This tutorial explain how to create antisite defects
import sys
from IPython.display import Image
from siman import header
from siman.calc_manage import smart_structure_read
from siman.geo import create_antisite_defect
%matplotlib inline
# st = smart_structure_read('geo/POSCAR_LiFePO4_s10_su_4uis_100_end') # read required structure
NCO = smart_structure_read('geo/POSCAR_NaCoO2_O3_su_s10_1uCo0LF_100_end')
NCO = smart_structure_read('geo/POSCAR_NaCoO2')
create_antisite_defect(NCO, 'Na', 'Co', max_sep = 6, iatom = 1)
-- I have found 1 non-equivalent positions for Na : dict_keys([0]) -- Atom numbers: {0: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]} -- I have found 1 non-equivalent positions for Co : dict_keys([32]) -- Atom numbers: {32: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]} -- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/xyz/POSCAR__NaCoO2_O3_su_s10_1uCo0LF_100_end_as1-34 -- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/xyz/POSCAR__NaCoO2_O3_su_s10_1uCo0LF_100_end_as1-33 -- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/xyz/POSCAR__NaCoO2_O3_su_s10_1uCo0LF_100_end_as1-32 -- File xyz/_NaCoO2_O3_su_s10_1uCo0LF_100_end.xyz was written -- List of antisites: +-------+-----------------+-------+-------+-----------------+ | No. | Antisite type | at1 | at2 | Separation, A | |-------+-----------------+-------+-------+-----------------| | 0 | (0, 32) | 2 | 35 | 3.091 | | 1 | (0, 32) | 2 | 34 | 4.247 | | 2 | (0, 32) | 2 | 33 | 5.15 | +-------+-----------------+-------+-------+-----------------+
([<siman.classes.Structure at 0x7fa9028a2518>, <siman.classes.Structure at 0x7fa9028a24a8>, <siman.classes.Structure at 0x7fa9028a2780>], [[0, (0, 32), 2, 35, 3.091], [1, (0, 32), 2, 34, 4.247], [2, (0, 32), 2, 33, 5.15]])