Pieter Tack | 25 Feb 11:20 2015
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Pb compound determination fitting issue

Hi everyone,

I recently acquired an EXAFS data set (albeit somewhat noisy) on the  
Pb-L3 edge. I have normalized it using Athena, and tried to fit the  
first shell using Artemis. I attached the Athena project file as well  
as the Artemis project file of what I obtained thus far.

We have reason to believe the unknown compound is PbO or PbS (or a  
mixture). However, when I look at the R space curve, the first  
coordination shell is at rather low path distance (1.7 A), whereas one  
would expect larger bond distances for PbO and PbS. I found that a  
similar bond distance as to what the experimental spectrum shows can  
be found in PbCO3, but a fit using the mineral data of PbCO3 also  
doesn't do the trick.

In any case, no matter what I try to fit in Artemis, nothing seems  
decent. Is the EXAFS fitting simply impossible due to the noisy data,  
did I extract my Chi(k) wrong or am I encountering some other issue?

I realize it's probably not much to go on, but I'm rather new to EXAFS  
analysis so any help/advice is appreciated.
Thanks a lot in advance!

Best regards,
Pieter Tack

--

-- 
X-Ray Micro-Spectroscopy and Imaging Group
Department of Analytical Chemistry
Ghent University
(Continue reading)

Stevan Ognjanovic | 18 Feb 10:21 2015
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Trouble installing demeter on Mint 17.1

Dear list,


After upgrading my Linux OS to Mint 17.1, I have trouble installing demeter again (on Mint 14 it used to install and run without problems).  sudo ./Build installdeps failed to install a few dependencies even after issuing the command several times (Wx and Regexp:Assemble), so I installed them manually from the Mint repositories. After that, perl ./Build.PL said that all dependencies were satisfied. I then ran ./Build which finished, I think, normally. The only lines that look remotely suspicious are:

Chantler data conversion tool 1.2 for Absorption 0.10
  Parsing lines ...
  Parsing element 5Argument "8.20144-01" isn't numeric in numeric le (<=) at lib/Xray/data/chantler2st.PL line 120, <CHANTLER> line 81.
 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90
  Getting energy list keys ... sorting energy list ... and making energy hash
  Saving new database, lib/Xray/data/../Absorption/chantler.db.

However, when I run ./Build test it shows that 2/44 tests fail (5/2681 subtests). Please find the terminal output below.

It might be usefull to mention that at first I tried to install demeter without root privileges (following the Dave Hughes' guide), with same tests failing. I went on to ./Build install anyway, and it succeded, but when trying to open previously saved projects, dathena would crash. I then removed demeter and the local perl directory, and tried installing demeter again, this time with root privileges following Bruce Ravel's guide.

Any help would be appreciated, thank you in advance!




./Build test terminal output:

t/000_ifeffit.t ......... ok
t/001_base.t ............ ok
t/002_types.t ........... ok

#   Failed test 'configuration system introspection works: groups 37 artemis'
#   at t/003_config.t line 61.

#   Failed test 'configuration system introspection works: main_groups 37'
#   at t/003_config.t line 63.

#   Failed test 'introspection after reading new group: groups'
#   at t/003_config.t line 74.

#   Failed test 'introspection after reading new group: main_groups'
#   at t/003_config.t line 76.
# Looks like you failed 4 tests of 24.
t/003_config.t ..........
Failed 4/24 subtests
t/004_data.t ............ ok
t/005_plot.t ............ ok
t/006_gds.t ............. ok
t/007_prj.t ............. ok
t/008_path.t ............ ok

