Tips for first-principles calculations for point defects

1. Symmetrization of point defects

As mentioned in the Tutorial of pydefect, the neighboring atoms near the defect are initially slightly perturbed to break the symmetry. However, some defects tend to move back to the symmetric configuration or recover a part of symmetry operations during the structure optimization.

Even in these cases, the relaxed structures are not obviously symmetric. Pydefect provides the refine_defect_poscar (= rdp) sub-command that allows for symmetrizing the defect structure. It is used as:

pydefect_vasp_util rdp -p Va_Mg1_0/CONTCAR-finish -d Va_Mg1_0/defect_entry.json -n POSCAR_new

which creates the POSCAR_new file as follows.

Mg7 Al16 O32
1.0
8.105607 0.000000 0.000000
0.000000 8.105607 0.000000
0.000000 0.000000 8.105607
Mg Al O
7 16 32
direct
0.749726 0.749738 0.249693 Mg
0.749726 0.249738 0.749693 Mg
0.249726 0.749738 0.749693 Mg
0.003191 0.003203 0.003158 Mg
0.496261 0.496273 0.003158 Mg
0.496261 0.003203 0.496228 Mg
0.003191 0.496273 0.496228 Mg
0.625112 0.373467 0.373422 Al
0.125997 0.874352 0.373422 Al
0.125997 0.373467 0.874307 Al
0.624659 0.874804 0.874760 Al
0.624659 0.624671 0.624626 Al
0.125997 0.126009 0.625079 Al
0.125997 0.625124 0.125964 Al
0.625112 0.126009 0.125964 Al
0.373455 0.625124 0.373422 Al
0.874340 0.126009 0.373422 Al
0.874792 0.624671 0.874760 Al
0.373455 0.126009 0.874307 Al
0.373455 0.373467 0.625079 Al
0.874792 0.874804 0.624626 Al
0.874340 0.373467 0.125964 Al
0.373455 0.874352 0.125964 Al
0.862178 0.862190 0.862145 O
0.361441 0.361453 0.859833 O
0.361441 0.859878 0.361408 O
0.859866 0.361453 0.361408 O
0.388922 0.611788 0.611743 O
0.887676 0.110542 0.611743 O
0.887676 0.611788 0.110497 O
0.393711 0.105752 0.105707 O
0.611776 0.611788 0.388889 O
0.105740 0.105752 0.393678 O
0.110530 0.611788 0.887643 O
0.611776 0.110542 0.887643 O
0.611776 0.388934 0.611743 O
0.110530 0.887688 0.611743 O
0.105740 0.393723 0.105707 O
0.611776 0.887688 0.110497 O
0.637273 0.637285 0.862145 O
0.138011 0.138023 0.859833 O
0.138011 0.639597 0.361408 O
0.639585 0.138023 0.361408 O
0.637273 0.862190 0.637241 O
0.138011 0.361453 0.639552 O
0.138011 0.859878 0.137978 O
0.639585 0.361453 0.137978 O
0.393711 0.393723 0.393678 O
0.887676 0.887688 0.388889 O
0.887676 0.388934 0.887643 O
0.388922 0.887688 0.887643 O
0.862178 0.637285 0.637241 O
0.361441 0.138023 0.639552 O
0.361441 0.639597 0.137978 O
0.859866 0.138023 0.137978 O

2. Tips for hybrid functional calculations

Hybrid functionals, namely the HSE06 functional, and those with different exchange mixing parameters and/or screening distances, have been regularly used for point-defect calculations recently.

Usually, their calculations are a few tens more expensive than those with a functional based on the local or semilocal density approximations. Therefore, we need to take a little ingenuity to reduce their computational costs.

For this purpose, we regularly prepare the WAVECAR files obtained using a GGA functional. (Relaxation of the atomic positions using GGA beforehand could be inappropriate for point-defect calculations, because site symmetry of a defect calculated by GGA could be different from that by hybrid functionals, and once the symmetry is increased by GGA, it never be decreased by hybrid functionals.)

One can create the INCAR file for generating WAVECAR files using the GGA with the following command, for instance,

grep -v LHFCALC INCAR | grep -v ALGO | sed s/"NSW     =  50"/"NSW     =   1"/ > INCAR-pre

and, then, move the WAVECAR file to the director for the hybrid functional calculation.