[Pw_forum] How to set the atomic position in ESM model with QE from Yuanqing Wang

[Minoru Otani]

Dear Yuanqing,

If you assume the unit cell is located from z=0 to z=L (L is the cell size along z-direction),
the slab will appear at bottom/top region of the cell. But in an ESM calculation, this is not
the case. The unit cell is located from z=-L/2 to z=L/2 and the slab located in the center
of the cell (around z=0). Please look at the following web site:
http://sugino.issp.u-tokyo.ac.jp/esm/index.php?SIESTA%2BESM%20Manual
Although this is a manual page for the SIESTA version of ESM, you can easily understand
the position of atoms and ESMs (see “Features” section).

Please remember that you need sufficient vacuum region (typically 8A each) between slab
and both ESMs.

Best regards,
Minoru

--------------------------------------------------------------------------------------------------------
Minoru Otani
National Institute of Advanced Industrial Science and Technology
Research Centre for Computational Design of Advanced Functional Materials
email : minoru.otani at aist.go.jp
---------------------------------------------------------------------------------------------------------

> On Mar 1, 2016, at 8:14 PM, ＷＡＮＧ ＹＵＡＮＱＩＮＧ <yuanqing.wang at riken.jp> wrote:
> 
> Dear all,
> 
> Hi. I have some puzzles when I study the ESM example in QE. The example shown below seems that there are two slabs in one unit cell if the unit cell does not repeat in the z direction in the ESM model. I am not sure if this understanding is correct. If I just want to simulate a electrochemical cell, should the metal slab just arrange in the position with z>0 ? Thank you very much!
> 
> Best regards,
> 
> Yuanqing Wang
> 
> 
> 
> 
> # scf calculation for Al(111) with ESM bc3 (vacuum-slab-metal), - charged
> &control
>    calculation='scf',
>    restart_mode='from_scratch',
>    prefix='Al111',
>    pseudo_dir = '/home/wang/Program/espresso-5.1.2/pseudo/',
>    outdir= './',
>    tprnfor = .TRUE.
> /
> &system
>    ibrav = 0, celldm(1) = 7.653393855, 
>    tot_charge = -0.005,
>    nat= 7, ntyp= 1,
>    ecutwfc = 20.0,
>    nosym=.TRUE.
>    occupations='smearing', smearing='mp', degauss=0.05
>    assume_isolated='esm', esm_bc='bc3'
> /
> &electrons
>    mixing_beta = 0.5
> /
> ATOMIC_SPECIES
> Al  26.981538   Al.pbe-rrkj.UPF
> CELL_PARAMETERS hexagonal
> 0.707106781    0.000000000  0.000000000
> 0.353553390    0.612372436  0.000000000
> 0.000000000    0.000000000 10.000000000
> ATOMIC_POSITIONS angstrom
> Al 0.00000    0.00000   -7.01481
> Al 0.00000    1.65341   -4.67654
> Al 1.43189    0.82670   -2.33827
> Al 0.00000    0.00000    0.00000
> Al 0.00000    1.65341    2.33827
> Al 1.43189    0.82670    4.67654
> Al 0.00000    0.00000    7.01481
> K_POINTS automatic
> 8 8 1 0 0 0
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum