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.