[QE-users] Dangling bonds with CdS

Thu Nov 12 18:10:01 CET 2020

Thank you for your quick response.
To create a dangling bond, I need to remove one atom of Cd (or S) form
periodic CdS system. Is it correct method to create a Dangling bond?
Dr. Sunil Kumar
Ph.D (Chemical Engg. IIT Delhi)
M.Tech (Chemical Engg. IIT Delhi)
B.Tech (Chemical Engg. IET-CSJMU Kanpur)
Scientist-C and Assistant Professor
CSIR-National Metallurgical Laboratory Jamshedpur-831007
http://www.nmlindia.org/
https://scholar.google.co.in/citations?user=OchYqugAAAAJ&hl=en&oi=sra

On Thu, Nov 12, 2020 at 10:28 PM Giuseppe Mattioli <
giuseppe.mattioli at ism.cnr.it> wrote:

>
> Dear Kumar
> In your attached file there is a correct and fully periodic CdS
> zincblend structure. I don't see any dangling bond.
>
>   >> I have one more question. Is it sufficient to remove one atom Cd (or
> S)
> >> form CdS crystal
>
> To obtain what?
>
> >> i need to modify/regenerate pseudo-potential file
> >> to calculate properties related to Dangling bond during DFT simulation?
>
> No, you don't
>
> HTH
> Giuseppe
>
> Quoting "Dr. SUNIL KUMAR" <suniliitd14 at gmail.com>:
>
> > I have carried out some dft simulations as attached file.
> > Dr. Sunil Kumar
> > Ph.D (Chemical Engg. IIT Delhi)
> > M.Tech (Chemical Engg. IIT Delhi)
> > B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> > Scientist-C and Assistant Professor
> > CSIR-National Metallurgical Laboratory Jamshedpur-831007
> > http://www.nmlindia.org/
> > https://scholar.google.co.in/citations?user=OchYqugAAAAJ&hl=en&oi=sra
> >
> >
> >
> > On Thu, Nov 12, 2020 at 10:10 PM Dr. SUNIL KUMAR <suniliitd14 at gmail.com>
> > wrote:
> >
> >> Thankyou for your explanation regarding Dangling bond.
> >> I have one more question. Is it sufficient to remove one atom Cd (or  S)
> >> form CdS crystal or also i need to modify/regenerate pseudo-potential
> file
> >> to calculate properties related to Dangling bond during DFT simulation?
> >> thanks
> >> Dr. Sunil Kumar
> >> Ph.D (Chemical Engg. IIT Delhi)
> >> M.Tech (Chemical Engg. IIT Delhi)
> >> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> >> Scientist-C and Assistant Professor
> >> CSIR-National Metallurgical Laboratory Jamshedpur-831007
> >> http://www.nmlindia.org/
> >> https://scholar.google.co.in/citations?user=OchYqugAAAAJ&hl=en&oi=sra
> >>
> >>
> >>
> >> On Thu, Nov 12, 2020 at 8:53 PM Giuseppe Mattioli <
> >> giuseppe.mattioli at ism.cnr.it> wrote:
> >>
> >>>
> >>> Dear Tamas and Kumar
> >>> only to add a few words to the (very pertinent) Tamas' reply:
> >>> 1) Semiconductor surfaces can undergoes very complex reconstruction
> >>> patterns (the 7x7 Si(111) reconstruction being likely the most famous
> >>> case). You will not find complex reconstructions by simply cutting and
> >>> relaxing the slabs, and it is best to search in experimental
> >>> literature, in order not to waste time simulating unphysical systems
> >>> which are never going to converge.
> >>>
> >>> 2) Dangling bonds can be also created inside crystals (e.g, by atomic
> >>> vacancies). It is not clear what kind of dangling bond you are
> >>> referring to.
> >>>
> >>> 3) There is an additional problem when you want to simulate some
> >>> process happening on the surface (e.g., adsorptions of molecules).
> >>> Various strategies can be used, including the saturation of dangling
> >>> bonds on one side of the slab by "pseudohydrogen atoms" having
> >>> fractional charge mimicking that of the pristine bond broken by
> >>> cleavage.
> >>>
> >>> This said, you should "make an educated guess" [cit. John Malkovich
> >>> :-)] and ask less general questions which may (or may not) generate
> >>> more useful answers.
> >>>
> >>> HTH
> >>> Giuseppe
> >>>
> >>> Quoting Tamas Karpati <tkarpati at gmail.com>:
