How to determine all the different configurations when doing alloying or doping

 

When we want to do alloying by substituting atoms by other atoms we find that there will be many configurations  of substitutions which lead to different energies.

To determine all the possible configurations we use a package called SOD to create all the possible POSCAR files related to the possible configurations 

For more information about the code click the following link:

https://github.com/gcmt-group/sod

Downloading

To download the package run the following command

git clone https://github.com/gcmt-group/sod.git

Installing

Change to sod directory

cd sod

 

Compile 

make all

 

The executables will be in the bin directory

Add the path to the  ~/.bashrc   file

#------ SOD path
SODROOT=/home/algerien1970/abinitio/sod_0.47/bin
export PATH=$PATH:$SODROOT
#------------------------------

Executing

We will take the example of MgO in NaCl structure. We make supercell 2x2x2 and replace 2 atoms of Mg by 2 atoms of Ca.

 

We need 2 input files which are INSOD and SGO inside the working directory MgCaO

INSOD

#Title
Ca-doped MgO

# a,b,c,alpha,beta,gamma
4.22  4.22  4.22  90.000  90.000  90.000

# nsp: Number of species
2

# symbol(1:nsp): Atom symbols
Mg O

# natsp0(1:nsp): Number of atoms for each species in the assymetric unit 
1 1 

# coords0(1:nat0,1:3): Coordinates of each atom (one line per atom)
0.0  0.0  0.0
0.5  0.5  0.5

# na,nb,nc (supercell definition)
2 2 2

# sptarget: Species to be substituted
1

# nsubs: Number of substitutions in the supercell
2

# newsymbol(1:2): Symbol of atom to be inserted in the selected position, 
#                 symbol to be inserted in the rest of the positions for the same species.
Ca Mg 

# FILER, MAPPER
# # FILER:   0 (no calc files generated), 1 (GULP), 2 (METADISE), 11 (VASP)
# # MAPPER:  0 (no mapping, use currect structure), >0 (map to structure in MAPTO file)
# # (each position in old structure is mapped to MAPPER positions in new structure)
11 0

# This section is not read if VASP files are being created
# If FILER=1 then: 
# ishell(1:nsp) 0 core only / 1 core and shell (for the species listed in symbol(1:nsp)) 
0 1
# newshell(1:2) 0 core only / 1 core and shell (for the species listed in newsymbol(1:2))
0 0

SGO 

cp /home/algerien1970/abinitio/sod_0.47/sgo/225.sgo  ./SGO

 

 List the input files

/MgCaO> ls

INSOD NGO

 

Execution

sod_comb.sh

 

Output

OUTSOD 

           2  substitutions in           32 sites
           5  configurations
     1     48    1    2
     2     48    1    4
     3     16    1    8
     4    192    1    9
     5    192    1   13

In the CALCS directory there are 5 POSCAR files for the 5 independent configurations

c00001.vasp  c00002.vasp  c00003.vasp  c00004.vasp  c00005.vasp  job_sender  OUTSOD