Phonon bands from AIMD for vacancy contaning supercell

[mvnayagam]

Dear Admin and users,
I am trying to calculate the thermal conductivity of two-dimensional Se and Te single layers with and without vacancy. For layers without vacany I am able to simualte the phonon bands.

But I face issues with vacancy-containing layers. I generated a 4x4 supercell of Te layer with a Te vacancy. Carried out AIMD simulation using VASP for more than 6 fs. I use the last 1300 frames (1.3 ps) for further process with Alamode. Within harmonic terms, I try to get phonon band strucutre. Since the layer contains a vacancy, the complete cell acts as primittive cell. There are 47 Te atoms in the cell and i expect 141 no of modes. I get 141 mode. But issue is to define &cell card for anphon simulation.

I got the following phonon (frequency unit: THz) from anphon

Setting for anphon calcaultion

&general
  PREFIX = sc
  MODE   = phonons
  NKD    = 1 ;  KD = Te
  #MASS  = 127.60
  FCSXML = sc.xml
  PRINTSYM = 1
/
&cell
1.889725988
    16.9599990845000015    0.0000000000000000    0.0000000000000000
     8.4800007677000000   14.6839988664999996    0.0000000000000000
     0.0000000000000000    0.0000000000000000   20.0000000000000000
/
&kpoint
  1  # KPMODE = 1: line modei
  G   0    0  0     M  1/2  0     0  51
  M  1/2 1/2 0   K  1/3  2/3  0  51
  K  1/3 2/3 0    G   0    0      0  51
/

Have anyone faces such a issue?

Is Alamode capable of solving phonon bands for defect containing systems ?

It would be more beneficial if you share your experience or comments on this issue.
Also If you need more information, please let me know

Looking forward to your mail !

Thank you

Best regards,
Muthu Vallinayagam
Reserach scholar
Hochschule für Technik und Wirtschaft Dresden
Germany

[ttadano]

Hi,

I am not sure if this is an issue of ALAMODE. It is possible that your supercell structure with a vacancy is not dynamically stable.