[xcrysden] Bismuth Titanate Structure

[Scott Beckman]

PWSCF is failing because there are atoms that are on top of each  
other.  Xcrysden compensates by deleting the mistake.

When I see this error it is because I made a mistake with the units.   
I think you might be mixing units because a,b,c are by default  
Angstrom, but you're using atomic positions in Bohr.  It isn't  
necessary to have a uniform unit scheme, but it is easier to avoid  
mistakes if you do.

For reference see:  http://www.quantum-espresso.org/input-syntax/ 
INPUT_PW.html


On Jul 17, 2009, at 5:36 AM, dev sharma wrote:

>
>
>
>
> Hi all,
>
> I am new to PWscf and XCrysden. My Input file for Bismuth Titanate  
> is below. The output structure in XCRYSden window is seemed to be  
> right but it is giving mssg ......... typed below. Please help or  
> give suggestion.
>
> Number of Atoms:  133
> Number of Frames: 12
> WARNING: Atom 1 and atom 12 are very close !!!
>          Atom 12 deleted !!!
> WARNING: Atom 2 and atom 122 are very close !!!
>          Atom 122 deleted !!!
> WARNING: Atom 3 and atom 14 are very close !!!
>          Atom 14 deleted !!!
> WARNING: Atom 4 and atom 123 are very close !!!
>          Atom 123 deleted !!!
> WARNING: Atom 5 and atom 16 are very close !!!
>          Atom 16 deleted !!!
> WARNING: Atom 6 and atom 124 are very close !!!
>          Atom 124 deleted !!!......
> .........................................................
> ......
>
>  and because of this PWScf  SCF run stops and gives the mssg wrong  
> atomic co-ordinates.
>
>
>  &control
>     calculation='scf',
>     restart_mode='from_scratch',
>     prefix='bit'
>     pseudo_dir = '/home/physics/pseudo/',
>     outdir='/home/physics/work/bit/temp'
>  /
>  &system
>     ibrav = 7, a=3.86334, b= 3.86334, c=33.2942
> , nat =38, ntyp= 3,
>     ecutwfc = 60.0,ecutrho=200,
>    occupations='smearing', smearing    = "methfessel-paxton",  
> degauss=0.01,
>
>  /
>  &electrons
>     mixing_beta = 0.50
>     conv_thr =  1.0e-6
> /
>  &ions
>  /
>
> ATOMIC_SPECIES
>   Bi     208.980     Bi.pbe-d-mt.UPF
>   Ti      47.867       Ti.pbe-sp-van_ak.UPF
>   O     15.9994      O.pbe-van_ak.UPF
> ATOMIC_POSITIONS {bohr}
> Bi             3.65032726386637    3.65032726386637     
> 4.24815040995715
> Bi             3.65032726386637    3.65032726386637    
> 13.30504053709336
> Ti             3.65032726386637    3.65032726386637    
> 23.32581852937194
> O             3.65032726386637    3.65032726386637   27.75265329698888
> O             3.65032726386637    3.65032726386637   19.74332980289407
> Bi             0.00000000000000    0.00000000000000    
> 35.70661018533794
> Bi             0.00000000000000    0.00000000000000    
> 44.76350031247415
> Ti             0.00000000000000    0.00000000000000    
> 54.78427830475272
> O             0.00000000000000    0.00000000000000   -3.70580647839191
> O             0.00000000000000    0.00000000000000   51.20178957827486
> Bi             3.65032726386637    3.65032726386637       
> 58.66876914080443
> Bi             3.65032726386637    3.65032726386637       
> 49.61187901366822
> Ti              3.65032726386637    3.65032726386637      
> 39.59110102138964
> O             3.65032726386637    3.65032726386637       
> 35.16426625377269
> O             3.65032726386637    3.65032726386637       
> 43.17358974786750
> Bi             0.00000000000000    0.00000000000000    
> 27.21030936542364
> Bi             0.00000000000000    0.00000000000000    
> 18.15341923828743
> Ti              0.00000000000000    0.00000000000000     
> 8.13264124600885
> O             0.00000000000000    0.00000000000000    3.70580647839191
> O              0.00000000000000    0.00000000000000    
> 11.71512997248671
> Ti              3.65032726386637    3.65032726386637    
> 31.45845977538078
> Ti              0.00000000000000    0.00000000000000     
> 0.00000000000000
> O             3.65032726386637    0.00000000000000    0.00000000000000
> O             0.00000000000000    3.65032726386637   31.45845977538078
> O             0.00000000000000    3.65032726386637    0.00000000000000
> O             3.65032726386637    0.00000000000000   31.45845977538078
> O             3.65032726386637    0.00000000000000   15.72922988769039
> O             0.00000000000000    3.65032726386637   15.72922988769039
> O             3.65032726386637    0.00000000000000   47.18768966307118
> O             0.00000000000000    3.65032726386637   47.18768966307118
> O             3.65032726386637    0.00000000000000    7.40406298501923
> O             0.00000000000000    3.65032726386637   38.86252276040002
> O             0.00000000000000    3.65032726386637    7.40406298501923
> O             3.65032726386637    0.00000000000000   38.86252276040002
> O             3.65032726386637    0.00000000000000   55.51285656574235
> O             0.00000000000000    3.65032726386637   24.05439679036155
> O             0.00000000000000    3.65032726386637   55.51285656574235
> O             3.65032726386637    0.00000000000000   24.05439679036155
>
> K_POINTS {automatic}
>   4 4 1 0 0 0
>
>
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