Re: [Ifeffit] Ni standard spectra

[Otal Eugenio]

Dear Qiang,
please check here for references:
https://urldefense.us/v3/__https://mdr.nims.go.jp/collections/qz20st57x?utf8=**B=ni=__;4pyT!!G_uCfscf7eWS!dMq5k-AqagWlGvPzorQwK2VKGoFbwtPLMPkwTX4fSPGlg9Xc9ZHCmD1aag9s7ZBJQk7TNBbnOvgfghOjnejnth5XqIHoRY9yF1y3ibn8mqqa$
 
Best regards.

(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp

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On Mon, Jul 8, 2024 at 12:15 PM Qiang  wrote:

> Hi, Dear XAFS community, does someone by chance have the standard spectra
> of some Ni compounds? Now in my hand I have Ni foil, NiO, and Ni2O3. I am
> still looking for α-Ni(OH)2, β-Ni(OH)2, γ-NiOOH, and β-NiOOH. I am very
> appreciated if someone
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> Hi,
>
> Dear XAFS community, does someone by chance have the standard spectra of some 
> Ni compounds? Now in my hand I have Ni foil, NiO, and Ni2O3. I am still 
> looking for α-Ni(OH)2, β-Ni(OH)2, γ-NiOOH, and β-NiOOH. I am very appreciated 
> if someone can share some spectra. Other related Ni compound spectra, if any, 
> are also thankful.
>
> Best regards,
> Qiang
>
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Re: [Ifeffit] Problem with cif files using Larch

[Otal Eugenio]

Hi,

Thank you for your answer.

I deleted Ni and Mn alternately, but it didn't work. I obtained a new one
from ICSD, and it is working fine. I have attached it.

Having atoms in the same position was not a problem with other CIF files,
like the FMN attached one. I am fitting now, but I was concerned about it.

Thank you again for your help.

Best regards.



(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates

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On Thu, Feb 15, 2024 at 4:03 PM 정은석  wrote:

> The site in Mn and Ni in cif is same. It makes your problem.
>  Make only Mn in cif. I mean that Mn instead of Ni is located.
>  And run feff.  You can get the path related with Mn.
> After that,  Make another structure in same cif, Ni instead of Mn. You can
> get the path of Ni.
> Then, use them
>
> 2024년 2월 15일 (목) 오후 3:36, Otal Eugenio 님이
> 작성:
>
>> Dear all.
>> I am trying to generate the path for fitting Mn and Ni K edge at
>> LiMn1.5Ni0.5O2 using cif files from ICSD.
>> I receive this error:
>>
>>
>>
>>
>>
>>
>>
>> *Elements: ['Li', 'Mn', 'Ni', 'O']Sites: [2.08337619 6.16682619
>> 6.08352381] Li:0.980Traceback (most recent calls last):  File
>> "C:\Users\Me\xraylarch_2023_10\Lib\site-packages\larch\wxlib\cif_browser.py",
>> line 447, in onShowCIFsites = ['%d' % (i+1) for i in
>> range(len(sites))]
>>  ^^TypeError: object of type 'PeriodicSite' has no len()*
>>
>> I also attached the cif.
>>
>> Any hint to go forward?
>>
>> Best regards.
>>
>> (^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)
>>
>> Eugenio H. OTAL
>> Assistant Professor
>> Dept. of Materials Chemistry
>> Shinshu University
>> 4-17-1 Wakasato, Nagano 380-8553, JAPAN
>> eugenio_o...@shinshu-u.ac.jp
>> https://sites.google.com/view/zettsu-laboratory/news-updates
>>
>> ¯\_(ツ)_/¯¯\_(ツ)_/¯
>>
>> Who is John Galt?
>>
>> ¯\_(ツ)_/¯¯\_(ツ)_/¯
>>
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LNMO_P4332_c.cif
Description: Binary data


O3 NaNiFeMnO.cif
Description: Binary data
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[Ifeffit] Problem with cif files using Larch

[Otal Eugenio]

