Dimitar Popmintchev | 4 May 03:02 2016
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Artemis/FEFF question

Dear All,

The database at http://cars9.uchicago.edu/~newville/adb/search.html is down and I am trying to create an input file (for feff calculation) for pure scandium ( http://www.periodni.com/sc.html ).

The problem is when the 'atoms', and 'feff' in Artemis calculate the scattering paths, they shows distances smaller than the expected 3.256A nearest neighbor distance. What is the error in the input file attached below ?

Thank you.
Dimitar

 ATOMS                  * this list contains 117 atoms
 *   x          y          z     ipot tag           distance
    0.00000    0.00000    0.00000  0  Sc1           0.00000
    0.00000    0.00000    2.63650  1  Sc1.1         2.63650
    0.00000    0.00000   -2.63650  1  Sc1.1         2.63650
    2.86568    1.65450    0.00000  1  Sc1.2         3.30900
   -2.86568    1.65450    0.00000  1  Sc1.2         3.30900


Input file for scandium

## This Atoms file was generated by Demeter 0.9.22
## Demeter written by and copyright (c) Bruce Ravel, 2006-2015

title = name:     scandium
title = formula:  Sc
title = sites:    Sc1
title = refer1:   Kittel, ISSP
title = refer2:
title = schoen:
title = notes1:   metal, hcp
space = P63/mmc
a = 3.30900  c = 5.27300000
rmax  =   9.00000    core  = Sc1
atoms
# el.     x           y           z        tag
  Sc     0.00000     0.00000     0.00000   Sc1     
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Anatoly I Frenkel | 4 May 02:39 2016

Postdoctoral position

Dear IFEFFIT subscribers:

A postdoctoral position in my group will be available on July 1, 2016. The postdoc will be employed by
Yeshiva University in New York City. She or he will be stationed in Brookhaven National Laboratory on Long
Island and utilize XAFS and XRD/PDF techniques for studying mechanisms of electrostriction in novel
electromechanical materials. Prior experience with these methods, including high energy resolution
XAS, is required. This position is part of international collaboration, and will involve occasional
travel to research sites outside of the US. For all inquiries please contact me.

Anatoly Frenkel, Ph.D.
Professor and Chair, Department of Physics, Yeshiva University
245 Lexington Avenue, New York, NY 10016
https://yu.edu/faculty-bios/frenkel/
Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc
Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel@...
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Matt Newville | 27 Apr 17:52 2016
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XASLIB (was Re: data availability)

Hi Nino,

Thanks for bringing this up and for the kind words.  I agree that not only is access to measured XAFS spectra a problem now, it's been a problem for a long time, as evidenced by the Farrel Lytle database.  In fact, it has long been a topic of discussion in the XAFS community of how to provide such databases, and developments over the past few years on data formats have been driven at least partly by the desire to have better spectral databases. 

For everyone: please try out XASLIB at  http://cars.uchicago.edu/xaslib  and let us know if you have any questions, comments, or suggestions for improving this database.   Right now, there is not a lot of data here, but it is enough to give you an idea of how it works.  

Comments can either come here or as github Issues at the source repository for this code:
   https://github.com/XraySpectroscopy/XASDataLibrary

There is a bit of documentation and wiki pages at
   https://github.com/XraySpectroscopy/XASDataLibrary/wiki


A longer explanation:

The standard XDI format for XAFS data (largely the work of Bruce)  was presented at an IXAS workshop (Q2XAFS) in Tsukuba, Japan in 2011.  At the most recent Q2XAFS meeting in Hamburg last August (as a satellite meeting of the XAFS conference), I presented an initial version of an on-line database based on this format, and intended for general use in the community.    With feedback from that meeting, the version linked above is now ready for beta testing and comments.

The plan is to move this to the IXAS Portal  http://www.ixasportal.net/ixas/,  but we'd like to get community suggestions and features and testing before we make that move.

The database uses proper relational database to store the actual data, and tries to use modern web technologies for the interface.

Some of the main features of this database are:
  -  spectra can be uploaded from XDI files through the web interface.  
  -  multiple spectra can be tagged as belonging to the same Suite.
  -  individual spectra or Suites can be rated and/or commented on by
     anyone, giving "Amazon-like" reviews.
  -  in order to upload or comment, one has to log in by email address.  

The ratings and reviews are meant to provide some mechanism for data quality assurance, but to avoid having one person "police" the data before it can be added.  This is trying to recognize that no one person can actually curate all the spectra, that truly bad data can be best identified by experts on that system, and also that there is actually some value to imperfect data.

