[QE-users] some queries about files to plot electrostatic potential for a mono/bi layer
rekha sharma
rekha1997jpr at gmail.com
Sat Jan 4 16:37:23 CET 2020
Dear Sir,
I have tried to understand the input files.
My system is a layered material very similar to MoS2, but both atoms are
from p-block and I assume the side of the layer is not charges (in
principle I do not know how to check whether the surface is charged or not)
and I am studying some DFT calculations of its mono/bi-layers.
The background of this email is "how to set vacuum for a layer and in reply
to my previous email it was suggested by Nicolás sir that I should check
the electrostatic potential plot. So I am doing it.
My cell parameters are (tetragonal structure)
6.67592997d0 0.000000000000d0 0.000000000000d0
0.000000000000d0 6.67592997d0 0.000000000000d0
0.000000000000d0 0.000000000000d0 $i (varying from 30:2:40)
below numbers (with tefield=.true., and dipfield=.true.,) I have
taken are from examples and I need some help to understand them.
&SYSTEM
edir=3, # The direction of the electric field or dipole
correction.
Que. Is it always a vacuum direction? i.e. for x(y)-axis it will be 1(2)?
emaxpos=0.55, # Position of the maximum of the saw-like potential
along crystal axis edir
Que. Why we apply a saw-like potential and how to fix set this value?
eopreg=0.06, # Zone in the unit cell where the saw-like potential
decreases
Que. Again, how to set this number?
eamp=0, # Zero electric field
Que. If we set " tefield=.true.," in the qe.in file it means we are
applying electric filed in a particular direction. But what does it mean
about " tefield=.true.," if eamp=0?
avg.in
N (*nfile)* # number of files produced by pp.x?
pp-$i.pot # mention all file names here
1.0 (*weight) # What does it mean?*
3000 (*npt) * # Should we do a convergence test for it of 3000 or it is a
well tested number?
3 # I am dealing a monolayer/bi-layer with a vacumm in z-direction.
How to set this idir? Is it same as edir?
2.59 (awin) # How to set this awin windiow?
Thank you for your support,
Best wishes
Rekha
On Sat, Jan 4, 2020 at 5:43 PM rekha sharma <rekha1997jpr at gmail.com> wrote:
> I could finish a test case.
> I need to define some variables in qe.in file.
>
> Will get back to you once I finish it.
>
> Thank you sir,
>
> best wishes
>
> Rekha
>
> On Sat, Jan 4, 2020 at 2:08 PM rekha sharma <rekha1997jpr at gmail.com>
> wrote:
>
>> Dear Sir,
>> Thanks for your reply.
>> It is very useful for me.
>> Consider my apology for late reply as my computer was not free.
>>
>> ecutrho 52 is by mistake. actually it is 520 (uspp).
>>
>> I tried to run calculations for "V" but I could not finish pp.x.
>> I run pw.x followed by pp.x.
>>
>> my pp.in is
>>
>> &inputPP
>> prefix = 'pwscf'
>> outdir='/tmp-$i',
>> plot_num=11
>> filplot = 'pp-$i.pot'
>> /
>>
>> &plot
>> iflag=3,
>> output_format=5
>> /
>>
>> where prefix and outdir is same as I used in in my scf file.
>>
>> I am getting below xml error
>>
>> Error in routine pw_readschemafile (1):
>> xml data file not found
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> stopping ...
>>
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine pw_readschemafile (1):
>> xml data file not found
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> stopping ..
>>
>> Please suggest me how to run pp.x.
>>
>> My problem is related with this issue
>> <https://lists.quantum-espresso.org/pipermail/users/2017-November/039771.html>
>> but I am not doing any restart_mode calculation.
>>
>>
>> Best Wishes,
>>
>> Rekha
>>
>>
>>
>> On Thu, Jan 2, 2020 at 6:50 PM Lucas Nicolás Lodeiro Moraga <
>> lucas.lodeiro at ug.uchile.cl> wrote:
>>
>>> Hello Rekha!
>>> I am not an expert in monolayers, I work with slabs, but the problems
>>> should be similar.
>>> First, the ecutrho value that you use (52) it is very low... I do not
>>> know wich type of pseudopotential do you use (NormConserving, UltraSoft,
>>> PAW), but the ecutrho must be 4 times the ecutwfc (For US and PAW form 6 to
>>> 12 times). Other thing, the convergence criteria of 1meV its good, but I
>>> prefer a criteria independent of number of atoms, as 1meV/atom... If you
>>> have the same system with more atoms, with your criteria you need a higher
>>> values to reach ir, but if use an independent atoms criteria, the values
>>> are the same for small and big systems.
>>>
>>> MONOLAYER:
>>> kpoints: I use 1 point in the vacuum direction, and I do not found any
>>> difference when I use 2 or more kpoints in this direction. The bands
>>> dispersion in this direction is negligible.
>>> cell: The 2Dshape flag does not change your cell because it does not
>>> change the xy area, how you have an orthogonal a,b vectors and a=b. The
>>> broken of this symmetry is energetically not allowed. For this, 2Dxy flag
>>> works and minimize the cell in xy directions, and reduce the stress.
>>> If is it okay the parameters deviates from the bulk? I do not know for
>>> the case of Monolayers... but for me makes sense, in your calculation the
>>> xy area reduces to maximize the interaction with the neighborhood. If you
>>> want do a vc-relax the 2Dxy is the correct flag.
>>> Vacuum: 30 bohr should be enough... In my systems I do a similar vacuum
>>> test, and 30 bohr gives the same result as 200 bohr.
>>> I guess your system have charged surfaces, dipoles or something like
>>> that. If is a bynary semiconductor AB... a monolayer gives you a "A type"
>>> and a "B Type" surfaces, how A and B have different electronegativities,
>>> exists a dipole between both surfaces, that could explain the energy
>>> behaviour with vacuum.
>>> I recommend, do a post-processing calculation for the monolayer,
>>> calculate the electrostatic potential (V) along the vacuum direction... If
>>> V is not plane in the vaccum region, do you have a dipole on the monolayer.
>>> You can fix it using a dip-field on the vacuum... with it you add a "V
>>> step" on the vacuum, giving you two V planes on vaccum, "two types of
>>> vaccum".
>>> Other way, is making a monolayer with equal surfaces, like A-A or B-B
>>> (adding a plane of atoms)... this fix the dipole in most cases... but I do
>>> not know if this is still a monolayer or what you want.
>>>
>>> Regards
>>>
>>> Lucas Lodeiro
>>>
>>>
>>
>> --
>>
>>
>>
>>
>> Best wishes
>>
>> Ms. Rekha
>> Ex-PG student,
>> LBS college, Jaipur
>> India
>> Mob.: +11 90-95 790 71 697
>> Email: rekha1997jpr at gmail.com
>>
>
>
> --
>
>
>
>
> Best wishes
>
> Ms. Rekha
> Ex-PG student,
> LBS college, Jaipur
> India
> Mob.: +11 90-95 790 71 697
> Email: rekha1997jpr at gmail.com
>
--
Best wishes
Ms. Rekha
Ex-PG student,
LBS college, Jaipur
India
Mob.: +11 90-95 790 71 697
Email: rekha1997jpr at gmail.com
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