[QE-users] Atoms crossing boundary of cell during relaxation

[Giovanni Cantele]

Hi,

I do not actually see atoms that "after relaxation" go in positions that
they did not occupy before relaxation. However, such effects can be
absolutely "normal", in that due to periodicity, if you did not center your
atomic positions around the middle of the cell along z direction, it can
happen
that an atom, let's say at z=0.0 at the beginning, after relaxation is
found at z=-0.1 Ang. The visualization of the file with any visualization
tool,
will display the atoms in the primitive cell, so that atom will be seen at
z = c - 0.1 Ang. Try to just replicate your cell twice along z and you'll
see that
the structure is correct.


By looking at the two files, also consider that:

i) although the total final force is small, strictly speaking your
calculation is not ended as far as relaxation is concerned
(see the message "The maximum number of steps has been reached." at the end
of the file)

ii) you're forcing pw.x to compute every time nbnd=1186 bands. However,
your system is composed of 1084 electrons that would correspond
to 542 occupied bands for a semiconductor. For a metallic system, using
occupation='smearing' automatically increases this
value (542) by some percentage (something like 20%). You can see that also
from the estimation of the Fermi level, 2.4851 eV, if compared with
your highest occupied bands, just slightly below 20 eV. This implies that
you're taking much more time than needed to converge scf cycles
and atomic position optimization. I would get rid of the nbnd variable,
complete the relaxation and only after that rerun the calculation with
the optimized structure and a larger number of bands, in the case you
really need them

iii) I would check convergence against k-point grid, only one k-point could
not be enough

iv) you have specified dipfield = .true. from the documentation you read
If .TRUE. and tefield==.TRUE. a dipole correction is also
added to the bare ionic potential - implements the recipe
of L. Bengtsson, PRB 59, 12301 (1999). See variables edir,
emaxpos, eopreg for the form of the correction. Must
be used ONLY in a slab geometry, for surface calculations,
with the discontinuity FALLING IN THE EMPTY SPACE.
So, I think that as you did, the variable is not effective. However, dipole
correction for your slab geometry might be needed due to the
asymmetry between the top and the bottom surface of the slab.

Giovanni

-- 

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 <giovanni.cantele at spin.cnr.it>
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: https://sites.google.com/view/giovanni-cantele/home


Il giorno gio 12 dic 2024 alle ore 06:18 Suraj P <surajp at iitkgp.ac.in> ha
scritto:

> Dear QE users,
>
> I have relaxed a Pd-doped anatase TiO2 (001) supercell using Quantum
> espresso. After relaxation, some atoms at the top surface of the slab is
> going outside the cell. I have attached the input file and output file.
> Kindly let me know why the atoms cross the boundaries of supercell.
>
> Input file:
> https://drive.google.com/file/d/10-Q4xL-V3GD_gMzZ3ZJaiO2CrY7PZSsC/view?usp=sharing
> Output file:
> https://drive.google.com/file/d/17Nm9q5oiexxhtn16k4lkRdT43ZvnpLhi/view?usp=drive_link
>
>
> Thanking you
> Suraj
> Research student
> IIT Indian institute of technology
>
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