[Pw_forum] bfgs optimization not going anywhere
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Thu Nov 26 11:16:25 CET 2015
> As for the dispersion correction, the discussion is still open :-)
And we will not close it soon :-)
> to summarize: what would be 'the best' DFT correction on to of
> *existing* functionals, e.g. PBE for molecule-metal-interaction?
There is likely no best correction, but the best correction for a given system may be found by trial and error.
> As far as I understood, vdw-DF must be used with the corresponding pseudopotential
> (BTW, where one can get them?).
Look into the corresponding papers. They usually say which GGA flavour should be used to build the PPs. Then build (with pslibrary and ld1.x, for
example) and test them! For vdwdf revPBE is suggested to perform better than PBE, but I suppose that it could be interesting to see what happens in
the case of systems a bit larger than Ar dimers... I expect to find negligible differences in, e.g., adsorption energies and geometries of large
molecules interacting with surfaces if you use old PBE PPs rather than "equivalent" revPBE ones. But I may be wrong...
HTH
Giuseppe
On Thursday, November 26, 2015 07:24:27 AM Matej Huš wrote:
> Found the culprit!
> When I turned off the dipole correction, the system converged.
> Digging deeper, I found the underlying problem.
>
> I had been reckless and used the 'emaxpos' value unchanged from a different set of calculation, inadvertently setting it to too close to the edge of
> the vacuum. A change from 0.70 to 0.50 solved the problem.
>
> Thanks for the all contributions!
>
> As for the dispersion correction, the discussion is still open :-)
>
> Matej
>
> -----Original Message-----
> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Ilya Ryabinkin
> Sent: Tuesday, November 24, 2015 8:03 PM
> To: PWSCF Forum <pw_forum at pwscf.org>
> Subject: Re: [Pw_forum] bfgs optimization not going anywhere
>
> Colleagues,
> to summarize: what would be 'the best' DFT correction on to of
> *existing* functionals, e.g. PBE for molecule-metal-interaction? As far as I understood, vdw-DF must be used with the corresponding pseudopotential
> (BTW, where one can get them?).
>
> --
> I.
>
> On Tue, Nov 24, 2015 at 8:30 AM, Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it> wrote:
> > Dear Matej (and all)
> >
> >> As for DFT-D2, I admit I am a bit in the dark here. How 'wrong' is
> >> it? Or to put differently, is it more wrong that not using dispersion
> >> correction at all?
> >
> > Regarding the dispersion correction(s) this is the Stephan Grimme's
> > paper which indicates that DFT-D2 doubles the DFT-D3 interaction energy between molecules and metal surfaces:
> >
> > J. Chem. Phys. (2010) 132, 154104
> >
> > In my experience of phthalocyanine/metal interactions (but if I
> > remember well Ari has also performed calculations on
> > porphyrin/phthalocyanine molecules adsorbed on metal surfaces and he
> > can add his own knowledge), adsorption geometries and energies are
> > very different, so that the results are also quite different. See for
> > example this paper (Cu phthalocyanine interacting with Ag (100) with
> > DFT-D2)
> >
> > PRL 105, 115702 (2010)
> >
> > And my paper (TiO phthalocyanine interacting with Ag (100) with
> > vdW-DF)
> >
> > J. Phys. Chem. C 2014, 118, 5255
> >
> > And, yes, of course: if you use no dispersion correction you badly underestimate the interaction between the molecule and the surface...
> >
> > 2 more hints:
> >
> > 1) In the case of molecule/metal systems, ab initio functionals
> > modeling long distance correlation between electrons should be (in my
> > opinion) preferred to semiempirical functional with add pairwise
> > forces based on tabulations (or partial calculations) of C6
> > coefficients. There is a nice perspective written by J. L. Bredas
> > which addresses the issue
> >
> > Nature Nanotechnology
> > 8,
> > 230–231
> > (2013)
> >
> > 2) Regarding lattice parameters, Ari is right in the case of vdwdf.
> > But I've tried to simulate gold (bulk and) surfaces in contact with
> > molecules by using the reparametrized vdwdf-c09 functional: lattice parameter of gold is ok, and also molecule-surface interactions are expected
> > to be improved with respect to vdwdf!>
> >> Also, if I change/switch off the dispersion correction, then I will
> >> have to re-optimize all already converged structures (metal, isolated
> >> molecules, adsorbed intermediates), right? Looks rather tedious
> >
> > Yes, you should recalculate everything...:-(
> >
> > HTH
> > Giuseppe
> >
> > On Tuesday, November 24, 2015 11:37:45 AM Matej Huš wrote:
> >> Thanks for very useful comments.
> >>
> >> Yes, vacuum region is indeed too low in this example (whoops, seems
> >> like I've attached an old input file). I also ran a calculation with
> >> 10 A of vacuum without any improvement. Open shell is unnecessary as
> >> it quickly converges to a closed shell solution. I've just wasted
> >> some CPU time with that.
