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

Fri Aug 4 13:38:13 CEST 2023

I"m really grateful for the time you're dedicating to me. I tried tonight
with lower tr2_ph and using a 4 4 1 k-point grid and the negative
frequencies disappeared. Now I'm trying again with nq1=nq2=3 in order to
improve the dispersion relation. In regards to occupation = 'smearing',
I'm using It because my advisor told me to use it for this system in order
to ease convergence but I'm working with a (indirect) semiconductor

Il ven 4 ago 2023, 13:16 Vahid Askarpour <vh261281 at dal.ca> ha scritto:

> 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> 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>
>> 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> 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>
>>> 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
>>>
>>> _______________________________________________
>>> The Quantum ESPRESSO community stands by the Ukrainian
>>> people and expresses its concerns about the devastating
>>> effects that the Russian military offensive has on their
>>> country and on the free and peaceful scientific, cultural,
>>> and economic cooperation amongst peoples
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>> _______________________________________________
>>> The Quantum ESPRESSO community stands by the Ukrainian
>>> people and expresses its concerns about the devastating
>>> effects that the Russian military offensive has on their
>>> country and on the free and peaceful scientific, cultural,
>>> and economic cooperation amongst peoples
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>> _______________________________________________
>>> The Quantum ESPRESSO community stands by the Ukrainian
>>> people and expresses its concerns about the devastating
>>> effects that the Russian military offensive has on their
>>> country and on the free and peaceful scientific, cultural,
>>> and economic cooperation amongst peoples
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>> _______________________________________________
>> The Quantum ESPRESSO community stands by the Ukrainian
>> people and expresses its concerns about the devastating
>> effects that the Russian military offensive has on their
>> country and on the free and peaceful scientific, cultural,
>> and economic cooperation amongst peoples
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20230804/c6194182/attachment.html>