In [1]:

    

import sys, numpy
sys.path.extend(['/home/aksenov/Simulation_wrapper/siman'])
from calc_manage import smart_structure_read
from geo import create_deintercalated_structure

st = smart_structure_read(input_geo_file = 'in/Na2FePO4F.POSCAR') #read initial structure from POSCAR

st1 = create_deintercalated_structure(st, 'Na', del_pos = 1)   #find non-equivalent positions of Na and remove position 1
st2 = create_deintercalated_structure(st, 'Na', del_pos = 2)   #find non-equivalent positions of Na and remove position 2


    

    




-- You provided the following geo file explicitly  in/Na2FePO4F.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- I have found  2 non-equivalent positions for Na : dict_keys([56, 64]) 

-- Choose from the following list using *del_pos*: 
--       1 ---> 56 
--       2 ---> 64 
-- You have chosen position: 56 

-- I have found  2 non-equivalent positions for Na : dict_keys([56, 64]) 

-- Choose from the following list using *del_pos*: 
--       1 ---> 56 
--       2 ---> 64 
-- You have chosen position: 64 

In [2]:

    

st.write_xyz()
st1.write_xyz()
st2.write_xyz()


    

    




-- File xyz/Na2FePO4F.xyz was written 

-- File xyz/Na2FePO4F.Na56del.xyz was written 

-- File xyz/Na2FePO4F.Na64del.xyz was written 

In [ ]:

    

stDS = st.remove_atoms(['Na'])