[Ifeffit] Looking of a K-edge spectrum of maghemite

[Lorenzo Stievano]

Hi everybody,

daes anybody have in his repository a Fe K-edge XAS spectrum of 
maghemite (gamma-Fe2O3)? I would need it as a reference material in a 
study on doped iron oxides.


Thanks a lot in advance!

Lorenzo

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Re: [Ifeffit] Energy Resolution

[Lorenzo Stievano]

  
  
Hi Julian,
Carlo is completely right about the S0^2, and the common way to
  handle it (measure it for a standard and then transfer it, keeping
  it fixed, to the other measured materials).
I would just like to add that it is preferable that the standard
  and the materials have similar thickness (absorption coefficient)
  and especially good homogeneity. In fact, while the first one has
  an important influence on the amplitude of the EXAFS oscillations
  (especially when you deal with thick samples at low energies), the
  second one might also induce you in a wrong evaluation of the real
  value of the edge jump and thus of the amplitude of the
  oscillations (with inhomogenoeus samples, you may obtain edge
  jumps of acceptable values with attenuated oscillations).

This just to stress that sample preparation is really extremely
  important also to obtain a correct evaluation of the S0^2 from a
  reference compound.
Yours, Lorenzo




On 10/05/2018 18:06, Carlo Segre wrote:


  
  Hi Julian:
  
  
  I would be happy to help with this.  Let me answer briefly on the
  list and afterward, if you like, just contact me privately and we
  can discuss in more depth.
  
  
  S02 is a property of the absorbing atom and is due to the change
  in electronic energy levels because of the present  of a core hole
  after the photoabsorption event.  It is usually considered to be
  transferable from material to material with the same element
  because it is really a local property.  However, in practice it
  does depend on the type of compound you are measuring and the
  beamline as well as the type of measurement you are making
  (transmission, fluorescence).  All of these factors can masquerade
  a amplitude reduction factor.
  
  
  What I do in practice is to measure a standard which has the same
  local environment and fit the EXAFS with the known structure to
  extract an S02 which I then use transferably.
  
  
  As for your question about delta R.  If your EXAFS cannot be fit
  using an isotropic expansion model (not always the best way
  anyway) then you most likely need to make the delta R parameters
  independent.  There is absolutely no reason to correlate a shorter
  path with a longer path even if it is the same element, unless you
  are using a known structure model out of which you are trying to
  extract specific parameters.
  
  
  Hope this helps.
  
  
  Carlo
  
  
  On Thu, 10 May 2018, Julian Ehwald wrote:
  
  
  Hi Carlo


Thank you for your answer. I have completely different question
as well: I

just started using Artemis, and have a question regarding the
amplitude

reduction factor: I use different So^2 for different elements,
correct? If I

start fitting and have paths involving the same kind of atom but
once at

distance 2A, and once maybe 3A, is this then the same So^2 or am
I supposed

to model the behaviour of So^2 somehow?

Similar for \Delta R: If I don?t have a nice simple cubic
structure and

can?t use isotropic expansion similar like alpha*R_eff, what
would be a

smart(or physically correct) way to connect \Delta R (as well as
sigma^2)

for the same element for different distances? The material I am
looking at

is Li2O2 and Li2IrO3, which don?t have a very simple structure.


I am aware that maybe I am asking a bit much, but if you could
help me in

any way I would be very delighted.


Best, Julian


-Ursprüngliche Nachricht-

Von: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov]
Im Auftrag

von Carlo Segre

Gesendet: Sonntag, 6. Mai 2018 01:07

An: XAFS Analysis using Ifeffit


Betreff: Re: [Ifeffit] Energy Resolution



Hi Julian:


With an edge energy of 543 eV, your monochromator resolution
should be at

least 0.1 eV.  If you are interested in XANES, you need to take
data at this

resolution or maybe even better.  ONce past the edge, there is
no need to

keep that step size.  If your beamline permits an EXAFS-type
step scan with

steps in k-space, you want to use a dk of 0.05 which is what
IFEFFIT

interpolates to.  Smaller step sizes 

Re: [Ifeffit] Strange EXAFS oscillations, never seen before

[Lorenzo Stievano]

  
  
Dear Rana,
you seem to have real EXAFS oscillations up to k=9, then there
  are surely some artefacts in your spectra, which are unusable from
  that point on. In fact, if you limit your spline range to 9 in
  Athena, you get oscillations that look real and seem to have some
  sense. 

