[QE-users] some queries about mono layer optimization and vacuum

[rekha sharma]

Dear Sir,

Good afternoon and happy new year to all of you.

I am new user here so I need a step by step reply.

Before sending this email I have read the posting rules.

I used Quantum Espresso 6.4.1 compiled with ifort on a 16 core CPU.

Without having any previous experience on any quantum simulation tool, I
spent almost six months to learn quantum espresso and for bulk system I
feel comfortable.

I have done some calculations with a binary semiconductor compound which
was vc-relxed for ecutwcf (65), ecurho (52) and k-mesh(9 9 3 0 0 0). The
convergence  criteria was less then 1meV for these parameters.
Pseudo-potentials are taken from PSlibrary (recommended there).

Now I want to do some calculation of its monolayer.
As I could not get any informative tutorials for this kind of calculations
so  I am asking here.
My doubts are on k-mesh, &CELL and vacuum for the mono-layer.

1. k-mesh:
Que. Should I keep the same k-mesh but reducing the k-point in
vacuum direction to 1?
i.e. 9 9 1 0 0 0 (9 9 3 0 0 0 was for bulk with 1meV convergence).
I have done a k-mesh convergence test and  no significant changes observed
after 9 9 1 0 0 0 k-grid.
My double arises here because materials cloud suggest 2 k-points in
vacuum direction.

2. &CELL
I have adopted two choices to do it.

A.

I have read the mailing list and found a link

where it is mentioned that how to do vc-relax of a mono-layer.
That user used
&CELL
cell_dofree='2Dshape'
/
to do a vc-relax.

With these flags (with k-mesh 9 9 1 0 0 0),
The relaxed data are below
Total force = 0.08 Total SCF correction = 0.00
  total   stress  (Ry/bohr**3)   (kbar) P=
-2.81# Stress
 Final enthalpy =-227.5797893621 Ry
Begin final coordinates
 new unit-cell volume =   1782.72164 a.u.^3 (   264.17209 Ang^3 )
 density =  0.85971 g/cm^3

CELL_PARAMETERS (alat=  1.)
   6.675929970   0.0   0.0 # Please note a,b,c are same
what I have supplied in the input file.
   0.0   6.675929970   0.0
   0.0   0.0  40.0

B.

from pw.x input descriptions, I found "cell_dofree='2Dxy' " do to a
vc-relax in x-y plane.
So with below flags
&CELL
cell_dofree='2Dxy'
/

My results are
 Total force = 0.13 Total SCF correction = 0.02
   total   stress  (Ry/bohr**3)   (kbar) P=
  -0.05# Stress is 0.5 kbar

 Final enthalpy =-227.5803704614 Ry
Begin final coordinates
 new unit-cell volume =   1742.44890 a.u.^3 (   258.20428 Ang^3 )
 density =  0.87958 g/cm^3

CELL_PARAMETERS (alat=  1.)
   6.600092607   0.0   0.0   # Please note here
that a and b has reduced from what I given into input file (6.675929970)
  -0.0   6.600092607   0.0
   0.0   0.0  40.0

My concern arises from the  stress and change in lattice parameters from
above two cases.
In the case-B  where I have adopted stress and Final enthalpy is more
stable then the case-A.

Que. Which approach I should use A or B?
Que. Is it okay if the cell parameters (a and b) deviates from the bulk
case?
Que. Or you can advice me how to do vc-relax for  a mono-layer.


C. For vacuum

Que. How to decide the vacuum size?
I have done a convergence test from 30 bohr to 50 bohr and the total energy
first decrease, reach to a lowest value of then starts to increase.

Below is the Total every for 30 Bohr to 50 Bohr vacuum size

-227.40963239 Ry   # 30
-227.43879270 Ry   # 31
-227.46529446 Ry   # 32
-227.48906558 Ry
-227.51005151 Ry
-227.52821961 Ry
-227.54356349 Ry
-227.55610674 Ry
-227.56589822 Ry
-227.57301424 Ry
-227.57755075 Ry
-227.57962022 Ry  # with vacuum 41 bohr
-227.57934725 Ry
-227.57686484 Ry
-227.57231253 Ry
-227.56583286 Ry
-227.55757040 Ry
-227.54767074 Ry
-227.53627785 Ry
-227.52353424 Ry# 49
-227.50957968 Ry# 50

Any step wise reply will help me a lot.