#   Failed test 'statistics reporting seems ok'
#   at t/009_fit.t line 97.
# Looks like you failed 1 test of 25.
t/009_fit.t .............
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/25 subtests
t/010_feff.t ............ ok
t/011_sp.t .............. ok
t/012_atoms.t ........... ok
t/013_spacegroups.t ..... ok
t/014_vpath.t ........... ok
t/015_sspath.t .......... ok
t/016_fspath.t .......... ok
t/017_structuralunit.t .. ok
t/018_multichannel.t .... ok
t/019_provenance.t ...... ok
t/020_indicator.t ....... ok
t/021_externalfeff.t .... ok
t/022_filetypes.t ....... ok
t/023_files.t ........... ok
t/024_graph.t ........... ok
t/025_lcf.t ............. ok
t/026_xes.t ............. ok
t/028_fpath.t ........... ok
t/029_threebody.t ....... ok
t/030_xdi.t ............. ok
t/031_quench.t .......... ok
t/032_miscellany.t ...... ok
t/100_elam.t ............ ok
t/101_mcmaster.t ........ ok
t/102_chantler.t ........ ok
t/103_henke.t ........... ok
t/104_shaltout.t ........ ok
t/105_fluo.t ............ ok
t/500_checker.t ......... ok
t/501_dataBlock.t ....... ok
t/502_dictionary.t ...... ok
t/503_filter.t .......... ok
t/504_parser.t .......... ok
t/505_writer.t .......... ok

Test Summary Report
-------------------
t/003_config.t        (Wstat: 0 Tests: 24 Failed: 4)
  Failed tests:  17-18, 23-24
t/009_fit.t           (Wstat: 256 Tests: 25 Failed: 1)
  Failed test:  17
  Non-zero exit status: 1
Files=44, Tests=2681, 69 wallclock secs ( 0.29 usr  0.06 sys + 67.36 cusr  2.64 csys = 70.35 CPU)
Result: FAIL
Failed 2/44 test programs. 5/2681 subtests failed.


Kind regards,
Stevan Ognjanovic
-- Stevan Ognjanovic, Dipl.-Ing. Nanoparticle Process Technology Department of Engineering Sciences University Duisburg-Essen Lotharstraße 1, MA 349 D-47057 Duisburg Phone: +49 (0)203 379 1783 Mobile phone: +49 (0)157 3820 6890 Fax: +49 (0)203 379 4453 web: www.nppt.de e-mail: stevan.ognjanovic-2ePcrahqm8iELgA04lAiVw@public.gmane.org
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Godfrey, Ian | 17 Feb 05:41 2015
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Feature request - Hephaestus: Plot multiple standards at once

Dear All,


I'm using Hephaestus' standards library to help with some XANES fingerprinting and it's very useful.


I would find it quite helpful to be able to select two (or more) standards from the list and plot them on the same graph for comparison.


Regards,


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-8xqbrEIV++l3+QwDJ9on6Q@public.gmane.org

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Khalid, Syed | 4 Feb 19:32 2015

Re: Ifeffit Digest, Vol 144, Issue 2

Thank you all, many nice suggestions and I will try them all.

For the first time the beamline 2-2 at SSRL is being used for XAS.
The control software is in LINUX and the output files automatically move to a
Windows computer, in binary and ASCII form, sitting next to it.
We were also able to see the ASCII file in wordpad and then saved it as text file after deleting all the text and
only keeping the data columns.
Athena was able to read it then.
I will have to write a program to add "#" before text lines. We will need that dealing with lot of data.
I will certainly check with the beamline scientist, why things are the way they are.
About the offsets, I did notice it was slightly negative, but we had other major problems to deal with, so did
not bother.

Syed Khalid

-----Original Message-----
From: ifeffit-bounces@...
[mailto:ifeffit-bounces@...] On
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Sent: Wednesday, February 04, 2015 1:00 PM
To: ifeffit@...
Subject: Ifeffit Digest, Vol 144, Issue 2

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When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..."

