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

Rendering of windows in Artemis and transferring paths from feff calculation
by Alison Tebo 23 Apr '14

23 Apr '14

Hi All, I am running Demeter 0.9.18 installed on a Mac 10.6.8 via the (very helpful!) Macports port. I've had nearly no problems with processing my data, but Artemis appears very strange. Most of the button can't be seen and are black instead (I've attached a screenshot). The bigger problem is that once I run a Feff calculation, I can't seem to transfer the paths from the Feff Window into the Data Window (see second screenshot). The program seems to think it's doing it--there are no error messages in the log and it even makes the little graphic as it 'grabs' the path--but it never transfers it over to the Data Window. I have attached a project file where I get this error, the feff input file that I run the calculation on, and two screenshots of what Artemis looks like for me. I don't think the input and project file matter much since this happens for me even with examples from the various courses Bruce has given. Any advice would be greatly appreciated. Sincerely, Alison

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Re: [Ifeffit] Rendering of windows in Artemis
by Martha W Schaefer 23 Apr '14

23 Apr '14

I am just now going through the tutorials for Artemis (from the 2011 Diamond Light Source course), so I am by no means familiar with Artemis, but I am seeing the same black buttons. I am running Demeter 0.9.18 from MacPorts, on a Mac 10.8.5, and I don't think I have ever played with the color theme. I can't speak about the feff transferring paths issue (yet). (In the ifeffit mailing list digest I can't seem to see Alison's screenshot, but what I see sounds the same.) Martha W. Schaefer Louisiana State University >> >>> On 03/24/2014 03:21 PM, Alison Tebo wrote: >>> >>>> I am running Demeter 0.9.18 installed on a Mac 10.6.8 via the (very >>>> helpful!) Macports port. I've had nearly no problems with processing my >>>> data, but Artemis appears very strange. Most of the button can't be seen >>>> and are black instead (I've attached a screenshot). The bigger problem >>>> is that once I run a Feff calculation, I can't seem to transfer the >>>> paths from the Feff Window into the Data Window (see second screenshot). >>>> The program seems to think it's doing it--there are no error messages in >>>> the log and it even makes the little graphic as it 'grabs' the path--but >>>> it never transfers it over to the Data Window. >>>> >>>> I have attached a project file where I get this error, the feff input >>>> file that I run the calculation on, and two screenshots of what Artemis >>>> looks like for me. I don't think the input and project file matter much >>>> since this happens for me even with examples from the various courses >>>> Bruce has given. >>>> >>>> Any advice would be greatly appreciated. >>>> >>> >>> Hi Alison, >>> >>> First off, I apologize that it has taken me so long to respond to this. >>> Busy time. >>> >>> I don't quite understand the bigger problem. This is certainly not a >>> problem I have on other platforms. Do other Mac users observe the same >>> behavior? >>> >>> As for the lesser problem, looking at the icons across the top in your >>> screenshots, it would seem that you are using some kind of color theme that >>> is different from a Mac out of the box. Is that right? If so, how does >>> the software behave if you change the theme back to the default? >>> >>> Cheers, >>> B >>> >>> >>> -- >>> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >>> >>> National Institute of Standards and Technology >>> Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 >>> Building 535A >>> Upton NY, 11973 >>> >>> Homepage: http://xafs.org/BruceRavel >>> Software: https://github.com/bruceravel >>> _______________________________________________ >>> 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 >> >> >

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Re: [Ifeffit] possible bug in Atoms
by Matt Frith 18 Apr '14

18 Apr '14

Bruce, thanks for taking a look at the problem- the effort is appreciated. Bests, Matt Frith On Thu, Apr 17, 2014 at 1:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Artemis Feature Request (Bruce Ravel) > 2. Re: possible bug in Atoms (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Apr 2014 16:49:26 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Artemis Feature Request > Message-ID: <534EECD6.2090707(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 04/15/2014 01:12 PM, Shelly Kelly wrote: > > Does Artemis have the ability to save the path list information in a > > format similar to the old intrp.dat file to disk? > > Done. Will be in the next release. > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > Homepage: http://xafs.org/BruceRavel > Software: https://github.com/bruceravel > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Apr 2014 08:44:51 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] possible bug in Atoms > Message-ID: <534FCCC3.9010407(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 04/03/2014 02:19 AM, Matt Frith wrote: > > I think I may have found a possible bug with the stand-alone version of > > (D) Atoms. If I generate an inp file in atoms, save it and then try and > > run feff on it later, Atoms crashes without attempting the calculation. > > However, if I load that same input file in (D)Artemis it will run feff > > without crashing. Stand-alone atoms will also fail if I generate the > > input file in Artemis, save it and then try and later open it using > > Atoms. Only Atoms or Artemis is open at a time, > > > > This will be fixed in the next release. Thanks for the bug report. > > > > This problem is occurring on both 32 and 64 bit Windows 7 computers > > running the current (0.9.18.2) package. The problem occurred using > > 0.9.17 also. Any ideas of why I am all of a sudden having this issue > > when it has not been a problem before? > > > > I suspect that it has long been a problem, but it takes a particular > action to trigger the problem. I think that you, like me, never noticed > it before. > > Cheers, > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > Homepage: http://xafs.org/BruceRavel > Software: https://github.com/bruceravel > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 134, Issue 16 > **************************************** >

