George Sterbinsky | 25 Mar 22:38 2015

Artemis on Yosemite

Hello,

When I attempt to open Artemis on OSX Yosemite (10.10.2) the error message copied below prints to the terminal. The initial image that indicates Artemis is opening does appear, although Artemis fails to open. Athena and Hephaestus open without error. Any suggestions as to how this could be resolved would be appreciated.

Thanks,
George

$ artemis
Can't locate Math/Round.pm in <at> INC ( <at> INC contains: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44.
BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44.
Compilation failed in require at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter.pm line 306.
BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Artemis.pm line 26.
Compilation failed in require at /opt/local/bin/artemis line 34.
BEGIN failed--compilation aborted at /opt/local/bin/artemis line 34.



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Johan Nilsson | 24 Mar 17:05 2015
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Incomplete source tarballs for larch?

Dear all,

Today I helped a colleague install larch on OSX Yosemite but we ran into some problems using the source tarball from CARS (larch-0.9.24.tar.gz). It was a bit of a learning curve for me as a linux user but we managed to install the prerequisites (exept for epics) using macports and then ran the larch installer without noticing any warnings or errors. The problem after that was that we could not locate the larch binary. The source tarball does not include a 'bin' directory and some other things that are found in the github source so we went ahead and installed larch from the github source instead. After that we could locate the binery and start the interpreter. Did we make some mistake here or are there things missing in the source tarballs?

Best regards,
Johan Nilsson


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Rana, Jatinkumar Kantilal | 21 Mar 14:06 2015
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Breaking down correlationships between parameters

Dear All,

I have stumbled upon a question regarding correlationships between various parameters in EXAFS fitting. As we know, the parameters S02*N and sigma2 are highly correlated (where N is the number of nearest neighbors).

I would like to determine the number of nearest neighbors for a series of sample subjected to some treatment. I can do this by simply setting S02 to a value for a given absorber (based on the literature or my own measurements of some reference compounds) and letting N and sigma2 vary in a fit. However, the problem is the physical process which changes the number of nearest neighbors, also introduces structural disorder in samples. Thus, I always get the values of N overestimated due to its correlationship with sigma2. 

I know of a method which can be used to breakdown the correlationship between S02 and sigma2 by setting a series of S02 values at different k-weights and refining the corresponding sigma2 as discussed in several literature. However, in this approach the explicit assumption is, S02 is the property of absorbing atoms and thus is independent of changes occurring inside the sample. In my case, however, both sigma2 and N vary with changes inside samples. Is there any way to break this correlationship ?

I look forward to your valuable suggestions and comments.

Best regards,
Jatin






Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
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D-14109 Berlin

http://www.helmholtz-berlin.de
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huyanyun | 19 Mar 23:32 2015
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amplitude parameter S02 larger than 1

Hi all,

I know this question has been asked for many times. S02 is expected to  
be around, but smaller than 1,  a fact that has been explained, such  
as in the following previous emails, in our mailing list.

http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg02237.html
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2003-February/000230.html

However, I am continually get S02 value larger than 1 for a series of  
similar samples when I fit data in Artemis. I think my fit is very  
good, because my suspected model(based on other technique) could be  
verified in XAFS analysis (i.e., defensible in physics), the  
statistics is good ( R=0.01, reduced chi-square=31.4, fit-range:1.5~6  
Angstrom, k-range: 3~14 angstrom-1) and all the parameters such as the  
bond length, sigma2 are physically reasonable. The only thing makes me  
uncomfortable is that parameter S02 keeps between 1.45 to 1.55 during  
the fitting.

In my system, the absorber atom occupies two crystallographic sites.  
So I built a model with paths generated from two FEFF calculations.  
For paths generated from the 1st and 2nd FEFF calculation, the  
amplitude parameters are set to be S02*P% and S02*(1-P%) respectively,  
where P% is the first site occupancy percentage. Both S02 and P are  
free parameters during the fit, and P is an important conclusion I  
want to extract from XAFS fitting.

