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orex / supercell

The program allows you to create regular structure supercell from cif file with partial occupancy and/or substitutions.
GNU General Public License v2.0
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Fe Supercell issues #26

Closed debbieLT closed 5 years ago

debbieLT commented 5 years ago

have recently started using the supercell software, however I’m having trouble with the symmetry outputs.

I’ve attached an example of the output I’m getting. In this example I have 16 Fe atoms (2x2x2 bcc unit cell) and have given 4 of them an occupancy of 0.5, which gives the initial system a formula of Fe14. However, the supercell formula is coming up as Fe12, which in this case is incorrect as this should be Fe14 (4 atoms at 0.5 = 2 and 12 at 1 occupancy = 12+2 = 14) It also comes up with 1 as the number of combinations, which again doesn’t make sense. I was hoping to get some pointers as to where im going wrong

i am using a Linux operating system and supercell version: 23rd May 2019 Attached is my input file (input_Fe_222.txt) and output file i get to my screen (output_Fe_222.txt) The command i use to launch supercell is ./supercell -i Fe_222.cif -m -q -g -o=supercell

input_Fe_222.txt supercell_coulomb_energy.txt output Fe_222.txt supercell_i0_w1.txt

Many Thanks Debbie

orex commented 5 years ago

Dear Debbie, Thank you very much for using supercell. Please, specify exactly the commenad line you used for supercell launch like ./supercell -i input_Fe_222.cif -s 2x2x2 etc and the output you get from the program to your screen.

debbieLT commented 5 years ago

This should be updated in the main query now but the command i use is ./supercell -i Fe_222.cif -m -q -g -o=supercell And the output i get to my screen is attached as a file: output Fe_222.txt

orex commented 5 years ago

Thank you, Debbie. Sorry, I missed the file. As I can see from the output in your cif file all Fe atoms a labeled differently. Supercell program treats it as different sites (despite all of them are Fe atoms). For detailed information please check https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0129-3#Sec5 Stage I. Therefore you should use another input file where all atoms from one site should have the same label. In you case, probably atoms Fe2, Fe6, Fe9, Fe16 should have a label FeB, and all the rest should have a label FeA. Same label is very important not only for permutations, but for summery algorithms also. Fe1 and Fe3 will be treated as different sites for symmetry search.

Sincerely yours, Kirill.

debbieLT commented 5 years ago

Thanks for your help Kirill this seems to have cleared up the problem Many Thanks

Debbie