The requirements for data to be uploaded are fairly minimal except that the data must be in XDI format (basically so that metadata can be parsed easily and the columns are well-labeled), and that the monochromator lattice constant must be provided (so that energy re-calibration can be done if needed).    We can help translate existing data into XDI so it can be uploaded into this database.

There are several features to add or improve including:
   - adding some information about energy resolution.
   - being able to export a Suite of spectra as a single zip file or Athena project.
   - better web page interface to setting citation information.
   - better web page interface to setting sample information.

But suggestions from anyone would be greatly appreciated.

Finally, although the database is meant to provide a public, on-line databases useful to anyone, and uses modern relational database engines as the backend, the software can actually run on an individual machine to provide a local, private database of XAS spectra, with the same web-based interface.  This is not very well documented at the moment, but if anyone is interested in trying to set such a database at their home institution, let me know.

--Matt Newville

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pereira | 26 Apr 21:54 2016
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data availability

New to this mailing list, so excuse my innocence:

Today I see two questions about standards. Some time ago I was
looking for what I think is similar, and was pointed to the XAS data base
http://cars.uchicago.edu/xaslib/about/.

If I understand the questions properly, this database may be of great
help. It was to me. I thank the people organizing it, Matt Newville and
Bruce Ravel, for their great service to the community in volunteering
to make seemingly reliable data available in a convenient way.

Nino

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Halder, Avik | 26 Apr 15:49 2016

Request for CuCl and CuSO4 XAFS/ XANES standard data

I was trying to find the bulk standards for CuCl and CuSO4. If you would have this data could you please share
with me.

Best regards,
Avik Halder
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bajnoczi | 26 Apr 12:05 2016
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Farrel Lytle IXAS XAFS database data energy calibration

Dear List Members,

  I need some nickel reference spectra, and I thought to use the Farrel 
Lytle IXAS XAFS database. I have found some proper ones, e.g.:
http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/Ni/nifl.090
and
http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/Ni/nicl.047 ,
but it is not clear from the files how these spectra are energy 
calibrated. Can somebody help and give some detailed information about 
it for me?

  Thank you for your help in advance.

Best Regards,
Eva Bajnoczi
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pereira | 13 Apr 04:08 2016
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how to use the data in the XAN library to estimate the transmission of an x-ray filter

Hi All,

new to this list and to the field, so please be patient and kind
and helpful in any response you may have. So far everyone I've
reached on this topic has been extraordinary good. I still have to
learn the lore though.

I'd like to compute the x-ray transmission as function of the x-ray
energy, for a particular mass per unit area of a substance, say Zn.
In the XAS data base I find Zn foil at room temperature, recently measured
and even more recently put into the data base just in time for
my purpose. Thank you!  The question is:  is there a ready-made program
to use those data? I see that your community has a whole slew of
programs that do the opposite, go from the attenuation and/or fluorescence
measured on a beam line to the attenuation coefficient, apparently without
having to know the mass per unit area of the filter. I see Demeter,
Athena, Larch, and various others but they all seem to go the wrong
way for (and much further than) what I need.

Instead, I'd like to pick up the data you guys measured on the synchrotron,
and convert those into the X-ray transmission of a filter for which I select
the mass per unit area.

In trying to figure out how to do this I look at the graphs in the database,
and the numbers behind Zn foil.xdi.

The graph on the top left side gives the "Raw XAFS" (y, say) as function 
of energy.
I interpret that as y = - ln (itrans/i0), where i0 and itrans are in    
  Zn foil.xdi
as the intensity of the incoming x-ray beam, and the beam behind the
particular filter. Far from the edge, at 9600 eV, I see i0=93769.049842
and itrans=56429.849906, so that y=0.508. I can't tell from the graph 
whether this
is indeed the case, so I go to the NIST tables. They give 35.05 cm^2/g 
on the
low side of the edge. Then, the mass per unit area of this particular foil
must have been 14.5 mg/cm^2.

At 10000 eV the same thing gives y=3.603. This is pretty close to what I
see in the graph, so I'm tempted to think that guessing "Raw XAFS"= 
ln(i0/itrans).
However, for (mu/rho) NIST gives 233.1 cm^2/g, so I get for the foil's mass
per unit area 16 mg/cm^2. Not quite right.

Any comments on what I might have done wrong?

It seems to me that by measuring the transmission of a particular filter on
some X-ray source we might have available would then in effect measure
the mass per unit area, so that this can be taken into account by simply
exponentiating itrans/i0 with the right exponent ( = multiplying the
logs with the right factor).

