Dear Gabriel,
1, The same box size everywhere, or not?
2, QE reports near the beginning of its output a series of 6 or 7 numbers,
each indicating a term in the functional. Cannot now recall which
but -if you cannot find- I can check in a week the source file that
actually lists them (just easy comments, no code).
Also, if a dispersion term is applied pw.x reports it somewhat below
(in connection with the vdw_corr input parameter).
I hope it helps to identify what theory you are actually using.
(Note: input_dft overwrites the functional specification of the UPF file
but vdW terms are just additive, not exclusive -if i'm correct).
HTH.
t
On Fri, Oct 9, 2020 at 3:28 PM Gabriel Bramley <[email protected]> wrote:
>
> Hello Thomas,
>
> 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.
>
> 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.
>
> Thank you for your input
>
> Kind regards,
> Gabriel
> ________________________________
> From: users <[email protected]> on behalf of Tamas
> Karpati <[email protected]>
> Sent: 08 October 2020 07:51
> To: Quantum ESPRESSO users Forum <[email protected]>
> Subject: Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW
>
> Dear Gabriel,
> By "consistent box" sizes do you mean that you have
> converged the box sizes for all three species?
> I rather meant the exact same box size for all
> (and this size be converged, ie. large enough for each).
>
> BTW, the systematic differences you observed might be
> due to a vdW (or another) term switched on/off
> (or a bug/error in code/functional).
> Make sure, everything is treated appropriately.
> For instance, input_dft can be trickier than you expect 1st.
> Doubly disperse the functional (in both input_dft and
> vdw_corr) might do sg. similar.
> Bests,
> t
>
> On Wed, Oct 7, 2020 at 2:17 PM Gabriel Bramley <[email protected]>
> wrote:
> >
> > Hello Thomas,
> >
> > 1/2
> >
> > 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.
> >
> > 2/2
> >
> > 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).
> >
> > And you're quite right, I do apologise, that should be written as:
> > E_adsorption = E_(slab+adsorbate) - (E_slab + E_adsorbate)
> >
> > Kind regards,
> > Gabriel
> >
> >
> > ________________________________
> > From: users <[email protected]> on behalf of Tamas
> > Karpati <[email protected]>
> > Sent: 07 October 2020 11:57
> > To: Quantum ESPRESSO users Forum <[email protected]>
> > Subject: Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW
> >
> > Dear Gabriel,
> >
> > 1/2, are your sims. reproducing *all* of the ref. params? (eg. are
> > cell parameters the same?)
> > any missing params. would contribute by adding an *unknown*
> > magnitude of error...
> > 2/2, my guess would be that your evaluation of dE_a is wrong due to
> > *different cell sizes*
> > (basis set superposition error?); this would explain the
> > systematic character of the deviation
> > and suggest (pain indeed) to increase cell sizes up to the same
> > (ie. the largest) of
> > E_slab+ads, E_slab and E_adsorbant.
> > +1, your eq. for the heat is recursive (kidding): LHS is to be renamed!
> >
> > HTH,
> > t
> >
> > On Wed, Oct 7, 2020 at 12:19 PM Gabriel Bramley <[email protected]>
> > wrote:
> > >
> > > Dear Users,
> > >
> > > Problem:
> > >
> > > 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.
> > >
> > > 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).
> > >
> > > The calculation for adsorption energy is performed as:
> > > E_ads = E_slab+ads - (E_slab + E_ads)
> > > 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).
> > >
> > > Question:
> > >
> > > 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?
> > >
> > > A previous email to this list has pointed out other issues with this
> > > functional
> > > (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).
> > > This might help, but could someone please clarify this as well?
> > >
> > > Additional information:
> > >
> > > 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.
> > >
> > > Please find below the input file:
> > >
> > > ___________________________________
> > >
> > > &CONTROL
> > > calculation = 'relax'
> > > restart_mode = 'from_scratch'
> > > prefix = 'Pt'
> > > disk_io = 'low'
> > > pseudo_dir = '/home/gab1u17/pslib-kj-paw/'
> > > nstep = 300
> > > /
> > > &SYSTEM
> > > ibrav = 0
> > > ecutwfc = 45
> > > ecutrho = 360
> > > occupations = 'smearing'
> > > degauss = 0.05
> > > smearing = 'gaussian'
> > > input_dft = 'vdw-df-obk8'
> > > assume_isolated = '2D'
> > > ntyp = 4
> > > nat = 48
> > > /
> > > &ELECTRONS
> > > electron_maxstep = 150
> > > conv_thr = 8e-08
> > > mixing_mode = 'local-TF'
> > > mixing_beta = 0.2
> > > /
> > > &IONS
> > > ion_dynamics = 'bfgs'
> > > /
> > > &CELL
> > > /
> > >
> > > ATOMIC_SPECIES
> > > Pt 195.084 Pt.pbe-n-kjpaw_psl.1.0.0.UPF
> > > C 12.011 C.pbe-n-kjpaw_psl.1.0.0.UPF
> > > O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF
> > > H 1.008 H.pbe-n-kjpaw_psl.1.0.0.UPF
> > >
> > > K_POINTS automatic
> > > 6 6 1 0 0 0
> > >
> > > CELL_PARAMETERS angstrom
> > > 7.42718991274627 0.00000000000000 0.00000000000000
> > > 3.71359495637314 6.43213514316980 0.00000000000000
> > > 0.00000000000000 0.00000000000000 29.000000000003126
> > >
> > > ATOMIC_POSITIONS angstrom
> > > Pt 2.5641489000 0.4594382200 8.0000000000 0 0 0
> > > Pt 5.2167167200 1.3783146700 8.0000000000 0 0 0
> > > ...
> > > Pt 4.1556895900 0.1531460700 17.1683222700
> > > Pt 6.8082574200 1.0720225200 17.1683222700
> > > Pt 2.0336353300 1.9908989700 17.1683222700
> > > ...
> > > H 0.3060672802 1.6388023741 19.1376040000
> > > H 2.7167357186 1.0284278006 19.1376040000
> > > H 4.4562891110 2.8078620154 19.1376040000
> > >
> > > ___________________________________
> > >
> > > Thank you in advance for your assistance.
> > >
> > > Kind regards,
> > > Gabriel Bramley
> > > PhD. Candidate
> > > University of Southampton
> > >
> > > _______________________________________________
> > > Quantum ESPRESSO is supported by MaX
> > > (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)
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> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX
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> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX
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> _______________________________________________
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