Looking forward for a supportive response.

thank you very much sir,

Best wishes

Ms. Rekha
Ex-PG student,
LBS college, Jaipur
India
Mob.: +11 90-95 790 71 697
Email: rekha1997...@gmail.com
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

[QE-users] Bader Charges for a Spin-Polarized System

[Victor Bermudez]

Happy New Year All, 

 I'm trying to compute Bader charges for a paramagnetic molecule (NO2) 
adsorbed on MoS2. Normally one would use the PAW wavefunction of the relaxed 
system as input to pp.x with plot_num=17 to obtain the electron density, which 
would then be processed with the Henkelman code 
(http://theory.cm.utexas.edu/henkelman/code/bader/) to get the Bader charges. 
Unfortunately, pp.x with plot_num=17 doesn't work for spin-unrestricted systems 
in Quantum Espresso version 6.4.1. The latest release notes say that this has 
been fixed in vers. 6.5, but I don't yet have access to this most-recent 
version. I also tried plot_num=21 in vers. 6.4.1, and that doesn't work either. 
Out of desperation I tried plot_num=0, which according to the pp.x 
input write-up produces "electron (pseudo-)charge density". That does work, and 
the results appear reasonable. The right total number of electrons is obtained, 
and all the atom charges look OK (Mo = +1.18, S = -0.59, N = +0.70, O = -0.37). 
The MoS2 is essentially charge-neutral and a very small negative charge appears 
on the electron-acceptor NO2. 
With that as background, my question is whether or not the use of 
the plot_num=0 density in this way is in fact valid. I'm not sure what the term 
"electron (pseudo-)charge density" actually means. Another disturbing point is 
that the atom volumes found by the Bader code are slightly different for S 
atoms that are related by symmetry (i.e., by reflection in a mirror plane), 
even in the absence of the adsorbed molecule. In one S layer the volumes are in 
the range of 833-841 bohr^3 while in the symmetrically-equivalent layer the 
range is 821-828 bohr^3. I should mention that I'm using a dipole correction 
layer (3 Angstroms wide) in the middle of the vacuum space (26 Angstroms wide) 
because of the finite molecular dipole. I'm assuming that this won't affect the 
Bader-charge calculation. 
Any expert advice would be much appreciated. 

Best Wishes,
Vic Bermudez
(US Naval Research Lab. - retired) 


___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Bader Charges for a Spin-Polarized System

[Alberto Otero de la Roza]

Hi Vic,

I haven't used pp.x for a while for spinpolarized systems so I'm not
sure about the state of the code in that regard but I can answer some
of your other questions. The plot_num=0 density (aka valence
pseudo-density) is built as the sum of the squares of the pseudo-KS
states, which have been smoothed near the nuclei. The valence
pseudo-density integrates to the number of valence electrons in your
calculation. Bader integration relies on having maxima at the nuclei
but the smoothing may cause some of them to be missing. Therefore, it
is a poor idea to use this density to partition the crystal space into
atomic regions.

In PAW, you can reconstruct the "correct" (i.e. not smoothed) valence
charge density. This is plot_num=17. If, on top of that, you add the
core density, then you have the all-electron charge density
(plot_num=21). These two densities are poorly represented by a uniform
grid and they do not integrate to an integer number of electrons. But
they are what you need to use to find the atomic basins. Once the
basins are found, you integrate the valence pseudo-density
(plot_num=0) inside them to find the atomic charges.

You can use plot_num=0 to find the basins. If you have enough valence
electrons and little charge transfer, you may very well have maxima on
top of all atoms. However, the results will be off. Also, regardless
of how you partition the system into atoms, the sum of all atomic
populations will trivially give the number of valence electrons
always, so that's not a good measure of quality.

I have some notes on the atomic integration topic here:

https://aoterodelaroza.github.io/critic2/examples/example_11_01_simple-integration/

using the critic2 program but I believe they should apply to
Henkelman's code as well.

As for why symmetry-equivalent atoms come out with different atomic
populations: because the uniform grid on which the density is written
doesn't have the same symmetry as the crystal. However, in the limit
of an infinitely fine grid the atomic populations should converge to
the same value. You may want to try the Yu and Trinkle method
implemented in critic2, which assigns fractional weights to grid
points and is in general a little more accurate than Henkelman's, but
I believe a finer grid is the ultimate solution.

Best,

Alberto

--
Dr. Alberto Otero de la Roza
Ramón y Cajal fellow,
Department of Physical and Analytical Chemistry, 
University of Oviedo

___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

[QE-users] Phonon not converging

[Mayuri Bora]

Hi,

I am not able to converge phonon calculation for monolayer CrX3. Can
anyone suggest what may be the reason. The input is given below:

BEGIN
phonons of ml
 &inputph
  tr2_ph=1.0d-14,
  ldisp=.true.,
  nq1=7, nq2=7, nq3=7,
  amass(1)=51.996,
  amass(2)=79.904,
  prefix='ml',
  outdir='/global/home/sushantk/mayuri/monolayer/'
  fildyn='ml.dyn',
 /
END


Mayuri Bora
INSPIRE Fellow
Advanced Functional Material Laboratory
Tezpur University
Napaam
http://www.tezu.ernet.in/afml/


* * * D I S C L A I M E R * * *
This e-mail may contain privileged information and is intended solely for the 
individual named. If you are not the named addressee you should not 
disseminate, distribute or copy this e-mail. Please notify the sender 
immediately by e-mail if you have received this e-mail in error and destroy it 
from your system. Though considerable effort has been made to deliver error 
free e-mail messages but it can not be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, delayed, or may 
contain viruses. The recipient must verify the integrity of this e-mail message.
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users