Larch and calculation of theoretical EXAFS via cif -files part 2
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
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.mangold@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 _______________________________________________ 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
-- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411
participants (2)
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Mangold, Stefan (IPS)
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Matt Newville