Re: [Ifeffit] Artemis\Plot mismatch\Artemis[Plot] [Feff] Atoms and Feff

[Ravel, Bruce]

Question 1:  As explained here:

 
https://bruceravel.github.io/demeter/documents/Artemis/feff/paths.html#path-plotting-and-path-geometry

the plot made form the paths tab of the Feff window make no effort to 
set parameters like S02 and sigma^2 to sensible values.  The plots made 
from the Data window probably have values for S02 and sigma^2 not equal 
to 1 and 0, respectively.

Question 2:  See

 
https://speakerdeck.com/bruceravel/the-ramsauer-townsend-effect-in-x-ray-absorption-spectroscopy

a topic which is also explained in many other places by many other people.

B



On 1/10/21 9:49 PM, Huaming wrote:
> Dear all,
> 
> I am using Artemis for EXAFS data fittingand found that the |χ(R)| plot 
> shown in "Artemis [Plot]" and "Artemis [Feff] Atoms and Feff" are in 
> great difference for a same scattering path. However, the |χ(k)| plots 
> shown in the above two windows is the same.   For the plot shown in 
> "Artemis [Feff] Atoms and Feff" window, one path is selected and 'Plot 
> path' is clicked. For the plot shown in "Artemis [Plot]", the same path 
> is dragged into the "Artemis window" and then transfered path and plot 
> in R by click "Action" menu.  I would like to know what is the 
> difference of data shown in the two windows.
> 
> BTW, whether it is possible to have two peaks in the |chi(R)| plot for a 
> single scattering path? For some scatters with high-Z, the f(k) may 
> feature multiple peaks.
> 
> Thanks,
> 
> All bests,
> 
> Huaming Hou
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data

[Ravel, Bruce]

Likeliest reason:

https://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units

Make sure "xmu" is selected in the indicated menu.

Good luck,
B




On 12/7/20 10:26 AM, Deka, N. wrote:
> Dear all
> 
> I am a new student trying to work with Athena for XAS data processing. 
> Attached is a data file which when I import does not show the background 
> and also Athena cannot plot “k” , “q” , “R” plots for the data. Please 
> suggest me a possible solution.
> 
> Thank you
> 
> Best Regards,
> 
> Nipon Deka
> 
> Leiden University
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Athena error on Linux mint

[Ravel, Bruce]

I would guess the problem is that Mint 20 uses a different version of 
perl than Mint 19.  Either downgrade to the same version of perl or 
reinstall.  Making it work as is, if even possible, would require A LOT 
of fiddling.

B





On 10/26/20 6:27 PM, Kyle Kluherz wrote:
> I recently successfully installed the Demeter suite on my Linux Mint 19 
> machine. Last week, I updated to Linux Mint 20, and now I get the 
> following error when trying to run athena from the command line:
> 
> Can't locate Demeter/Here.pm in @INC (you may need to install the 
> Demeter::Here module) (@INC contains: /etc/perl 
> /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 
> /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 
> /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 
> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at 
> /usr/local/bin/dathena line 7.
> BEGIN failed--compilation aborted at /usr/local/bin/dathena line 7.
> 
> I was wondering if there was a relatively easy way to fix this, or if 
> the best recourse is to simply reinstall Demeter? It took some fiddling 
> to install initially, so I don't want to reinstall it unless that's the 
> easiest way to fix the issue.
> 
> Also, the mailing list link on the Demeter home page 
> (http://cars9.uchicago.edu/mailman/listinfo/ifeffit/) times out. 
> Fortunately I was able to get a working link 
> (https://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) from a friend.
> 
> Sincerely,
> 
> Kyle Kluherz
> 
> -- 
> Kyle (Tk) Kluherz
> Graduate Student
> Gamelin & De Yoreo groups
> Department of Chemistry, UW
> Materials Science Division, PNNL
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Requesting guidance in understanding results from Athena

[Ravel, Bruce]

You should read this: 
https://bruceravel.github.io/demeter/documents/Athena/bkg/rbkg.html

B


On 9/13/20 1:45 PM, Deepak Varanasi wrote:
> Good afternoon
> 
> I hope that you are doing well and are healthy. My name is Deepak
> 
> Varanasi and ii am an undergraduate student at Middle Tennessee State 
> University In need of your guidance for my thesis project. I am having  
> trouble interpreting results for my EXAFS analysis done on Athena – 
> specifically, the emergence of a signal in R-space, below the 1 – 
> angstrom mark,  after suppressing it via its rbkg parameter (signified 
> by the black arrows). I have checked my back ground reduction and 
> normalization multiple time sand have failed to isolate the reason 
> behind my results or maybe it is the due to the gaps in my knowledge 
> that prohibit my understanding of the results. At the risk of sounding 
> armature, may I request your guidance in resolving my conundrum please? 
> I would be honored to have your council in solving, understanding and 
> comprehending the physical and chemical implications of my results. For 
> your convenience, I have also appended a picture of my results to 
> illustrate my query. Kindly contact me at your earliest convenience and 
> please stay safe and healthy.
> 
> Yours Sincerely
> 
> Deepak Varanasi
> 
> P.S.: For your convenience, I have also appended a picture of my results 
> to illustrate my query.
> 
> Resulting R – space graphs: -
> 
> An Ink Drawing With Ink Annotations
> 
> Resulting R – space graphs: -
> 
> An Ink Drawing
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Unable to Import Data In Athena

[Ravel, Bruce]

Aha!  Attached log file.  Sorry.  Didn't notice that on my phone :(

I concur with Matt about Larch.

And at the risk of irking Matt, you could try forcing the use of 
Ifeffit.  While maybe not the best choice, it would isolate problems 
with Demeter from problems with Larch and your python installation.

B





On 9/3/20 11:00 AM, Matt Newville wrote:
> Hi Angshuman,
> 
> The logfileyou attached says that Athena is using Larch and that is 
> where the error is coming from.
> A few comments on that:
>    a) it looks like it is using Python 2.7 which actually has not been 
> supported for xraylarch for some time now (well over a year)
>    b) that the `pyfai` module is not installed, which should not be 
> required but is what is causing the actual error.
> 
> Having `pyfai` not installed should not cause an error, but this all 
> suggests that your xraylarch installation is quite all.
> I would suggest reinstalling xraylarch using Python3 and see if that 
> fixes the problem.
> 
> 
> 
> On Thu, Sep 3, 2020 at 8:57 AM Angshuman Gupta  > wrote:
> 
> Dear sir,
> I am new to this mailing list and excuse me if the question had
> already been asked. I am not able to import data in the Athena
> software. I tried to import some of the examples data like
> Fe_lepidocrocite.000 in the Fe standards folder while importing the
> data I encountered an error (screenshot has been attached along with
> the log file generated in the terminal).
> I am using Linux Mint 18.3 Sylvia OS and perl 5, version 22,
> subversion 1 (v5.22.1).
> I followed the instruction for installation here
> 
> "https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html
> 
> "
> I will be thankful if you could suggest something to getting rid of
> this issue.
> Thank you
> Angshuman Gupta
> PhD scholar
> IIT Bombay
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> 
> 
> --Matt
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Unable to Import Data In Athena

[Ravel, Bruce]

I do not recognize that error message.  I would need to see what is 
written underneath the details button and/or what is written in green 
text in the terminal window behind Athena.

B


On 9/3/20 9:56 AM, Angshuman Gupta wrote:
> Dear sir,
> I am new to this mailing list and excuse me if the question had already 
> been asked. I am not able to import data in the Athena software. I tried 
> to import some of the examples data like Fe_lepidocrocite.000 in the Fe 
> standards folder while importing the data I encountered an error 
> (screenshot has been attached along with the log file generated in the 
> terminal).
> I am using Linux Mint 18.3 Sylvia OS and perl 5, version 22, subversion 
> 1 (v5.22.1).
> I followed the instruction for installation here 
> "https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html
>  
> "
> I will be thankful if you could suggest something to getting rid of this 
> issue.
> Thank you
> Angshuman Gupta
> PhD scholar
> IIT Bombay
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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[Ifeffit] interesting job posting at NSLS-II

[Ravel, Bruce]

Hi all,

A colleague of mine here at NSLS-II has an interesting post-doc position 
open right now.

https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-in-total-scattering-and-machine-learning/3437/14611841

This position is for a person doing total scattering (aka PDF). Strictly 
speaking, not an XAS position, but perhaps of interest to someone with 
an XAS background who is looking for a post-doc.

Regards,
Bruce


-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Trouble with energy spacing in .nor files Athena

[Ravel, Bruce]

This bug is explained here:

https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06572.html

and in the next message by thread.

Executive summary: the problem is a bug in Athena interpreting an energy 
column expressed in keV.

It has since been fixed at GitHub.  I am struggling to find the time to 
build a new Windows installer, but when I di, this problem will be fixed.

In the short term, find a way to edit your data files to convert keV 
units to eV units.  Or politely ask your beamline scientist to write out 
the data in eV units.

HTH,
B


On 11/22/19 12:22 PM, Berryman, Eleanor (NRCAN/RNCAN) wrote:
> I have run into a problem with Athena binning the energies of my 
> imported spectra without being told to. This problem is best explained 
> by example:
> 
> I am processing XANES data collected around the Cr edge (5989 eV). I 
> load a datafile that has data collected in 5 eV steps from 5789.2 to 
> 5969.2 eV; in 0.5 eV steps from 5969.2 to 6019.2 eV; in 1 eV steps from 
> 6019.2 to 6139.2 eV.
> 
> In the ‘Import Data’ popup window (Athena: column selection), the 
> preview of the raw data shows the current energy resolution. The raw 
> data is processed in Athena using column 1 as Energy, column 10 as 
> Numerator, and column 4 as denominator. ‘Perform rebinning’ is 
> unselected.  I save the processed data as norm(E) to produce the 
> attached result, which has data in the following steps: 5 eV steps from 
> 5789.2 to 5969.2 eV; 1 or 1.5 eV steps from 5970.2 to 6018.7; 1 or 2 eV 
> steps from 6020.2 eV to 6138.2 eV.
> 
> I have used the rebinning feature during import to circumvent this 
> problem. When I rebin, the saved .nor file obeys the rebinned energy 
> spacing. I need to find a better solution than this. I need to find a 
> way for Athena to obey the energy spacing of the imported dataset.
> 
> Details on my version of Athena:
> 
> Demeter 0.9.26
> 
> Downloaded last week and today.
> 
> Installation run as user and as administrator. The problem persists even 
> after reinstallation.
> 
> System details:  64-bit Windows 10 Operating System
> 
> Thanks in advance for any direction in finding a solution to this problem.
> 
> *Eleanor Berryman, PhD*
> 
> Mineralogist & Geochemist, CanmetMINING
> 
> Land & Minerals / Natural Resources Canada / Government of Canada
> 
> eleanor.berry...@canada.ca  / Tel : 
> 613-995-4479
> 
> Minéralogiste & Géochimiste, CanmetMINES
> 
> Secteur des terres et des minéraux / Ressources naturelles Canada / 
> Gouvernement du Canada
> 
> eleanor.berry...@canada.ca  / Tél : 
> 613-995-4479
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] no plot window with Demeter on Ubuntu 18.04

[Ravel, Bruce]

Hi Joseph,

You did the first few troubleshooting steps.  Good to know that gnuplot 
works by itself.

What is the value of preferences->gnuplot->program ?  On a linux 
machine, this parameter should simply be set to "gnuplot".  That means 
that gnuplot needs to be in the execution path.  Perhaps gnuplot is in 
an unexpected place on your machine?  Or perhaps it is called by an 
unexpected name?  If it is not in the normal execution path, try setting 
that parameter to the full path to the gnuplot executable.

The Gtk-CRITICAL warning is almost certainly a red herring.  That has to 
do with how one of the widgets in the main display gets sized when 
Athena is created.  It is noisy and annoying, but almost certainly not 
harmful or related to your plotting problem.

B


On 11/19/19 11:37 AM, Joseph Zsombor-Pindera wrote:
> Dear mailing list members;
> 
> I've successfully built Demeter from source on my computer running 
> Ubuntu 18.04. Running "dathena", for example opens the familiar Athena 
> window. Once I try to plot something, however, I get no plot window. It 
> appears as if the program has done something, but the window just 
> doesn't appear.
> 
> I have installed gnuplot-x11.
> running 'gnuplot -e "plot sin(x)"' produces no window, but
> 'gnuplot -p -e "plot sin(x)"' produces a plot, and if I just run
> 'plot sin(x)' within gnuplot, then I get the plot, so it appears that 
> gnuplot itself is working correctly.
> 'show terminal' results in:
> terminal type is wxt 0 enhanced
> I have tried changing the terminal to 'wxt' under 
> preferences>gnuplot>terminal in Athena, which didn't fix the problem.
> I have also tried changing the terminal to 'qt' and installing 
> gnuplot-qt. This didn't work, so I purged it and switched back to 
> gnuplot-x11.
> I haven't managed to get gnuplot to run with x11 as its default 
> terminal. It seems that the default terminal of gnuplot-x11 is wxt.
> 
> I'm not sure if these matter, but when I run Athena, I get errors in the 
> terminal like this:
> (dathena:16207): Gtk-CRITICAL **: 11:55:29.414: 
> gtk_box_gadget_distribute: assertion 'size >= 0' failed in GtkCheckButton
> 
> thanks,
> Joseph
> -- 
> *Joseph Zsombor-Pindera, BSc*
> PhD Student, UBC Chemistry
> 
> C
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] about WebAoms

[Ravel, Bruce]

On 11/20/19 7:49 PM, Park Gyuchul wrote:
> I appreciate for your precious comments. Your suggestion makes my life 
> easier!  Is "distance" column is not required information in feff.inp 
> format? (please find the part of the feff file attached. This is what I 
> got from WebAtoms (typical cif file is used here).


Quoting from 
https://bruceravel.github.io/demeter/documents/Artemis/atoms/example.html#the-feff-input-file

"The atom list is printed in the format required by FEFF. The atom list 
has two comment columns. The indexed atomic symbol and radial distance 
are written by ATOMS for your use when reading feff.inp and are ignored 
by FEFF."


-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] about WebAoms

[Ravel, Bruce]

Hi,

I am wondering whether you are thinking about your problem in the most 
straight-forward way.  Atoms is a tool to expand crystal data into a 
cluster.  From lammps, you already have a cluster, you just don't have 
your cluster expressed in a form that Feff knows how to read.

Unless I am significantly misunderstanding your question, I dont think 
Atoms is your best tool.  You just need to take some (or all) of the 
atoms from the output cluster from your MD simulation and wrap it up in 
the correct dressing for Feff.

Here is what I mean, explained for a much smaller problem (in terms of 
number of atoms):

https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples?slide=11

Note what I say on the next page -- the absorber DOES NOT need to be at 
(0,0,0) and the absorber does not need to be the first item in the list.

You can just edit (or write a short script/program) your lammps output 
to cut out the atomic coordinates, assign unique potential indeces to 
all the atoms, and put the correct boilerplate at the top of the file. 
Voila!  You have a feff input file.

While it is true that you can, in principle, convert your lampps file to 
a CIF file, it just doesn't seem like a necessary or helpful step.  I'd 
really recommend taking the time to understand how to move the MD output 
into the proper form for feff input.

HTH,
B


On 11/19/19 9:27 PM, Park Gyuchul wrote:
> Hi All,
> 
> I am trying to simulate the EXAFS spectrum of pure molybdenum through 
> FEFF9 software. I got the atomic configurations of molybdenum from 
> molecular dynamics simulations, and I'd like to import it into FEFF 9. 
> In order to do that, I converted lammps file into cif file, and I am 
> trying to convert cif file into feff.inp. I am using Webatoms to convert 
> cif file into feff.inp. The default value of cluster size and longest 
> path is 8 and 5, respectively (in angs). However, when I try to increase 
> the cluster size and the longest path to 10, it stops working, and I got 
> the internal error. I am working with 1024 atoms (8x8x8 cells, bcc 
> crystal structure). Are 1024 atoms too many to deal with in webatoms? or 
> is there other ways to convert cif file into feff.inp?
> I don't have any problems when I use the ideal cif file (not from 
> molecular dynamics simulations).
> 
> Sincerely,
> Gyuchul Park
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Installation problems for Demeter on Ubuntu 16.04

[Ravel, Bruce]

Hi Jo,

I am sorry this is proving so difficult.  Just the other day, I 
installed everything on a machine with Ubuntu 19.10 and saw none of 
these problems.

The problem you are seeing is not one I have ever run into, so it;s a 
bit hard to comment on.  It is clearly a Wx problem.  Your traceback 
identifies it as a Wx problem.

If upgrading your machine to 19.10 is not an option (I /am/ pretty happy 
with the 19.10...) then I have a suggestion for you to try.  This 
suggestion assumes that you let Demeter's build script install the 
perl/Wx interface for you.  This will be a little hands-on -- sorry for 
that, but it's hard to do better from afar

First uninstall some of the things that Demeter installed.  I think the 
best way to do this will be:

cpanp uninistall Wx

"cpanp" is a program that comes with perl itself.  Yo willprobably have 
to sudo that command.

