In [10]:

    

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


    

In [5]:

    

# 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')


    

In [12]:

    

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  |
+-------+-----------------+-------+-------+-----------------+ 







    
Out[12]:





([<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]])