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Hello Thomas,</div>
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Yes, the box size should be converged for the dipole corrections specified (over twice the length in the z-direction of the initial system itself). I've just ran a few tests using an incredibly large box size (50 Ang) and the enthalpy value remains similarly
low compared to literature values. <br>
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I'm thinking your second suggestion is quite likely. The calculation does output a non-local correlation energy in the high verbosity mode, but perhaps the relevant terms aren't being added correctly in the final total energy. I will report back once I've looked
into this more thoroughly. <br>
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Thank you for your input<br>
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Kind regards,</div>
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Gabriel <br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Tamas Karpati <tkarpati@gmail.com><br>
<b>Sent:</b> 08 October 2020 07:51<br>
<b>To:</b> Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
<b>Subject:</b> Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW</font>
<div> </div>
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<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Dear Gabriel,<br>
By "consistent box" sizes do you mean that you have<br>
converged the box sizes for all three species?<br>
I rather meant the exact same box size for all<br>
(and this size be converged, ie. large enough for each).<br>
<br>
BTW, the systematic differences you observed might be<br>
due to a vdW (or another) term switched on/off<br>
(or a bug/error in code/functional).<br>
Make sure, everything is treated appropriately.<br>
For instance, input_dft can be trickier than you expect 1st.<br>
Doubly disperse the functional (in both input_dft and<br>
vdw_corr) might do sg. similar.<br>
Bests,<br>
t<br>
<br>
On Wed, Oct 7, 2020 at 2:17 PM Gabriel Bramley <G.A.Bramley@soton.ac.uk> wrote:<br>
><br>
> Hello Thomas,<br>
><br>
> 1/2<br>
><br>
> They haven't specified any parameters to my knowledge that would lead to such a large error. There may be slight difference in the thresholds of energetic convergence, but they should yield errors on a much smaller scale.<br>
><br>
> 2/2<br>
><br>
> RE: box sizes - We did briefly fall foul of having inconsistent box sizes for one or two calculations, but this is definitely a problem we've addressed. (We use slightly different box sizes for the adsorbate, but I've ran a few different cell sizes for this
small molecules and it yielded very small differences).<br>
><br>
> And you're quite right, I do apologise, that should be written as:<br>
> E_adsorption = E_(slab+adsorbate) - (E_slab + E_adsorbate)<br>
><br>
> Kind regards,<br>
> Gabriel<br>
><br>
><br>
> ________________________________<br>
> From: users <users-bounces@lists.quantum-espresso.org> on behalf of Tamas Karpati <tkarpati@gmail.com><br>
> Sent: 07 October 2020 11:57<br>
> To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
> Subject: Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW<br>
><br>
> Dear Gabriel,<br>
><br>
> 1/2, are your sims. reproducing *all* of the ref. params? (eg. are<br>
> cell parameters the same?)<br>
> any missing params. would contribute by adding an *unknown*<br>
> magnitude of error...<br>
> 2/2, my guess would be that your evaluation of dE_a is wrong due to<br>
> *different cell sizes*<br>
> (basis set superposition error?); this would explain the<br>
> systematic character of the deviation<br>
> and suggest (pain indeed) to increase cell sizes up to the same<br>
> (ie. the largest) of<br>
> E_slab+ads, E_slab and E_adsorbant.<br>
> +1, your eq. for the heat is recursive (kidding): LHS is to be renamed!<br>
><br>
> HTH,<br>
> t<br>
><br>
> On Wed, Oct 7, 2020 at 12:19 PM Gabriel Bramley <G.A.Bramley@soton.ac.uk> wrote:<br>
> ><br>
> > Dear Users,<br>
> ><br>
> > Problem:<br>
> ><br>
> > I am performing calculations with the optB88-vdW functional to obtain adsorption energies of small aromatic molecules on metallic surface facets (Pt(111) and phenol for the cases discussed here). Unfortunately, the adsorption energies obtained from these
calculations are systematically 50 kJ mol^-1 below comparable studies performed with VASP. I have replicated their parameters as closely as possible - as such I am also using PBE PAW pseudopotentials from the psl pseudopotential library.<br>
> ><br>
> > The above underestimation occurs for a fully periodic calculation. Using the dipole corrections (2D and ESM (bc1)) appears to exacerbate these issues, leading to a 70 kJ mol^-1 underestimation of the adsorption energy. (The system is centred in the centre
of the cell with 8 Ang of vacuum either side of the system for 2D, and the system is centred around z=0 for ESM).<br>
> ><br>
> > The calculation for adsorption energy is performed as:<br>
> > E_ads = E_slab+ads - (E_slab + E_ads)<br>
> > Where the adsorbate is calculated in a 30x30x30 Ang cell with the Markov-Payne dipole correction (Though this give negligable difference compared to full PBC).<br>
> ><br>
> > Question:<br>
> ><br>
> > The PBE+rvv10 functional performs significantly better with PBC and 2D Coulomb Cutoff, giving sensible and expected values for the adsorption energy. However, I am cautious in trusting these results given the large errors for the optB88-vdW functional.
