Hi all / anyone,
I've been trying to use the exhaustive symmetry search method described here:
http://community.dur.ac.uk/john.evans/topas_workshop/tutorial_exhaustive_symmetry.htm
and here:
https://pubs.acs.org/doi/abs/10.1021/jacs.6b04947
but haven't had much luck so far.
After boldly trying (and failing) to jump straight to using my own data, I conceded to attempt to work through the tutorial. I've got an error though and my python skills aren't yet up to solving it so wanted to know if anyone else has had the same issues:
Going through the steps: 1-4 go smoothly and the parent .inp seems to run fine.
In step 5, I've followed i-v without issue.
But when trying to run the script (5.vi) I get back an error (the same error from when I tried to run with my own data).
"
runfile('C:/USER_DATA/Colman/2019_July_GEM/PDF_refinements/Exhaustive_search/Tutorial/All_in_one_Exhaustive_Searcher_tutorial.py', wdir='C:/USER_DATA/Colman/2019_July_GEM/PDF_refinements/Exhaustive_search/Tutorial')
Initialising refinements of all subgroups
tetragonal space group detected!
Traceback (most recent call last):
File "<ipython-input-13-450dd9db16bd>", line 1, in <module>
runfile('C:/USER_DATA/Colman/2019_July_GEM/PDF_refinements/Exhaustive_search/Tutorial/All_in_one_Exhaustive_Searcher_tutorial.py', wdir='C:/USER_DATA/Colman/2019_July_GEM/PDF_refinements/Exhaustive_search/Tutorial')
File "C:\Users\Topas-soft\Anaconda2\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 827, in runfile
execfile(filename, namespace)
File "C:\Users\Topas-soft\Anaconda2\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 95, in execfile
exec(compile(scripttext, filename, 'exec'), glob, loc)
File "C:/USER_DATA/Colman/2019_July_GEM/PDF_refinements/Exhaustive_search/Tutorial/All_in_one_Exhaustive_Searcher_tutorial.py", line 213, in <module>
inp_maker(basefile, subgroup, thermal_prms)
File "C:/USER_DATA/Colman/2019_July_GEM/PDF_refinements/Exhaustive_search/Tutorial/All_in_one_Exhaustive_Searcher_tutorial.py", line 81, in inp_maker
add_structural_info(new_inp_file_stream, structure_lines, thermal_prms)
File "C:/USER_DATA/Colman/2019_July_GEM/PDF_refinements/Exhaustive_search/Tutorial/All_in_one_Exhaustive_Searcher_tutorial.py", line 104, in add_structural_info
new_inp_file_stream.write(line.replace("beq 0.0", "beq %f" % (thermal_prms[site])).replace(";", ";: 1.00000 "))
KeyError: None
"
Looking at the partially produced .inp file, it seems to have correctly written all sites, and their thermal parameters but then stopped.
I'd love to know if anyone else has this error when attempting the tutorial?
Just a guess but, I'm wondering if it is to do with the ISODISTORT .str outputs as they also include an 'origin' site, and perhaps when this tutorial was written the .str outputs did not also include this extra site (so the script is confused by the additional lines):
"
'{{{mode-dependent sites
site W_1 num_posns 0 x = W_1_x;:0 y = W_1_y;:0 z = W_1_z;:0 occ W = W_1_occ;beq 0.0
site O_1 num_posns 0 x = O_1_x;:0 y = O_1_y;:0 z = O_1_z;:0 occ O = O_1_occ;beq 0.0
site origin num_posns 0 x 0.00000 y 0.00000 z 0.00000 occ D 0
'}}}
"
If that is the cause of the issue, is anyone skilled enough at python to give me some guidance on how to adapt the script to work around this?
Many thanks and kind regards,
Ross