[QE-users] pw.x - regrouping atoms

[Fnukal Frantisek]

Dear QE users,


I'm performing calculations on organic molecular crystal structures using pw.x. For organic molecular structures, it is quite common that a part of a molecule is positioned across a boundary of two neighboring cells (meaning not all atoms are positioned inside the basic cell). When I use pw.x (doing SCF calculations), the atoms that do not lie inside the basic cell are automatically re-positioned so that they do lie inside the basic cell (I came to this conclusion by analyzing the pw.x output file). As a result, the molecules of the structure get cut into pieces. I wasn't sure if this had to do with the symmetry specification - I tried to specify symmetry using either the "space_group" keyword or using "ibrav = 0", but I ended with the same result for either approach.

This is a little bit troublesome for me, because I later use the SCF results to plot the charge density using pp.x and I would very much like if the molecules were preserved. If I understand correctly, I could potentially fix this by editing the pp.x output manually, however, is there another way to bypass this problem? The version I'm using is "PWSCF v.6.4.1".

Thank you for any recommendations.

Sincerely,

F.Fňukal

UCT Prague
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