------------------------------------------------------------------------------------------------------------------- Local polarization in oxygen-deficient LaMnO3 induced by charge localization in the Jahn-Teller distorted structure C. Ricca and U. Aschauer ------------------------------------------------------------------------------------------------------------------- The data in the paper can be reproduced executing (sequentially) the jupyter notebook paper_LMO_VO_def.ipynb The jupyter notebook should explain the directory structure sufficiently and allow the reader to follow the post-processing. The tables and pictures in jupyter notebook file, written in python 2, report the same numbering of the tables/figures one can find in the paper. ABBREVIATIONS: "LMO" refers to LaMnO3 "V_OOP" refers to an in-plane oxygen vacancy "V_OIP" refers to an out-of-plane oxygen vacancy "scVO" refers to singly charged defects "nVO" referes to neutral defects "dcVO" refers to doubly charged defects "AFM" anti-ferromagnetic "OP" stands for out-of-plane "IP" stands for in-plane FOLDERS CONTENT: ./stoichiometric contains the data for stoichiometric LaMnO3 (LMO) unstrained and epitaxially or isostatically strained structures ./V_OOP contains results for the neutral OP oxygen vacancy in the unstrained and epitaxially or isostatically strained LMO structures ./V_OIP contains results for the neutral IP oxygen vacancy in the unstrained and epitaxially or isostatically strained LMO structures ./singly_charged_VO contains results for the singly charged oxygen vacancy ./doubly_charged_VO contains results for the doubly charged oxygen vacancy ./O2 contains the data relative to the O2 molecule used to compute the defect formation energies ./cplap contains the results of the phase diagram determination ./MnO contains the data for the MnO calculation ./Mn2O3 contains the data for the Mn2O3 calculation ./Mn_metal contains the data for the Mn metal calculation ./La_metal contains the data for the La metal calculation ./La2O3 contains the data for the La2O3 calculation ./Mn3O4 contains the data for the Mn3O4 calculation ./BaTiO3 contained the data for the Berry phase calculation in BaTiO3 ./scratch is an empty folder in which files will be created during the exectution of the jupyter notebook SCRIPTS: - site_pot.sh: bash script used to compute the spherically averaged electrostatic potentials necessary for the potential alignment /path/site_pot_pp.sh tmp.pp (where tmp.pp file is the file of the FFT grid containing the electrostatic potential of a system obtained through a pp.x calculation in which plot_num=10). The output is the "file.dat" file and it is used in the jupyter notebook to derive the potential alignment according to the Lany-Zunger scheme. When necessary this file has been created as saved in the appropriate folder. WARNING: Line 18 needs to be uptated before use for each structure, by substituting XX with the exact number of lines appearing in the tmp.pp file prior the atomic positions - Q3.sh: bash script used to compute the Jahn-Teller distortion. Usage: /path/Q3.sh POSCAR. The POSCAR files necessary to run the script for the stoichiometric LMO structures can be found in the corresponding folders. NOTE: The calculation of the position of the dz2 and dx2-y2 orbital in selected cases is performed computing the center of mass of the peak associated with the dz2/dx2-y2 orbitals observed in the corresponding density of states (DOS). Due to the large size of the DOS files, the contribution of the eg and t2g states per atom to the DOS has been saved in text files: XMnpdos_eg.dat and XMnpdos_t2g.dat files can be found in the appropriate folders, where X indicates the number of the Mn atom in the structure.