Is there something obvious I am missing in these calculations or is this a known issue?<br>
> ><br>
> > A previous email to this list has pointed out other issues with this functional (<a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mail-archive.com%2Fusers%40lists.quantum-espresso.org%2Fmsg35965.html&data=01%7C01%7CG.A.Bramley%40soton.ac.uk%7Ca960b2172e5c4a00549408d86b5656b7%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=P4%2Fh0MgP2GH7WkQExoP3zUqs81S5rZUt7PLfswiF9jE%3D&reserved=0">https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mail-archive.com%2Fusers%40lists.quantum-espresso.org%2Fmsg35965.html&data=01%7C01%7CG.A.Bramley%40soton.ac.uk%7Ca960b2172e5c4a00549408d86b5656b7%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=P4%2Fh0MgP2GH7WkQExoP3zUqs81S5rZUt7PLfswiF9jE%3D&reserved=0</a>).
This might help, but could someone please clarify this as well?<br>
> ><br>
> > Additional information:<br>
> ><br>
> > I am using QE v.6.5 compiled with Intel-2018 with the ELPA 2017 library. Enivron Module installed but not used in these calculations. All QC tests pass without error.<br>
> ><br>
> > Please find below the input file:<br>
> ><br>
> > ___________________________________<br>
> ><br>
> > &CONTROL<br>
> > calculation = 'relax'<br>
> > restart_mode = 'from_scratch'<br>
> > prefix = 'Pt'<br>
> > disk_io = 'low'<br>
> > pseudo_dir = '/home/gab1u17/pslib-kj-paw/'<br>
> > nstep = 300<br>
> > /<br>
> > &SYSTEM<br>
> > ibrav = 0<br>
> > ecutwfc = 45<br>
> > ecutrho = 360<br>
> > occupations = 'smearing'<br>
> > degauss = 0.05<br>
> > smearing = 'gaussian'<br>
> > input_dft = 'vdw-df-obk8'<br>
> > assume_isolated = '2D'<br>
> > ntyp = 4<br>
> > nat = 48<br>
> > /<br>
> > &ELECTRONS<br>
> > electron_maxstep = 150<br>
> > conv_thr = 8e-08<br>
> > mixing_mode = 'local-TF'<br>
> > mixing_beta = 0.2<br>
> > /<br>
> > &IONS<br>
> > ion_dynamics = 'bfgs'<br>
> > /<br>
> > &CELL<br>
> > /<br>
> ><br>
> > ATOMIC_SPECIES<br>
> > Pt 195.084 Pt.pbe-n-kjpaw_psl.1.0.0.UPF<br>
> > C 12.011 C.pbe-n-kjpaw_psl.1.0.0.UPF<br>
> > O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF<br>
> > H 1.008 H.pbe-n-kjpaw_psl.1.0.0.UPF<br>
> ><br>
> > K_POINTS automatic<br>
> > 6 6 1 0 0 0<br>
> ><br>
> > CELL_PARAMETERS angstrom<br>
> > 7.42718991274627 0.00000000000000 0.00000000000000<br>
> > 3.71359495637314 6.43213514316980 0.00000000000000<br>
> > 0.00000000000000 0.00000000000000 29.000000000003126<br>
> ><br>
> > ATOMIC_POSITIONS angstrom<br>
> > Pt 2.5641489000 0.4594382200 8.0000000000 0 0 0<br>
> > Pt 5.2167167200 1.3783146700 8.0000000000 0 0 0<br>
> > ...<br>
> > Pt 4.1556895900 0.1531460700 17.1683222700<br>
> > Pt 6.8082574200 1.0720225200 17.1683222700<br>
> > Pt 2.0336353300 1.9908989700 17.1683222700<br>
> > ...<br>
> > H 0.3060672802 1.6388023741 19.1376040000<br>
> > H 2.7167357186 1.0284278006 19.1376040000<br>
> > H 4.4562891110 2.8078620154 19.1376040000<br>
> ><br>
> > ___________________________________<br>
> ><br>
> > Thank you in advance for your assistance.<br>
> ><br>
> > Kind regards,<br>
> > Gabriel Bramley<br>
> > PhD. Candidate<br>
> > University of Southampton<br>
> ><br>
> > _______________________________________________<br>
> > Quantum ESPRESSO is supported by MaX (<a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=01%7C01%7CG.A.Bramley%40soton.ac.uk%7Ca960b2172e5c4a00549408d86b5656b7%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=eJ6nJJX91k68emovHJF3H0dqCnEnAB5Hdpx4U12hujY%3D&reserved=0">https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=01%7C01%7CG.A.Bramley%40soton.ac.uk%7Ca960b2172e5c4a00549408d86b5656b7%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=eJ6nJJX91k68emovHJF3H0dqCnEnAB5Hdpx4U12hujY%3D&reserved=0</a>)<br>
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