These artefacts are probably of experimental origin (shit
  happens), I do not think you can do much about them,with the
  exception of remesuring your spectra.
Yours sincerely,
Lorenzo

Le 19/03/2017 à 17:13, Rana, Jatinkumar Kantilal a écrit :


  
  
  Dear all,


I observed strange EXAFS oscillations in my data up to
  about 1000 eV beyond the K-edge, I would like to share this
  situation with you and hope to get some feedback. Please find
  attached the athena project file of the data.


The chemical composition of the material is
  (Fe0.5Cu0.5)Sn5. The EXAFS sample was prepared by taking the
  material equal to 2 absorption lengths at the Cu K-edge,
  mixing it with graphite and pressing into the pellet, which
  was sealed between the Kapton tape.


The measurements were carried out at the Cu K-edge of the
  material in the transmission mode at the beamline 5BM of APS.


Here are my concerns:


(1) In the athena project file, the data files
  "Cu_S1_scan003" and "Cu_S1_scan004"
are the two scans of the same sample measured one after the
other. As can be seen, there are strong oscillations even at
1000 eV from the Cu K-edge, which is strange because
generally EXAFS oscillations "wash out" as we go higher in
energy. Nevertheless, the two scans appear reproducible.

  
(2) Once I removed the
sample and remeasured it after some time (because I did not
believe the previous 2 scans), I found completely different
data (i.e., data "Cu_S1_scan005"). 

  
(3) The Cu reference
foil measured simultaneously along with the sample for each
of these scans appear quite reproducible.

  
I am puzzled as to what
can contribute to such effects. I have never seen such
effects before. 


We can rule out the possibility of beam damage, since I
  have measured up to 3 scans (25 min per scan) and they all
  look reproducible. However, once I remove the sample and
  remeasure it after some time to reproduce the previous 3
  scans, the scan looks totally different.


Also, we can rule out the chemical instability of the
  material, since the material is quite air-stable.


I have measured a series of samples with this composition
  and all of them have the same effect. 


I would very much appreciate your feedback!


Best regards
Jatin




  
  
  
  
Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

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

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv.
Vorsitzende Dr. Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de
  
  
  
  
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-- 
  
  

  

    
  
Lorenzo
Stievano
  
  Professeur
  
  Tel : +33(0) 4 67 14 33 46
  
  aime.icgm.fr/spip.php?article102



  

  
  

  
  Institut Charles Gerhardt Montpellier
  UMR 5253 CNRS-UM-ENSCM
  Université de Montpellier, Place E. Bataillon, Bât 15,
  cc 1502
  34095 Montpellier cedex 5 - France

  

  

  

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Re: [Ifeffit] Bug report

[Lorenzo Stievano]

There must have been something corrupted in the AppData\Roaming\Demeter 
directory. It crachesd even with your data file (as for mine), but now 
it works fine since I reinstalled it AFTER removing the Roaming directory.


Thanks for your help,

Lorenzo

Le 10/04/2016 08:20, Robert Gordon a écrit :

The log file was attached, not a data file.
I have attached a datafile that is just text. Try importing it, 
please. It imports without issue for me.


Another thought: When you uninstalled/reinstalled, did you delete the 
AppData\Roaming\Demeter directory?
This may not get removed when an uninstall occurs and if it has a 
corrupted setting somehow, then

deleting it before reinstall may clear that.


