[Pw_forum] bfgs optimization not going anywhere
Matej Huš
matej.hus at gmail.com
Thu Nov 26 07:24:27 CET 2015
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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>
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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
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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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