Dear Cameron,
I expect this simulation to allow the _atomic positions_ to relax
leaving the actual lattice constant unchanged. I also expect the
atomic positions to relax in all 3 directions (hence the 1 1 1 after
each coordinate specification) but I have seen the x and y coordinates
remain relatively unchanged. Again I am really after the Se-Se distance.
Why would you expect in-plane relaxation of atoms? You're calculating
1x1 surface cell, so any Se in-plane movement wouldn't change anything,
next set of neighbour Se atoms would still be arrange respectively with
presented lattice constant. Of course, in-plane position of Mo atom
could change with the respect to Se however, it would distorted the
MoSe2 structure. Normally from the top view you see hexagonal structure
for TMDC materials and a change of in-plane relative positions of Mo and
Se would affect this symmetry.
I don't recall MoSe2 reconstructions, but maybe literature say other
ways. If so you should just repeat relaxation if right supercell.
My questions are: is this relaxation calculation doing what I expect
it to do? And is the equilibrium structure guaranteed if convergence
is achieved? The motivation for the second question is that, I have
run a relaxation calculation with this input file, it converges, but
then I find negative frequencies in the phonon dispersion particularly
with the ZA and TA modes (the ZA mode being the characteristic
quadratic mode found in 2D monolayers such as graphene and would be
most susceptible to variations in the Se-Se distance). As the
simulation experienced no interruptions I suspect the negative
frequencies to be a result of numerical issues with the atomic
positions and/or the MP grid size (note I used an 8 8 1 grid size for
the phonon calculation, not 6 6 4 as mentioned above)
If you think that atomic positions could be the source of your problems,
than maybe should try different functionals (PBE should provide
different distances).
Regards,
Maciej
Maciej Szary,
PhD student,
Computational Physics and Semiconductors Division,
Poznan University of Technology,
Poland
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