Hello all,
I am studying a compound in which a certain concentration of fluorine sites are replaced with a pair of fluorine atoms. The occurrences are disordered, so my plan was to implement the mcsqs code. However, is it possible to simulate this type of disordering? Such that single atoms are replaced by pairs of atoms?
Any help would be much appreciated. Thank you very much in advance.
This is not directly possible, but with minimal programming, it should be possible.
You would need worry of the orientation of the dimer as well, I think.
If the possible orientations are discrete, then you can just use as many atom labels as there are orientations. And then run mcsqs as usual.
Next, a little script would be needed to convert the labels into dimers, e.g.
awk '{if ($4!="F_x") {print $0} else {print $1+0.6,$2,$3,"F"; print $1-0.6,$2,$3,"F";}' < bestsqs.out > str.out
Of course you can add cases with F_y and F_z if these are the possible orientations. You may need to adjust the 0.6 shift too.
If this is mysterious, read
man awk
Great, thank you very much for the reply. I will implement your suggestions.