[QE-users] N2 adsorption on Na surface
Kazume NISHIDATE
nisidate at iwate-u.ac.jp
Fri Nov 8 23:18:14 CET 2024
Dear Federico
You specify the option assume_isolated = '2D' to truncate the
periodic Coulomb interaction along the c axis. However, your structure
may need to be revised for this purpose.
I think you need to shift all of the atomic positions upward by 7.5 A,
half of the vacuum gap (15 A) so that the center of the vacuum region
will be at the boundary.
Also, in general, it is not necessary to put the N2 molecule on both
sides of the slab if you securely truncate the Coulomb interaction over
the cyclic boundary.
Before you proceed, you should check the potential distribution along
the c-axis which can be done by pp.x (plot_num=11) and average it in
the xy plane with the average.x.
Also, the bond length of the molecule may be different from its isolated
neutral state if there is a significant charge transfer between the
molecule and the surface.
Good luck.
Sincerely,
Kazume
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> 2024/11/09 1:29?Federico Verdicchio <federico.verdicchio at unicam.it>????:
>
> Dear all
> I am attempting to simulate the adsorption of an N? molecule on a Na(100) slab using QE. In my input file, I?m using a 12-layer Na 2x2 supercell with a 15 ? vacuum gap. I have kept the interlayers fixed, allowing only the top 3 surface layers on both ends to relax, with an N? molecule on each surface oriented perpendicular to the slab.
> Additionally, I am using:
> ? The DFT-D3 van der Waals correction
> ? assume_isolated=2D to truncate interactions along the z-axis
> ? nspin=2 to allow for unconstrained polarization
> The calculation has not yet converged, but it appears to be resulting in a shortening of the N?N bond, which is the opposite of what I expected.
> Am I missing something here?
> Thank you for any suggestions!
>
> Sincerely,
> Federico
>
> Input file:
> &CONTROL
> calculation = 'relax'
> etot_conv_thr = 1.0000000000d-04
> forc_conv_thr = 1.0000000000d-03
> outdir = ""
> prefix = ""
> pseudo_dir = "./SSSP_precision_pseudos"
> verbosity = 'low'
> restart_mode='from_scratch'
> /
>
> &SYSTEM
> ibrav = 0
> A = 8.30638
> nat = 52
> ntyp = 2
> ecutrho = 385 ! *11
> ecutwfc = 35
> occupations = 'smearing'
> smearing = 'gaussian'
> degauss = 0.01
> assume_isolated = '2D'
> vdw_corr = 'dft-d3'
> nspin = 2
> starting_magnetization(1)= 0 ! Na
> starting_magnetization(2)= 0.1 ! N
> /
>
> &ELECTRONS
> conv_thr = 1.0000000000d-6 ! Default
> electron_maxstep = 200
> mixing_beta = 4.0000000000d-01
> /
>
> &IONS
> ion_dynamics = 'bfgs'
> /
>
> CELL_PARAMETERS {alat}
> 1.000000000000000 0.000000000000000 0.000000000000000
> 0.000000000000000 1.000000000000000 0.000000000000000
> 0.000000000000000 0.000000000000000 4.683585508970213
> ATOMIC_SPECIES
> Na 22.98900 Na.paw.z_9.ld1.psl.v1.0.0-low.upf
> N 14.00650 N.oncvpsp.upf
> ATOMIC_POSITIONS {crystal}
> Na 0.000000000000000 0.000000000000000 -0.000032000000000 1 1 1
> Na 0.000000000000000 0.500000000000000 -0.000032000000000 1 1 1
> Na 0.500000000000000 0.000000000000000 -0.000032000000000 1 1 1
> Na 0.500000000000000 0.500000000000000 -0.000032000000000 1 1 1
> Na 0.000000000000000 0.000000000000000 0.106684000000000 1 1 1
> Na 0.000000000000000 0.500000000000000 0.106684000000000 1 1 1
> Na 0.500000000000000 0.000000000000000 0.106684000000000 1 1 1
