Dear Gabriel, Good news. I assume ecutwfc (+ecutrho) and k point density are also the same (thus having the same amount of systematic offset). I guess the deviation is from another source. One more thing I can think of is the basis being used. Is it possible for you to use the exact same PW basis in each software? I hope so. If not, I have no idea -except for an implementation difference...
I rechecked the corresponding source and found (also referred to by INPUT_PW.html @ input_dft) it to be Modules/funct.f90. I do not know how it relates to the LIBXC+QE combo, guess it's just the QE internal machinery -with a useful list of functionals and numbering in the lengthy comments. I hope it helps but I cannot contribute more to this. Good luck, t On Thu, Oct 15, 2020 at 12:32 AM Gabriel Bramley <g.a.bram...@soton.ac.uk> wrote: > > Dear Thomas, > > Apologies for the lack of clarity. Yes, they are. > I have checked this and they appear correct. I believe the numbers represent > (exchange, correlation, gradient corrected exchange, gradient corrected > correlation, meta GGA and vdW (non-local correlation) correction). obk8 is > specified as (slater, Perdew Wang, optB88x, p86c, no meta GGA, no vdW > correction) and vdwdf-obk8 is specified as (slater, Perdew Wang, optB88x, no > gradient corrected correlation, no meta GGA, DF-vdW1), which looks correct to > me, as the E_xc term in the original optB88-vdW paper consists of E_xc = > E^GGA_x + E^LDA_c + E^nl(vdW)_c. However, there might be some nuance I am > missing. Further, I've had a look in the code itself (xc_df_vdW) and how it > relates to the core PW-SCF and nothing jumps out as being out of the > ordinary, but I'm not familiar enough with the QE code to make a complete > judgement on that. > > I've run further calculations with the LIBXC library (using their > version of optb88 exchange), and that doesn't yield improvement either. > > Kind regards, > Gabriel Bramley > ________________________________ > From: users <users-boun...@lists.quantum-espresso.org> on behalf of Tamas > Karpati <tkarp...@gmail.com> > Sent: 12 October 2020 12:53 > To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> > Subject: Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW > > 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 <g.a.bram...@soton.ac.uk> > 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 <users-boun...@lists.quantum-espresso.org> on behalf of Tamas > > Karpati <tkarp...@gmail.com> > > Sent: 08 October 2020 07:51 > > To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> > > 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 <g.a.bram...@soton.ac.uk> > > 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 <users-boun...@lists.quantum-espresso.org> on behalf of Tamas > > > Karpati <tkarp...@gmail.com> > > > Sent: 07 October 2020 11:57 > > > To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> > > > 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 <g.a.bram...@soton.ac.uk> > > > 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%7Ce7b35ab073dc4cc9a68a08d86ea51d66%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=zfeVtqdRVTvvp3MYkR8pF3I5PdmU2zAntcOC5GqNx20%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. 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