Structure Ordering

Example: NaSiCON $\mathrm{Na}{}_x\mathrm{Zr}{}_2\mathrm{Si}{}_{x-1}\mathrm{P}{}_{4-x}\mathrm{O}{}_{12}$(x = 1-4)

Primitive Cell

For the primitive cell (2 f.u.), 2x is an integer between 2-8. Then x is

[2,3,4..8]/2 = 1, 1.5, 2, 2.5, 3, 3.5 and 4

$2\times 1\times 1$ Super Cell

In 211 supercell (4 f.u.) 4x is a integer between 4-16. Then the ‘x’ in my script is:

[4,5,6…16]/4 = [1,1.25,2.5 …3.75,4]

The site occupancy for each Na is x/4 =  [0.25,0.3125, …,1] which is reasonable. And I think Si and P are correct as well.

As a double check: 

‘x = 1.25’: the code generated $\mathrm{Na}{}_5\mathrm{Zr}{}_8\mathrm{Si}{}_1\mathrm{P}{}_{10}\mathrm{O}{}_{48}$ which is reduced as: $\mathrm{Na}{}_{1.25}\mathrm{Zr}{}_2\mathrm{Si}{}_{0.25}\mathrm{P}{}_{2.5}\mathrm{O}{}_{12}$ ‘x = 2.25’: the code generated $\mathrm{Na}{}_9\mathrm{Zr}{}_8\mathrm{Si}{}_5\mathrm{P}{}_7\mathrm{O}{}_{48}$ which is reduced as: $\mathrm{Na}{}_{2.25}\mathrm{Zr}{}_2\mathrm{Si}{}_{1.25}\mathrm{P}{}_{1.75}\mathrm{O}{}_{12}$

from pymatgen.transformations.standard_transformations import OrderDisorderedStructureTransformation, SubstitutionTransformation, AutoOxiStateDecorationTransformation,SupercellTransformation`
 
from pymatgen.alchemy.transmuters import PoscarTransmuter, CifTransmuter
from pymatgen.io.vasp.sets import MVLScanRelaxSet
from pymatgen.alchemy.filters import RemoveDuplicatesFilter
import re,os,multiprocessing
 
import numpy as np
 
from joblib import Parallel, delayed
 
source ="../EntryWithCollCode15546_Na4Zr2Si3O12_573K.cif"
 
home_dir = os.getcwd()
 
def ordering(x):
	work_dir = home_dir+'/Na'+str(x)
	os.mkdir(work_dir)
	os.chdir(work_dir)
 
nasiconT = CifTransmuter.from_filenames([source], transformations=[AutoOxiStateDecorationTransformation()], primitive = True)
 
nasiconT.append_transformation(SupercellTransformation(scaling_matrix=((2, 0, 0), (0, 1, 0), (0, 0, 1))))
 
# Nax Zr2 Six-1 P4-x O12, x = 1-4`
 
chem_dict = {"Na+": {"Na+": x/4.0}, "Si4+" : {"Si4+": (x-1)/3.0, "P5+": (4-x)/3.0}}
 
nasiconT.append_transformation(SubstitutionTransformation(chem_dict))
 
nasiconT.append_transformation(OrderDisorderedStructureTransformation(),extend_collection=500)
 
print ("Total ordering:", len(nasiconT),chem_dict)
 
nasiconT.apply_filter(RemoveDuplicatesFilter())
 
print ("Reduce ordering:",len(nasiconT),chem_dict)
 
incar_mod = {"EDIFF" : 1e-5, "EDIFFG" : -0.01, "NSW" : 150, "NCORE" : 12, "LPLANE" : "True", "NSIM" : 4, "ISYM" : 0, "NELMIN" : 4, "ISPIN" : 1, "ISMEAR": 0}
 
nasiconT.write_vasp_input(vasp_input_set=MVLScanRelaxSet,potcar_functional='PBE_54', user_incar_settings=incar_mod, include_cif=True)
 
x_list = np.arange(4,16)/4
num_cores = multiprocessing.cpu_count()
 
print('Start structure generation over',num_cores,'Cores........')
 
Parallel(n_jobs=num_cores)(delayed(ordering)(x) for x in x_list)