> Na 0.500000000000000 0.500000000000000 0.106684000000000 1 1 1
> Na 0.000000000000000 0.000000000000000 0.213377000000000 0 0 0
> Na 0.000000000000000 0.500000000000000 0.213377000000000 0 0 0
> Na 0.500000000000000 0.000000000000000 0.213377000000000 0 0 0
> Na 0.500000000000000 0.500000000000000 0.213377000000000 0 0 0
> Na 0.000000000000000 0.000000000000000 0.320068000000000 0 0 0
> Na 0.000000000000000 0.500000000000000 0.320068000000000 0 0 0
> Na 0.500000000000000 0.000000000000000 0.320068000000000 0 0 0
> Na 0.500000000000000 0.500000000000000 0.320068000000000 0 0 0
> Na 0.000000000000000 0.000000000000000 0.426760000000000 0 0 0
> Na 0.000000000000000 0.500000000000000 0.426760000000000 0 0 0
> Na 0.500000000000000 0.000000000000000 0.426760000000000 0 0 0
> Na 0.500000000000000 0.500000000000000 0.426760000000000 0 0 0
> Na 0.000000000000000 0.000000000000000 0.533446000000000 1 1 1
> Na 0.000000000000000 0.500000000000000 0.533446000000000 1 1 1
> Na 0.500000000000000 0.000000000000000 0.533446000000000 1 1 1
> Na 0.500000000000000 0.500000000000000 0.533446000000000 1 1 1
> Na 0.250000000000000 0.250000000000000 0.053371000000000 1 1 1
> Na 0.250000000000000 0.750000000000000 0.053371000000000 1 1 1
> Na 0.750000000000000 0.250000000000000 0.053371000000000 1 1 1
> Na 0.750000000000000 0.750000000000000 0.053371000000000 1 1 1
> Na 0.250000000000000 0.250000000000000 0.160012000000000 0 0 0
> Na 0.250000000000000 0.750000000000000 0.160012000000000 0 0 0
> Na 0.750000000000000 0.250000000000000 0.160012000000000 0 0 0
> Na 0.750000000000000 0.750000000000000 0.160012000000000 0 0 0
> Na 0.250000000000000 0.250000000000000 0.266740000000000 0 0 0
> Na 0.250000000000000 0.750000000000000 0.266740000000000 0 0 0
> Na 0.750000000000000 0.250000000000000 0.266740000000000 0 0 0
> Na 0.750000000000000 0.750000000000000 0.266740000000000 0 0 0
> Na 0.250000000000000 0.250000000000000 0.373399000000000 0 0 0
> Na 0.250000000000000 0.750000000000000 0.373399000000000 0 0 0
> Na 0.750000000000000 0.250000000000000 0.373399000000000 0 0 0
> Na 0.750000000000000 0.750000000000000 0.373399000000000 0 0 0
> Na 0.250000000000000 0.250000000000000 0.480132000000000 1 1 1
> Na 0.250000000000000 0.750000000000000 0.480132000000000 1 1 1
> Na 0.750000000000000 0.250000000000000 0.480132000000000 1 1 1
> Na 0.750000000000000 0.750000000000000 0.480132000000000 1 1 1
> Na 0.250000000000000 0.250000000000000 0.586794000000000 1 1 1
> Na 0.250000000000000 0.750000000000000 0.586794000000000 1 1 1
> Na 0.750000000000000 0.250000000000000 0.586794000000000 1 1 1
> Na 0.750000000000000 0.750000000000000 0.586794000000000 1 1 1
> N 0.500000000000000 0.250000000000000 0.638203000000000 1 1 1
> N 0.500000000000000 0.250000000000000 0.667799000000000 1 1 1
> N 0.250000000000000 0.000000000000000 0.948559000000000 1 1 1
> N 0.250000000000000 0.000000000000000 0.918963000000000 1 1 1
> K_POINTS automatic
> 7 7 1 0 0 0
>
>
> --
> Federico Verdicchio
> Ph.D. in Chemical Sciences
> School of Science and Technology - Chemistry Division
> Via S. Agostino, 1
> 62032 Camerino (MC)
> Italy
> Phone: +39 334 2758061
>
????
Kazume NISHIDATE Ph.D
Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishidate at gmail.com, nisidate at iwate-u.ac.jp
https://sites.google.com/site/nisidatelab/
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