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Formation energy of charged defects in 2D
Date: 2023/04/12 04:00
Name: Roozbeh Anvari   <roozbeh.anvari@gmail.com>


Dear OpenMX developers,

I have a question regarding the formation energy of charged defects in 2D,

Although the calculated formation energy of neutral defect converges with increasing size of the supercell,that of charged defects does not, 

here is a summary of calculated formation energies of a single sulfur vacancy in MoS2 in the neutral, +1e and -1e charge states,
(neutral and charged structures are fully relaxed) :


    cell size    vacuum size (\AA)      E_charge_0 - E_charge_-1e (eV)      E_charge_0 - E_charge_+1e  (eV)       
    ------------------------------------------------------------------------------------------------------------------
    6x6          30                    2.56                                -7.86 
    6x6          40                    1.85                                -8.57 
    6x6          50                    1.14                                -9.28 
    6x6          60                    0.43                                -9.9   
    6x6          70                    -0.27                                -10.7   
    7x7          70                    3.08                                -7.3     
    8x8          70                    1.8                                  -8.6 


and here is the setup for my calculations,


System.CurrrentDirectory        ./ 
System.Name                      MoS2
level.of.stdout                  1 
level.of.fileout                  0 
DATA.PATH    ../DFT_DATA19 

Species.Number      3
<Definition.of.Atomic.Species
Mo Mo7.0-s3p2d2  Mo_PBE19
S  S7.0-s2p2d1f1 S_PBE19
E  S7.0-s2p2d1f1 E
Definition.of.Atomic.Species>

Atoms.Number    192
Atoms.SpeciesAndCoordinates.Unit  Ang  # FRAC|Ang|AU
<Atoms.SpeciesAndCoordinates
  1  Mo    0.00050700702568    1.84986620739400  10.03839357433526    7    7   
  2  Mo  -1.59486367279878    4.61627463816083  10.02977818816547    7    7   
  ...
  65    S    1.59653623202201    0.92442474871844    8.45598659923796    3    3   
  66    S    0.00424403169950    3.69234160850257    8.44975400086947    3    3   
  ...
155    S    7.97398629435223    6.48685004433369  11.58888111322887    3    3   
156    S    6.36307626517883    9.31663467513011  11.54168942826534    3    3   
157    E    4.67775002088586  12.04343751441682  10.49528937300338    0    0
...   
192    S  12.76124458787810  20.28256653780570  11.62440840719757    3    3       
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit  Ang
<Atoms.UnitVectors
  0.000000000000000  0.000000000000000  33.378293991100001
25.549865722699987  0.000000000000000  0.000000000000000
-12.783150427300001  22.131666175499987  0.000000000000000
Atoms.UnitVectors>

#-------------------------------------------------------------------------------------------------

scf.XcType                  GGA-PBE    # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization        On        # On|Off|NC
scf.ElectronicTemperature  300.0      # default=300 (K)
scf.energycutoff          300.0      # default=150 (Ry)
scf.maxIter                100        # default=40
scf.EigenvalueSolver      band        # DC|GDC|Cluster|Band

scf.Kgrid                5  5  1    # 5x5x1 for relax and 12x12x1 for energy
scf.Mixing.Type          rmm-diisk    # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight    0.010        # default=0.30
scf.Min.Mixing.Weight      0.01      # default=0.001
scf.Max.Mixing.Weight      0.100      # default=0.40
scf.Mixing.History          20          # default=5
scf.Mixing.StartPulay      15          # default=6
scf.criterion            1.0e-10      # default=1.0e-6 (Hartree)


scf.system.charge    -1.0 
scf.coulomb.cutoff      on

ESM.switch                  on2      # off, on1=v|v|v, on2=m|v|m, on3=v|v|m, on4=on2+EF
ESM.potential.difference    0.0      # default=0.0 (eV)
ESM.wall.switch              off
ESM.wall.position            6.0      # default=10.0 (ang)  , distance pf the u[pper edge and the barrier of the potentil, cell length - xB,
ESM.wall.height            100.0      # default=100.0 (eV)
ESM.buffer.range            10      # default=10.0 (ang)
ESM.direction                z      # x|y|z, default=x
                                     

#MD.Type                    nomd      # Nomd|Opt|NVE|NVT_VS|NVT_NH
#MD.maxIter                    1        # default=1
#MD.TimeStep                  1        # default=0.5 (fs)
#MD.Opt.criterion        1.0e-5        # default=1.0e-4 (Hartree/bohr)

# 1. - - - - - - - - - - - - - - - -
MD.Type                    EF        # Opt|DIIS|BFGS|RF|EF  , 
MD.Opt.DIIS.History          3        # default=3
MD.Opt.StartDIIS            5        # default=5
MD.Opt.EveryDIIS            300        # default=200
MD.maxIter                  200        # default=1
MD.Opt.criterion          1.0e-5      # default=0.0003 (Hartree/Bohr)



Thank you for your help,
Roozbeh Anvari
UT, Austin,     



 

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Re: Formation energy of charged defects in 2D ( No.1 )
Date: 2023/04/12 14:01
Name: T. Ozaki

Hi,

Even if you specify the following two keywords:

scf.system.charge    -1.0
scf.coulomb.cutoff      on

the Coulomb cutoff scheme does not work properly because of absence
of the reference charge density for the neutral system.
You may follow the way to perform the XPS calculation explained at
https://www.openmx-square.org/openmx_man3.9/node193.html

I do not see studies in which the Coulomb cutoff scheme is properly used to calculate
charged defects in a bulk system. At this moment, I am not sure that the method works
well to study the charged defects, though it looks an interesting topic.

Regards,

TO

メンテ
Re: Formation energy of charged defects in 2D ( No.2 )
Date: 2023/05/13 06:00
Name: Roozbeh Anvari  <roozbeh.anvari@gmail.com>



Thank you Professor Ozaki,

Best regards,

Roozbeh


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