Dear all.
I am trying to generate the path for fitting Mn and Ni K edge at
LiMn1.5Ni0.5O2 using cif files from ICSD.
I receive this error:







*Elements: ['Li', 'Mn', 'Ni', 'O']Sites: [2.08337619 6.16682619 6.08352381]
Li:0.980Traceback (most recent calls last):  File
"C:\Users\Me\xraylarch_2023_10\Lib\site-packages\larch\wxlib\cif_browser.py",
line 447, in onShowCIFsites = ['%d' % (i+1) for i in
range(len(sites))]
 ^^TypeError: object of type 'PeriodicSite' has no len()*

I also attached the cif.

Any hint to go forward?

Best regards.

(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates

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LNMO P4332_ICSD.cif
Description: CIF chemical test
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Re: [Ifeffit] Ir standards

[Otal Eugenio]

Dear Olga,
Check here:
https://mdr.nims.go.jp/catalog?utf8=%E2%9C%93=en_field=all_fields=IrO2
https://mdr.nims.go.jp/catalog?utf8=%E2%9C%93=en_field=all_fields=Ir
Best regards.

(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates

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On Mon, Feb 12, 2024 at 12:46 AM Ольга Филимонова 
wrote:

> Hello!
>
>
> Does everyone have standards of metallic Ir, IrO2 etc.? (L3-edge, both
> XANES and EXAFS would work).
>
> Thank you!
>
>
> Sincerely,
> Olga
> --
> Olga Filimonova
> Post-doc researcher - BM28 - XMaS
> Office: 30-1-24
> Extension: 2436
> European Synchrotron Radiation Facility (ESRF), Grenoble, France
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Re: [Ifeffit] Fe K-edge maghemite (gamma-Fe2O3)

[Otal Eugenio]

Dear Christian,
Check this database:
https://mdr.nims.go.jp/concern/datasets/1n79h782t?locale=en
I hope it helps.
Best regards.


(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates

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Who is John Galt?

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On Fri, Feb 9, 2024 at 4:12 AM Christian Wittee Lopes 
wrote:

> Dear XAFS community,
>
> Does anyone have a Fe K-edge XAS spectrum of maghemite (gamma-Fe2O3)
> sample or standard?
>
> Thank you in advance.
>
> Best,
>
> Christian Wittee Lopes
>
> --
>
> Christian Wittee Lopes
>
> Professor Adjunto
>
> *Departamento de Química - Setor de Ciências Exatas*
>
> Universidade Federal do Paraná (UFPR)
>
> *Curitiba - Paraná*
>
> *LinkedIn 
> | ORCID  | Lattes
> *
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[Ifeffit] O K-edge energy shift in feff8

[Otal Eugenio]

Dear all,
I am simulating O K-edge from LiNi0.5Mn1.5O4 with partial fluoride
substitution.
I am starting from a DFT simulated cif file with 30 different oxygen atoms,
so I am simulating each Oxygen for a later average and comparing them with
experimental results.
I am using these flags:

 *  O K edge energy = ##.## eV
EDGEK
S02 1.0
 * potxsph  fms   paths genfmt ff2chi
 CONTROL   1  1 1 1 1  1
 PRINT 1  0 0 0 0  0

 * ixc  [ Vr  Vi ]
 EXCHANGE  0

 * r_scf  [ l_scf   n_scf   ca ]
 SCF   6.50

 * kmax   [ delta_k  delta_e ]
 XANES 4.0   0.05 0.3

 * r_fms l_fms
 FMS6.50  0

 * emin  emax   eimag
 LDOS  -30   20 0.1

 RPATH 0.1
 *EXAFS 20

POTENTIALS
*IPOT  Z   Tag
  0 8   O
  1 8   O
  225   Mn
  328   Ni
  4 3   Li
  5 9   F

ATOMS
*x y z   ipot  tag   distance  site_info
0.0   0.0   0.00   O 0.0  * O_25
(...)