Now use Ubuntu's package manager to satisfy the wxperl requirement:

sudo apt install libwx-perl

say yes to all of the dependencies.  Now try building and installing 
Demeter again.  Do:

./Build dist-clean

then

perl -I. Build.PL
./Build
./Build test
./Build install

No guarantee that this will actually improve the situation.  Wx is a 
difficult thing to build.  It seems more reliable to use the one already 
built by the Ubuntu package manager.

Good luck!
B





On 11/13/19 4:12 PM, Jo Melville wrote:
> Hello all,
> 
> I am having some troubles successfully building Demeter from source on 
> my Linux machine. All dependencies appeared to install correctly -- a 
> few errors pop up upon running ./Build test (full error report 
> attached), but as best I could discern, the errors produced were the 
> same as those reported in this recent message 
> 
>  
> (https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html 
> ).
> 
> Athena appear to install correctly and even start correctly, but upon 
> attempting to import /any/ data file into Athena, the following error 
> message pops up (screenshot also attached):
> 
> 03:50:59 PM: Unknown warnings category 'experimental::script_run' at
> /usr/share/perl/5.22/warnings.pm
> 
> 
> line 254.
> warnings::Croaker("Unknown warnings category
> 'experimental::script_run'") called at
> /usr/share/perl/5.22/warnings.pm
> 
> 
> line 332
> warnings::unimport("warnings", "experimental::script_run") called at
> (eval 2455) line 1
> Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1
> eval {...} called at (eval 2455) line 1
> eval 'no warnings "experimental::script_run";
>                            qr/(*script_run: ^ .* $ )/x' called at
> /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74
> require Pod/Simple/BlackBox.pm called at
> /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7
> Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1
> eval {...} called at (eval 2455) line 1
> require Pod/Simple/LinkSection.pm called at
> /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9
> Pod::Simple::BEGIN() called at (eval 2455) line 1
> eval {...} called at (eval 2455) line 1
> require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34
> Pod::Text::BEGIN() called at (eval 2455) line 1
> eval {...} called at (eval 2455) line 1
> require Pod/Text.pm called at
> 
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm
> line 13
> Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455)
> line 1
> eval {...} called at (eval 2455) line 1
> require Demeter/UI/Athena/PluginRegistry.pm called at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm
> line 2114
> Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0),
> "PluginRegistry") called at
> 

Re: [Ifeffit] Solved concatenation bug Arrays.pm line 115

[Ravel, Bruce]

I'm glad you found a solution.

I wish that Athena played better with languages that use unicode text. 
I imagine that there are plenty of places where I make -- intentionally 
or not -- that kind of assumption about user-supplied text.  So there 
are probably other places where Athena might break for the same reason.

The general solution of making a place on your computer that 
English/western characters in the folder names is a good way of avoiding 
this sort of problem.  Again ... that's a functional solution, but not a 
very appropriate one.

B


On 11/5/19 8:53 PM, FonsPaul wrote:
> I wanted to update the mailing list on my encounter with a concatenation 
> bug. I discovered that the cause was having (Japanese) Chinese 
> characters in the pathname. Moving the folder solved the problem.
> 
> Paul Fons
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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[Ifeffit] Fwd: 32 bit package for install

[Ravel, Bruce]

http://bruceravel.github.io/demeter/#old

 Forwarded Message 
Subject:32 bit package for install
Date:   Mon, 28 Oct 2019 20:30:40 +0200
From:   Margaret Blazhynska 
To: ifeffit-ow...@millenia.cars.aps.anl.gov



To whom it may concern,

Could you please send me the 32-bit installer package of ifeffit?
I am a student of a masters degree in Chemistry and I really need this 
pack to practice on XAS
Thank you in advance
-- 
Best regards,
Margaret Blazhynska

-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Issue with the Athena software - Athena Warning: redundant argument in sprintf

[Ravel, Bruce]

Hi,

It's hard for me to really troubleshoot the problem without seeing the 
data.  It looks like the fit ran to completion, that is, the plot looks OK.

A couple of your standards don't actually seem to be represented in your 
fit.  Augite has a negative weight and Olivine is barely outside its 
error bar.  Also, the R factor for fit "B,D,E" is barely different from 
those above, which further suggests that those two are not actually in 
your sample.

What happens if you exclude those two from the combinatorial fit?  Do 
you see the same error message?

What happens if you unclick the button that says "Force weights to sum 
to 1"?  (I suspect that button is the culprit behind the negative weight 
for Augite)

Does the same error message happen if the fit in mu(E) rather than the 
derivative, as shown?

B


On 10/14/19 7:00 AM, Clarissa Baldo wrote:
> Good Afternoon,
> 
> I am a new user of the Athena software.
> 
> I am trying to fit my XANES spectra using the linear combination fitting 
> tools in Athena.
> 
> However, every time I run the fitting I receive the following warning 
> message:
> 
> Would you please give me some advice to solve this problem?
> 
> I am using the latest version of the Demeter system (version 0.9.26) for 
> windows.
> 
> I have attached a copy of the warning log and a screenshot of the error.
> 
> Thanks,
> 
> Clarissa
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] software installation

[Ravel, Bruce]

By a very long stretch, the most common explanation for problems on 
Windows is that your anti-virus software is blocking something that the 
software needs.

You might try digging through the AV log files to see if a file 
installed with Demeter shows up.  If you are your administrator can 
grant an exception, that will likely solve the problem,

Useful reading:
http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html



On 10/11/19 4:01 PM, Shultz, Mary Jane wrote:
> Has anyone had issues with software installation? I have installed it on 
> a Windows machine (64 bit, 7 pro). It appears to install, but when I try 
> to run it, it starts but immediately shuts down. Am I missing something?
> 
> Thanks
> 
> M
> 
> Three colleagues are having the same issue.
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Install for Mac error

[Ravel, Bruce]

Here's one time recently that question was answered:

 
https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-June/009822.html



The archives of this mailing list are quite useful:

https://millenia.cars.aps.anl.gov/pipermail/ifeffit/


B



On 10/2/19 6:04 PM, Wu Xiaohan wrote:
> Hello everyone,
> 
> I tried to install demeter on my Mac and run Athena. And get the error 
> shown below:
> 
> 16:59:44: Name "Demeter::Templates::DS" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572,  
> line 236.
> 
> 16:59:44: Name "Demeter::Templates::S" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572,  
> line 236.
> 
> 16:59:44: Name "Demeter::Templates::F" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572,  
> line 236.
> 
> 16:59:44: Name "Demeter::Templates::PT" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572,  
> line 236.
> 
> 16:59:44: Name "Demeter::Templates::T" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572,  
> line 236.
> 
> 16:59:44: Name "Demeter::Templates::D" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572,  
> line 236.
> 
> I would like to ask help to correct this error.
> 
> Thank you so much.
> 
> Best regards
> Kelsey
> 
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Athena data uploading: Fourier transform parameters are not showing

[Ravel, Bruce]

http://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units

On 9/30/19 2:42 AM, Pankaj Singh Rawat wrote:
> Hey There, Do anyone have idea about following problem:
> 
> I uploaded C-k edge on Athena but fourier transform parameters are not 
> showing/open for modifications.
> 
> Attaching the screenshot. Is this because of the data format of any 
> software issue ? any suggestions?
> 
> I'll be grateful to you for valuable suggestions.
> -- 
> Pankaj Singh Rawat
> PhD Research Scholar
> GBPUA Pantnagar
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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[Ifeffit] Fwd: 64-bit Demeter not able to use on Windows computer

[Ravel, Bruce]

Brittany,

In your first post to the mailing list, you said you could not get the 
software to run on "a Windows computer".  That you are looking for a 32 
bit installer seems like extremely relevant information.

I no longer have the capacity to build 32 bit versions of the installer, 
but I keep links to old versions available on the Demeter website.

http://bruceravel.github.io/demeter/#old

The most recent version for which a 32 bit installer exists is 0.9.25. 
Somewhat dated, but should still be useful.

B

PS: Please send email to the mailing list 
ifeffit@millenia.cars.aps.anl.gov and please do not send email directly 
to ifeffit-owner.  Matt and I are the only ones who read mail sent to 
ifeffit-owner and we don't guarantee a response to email sent to that 
address.


 Forwarded Message 
Subject:64-bit Demeter not able to use on Windows computer
Date:   Wed, 28 Aug 2019 09:10:17 -0400
From:   Brittaney Courchesne 
To: ifeffit-ow...@millenia.cars.aps.anl.gov



Hi everyone,

The 64-bit version of Demeter is not able to be used on my Windows 
computer I have, since it is a 32-bit version. Is there a way around 
this or does someone have the 32-bit version they can email me?
I have tried disabling my firewall completely and trying to "allow" the 
programs through the firewall, and running as an administrator, but the 
64-bit just doesn't seem to work.

Thank you,
Brittaney

-- 
*/Brittaney Courchesne, G.I.T./*
MSc Geology Candidate
Harquail School of Earth Sciences
Laurentian University
Sudbury, ON
/bcourche...@laurentian.ca /

-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Unable to use 64-bit Demeter on Windows computer

[Ravel, Bruce]

I am always suspicious of anti-virus in this situation. I have seen many 
times where AV is flagging one of the libraries used by the software. 
Definitely my first guess ofr troubleshooting.

The AV software should have a log that reports what it's unhappy with. 
The administrator can then put an exception in that allows the software 
to run.

HTH,
B

On 8/21/19 11:29 AM, Brittaney Courchesne wrote:
> Hello,
> 
> I am just sending this email to see if anyone has encountered the 
> following problem:
> I downloaded the newest 64-bit version of Demeter on my Windows 
> computer, and it downloaded successfully, but now when I double click on 
> the program, a tiny window pops up for about 0.5 seconds and then 
> disappears. I have tried redownloading twice.
> 
> Thank you very much,
> Brittaney
> 
> -- 
> */Brittaney Courchesne, G.I.T./*
> MSc Geology Candidate
> Harquail School of Earth Sciences
> Laurentian University
> Sudbury, ON
> /bcourche...@laurentian.ca /
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Trouble with MacOS 10.14 Mojave

[Ravel, Bruce]

Fun fact: our mailing lists has an archive of previous posts.

https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-June/009821.html

and

https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-June/009822.html

On 7/25/19 5:03 AM, christophe den auwer wrote:
> Hi all,
> 
> I have to re-install Demeter on my Mojave MacBook (version 10.14.5).
> X code version 10.2.1
> 
> Well it didn't totally worked out….
> 
> When I launch either Athena or Artemis, this is what I get (bellow).
> I also notice I have a new « opt » directory directly on the hard disk 
> (this seems a strange location).
> 
> Does anybody have an idea about that ?
> 
> Thanks a lot for your help
> 
> Christophe
> 
> 
> 
> --
> Christophe Den Auwer
> Professeur
> Université Côte d’Azur
> Institut de Chimie de Nice
> Parc Valrose
> 06108 Nice, France
> christophe.denau...@univ-cotedazur.fr 
> 
> --
> 
> 
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] averaging data

[Ravel, Bruce]

http://bruceravel.github.io/demeter/documents/Athena/process/merge.html

On 7/18/19 2:15 PM, Danielle Brown wrote:
> How do I average two data sets in Athena?
> 
> Thanks!
> —
> 
> Danielle Brown
> Office: CSE L180
> Cell: 317-605-9311
> IIT '20 - BS Physics
> IIT ID: A20417782
> dbrow...@hawk.iit.edu 
> d.e.brow...@gmail.com 
> 
> 
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] How to install Demeter on ubuntu 18.04

[Ravel, Bruce]

William,

I'm a bit confused by the information you've given, but it seems that 
the installation location of Athena is not in perl's path.

Try this:

At the command line type

 export PERL5LIB=/home/opd30/demeter

Then perl should find the "missing" module.  If that does the trick on 
your machine, you can set that environment variable in your ~/.bashrc 
file (or the start-up file for whatever shell you actually use).

More information: 
https://perlmaven.com/how-to-change-inc-to-find-perl-modules-in-non-standard-locations

HTH,
B



On 7/3/19 9:36 AM, William Del Net wrote:
> Dear people
> I tried to install demeter on computer with ubuntu 18.04.
> I ve found the Deavd Hughes guide to demeter installation on Ubuntu 12.04
> 
> There are some differencies and I tried to follow everything. Well, 
> everything seem to be installed, but when I run dathena, i have the 
> following error message
> opd30@joconde:~/demeter$ ./bin/dathena
> Can't locate Demeter/Here.pm in @INC (you may need to install the 
> Demeter::Here module) (@INC contains: 
> /home/opd30/perl5/lib/perl5/5.26.1/x86_64-linux-gnu-thread-multi 
> /home/opd30/perl5/lib/perl5/5.26.1 
> /home/opd30/perl5/lib/perl5/x86_64-linux-gnu-thread-multi 
> /home/opd30/perl5/lib/perl5 /etc/perl 
> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 
> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 
> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 
> /home/opd30/perl5/lib/perl5/5.26.0 
> /home/opd30/perl5/lib/perl5/5.26.0/x86_64-linux-gnu-thread-multi 
> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at 
> ./bin/dathena line 7.
> BEGIN failed--compilation aborted at ./bin/dathena line 7.
> 
> Here.pm is located in~/demeter/lib/Demeter. And yes, it's not in @INC.
> My home directory is /home/opd30
> 
> 
> Do you have a solution, or a guide to install properly demeter on Ubuntu 
> 18.04
> Thanks a lot
> william
> 
> -- 
> 
>>
> DEL NET William
> ESRF  CRG-FAME
> 71 avenue des Martyrs
> F-38043 GRENOBLE CEDEX 9
> 
> tel: +33 4 76 88 25 46
> 
> fax: +33 4 76 88 27 43
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Problem with Demeter installation on mac OS Mojave

[Ravel, Bruce]

A frequently asked question on this mailing list

Here's one solution to the problem:

Find the file Demeter.pm where ever it is installed on your computer. 
Open it in a text editor (not a word processor, if you use Word, you 
will make more problems for yourself) and scroll down to about line 
1000.  You should find a couple of lines that say:

__PACKAGE__->meta->make_immutable;
1;


Add the following three lines:

package Demeter::Templates;
use vars qw($S $D $P $C $F $DS $T $PT);
1;


It should end up looking like this:

https://github.com/bruceravel/demeter/blob/master/lib/Demeter.pm#L991-L997

To the best of my understanding, that will fix the problem.

B


On 6/12/19 4:52 PM, Gaëlle Creff wrote:
> I have some troubles with the installation of Demeter on my mac (under 
> OS Mojave since this week end).
> Athena crashed after the following message:
> "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572,  
> line 236.
> 
> 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572,  
> line 236.
> 
> 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572,  
> line 236.
> 
> 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572,  
> line 236.
> 
> 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572,  
> line 236.
> 
> 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at 
> /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572,  
> line 236. »
> 


-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Athena labels

[Ravel, Bruce]

Not easily (*).  The plotting in Athena is pretty proscriptive.  The 
user does not have a much freedom to change what gets plotted.

That was by design.  On one hand, I didn't want to write a support a 
full featured plotting tool.  On the other hand, I didn't want the user 
to spend time fussing with details of the plots rather than thinking 
hard about their data.

There are a number of ways to get data out of Athena in useful forms so 
that you can make beautiful plots that look exactly how you want them 
using your favorite plotting tool.

   http://bruceravel.github.io/demeter/documents/Athena/output/column.html

B


(*) To change the plot labels, you would have to alter the source code. 
Those strings are hard-wired.


On 5/24/19 10:22 AM, Stoll, Andreas (IAM) wrote:
> Hi,
> 
> Is it possible to change the x- and y-axes labels in the athena plots 
> (energy against normalized xµE)?
> 
> Greetings
> 
> Andi
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Pseudo Voigt crash Athena

[Ravel, Bruce]

On 05/01/2019 10:57 PM, Matt Newville wrote:
> Larch (and the lmfit library it uses) and the XAS Viewer GUI are all 
> supported. Peak-fitting of XANES is one feature which I am confident to 
> say is definitely better than Athena. I'm willing to take 100% of the 
> blame for this, but peak-fitting does not work well in Athena.

That's not necessary, Matt.  I have said before on this mailing list and 
elsewhere that peak fitting is a very weak part of Athena.  While it is 
true that Ifeffit's capabilities in this area were limited, Athena's 
implementation was poor.

I completely agree that XAS Viewer would be a better choice for this task.

B

-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] can't open Athena 0.9.26!

[Ravel, Bruce]

Or use one of the older releases from back when I still had a 32 bit 
computer on which to build installer packages.

http://bruceravel.github.io/demeter/#old

B

On 04/23/2019 07:48 AM, Matt Newville wrote:
> 
> 
> On Tue, Apr 23, 2019 at 6:24 AM m.rezaie  > wrote:
> 
> Hi,
> 
> I upgraded my DEMETER to DEMETER 0.9.26 but I can't open it on my
> computer which is Win 7, 32 bit. How can I solve this problem?
> 
> 
> 
> I believe the installer for Demeter 0.9.26 works only with 64-bit machines.
> 
> You (or someone else) might be able to build it from source on 32-bit 
> machines.  I don't think there have been very many requests for that.
> 
> --Matt
> 
> 
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Demeter - Athena Warning, crashing

[Ravel, Bruce]

Hi,

The Demeter problem that presents itself with error messages like:

   15:36:09: Name "Demeter::Templates::S" used only once: possible typo 
at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, 
 line 236.

is one that comes up pretty often here on the mailing list.  It is also 
a problem that is already solved on github, but I haven't made a new 
release in quite some time.

