In this example part of Na ions is removed from fully intercalated structure of Na2FePO4F
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
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
To remover all atoms a general method can be used
stDS = st.remove_atoms(['Na'])