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 PS: please sing your emails with your affiliation as to comply with the mailing list rules. -- 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? > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espre > sso) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list [email protected] https://lists.quantum-espresso.org/mailman/listinfo/users
