[QE-users] Negative frequencies for phonon dispersion in Bilayer MoS2

[Vahid Askarpour]

A few points about your inputs:

1. You may want to lower both force and energy convergence thresholds by a factor of 10

2. You are using smearing. Is this a metal? If not, try a fixed occupation

3. For a bilayer, the KPOINTS should be like 4 4 1 or 6 6 1. From experience, since your a=3 angstrom, I would start by a K-grid of 1010 1.

4. For phonon calculations, nq3=1. Your nq1 and nq2 are too small. So when interpolating for phonon dispersion calculations, you do not have enough q-points in the BZ to get a nice dispersion.

5. You may like to lower the tr2_ph to 1.0d-16. I have even gone to 1.0d-22 to avoid some negative frequencies.

6. Last but not least, the PSP may be the issue.

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University
Halifax, NS
CANADA

On Aug 4, 2023, at 8:00 AM, Vahid Askarpour <vh261281 at dal.ca> wrote:

If the coordinates of the atoms are correct for the bilayer, you just need to add vacuum by adding 15 to 20 Ang to the c value.

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University
Halifax, NS
CANADA

On Aug 4, 2023, at 7:08 AM, Giuseppe Scala <g.scala2 at campus.unimib.it> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
The c parameter is set in that way in order to have 10 angstrom vacuum between two sets of Bilayer in my structure. If I reduce the c parameter i think that my system won't be a Bilayer anymore. Is that line of reasoning wrong?

Il ven 4 ago 2023, 05:15 ANAND JHA <anandkj21 at iitk.ac.in<mailto:anandkj21 at iitk.ac.in>> ha scritto:
C parameter and a parameter are wrong they are too high and low

On Thu, 3 Aug 2023 at 20:01, Giuseppe Scala <g.scala2 at campus.unimib.it<mailto:g.scala2 at campus.unimib.it>> wrote:
Hi ANAND,

Would you mind if I ask you to tell me where's the problem in the structure? Maybe that c parameter is too high or low?
Il gio 3 ago 2023, 12:58 ANAND JHA <anandkj21 at iitk.ac.in<mailto:anandkj21 at iitk.ac.in>> ha scritto:
There is some issue in your bilayer
Try to make a new bilayer with CRYSTAL SOFTWARE

On Thu, 3 Aug 2023 at 03:55, Giuseppe Scala <g.scala2 at campus.unimib.it<mailto:g.scala2 at campus.unimib.it>> wrote:
I get negative frequencies at gamma points for Bilayer MoS2. I relaxed my structure and checked convergence with respect to energy cutoff. That's my input file for the scf calculation:

##############

&CONTROL
calculation ='scf'
prefix = 'MoS2_BI'
pseudo_dir = '/home/Giuseppe'
outdir = './'
tstress = .true.
tprnfor = .true.
forc_conv_thr = 1.0d-3
nstep = 200
/

     &SYSTEM
ibrav = 4
a = 3.1429635960300000000
c = 20.006663000000000000
nat = 6
ntyp = 2
ecutwfc = 60
ecutrho = 240
occupations = 'smearing'
degauss = 0.01
/

    &ELECTRONS
mixing_beta = 0.7
conv_thr = 1.0d-8
diagonalization = 'david'
electron_maxstep=200
/

    &IONS
trust_radius_max = 0.2
/
    &CELL
cell_dynamics = "bfgs"
cell_dofree = '2Dxy'
/

ATOMIC_SPECIES
Mo 95.9400 Mo.pbesol-spn-kjpaw_psl.1.0.0.UPF
S 32.0660 S.pbesol-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Mo 1.5714815237 0.9072955423 6.6890512735
Mo 0.0000000000 1.8145901001 13.377562735
 S 1.5714815237 0.9072955423 11.825385701
 S 1.5714815237 0.9072955423 14.928508325
 S 0.0000000000 1.8145901001 8.2412092563
 S 0.0000000000 1.8145901001 5.1381015776

K_POINTS {automatic}
4 4 4 0 0 0

#########


And here my input file for ph.x


#######

&inputph
prefix = 'MoS2_BI'
fildvscf = 'dvscf'
ldisp = .true.
fildyn = 'MoS2_BI.dyn'
alpha_mix(1) = 0.3
nq1 = 2,
nq2 = 2,
nq3 = 2,
tr2_ph = 1.0d-12
/
########

Is my bilayer wrong? I've come the exact same calculations for Bulk and Monolayer MoS2 and everything went smoothly

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people and expresses its concerns about the devastating
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