[Pw_forum] graphen with adatoms input

[yelena]

I tried to make input for graphene with adatoms in two ways, but 
everytime when i open it in crysden to check if it looks ok and I got 
this image (in attachment).
Here are inputs:
&CONTROL
     prefix='gradat',
     calculation='scf',
     restart_mode='from_scratch',
     outdir = '/home/ipb167/Desktop/espresso/gradat' ,
     pseudo_dir = '/home/ipb167/Desktop/espresso/pseudo' ,
  /
  &SYSTEM
     ibrav=  0, celldm(1) = 4.66, nat=3, ntyp= 2,
     ecutwfc = 65.D0,
     occupations='smearing',
     smearing='methfessel-paxton',
     degauss=0.01,
/
  &ELECTRONS
     conv_thr=1.D-12,
     diagonalization='david',
     mixing_mode='plain'
  /
ATOMIC_SPECIES {alat}
  C  12.0107  C.pz-vbc.UPF
Li  6.941    Li.pz-n-vbc.UPF
CELL_PARAMETERS (alat=4.66000000){hexagonal}
    0.999984012   0.000000000   0.000000000
   -0.499992006   0.866011558   0.000000000
    0.000000000   0.000000000   12.188495864

ATOMIC_POSITIONS crystal
  C 0.000000  0.000000 0.000000
  C 0.333333  -0.33333 0.000000
Li 0.666666  0.333333 0.000000
K_POINTS automatic
32 32 1 0 0 0


And other:

&CONTROL
     prefix='gradat',
     calculation='scf',
     restart_mode='from_scratch',
     outdir = '/home/ipb167/Desktop/espresso/gradat' ,
     pseudo_dir = '/home/ipb167/Desktop/espresso/pseudo' ,


  /
  &SYSTEM
     ibrav=  4, celldm(1) = 4.66, celldm(3)= 6.0, nat=3, ntyp= 2,
     ecutwfc = 65.D0,
     occupations='smearing',
     smearing='methfessel-paxton',
     degauss=0.01,
/
  &ELECTRONS
     conv_thr=1.D-12,
     diagonalization='david',
     mixing_mode='plain'
  /
ATOMIC_SPECIES
  C  12.0107  C.pz-vbc.UPF
Li  6.941    Li.pz-n-vbc.UPF
ATOMIC_POSITIONS crystal
  C 0.000000  0.000000 0.000000
  C 0.333333  -0.33333 0.000000
Li 0.666666  0.333333 0.000000
K_POINTS automatic
32 32 1 0 0 0

Both give same image and I'm not sure if Li and C should be connected 
it that way.
Any suggestions?

Jelena


On 08 May 2013 15:03, Stefano de Gironcoli wrote:
> you can use the cell you have created for the pure graphene, or a 
> 2x2,
> 3x3 version of it and then simply add the adatom in the desired place 
> .
> the code will recognize the reduced symmetry and will adapt the list 
> of
> kpoints accordingly.
>
> stefano
>
> On 05/08/2013 02:23 PM, yelena wrote:
>> Hello everyone!
>> I am asking for suggestion. I'm trying to make input for scf
>> calculation (and then for electron-phonon... ) for graphene with
>> adatoms.
>> I've been doing calculation with monolayer graphene and I used
>> hexagonal lattice to describe it and large c/a with vacuum to 
>> simulate
>> monolayer. I've been using GPU version of code and it works 
>> perfectly
>> (I'll write something more about that on GPU message board)
>> Now I'd like to add adatoms in the middle of lattice and I'm not 
>> sure
>> how to do that. Is there any way to make input for hexagonal lattice
>> with adatom or I have to make free lattice ibrav=0 and then use CELL
>> PARAMETER card?
>>
>> Looking forward to your answers,
>>
>> Jelena Pesic
>> PhD Student,
>> Institute of Physics Belgrade, Serbia
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
-------------- next part --------------
A non-text attachment was scrubbed...
Name: adatoms.png
Type: image/png
Size: 106675 bytes
Desc: not available
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20130530/5a648dae/attachment.png>