> >>>
> >>> > Dear Dr. Kumar,
> >>> >
> >>> > I guess dangling bonds are written about in DFT textbooks of the
> >>> > physicists' style
> >>> > (in quantum chemistry, ie. clusters rather than crystals, it is less
> >>> > of a problem).
> >>> >
> >>> > The typical problem is that you cut chemical bonds when cleave the
> >>> > crystal (to get a slab).
> >>> > In case of bonds originally dominated by ionic (Coulomb) forces you
> >>> > may still have a closed
> >>> > shell system (ie. just paired electrons) after the cleavage. As for
> >>> > the more covalent
> >>> > bonds, radicals are generated and such high multiplicity electronic
> >>> > states (large
> >>> > magnetizations in terms of QE/PW.x inputs) reorganize to the more
> >>> > stable closed
> >>> > shell systems by changing geometry (you need to reoptimize their
> >>> > geometry) and
> >>> > simultaneously forming new bonds. This way every few surface atom
> >>> > pairs get closer
> >>> > and such bonds form, ie. bonds that were dangling after you made the
> >>> > cut are now
> >>> > in covalent bonds again (no dangling anymore).
> >>> > This you can model by reoptimizing with low (not sure but probably
> >>> > zero) magnetization.
> >>> >
> >>> > CdS has strong bonds carrying both ionic (maybe less) and covalent
> >>> nature
> >>> > (more of the latter). Depending on the cleaving plane you applied to
> >>> > the crystal,
> >>> > you have a high chance to see new Cd-S bonds form. Less probable is
> >>> > that you'll
> >>> > have Cd-Cd bonds or -S-S- bridges but these are also possible if your
> >>> surface
> >>> > atoms are situated so.
> >>> >
> >>> > Another way of treating such systems is to keep the structure as you
> >>> have cut
> >>> > from the crystal and apply a high starting_magnetization in a
> PW/relax
> >>> job.
> >>> >
> >>> > Be careful, though, as the chemistries you describe by the above two
> >>> methods
> >>> > (reorganization vs. high magnetization) are living in two distant
> >>> Universes.
> >>> >
> >>> > I hope this helps,
> >>> >   Tamas
> >>> >
> >>> > On Thu, Nov 12, 2020 at 8:13 AM Dr. SUNIL KUMAR
> >>> > <suniliitd14 at gmail.com> wrote:
> >>> >>
> >>> >> Dear QE developers and Users.
> >>> >> I am struggling to carry out a DFT simulation of CdS with dangling
> >>> >> bonds using Quantum Espresso DFT packages. I am unable to
> >>> >> understand the phenomena of Dangling bond and its implementation in
> >>> >> QE DFT simulation. I would like to request to you all, kindly
> >>> >> suggest me some tutorial and sample QE scripts for CdS with
> >>> >> Dangling bonds. I will be grateful to you.
> >>> >>
> >>> >> Thanks
> >>> >> With regards
> >>> >> SUNIL
> >>> >> Dr. Sunil Kumar
> >>> >> Ph.D (Chemical Engg. IIT Delhi)
> >>> >> M.Tech (Chemical Engg. IIT Delhi)
> >>> >> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> >>> >> Scientist-C and Assistant Professor
> >>> >> CSIR-National Metallurgical Laboratory Jamshedpur-831007
> >>> >> http://www.nmlindia.org/
> >>> >>
> https://scholar.google.co.in/citations?user=OchYqugAAAAJ&hl=en&oi=sra
> >>> >>
> >>> >> _______________________________________________
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> >>>
> >>>
> >>>
> >>> GIUSEPPE MATTIOLI
> >>> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> >>> Via Salaria Km 29,300 - C.P. 10
> >>> I-00015 - Monterotondo Scalo (RM)
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> >>> Tel + 39 06 90672342 - Fax +39 06 90672316
> >>> E-mail: <giuseppe.mattioli at ism.cnr.it>
> >>>
> >>> _______________________________________________
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> >>>
> >>
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
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