[CP2K-user] [CP2K:14238] Re: Geometry optimisation of organic molecule on fcc Au(111) slab

[DMITRII Drugov]

Dear Anton, thank you a lot for your reply!

Could you please have a look at cell setting for my other surfaces? I would 
like to know that I got it correct.
I have Li(100) bcc here, with a=b=c= 3.51 A 
my XZY file gave me  14.04000000  14.04000000   3.51000000. My CP2K cell 
parameters should be ABC 14.04000000  14.04000000   50.0000 with 
ALPHA_BETA_GAMMA 90 90 90

For graphite as length = 2*sqrt(3)*a , where a=b=2.46 and c (interlayer 
distance) = 6.71A. The surface has about 4 a in xy and it is hexagonal. So 
CP2K cell parameters will be ABC 13.84 13.32 50 with ALPHA_BETA_GAMMA 90 90 
120

For Si(100), a = 3.867 A. It's also fcc and hexagonal, I found ABC 21.87 
21.87 50.00 ALPHA_BETA_GAMMA 90 90 120
Do you think it's correct?

Also, do you think I need to set up different GPW cutoff and real_cutoff 
for each system individually? Or I can use one cutoff for these four 
different surfaces to calculate adsorption of organic molecule?

When I do geometry optimisation with GC optimiser, I use only following in 
QS section.
 &QS
      EPS_DEFAULT 1.0E-12
      WF_INTERPOLATION ASPC
    &END QS
However, I saw people specify it in this way to highlight GPW method
    &QS
      METHOD GPW
      EXTRAPOLATION USE_GUESS
    &END QS
Do you think which one is correct for geometry optimisation? For 
calculation of Eab, I can use total energy of system for the last step of 
optimization? I don't need to take final structure and run energy 
calculation again, unless I need some charge density distribution etc?

Regards,
Dmitrii
[image: Screen Shot 2020-11-18 at 4.54.18 pm.png][image: Screen Shot 
2020-11-18 at 5.07.10 pm.png]


On Tuesday, November 17, 2020 at 11:26:07 PM UTC+11 ant... at gmail.com 
wrote:

> Dear Dmitrii,
>
> 17.11.20 03:37, DMITRII Drugov пише:
> > I built Au(111) slab with a= 4.07825 
>
> a= 4.07825 is the cell dimension of the gold structure itself. The
> symmetry of the (111) slab is hexagonal with a = b = 5.76752
> (4.07825*sqrt(2)) and gamma = 120. You can use Avogadro to build the
> slab and calculate the dimensions of the new "cell", but better consider
> this topic to choose
>
> https://groups.google.com/d/msgid/cp2k/9d5922dc-c114-4bf1-bbc8-4b576728d29bn%40googlegroups.com?utm_medium=email&utm_source=footer
> , as Avogadro could be a bit tricky in this regard.
>
> So finally you have:
>
> ABC 17.30256 17.30256 50.0
>
> ALPHA_BETA_GAMMA 90.0 90.0 120.0
>
> You should leave enough layers of gold atoms ("thickness") in the slab
> and enough space for vacuum. Ideally, you should start from 4--6 layers
> and 30-50 A for the third dimension and check convergence of the results
> in respect to these parameters. Use that paper to see what to expect
> (however, you should be aware of the metallic nature of your system).
>
> In principle, I see no reason to fix any atom in the DFT optimization
> (it could be reasonable for MM or semiempirics, but Au-Au and
> Au-whatever interactions are well described via DFT). If the geometry is
> built correctly, no devastation of the metal layer will happen. If you
> see any notable disorder at the equilibrium, I would double-check the
> setup rather than try to fix the atoms.
>
> Periodicity in x and y dimensions (within the slab plane) is a must in
> your case (if you want to deal with 2D layer rather than nanoparticle).
> Regarding Z direction, it depends on your study, you can try both cases
> and compare the results. With PBC along z axis, you should provide
> really large z to exclude spurious self-interactions. Without PBC along
> z, you might be unable to provide some studies reasonably, face
> unexpected issues or just have scarce literature base for comparison.
>
> Hope that helps.
>
> Yours,
>
> Anton
>
>
>
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