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 onShowCIF sites = ['%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_otal@shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates ¯\_(ツ)_/¯¯\_(ツ)_/¯ Who is John Galt? ¯\_(ツ)_/¯¯\_(ツ)_/¯
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
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 onShowCIF sites = ['%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_otal@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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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_otal@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
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 onShowCIF sites = ['%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_otal@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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Dear 정은석, Thank you for initiating a discussion on this topic and sharing your approach for addressing partial occupancy in FEFF method. When I was a student, I used exactly the method you described to fit the NMC111 EXAFS data across Ni, Co, and Mn K-edges. At the time, I faced significant skepticism from a colleague that was working with RMC method! It is reassuring to see that this approach is indeed correct for handling partial occupancy. Thanks, Esmael On 2/15/2024 8:01 AM, 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:0.980 Traceback (most recent calls last): File "C:\Users\Me\xraylarch_2023_10\Lib\site-packages\larch\wxlib\cif_browser.py", line 447, in onShowCIF sites = ['%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_otal@shinshu-u.ac.jp mailto:eugenio_otal@shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates https://sites.google.com/view/zettsu-laboratory/news-updates
¯\_(ツ)_/¯¯\_(ツ)_/¯
Who is John Galt?
¯\_(ツ)_/¯¯\_(ツ)_/¯
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participants (3)
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Esmael Balaghi
-
Otal Eugenio
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정은석