I just finished some simulations and I found the energy limits are shifted
in xmu.dat for the different oxygen sites, just in absolute (omega) and
relative (e) energy.
As I want to see the relative intensities in the pre-edge, I am
worried about normalizing the energy before averaging all the spectra.
Is this ok? Is there a way to normalize the energies or am I making any
mistakes? I m attaching a plot of three spectra.
Best regards.

(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates

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Re: [Ifeffit] Shift in Eo when fitting PtO2 and similar samples

[Otal Eugenio]

Dear Chen,
Did you compare the spectra of Pt with the reference available here:
https://www.aps.anl.gov/files/APS-Uploads/DET/Detector-Pool/Beamline-Components/EXAFS_Filters/Reference_XRay_Spectra.pdf
Some edges, like Pd, are tricky.
Best, euG


(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)




On Thu, Aug 24, 2023 at 5:02 AM alexeyboubnov 
wrote:

> Dear Yanny, dear Shelly,
>
> I also came across this issue, with Pt and Ir L3 XAS. For these spectra,
> deltaE0 is systematically 10-12 eV, compared to K edge XAS spectra, where
> it is typically +/- a few eV.
>
> My explanation is as follows; if I am wrong or there are other
> explanations in the community, I would like to know:
>
> In the K edge case you define the actual edge step as your edge position
> E0 in Athena, which matches pretty well with the "E0" point that Artemis
> takes as k=0Å-1 when calculating the paths in FEFF. The difference deltaE0
> between what Artemis defines and what you define in Athena is thus small.
> Note that the pre edge peak (transition to bound states, 1s to 3d is weak)
> is left on the low energy side and typically ignored when choosing E0,
> because it is usually significantly smaller than the edge step.
>
> For L3 XAS, the white line is your transition to bound states, 2p to 3d,
> and is very intensive compared to the edge step. The actual edge step is
> then buried about 10 eV higher than where the white line onset is found. So
> when you define E0 as the white line onset, you "underestimate" the actual
> edge position by about 10 eV or higher. Artemis then corrects it and
> everything matches. If you define E0 at the white line peak as Shelly
> suggested, or maybe even after the white line, you will definitely be
> closer to theory, but that will also affect the background subtraction.
>
> Hopefully this is helpful!
>
> Cheers,
> Alexey
>
>
>  Original message 
> From: "Kelly, Shelly Diane" 
> Date: 8/23/23 16:11 (GMT+01:00)
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] Shift in Eo when fitting PtO2 and similar samples
>
> Hello Yanny:
>
>
>
> I’ve modeled a few Pt EXAFS spectra and have found that using an E0 at the
> top of the white line usually does a better job of getting the data close
> to the theory. This seems to be often the case with the L3-edges as they
> are rather broad compared to the K-edges of transition metals.  If you
> would like to share your project files with me. I can take a look.  14 eV
> seems to be too much and maybe an indication that there is a different type
> of atom in the first shell.
>
>
>
> B.T.W. Using the first derivative is great for XANES analysis, but often
> not the best choice for EXAFS.
>
>
>
> Kind regards,
>
> Shelly Kelly (ske...@anl.gov)
>
>
>
> *From:* Ifeffit  *On Behalf Of
> *Zi Qi Chen
> *Sent:* Tuesday, August 22, 2023 9:53 AM
> *To:* ifeffit@millenia.cars.aps.anl.gov
> *Subject:* [Ifeffit] Shift in Eo when fitting PtO2 and similar samples
>
>
>
> Dear all,
>
>
>
> I am looking at EXAFS of PtO2 powders and Pt particles supported on TiO2.
> I used a beta-PtO2 crystal structure data for the PtO2 EXAFS and after
> the first shell fit, I observed a large shift in Eo (delta Eo of ~14 eV) in
> my fit parameters. When I tried to fit the Pt foil to obtain the So2, the
> energy shift also seemed high (delta Eo of ~7 eV). I am wondering if there
> could be a problem in the selection of Eo prior to EXAFS analysis? I left
> the Eo as the energy at the first peak of first derivative (ifeffit
> default).
>
> All of the data were also aligned using the reference foil in Athena
> before looking at EXAFS. I am wondering what would have caused this shift?
> Any help is appreciated, thank you.
>
>
>
> Best regards,
>
> Yanny
>
>
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[Ifeffit] White line position shift