However, the fit result gives me S02=1.45 ~ 1.55 and P=0.51 ~ 0.56 all  
the time (i.e., for each path the 'total amplitude' S02*P% or  
S02*(1-P%) are about 0.7~0.8, smaller than 1). It looks to me that I  
got a 'perfect' fit but I am not sure if S02 larger than one is  
defensible. So I have to ask:

1) Is my current fit with S02 larger than one reasonable? If not, what  
could be suggested to get around it?

2) What's the meaning of S02? It is interpreted in physics that it is  
a reduced electron excitation parameter, but is it possible that S02  
will be affected by any experimental condition?

3) Can anyone share whether you had the multiple site system that gets  
S02 larger than one?

Looking forward to your help.

Best,
Yanyun
Anders Glans | 19 Mar 22:21 2015

Installing demeter from source on Yosemite?

Dear all,

Has anybody succeeded with installing demeter from source on a Mac? I have attempted to install demeter from source on OS X 10.10.2, but so far without success.

I have followed the installation procedure for Installing source code at http://bruceravel.github.io/demeter/pods/installation.pod.html, except I installed pgplot from source instead of using the install script provided through ifeffit. I don’t get any errors installing either pgplot or ifeffit.

All dependencies for demeter should be met:

$ sudo perl ./Build.PL
Password:
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Demeter' version '0.9.21'

If all dependencies are met, build and install Demeter by doing:
<snip>

The build seems to go fine:

$ sudo ./Build
Simple test for presence of gnuplot ---> found it!  Using gnuplot with the x11 terminal.
Building Demeter
Building Artemis User's Guide
Building Athena User's Guide

But the tests fail miserably. Already before the actual testing starts, there is a message that loading of Ifeffit.bundle fails:

$ sudo ./Build test
t/000_ifeffit.t ......... Can't load '/Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle' for module Ifeffit: dlopen(/Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle, 2): Symbol not found: _ifeffit
  Referenced from: /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle
  Expected in: flat namespace
 in /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle at /System/Library/Perl/5.18/darwin-thread-multi-2level/DynaLoader.pm line 194.
 at t/000_ifeffit.t line 9.
Compilation failed in require at t/000_ifeffit.t line 9.
BEGIN failed--compilation aborted at t/000_ifeffit.t line 12.
# Looks like your test exited with 255 before it could output anything.
t/000_ifeffit.t ......... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 6/6 subtests
<snip>


However, the bundle exists:
$ ls -l /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/
total 152
-r-xr-xr-x  1 root  wheel  76208 Mar 18 13:09 Ifeffit.bundle

and the symbol in question is part of the bundle (well, at least the string exists):

$ grep _ifeffit /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/*
Binary file /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle matches

Does anybody know what is going on? Am I missing something?

A couple of more bits of information:

$ which ifeffit
/usr/local/bin/ifeffit

$ ifeffit
 Ifeffit   1.2.12 Copyright (c) 2005 Matt Newville, Univ of Chicago
                command-line shell version 1.1 with GNU Readline
Ifeffit> testplot
 %PGPLOT, Unrecognized device type
 %PGPLOT, Invalid device specification: /AQT
 %PGPLOT, PGBBUF: selected graphics device is not open
 %PGPLOT, PGQCI: selected graphics device is not open
 %PGPLOT, PGQFS: selected graphics device is not open
 %PGPLOT, PGSCI: selected graphics device is not open
 %PGPLOT, PGSFS: selected graphics device is not open
 %PGPLOT, PGSVP: selected graphics device is not open
 %PGPLOT, PGBBUF: selected graphics device is not open
 %PGPLOT, PGEBUF: selected graphics device is not open
 %PGPLOT, PGSVP: selected graphics device is not open
 %PGPLOT, PGSCI: selected graphics device is not open
 %PGPLOT, PGSFS: selected graphics device is not open
 %PGPLOT, PGEBUF: selected graphics device is not open
  ** plot error: cannot open device:
 %PGPLOT, Unrecognized device type
 %PGPLOT, Invalid device specification: /AQT
  ** plot error: cannot open device:
Ifeffit> exit