The solution to this particular problem is shown here:

 
https://github.com/bruceravel/demeter/blob/master/lib/Demeter.pm#L994-L996

You could simply edit the copy of Demeter.pm on your computer to have 
the three lines highlighted at that link.

Or you could click the "Raw" button at the top of that page, then save 
the raw file in place of Demeter.pm on your computer.

A bit more effort would be to remove the version of Text::Template that 
is on your computer and install an older version of Text::Template on 
your computer.  This one should work:

   https://metacpan.org/release/MJD/Text-Template-1.46


The bottom line is that Demeter uses a perl module for which the 
documentation of a feature and its implementation used to agree and, at 
some point, stopped agreeing.  The fix that I link to above addresses 
that problem, but the specific combination of Demeter and Text::Template 
that makes it onto some people computers expose this problem.  Any of 
the solutions explained above should address this in the short term.

Eventually I will make a new release and this problem will go away. 
Until then, hopefully people will find this email.

B



-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Import Error

[Ravel, Bruce]

I did not remember when you asked the other day, but it occurred to me 
that your data-in-keV problem was reported a few months ago.

https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-January/009688.html

I have not yet made a new Windows release with the fix.  However, it is 
not too hard to apply the fix by editing a small amount of Athena's 
source code.


I think this is the easiest way to explain the small changes.  Find the
file "lib/Demeter/Data.pm" underneath the location on your computer that
the software was installed.  Look at this link:

https://github.com/bruceravel/demeter/commit/1b586b88d36336cad00b13d73913ebdb48b1d132#diff-74dd62af0fb82fb27595c1edcf73041f

Make the indicated change at line 22 (i.e. add $EPSILON6 to the argument
list of qw().)

Make the indicated changes around 885 (i.e. add the two lines before the
while block and alter the argument of the greater-than comparison in the
first line of the while block).

The change at line 871 is irrelevant and has no impact on Athena's 
operations.

That should do it.  You can then drop the edited file into place on any
other computer.

B



On 04/05/2019 10:33 AM, Clark Adam Hugh (PSI) wrote:
> Dear Bruce and Lucy
> 
> Thanks for your work around Lucy, it works perfectly but still doesn't 
> explain the behavior I am observing.
> 
> Bruce what other information would be useful to diagnose the problem I am 
> currently having? I have attached two figures, one showing the import window 
> with the setting I have been using, specifically that I am not using the 
> rebin feature. The second figure shows the difference in the pre-edge region 
> between importing the data with eV and keV units for the energy column to 
> demonstrate clearly that resampling is occurring when importing with data 
> that has an energy column of KeV.
> 
> Many Thanks
> Adam Clark
> 
> __
> Paul Scherrer Institut
> Adam Hugh Clark
> WLGA/129
> Forschungsstrasse 111
> 5232 Villigen PSI
> Schweiz
> 
> Telefon: +41 56 310 41 51
> E-Mail: adam.cl...@psi.ch
> -Original Message-
> From: Ifeffit  On Behalf Of 
> ifeffit-requ...@millenia.cars.aps.anl.gov
> Sent: Freitag, 5. April 2019 15:20
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: Ifeffit Digest, Vol 194, Issue 4
> 
> Send Ifeffit mailing list submissions to
>   ifeffit@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-requ...@millenia.cars.aps.anl.gov
> 
> You can reach the person managing the list at
>   ifeffit-ow...@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. Data Import Bug (Athena 0.9.26) (Clark Adam Hugh (PSI))
> 2. Re: Data Import Bug (Athena 0.9.26) (Ravel, Bruce)
> 3. Re: Data Import Bug (Athena 0.9.26) (Lucy M Mottram)
> 
> 
> --
> 
> Message: 1
> Date: Fri, 5 Apr 2019 11:33:13 +
> From: "Clark Adam Hugh (PSI)" 
> To: "ifeffit@millenia.cars.aps.anl.gov"
>   
> Subject: [Ifeffit] Data Import Bug (Athena 0.9.26)
> Message-ID:
>   
> Content-Type: text/plain; charset="us-ascii"
> 
> Dear Mailing List
> 
> I have recently come across a data import error when using Athena version 
> 0.9.26. When importing data there appears to be a resampling which 
> significantly reduces the resolution of the data. Attached is an example 
> dataset with an energy step of 0.5 eV on the Cu K edge. When importing with 
> Athena 0.9.26 this data is significantly resampled resulting in an energy 
> resolution on the edge of 1.5 eV which can either be seen by plotting or by 
> exporting and inspecting the datafile. Using version 0.9.25 resolves this 
> issue entirely. The data itself appears to actually be visible correctly 
> during the import process (the import tab shows the data listed correctly 
> when choosing which columns to import).
> 
> Is there a setting somewhere within Athena 0.9.26 that sets the default 
> behavior to resample the imported data?
> 
> Thanks
> Adam Clark
> 
> __
> Paul Scherrer Institut
> Adam Hugh Clark
> WLGA/129
> Forschungsstrasse 111
> 5232 Villigen PSI
> Schweiz
> 
> Telefon: +41 56 310 41 51
> E-Mail: adam.cl...@psi.ch
> -- next part --
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> <http://millenia.cars.aps.anl.go

Re: [Ifeffit] [SUSPECTED SPAM] - How to use deconvolution function in larch using athena

[Ravel, Bruce]

There isn't any major functionality in Demeter that is not explained in 
the documentation.  The thing you are asking for is not documented, thus 
it's not available.

If you need larch's deconvolution function you might consider, you know, 
using larch

B




On 04/06/2019 08:56 AM, wangshaof...@iae.ac.cn wrote:
> Dear all,
> 
> I am trying to deconvolute some xafs data. Can anybody show me how to 
> use larch deconvolution function in demeter?


-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Data Import Bug (Athena 0.9.26)

[Ravel, Bruce]

Unfortunately, I don't observe what you are describing.

Grasping at straws here, but are you inadvertently using this import 
feature?

 
http://bruceravel.github.io/demeter/documents/Athena/import/preproc.html#rebinning-quick-scan-data

B

On 04/05/2019 07:33 AM, Clark Adam Hugh (PSI) wrote:
> Dear Mailing List
> 
> I have recently come across a data import error when using Athena 
> version 0.9.26. When importing data there appears to be a resampling 
> which significantly reduces the resolution of the data. Attached is an 
> example dataset with an energy step of 0.5 eV on the Cu K edge. When 
> importing with Athena 0.9.26 this data is significantly resampled 
> resulting in an energy resolution on the edge of 1.5 eV which can either 
> be seen by plotting or by exporting and inspecting the datafile. Using 
> version 0.9.25 resolves this issue entirely. The data itself appears to 
> actually be visible correctly during the import process (the import tab 
> shows the data listed correctly when choosing which columns to import).
> 
> Is there a setting somewhere within Athena 0.9.26 that sets the default 
> behavior to resample the imported data?
> 
> Thanks
> 
> Adam Clark
> 
> __
> Paul Scherrer Institut
> Adam Hugh Clark
> WLGA/129
> Forschungsstrasse 111
> 5232 Villigen PSI
> Schweiz
> 
> Telefon: +41 56 310 41 51
> E-Mail: adam.cl...@psi.ch
> 
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Export measured difference integrated areas

[Ravel, Bruce]

That would certainly be a good feature

B


On 04/04/2019 09:29 AM, Patridge, Christopher wrote:
> Hello everyone,
> 
> Is there an export option for the integrated areas found in difference 
> spectra from Athena?  It appears the only option is exporting the 
> picture of plotted values?  I was hoping to save a little from 
> transcribing each value inside Athena.
> 
> Thanks everyone,
> 
> Chris
> **
> Dr Christopher Patridge
> Assistant Professor
> Department of Chemistry
> SASE 315
> D’Youville College
> 320 Porter Ave.
> Buffalo, NY 14201
> 716-829-8096 / 315-529-0501
> patri...@dyc.edu 
> 
> 
> 
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] how to best implement fitting u (oxygen parameter) in an spinel

[Ravel, Bruce]

The assumption we make when doing EXAFS analysis with Feff and any 
Feff-using tool (Artemis, for example, but there are others) is that a 
small change in local configuration affects the argument of the sin() in 
the EXAFS equation significantly, but the scattering function negligibly.

To say that another way, a small change in length between absorber and 
scatterer is clearly visible in sin(2kr).  However, if you were to 
recalculate the scattering function upon making that small change in 
configuration, you would find that the scattering function changes very 
little.

Thus, to a good approximation, we can compute the scattering functions 
using a starting configuration, then model changes in configuration as 
deltaR terms in the analysis.

In Artemis, this means writing interesting math expressions in the 
deltaR fields for the paths that you include in the fit.  Those math 
expressions should encapsulate the way that a change in your u parameter 
changes the absorber-scatterer distances.

This is discussed in the Artemis user manual and in LOTS of EXAFS 
analysis papers in the literature that do this.  Look up papers by names 
that you recognize from this mailing list.

HTH,
B


On 04/01/2019 01:46 PM, Juan de la figuera wrote:
> Dear all,
> 
> I have a naive question. I have some mixed spinels, of which I want to 
> fit among other parameters the oxygen parameter u which indicates the 
> distortions around the oxygen anions, using only the single scattering 
> paths.
> 
> What would be the simplest way of fitting that? In the tests I did 
> before using Artemis, I would start with the structure (usually with a 
> cif file), using atoms/FEFF to calculate all the paths. But changing u 
> changes the initial structure.
> 
> One way I can think of is to apply a correction, obtained by hand, to 
> deltaR on each O-M path. Of course, this is not a general solution but 
> only good for a few paths. Am I missing something?
> 
> Thanks in advance,
> Juan
> 
> 
> 
> 
> Juan de la Figuera
> Instituto de Quimica Fisica "Rocasolano"
> c/ serrano, 119
> Madrid, Spain 28006
> Phone: +34 91 745 9517
> http://surfmoss.iqfr.csic.es/ 
> 
> http://scholar.google.com/citations?user=GOiP624J
> -
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] ????Athena????32??????????????????

[Ravel, Bruce]

On 01/16/2019 06:41 AM, 2225295803 wrote:
> 32?? 
> ??32EXAFSAthena??

With the help of Google Translate, I was able to understand that you are
looking for a 32 bit version of my software.

32 bit versions of the software were built until a couple years ago.  I
no longer have a computer on which to build the 32 bit version.

Historical releases, including 32 bit packages, of the software are
available at the website.

http://bruceravel.github.io/demeter/

Scroll all the way to the bottom.

B


-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Unwanted rescaling of energy axis when importing ascii file into Athena (Demeter 0.9.26)

[Ravel, Bruce]

Lukas,

A mistake is made related to the keV units in the first column of your 
data file.  This mistake is made only with the Ifeffit backend and only 
for data with keV energy units.  The Larch backend does not suffer from 
this problem.  Nor do data files with eV energy units.

I just checked a fix for this into github.  I hope to make a new windows 
release sometime soon ... it will have this fix.

Two possible work-arounds:

1. Use data files with eV energy units.  The problem only effects data 
measured in keV units.

2. If you cannot wait for a new Windows release, I can explain how to 
modify the relevant source code file to correct the mistake.  It would 
involve editing 3 lines of a file installed on your computer.

B

On 01/09/2019 09:35 AM, Lukas Grote wrote:
> Hello,
> 
> I am reporting an apparent bug in Athena (Demeter 0.9.26, Windows 10). 
> When I import high energy resolution XAS data from an ascii file, the 
> energy axis is automatically rescaled to 1.2eV step size, thus 
> drastically reducing the resolution of the data. When the imported data 
> has energy steps larger than 1.2eV, no rescaling occurs.
> 
> This issue may be similar to the one reported in March 2018 under the 
> topic "Athena (Demeter 0.9.26) does not import all datapoints from ascci 
> file". However, the issue I am seeing always results in 1.2eV steps in 
> the imported data. If my original file hast 0.3eV steps, the number of 
> points is reduced by a factor of 4. If it has 0.6eV steps, the number of 
> points is reduced by a factor of 2.
> 
> I couldn't find any option to switch this recaling on / off, or to 
> change the target energy step size.
> 
> The problem does not occur with Demeter 0.9.25. Attached please find two 
> screenshots of the data import dialog for both versions of Demeter. The 
> plots show the difference in energy scale. I also attached the original 
> data file "no_rebin.dat" as well as spectra exported from both Demeter 
> versions, one of them showing the 1.2eV steps.
> 
> Thank you and all the best,
> Lukas
> 
> -- 
> Lukas Grote
> 
> University of Hamburg
> Center for Hybrid Nanostructures
> Institute for Nanostructures and Solid State Physics
> Luruper Chaussee 149, Bld. 600, Room 2.62
> 22761 Hamburg
> Germany
> 
> +49 40 42838 1614
> 
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Extrating standard deviation value from merged dataset in Athena

[Ravel, Bruce]

That doesn't get exported by any of the export options.

That's kind of a weird oversight.  I am surprised no one has ever 
pointed that out and I am surprised that I never thought to put that 
into one of the export files.  It's available and is saved to and 
restored from the project file.  Odd oversight ... after all these years

Sorry for the bad news.
B


On 11/15/2018 12:02 PM, Christian Rein wrote:
> Hi,
> 
> Do anyone know how to obtain the standard deviation value that Athena 
> calculates when merging the data?
> 
> Best,
> 
> Christian
> 
> **
> 
> *Christian Rein*
> 
> Postdoc
> 
> DTU Energy
> 
> *Technical University of Denmark*
> 
>   
> 
> http://www.dtu.dk/~/media/DTU_Generelt/Andet/DTU_email_logo_01.gif
> 
> Department of Energy Conversion and Storage
> 
> Building 771, room 010
> 
> 4000 Roskilde
> 
> Denmark
> 
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] difference of feff interpretation generated by different version of artemis

[Ravel, Bruce]

As I have said before, that's a feature, not a bug.

http://bruceravel.github.io/demeter/documents/Artemis/extended/fuzzy.html

B

On 10/17/2018 10:19 AM, woschangqi...@126.com wrote:
> Hello, everyone. I recently ran into an issue in using Artemis software.
> 
> I  used two versions of Artemis  (Artemis 0.8.012 and Demeter 0.9.25) to 
> generate the paths from the same input file (FeS2.inp), but there is big 
> difference between the two path results.
> 
> e.g. 1, the path4 and path6 generated in Demeter 0.9.25  are not 
> generated in Artemis 0.8.012, though they have a very low applitude.
> 
> e.g. 2, the path7 in Demeter 0.9.25 is likely identical to path5 in 
> Artemis 0.8.012 judging from the degenracy, reff, and amplitude, but 
> their scattering name are different: (+)-S1-S2-(+) in Demeter 0.9.25 and 
> (+)-S2-S1-(+) in Artemis 0.8.012. In my opinion, the scattring sequence 
> of photoelectron in multiple scattering affect the paramters of paths. 
> Why do these two paths have different scattering sequence? Thanks very 
> much for your help.
> 
>>> Qiang Chang
>>> Institute of Coal Chemistry, CAS
>>> Leyuan South II Street 1, Yanqi Development Zone
>>> Huairou District, Beijing, POB. 101407
>>> P.R. China
>>> Email: w oschangqi...@163.com 
>>> 
>>
> 
> 
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-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 06BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

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[Ifeffit] larch warning that I don't understand

[Ravel, Bruce]

Matt,

When Larch starts, what is meant by warnings like this:

  No handlers could be found for logger "pyFAI.opencl.common"

or 

  No handlers could be found for logger "pyFAI.gui.matplotlib"

The first one went away by installing python's opencl interface -- a rather 
sizable prerequisite! I haven't figured out how to make the second one happy.

Thanks,
B

--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage: http://bruceravel.github.io/home
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter


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Re: [Ifeffit] determining reasonable fitting parameters

[Ravel, Bruce]

That's my understanding also.
B

--
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/


On July 27, 2016, at 7:01 PM, Scott Calvin  wrote:

This is also related to whether it is appropriate to apply a McMaster 
correction to sigma2 after fitting, right? (Or “during,” but since it’s just an 
offset, it amounts to the same thing.) In Bruce’s method, a McMaster correction 
is appropriate, although often it’s small in comparison with the reported 
uncertainties anyway. In Matthew’s method, there is no need for a McMaster 
correction. Essentially McMaster attempts to correct for using a constant 
normalization instead of the expected smooth decrease in the normalization 
factor after the edge. Or am I remembering the meaning of that correction wrong?

—Scott Calvin
Sarah Lawrence College

> On Jul 27, 2016, at 5:26 PM, Matthew Marcus  wrote:
>
> I think that if the wiggliness in the spline is enough to cause trouble by 
> the mulriplicative effect, then it's probably eating up the wiggles by 
> subtraction, anyway.
> However, I can see that you wouldn't want the bother and potential for 
> trouble involved in having a second curve for the post-edge division.
>mam
>
> On 7/27/2016 2:08 PM, Bruce Ravel wrote:
>> On 07/27/2016 04:56 PM, Matthew Marcus wrote:
>>> Oh, so it assumes that chi(k) = (mu(E(k))-spline(k))/const.?  Mine does
>>> (mu(E(k))-spline(k))/spline(k), which I guess has its own problems
>>
>> Exactly.  Both solutions have problems.  The potential for trouble with 
>> "/const" seems less severe to me and easier to support (in the sense of 
>> supporting the use of a software package).  So that's why Athena does what 
>> she does.
>>
>> B
>>
>>
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Re: [Ifeffit] PGPLOT intallation error!

