Problem with cif file in larch
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_otal@shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates
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
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_otal@shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates
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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_otal@shinshu-u.ac.jp
https://sites.google.com/view/zettsu-laboratory/news-updates
On Fri, Mar 24, 2023 at 11:08 PM Matt Newville
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_otal@shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates
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participants (2)
-
Matt Newville
-
Otal Eugenio