JOLLIVET Patrick | 18 Apr 15:01 2014
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D-ARTEMIS

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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Ronald A. Quinlan | 15 Apr 21:25 2014
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reporting a problem

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
Shelly Kelly | 15 Apr 19:12 2014
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Artemis Feature Request

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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Matt Newville | 14 Apr 22:44 2014

wavelet transforms for EXAFS

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.py)
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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George Sterbinsky | 12 Apr 00:45 2014

Demeter: Problem closing communication to gnuplot

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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David Pickup | 10 Apr 12:27 2014
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Athena Ubuntu 12.04 LTS

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

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Dr Dave Pickup
School of Physical Sciences
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Tel. 01227 823276
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Alessandro Lisboa | 9 Apr 22:39 2014
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Dafs - DIFFKK

Dear, 

My name is Alessandro Lisboa. I am a phd student of physics in Brazil - University of Brasilia. In the last February was held the first experiment DAFS in the Laboratório Nacional de Luz Síncrotron of Brazil. I performed this experiment and now I'm trying to analyze the data. I am having difficulty to establishing a procedure for analysis. I've read many things about. 
I tried to generate the diffkk.inp but I can not get result. I do not know what I'm doing wrong.
I ask, please, help me with a procedure to analyze. For example, what is the sequence of files that need to create and run? 


I would be eternally grateful for your help. 

Regards, 

Alessandro Lisboa

--
-----
M.Sc. Alessandro F. Lisboa Moreira
Ph.D. Student
Complex Fluids Group
Universidade de Brasília (UnB) - Instituto de Física
Brasília/DF (Brazil)
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Johan Nilsson | 9 Apr 16:03 2014
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Larch: problems importing feff paths

Hello,

I'm experimenting a bit with exafs fitting in Larch but I've come across a problem when I try to import my feff paths. Basically what happens is:

$ larch
  Larch 0.9.22 (12-Dec-2013) M. Newville, T. Trainor
  using python 2.7.5, numpy 1.7.1, wx-enabled, wx version 2.8.12.1
larch> path = feffpath('feff0001.dat')
file <stdin>, line 0
IndexError: list index out of range
    path = feffpath('feff0001.dat')
           ^^^
larch>

I don't know if this is an issue with my input file to feff or if this is some sort of bug in Larch. I wrote the feff.inp from scratch using a template and the structure is supposed to be bulk PdO. I've attached my feff.inp and feff0001.dat if someone wants to try and reproduce the problem. I tried another set of paths that was calculated for FeO using an input file from webatoms and those appear to import without issues. I've attached those as well in a zip if someone wants to compare the two sets. I'm running Ubuntu 13.10 on my PC.

Best regards,
Johan
Attachment (feff.inp): chemical/x-gamess-input, 1155 bytes
Attachment (feff0001.dat): chemical/x-mopac-input, 7222 bytes
Attachment (FeO_feff.zip): application/zip, 4645 bytes
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Bruce Ravel | 8 Apr 20:07 2014

my backlog of Demeter chores


Hi everyone,

For the last couple of weeks, I have been having trouble finding time
to address the bugs that have been reported.  Moneed Shatnawi,
Alexander Britz, Matt Frith, Mengling Stuckman, Alison Tebo, and
Thomas Huthwelker have all asked reasonable questions about actual
issues with the software.  I am writing today to assure them that they
are on my mind, but there haven't been enough hours in the day or days
in the week recently for me to address the problems.  But I will!
Soon, I hope.

Cheers,
B

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  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:    http://xafs.org/BruceRavel
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Matt Newville | 7 Apr 17:17 2014

Re: Problem with importing projects from ATHENA into ARTEMIS

Hi Alexander,

I think you may not alone in having this issue.   You should be using
normalized chi(k) in Artemis, but I don't think Artemis would be
reading chi(k) from the project file incorrectly.... Perhaps there is
something strange about how you're doing the normalization?   Or
perhaps it is just a question of what k-weighting is being used for
the plot. Unfortunately, the PNGs I see have been cropped and don't
show the labels of the axes.

I'm sending this to the Ifeffit mailing list, where you'll probably
get a more complete answer.

On Mon, Apr 7, 2014 at 9:57 AM, Britz, Alexander
<alexander.britz@...> wrote:
> Dear Mr. Newville,
>
> I came across a problem when I import an ATHENA project after normalization into ARTEMIS. Maybe you could
tell me who to contact about this problem. Let me try to explain it in few words:
>
> I normalize my EXAFS data in ATHENA and safe it a s a .prj file. When I open the .prj file in ARTEMIS I noticed,
that the amplitude of some oscillations have changed. When I save the chi(k) as .txt, this problem does not
occur. When I open the chi(k) text file in ARTEMIS, the normalization and the amplitude of the
oscillations are exactly the same as in ATHEN.
>
> I have attached a .png file for the EXAFS in k-space. It is the same .prj file, one time opened in ARTEMIS, one
time in ATHENA. To be more specific, the amplitude of the oscillation at k=3 is -1.4 and -1.6, respectively.
>
> Thank you very much for your help in advance!
>
> Best regards from Hamburg,
> Alexander
>
> ________________________________________
> Alexander Britz
> European XFEL GmbH
> alexander.britz@...
> Tel. +49 (0)40 8998-6986
> Fax +49 (0)40 8998-1905
> www.xfel.eu/de
>
> Postadresse: Notkestraße 85, 22607 Hamburg
> Sitz: Albert-Einstein-Ring 19, 22761 Hamburg
>
> Geschäftsführer: Prof. Dr. Massimo Altarelli, Dr. Claudia Burger
> Registriert als European X-Ray Free-Electron Laser Facility GmbH
> beim Amtsgericht Hamburg, HRB 111165
>
>
>
>

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Moneeb Shatnawi | 5 Apr 11:54 2014
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D-Atoms program, common positions and occupancies

Dear Bruce Ravel,
Hello,
 I am Moneeb Shatnawi from the University of Jordan. I have a question and I appreciate your help in advance.
 I have installed the Demeter program (version 0.9.18) and I tried to use your (D)Atoms program using the attached input files.

When I try to run atoms, I get a warning message stating that two sites generate one or more common positions and their occupancies sum to more than 1. (attached also the warning message that I got).
If I ignore this warning message and try to run FEFF, the program crashes.
When I change the space group to P 1 (as indicated by the message) , the program runs well.
My question is, could you please figure out the problem with these input files, so that I can run them with the correct space group?
Thank you so much in advance,
 Moneeb
Attachment (Atoms_Cd-Se.inp): application/octet-stream, 1038 bytes
Attachment (Atoms_CdSe_2.inp): application/octet-stream, 1196 bytes
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