[Ravel, Bruce]

"Debutant". Thanks spell-check!

I meant "debian"

B


On May 26, 2016, at 1:45 PM, "Ravel, Bruce" <bra...@bnl.gov> wrote:


Ernesto,

That cannot possibly be the entire screen output. If you don't know enough to 
interpret and troubleshoot the screen output, then you cannot reliably edit it.

Capture everything. Post everything. If you do not provide sufficient context, 
you cannot expect me to be able to help.

It would be useful to tell us what kind of computer you are using.  The 
debutant answer may be different from the Mac answer or from the Red Hat answer.

B


On May 26, 2016, at 1:38 PM, Ernesto Ramos <jer...@hotmail.com> wrote:


Dear all,
after running the PGPLOT_install script, I'm trying to continue the 
installation using ./configure, and sudo make, but in this step appears the 
following error message,


collect2: error: ld returned 1 exit status
make[3]: *** [libifeffit.so] Error 1
make[3]: Leaving directory `/home/ernesto/ifeffit-master/src/lib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/ernesto/ifeffit-master/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/ernesto/ifeffit-master'
make: *** [all-recursive-am] Error 2

Could you help me to overcome this error?

Thanks a lot!



---
Ernesto Ramos
Physical Engineer
University of Brasilia, Campus Darcy Ribeiro
70910900 Brasilia
DF, Brazil
Tel.  (+55) 61 30343370
Cel.  (+55) 61 82317244
---
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Re: [Ifeffit] PGPLOT intallation error!

[Ravel, Bruce]

Ernesto,

That cannot possibly be the entire screen output. If you don't know enough to 
interpret and troubleshoot the screen output, then you cannot reliably edit it.

Capture everything. Post everything. If you do not provide sufficient context, 
you cannot expect me to be able to help.

It would be useful to tell us what kind of computer you are using.  The 
debutant answer may be different from the Mac answer or from the Red Hat answer.

B


On May 26, 2016, at 1:38 PM, Ernesto Ramos  wrote:


Dear all,
after running the PGPLOT_install script, I'm trying to continue the 
installation using ./configure, and sudo make, but in this step appears the 
following error message,


collect2: error: ld returned 1 exit status
make[3]: *** [libifeffit.so] Error 1
make[3]: Leaving directory `/home/ernesto/ifeffit-master/src/lib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/ernesto/ifeffit-master/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/ernesto/ifeffit-master'
make: *** [all-recursive-am] Error 2

Could you help me to overcome this error?

Thanks a lot!



---
Ernesto Ramos
Physical Engineer
University of Brasilia, Campus Darcy Ribeiro
70910900 Brasilia
DF, Brazil
Tel.  (+55) 61 30343370
Cel.  (+55) 61 82317244
---
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Re: [Ifeffit] Bug report ATHENA (Demeter 0.9.24)

[Ravel, Bruce]

Sunil,

You are correct.  Athena does not save settings from the LCF tool.  That's not 
so much a bug as it is a missing feature.

It's on my to do list (there's a link to the to do list on the Demeter home 
page).  I am hoping to make a new release next month ... I will try to address 
this before then.

B


--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage: http://bruceravel.github.io/home
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter


From: Ifeffit [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Patel, 
Sunil [sunil.pa...@honeywell.com]
Sent: Monday, May 16, 2016 5:54 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Bug report ATHENA (Demeter 0.9.24)

Hello All,
I am using the latest version of Demeter (0.9.24) in Windows 7 Enterprise 
(64-bit).
In the process of doing LCF, the fit details (for ex. standards used for 
fitting, fitting range, phase fractions etc.) are not saved into the project 
file. This (very useful!) feature was available in the older version of ATHENA.

Please find attached a project file. To reproduce the problem:

  1.  Open the project file in new ATHENA.
  2.  Do LCF for marked datasets (Data_1 to Data_6) using standards (Standard_1 
and Standard_2), with LCF range= -20 to 40 eV and hitting the “Fit marked 
groups” tab.
  3.  Save the project file and close it.
  4.  Re-open the file and go to the LCF page. The details are not saved. We 
need to re-do the fits to get the values.
  5.  To check, open the ATHENA project file in older version of ATHENA and 
repeat the above steps. LCF details are shown on re-opening the file.

A similar bug report was made last year for an earlier version of Demeter 
(0.9.21).

(http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05057.html )

Thanks & regards,
Sunil Patel

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Re: [Ifeffit] low and negative ss2 and bug in the log file of fit history

[Ravel, Bruce]

 Further i have found a small bug in the fit history window. After each fit, 
 earlier data set in the log file of
 fit history is found to overwritten with the latest fitting parameters (like 
 k range, dk, etc..). Here in my
 log file window, all fit data set contain the same data set value as like the 
 last fit (fit9).

This appears to be the same issue discussed in this thread:

  
http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04877.htmlhttp://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04877.html

If you try one of the so-called pre-release versions at

  http://bruceravel.github.io/demeter/#windows

I think you'll find that the problem goes away.

B

--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage: http://bruceravel.github.io/home
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Raj kumar 
[rajr...@gmail.com]
Sent: Monday, June 01, 2015 11:42 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] low and negative ss2 and bug in the log file of fit history

Dear All,

I am trying to fit the first shell FT of bulk YbVO4 (measured in dispersive 
EXAFS) with the reference YbVO4. The resultant SS2 value for the first shell is 
found to be low for wide k-range selection, whereas approaching negative for 
the relatively short k-range window. While approaching negative value (of ss2), 
i have tried to constraint the ss2 value using expression abs(ss). In that 
case, ss2 value is found to take value 0. Please help me to figure out the 
problem.


Regards,
Raj

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Re: [Ifeffit] Create Atoms input with just coordinates

[Ravel, Bruce]

Maryline,

Vasiliy's is the correct answer.  You don't have a crystal.  Atoms is the right 
 tool for interpreting crystal data, but not the right tool in your case.

See page 7 and following in

  https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples

and/or watch my Modelling non crystalline samples using Artemis talk at

  http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html

B

--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage: http://bruceravel.github.io/home
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Василий Прядченко 
[vasiliy.pryadche...@gmail.com]
Sent: Monday, June 01, 2015 11:04 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Create Atoms input with just coordinates


You can simply replace atomic coordinates in ATOMS card in feff.inp file.

01 Июн 2015 г. 17:58 пользователь M Ferrier 
mferr...@hotmail.commailto:mferr...@hotmail.com написал:
Hi,

I am trying to create an Atoms input file for actinium. Since not a lot is 
known about this element we run some DT calculations. One molecule of Ac 
acetate in a box surrounded by water.
I have the coordinate of each elements. I was told the symmetry was P1 (I guess 
for the box) but unfortunately their is no symmetry in liquid and thus we 
cannot input the cell parameters (distances a, b, c and angles alpha, beta, 
gamma). I was wondering if their were a way to make Atoms run to obtain the 
Feff calculations. Or we should use a different model with a known solid?

Thank you for your help

Maryline Ferrier

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Re: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED]

[Ravel, Bruce]

Zhaoming,

This conversation should be happening on the Ifeffit Mailing List.  I did not 
notice that last night when I replied to your first email.  Yet another reason 
not to answer email late at night!

I continue to be sceptical of your claims.  I have no problems with the data 
file you sent on either Windows or Linux once I correctly select the columns in 
the column selection dialog.  Once imported, the default values for 
normalization are set as I expect and the data is interactive in the normal 
manner.

Here are some hints about how to provide a useful bug report:
   http://bruceravel.github.io/demeter/pods/bugs.pod.html
Please read it carefully.

If there is more to this conversation, please use the mailing list.

B


--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage: http://bruceravel.github.io/home
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter


From: ZHANG, Zhaoming [z...@ansto.gov.au]
Sent: Thursday, April 02, 2015 1:00 AM
To: Ravel, Bruce
Subject: RE: [Ifeffit] Importing data with the new version of Athena 
[SEC=UNCLASSIFIED]

Hi Bruce,
Sorry, I did have to specify column 4 as energy, 7 as Io and 8 
as It. The new version of Athena does read the .dat file in, but the default 
values for normalization are way wrong, and it doesn’t work by manually change 
them either.
I’m happy to send you screen shots if necessary. Thanks again 
for your help.
Zhaoming

From: Ravel, Bruce [mailto:bra...@bnl.gov]
Sent: Thursday, 2 April 2015 12:43 PM
To: ZHANG, Zhaoming
Subject: RE: [Ifeffit] Importing data with the new version of Athena 
[SEC=UNCLASSIFIED]


Zhaoming,

I'm afraid I am sceptical of your story.  I have no trouble reading this file 
and I don't believe that any change I've made since 0.9.20 would have affected 
this.  Who knows, though.  I'll take a lok on a windows machine when I get into 
work tomorrow morning.

It's a rather awkward file.  The first column is an index, not energy.  That's 
one of my pet peeves -- just a ridiculous way to present the data and kind of 
mean-spirited to the user.  When something is measured in energy, the first 
column should be energy.

That means you have to explicitly select column 2 as the energy.  Column 2 
appears to be in keV, so you need to explicitly set that in the column 
selection dialog.  Because column 1 was not the energy, Athena had no way of 
figuring that out.

I have no idea which columns have data in them.  7 and 8 look rather like I0 
and It.  So you need to explicitly set your data columns, as well.

I've attached a screenshot of the column selection dialog with all those 
settings.

When data are presented as obfuscated as they are in this data file, it is not 
reasonable to expect that Athena will magically know how to disentangle 
everything without your help.  You have to be responsible for knowing which 
columns to combine to turn your raw data into mu(E).

B

--
 Bruce Ravel   
bra...@bnl.govmailto:bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage: http://bruceravel.github.io/home
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter

From: ZHANG, Zhaoming [z...@ansto.gov.au]
Sent: Wednesday, April 01, 2015 7:34 PM
To: Ravel, Bruce
Subject: [Ifeffit] Importing data with the new version of Athena 
[SEC=UNCLASSIFIED]
Dear Bruce,
I’ve encountered the same problem as Sander Bruun. My data were 
obtained from the Australian Synchrotron. In the past, I could read the .dat 
file (see attached example) directly into Athena. But it doesn’t work with the 
new version (0.9.20), and the beamline scientist doesn’t know why either.
I would really appreciate if you could let me know what ‘fix’ 
we need! Thanks so much.
Warm regards,
Zhaoming

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Re: [Ifeffit] Athena does not React after 2-4 steps

[Ravel, Bruce]

I need to see the C:\Users\Michael\AppData\Roaming\demeter\dathena.log file.

You don't need to guess what information to send me.  I explain it clearly here:

  
http://bruceravel.github.io/demeter/pods/bugs.pod.html#The_basic_rules_to_good_bug_reportin

B

--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage: http://bruceravel.github.io/home
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter



From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Michael Kömm 
[michael.ko...@uni-jena.de]
Sent: Wednesday, October 22, 2014 9:16 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Athena does not React after 2-4 steps

Dear Bruce and dear mailing list,

Athena stops working after doing a maximum of four steps (f.e. removing
points, import data,...) when running on my PC with Windows 8. It either
says not responding or just shuts down. Whenever Athena shuts down the
errors in the .txt in the directory of the project differs. But it
always looks like this:

  line 0: warning: Skipping unreadable file
C:\Users\Michael\AppData\Roaming\demeter\stash\gp_leqfnhqh
  line 0: No data in plot

only the file name changes. But there's never a file with that name in
that directory.

Sometimes there is as well a window opened that says: gnuplot.exe is not
working anymore.
I've deleted the Roaming\demeter folder but it didn't end the troubles.

Hope there is a way to end this problem.

Sincerely yours

Michael Koemm


PS: There is also one of my projects in the attachment.


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Re: [Ifeffit] Artemis closes when I try to open a project file or import data

[Ravel, Bruce]

I cannot solve a problem that I cannot reproduce on my own computer.  Please 
read and follow these hints on submitting a useful bug report:

http://bruceravel.github.io/demeter/pods/bugs.pod.html#The_basic_rules_to_good_bug_reportin

In particular note the location of the error message -- something that has been 
discussed dozens of times on this mailing list -- which I will need to see.

In this case, you seem to be saying that one day Artemis worked and the next 
day Artemis didn't work.  What changed on your computer in the interim?

B


--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage: http://bruceravel.github.io/home
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Kurinji Krishnamoorthy 
[kurinjikrishnamoorthy2...@u.northwestern.edu]
Sent: Monday, October 20, 2014 11:31 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Artemis closes when I try to open a project file or import 
data

Hi,
Artemis had been working well on my laptop for a while. But today when I 
attempted to open a saved project file ( with a *.fpj extension), the program 
tried to open it for a while but then ultimately closed without any error 
messages. A similar thing occurred when I tried to import an Athena data file 
into Artemis. I was wondering if anybody had any idea how to fix this problem?

Thanks,
Kurinji
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Re: [Ifeffit] to use scattering path in different model or to construct a new model which is the combination of different simple compound

[Ravel, Bruce]

Chances,

You should read this paper by Shelly Kelly: 
http://dx.doi.org/10.1016/S0016-7037(02)00947-X

It shows an example that is, I think, similar to your question.  She fits an 
unknown by combining paths from different FEFF calculations.

B


On June 29, 2014, at 2:19PM, ZHAN Fei wrote:


Dear all,

  I have a confusion.For instance,when I want to fit a simple which has  
Pt-O,Pt-S,Pt-N,Pt-Pt cordination shell;when can not find a compound with all 
same shell or can not find one with all suitable bond length,can I use 
different scattering path from different model to fit diffferent shell? and if 
do so atom may in different pot in feff ,are the phase and amplitude still 
transformable?  Other choice is to use path-like object in demeter to construcr 
a more suitable distance scattering path,or construct a new cluster model 
according to several cif files, myself,which proticol is feasible or better ?



sincerely

zhanfei
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Re: [Ifeffit] to use scattering path in different model or to construct a new model which is the combination of different simple compound

[Ravel, Bruce]

Chances???  Damn autocorrect!

Sorry about that Zhanfei.

B


On June 30, 2014, at 10:09AM, Ravel, Bruce wrote:


Chances,

You should read this paper by Shelly Kelly: 
http://dx.doi.org/10.1016/S0016-7037(02)00947-X

It shows an example that is, I think, similar to your question.  She fits an 
unknown by combining paths from different FEFF calculations.

B


On June 29, 2014, at 2:19PM, ZHAN Fei wrote:


Dear all,

  I have a confusion.For instance,when I want to fit a simple which has  
Pt-O,Pt-S,Pt-N,Pt-Pt cordination shell;when can not find a compound with all 
same shell or can not find one with all suitable bond length,can I use 
different scattering path from different model to fit diffferent shell? and if 
do so atom may in different pot in feff ,are the phase and amplitude still 
transformable?  Other choice is to use path-like object in demeter to construcr 
a more suitable distance scattering path,or construct a new cluster model 
according to several cif files, myself,which proticol is feasible or better ?



sincerely

zhanfei
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Re: [Ifeffit] Demeter on Ubuntu 14.04

[Ravel, Bruce]

I'm on vacation right now and only have my tablet, so typing a decent response 
is a challenge.

From what you included, it looks as though you pulled or cloned the latest 
from within, but did not do the perl Build.pl or ./Build installdeps 
steps.  If not starting from a clean install, it may help to also ./Build 
touch_wrapper.

I'll be with email only sporadically for a while, unfortunately.

B


On May 21, 2014, at 11:27AM, Denis TESTEMALE wrote:

Dear members of the list,

it's that time of the (Linux) Ubuntu life cycles where you do upgrades and 
break previously working programs... Upgrading to Ubuntu 14.04 made no 
exception for me. It also broke the old Hephaestus programs, but I think it is 
definitely time that I stop being lazy and switch to Demeter. So I'll focus on 
the Demeter problems. Sorry about the lengthy post full of pasted error 
messages.

--
Context: I'm running Ubuntu 64 bits 14.04. Demeter version 0.9.20. I followed 
Ubuntu specific instructions found here:
https://gist.github.com/3959252
Demeter once worked but I cannot guarantee that it did just before the upgrade 
to 14.04. After the upgrade, both trying to run dathena or to rebuild the 
package ran into errors such as:

denis@huchet4:~/demeter$ ./Build
Building Demeter
Perl API version v5.14.0 of DateTime does not match v5.18.0 at 
/usr/share/perl/5.18/XSLoader.pm line 92.
Compilation failed in require at lib/Xray/data/elam2st.PL line 405.
BEGIN failed--compilation aborted at lib/Xray/data/elam2st.PL line 405.
lib/Xray/data/elam2st.PL failed at 
/home/denis/perl5/lib/perl5/Module/Build/Base.pm line 2963.

denis@huchet4:~/demeter$ dathena
Perl API version v5.14.0 of Wx does not match v5.18.0 at 
/usr/lib/perl/5.18/DynaLoader.pm line 207.
Compilation failed in require at /home/denis/perl5/bin/dathena line 11.
BEGIN failed--compilation aborted at /home/denis/perl5/bin/dathena line 11.

