[Pw_forum] Structural Optimization Calculation

[Cameron Foss]

Hello all,

I am trying to run a relaxation calculation on a monolayer of a transition
metal dichalcogenide of Molydenum Diselenide (MoSe2) to then further obtain
vibrational modes of that monolayer. I am using QE-5.1 with LDA
functionals. I want the monolayer material so vdW corrections are neglected
in this case. I am somewhat confident in the in-plane lattice constant but
I am trying to relax the Se-Se distance to the equilibrium structure. Below
is the input file for the relaxation:

&control
    calculation='relax'
    restart_mode='from_scratch',
    !pseudo_dir='directory where pseudopotentials are stored/',
    !outdir='directory where large files are written/'
    pseudo_dir='/home/cjfoss/espresso-5.1/pseudo/',
    outdir='/home/cjfoss/espresso-5.1/2dout'
    prefix='mose2PH_v7',
 /
 &system
    ibrav=4, celldm(1)=6.2134195, celldm(3)=8,
    nat=3, ntyp=2, ecutwfc =140
 /
 &electrons
    conv_thr =  1.0d-14
    mixing_beta = 0.7
 /
&ions
    ion_dynamics='bfgs'
/
ATOMIC_SPECIES
 Mo  95.94    Mo.pw-mt_fhi.UPF
 Se  78.96    Se.pw-mt_fhi.UPF
ATOMIC_POSITIONS alat
Se       0.000000000   0.000000000   3.000000000 1 1 1
Mo       0.500000000   0.288675135   3.493465193 1 1 1
Se       0.000000000   0.000000000   3.986930347 1 1 1
K_POINTS automatic
 6 6 4 1 1 1

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.

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)

A third question: Is there perhaps a better way to perform a relaxation
calculation? or am I oversimplifying the system -- that is MoSe2 consists
of a transition metal (Mo) and 2 chalcogens (Se), are there additional
parameters that should be stated that I am leaving out?

Best regards,
Cameron
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