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D-ARTEMIS
by JOLLIVET Patrick 18 Apr '14

18 Apr '14

Dear Dr Ravel, In the previous version of ARTEMIS, it was possible to separately do FEFF calculations (with FEFF7, FEFF8 or FEFF9) and then to import all paths or one by one in ARTEMIS (theory menu) to fit the experimental data. Is it still possible with the new version D-ARTEMIS ? If yes, how to proceed to do that because I did not manage to do it. Thank you for your answer. Sincerely yours

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possible bug in Atoms
by Matt Frith 17 Apr '14

17 Apr '14

Dear All, I think I may have found a possible bug with the stand-alone version of (D) Atoms. If I generate an inp file in atoms, save it and then try and run feff on it later, Atoms crashes without attempting the calculation. However, if I load that same input file in (D)Artemis it will run feff without crashing. Stand-alone atoms will also fail if I generate the input file in Artemis, save it and then try and later open it using Atoms. Only Atoms or Artemis is open at a time, This problem is occurring on both 32 and 64 bit Windows 7 computers running the current (0.9.18.2) package. The problem occurred using 0.9.17 also. Any ideas of why I am all of a sudden having this issue when it has not been a problem before? The cif file, inp file, and atoms log file are all attached. Sincerely, Matt Frith

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Artemis Feature Request
by Shelly Kelly 16 Apr '14

16 Apr '14

Bruce: Does Artemis have the ability to save the path list information in a format similar to the old intrp.dat file to disk? Seems like this feature could go on the "export" button on the Atoms tab. Or it might also belong on the "Save calc" on the Paths tab. This button gave me a feff.yaml file that I don't know how to open, maybe it is in there? Thank-you for considering this suggestion. Shelly

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reporting a problem
by Ronald A. Quinlan 16 Apr '14

16 Apr '14

To whom it may concern: I recently downloaded the new Demeter (Athena). However, every time I attempt to do a LCF the system closes. I have installed Xcode and Line Command Tools for my operating systems (OS X 10.8.5). Any advice would be appreciated. RAQ

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wavelet transforms for EXAFS
by Matt Newville 14 Apr '14

14 Apr '14

Hi Folks, It's been on my To-Do list for many years, and was one of the arguments for needing to be able to handle multi-dimensional arrays for EXAFS analysis. So I'm happy to say that the Continuous Cauchy Wavelet transform of Munuz, Argoul, and Farges (from American Mineralogist 2003) is now (only ten years late) available in Larch. See http://xraypy.github.io/xraylarch/xafs/wavelets.html for an example. The code (see https://github.com/xraypy/xraylarch/blob/master/plugins/xafs/cauchy_wavelet… ) is adopted from the matlab code of M Munoz and F Farges, and that publication should be used as the citation for this routine. I know there are other implementations of wavelet transforms for EXAFS.... suggestions for changes or additions are welcome, as is additional code. The ability to actually fit data in wavelet space is not yet implemented. This was sort of planned for, and so shouldn't be too difficult to do. If anyone is interested in trying to fit EXAFS data in wavelet space, please let me know. I try to avoid too many announcements about why you should be using Larch instead of Ifeffit, but this is a clear case of something that was impossible in Ifeffit, but added as a single file of code (less than 150 lines, including code documentation) to Larch. --Matt

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Demeter: Problem closing communication to gnuplot
by George Sterbinsky 13 Apr '14

13 Apr '14

Hello, I am trying to learn to use Demeter following The Demeter Programmer Guide. When I attempt to run the first example script in the importing data section I get the following error message: Graphics::GnuplotIF (object 1): problem closing communication to gnuplot I also see the plot window flash open and then closed on my screen. I am using perl 5.16.1 on mac OSX 10.8.5. If anyone can provide any suggestions as to how I might correct this please let me know. Thank you, George

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Athena Ubuntu 12.04 LTS
by David Pickup 10 Apr '14

10 Apr '14

Hello, I'm running Athena (Demeter 0.9.20) with Ubuntu 12.04 LTS. Every time I go to the 'align data' window (with data open), Athena closes and the following message appears in the terminal: Usage: Wx::ComboBox::GetClientData(THIS, n) at /home/dave/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Align.pm line 161, <F> line 1. Any suggestions on how to fix this problem. Thanks, Dave -- ----------------------------------------------------- Dr Dave Pickup School of Physical Sciences Ingram Building University of Kent Canterbury CT2 7NH Tel. 01227 823276 Fax. 01227 827558

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