Is something like this already implemented in one of your programs? If so,
which one?

Thank you,

Nino

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Ritimukta Sarangi | 12 Apr 22:45 2016
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SSRL XAS Summer School 2016 - update

Hello Everyone,
The agenda and application pages are online for the XAS summer school at SSRL in July. Please note that there are two hands-on tracks and you can choose to attend one of either XAS-imaging or EXAFS sessions. The lecture part is the same for both the sessions and both sessions will benefit from the XANES and advanced spectroscopy lectures on the final day of the summer school. Note that the deadline for application is May10th. Accepted participants will be emailed before the 20th of May.


Best Wishes,
-Riti Sarangi
Staff Scientist
SSRL, SLAC






On Apr 4, 2016, at 12:32 PM, Ritimukta Sarangi <ritimukta-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Hello Everyone,
This is an announcement for the XAS summer school to be held at SSRL between July 18-22, 2016. We will cover XAS, EXAFS and Imaging beamlines with hands on data collection sessions at beamlines, followed by in-depth data analysis in a classroom setting. You can find more information at :http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html. The agenda and application pages will be finalized within a week and I will post an update once it is up and running. But I wanted interested users and participants to get a heads up.






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Matteo Busi | 12 Apr 13:50 2016
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Importing chi(k) data

Hi,
I am experiencing several bugs when trying to import data as chi(k).

I have the data as a .dat ascii files with k the second column and the relevant chi(k) and corrected chi(k) as the 4th and 5th columns. This data was  previously exported as .xmu from athena, the k grid column was obtained as k ~= sqrt(0.262468*(E-E0)). When I try to import this new data back in athena, I get something totally different from expectations! 
However sometimes by clicking repeatedly in the importing menu I get the expected result. 
This looks like a bug to me!

You can find the file as attachment.

Regards
Attachment (Corr_2nd.dat): application/octet-stream, 197 KiB
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Lorenzo Stievano | 9 Apr 21:43 2016
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Bug report

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is installed.

Athena worked fine until a few days ago, but from a certain point it 
started to crash when I try to import a simple text data file (which 
worked well before). I have tried reinstalling Demeter (I actually did 
it twice) but the problem persist. The computer works under WIndows 7 
Professional, SP1, 64 bits.

Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.
Attachment (dathena.log): application/octet-stream, 4375 bytes
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Matteo Busi | 8 Apr 16:22 2016
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(no subject)

Hi Matt.

Thanks for the hints, they are very useful.

What would you suggest to use if not the bkg?
Regarding the xmu(E) I have been using exactly the values exported through
the .xmu ascii file.
I have been reading though the Athena's user guide and I didn't find any
hint about which unit I could assign to them.
Anyway I would like to get them with the cm^-1 units which would suit with
the correction expression I want to perform. How can this be done?
My idea was to divide the xmu data by the penetration depth in the sample
(i.e. the radius of the capillar sample). Is this correct? Can this be
applied to the bkg data aswell?

Moreover the data I have is not scanned through the Cu fluorescence energy
you have mentioned (8046 eV). Would you recommend to use data from Chantler
or Cromer-Liberman? And how can I merge it with my other measured data to
make it unit meaningful?

Thanks and regards,
Matteo

I report our previous conversation for reference:

> What I am trying to do is to perform a new developed self-absorption
> correction using collected fluorescence absorption coefficient data on a
> CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as
> absorber, having different values of molarity and penetration depth.
> The correction expression requires these measured quantity:
> ?X(E) : the absorption coefficient due to a given core excitation of the
> absorbing atom
>               - I used the background function for this ( bkg(E))

Wouldn't using bkg(E) suppress the fine-structure you are trying to
recover?  Anyway what are the units, are you normalizing bkg(E) to
something meaningful?  I would suggest using data from Chantler or
Cromer-Liberman here.   Or perhaps match mu(E) or bkg(E) to these.


> ?o = ?(E) : photoelectric total linear absorption coefficient of the
> sample at incident energy E
>                    - I used the xmu(E) for this
>

Again, be mindful of what the units are.

> ?h = ?(E) :photoelectric total linear absorption coefficient of the sample
> at fluorescence emission Ef
>                    - I used the xmu(Ef) with Ef the K absorption edge of
> Cu ( 8.9789 eV)
>

I am pretty sure that this is not what you want.  You probably want mu(E)
at the Cu fluorescence energy (8.046  keV). This can make a significant
difference.
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