[Otal Eugenio]

Hi all,
I am dealing with in-situ battery measurements.
While I am changing the voltage, the white line of TM is changing its
position and intensity.
The change in intensity can be related to the order as pointed out here:
https://pubs.acs.org/doi/10.1021/acsami.0c13161
But what about energy shifts when there is no change in the oxidation
state? Any reference where to dig?
Best regards.

(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates
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Re: [Ifeffit] Problem with cif file in larch

[Otal Eugenio]

Dear Matt,
Thanks for your answer!
I tested the same .cif on another computer and works fine, even if it is an
older version, 0.9.65.
On the computer I had a problem, I have 0.9.67. I reinstalled Larch
completely and now works fine.
Thanks for taking the time to work on Larch,
Best regards.



(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates



On Fri, Mar 24, 2023 at 11:08 PM Matt Newville 
wrote:

> Hi Eugenio,
>
> Sorry for the trouble.  For sure, interpreting CIF files can be tricky!
> But, I can read that CIF file with XAS Viewer, larch version 0.9.67.  It
> doesn't fully read all the data about the publication, and it can generate
> a plausible Feff.inp file.
> Can you verify that you have a fairly recent version?
>
> I see that there are Unicode characters in the file, but these seem to me
> to be UTF-8 compatible.   If you are still seeing trouble, this might be
> part of the problem.  You might have better luck if you remove these
> (specifically the line with "_chemical_name_structure_type", which I
> think you can just remove).   If that *does* help, can you also report
> what your default Unicode encoding is: from either Python or the Larch
> buffer in XAS Viewer, do
>
>import sys
>print(sys.getdefaultencoding())
>
>
> Unfortunately, the current code is not super helpful in reporting why it
> couldn't read the CIF file - this should be improved!
>
>
>
> On Fri, Mar 24, 2023 at 2:20 AM Otal Eugenio 
> wrote:
>
>> Hi all,
>> In November I was generating the feff-path in Larch using the .cif file I
>> attached.
>> Now I am generating additional paths from another absorbing atom and I am
>> getting the error message "Error opening .cif file" using the same .cif
>> file.
>> Any ideas?
>> Best regards.
>>
>>
>>
>> (^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)
>>
>> Eugenio H. OTAL
>> Assistant Professor
>> Dept. of Materials Chemistry
>> Shinshu University
>> 4-17-1 Wakasato, Nagano 380-8553, JAPAN
>> eugenio_o...@shinshu-u.ac.jp
>> https://sites.google.com/view/zettsu-laboratory/news-updates
>>
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>
>
>
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[Ifeffit] Problem with cif file in larch

[Otal Eugenio]

Hi all,
In November I was generating the feff-path in Larch using the .cif file I
attached.
Now I am generating additional paths from another absorbing atom and I am
getting the error message "Error opening .cif file" using the same .cif
file.
Any ideas?
Best regards.



(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates


FMN.cif
Description: CIF chemical test
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[Ifeffit] Y2O3 E0

[Otal Eugenio]

Hi all,
I am aligning in energy Y substituted sample but using Zr foil as a
reference, no Y metal is available at the BL.
Does anyone have well-calibrated in-energy Y2O3 spectra?
Best regards.

(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates
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[Ifeffit] Yttrium standars for oxidation state

[Otal Eugenio]

Hi all,
I need to confirm the oxidation state of Y in a sample.
I found some reports about Y(II), does someone have something like it?
I was looking in the databases and had no luck.
Best regards.

(^ㅇᆽㅇ^)(=˃ᆺ˂=)(= ༝ =)

Eugenio H. OTAL
Assistant Professor
Dept. of Materials Chemistry
Shinshu University
4-17-1 Wakasato, Nagano 380-8553, JAPAN
eugenio_o...@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates
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