On 4/9/2016 11:04 PM, Lorenzo Stievano wrote:

It was actually attached... anyway, now I just paste it in the message:

--

Started at 2016-04-09T21:33:05
Win7Professional (64-bit) Service Pack 1Service Pack 16176012102561

PATH is:
C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program 
Files\DemeterPerl\c\bin;C:\Program 
Files\DemeterPerl\perl\site\bin;C:\Program 
Files\DemeterPerl\perl\bin;C:\Program 
Files\DemeterPerl\c\bin\gnuplot\bin


perl version: v5.18.2
backend: ifeffit

@INC:
C:/Program Files/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
C:/Program Files/DemeterPerl/perl/site/lib
C:/Program Files/DemeterPerl/perl/vendor/lib
C:/Program Files/DemeterPerl/perl/lib
.
Demeter version 0.9.24

YAML::Tiny failed to classify line ' ' at C:/Program 
Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 783.
YAML::Tiny::_error(YAML::Tiny=ARRAY(0x10c7d818), "YAML::Tiny 
failed to classify line 
'\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm 
line 303
YAML::Tiny::_load_string("YAML::Tiny", 
"\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm 
line 37
YAML::Tiny::Load("\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm line 296
Demeter::UI::Athena::IO::_data(Demeter::UI::Athena=HASH(0x4bbae8), 
"C:\\Users\\Utilisateur\\Desktop\\Ge K-edge 
Operando_ROCK\\operando"..., "C:\\Users\\Utilisateur\\Desktop\\Ge 
K-edge Operando_ROCK\\operando"..., 1, 0) called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm line 165
Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x4bbae8)) 
called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 859
Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30), 
Demeter::UI::Athena=HASH(0x4bbae8)) called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 782
Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30)) called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47
eval {...} called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47



--

Le 10/04/2016 07:53, Robert Gordon a écrit :

The data file?

On 4/9/2016 10:19 PM, Lorenzo Stievano wrote:

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

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.


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Re: [Ifeffit] Bug report

[Lorenzo Stievano]

It crashes with any text data file I try to import. It opens normally 
already saved .prj files.


Le 10/04/2016 07:56, Robert Gordon a écrit :
Another thought: Does this crash happen with other data files, or just 
this one?


On 4/9/2016 10:19 PM, Lorenzo Stievano wrote:

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

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.


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Re: [Ifeffit] Bug report

[Lorenzo Stievano]

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

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.


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Started at 2016-04-09T21:33:05
Win7Professional (64-bit) Service Pack 1Service Pack 16176012102561

PATH is:
C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program 
Files\DemeterPerl\c\bin;C:\Program Files\DemeterPerl\perl\site\bin;C:\Program 
Files\DemeterPerl\perl\bin;C:\Program Files\DemeterPerl\c\bin\gnuplot\bin

perl version: v5.18.2
backend: ifeffit

@INC:
C:/Program Files/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
C:/Program Files/DemeterPerl/perl/site/lib
C:/Program Files/DemeterPerl/perl/vendor/lib
C:/Program Files/DemeterPerl/perl/lib
.
Demeter version 0.9.24

YAML::Tiny failed to classify line 
''
 at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 783.
YAML::Tiny::_error(YAML::Tiny=ARRAY(0x10c7d818), "YAML::Tiny failed to 
classify line 
'\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...)
 called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 303
YAML::Tiny::_load_string("YAML::Tiny", 
"\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...)
 called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 37

YAML::Tiny::Load("\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...)
 called at C:/Program Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm 
line 296
Demeter::UI::Athena::IO::_data(Demeter::UI::Athena=HASH(0x4bbae8), 
"C:\\Users\\Utilisateur\\Desktop\\Ge K-edge Operando_ROCK\\operando"..., 
"C:\\Users\\Utilisateur\\Desktop\\Ge K-edge Operando_ROCK\\operando"..., 1, 0) 
called at C:/Program Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm 
line 165
Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x4bbae8)) 
called at C:/Program Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 
859
Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30), Demeter::UI::Athena=HASH(0x4bbae8)) called 
at C:/Program Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 782
Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30)) called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47
eval {...} called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47
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[Ifeffit] Bug report

[Lorenzo Stievano]

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.


dathena.log
Description: Binary data
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