[QE-users] Dangling bonds with CdS

Thu Nov 12 17:43:18 CET 2020

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)
>> Mob (*preferred*) +39 373 7305625
>> Tel + 39 06 90672342 - Fax +39 06 90672316
>> E-mail: <giuseppe.mattioli at ism.cnr.it>
>>
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