[QE-users] Implementing a bias potential in a Si slab

[Giovanni Cantele]

There are three issues that might be among the causes of the strange behaviour you observe:

1) you should add dipfield = .true. , the dipole correction is needed due to the periodic boundary corrections

2) you set edir=3, emaxpos=0.9 and eopreg=0.1: the saw-like potential decreases from emaxpos within an eopreg interval,
that is, from 0.9 to 0.9 + 0.1 in units of the unit cell parameter along edir. Since along the z direction you have atoms at z=0
that, due to the periodic boundary conditions are replicated at z=1, the (unphysical but needed) decrease of the saw-like potential
occurs in a region of not zero charge density, thus adding spurious interaction to the calculation.
Usually you set emaxpos in the middle of the vacuum space separating two periodic replicas along z. For example, if I’m not wrong,
you have atoms ranging from z=0 to z=0.5, so I would set emaxpos=0.75. Moreover, I would choose a small eopreg.

3) You should also check whether the 28 Ry cutoff is enough to get converged properties with all the pseudo potentials included in your
calculation.

Giovanni

> On 30 Jul 2019, at 13:31, Helen Eisenberg <helen at fh.huji.ac.il> wrote:
> 
> Dear Users,
> 
> I am trying to implement a bias potential on a Si slab with a Li ion in the vacuum, and I am getting unphysical things happening to the Si slab (it gets squashed or stretched depending on which bias I use). This makes me think I'm doing something wrong...Do I need to use a dipole correction (dipfield=TRUE)? Am I doing something else wrong? Does it not work with molecular dynamics only ionic relaxation?
> 
> Thank you for your help (I have copied my input file below, note the various parameters, such as kpoints and ecutwfc are not yet converged, as these are initial calculations )
> 
> Dr. Helen Eisenberg,
> 
> Fritz Haber Center for Molecular Dynamics,
> 
> Hebrew University
> 
> 
> &CONTROL
>   calculation = "md",
>   restart_mode='from_scratch',
>   pseudo_dir  = "$PSEUDO_DIR",
>   prefix      = "Energy_Si_2x2",
>   tstress     = .true.
>   tprnfor     = .true.
>   outdir      = "$TMP_DIR"
> dt=40,
> nstep=800
> tefield=TRUE
> /
> &SYSTEM
>   ibrav       = 0,
>   nat         = 33,
>   ntyp        = 3,
>   ecutwfc     = 28.D0,
>   occupations = 'smearing',
>   smearing    = 'mv',
>   degauss     = 0.0001,
>   tot_charge  = 0.0,
>   nspin       = 2,
>   starting_magnetization(1)=0.0
> edir=3
> emaxpos=0.9
> eopreg=0.1
> eamp=0.01
> /
> &ELECTRONS
> electron_maxstep=500
>  mixing_mode = 'plain'
>   mixing_beta = 0.7
>   conv_thr =  1.0d-6
> /
>  &ions
>     pot_extrapolation='second-order'
>     wfc_extrapolation='second-order'
>  /
> 
> ATOMIC_SPECIES
> Si  28.086  Si.pbe-mt_gipaw.UPF
> H 1.00794 H.pbe-vbc.UPF
> Li   6.941  Li.pbe-s-mt.UPF
> ATOMIC_POSITIONS (crystal)
> H 0.25  -0.00517        0 0 0 0
> H 0.75  -0.00517        0 0 0 0
> Si 0.51097      0.49804 0.16473
> Si 0.35376      0.49734 0.35774
> Si 0.25 0.24742 0.05541 0 0 0
> Si 0.24944      0.24765 0.27061
> Si 0.75 0.24742 0.05541 0 0 0
> Si 0.75919      0.24761 0.28048
> Si 6.33534E-4   0.49808 0.16495
> Si 0.07141      0.49748 0.38744
> Si -5.17962E-4  0.2482  0.10971
> Si 0.01902      0.24763 0.33382
> Si 0.75553      0.49764 0.22403
> Si 0.50177      0.24816 0.10965
> Si 0.4958       0.24746 0.33137
> Si 0.25633      0.49758 0.21703
> H 0.25  0.49483 0 0 0 0
> H 0.75  0.49483 0 0 0 0
> Si 0.51097      0.99804 0.16473
> Si 0.35376      0.99734 0.35774
> Si 0.25 0.74742 0.05541 0 0 0
> Si 0.24944      0.74765 0.27061
> Si 0.75 0.74742 0.05541 0 0 0
> Si 0.75919      0.74761 0.28048
> Si 6.33534E-4   0.99808 0.16495
> Si 0.07141      0.99748 0.38744
> Si -5.17962E-4  0.7482  0.10971
> Si 0.01902      0.74763 0.33382
> Si 0.75553      0.99764 0.22403
> Si 0.50177      0.74816 0.10965
> Si 0.4958       0.74746 0.33137
> Si 0.25633      0.99758 0.21703
> Li       0.625           0.5           0.5
> K_POINTS automatic
> 2 2  1  0  0  0
> CELL_PARAMETERS {angstrom}
>                 7.6801695932    0.0000000000    0.0000000000
>                 0.0000000000    7.76034    0.0000000000
>                 0.0000000000    0.0000000000   24.5037250000
> EOF
> 
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-- 

Giovanni Cantele, PhD

CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy

e-mail: giovanni.cantele at spin.cnr.it
            gcantele at gmail.com
Phone: +39 081 676910
Skype contact: giocan74
Web page: https://sites.google.com/view/giovanni-cantele

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