[QE-users] Dangling bonds with CdS

Thu Nov 12 18:48:30 CET 2020

Dear Kumar
There is some sort of misunderstanding here. If you remove one (S or  
Cd) atom, you create a (S or Cd) vacancy, which is a point defect and  
is not generally referred to as "dangling bond", even if its formation  
may involve the creation of internal dangling bonds. First of all you  
should use a supercell (I would say at least a 2x2x2 64-atom  
supercell) to investigate the properties of a vacancy, because in a  
1x1x1 simple cubic cell you would have an unphysical 25% concentration  
of vacancies. You don't need to have particular care in the simulation  
(e.g. use of different pseudopotentials), but try to compare results  
obtained by relaxing the fully symmetric system and a less symmetric  
system obtained by very small (0.01 A) and randomized displacements of  
atoms in the supercell (by hand or by using some tool such as atomsk).  
Generally the latter starting configuration ensures the possibility  
that the vacancy site relaxes its geometry along less symmetric (and  
sometimes more stable) paths.
HTH
Giuseppe

Quoting "Dr. SUNIL KUMAR" <suniliitd14 at gmail.com>:

> 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
>> >>> >>
>> >>> >> _______________________________________________
>> >>> >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
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>> >>> > _______________________________________________
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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>
>>
>> _______________________________________________
>> 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>