Dear Hamed,

Your oxygen atoms are positioned more or less exactly on top of the other atoms, that's why you don't see them.


E.g.

Fe    5.2187500    5.2187500    5.2187500
O    5.1185500    5.3189500    5.3189500


Fe    3.1312500    7.3062500    7.3062500
O    3.0310500    7.2060500    7.4064500

Best wishes,

Lars
PhD Student
Imperial College London


On 11/08/18 14:00, hamed asadi wrote:

Dear users;
I have faced a tricky problem to construction of CoFe2O4 input file, in the following input, When I open the structure with Xcrysden, there are no oxygen in it. I'll appreciate any helps in this problem. Indeed, if anyone has the correct structure, I'm grateful to give it to me.


&CONTROL
calculation = 'scf' ,
restart_mode = 'from_scratch' ,
etot_conv_thr = 1.0E-8  ,
forc_conv_thr = 1.0D-8 ,
outdir='/home/asa/Desktop/drgerami/out',
pseudo_dir = '/home/asa/Desktop/drgerami/pp',
wf_collect=.true.
tprnfor   = .true.
tstress = .true.
verbosity= 'low',

 /
 &SYSTEM
ibrav = 1,
celldm(1) =15.86667684,
nbnd = 400,
nat = 56,
ntyp = 3,
ecutwfc = 40 ,
ecutrho = 400,
occupations = 'smearing' ,
degauss= 0.01 ,
smearing= 'gaussian',

 /
 &ELECTRONS
mixing_beta = 0.7
conv_thr = 1.D-8 ,
 /
&IONS
ion_dynamics= 'bfgs'

/
 &CELL
cell_dynamics = 'bfgs' ,
cell_factor = 2
 /
ATOMIC_SPECIES
Co    58.933   Co.pbe-spn-rrkjus_psl.0.3.1.UPF
Fe    55.845   Fe.pbe-spn-rrkjus_psl.0.2.1.UPF
O     15.999    O.pbe-n-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS (angstrom)
Co 0.0000000    0.0000000 <callto:0.0000000%200.0000000> 0.0000000
Fe 5.2187500    5.2187500 <callto:5.2187500%205.2187500> 5.2187500
O 3.2314500    3.2314500 <callto:3.2314500%203.2314500> 3.2314500
Co 0.0000000    2.0875000 <callto:0.0000000%202.0875000> 2.0875000
Co 6.2625000    2.0875000 <callto:6.2625000%202.0875000> 4.1750000
Co 6.2625000    0.0000000 <callto:6.2625000%200.0000000> 6.2625000
Co 4.1750000    6.2625000 <callto:4.1750000%206.2625000> 2.0875000
Co 2.0875000    6.2625000 <callto:2.0875000%206.2625000> 4.1750000
Co 2.0875000    4.1750000 <callto:2.0875000%204.1750000> 6.2625000
Co 0.0000000    4.1750000 <callto:0.0000000%204.1750000> 4.1750000
Co 2.0875000    2.0875000 <callto:2.0875000%202.0875000> 0.0000000
Co 2.0875000    0.0000000 <callto:2.0875000%200.0000000> 2.0875000
Co 4.1750000    2.0875000 <callto:4.1750000%202.0875000> 6.2625000
Co 0.0000000    6.2625000 <callto:0.0000000%206.2625000> 6.2625000
Co 6.2625000    4.1750000 <callto:6.2625000%204.1750000> 2.0875000
Co 6.2625000    6.2625000 <callto:6.2625000%206.2625000> 0.0000000
Co 4.1750000    0.0000000 <callto:4.1750000%200.0000000> 4.1750000
Co 4.1750000    4.1750000 <callto:4.1750000%204.1750000> 0.0000000
Fe 3.1312500    7.3062500 <callto:3.1312500%207.3062500> 7.3062500
Fe 1.0437500    5.2187500 <callto:1.0437500%205.2187500> 1.0437500
Fe 3.1312500    3.1312500 <callto:3.1312500%203.1312500> 3.1312500
Fe 1.0437500    1.0437500 <callto:1.0437500%201.0437500> 5.2187500
Fe 7.3062500    3.1312500 <callto:7.3062500%203.1312500> 7.3062500
Fe 5.2187500    1.0437500 <callto:5.2187500%201.0437500> 1.0437500
Fe 7.3062500    7.3062500 <callto:7.3062500%207.3062500> 3.1312500
O 5.1185500    5.3189500 <callto:5.1185500%205.3189500> 5.3189500
O 3.0310500    7.2060500 <callto:3.0310500%207.2060500> 7.4064500
O 1.1439500    5.1185500 <callto:1.1439500%205.1185500> 1.1439500
O 3.2314500    7.2060500 <callto:3.2314500%207.2060500> 7.2060500
O 1.1439500    5.3189500 <callto:1.1439500%205.3189500> 0.9435500
O 3.0310500    3.2314500 <callto:3.0310500%203.2314500> 3.0310500
O 5.1185500    5.1185500 <callto:5.1185500%205.1185500> 5.1185500
O 7.4064500    3.0310500 <callto:7.4064500%203.0310500> 7.2060500
O 5.3189500    1.1439500 <callto:5.3189500%201.1439500> 0.9435500
O 7.2060500    7.4064500 <callto:7.2060500%207.4064500> 3.0310500
O 5.1185500    0.9435500 <callto:5.1185500%200.9435500> 0.9435500
O 7.2060500    7.2060500 <callto:7.2060500%207.2060500> 3.2314500
O 5.3189500    5.1185500 <callto:5.3189500%205.1185500> 5.3189500
O 0.9435500    5.3189500 <callto:0.9435500%205.3189500> 1.1439500
O 3.2314500    3.0310500 <callto:3.2314500%203.0310500> 3.0310500
O 7.2060500    3.2314500 <callto:7.2060500%203.2314500> 7.2060500
O 5.1185500    1.1439500 <callto:5.1185500%201.1439500> 1.1439500
O 7.2060500    3.0310500 <callto:7.2060500%203.0310500> 7.4064500
O 1.1439500    0.9435500 <callto:1.1439500%200.9435500> 5.3189500
O 3.2314500    7.4064500 <callto:3.2314500%207.4064500> 7.4064500
O 1.1439500    1.1439500 <callto:1.1439500%201.1439500> 5.1185500
O 3.0310500    3.0310500 <callto:3.0310500%203.0310500> 3.2314500
O 3.0310500    7.4064500 <callto:3.0310500%207.4064500> 7.2060500
O 7.4064500    7.2060500 <callto:7.4064500%207.2060500> 3.0310500
O 5.3189500    5.3189500 <callto:5.3189500%205.3189500> 5.1185500
O 5.3189500    0.9435500 <callto:5.3189500%200.9435500> 1.1439500
O 0.9435500    1.1439500 <callto:0.9435500%201.1439500> 5.3189500
O 7.4064500    3.2314500 <callto:7.4064500%203.2314500> 7.4064500
O 0.9435500    5.1185500 <callto:0.9435500%205.1185500> 0.9435500
O 0.9435500    0.9435500 <callto:0.9435500%200.9435500> 5.1185500
O 7.4064500    7.4064500 <callto:7.4064500%207.4064500> 3.2314500
K_POINTS {automatic}
6 6 6   0 0 0 <callto:6%206%206%200%200%200>

best regards,
Hamed Asadi,
KN Toosi university of Technology, Faculty of physics



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