Script for generating various vacancy patterns in perovskite matrix.
Unlike conventional structure-generation algorithms, this code starts from close-packed planes in ABO3 perovskite, which is (111) plane. Poeppelmeier et al. made an elegant observation of oxygen-deficient perovskites that each phase possesses a specific layer vacancy pattern on AO3 layers. By reversing this finding, we generate planer vacancy patterns and stack along [100] perovskite direction to construct 3-dimensional atomic structure. We adopt the sample stoichiometry of ABO2.5, and the 50 structures generated with this algorithm covers prototypical examples of oxygen-deficient perovskites with ordered vacancies.
We additionally developed GUI-version of this code on MATLAB environment.
You can run StructureGenerator.m, which will generate a POSCAR file (structure file for VASP) of oxygen-deficient ABO2.5 structure with input parameters of your choice. Among parameters shown in the figure below, the pattern length, pattern, and translational vector are key parameters determining vacancy pattern.
The parameters covered by this code can generate 50 structures of oxygen-deficient perovskites, which are collected in Generated_structures folder. The filename of structure is defined based on the length of unit later, vacancy pattern, translation vector upon stacking, and the use of alternative stacking.
For example L2_vac1_t0.17_alt.vasp is generated from vacancy pattern 1 with length of L=2 (double vertical length of atomic plane shown in GUI), and translation vector of L*1/6 (=0.17L). And the 'alt' in the filename implies that layer pattern is mirrored upon every stacking layer.
We note that the structures are defined by AO2.5 layer and stacking, which makes the outlook of structures parallelopied regardless of space group of each structure. To use them for first-principles calculations, we recommend users to convert the generated structures to cif file and export to POSCAR format so that structures to have conventional unit cell shape with corresponding symmetry.