[QE-users] Dangling bonds with CdS

[Giuseppe Mattioli]

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)
>>> 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
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>



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>