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%7Cff146e0c9f8442a6502408d86aaf85d0%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=XIGDLm5GiwsmCuyJjhxr3hvWbAc7nah5%2BXHAw1JzxHY%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%7Cff146e0c9f8442a6502408d86aaf85d0%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=1iFjhj4tqm%2FF7Zmv5ob6KOGFn328kB6fdI5BpmoeUSY%3D&reserved=0) > > users mailing list [email protected] > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=01%7C01%7CG.A.Bramley%40soton.ac.uk%7Cff146e0c9f8442a6502408d86aaf85d0%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=Lv7plWOT%2B3hGuARAi%2BVgBKu51t94mxKdcmCP5J%2BIZug%3D&reserved=0 > _______________________________________________ > 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%7Cff146e0c9f8442a6502408d86aaf85d0%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=1iFjhj4tqm%2FF7Zmv5ob6KOGFn328kB6fdI5BpmoeUSY%3D&reserved=0) > users mailing list [email protected] > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=01%7C01%7CG.A.Bramley%40soton.ac.uk%7Cff146e0c9f8442a6502408d86aaf85d0%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=Lv7plWOT%2B3hGuARAi%2BVgBKu51t94mxKdcmCP5J%2BIZug%3D&reserved=0 > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list [email protected] https://lists.quantum-espresso.org/mailman/listinfo/users