---

So I erased the folders and reinstalled everything. The installation ran 
smoothly (except I had to install missing deps several times, but no error 
messages at the end). Now I can start the programs but run into problems:

For Dephaestus: everything works, I can plot f' and f (gnuplot is working) but 
when I try to plot some XANES references in the standards tab, it crashes with:

Attribute (bkg_nc0) does not pass the type constraint because: Validation 
failed for 'LaxNum' with value 0,00 at 
/usr/local/lib/perl/5.18.2/Moose/Exception.pm line 37

Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)')
 called at reader Moose::Exception::trace (defined at 
/usr/local/lib/perl/5.18.2/Moose/Exception.pm line 9) line 7

Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)')
 called at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 49

Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)',
 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Class/MOP/Method.pm 
line 128
Class::MOP::Method::execute('Moose::Meta::Method=HASH(0xa44deb8)', 
'Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)', 
'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 56

Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)',
 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Meta/Class.pm 
line 282
Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0x9a3f0d8)', 
'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 27

Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConstraint', 
'type_constraint_message', 'Validation failed for \'LaxNum\' with value 
0,00', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 
'value', '0,00') called at /usr/local/lib/perl/5.18.2/Moose/Util.pm 
line 52
Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint', 
'type_constraint_message', 'Validation failed for \'LaxNum\' with value 
0,00', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 
'value', '0,00') called at accessor Demeter::Data::bkg_nc0 (defined 
at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm 
line 309) line 4
Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xa372058)', '0,00') 
called at 
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm 
line 323
Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xa372058)') called at 
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 
674

Re: [Ifeffit] XANES + EXAFS for light elements in diluted samples

[Ravel, Bruce]

Federico Boschirini's compilation of the world's XAFS beamlines should help:

http://www.iucr.org/resources/commissions/xafs

B


On May 10, 2014, at 12:04PM, Marcelo Alves wrote:

Dear all,

I am interested in running some measurements of XANES and EXAFS K-edge spectra 
of elements such as  Ca and S sorbed onto commonly found oxisol minerals, i.e 
natural kaolinite, gibbsite, hematite, and goethite. Besides appropiate filters 
to attenuate the fluorescence signals that come from elements such as Al and 
Si, what would the other instrumental conditions (e.g detector type, photon 
flux, etc...) needed for getting usable spectra of those elements in diluted 
samples? Any suggestion on the more adequate beamline to carry out such 
measurements?

Kind regards,

Marcelo.
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Re: [Ifeffit] XANES + EXAFS for light elements in diluted samples

[Ravel, Bruce]

There are three links, right there in the sidebar.
B


On May 11, 2014, at 6:18PM, Matthew Marcus wrote:

It took some clicking to get from the link below to where there's actually such 
a compilation: http://www.xafs.org/Experiment .  Is that the one you meant?
mam

On 5/11/2014 3:04 PM, Ravel, Bruce wrote:
 Federico Boschirini's compilation of the world's XAFS beamlines should help:

 http://www.iucr.org/resources/commissions/xafs

 B



 On May 10, 2014, at 12:04PM, Marcelo Alves wrote:

 Dear all,

 I am interested in running some measurements of XANES and EXAFS K-edge 
 spectra of elements such as  Ca and S sorbed onto commonly found oxisol 
 minerals, i.e natural kaolinite, gibbsite, hematite, and goethite. Besides 
 appropiate filters to attenuate the fluorescence signals that come from 
 elements such as Al and Si, what would the other instrumental conditions (e.g 
 detector type, photon flux, etc...) needed for getting usable spectra of 
 those elements in diluted samples? Any suggestion on the more adequate 
 beamline to carry out such measurements?

 Kind regards,

 Marcelo.


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Re: [Ifeffit] LCF fitting marked groups in Athena

[Ravel, Bruce]

Thanks as always for the bug report, Fred.  I am on travel right now, but I am 
hoping to make a new release in the next few weeks.  I will put this on the to 
do list.

The work-around is, as I am sure you know, rather obvious.  You'll have to do 
the fits one-by-one.

B


 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 Homepage:http://xafs.org/BruceRavel
 Software:https://github.com/bruceravel

From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of 
fred.mosselm...@diamond.ac.uk [fred.mosselm...@diamond.ac.uk]
Sent: Saturday, November 09, 2013 6:49 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] LCF fitting marked groups in Athena


Dear Bruce,
The PCA fitting marked groups on Athena seems to have a problem in windows. 
Using your teaching example if you highlight several (e.g. 3 spectra ) and try 
to fit them to some standard using the fit marked group button the programme 
does some LCF fitting and then seems to be about to report the results but 
instead crashes. I have tried this on both windows xp and windows 7 platforms 
with the same results. Individual spectrum fitting works fine.

Log file attached
Thanks
Fred





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Re: [Ifeffit] Problem with Demeter 0.9.18 pluck tool

[Ravel, Bruce]

Denis,

I have a question.  What gnuplot terminal do you use?  That is, what's the 
value of the gnuplot-terminal configuration parameter?

It seems that the way I do the pluck buttons does not work with the X11 
terminal, but it should work with the wxt terminal.  So if that parameter is 
set to X11, change it to wxt, then try plucking again.

B


 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 Homepage:http://xafs.org/BruceRavel
 Software:https://github.com/bruceravel


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Denis Testemale 
[denis.testem...@grenoble.cnrs.fr]
Sent: Friday, September 27, 2013 8:24 AM
To: ifeffit mailing list
Subject: [Ifeffit] Problem with Demeter 0.9.18 pluck tool

Dear members of the list,
I finally got the opportunity to start using Dathena. I don't know if
I've found a bug or if I'm doing something stupid (chances are not too
low, actually...).

- I am using Ubuntu 13.04
- Demeter 0.9.18 (I did the upgrade to 0.9.18 but ran into some error
messages as reported on September 10th on this list, could they be
related to the behaviour I am reporting here?).
- I cannot say if it worked before the upgrade to 0.9.18 since I never
took the time to use Demeter properly until now.

I'm trying to pick/pluck a value from the graph.
- When I first launch Dathena, and I press a pluck button for the first
time I can see the expected message at the bottom of the GUI (Double
click on a point to pluck its value ...): as hard as I tried (I tried
many different combinations) I could never get the thing to work
(parameter value in the 'box' never records the value where I double
click). After 10s I see the 'Pluck timed out' message.
- Then, when I click again on the pluck button, a value is recorded
instantly in the 'box' without any double-clicking from me, and this
value is crazy. An example: for a low k parameter of the FT I get
-10. The example in the attached screenshot shows a value for the
normalization range low limit at -107112.52eV (note that the E0 value is
'integrated' in this number: the iron edge at 7112.52, see screenshot. I
tried another set of data, silver K edge and the same thing occured: a
weird number, with the E0 value inside, got recorded in the 'box).
- Same problem with Dartemis.

Tell me what I can do to help... or what I'm doing stupid.
Thanks.
denis

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Re: [Ifeffit] Problem with Demeter 0.9.18 pluck tool

[Ravel, Bruce]

Hi Denis,

The plucking thing is odd.  Both the X11 and wxt terminals seem to interact 
with the clipboard in the same way, but my code only successfully retrieves the 
point from the clipboard when I use the wxt terminal.

B


 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 Homepage:http://xafs.org/BruceRavel
 Software:https://github.com/bruceravel

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Re: [Ifeffit] Athena- Demeter 0.9.14 importing data

[Ravel, Bruce]

As I have said many, many, many times on this mailing list, there is nothing I 
can do to fix -- much less understand -- a problem without being able to 
reproduce it on my own computer.

Atul, the reason you have not gotten a response to your post is because you did 
not provide an example of the data that triggers the problem.  Without that, 
there truly is nothing I or anyone else can do to help you.

If anyone out there has a suggestion for how I can explain this point, either 
in this forum in in another location, in a way that will result in people 
submitting actionable bug reports, I would be very grateful.

B



From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Atul Bansode 
[abans...@iciq.es]
Sent: Friday, May 03, 2013 6:28 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Athena- Demeter 0.9.14 importing data

Hi All,
I am using Athena (Demeter 0.9.14) to process the EXAFS data of Copper samples.
Athena reads the data correctly however my problem is concerned with the 
importing the data.
When I import the data, in the Athena: Column Selection dialog box the Energy 
units is shown in keV by default. Since my data is in eV, I can always change 
the keV to eV and work when it’s a single file.
My problem starts when I try to import multiple files where I choose Energy 
units as eV in the dialog box however this setting gets applied to the first 
file only. Remaining data files are read as keV which creates a problem for me 
to process the data.

Is there any way to apply same Energy units to all the files while they are 
getting imported ?
Or is it possible to change the Energy units after importing files ?

I appreciate all your help.

Thanks in advance !

Best regards
Atul
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Re: [Ifeffit] Problem with running Demeter

[Ravel, Bruce]

Amitava,

It is very difficult for me to take your email seriously.  In fact, I just 
wrote an extremely sarcastic email, then thought better of it.

Looking up the web page of the cleaning tool you used, it seems that one of the 
purposes of that thing is to target third party applications (like Demeter).  
It promises to remove DLLs that it considers old or unused.  If I had to guess, 
it removed some DLLs from the system space that Demeter was relying on.  Given 
that you reinstalled Demeter and still have the same problem, it seems quite 
likely that your helpful tool did, in fact, remove DLLs from system folders.

I have not the foggiest clue how to solve your problem.  It is hard enough work 
for me to maintain a software package in a state that works on virtually 
everyone's computer.  Expecting me to be your system administrator as well 
seems outside the realm of my responsibilities.

B




From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Amitava D Roy 
[re...@lsu.edu]
Sent: Wednesday, May 01, 2013 2:23 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Problem with running Demeter

Dear Bruce,

I am having this strange problem since I used CC Cleaner to clean up my 
computer. (This may be coincidental.)

[cid:image001.jpg@01CE466F.10C0D470]


The following is the output of the dartemis.log file:

Can't load 'C:/strawberry/perl/site/lib/auto/Wx/Wx.dll' for module Wx: 
load_file:The specified procedure could not be found at 
C:/strawberry/perl/lib/DynaLoader.pm line 200.
at C:/strawberry/perl/site/lib/Wx/Perl/SplashFast.pm line 60
Compilation failed in require at C:\strawberry\perl\site\bin\dartemis.bat line 
23.
BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dartemis.bat 
line 23.

I have uninstalled and installed Demeter several times but the problem remains 
the same.

This happened just when I needed to use Demeter the most.


Thanks in advance,

Amitava Roy
J. Bennett Johnston, Sr., Center for Advanced Microstructures and Devices (CAMD)
Louisiana State University, Baton Rouge, LA 70806

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Re: [Ifeffit] artemis can not use a cif file

[Ravel, Bruce]

Shaofeng,

What have you tried so far to address your problem?

B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Shaofeng Wang 
[wangshaof...@iae.ac.cn]
Sent: Monday, April 22, 2013 10:54 PM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] artemis can not use a cif file

Hi Bruce,

I want to use a crystal structure file to calculate the path. But the software 
remind me it can not use crystal data whick has sites of partial occupancy. How 
can I solve this problem. See the file in attachment.

Shaofeng
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Re: [Ifeffit] problem with importing data between version of artemis

[Ravel, Bruce]

Georges,

Thanks for the bug report.  I'll look into it soon, although it may have to 
wait until next week.  Things are pretty busy at the beamline this week.

Cheers,
B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Georges Siddiqi 
[siddi...@inorg.chem.ethz.ch]
Sent: Monday, April 22, 2013 10:05 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] problem with importing data between version of artemis

Hi All,

I've done a fit in the old version of Artemis (0.8.014), and wanted to import 
this fit into the new version of artemis (demeter 0.9.15) that I have to play 
around with it a bit more.

The problem is, when I import the the old-style artemis project, and do the 
same fit, the values, and fit itself are nowhere near similar to what i got 
with the old version of Artemis.

what is the cause of this discrepancy? As far as I can tell from double 
checking all the fitting parameters, windows, variables, etc, they are all 
exactly the same.  Even if I try to just do a summation in the new version with 
my best-fit values from the old version, the fit is completely different.

Previously when I was importing fits between versions I had no issues 
whatsoever.

I've attached the artemis project file (W EXAFS.apj) that gives me a good fit 
in the old version, and a poor fit in the new version.

thanks,
georges
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Re: [Ifeffit] generating high res figures

[Ravel, Bruce]

As others said, it is not my intention that AA be used for publication quality 
plots, although part of the motivation to make Demeter, as compared to the 
earlier version, was not make prettier plots.  I, in fact, use screen captures 
of the plot window regularly in presentations and posters.  But I also do as 
the others advised -- I export the data to ascii column files and make 
dedicated plots for my publications.

Even aside from the fact that I chose not to make Demeter into a fully featured 
scientific plotting tool, it is wise to spend some time thinking hard about 
your plots for publication.  Figures are part of the story you are telling in 
your paper.  It is good for you and good for your reader if you spend the time 
to make beautiful, expressive plots using a highly capable plotting tool.

 Can I change the figure legends? I used sample 1 and I want to give it a 
 different name

Yes.  That's easy.  Group menu - Rename current group.  Or Shift-ctrl-l.  Or 
double click on the data group in the group list.

 Can I use special characters (e.g. Greek letters)?

Not conveniently.  Strictly speaking, if you observe the weird formatting rules 
of the underlying plotting tool, you can do so.  For example, if you you change 
Sample 1 to Sample {/Symbol a} it will be printed in the legend of the plot 
as Sample α.  But then you will have a weirdly named data group in the group 
list.  (The rest of the Greek characters are made in the same way.  Sample 
{/Symbol S} = Sample Σ and so on.)

I have never actually thought about how to make it possible to give a group a 
sensible name and have special characters plotted in the legend.  It doesn't 
seem like a high priority, but I could be persuaded.

 Can I adjust the resolution for different formats (talk vs. publication)?

Your best bet by FAR is to export the data as ascii column files and use your 
favorite plotting tool to export into a vector format, such as PDF or SVG.  The 
beauty of vector formats is that they can rescale without loss of quality.

 I am running Demeter 0.9.9.9 under XP.

You might consider upgrading.  There have been a lot of bug fixes and new 
features since then.   One such feature is the ability to export the most 
recent plot as a PNG or PDF file.

B

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Re: [Ifeffit] demeter windows download

[Ravel, Bruce]

Darren,

Erik's answer was the right one.

I updated that wiki page.  Thanks for reporting the documentation bug.

Cheers,
B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Darren Dale 
[dsdal...@gmail.com]
Sent: Sunday, February 17, 2013 10:10 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] demeter windows download

Hello Bruce, All,

I wanted to install Demeter on my windows computer this morning. I
followed links to instructions at
http://cars9.uchicago.edu/ifeffit/Demeter/WindowsUpdater , which in
turns links to https://github.com/bruceravel/demeter/downloads .
Unfortunately, github recently discontinued the downloads service, so
that is not a functioning link anymore. Is there a new location
available to find the installer?

Thanks,
Darren
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Re: [Ifeffit] Hephaestus crash

[Ravel, Bruce]

Darren,

This is fixed at github.  You can git pull and reinstall.

Since I am working on integrating Matt's larch with Demeter, I have 
instrumented one of the main choke points in Demeter with a useful (to me) 
screen message that helps me track the flow through the parts of the program 
relevant to switching between Larch and Ifeffit.  Unsurprisingly, I hadn't 
tested it quite all the situations, one of which was borken and is found in 
Hephaestus' f'/f tool.

Thanks for the heads-up.

B



From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Darren Dale 
[darren.d...@cornell.edu]
Sent: Saturday, February 16, 2013 4:09 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Hephaestus crash

Hello all,

I'm working on getting my ifeffit/demeter environment together,
following the instructions at
http://bruceravel.github.com/demeter/pods/installation.pod.html . When
I run hephaestus, select F'/F'', and then select any element in the
table, the program bails and I get some feedback in the terminal:

Can't use string (Demeter) as a HASH ref while strict refs in use
at accessor Demeter::devflag (defined at
/home/darren/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter.pm
line 100) line 8.

Sometimes, F line 29. is appended to that error message.

I'm running the forthcoming kubuntu 13.04. Any ideas how I can improve
my install?

Thanks,
Darren
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Re: [Ifeffit] Athena doesn't start - Larch server not running

[Ravel, Bruce]

I'm really sorry.  I left Demeter in a broken state on github.  I am currently 
at work getting Demeter to use Larch, but it is most certainly not ready for 
prime-time.

I will disable the use of larch in Demeter and push that to github.  I am 
currently at the beamline, so it will be an hour or two before I get to that.  
I'll post to the list when I do so.

At that time, do a git pull then rebuild and re-install Demeter.

Again, sorry for the confusion.  100% my fault for being sloppy.

B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Ivan Stijepovic 
[ivan.stijepo...@gmail.com]
Sent: Thursday, February 14, 2013 5:33 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Athena doesn't start - Larch server not running

Dear Bruce and other people in the list,

I have just installed Demeter from the git on Ubuntu 12.04 using instructions 
given by Dave Hughes (https://gist.github.com/waveform80/3959252). Everything 
went fine during installation but then I tried to start Athena using dathena 
command from the terminal and I got this message:

Demeter says: Uh oh! You have requested using Larch, but there is no Larch 
server running!