Today's Topics:

   1. Re: SSRL-data (Shoaib Muhammad)
   2. Re: SSRL-data (Matt Newville)
   3. Re: SSRL-data (Matthew Marcus)

----------------------------------------------------------------------

Message: 1
Date: Wed, 4 Feb 2015 10:31:56 +0900
From: "Shoaib Muhammad" <mshoaibce@...>
To: "'XAFS Analysis using Ifeffit'"
	<ifeffit@...>
Subject: Re: [Ifeffit] SSRL-data
Message-ID: <002401d0401a$5e97d300$1bc77900$ <at> gmail.com>
Content-Type: text/plain; charset="us-ascii"

Dear Syed Khalid,

One simple work around can be to select "Plugin Registry" and enable SSRL related plugins. By doing this I
was able to successfully read both the attached files in Demeter Athena. Further details to enable
plugins can be found here:

http://bruceravel.github.io/demeter/aug/other/plugin.html

/Shoaib

SKKU (South Korea)

From: ifeffit-bounces@...
[mailto:ifeffit-bounces@...] On
Behalf Of Khalid, Syed
Sent: Monday, February 2, 2015 5:11 AM
To: ifeffit@...
Subject: [Ifeffit] SSRL-data

How to handle SSRL, beamline 2-2 data.

Attached is a binary and an ASCII file(with under score A).

Wordpad reads it, first column is time (data point duration), second energy it must go to, third real energy
where mono went, fourth I0 and fifth It. It is gold foil transmission data.

Syed Khalid

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Message: 2
Date: Tue, 3 Feb 2015 21:38:58 -0600
From: Matt Newville <newville@...>
To: XAFS Analysis using Ifeffit <ifeffit@...>
Subject: Re: [Ifeffit] SSRL-data
Message-ID:
	<CA+7ESbp06KLZd+U-n9gFjjd=fNNKTFuKdTm3xmjKEdszifQx5g@...>
Content-Type: text/plain; charset="utf-8"

Hi Syed,

If any beamline is giving you data in a non-standard binary format and not providing software to deal with
the data, either complain very loudly (and not to the people at the beamline -- complain to the people
*paying* the
people who are running the beamline), or use another beamline.    I'd
recommend both.

There is absolutely no excuse for undocumented binary data formats.  It is completely unacceptable.  If
there is a program to convert to a portable format, demand the source code for that program.

That said, the ASCII file you have would be easily read by Athena if you added a '#' sign to the first column of
every line before the actual array data starts.  If you had the source code for the program that converted
the binary file to the ASCII file, it would probably be easy to make such a change.  If you don't have that
source code, the binary data files are worthless.

--Matt
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Message: 3
Date: Wed, 04 Feb 2015 08:00:06 -0800
From: Matthew Marcus <mamarcus@...>
To: XAFS Analysis using Ifeffit <ifeffit@...>
Subject: Re: [Ifeffit] SSRL-data
Message-ID: <54D24206.4020207@...>
Content-Type: text/plain; charset=windows-1252; format=flowed

Seems to me that in this era of nigh-infinite disk space, there's no need for binaries for EXAFS files like
this.  The ASCII is perfectly fine.
One question to ask:  Is the offset already subtracted from the data count?  I assume that it is, because the
last column has numbers that are smaller than the offset numbers.

Another question is which energy to believe.  On 10.3.2, it turns out that the requested energy seems to be
more accurate than the reported energy.  This becomes clear when you look at XANES and find it much
smoother, especially in the derivative, when you use the requested energy.
	mam

On 2/1/2015 12:10 PM, Khalid, Syed wrote:
> How to handle SSRL, beamline 2-2 data.
>
> Attached is a binary and an ASCII file(with under score A).
>
> Wordpad reads it, first column is time (data point duration), second energy it must go to, third real
energy where mono went, fourth I0 and fifth It. It is gold foil transmission data.
>
> Syed Khalid
>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@...
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>

------------------------------

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End of Ifeffit Digest, Vol 144, Issue 2
***************************************
Khalid, Syed | 1 Feb 21:10 2015

SSRL-data

How to handle SSRL, beamline 2-2 data.

Attached is a binary and an ASCII file(with under score A).

Wordpad reads it, first column is time (data point duration), second energy it must go to, third real energy where mono went, fourth I0 and fifth It. It is gold foil transmission data.

 

Syed Khalid

Attachment (au-testrun_010_A.001): application/octet-stream, 38 KiB
SSRL - EXAFS Data Collector 2.0       
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Marcelo Alves | 16 Jan 16:21 2015
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Exploring XANES data for getting EXAFS results

Hi all,

I wonder if it is possible from XANES unusual data treatment to get information such as number and distances of neigbhors in the first and second shells.