> >>
> >> Ectuwfc, ecutrhc are large enough (converged). I believe K points
> >> should also not be the source of a problem.
> >>
> >> As for DFT-D2, I admit I am a bit in the dark here. How 'wrong' is
> >> it? Or to put differently, is it more wrong that not using dispersion
> >> correction at all? How about vdw-DF, how do I turn it on and does it
> >> perform better? Where can I find more important about that?
> >>
> >> Also, if I change/switch off the dispersion correction, then I will
> >> have to re-optimize all already converged structures (metal, isolated
> >> molecules, adsorbed intermediates), right? Looks rather tedious
> >>
> >>
> >> Matej
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org]
> >> On Behalf Of Ari P Seitsonen
> >> Sent: Tuesday, November 24, 2015 11:22 AM
> >> To: PWSCF Forum <pw_forum at pwscf.org>
> >> Subject: Re: [Pw_forum] bfgs optimization not going anywhere
> >>
> >>
> >> Dear Matej Hus,
> >>
> >> Adding to the previous comments (I think that it is ok to use the
> >>
> >> k points, even though you might gain some CPU time by first indeed
> >> using Gamma-only and then increasing, as your cell is quite large),
> >> have you checked the length of your vacuum/lattice vector along the surface normal?
> >> If I see correctly, you have only about six Ångströms, which is
> >> already very
> >> (too) little, plus the DFT-D2 (Grimme-D2) adds quite strong an
> >> interaction through the vacuum at such distances I believe, plus the
> >> dipole correction...
> >>
> >> Greetings from Peaceful Montrouge/France,
> >>
> >> apsi
> >>
> >> PS My personal opinion of the vdW-DF* is, yes, they might be better,
> >> but first check the literature about a "suitable empirical choice of
> >> the particular mixture" of the functional, as some of the choices
> >> give quite large lattice constants already (4-5 % larger than
> >> experimental, which, of course, is not necessarily the target, rather
> >> a good adsorption geometry and energy). And often the best agreement
> >> is found by tuning the exchange functional, which naturally should
> >> have not nothing to do with the vdW/London dispersion, which is pure
> >> correlation... So much about "ab initio". ;) The good news of the
> >> day is that it seems that seldomly things seem to go completely
> >> wrong, no matter which choice of the vdW-DF* you take, but still, I
> >> would study a bit the literature first. If any one has a reference
> >> for a good review on the vdW-DF* et co applied to surfaces and
> >> adsorption, I would also be very thankful! :)
> >>
> >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
> >> =*=-=*=
> >> -
> >>
> >> Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
> >> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
> >> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935
> >>
> >> On Tue, 24 Nov 2015, Matej Huš wrote:
> >> > Dear PW community
> >> >
> >> > I have a problem when trying to find optimized geometry of an
> >> > adsorbed intermediate in "benzene" hydrogenation on Ru surface (see input below).
> >> >
> >> > I believe I am fairly close to optimised structure since I'm only
> >> > adding one hydrogen atom to an already optimised reactant and only
> >> > slight displacing the adjacent atoms.
> >> >
> >> >
> >> >
> >> > The problem is that BFGS doesn't seem to go anywhere. Energy only
> >> > fluctuates, which to my understanding is a sign of being close to a
> >>
> >> minimum.
> >>
> >> > However, forces remain large.
> >> >
> >> >
> >> >
> >> > I've switched to the damp algorithm and the problem persists. I've
> >> > searched through the forum and the usual approaches of tackling
> >> > this issue do not seem to work.
> >> >
> >> >
> >> >
> >> > Any ideas? Thank you!
> >> >
> >> > Matej Hus
> >> >
> >> > Laboratory of Catalysis and Chemcial Reaction Engineering
> >> >
> >> > National Institute of Chemistry
> >> >
> >> > Ljubljana, Slovenia
> >>
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> > Giuseppe Mattioli
> > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> > v. Salaria Km 29,300 - C.P. 10
> > I 00015 - Monterotondo Stazione (RM), Italy
> > Tel + 39 06 90672836 - Fax +39 06 90672316
> > E-mail: <giuseppe.mattioli at ism.cnr.it>
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> --
> *******************************************************
> Ilya Ryabinkin
> Postdoctoral Scholar
> Physical and Environmental Sciences
> University of Toronto Scarborough
> http://www.utsc.utoronto.ca/~aizmaylov/Members.html
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********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ègaux en droits. Les distinctions sociales
ne peuvent être fondèes que sur l'utilitè commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la libertè,
la propriètè, la sùretè et la rèsistance à l'oppression.
********************************************************
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM), Italy
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
http://www.ism.cnr.it/english/staff/mattiolig
ResearcherID: F-6308-2012
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