$ which athena
/usr/local/bin/athena

$ athena
dyld: lazy symbol binding failed: Symbol not found: _iff_exec
  Referenced from: /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle
  Expected in: flat namespace

dyld: Symbol not found: _iff_exec
  Referenced from: /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle
  Expected in: flat namespace

Trace/BPT trap: 5



Regards,
Anders


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Samy OuldChikh | 15 Mar 14:50 2015
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Evaluation of uncertainty using correlated Debye model + advices for the fitting of an hexagonal Co-foil

Dear all,

I would like to go beyond the fitting of the first shell for a cobalt metallic foil acquired at FAME beamlime (ESRF).
It's not mandatory for the determination of So in this case, but I just would like to improve myself in EXAFS fitting.

The cobalt foil has an hexagonal structure (P 63/mmc, a =b=2.507 A, c= 4.068 A) according to the supplier.
The first 49 scattering paths calculated with FEFF were selected to cover the R range up to 5.1 A. This
include multiple scattering paths.
The parametrization of those scattering paths is as follow (.apj enclosed) :

- Distances :
1) a spherical expansion term was used to describe distance variation in [hkl] direction (reff*alpha1)
with l considered as "large"  when compared to h,k (reff*alpha1)
2) another spherical expansion term was used to describe distance variation in pure [hk0] direction (reff*alpha2)
3) a rough average of two previous expansion terms for [hkl] direction when h,k are comparable to l (reff*(alpha2+alpha1)/2).

- For modeling disorder, the correlated Debye model was used with 3 parameters dt, dt2, dt3 (t =293K):
1) [hkl] direction with l considered as "large" : debye(t,dt)
2) pure [hk0] direction: debye(t,dt2)
3)  for [hkl] direction with h,k comparable to l : debye(t,(dt+dt2)/2)

But does this choice of parametrization is really reasonable?
It seems very rough to me but when I look at the fit results it looks ok.

- Uncertainty on :

1) Distances :  is it simply delta(r) = reff*delta(alpha) ?
2) Debye-Waller : I can't figure out how to relate the uncertainty computed for the Debye temperatures (dt,
dt2) to the uncertainties of the debye-waller terms for each scattering paths. Although I spent some
times trying to understand this paper,
http://journals.aps.org/prb/pdf/10.1103/PhysRevB.20.4908, I can't write a simple relation at the end.

Many thanks for your kind help,

Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldchikh@...
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx

________________________________

This message and its contents including attachments are intended solely for the original recipient. If
you are not the intended recipient or have received this message in error, please notify me immediately
and delete this message from your computer system. Any unauthorized use or distribution is prohibited.
Please consider the environment before printing this email.
Attachment (Co-Foil-700C-hex.apj): application/octet-stream, 583 KiB
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Raj kumar | 11 Mar 09:59 2015
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(D)Artemis shutting down automatically

Dear All,

Recently, i have faced automatic shutting down of artemis during the import of chi file. For more clarification, please see the first log file.

Also, i observed emptying of .fpj files. This happens during the saving of old .apj to .fpj or/and during the frequent saving of .fpj files after .apj conversion. Please see the second log file for this problem.


Regards,
Raj
Attachment (dartemis.log): application/octet-stream, 749 bytes
Attachment (dartemis.log): application/octet-stream, 522 bytes
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Raj kumar | 10 Mar 17:11 2015
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Increase in uncertainty of Eo and fitting mismatch

Dear All,

Recently, I recorded Copper foil EXAFS as a reference in (Dispersive EXAFS) transmission mode at Soleil, Paris. For understanding the data quality (of my sample), i started fitting copper EXAFS through Artemis. After the DATA extraction, i fitted copper in Artemis and found a shift in energy. For this reason, i have modeled with and without corrected Copper EXAFS in Artemis. Initially, i started with first shell and progressed to three shell fit through step by step. During the course of fitting, some of the following troubles have been faced. Please help me to rectify it.