I think that could be very interesting for low Z elements such as P, S, Ca, K, Al, etc in diluted samples.

Thanks in advance.

Marcelo.
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Miller, BradleyW | 14 Jan 16:53 2015
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Demeter installation

Hi,

 

I’m trying to install Demeter software package on my govt. computer which is under a degree of lock down. I have full admin rights but its still not running.

 

Here is the explanation from IT support.

 

it wants to install on C:\strawberry and the C: drive is locked down here and all our programs need to be installed to C:\program files (x86) and when I tried to install there it told me that it didn't like spaces in the directory and I went ahead and install where it wanted and now program will not run due to security “

 

 

Any suggestions?

 

Thanks for your time.

 

 

Respectfully,

Bradley W Miller, PhD

Environmental Scientist

US Environmental Protection Agency

National Enforcement Investigations Center

Denver Federal Center, Bldg 25 Door E3

PO Box 25227

Denver, CO  80225

Office: 303-462-9150

Mobile: 863-258-7989

Fax: 303-462-9028

 

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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Angel Yanguas-Gil | 31 Dec 05:46 2014
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is there any ongoing effort to integrate feff and larch?

So far it seems from the sphinx doc that feff cannot be called from
larch. Is there any ongoing effort to implement that? The simplest way
would be to create a python module to generate the corresponding
feff.inp file, but I'd hate to duplicate someone else's work.

Thanks!

Angel
Edmund Welter | 22 Dec 15:23 2014
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Job offer at DESY

Dear colleagues,

DESY offers a postdoc position at the new PETRA III extension EXAFS
beamline P64. If you are interested in details please visit:

http://www.desy.de/v2/docs/1418221001-e.pdf

If you should know of a colleague who might be interested in the
advertised position please feel free to forward this mail. In case you
have any question please do not hesitate to contact me (preferentially
not via this mail list...)

Best regards,

Edmund Welter
Godfrey, Ian | 18 Dec 10:19 2014
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Handling large data sets in Athena (and energy dispersive calibration)

Dear All,

 

Here’s an issue I recently encountered while trying to handle some very large in situ datasets in Athena; it may be by design/an inherent limitation, rather than a bug, though:

 

(I am running Demeter 0.9.21 pre and Demeter 0.9.20 , both x64 on Windows 8.1 x64 on separate machines).

 

Each of my datafiles contains over 300 columns of u(E) data as space delimited plain text, however when I try and import them to Athena the import window will only display checkboxes up to column 87.

 

I’ve attached an example datafile and a logfile to this email. (The data is very poor, but that shouldn’t be an issue for debugging…) I’ve also attached a copy of the datafile as it came from the beamline – this also displays the issue, so it’s nothing I’ve done to the file.

 

On a related note, is it possible for the energy dispersive data calibration to be added back to Athena? To get the calibration parameters for this data I had to use the (very) old version!

 

Thanks,

 

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-8xqbrEIV++l3+QwDJ9on6Q@public.gmane.org

 

Attachment (dathena.log): application/octet-stream, 1678 bytes
Attachment (citrate_003_log_0_calibrated): application/octet-stream, 2921 KiB
Attachment (citrate_003_log_0): application/octet-stream, 3879 KiB
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Jean-Baptiste ABBE | 9 Dec 10:46 2014
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Bug report - autosave on mac

Hi everybody,

I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days.
Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue.
Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens :
1) athena launch, a little bit longer than usual
2) a box appear to give me choice to recover data by importing it from autosave or not
3) I can’t select anaything and the rainbow wheel of death appears.
After a few hours, nothing changes… and I have to terminate the programm manually.

So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions :

I tried to find the autosave file : nothing
I tried to uninstall and reinstall macports : nothing
I tried to uninstall macports and install the demeter-devel : nothing
In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment.

I will try again other solutions, but I will gladly accept any kind of help to solve my issues.


Thank you

ABBE J-Baptiste
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