Then I installed Larch (with some problems during installation, but that is 
different story) and again tried starting Athena with the same result. When I 
tried starting Larch in a server mode with larch -r command it didn't offer a 
possibility to start Athena in the same terminal window. Then I opened a new 
tab in the terminal and just typed dathena and the GUI appeared. Now, I have 
two questions:
1. Do I have to start Larch server every time like this before using Athena or 
is there some other solution for this?
2. I tried Artemis without Larch server running and didn't get the error 
message. Is Artemis independent from Larch or are there some problems that 
might occur later?

--
Best wishes,
Dr Ivan Stijepović

Department of Materials Engineering
Faculty of Technology
University of Novi Sad
Bul. cara Lazara 1
21000 Novi Sad
Serbia

tel: +381 21 485 3750
fax: +381 21 450 413
e-mail: ivan.stijepo...@gmail.commailto:ivan.stijepo...@gmail.com
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Re: [Ifeffit] Basic question in normalization and background removal

[Ravel, Bruce]

Cyril,

My favorite answer is don't measure data that way.  At the very least, add a 
few widely spaced points in the pre- and post edge regions so that 
normalization can be done.  If you added 10 points spaced 20 volts apart to the 
data on the right, then normalization would be much less ambiguous.

The concept of the normalization algorithm is that the fine structure 
eventually damps away and all spectra approach the bare atoms spectrum.  In 
short, all data eventually approach an exponentially decaying edge step.

If you only measure a few volts above the edge, you have no clue how your 
specific data relates to that decaying edge step, thus you don't really know 
how to do the normalization.  The problem is compounded by the fact that shape 
of the actual measured data is affected by how it is measured.  If you somehow 
prepare the same material in a way that is suitable for high quality 
transmission and fluorescence, the raw data will look rather different -- the 
transmission data will tend to slope downwards from the beginning of the data 
to their end, while the fluorescence data will tend to slope upwards.  And a 
fluorescence sample with relatively high concentration will look different from 
the same material with relatively low concentration due to the relative sizes 
of the fluorescence line and the Compton/elastic contribution.  And data 
measured with an integrating detector will look somewhat different from data 
measured with an energy discriminating detector. 

If you measure enough data to do a good job of normalization, all of those 
differences can be handled in a defensible way.  If you do not, well 

While the correct answer is don't do that, it would seem that the reality is 
you've already done that.  So what now?

Someone may suggest using an algorithm that compare the measured data to 
tabulated values of the bare atom absorption.  Ifeffit does this, but that 
feature is not currently enabled in Athena.  (It's on  the to-do list, FWTW)  
Or do a google scholar search for the paper about MBACK.  That will sort of 
solve the problem in the sense that it offers a somewhat more stable way of 
dealing with short-range data.  But it's not a perfect solution for all the 
same reasons I described above.

An empirical solution would be to measure at least one proper spectrum (i.e. 
with a decent pre- and post-edge range).  Then play around with the 
normalization parameters until your short-range data on that sample looks like 
your long-range data on that same sample.  Then use that set of normalization 
parameters for your entire ensemble of short-range data and keep your fingers 
crossed that it works across the ensemble.

I understand the motivation to measure very short-range data.  You are doing a 
time-resolved experiment, or you have a bazillion samples to measure  -- one of 
the standard reasons.  The thing you must ask yourself is whether you will be 
able to interpret reliably and defensibly the data and the quantity of data 
that you measure.  Yes means *you* (and I really mean you, not Athena ... 
you) have a reliable way of overcoming the limitation that you are imposing 
upon the set of measurement.  No means you need to perform the measurement 
differently next time.

Good luck,
B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Bajamundi Cyril 
[cyril.bajamu...@vtt.fi]
Sent: Friday, February 08, 2013 2:28 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Basic question in normalization and background removal

Hello,

I have here a very basic XANES data processing. I am but a novice in this XANES 
analysis.

In Bruce’s lecture  “Athena: Data processing 
Imms://diamstream02.diamond.ac.uk/xafs-2011-2” posted in the Diamond Light 
Source website, he used the Fe_lepidocrocite.000 example to show how background 
removal and normalization is done.  For the normalization range  he used the 
range 150 – 742.610 because his original photon energy scan range is quite long 
[ Emin: -200 and Emax: 800].

However, say that your original scan range is only short e.g. within the range 
Emin : -30 to Emax: 80, such that you don’t see the non-wiggly range  and you 
only see the a short portion of the post edge range, how does one set the 
normalization range for this data? Since I’m very new to XANES analysis, I keep 
second-guessing my choice  of normalization range.

Your patience for answering this simple question will definitely help me in 
moving to the actual fingerprinting analysis that I need to do with my sample.
Many thanks.


Warm regards,
Cyril

[cid:image004.jpg@01CE05DE.B8F89320] [cid:image007.jpg@01CE05DE.B8F89320]


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Re: [Ifeffit] Problem downloading windows installer for Demeter

[Ravel, Bruce]

Javier,

Thanks for reporting this problem.  This is related to a recent change in how 
GitHub handles large binary files. I thought I had fashioned a solution.  Turns 
out that I was mistaken.

I have come up with a different solution for distributing the Installer and 
Updater files and I've updated the links at 
http://bruceravel.github.com/demeter/

Please go back and try again.  Sorry for the inconvenience.

Also, please use the Ifeffit mailing list 
(http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) for this sort of 
thing rather than emailing me directly.

Cheers,
B



From: Javier Alonso [jalonsom...@gmail.com]
Sent: Sunday, January 06, 2013 7:59 AM
To: Ravel, Bruce
Subject: Problem downloading windows installer for Demeter

Dear Dr. Ravel,

Firts, I'd like to personally thank you for Demeter: it really helps me a lot 
with my XAS data analysis. And now the problem:

I'm trying to download the windows installer for Demeter from the webpage:

http://bruceravel.github.com/demeter/

but I keep receiving the same error message again and again:

Error: blob is too big

I think this is something related to Github and the limit of file sizes, but I 
haven't been able to find an alternative downloading site or similar.

Thanks in advance,

Javier Alonso

--
Javier Alonso Masa
Departamento de Electricidad y Electrónica
Facultad de Ciencia y Tecnología.
Universidad del País Vasco
48940 Leioa(Spain)

http://www.gmmmt.net/

Phone: +34 94 601 5400 / +34 695325749
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[Ifeffit] Using this mailing list effectively

[Ravel, Bruce]

 I think you are really right, I am in too great a hurry that I lost my 
 patience to set a time to learn basics quietly. Thanks for reminding.
 And for my second question, could you give me some suggestion too?


Mr. Tian,

Asking questions is an art.  Anyone can barf out sentences that end with a 
question mark, but asking questions that will prompt a useful and constructive 
discussion is a subtle and skillful business.  Both Chris and I tried to tell 
you that in our earlier responses, but apparently there is a need to be more 
explicit.

You are doing some things wrongly.  I say this not to be mean and not to 
diminish you, but because I spend a lot of my professional time teaching people 
how to do XAS.  It is important to me that people practice our craft well.  
This mailing list is a powerful tool to that end.  When it is used well, the 
people who solicit help from this list profit significantly.  When it used 
poorly, the people who volunteer their time answering questions become 
frustrated and the person asking the questions goes away with nothing.

So ... here are three comments:

(1) I am frustrated that you are not using the most recent version of my 
software.  You are using a version of Artemis that is about 4 years old.  I 
have no intention of continuing support for the older versions of my software.

(2) Your second question refers to 4 sets of data, which you posted to the 
mailing list not in an Athena project file, but in an Artemis project file.  
That's odd.  It would be much easier to examine the data in the form of an 
Athena project file.  Many of the issues in your recent line of questioning 
referred to S02.  As Scott pointed out, the evaluation of S02 is related to the 
determination of the normalization and background.  If you want people to help 
you with your actual question, it would be prudent to provide the data in a 
form that allows examination of all steps of the data processing.  My point 
here is that you simply must think about how you pose your question -- that 
includes thinking hard about how to present your data to the person whose help 
you are soliciting.

(3) Your first email on the topic of these Cu films was somewhat misleading in 
that your initial complaint seemed to be about a strange measure of 
coordination number on a Cu foil.  In that email, you gave a hint as to the 
actual form of the data, but scant information about how the data were measured 
and none about how the data were processed and analyzed.  After prompts from 
Scott and other, you have provided a bit more information about your actual 
measurement, but not enough to actually know what's going on.  As long as your 
line of questioning remains vague as to the details of the problem, the best 
you can expect are vague answers of the sort that you have already received.


Since I am suggesting that you be more thoughtful and explicit in how you 
communicate here on the list, it is important that I do the same.  Here is an 
example of what I consider to be a well-asked question.  My example comes from 
a posting that I myself made to the WxPerl mailing list last year.  WxPerl is 
the programming tool I use to make the GUIs Athena, Artemis, and Hephaestus.  
At the time, I was having a problem getting menus to post properly when making 
right-mouse clicks in various places in Athena.  While the question is rather 
technical and I don't expect a non-programmer to follow all the details, it is 
still instructive:

http://www.nntp.perl.org/group/perl.wxperl.users/2011/03/msg7929.html

Note first that in five brief lines of text I summarized my problem.  I then 
gave a complete example of how someone else could reproduce my problem on their 
own computer.  I then explained both what I expected to happen and what 
actually happened.

The point here is that I took the time to condense my question into a form that 
the people at the other end could understand and address with a minimum of 
effort.  Sure enough, I got useful responses from 2 knowledgeable (and, no 
doubt, very busy) people.


Mr. Tian, to the extent that it seems like I am singling you out for special 
criticism, I sincerely apologize.  But you have been posting to this mailing 
list rather often of late and you are doing so in a way that is probably not 
getting you the sort of results you would like to see.  I understand that this 
is an English language mailing list and that it is difficult to be as 
expressive in another tongue as you can be in your own.  (I really do 
understand that -- I have suffered through learning two other languages in my 
life.  It really is hard.)  But you have to try if you want to get useful 
results.

B
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Re: [Ifeffit] The degeneracy and the coordination number

[Ravel, Bruce]

Go the archives for this mailing list: 
http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/index.html

Enter the words coordination and degeneracy in the box at the top of the 
page, then click the button labeled Search.

I suspect the answers from the many times this question has been asked before 
will be helpful to you.  For example, this post from Scott -- 
http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03435.html -- 
in response to a thread on this very topic -- is quite helpful.

If it's still not clear, then ask again about the part that remains confusing 
to you.

Cheers,
B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Zhaomo Tian 
[zhaomo1...@postech.ac.kr]
Sent: Wednesday, December 26, 2012 6:23 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] The degeneracy and the coordination number

Dear all,

I am confused about the degeneracy and the coordination number used in the 
Artemis program.
I want to get the coordination number of 1st shell of my copper sample, so I 
set a guess number N1=12(initial guess) as the coordination number which will 
vary during the fitting iteration, but when I am looking at the 1st path's 
parameters, there is another N appear which may stand for the degeneracy.The 
1st path of copper model is single scattering, so the degeneracy N equals 
coordination number . But when I set N=12, the guessed N1 will have a value 
which is closed to 1, only when I set N=1, the guessed N1 will have a value 
which is closed to 12. It seems that N and N1 are reciprocals. But I think N 
actually equals N1 in the single scattering case.

So I am really confused, If I want to get coordination number of a shell in a 
fitting, how can I deal with floated coordination number and its path 
degeneracy N?

Thanks so much.

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Re: [Ifeffit] Plot multiple fits in (D)Artemis and statistical errors

[Ravel, Bruce]

Hi,

I am aware of both of these problems.  The tool for overplotting fits from the 
fit history is currently broken.  So is the tool for restoring an old fit.  
Fixing both of those is on my list of things to do.  Sorry for the 
inconvenience.

B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Nilmar Camilo 
[nil...@fis.ufu.br]
Sent: Friday, October 26, 2012 8:42 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Plot multiple fits in (D)Artemis and statistical errors

Dear Bruce,

I am new in the list and really don’t know if the points raised below were 
already discussed.
In the (D)Artemis (Demeter version 0.9.13) how may I:

-  Plot different fits with the experimental data (to visually compare 
the results)

-  I don’t know if this is a (new) bug of the program but when I try to 
restore a fit the program closes. In the log file the following line is 
written: “Can't use an undefined value as a HASH reference at 
C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558.”
Obs.:  I am running Demeter in Windows 7 (Pro).

Another problem is related to the statistical errors when constraining the S0^2 
parameter to float between two limits.  The program doesn’t return the error 
for all others parameters (but just zero as the error value) as you can see 
below:

guess parameters:
  amp=   0.79284158# +/-   0. [0.95]
  enot   =   5.29826510# +/-   0. [0]
  delrIn11   =   0.00235278# +/-   0. [0]
  ssIn11 =   0.00155959# +/-   0. [0.00300]
  delrCe1=  -0.00231455# +/-   0. [0]
  ssCe1  =   0.00192778# +/-   0. [0.00300]
  delrIn11In11   =   0.02070081# +/-   0. [0]
  delrIr1=  -0.00435502# +/-   0. [0]
  ssIr1  =   0.00386517# +/-   0. [0.00300]
  delrIn31   =   0.00648507# +/-   0. [0]
  ssIn31 =   0.00669602# +/-   0. [0.00300]
  delrIn12   =   0.00255704# +/-   0. [0]
  ssIn12 =   0.00305432# +/-   0. [0.00300]

def parameters:
  b  =   0.8000# [min(max(0.8,amp),1.0)]


Thanks so much in advance.
Nilmar


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Re: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos

[Ravel, Bruce]

Ku-Ding,

I don't know what to tell you.  On the computer I am sitting in front of right 
now, I opened your two project files and hit the fit buttons, I get the same 
fit with only numerical differences.  Here I am cutting and pasting from the 
two log files:

old artemis:

  Chi-square  =4334.684537717
  Reduced Chi-square  = 691.819976095
  R-factor=   0.004250325

  amp = 0.8649100   +/-  0.0412220(1.)
  enot= 5.6049380   +/-  0.2950270(0.)
  delr=-0.0226780   +/-  0.0023790(0.)
  ss  = 0.0082230   +/-  0.0003250(0.0030)


new artemis:

  Chi-square  : 4348.7359268
  Reduced chi-square  : 694.0625918 
   
  R-factor: 0.0042652   

  amp=   0.86526150# +/-   0.04129645 [1.0]
  enot   =   5.61081742# +/-   0.29527844 [0]
  delr   =  -0.02266589# +/-   0.00238341 [0]
  ss =   0.00822546# +/-   0.00032571 [0.00300]


I don't acknowledge that there is a problem.

B



From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Tsuei, Ku-Ding 
[ts...@nsrrc.org.tw]
Sent: Thursday, October 18, 2012 1:15 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Running (D)Artemis yields different result from that shown 
in (D)Artemis instruction videos

Hi Bruce,

I went through your (D)Artemis instruction videos and ran the latest
Demetris 0.9.12 with 0.9.13 update side by side to reproduce the
results. However, my running yields much poorer fitting results on Au
foil EXAFS, even the first shell (video 03). Actually it happened using
the older 0.9.11 too. I also went through your Lecture videos shot at
Diamond and ran (D)Artemis but could reproduce your results closely. I
have felt puzzled for quite a while why the simplest case Au foil does
work well. Today I tried to run the same Au data and fitting by the old,
last version of Artemis 0.8.014. I could produce very good fitting on
the first shell with the R-factor very near that shown in the video. I
made sure the math expressions for the fitting parameters amp, enot,
delr and ss are set exactly the same, with fitting range exactly the
same, in both programs. Their screen outputs file is attached. The saved
respective project files are also attached. I copied the fit outputs
into their journals. I would appreciate if you may review these results
and help clear my puzzle.

Best regards,

Ku-Ding

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Re: [Ifeffit] path averaging in Artemis

[Ravel, Bruce]

Hi Simon,

That's not a problem.  Quite the contrary.  It is by design and is something 
that I consider to be one of the compelling new features in Artemis.

In the new versions of Atoms and Artemis, I introduced a concept called fuzzy 
degeneracy whose purpose is explicitly to combine together paths that differ 
very little in distance and/or scattering angle.  I explain it in some detail 
here:

http://bruceravel.github.com/demeter/dpg/feff/pathfinder.html#Fuzzydegeneracy

This feature is entirely user-configurable.  That is, you can set the width of 
the bin used to group together fuzzily degenerate paths.  In Artemis, this can 
be set by selecting Edit Preferences from the File menu on the main window.  
In the preferences window, select pathfinder then fuzz.  The default value 
is 0.003 Angstroms.  In your case, you want to set this to be 0.01 or smaller 
if, in fact, you want to retain the split degeneracy in your fitting model.  
Click Apply or Apply and save and rerun the Feff calculation.

Setting the fuzz to 0 will make the new pathfinder behave just like the 
pathfinder in Feff6.

