Good luck, >>>> >>>> Alison >>>> >>>> On Mon, Sep 21, 2015 at 10:15 PM, Raimundo Lora Serrano < >>>> rloraserrano(a)infis.ufu.br> wrote: >>>> >>>>> Dear all, >>>>> >>>>> I have the same problems installing Athena/Demeter on Yosemite (10.10.5) >>>>> as Remi. >>>>> Also in my case (as for R?mi) - I use the R?mi?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, ?(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 >>>>> >>>>>

1 0

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

22 Sep '15

Hi again, I just reinstalled “xorg-server demeter”, now I get: /private/tmp/com.apple.launchd.lXiE4HyZ2W/org.macports:0 but there is no plot window. The problem remains. > Em 22/09/2015, 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. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (George Sterbinsky) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Sep 2015 10:05:29 -0500 > From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X > Yosemite > Message-ID: > <CALoY8Yx1Y4dodQ7ywgUFX5wuLEnauF9ib9LjJQLyi_Awf-T1Kg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi All, > > The result I get is > /private/tmp/com.apple.launchd.a2i2wnuP2l/org.macosforge.xquartz:0 and > Athena is working fine on my system. > > George > > On Tue, Sep 22, 2015 at 6:50 AM, Alison Tebo <agtebo(a)umich.edu> wrote: > >> Hi Raimundo (and R?mi), >> >> I'm not a pro here but, have you installed xorg-server? It seems like your >> $DISPLAY variables are not being set correctly. The problem might be >> XQuartz. The demeter build from Macports doesn't know to use that X windows >> server (everything is installed in different places) and is looking for the >> macports version. Your $DISPLAY variable should be something with >> org.macports rather than org.macosforge.xquartz:0. FWIW, xorg-server is >> maintained by and updated with XQuartz. >> >> Good luck, >> >> Alison >> >> On Mon, Sep 21, 2015 at 10:15 PM, Raimundo Lora Serrano < >> rloraserrano(a)infis.ufu.br> wrote: >> >>> Dear all, >>> >>> I have the same problems installing Athena/Demeter on Yosemite (10.10.5) >>> as Remi. >>> Also in my case (as for R?mi) - I use the R?mi?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, ?(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 >>> >>>

2 1