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Dear Cameron,<br>
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<div>I expect this simulation to allow the <u>atomic positions</u> 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.</div>
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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. <br>
<br>
I don't recall MoSe2 reconstructions, but maybe literature say other
ways. If so you should just repeat relaxation if right supercell.<br>
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<div>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)</div>
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<br>
If you think that atomic positions could be the source of your
problems, than maybe should try different functionals (PBE should
provide different distances).<br>
<br>
Regards,<br>
Maciej<br>
<br>
Maciej Szary,<br>
PhD student,
<br>
Computational Physics and Semiconductors Division,
<br>
Poznan University of Technology,
<br>
Poland
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