Dear Anton, thank you a lot for your reply!<div><br></div><div>Could you please have a look at cell setting for my other surfaces? I would like to know that I got it correct.</div><div>I have Li(100) bcc here, with a=b=c= 3.51 A </div><div>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</div><div><br></div><div>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</div><div><br></div><div>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</div><div>Do you think it's correct?</div><div><br></div><div>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?</div><div><br></div><div>When I do geometry optimisation with GC optimiser, I use only following in QS section.</div><div> &QS</div><div> EPS_DEFAULT 1.0E-12</div><div> WF_INTERPOLATION ASPC</div><div> &END QS</div><div>However, I saw people specify it in this way to highlight GPW method</div><div><div> &QS</div><div> METHOD GPW</div><div> EXTRAPOLATION USE_GUESS</div><div> &END QS</div></div><div>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?</div><div><br></div><div>Regards,</div><div>Dmitrii</div><div><img alt="Screen Shot 2020-11-18 at 4.54.18 pm.png" data-iml="1626782.4200000032" width="756px" height="477px" src="cid:13c4b00b-3c1b-4c52-b684-e21f229cb1c1"><img alt="Screen Shot 2020-11-18 at 5.07.10 pm.png" data-iml="1626782.5350000057" width="756px" height="488px" src="cid:eba7b863-fdab-495f-a9fd-6a8a6cba8ef6"></div><div><br></div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, November 17, 2020 at 11:26:07 PM UTC+11 ant...@gmail.com wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear Dmitrii,
<br>
<br>17.11.20 03:37, DMITRII Drugov пише:
<br>> I built Au(111) slab with a= 4.07825
<br>
<br>a= 4.07825 is the cell dimension of the gold structure itself. The
<br>symmetry of the (111) slab is hexagonal with a = b = 5.76752
<br>(4.07825*sqrt(2)) and gamma = 120. You can use Avogadro to build the
<br>slab and calculate the dimensions of the new "cell", but better consider
<br>this topic to choose
<br><a href="https://groups.google.com/d/msgid/cp2k/9d5922dc-c114-4bf1-bbc8-4b576728d29bn%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/9d5922dc-c114-4bf1-bbc8-4b576728d29bn%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1605764628157000&usg=AFQjCNEFcjggErSbwdDk9qfVkgKjziOojA">https://groups.google.com/d/msgid/cp2k/9d5922dc-c114-4bf1-bbc8-4b576728d29bn%40googlegroups.com?utm_medium=email&utm_source=footer</a>
<br>, as Avogadro could be a bit tricky in this regard.
<br>
<br>So finally you have:
<br>
<br>ABC 17.30256 17.30256 50.0
<br>
<br>ALPHA_BETA_GAMMA 90.0 90.0 120.0
<br>
<br>You should leave enough layers of gold atoms ("thickness") in the slab
<br>and enough space for vacuum. Ideally, you should start from 4--6 layers
<br>and 30-50 A for the third dimension and check convergence of the results
<br>in respect to these parameters. Use that paper to see what to expect
<br>(however, you should be aware of the metallic nature of your system).
<br>
<br>In principle, I see no reason to fix any atom in the DFT optimization
<br>(it could be reasonable for MM or semiempirics, but Au-Au and
<br>Au-whatever interactions are well described via DFT). If the geometry is
<br>built correctly, no devastation of the metal layer will happen. If you
<br>see any notable disorder at the equilibrium, I would double-check the
<br>setup rather than try to fix the atoms.
<br>
<br>Periodicity in x and y dimensions (within the slab plane) is a must in
<br>your case (if you want to deal with 2D layer rather than nanoparticle).
<br>Regarding Z direction, it depends on your study, you can try both cases
<br>and compare the results. With PBC along z axis, you should provide
<br>really large z to exclude spurious self-interactions. Without PBC along
<br>z, you might be unable to provide some studies reasonably, face
<br>unexpected issues or just have scarce literature base for comparison.
<br>
<br>Hope that helps.
<br>
<br>Yours,
<br>
<br>Anton
<br>
<br>
<br></blockquote></div>