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Clustering uses incorrect mu_symbol and particle_mass #61
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Is the SPECIES_MASS block written correctly or not? |
No.
The output *.cell files are like this one below:
#######################################################
#CASTEP cell file: srtio3_clusters/uep/srtio3_uep_min_cluster_2.cell
#Created using the Atomic Simulation Environment (ASE)#
#######################################################
%BLOCK LATTICE_CART
3.907000 0.000000 0.000000
0.000000 3.907000 0.000000
0.000000 0.000000 3.907000
%ENDBLOCK LATTICE_CART
%BLOCK POSITIONS_ABS
O 1.953500 1.953500 0.000000
O 0.000000 1.953500 1.953500
O 1.953500 0.000000 1.953500
Ti 1.953500 1.953500 1.953500
Sr 0.000000 0.000000 0.000000
H 1.952778 3.197325 -0.002414
%ENDBLOCK POSITIONS_ABS
…On Fri, 8 Apr 2022 at 12:19, elichad ***@***.***> wrote:
Is the SPECIES_MASS block written correctly or not?
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Ok, I see the issue: When Related: When |
The symbols should now be written correctly as of 0.2.2.dev0 . The SPECIES_MASS stuff might take longer as I'd like to see if we can get this fixed in ASE directly - https://gitlab.com/ase/ase/-/issues/1079 [edit 24/10/2022: the issue has been fixed, but there has not yet been an ASE release that contains the fix. Current release is 3.22.1 which came out back in Dec 2021.] |
Run pymuonsuite for Al2O3 in the venv_eli virtual environemnt.
*.yaml
file is this one:It runs, and a stopping site is found. However, the variables
clustering_save_type: structures
andclustering_save_format: cell
create structural*.cell
files with the resulting minimum energy muonated structures. One of this*.cell
files looks like this:The line H 0.408641 -2.098837 4.363707 should have read Li:i 0.408641 -2.098837 4.363707. The command
mu_symbol: Li:i
in*.yaml
is not doing what it is suppose to do.The text was updated successfully, but these errors were encountered: