[QE-users] Calculation of energy due to vacancy

[Tone Kokalj]

Dear Pooja Vyas

Your input opens just fine in xcrysden. However, to create a vacancy,
you first need to generate a supercell and only then delete a given
atom. Otherwise if you stay with the unit-cell, you will either delete
all Ca or all O atoms.

You can generate a "diagonal" supercell with xcrysden (simply multiply
the cells), but before saving the XSF shift to "translational
asymmetric unit" display mode (the 2nd little black button at the
bottom toolbox). Then you can use the coordinates from the "ATOMS"
section of the XSF file. Note that if you do not shift to
"translational asymmetric unit" display mode the atoms listed in ATOMS
section will contain some periodic replicas.

Best regards, Tone

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Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax: +386-1-251-9385)


On Wed, 2020-01-08 at 11:43 +0530, Pooja Vyas wrote:
> I want to calculate energy due to vacancy. I opened the following
> input
> file in x-crysden.
> 
> &control
> calculation = 'scf',
> prefix = '9.1334'
> tstress= .true.
> tprnfor= .true.
> outdir = '/home/user/cao.oct/'
> pseudo_dir = '/home/user/cao.oct/pseudo/'
> /
> &system
> ibrav = 2,
> celldm(1) = 9.1334,
> nat = 2,
> ntyp = 2,
> ecutwfc = 100,
> /
> &electrons
> mixing_beta = 0.7
> /
> 
> ATOMIC_SPECIES
> 
> Ca 40.078 Ca.pbe-nsp-van.UPF
> O 15.999 O.pbe-van_ak.UPF
> 
> ATOMIC_POSITIONS
> Ca 0.0 0.0 0.0
> O 0.50 0.50 0.50
> K_POINTS (automatic)
> 11 11 11 1 1 1
> 
> when I opened this structure in x-crysden, it showed me around 27
> atoms.
> Now I planned to create one vacancy by removing an atom and included
> rest
> all the atomic position in my input file and gave a run. But at that
> time I
> faced an error.
> 
> Following are the atomic positions which I read from x-crysden
> Ca 0.0 0.0 0.0
> O 0.5 0.0 0.0
> O 0.0 0.5 0.0
> O 0.0 0.0 0.5
> Ca 0.5 0.5 0.0
> Ca 0.5 0.0 0.5
> Ca 0.0 0.5 0.5
> O 0.5 0.5 0.5
> 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
> 
> Out of all these positions only
> Ca 0.0 0.0 0.0
> O 0.5 0.5 0.5
> are needed. rest are automatically ignored by quantum espresso. Then
> how do
> I create vacancy?
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