For first shell fit: Everything goes well and converged to reasonable physical values of copper foil. Whereas for further increment in copper shells leads to increase in Debye-waller factor for all three shells and increase in uncertainty value of E0 than the actual value.

Moreover, i have noticed that the (increase of shells in the fit) not only changes the physical parameters and also modifies the Fourier transform.  The inference are the following: A shift in first and third shell of Cu-Cu are observed, respectively, to larger and shorter distance than the experimental spectrum with diminished second shell amplitude.

Although Copper foil EXAFS is standard and well known sample, i am stuck with fitting. Please help me to overcome these problems. For your reference, project file of Copper file is attached with this email.

Regards.
Raj

Attachment (Cu_ODE_three-shell_fin_10-03-15.apj): application/octet-stream, 344 KiB
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Matthias Filez | 10 Mar 16:43 2015
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wavelet transformed XAS in Larch-0.9.24

Dear mailing list user,
 
I am currently trying to use the cauchy_wavelet.py plugin of Larch-0.9.24 to wavelet transform some k-space EXAFS data. In principle, everything works properly, but I would like to adjust the order of the Cauchy wavelet to 50. However, a view inside the script does not make clear what changes are necessary. How can this be done?
 
Please provide me your suggestions,
Many thanks,
 
Matthias Filez
 
PhD student
Ghent University / Laboratory for Chemical Technology
Technologiepark 914,  B-9052 Ghent - Belgium
http://www.lct.UGent.be
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Bruce Ravel | 9 Mar 14:09 2015

Importing data with the new version of Athena


Hi,

This question was sent to our mailing list by someone who is not
subscribed.  For some reason, it was not in the administration queue
on the list server, so I couldn't forward it along in the normal
fashion.

Here is Sander Bruun's question:

> For some reason I am unable to import data directly from *.dat files
> in the new version of Athena. It says I may be needing a plugin, but
> I do not know how to install it. Can anybody help. It worked fine in
> some of the older versions of Athena, but I cannot find and install
> them now.

Sander,

That's not enough information for me to answer the question.  "*.dat"
is not a file format.  A file called "*.dat" can (and usually does!)
contain almost anything.  Without an example of the sort of file that
is giving you trouble, I cannot possibly know what's going on.

If your data comes from a particular beamline, it's possible that you
simply need to enable that beamline's plugin.  There are a couple
plugins that come with the software related to specific beamlines at
ESRF....

http://bruceravel.github.io/demeter/aug/other/plugin.html#athena%27spluginregistry

Cheers,
B

PS: If you subscribe to the mailing list (see
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit), then you
mail will be posted to the list without my intervention.

--

-- 
  Bruce Ravel  ------------------------------------ bravel@...

  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/
Godfrey, Ian | 9 Mar 09:17 2015
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Data being overwritten in Artemis history window

​Dear All,


Sorry... another bug report! Hopefully the last one for a while!


In the history window some, but not all, data from previous fits seems to get overwritten when running a new fit. Specifically I've noticed this happening with the information in the "Data set" section. To reproduce run a QFS fit with some R-space fitting windows (say 2-4); at this point the log will be displayed correctly in the history window. Now change the R window (say 1.5-3.5) and run the fit again. When you go to the history window the R window information will be displayed correctly for the most recent fit but, for the previous fit it will have been overwritten by the newer fit. Some of the other info, such as R-factor by k-weight seems to get overwritten too.


A video of this behaviour can be found here: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_info&id=29d3e5c2 password: 54c8545f


System info: Win 8.1 Enterprise x64 running Demeter 0.9.22 pre release x64; log attached.


All the best,


Ian

----

Ian Godfrey

 

PhD Student,

UCL/JAIST Programme


Industrial Doctorate Centre in Molecular Modelling and Materials Science,

Department of Chemistry,

University College London

 

and

 

School of Materials Science,

Japan Advanced Institute of Science and Technology

 

i.godfrey-hclig2XLE9Zaa/9Udqfwiw@public.gmane.org i.godfrey <at> jaist.ac.jp

Attachment (dartemis.log): application/octet-stream, 714 bytes
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