Regards,
B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Simon Cassidy 
[simon.cass...@stcatz.ox.ac.uk]
Sent: Wednesday, September 19, 2012 10:18 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] path averaging in Artemis

Dear Bruce,

I've run into a problem with the new artemis' path finder. When running the 
attached feff.inp file in atoms, two separate paths are merged together.

The two paths it is merging are Se-Fe2 (N=4, reff=4.456) and Se-Fe3 (N=8, 
reff=4.465) which it gives as (N=12, reff=4.4621). The same problem occurs for 
these paths when starting with the Fe core.

The same feff.inp file generates the right path list when run in the old 
version of artemis. Please could you take a look at this?

Many thanks,

Simon


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Re: [Ifeffit] Importing Multiple Data Sets into Athena

[Ravel, Bruce]

I feel I should weigh in here.

There were two separate issues in the files Dan sent the other day -- one was 
the issue he intended to report, the other was a problem of his own creation.

The intended issue was a problem importing data for which the reference 
spectrum was of a different element than the main data.  In that case, the 
element and edge of the reference were being incorrectly identified.  This was 
a legitimate bug and a legitimate bug report.  I fixed the problem and pushed 
the fix to github.  It will be included in the next release of the Windows 
installer.  I will say now, as I have said many times before, that the software 
benefits enormously by users who are kind and diligent enough take the time to 
report their issues to me in a way that I can take action on.  My software is 
much better today thanks to bug reports like the one Dan submitted.  Obviously, 
I am quite grateful to him and to everyone else who has ever reported a 
software issue.

The unintended issue was that the data files he sent had been altered 
(apparently by reading into and saving from WordPad) in a way that rendered 
them unreadable by Athena.  Happily another member of our community supplied 
the original, unaltered data files.  Because I wanted to get to work on the 
primary problem, that of the incorrectly imported reference, I had to fritter 
away a good 20 or 30 minutes writing a one-off program to undo the damage that 
had been done to the files that were sent.  A bit of understand of what 
constitutes a data file would have spared me that effort. On that topic I have 
another comment.

Although Athena attempts to hide the details of interpreting the contents of 
data files form the user and (if I pay pat myself on the back) does a pretty 
good job of it, it is still worth while for the scientist to have a passing 
understanding of the contents of a data file.  All data files contain a 
sequence of numbers measured at a sequence of energy points.  By far the most 
common way of indicating the separation between a group of numbers (such as the 
signal on I0) measured at successive data points is by placing those numbers 
all on one line of the file and separating lines by a line break.  Athena has 
to make some assumptions about how the numbers are presented in the file or it 
will not be able to correctly interpret those numbers and the relationships 
between them.  If you insert line breaks willy-nilly into the file, it should 
not be surprising that Athena will get confused.  My point here is that, 
although Athena is largely successful at hiding uninteresting detail!
 s from the user, there is merit in having a basic understanding of how data is 
transmitted from the beamline all the way to your computer.  Thus, I took the 
time to write this paragraph.

B




From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Daniel Whittaker 
[daniel.whitta...@postgrad.manchester.ac.uk]
Sent: Friday, September 07, 2012 8:53 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena

Hi all,

I think that the issue that Bruce is referring to is due to a difference of
operating system and programs. The data i receive, as Kathy points out, is
absolutely fine and i have had no issue whatsoever with the beamline or the
files it produces. So, i think it might be an idea from now for all issues
posted to the list to be preceded with OS/programs (and potentially
computer) details so that such problems aren't misassigned and blame (or
problem) pointed in the wrong direction?

So in the interests of clarity and practicing my own suggestion:

Windows XP SP3, Using native Wordpad (not native Notepad - as this removes
formatting).
NB: it would seem that other software does something similar to what Bruce
is reporting (Win7 perhaps?).

The issue had already been overcome by the methodology as Kathy suggested.
So thanks for that. However, i was merely pointing out the fact that group
importing did not work as a point for 'looking at' before future releases in
the interests of software development and improvement. That being said i
appreciate the effort put in by the people on the lists, so thanks for the
hard work and perseverance.

Dan

--
From: Bruce Ravel bra...@bnl.gov
Sent: Thursday, September 06, 2012 3:04 PM
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena

 On Thursday, September 06, 2012 10:29:43 AM Daniel Whittaker wrote:
 Hi Scott,

 I have attached 3 of the data files and the Zr foil ref scan (already
 calibrated). I first import the reference Zr foil scan and then the 3
 files.
 The Numerator for the data is column 30 and i also import the ref channel
 where the numerator is column 7. If i choose to set ref to standard
 values
 (as you would expect that 

Re: [Ifeffit] Problem with Demeter Artemis 0.9.10

[Ravel, Bruce]

Hi Matt,

Thanks for the report.  I'll look into it and let you know what I find.

Clearly the only work-around right now is to recreate your fitting model from 
scratch in the new Athena.  Admittedly not a very satisfying answer,...

B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Matt Frith 
[matt.fr...@gmail.com]
Sent: Friday, September 07, 2012 12:01 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Problem with Demeter Artemis 0.9.10

Hi All,

I have come across an bug with Demeter 0.9.10.  When I go to open an old format 
Artemis project file I will see,

Converting old-style project file to Demeter serialization

written in the progress bar, and then the program will quit without opening the 
file. The problem occurs on both 32 and 64bit Windows 7.  I uninstalled the 
program and reinstalled Demeter 0.9.9 and there are no issues with 0.9.9.

The dartemis.log contains:


Can't locate object method inp_is_feff8 via package Demeter::Feff::External 
at C:/strawberry/perl/site/lib/Demeter/Fit/Horae.pm line 110.


I hope this is helpful.  It seems to be similar to the problem posted by 
Riamundo, and I hope that I have not missed a previously posted solution.

Attached is one of the project files that I have used.

Sincerely,

Matt Frith



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Re: [Ifeffit] Importing data to Athena crashes on WinXP

[Ravel, Bruce]

Hi Bradley,

This appears to be an example of a problem that I thought I had fixed some time 
ago.  The thing making Athena unhappy is the length of the line of column 
labels in your file.  This triggers a mistake in how Athena communicates with 
Ifeffit.

I will fix this for the next release.

For the short term, the best work-around I can suggest is delete the line with 
the column labels and replace it with hash (#) character.  This will avoid the 
mistake Athena is making and present the column labels as numbers (1 2 3 etc) 
in the column selection dialog.  Obviously that will be a hassle if you have a 
mountain of data

B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of BradleyW Miller 
[miller.bradl...@epamail.epa.gov]
Sent: Monday, August 13, 2012 9:22 AM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Importing data to Athena crashes on WinXP

Hi,

I've looked through the FAQ and help pages but don't see any comments about my 
issue. When importing new data into Athena it crashes on my Window XP computer. 
The column selection window opens and it freezes. I've attached a file for you. 
I don't have the same problem with project files. If I create a prj file in the 
old Athena I can then import it to the newest version of Athena and operate 
with no problems. I know at least one other person who has the same issue. 
Thanks for your time.

(See attached file: As_P2.002)


Respectfully,
Bradley W. Miller, Ph.D.
Post Doctoral Fellow
Oak Ridge Institute for Science and Education
U. S. Environmental Protection Agency
National Risk Management Research Laboratory
Land Remediation and Pollution Control Division
5995 Center Hill Avenue, Cincinnati, OH 45224-1702

Office: (513) 487-2889 miller.bradl...@epa.gov
Fax: (513) 569-7879 www.epa.gov

www.tinyurl.com/bwmiller

The great tragedy of Science—the slaying of beautiful hypothesis by an ugly 
fact.— Thomas H. Huxley


Views or Opinions expressed in this email is solely representative of the 
sender and does not represents those of the EPA or any other agency.


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Re: [Ifeffit] first official relezse of my new software

[Ravel, Bruce]

 Thanks a lot also to Matt Newville for IFEFFIT.

Ismael,

Thank you for mentioning that.  I neglected to do so in my email.  Obviously, 
there wouldn't be an Athena or an Artemis without an Ifeffit.  Matt does a lot 
for all of us.

B

PS:  Did everyone notice how I misspelled release in the subject line?  Yup, 
this is certainly a quality operation I'm running here! :)

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Re: [Ifeffit] Artemis: How to treat Neglected? DS path

[Ravel, Bruce]

Hi Takahide,

See the first full paragraph below equation A.1 in Zabinski et al, Phys. Rev. B 
52, 2995–3009 (1995), http://dx.doi.org/10.1103/PhysRevB.52.2995

Regards,
B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Takahide Yamaguchi 
[11nm0...@mcs.ibaraki.ac.jp]
Sent: Friday, February 03, 2012 3:31 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Artemis: How to treat Neglected? DS path

Dear all,

I have been analyzing some EXAFS data based on crystal structure by Artemis.

The model construction and analysis within the First shell had come
along OK.
And I would like to refine the analysis of higher shell including
multiple scattering.

But the problem about How to treat the MS path(especially DS) is
existing in the way to goal.

Generally, Considering triangle arrangement (A-B-C; A is Absorber, B is
nearest neighbor, C is the next neighbor)
offers the possibility of two double scattering paths.
Stated another way, the following two type can be readily considerable.

Type I: A--B--C--A and Type II; A--C--B--A

By calculation of FEFF on Artemis, a number of DS is computed and
listed, of course on my computer.
However, I could find JUST ONLY type II double scatter, no type I.

In this case, should I simply multiply the amplitude by two?

Or, are there reasonable answer to neglected type I path?

I will be glad with your help.

Best regards,
Takahide





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Re: [Ifeffit] Distortion of transmission spectra due to particlesize

[Ravel, Bruce]

 I think you are correct in principle that more layers can reduce the
 thickness effect problem.  If harmonics were not an issue, eventually if
 you pile up enough random layers, the thickness will be uniform.
 Whether this is useful in practice is another matter, but suspect it may
 not be when single particle absorption is large.

I think I agree with this.  Among my beamline's users, a very common problem is 
preping samples that, as Matthew suggested, have boulders either on tape or in 
BN.  If the individual particles/agglomerates are 10's of absorption lengths 
(which *is* a common problem among my users) then ignoring harmonics and 
stackin' 'em up won't help.

So stacking as a solution to pinholes only works if the particles are small 
enough to begin with -- in which case it won't be that hard to make a good 
sample in the first place!

B

--
 Bruce Ravel  --- bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
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Re: [Ifeffit] Primitive unit cell from .cif file

[Ravel, Bruce]

I don't really understand what you are driving at, but it seems as though you 
want to express Diamond as a simple cubic cell with a two atom basis?  Isn't 
that Pm3m with atoms at 0,0,0 and 1/4,1/4,1/4, or some such.  I don't really 
understand how that will save you time in abinit, but, of course, I am not a 
crystallographer

B

PS. Doesn't abinit understand crystal symmetry?  Why can't you just tell it 
that it's diamond and has the symmetry of diamond?

--
 Bruce Ravel  --- bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of joshua jason kas
Sent: Thu 6/18/2009 2:41 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Primitive unit cell from .cif file
 
Thanks everyone for your suggestions! I have tried the following things.
I used atoms (webATOMS) to generate a p1.inp file using diamond as an 
example, but this gives me the conventional cell with 8 atoms in 
it instead of the 2 atom primitive cell. Am I doing something wrong?
The input file came from the atoms database and the output is as follows:

  *
  *   F d -3 m appears in the International Tables with
  *   multiple choices of origin.  If the atoms list seems wrong, you
  *   should use a shift vector of:
  * -0.125, -0.125, -0.125
  *
  *
! This p1.inp file was generated by WebAtoms 1.8 (Atoms 3.0beta10)
! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
title = name: diamond
title = formula:  C
title = sites:C1
title = refer1:   Kittel, ISSP
title = refer2:
title = schoen:
title = notes1:   diamond structure
space   p 1 ! original space group: F d -3 m
a =   3.5670b =   3.5670c =   3.5670
alpha =  90.0   beta =   90.0   gamma =  90.0
core =  C1_1edge =  K   rmax =6.0
atoms
! elem   x  y  z   tag occ
   C 0.125000.125000.12500  C1_1   1
   C 0.125000.625000.62500  C1_2   1
   C 0.625000.125000.62500  C1_3   1
   C 0.625000.625000.12500  C1_4   1
   C 0.875000.375000.37500  C1_5   1
   C 0.875000.875000.87500  C1_6   1
   C 0.375000.375000.87500  C1_7   1
   C 0.375000.875000.37500  C1_8   1

I also tried the Mercury demo, but all editing features are disabled.

I will try Diamond now.

Just to give some motivation here, I am working with abinit (along with 
feff) to produce optical spectra. If I use a conventional cell, the 
calculations become much more time consuming, so ideally I want to use a 
primitive cell. 
Thanks again for all your help!
Josh

 Hi Josh,
  You may try Diamond Demo version which is free.

 http://www.crystalimpact.com/diamond/download.htm
I will give this a try.



 Hi Josh,

 If I understand your question, I think that Atoms does what you want.  
 Running the command line tool as atoms -p turns the attached cif file into 
 the attached p1.inp file.  You can do the same thing inside of Artemis 
 using write special output in the Theory menu.


 B

 --
 Bruce Ravel  --- bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




 -Original Message-
 From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of joshua jason kas
 Sent: Wed 6/17/2009 2:16 PM
 To: ifeffit@millenia.cars.aps.anl.gov
 Subject: [Ifeffit] Primitive unit cell from .cif file

 Hi everyone,
 I was wondering if there is a simple (free) utility for producing a
 primitive cell (not conventional) from an asymmetric cell and space group.
 Basically, I want to be able to easily go from a crystallographic
 information file to a primitive unit cell. I know that there are ways to
 do this within applications like material studio, but these are expensive.
 Any help would be appreciated.
 Thanks,
 Josh Kas
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 Message: 4
 Date: Wed, 17 Jun 2009 23:40:10 -0300
 From: Eugenio Otal eugen...@gmail.com
 Subject: [Ifeffit] Radial 

Re: [Ifeffit] Primitive unit cell from .cif file

[Ravel, Bruce]

Hi Josh,

If I understand your question, I think that Atoms does what you want.  Running 
the command line tool as atoms -p turns the attached cif file into the 
attached p1.inp file.  You can do the same thing inside of Artemis using 
write special output in the Theory menu.

B

--
 Bruce Ravel  --- bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of joshua jason kas
Sent: Wed 6/17/2009 2:16 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Primitive unit cell from .cif file
 
Hi everyone,
I was wondering if there is a simple (free) utility for producing a
primitive cell (not conventional) from an asymmetric cell and space group.
Basically, I want to be able to easily go from a crystallographic
information file to a primitive unit cell. I know that there are ways to
do this within applications like material studio, but these are expensive.
Any help would be appreciated.
Thanks,
Josh Kas
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Re: [Ifeffit] about wolframite crystallographic file

[Ravel, Bruce]

Yordy,

I'll look into this when I get a chance, but that might not be until later in 
the week (I am on travel at the moment).

B 

--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: [EMAIL PROTECTED] on behalf of Yordy Licea Fonseca
Sent: Sat 11/15/2008 6:36 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] about wolframite crystallographic file
 
Hi all,

As soon as I load this attached CIF crystallographic file from ISCD in
Artemis0.8.012 the software says:
Artemis trapped one or more errors!  Error message dumped to screen.
I can`t go on runnig Atoms as it seems to be a problem with the file. I have
read the suggestion made in FAQ, but I can not manage to find the error.
Could you help me, please?
It would be nice once the problem been fixed to add this structure to Matt's
atoms.inp database.

Thanks you very much, Yordy

-- 
Yordy E. Licea Fonseca
Departamento de Físico-Química
Instituto de Química-IQ/UFRJ
Laboratório de Catálise Heterogênea
Rio de Janeiro, RJ, CEP 21.949-909
Brasil
Email: [EMAIL PROTECTED]

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Re: [Ifeffit] Athena can not open any file

[Ravel, Bruce]

Gilberto,

Great to hear!!  I'll fix the instuctions for installing from source on my web 
page as soon as I can.

Thanks,
B

--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: [EMAIL PROTECTED] on behalf of Gilberto Fernandes Lopes Fabbris
Sent: Thu 8/14/2008 2:08 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Athena can not open any file
 
Hello,

I made as you said and now everything is working!

Thanks!!

Gilberto



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Re: [Ifeffit] X-ray absorption measurements for Fluorescence detection.

[Ravel, Bruce]

The sotfware is certanly capable of dealing with fluorescence and tranmission 
equally.  You need tomake sure to import your data correctly into Athena:

  http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/columns.html

Regards,
B


--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: [EMAIL PROTECTED] on behalf of
Sent: Mon 3/24/2008 7:15 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] X-ray absorption measurements for Fluorescence detection.

Dear Authors:
The Athena, Artemis fitting programs is suitable for X-ray absorption 
measurements
  for Fluorescence detection mode? Because transmission have different physical
   describing with  Fluorescence mode. Or maybe you have more descriptions about
  Fluorescense detection mode fitting about X-ray absorption measurement?
  
  Thanks for your time and help!
  
  Pei
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Re: [Ifeffit] sorting files in Athena

[Ravel, Bruce]

 if I can suggest, whould be useful the posibility of move marked groups
 in Athena, like copy and paste...

Ctrl-y copies a group and places it at the end of the list.

I haven't implemented cut and paste or other ways of moving groups
around in the list, but inertia is the only reason.  I'll think about
it.

