Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files part 2

[Matt Newville]

Hi Stefan,

Hmm, it looks like the pymatgen CIF parser is having a hard time with that
file.
I'll investigate...

On Mon, Aug 14, 2023 at 10:12 AM Mangold, Stefan (IPS) <
stefan.mang...@kit.edu> wrote:

> Dear all,
>
> i have another set of cif files, which also don't work on larch. They work
> with Artemis, except that they hit the 500 atoms limit per cluster. This
> won't be a problem in larch, because of the option to exclude the H-atoms.
>
> One problem seems to occur on the line
>
> _chemical_formula_moiety
> ;
> 2(C18 H36 K1 N2 O6 1+),Bi2 2-
> ;
>
> which I rewrote to
>
> _chemical_formula_moiety '2(C18 H36 K1 N2 O6 1+),Bi2 2-'
>
>
> but still I got the message
>
> Error reading CIF File:
> /Users/stefanmangold/Documents/eigene_Daten/Messdaten/PrepMessungen/XPS-Proben/Bi2-crypt-222_e.cif
> Traceback (most recent calls last):
>   File
> "/Users/stefanmangold/xraylarch/lib/python3.10/site-packages/larch/wxlib/cif_browser.py",
> line 618, in onImportCIF
> cif_data = parse_cif_file(path)
>   File
> "/Users/stefanmangold/xraylarch/lib/python3.10/site-packages/larch/xrd/amcsd.py",
> line 142, in parse_cif_file
> raise ValueError(f'Cannot read symmetries from file {filename:s}')
> ValueError: Cannot read symmetries from file
> /Users/stefanmangold/Documents/eigene_Daten/Messdaten/PrepMessungen/XPS-Proben/Bi2-crypt-222_e.cif
>
>
> Anybody an idea, I attached the unchanged file (Bi2-crypt-222.cif) and the
> edited file (Bi2-crypt-222_e.cif). Any idea what’s wrong?
>
>
>
>
> best regards
>
> Stefan
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Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Mangold, Stefan (IPS)]

Thanks for the support, will do the quick fix to proceed with my work, Thanks 
for the fast feedback.

Am 09.08.2023 um 20:17 schrieb Matt Newville :

Hi Stefan,

OK, yes I see that too.  I have this fixed in the code.  For a quick 
workaround, changing

_chemical_name_common 'Bismuth potassium (2/1)'

to

_chemical_name_common 'Bismuth potassium'

will fix the problem.


On Wed, Aug 9, 2023 at 11:25 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:



Am 09.08.2023 um 17:17 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan,

Can you send a CIF file that is not working? I tried the one for BiK3 from the 
built-in AmMin database, and it worked for me.  But, for sure it is possible to 
come up with a CIF file that doesn't work!  They are surprisingly tricky.

On Wed, Aug 9, 2023 at 9:51 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Dear all,

i have some cif files, which doesn’t work on larch. One example is KBi2, which 
works well on Artmenis with feff6. The same file (and also the cifs found in 
the database) won't work on larch (not with feff 6 nor feff8). There is no 
error message displayed -> just, that feff is started.


###
# Run Feff in folder: 
/Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
###
###

no result even after hours.

Any ideas?

Best regards

Stefan



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Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Matt Newville]

Hi Stefan,

OK, yes I see that too.  I have this fixed in the code.  For a quick
workaround, changing

_chemical_name_common 'Bismuth potassium (2/1)'

to

_chemical_name_common 'Bismuth potassium'

will fix the problem.


On Wed, Aug 9, 2023 at 11:25 AM Mangold, Stefan (IPS) <
stefan.mang...@kit.edu> wrote:

>
>
>
> Am 09.08.2023 um 17:17 schrieb Matt Newville :
>
> Hi Stefan,
>
> Can you send a CIF file that is not working? I tried the one for BiK3 from
> the built-in AmMin database, and it worked for me.  But, for sure it is
> possible to come up with a CIF file that doesn't work!  They are
> surprisingly tricky.
>
> On Wed, Aug 9, 2023 at 9:51 AM Mangold, Stefan (IPS) <
> stefan.mang...@kit.edu> wrote:
>
> Dear all,
>
> i have some cif files, which doesn’t work on larch. One example is KBi2,
> which works well on Artmenis with feff6. The same file (and also the cifs
> found in the database) won't work on larch (not with feff 6 nor feff8).
> There is no error message displayed -> just, that feff is started.
>
> 
> ###
> # Run Feff in folder:
> /Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
> ###
> ###
>
> no result even after hours.
>
> Any ideas?
>
> Best regards
>
> Stefan
>
>
>
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>
>
> --
> --Matt Newville  630-327-7411
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>
>

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Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Mangold, Stefan (IPS)]

Am 09.08.2023 um 17:17 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan,

Can you send a CIF file that is not working? I tried the one for BiK3 from the 
built-in AmMin database, and it worked for me.  But, for sure it is possible to 
come up with a CIF file that doesn't work!  They are surprisingly tricky.

On Wed, Aug 9, 2023 at 9:51 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Dear all,

i have some cif files, which doesn’t work on larch. One example is KBi2, which 
works well on Artmenis with feff6. The same file (and also the cifs found in 
the database) won't work on larch (not with feff 6 nor feff8). There is no 
error message displayed -> just, that feff is started.


###
# Run Feff in folder: 
/Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
###
###

no result even after hours.

Any ideas?

Best regards

Stefan



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KBi2.cif
Description: KBi2.cif
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Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Matt Newville]

Hi Stefan,

Can you send a CIF file that is not working? I tried the one for BiK3 from
the built-in AmMin database, and it worked for me.  But, for sure it is
possible to come up with a CIF file that doesn't work!  They are
surprisingly tricky.

On Wed, Aug 9, 2023 at 9:51 AM Mangold, Stefan (IPS) 
wrote:

> Dear all,
>
> i have some cif files, which doesn’t work on larch. One example is KBi2,
> which works well on Artmenis with feff6. The same file (and also the cifs
> found in the database) won't work on larch (not with feff 6 nor feff8).
> There is no error message displayed -> just, that feff is started.
>
> 
> ###
> # Run Feff in folder:
> /Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
> ###
> ###
>
> no result even after hours.
>
> Any ideas?
>
> Best regards
>
> Stefan
>
>
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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>

-- 
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Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Mangold, Stefan (IPS)]

calculations are done on a Macbook-Air with the current uptodate OS. 

best regards 

Stefan

> Am 09.08.2023 um 16:51 schrieb Mangold, Stefan (IPS) :
> 
> Dear all,
> 
> i have some cif files, which doesn’t work on larch. One example is KBi2, 
> which works well on Artmenis with feff6. The same file (and also the cifs 
> found in the database) won't work on larch (not with feff 6 nor feff8). There 
> is no error message displayed -> just, that feff is started. 
> 
> 
> ###
> # Run Feff in folder: 
> /Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
> ###
> ###   
> 
> no result even after hours. 
> 
> Any ideas?
> 
> Best regards
> 
> Stefan
> 
> 
> 
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