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

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

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

22 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 >>>> >>>>

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

22 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 >>>>> >>>>>

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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 >>> >>>

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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

1 0

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)

3 2

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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