B


--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
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Re: [Ifeffit] sorting files in Athena

[Ravel, Bruce]

 but then you have to ask every beamline owner to
 change the file names, at each synchrotron...

 Not necessarily, it really only applies to those generating 10's or
 100's of scans such as scanning in QEXAFS mode.  Not to mention that it
 is already implemented in many beamlines that had the foresight on this
 issue and implemented a solution when the beamlines were first created.
 :-)  However, I do agree that some level of group cut/paste could be
 helpful in Athena.


I am willing to go out on a limb and state in a public forum that the
people who run beamlines and write data acquisition software have a
responsibility to their users to think hard about the decisions they
make, acknowledging that even the smallest detail may end up being
important to someone.

Darek's problem is *not* an Athena-specific problem.  It is both
well-known and correct to state that numbers should be zero-padded if
sorting strings containing those numbers should be the same when done
numerically as alphabetically.  Athena is hardly the only program that
would order these files other than how Darek wanted them.  The
beamlines DAQ software shares responsibility for this failure of
Athena.

You could argue that Athena should consider file time stamp when
ordering files as they are read in, but sorting alphabetically is a
valid and unsurprising choice.  That Athena should be more flexible in
resorting the data in the group list is a completely valid feature
request and will get my attention.

All that said, I agree with Dan.  If there is a problem at the
beamline, the user has a right to complain loudly (but politely, of
course).

Oh, and I, too, am a beamline owner.

B



--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
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Re: [Ifeffit] sorting files in Athena

[Ravel, Bruce]

 
 Hi,
 I can not find one small thing - sorting files in Athena - it makes me
 crazy ;)
 I work with QEXAFS data  - usualy few tens of files or even more. Files
 are named in such way: file_namerXX.fio where XX is next file number
 (1, 2, 3, ... ,10, 11, 12, ... , 20, 21, etc.).
 I use Iffefit under Win XP, and every time when I open (import) more
 files I have them in such order: 1, 11, 12, 13, ... , 19, 2, 20, 21, 22,
 ... , 29, 3, 30, 31 ... etc.
 So, my question is if there is some hidden way to sort automatically
 files during importing or in the menue. Do you know something about? Is
 the sorting lexigraphical (from Windows)? 

The file selection dialog sorts alphabetically.  

There is no quick-n-easy way to resort the data groups once in
Athena.  The best solution would be to name the files in a way that
alphabetical sorting will be the same as time sorting.  The way to do
that will be to name the first file f01.fio rather than r1.fio.

 another problem which apears, is the limitation of the memmory...

That is a well known, well discussed problem.  Ifeffit is written in
fortran.  Fortran does not have dynamic memory allocation.  The only
practical solution is tonot read so many data files in at a time.

I wish it were different, but it's not.

B


--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/


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Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?

[Ravel, Bruce]

 
 Hi Bruce

 I have spent 1 month to learn the Athena by using your ATHENA User's Guide
 updated at Aug. 31,2007. I am very satisfied with it and thank you very
 much. Now I am learning the ARTEMIS. However, till now I can not find a
 suitable guide for a beginner. The PPT wrote by Shelly is not suitable for
 me. And the artemisdoc.pod is also puzzled me. Is there a Artemis User's
 Guide like the Athena?

 Thanks

 Kefan

 -- 
 Kefan Wang
 School of Physics and Electronics
 Henan University, 475004
 E-mail: [EMAIL PROTECTED]; [EMAIL PROTECTED]


Hi Kefan,

I suspect that my answer to this question will be of broad interest,
so I am taking the liberty of CCing the Ifeffit mailing list.

Thank you for the very kind words regaridng Athena.  I am pleased that
you found the Athena User's Guide so helpful.  Sadly, I have not yet
written a document of comparable extent for Artemis.  I certainly
understand that there is a need for comparable user guide, but finding
the time and energy to write one has not yet happened.  Writing the
Athena User's Guide was fairly exhausting and I need to take a break
before embarking on a similarly large document for Artemis.

I have to defend Shelly's various presentations.  I think they have a
lot of good information in them.  I think that using them along with
other resources can give you enough of an overview of Artemis to get
started.  I strongly recommend that you work through Scott Calvin's
ZnO example, which can be foun at 
   http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib
ZnO is somewhat of an idealized example -- many of us work on
problems that are pretty far removed from a simple crystal like ZnO.
However, Scott's example is quite thorough.  Working through it while
carefully following his comments in the project journals will
introduce many of Artemis' features.

As for the pod file -- those are the files that get displayed when you
click on one of the documentation buttons from within Artemis.  I
acknowledge that they are thin on details and somewhat out of date.

The last bit of advice I can give you is to read the papers written by
the names you see on the Ifeffit mailing list.  The folks who offer
answers to question on the list are also some of the best
practitioners of EXAFS analysis using Feff.  Although it might seem
funny to read papers by Anatoly Frenkel or Paul Fons if you are
studying environmental science (or Shelly Kelly's if you are a
materials scientist), I strongly recommend doing so anyway.  Their
science might be pretty far away from what you do, but the EXAFS
analysis strategies are quite instructive and are certainly
transferable.

I know that is not the answer you were hoping for, but it may be
helpful nonetheless.

Regards,
B

--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?

[Ravel, Bruce]

 
 What would be really useful is to make a searchable database with links
 to original publications (many of them are more than 20 years old but
 are still the best resources on many issues) on many subjects discussed
 in this list. 

Anatoly,

This seems like an awfully good start:

   http://scon155.phys.msu.su/~papers/

In fact, you seem to be the first hit for a search of cumulants!

Alexander seems to have done a very nice job.  Some more web-fu would
be nice -- for instance, actual links to the articles or to their DOI
numbers would be very helpful for those of us lucky enough tobe at
institutions with extensive subscription collections.  Mirrors of the
database and web page on other continents might also be helpful.

B


--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
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[Ifeffit] two issues with Athena on Windows and one with Artemis

[Ravel, Bruce]

Hi,

For the last few weeks, I have been doing experiments at beamlines
with Windows machines.  This has afforded me more time than normal
using my programs under Windows.  I am appreciating my linux machines
more than normal, but that is not the point of this email ;-)

I have found a few issues that I wanted to address even though no one
has yet mentioned them on this list.

 1. Combo-box menus:  In Athena, combo boxes are used for a variety of
purposes.  For instance, in the alignment dialog, a combo box is
used to select the data group for use as the alignment standard.
It seems that selecting items from the drop-down list does not
work as expected.  Clicking to post the drop down menu then
clicking on your choice does not cause your choice to be inserted
into the combo-box text area.

The work-around that I have found is to first *right* click on
your selection, then *left* click on it.  I cannot explain why
this works and I wish the whole thing just worked correctly.  At
least there is a work-around!  (Another work-around is to move
the appropriate group to the top of the list, but I dislike the
right-click/left-click solution less ;-/ .)

 2. Several people have mentioned privately that the most recent
version of Athena seems very sluggish on Windows.  I agree and so,
I think, does Matt.  We changed how the compiled parts get
compiled for the most recent release and perhaps some bed seeting
were used.  We'll look into for the next release.

While doing some profiling on my new coding project, Demeter, I
figured out a reasonably simple and very fruitful optimization for
the interaction between my perl code and the Ifeffit library.  I
will implement that for the next release of Athena.  Hopefully the
next version will be snappier.  For now, I apologize that the
performance of Athena is less than it should be.

 3. In Artemis, there are two or three menu items which involve
importing something from a file.  One example is Import variables
from text file under the GDS menu.  On Windows, this fails to
post the file selection dialog and spews error messages to the
console.  This bug will be fixed in the next release.  Sadly,
there is no work-around that I know of.

Regards,
B


--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/



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Re: [Ifeffit] different edge step by linux and window vista

[Ravel, Bruce]

Hi Shanshan,

A few questions:

  1. Are the normalization orders the same?  (Click the Show additional 
parameters button in the background removal section to see that parameter.)
  2. Are the values of spline clamps the same.  (Also visible among the 
additional parameters.)
  3. Are the numerical values associated with the spline clamps the same?  (The 
values are set among the preferences.  Look for the Clamp group on the 
preferences dialog.)

Another thing to look at is the contents of the Ifeffit buffer immediately 
after making those plots.  Are there any obvious differences in the commands 
sent to Ifeffit on the two platforms?

B



--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: [EMAIL PROTECTED] on behalf of Shanshan Liu
Sent: Wed 12/12/2007 12:58 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] different edge step by linux and window vista
 
Dear all,

It seems there is a problem when I use athena to open the file under the
windows vista environment.
 
According to the specific scan channel, the data gave the big different
edge step by linux and windows.(Other parameters are similar), and the
figures seem strange(I do not know what caused it). Now I am sending the
screen-shot that I see. Please help me about that.


Thank a lot.

Shanshan Liu

BCPS Dept.
Illinois Institute of Technology 


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Re: [Ifeffit] Graphics Problems in ATHENA

[Ravel, Bruce]

Hi Sola,

This is the sort of question that should go to the Ifeffit mailing
list, so I am taking the liberty of CCing my answer there.
 

 I recently encountered a problem with a .prj file in ATHENA. The first
 issue was the notification that ATHENA may be out of memory and when I
 checked the memory usage under the help menu, I found out that I was not
 even using up to 1% of the memory. So, after closing the saved .prj
 files, one with some groups removed and another one without removing
 some groups, I tried to reopen the .prj but the graphics refused to
 display. I have since rebooted the system and updated IFEFFIT, but still
 no luck!


This is not really enough information for me to figure out the nature
of the problem you are seeing and I have never seen the behavior you
describe, but I can give you a few hints.

1. Athena's way of guessing memory usage is extremely unreliable.
   In general it is a poor idea to import more than about 60 scans
   into Athena (that is, 60 scans of the typical step-scan variety
   with 10 volts steps in pre-edge, 1/2 volt steps through the edge,
   and 0.05 A^-1 steps in the EXAFS) or fewer if you are importing MED
   files with lots of columns or quick scans with lots of data
   points.  This is not a shortcoming of Athena, rather it is a result
   of Ifeffit being written in Fortran.  If you are running into
   memory issues, you should group your data in smaller chunks for
   import into Athena.

2. Perhaps there is something abnormal about the prj file, but I
   cannot know unless you attach an example that produces the poblem
   reliably.

3. Are there any messages in the console window that starts when you
   start Athena?  That's the window that stays on the task bar after
   Athena starts.  The messages i that window may be gobbledigoop to
   you, but they may provide me with information about the nature o
   fthe problem.  If Athena is exiting before you can look at the
   console, try opening up a command window, changing directory to 
   C:\Program Files\Ifeffit\bin (or wherever Ifeffit is installed) and
   running athena from the command line.  That way, any error messages
   will be preserved.

 
B


--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/


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Re: [Ifeffit] phase shift correction

[Ravel, Bruce]

 

Hi Bindu,

  Why the peak in the Fourier transform of the experimental 
  spectrum is less than the actual one. 

 The EXAFS equation is:

   N S02 F(K)
 chi(k) = --- exp(-2k^2 sigma^2) sin(2kR + phi(k))
 2kR^2

 In the oscillatory term, there is a piece that is the phase shift
 associated with the scattering of the photoelectron.  When you do a
 Fourier transform, the peak of the sin wave is not at R, rather it is
 shifted by an amount that depends on the size of phi(k).

That should be, of course, ...the peak of the *Fourier transform* of
the sine wave...


B


--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/


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Re: [Ifeffit] excuse me!

[Ravel, Bruce]

Hi Yuzhiguo,

This chapter of the Athena manual explains in some detail how to move data into 
Athena.

   http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/index.html

As you can see there, Athena is capable of importing data without modification 
from many different beamlines.

If you continue to have trouble, you might consider posting an example of the 
data that Athena is unable to read.

B


--
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at Brookhaven National Laboratory
 Building 535A
 Upton NY, 11973

 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: [EMAIL PROTECTED] on behalf of ???
Sent: Thu 11/22/2007 12:57 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] excuse me!
 
Dear prof:
 
 I am a postgraduated student in envirnmental science,so i have litte 
knowlege of this field ,now,i want to use athena to process date of XANES from 
Bsrf. but which format can be used in athena? my data format is .dat  ,how 
can i to convert it to fit athena!
 Thank you very much!
 
yuzhiguo
 
 


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Re: [Ifeffit] space group C-1

[Ravel, Bruce]

Nan,

You haven't quite given me enough information to actually help.  In this case, 
I'd need to see the crystallographic reference, or at least the input data, for 
the problem at hand.  This is point #5 at 
http://cars9.uchicago.edu/~ravel/software/bugs.html.

B


--
 Bruce Ravel  --- [EMAIL PROTECTED]


 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: Nan Jiang [mailto:[EMAIL PROTECTED]
Sent: Tue 10/9/2007 5:59 PM
To: [EMAIL PROTECTED]
Subject: space group C-1
 
Dear Dr Ravel

 

I use Atoms to generate clusters for FEFF calculations. My space group
is C-1, which is not included in your table. I tried to use P-1 instead,
but it does not work properly. There are four symmetries in C-4, but
only 2 in P-1. Could you advise me on this?

 

Thanks for your time.

 

Nan Jiang

 

 



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Re: [Ifeffit] The common question!

[Ravel, Bruce]

Hi Pei-chang,

Regarding questions 1 and 2: Go to http://xafs.org/Tutorials and read Matt 
Newville's The Fundamentals of XAFS.

Regarding question 3 - 5: On that same page, Matt's and Shelly's tutorials 
cover that information.  This part of the Athena document is also relevant: 
http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/rbkg.html

HTH,
B


--
 Bruce Ravel  --- [EMAIL PROTECTED]


 My homepage:http://cars9.uchicago.edu/~ravel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




-Original Message-
From: [EMAIL PROTECTED] on behalf of ?? ?
Sent: Tue 10/2/2007 8:56 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] The common question!
 
To Dear Authors;
We have accumulate some questions on attach ptt.file,
  that including theoretical and athena background removal
  file. In order to present our questions more clear and short,
  we make this way, Thanks for your time and help!
   
  Pei-chang Tsai
   

   ??,?? -  Yahoo!??!

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Re: [Ifeffit] Using windows apj files on linux

[Ravel, Bruce D.]

Hi all,

I spent some time on an airplane this morning fixing this problem that Josh 
reported.  It should be fixed in the next release.  In light of this being a 
linux-only problem, I will probably make a source code release before the new 
windows executables are ready.

B

P.S.  In case you are curious, \x is perl's way of explicitly specifying a 
unicode character and the argument in braces is the character number expressed 
in hex.  \x{d} is, therefore, the carriage return character, sometimes 
written \r.  So basically, perl was trying to tell me that I was handling the 
dos/unix end of line issue incorrectly, but it was telling me in a really 
obfuscated way.  Fascinating stuff ... not!

-Original Message-
From: [EMAIL PROTECTED] on behalf of joshua jason kas
Sent: Tue 5/29/2007 12:13 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Using windows apj files on linux
 
Hi,
I recently updated to redhat 4. I am running:
artemis 0.8.009
IFEFFIT 1.2.9
Tk-804.027
perl 5.8.5

I have an artemis project file that I 
started on my win xp machine and would like to use on the linux machine. 
When I open the apj file on linux, some of the information about the fits 
seems to be scrambled. Here are some of the symptoms.

1) The raw logs seem to have aquired the following
escape character at the end of each line: \x{d}
   This shows up as a carriage return or end of line on this screen.

2) Quick summary of selected fits gives 0 for all reported values
   (chisq, rfactor, nidp, etc) and does not report any guessed
parameters.

Here is one of the quick summaries. Note that the \x{d} do not show up 
here, but they do in the artemis message palette. I am also attatching the 
project file.
Thanks for any help,
Josh Kas

Project title   : Fitting pt1_amine_165_he_573.chi

Comment : fer dw, constant delr, ei=0, kw=1, kmin=2.0, rmin=1.2

Figure of merit : 17


Fitting statistics
   Number of independent points : 0
   Number of variables  : 0
   Chi-square   : 0
   Reduced chi-square   : 0
   R-factor : 0
   Measurement uncertainty (k)  : 0
   Measurement uncertainty (R)  : 0

Guess parameters

=*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*=




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RE: [Ifeffit] Problems with the flatten option in Athena

[Ravel, Bruce D.]

Flattening involves removing from the data the difference in slope and 
quadrature between the pre-and post-edge lines.  Because this does not make 
sense in the pre-edge, Athena multiplies this difference array by a step 
function centered at E0.  If your E0 is not somewhere sensible (i.e. in the 
swiftly rising part of the spectrum) then you amy see something funny.
 
This question would have been easier to answer had you attached a one-group 
project file conatining the data in question.  Without seeing the data, the 
only thing any of us can do is speculate as to what is happening.  That said, a 
misplaced E0 value seems like the likeliest answer.
 
HTH,
B



From: [EMAIL PROTECTED] on behalf of Jens Kruse
Sent: Wed 10/01/2007 08:56
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Problems with the flatten option in Athena



Hi,

I have a normalization problem with Athena. If I turn on the flatten
option in the background removal section, Athena creates in some of the
normalized spectra a step in the pre-edge range.  How can I  get rid of it?

Thanks,

jens
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