[QE-users] Atomic positions

[Pooja Vyas]

Respected Sir/Madam,
I want to calculate the energy due to vacancy in CaO. I need to create a
supercell. So for that, don't I need all the above atomic positions of CaO
in input file? Are only two atomic positions (0,0,0) and (0.5,0.5,0.5)
enough? If yes, how can I create vacancy with just two atomic positions? I
searched for a query similar to mine, but couldn't get any.

For instance, I tried calculation for Si-Ge alloy with the following
script, but there was no such error faced here.

&control
    calculation = 'scf',
    prefix = 'sige'
    tstress= .true.
    tprnfor= .true.
    outdir = '/home/userpooja/cao.oct/'
    pseudo_dir = '/home/userpooja/cao.oct/pseudo/'
 /
 &system
    ibrav =  0,
    celldm(1) = 5.4492,
    nat =  16,
    ntyp = 2,
    ecutwfc = 100,
/
&electrons
    mixing_beta = 0.7
 /

ATOMIC_SPECIES

Si 28.0855 Si.pz-vbc.UPF
Ge 72.64 Ge.pz-bhs.UPF

ATOMIC_POSITIONS
Si 0.0 0.0 0.0
Si 0.5 0.5 0.0
Si 0.5 0.0 0.5
Ge 0.0 0.5 0.5
Ge 0.25 0.25 0.25
Ge 0.75 0.75 0.25
Ge 0.75 0.25 0.75
Ge 0.25 0.75 0.75
Si 1.0 0.5 0.5
Si 1.0 1.0 0.0
Ge 1.25 0.25 0.25
Ge 1.5 0.0 0.5
Ge 1.5 0.5 0.0
Si 1.75 0.75 0.25
Si 1.75 0.25 0.75
Si 1.25 0.75 0.75

CELL_PARAMETERS
2.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0

Talking in detail about my procedure,
I opened the following input file (which is for equlibrium lattice
parameter of CaO) which has two atomic positions in X-crysden. Then it
showed me a structure with 27 atoms whose co-ordinates (read by atoms info)
are as follows:
Ca 0.5 0.5 0.0
Ca 0.0 0.0 0.0
Ca 0.5 0.0 0.5
Ca 0.0 0.5 0.5
O  0.0 0.0 0.5
O  0.5 0.5 0.5
O  0.0 0.5 0.0
O  0.5 0.0 0.0
Ca 0.5 0.5 1.0
Ca 0.0 0.0 1.0
O  0.0 0.5 1.0
O  0.5 0.0 1.0
Ca 0.0 1.0 0.0
Ca 0.5 1.0 0.5
O  0.0 1.0 0.5
O  0.5 1.0 0.0
Ca 0.0 1.0 1.0
O  0.5 1.0 1.0
Ca 1.0 0.0 0.0
Ca 1.0 0.5 0.5
O  1.0 0.0 0.5
O  1.0 0.5 0.0
Ca 1.0 0.0 1.0
O  1.0 0.5 1.0
Ca 1.0 1.0 0.0
O  1.0 1.0 0.5
Ca 1.0 1.0 1.0

So, don't I have to include all this atomic positions while calculating
energy due to vacancy? how can I create vacancy with just two atomic
positions?
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