Vacancy make#
Step 1. The VacancyGenerator
module in pymatgen.analysis.defects.generators is used to generate a set of structures with vacancy.
Step 2. If there are init_from_suffix
and output_suffix
parameter in the properties
part, the refine process follows. If reproduce is evoked, the reproduce process follows. Otherwise, the vacancy structure (POSCAR
) and supercell information (supercell.out
) are written in the task directory, for example, in confs/mp-*/vacancy_00/task.000000
with the check and possible removing of the old input files like before.
Step 3. When doing vacancy
by VASP, ISIF = 3
. When doing vacancy
by LAMMPS, the same in.lammps
as that in EOS (change_box is True) would be generated with scale
set to one.