I am using Quantum Espresso to study defects in III-V materials, and recently I relaxed my defect system in a 64-atom supercell. Currently, I am trying to determine the ionic displacements relative to my defect center (0,0,0), but I first need to develop code (Python) that undoes the PBCs. Ultimately, I would like a histogram that reports the number of atoms in spherical shells and a plot that shows whether an ion moved closer or further from the defect (0,0,0).

Does anyone have any insight as to how I might accomplish this task?

  • $\begingroup$ What do you mean by "undoes the PBC"? Do you mean to re-do the calculations without PBC? Export the output without PBC? $\endgroup$
    – Camps
    Apr 10 at 11:25
  • $\begingroup$ I think what you mean is to 'unwrap' the coordinates? I.e. if an atom crosses a cell boundary, you do NOT want it to jump to the otherside of the cell? You can fix this by comparing the coordinates before relaxation and after. If the atom has jumped by more than a box vector, shift it back by a box vector. The basic idea is called the 'minimum image convention'. See e.g. here: en.wikipedia.org/wiki/… $\endgroup$ Apr 10 at 16:56
  • $\begingroup$ Is this the answer that you are looking for? $\endgroup$ Apr 10 at 18:46


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