[QE-users] Dangling bonds with CdS
Dr. SUNIL KUMAR
suniliitd14 at gmail.com
Thu Nov 19 06:47:20 CET 2020
Dear Prof. Giuseppe Mattioli
I would like to thank you for your insightful suggestions/guidance for the
DFT simulation of CdS with and without Dangling bonds. I have carried out a
large number of simulations of CdS supercell like 1x1x1, 2x2x1, and 2x2x2
and the results are very much satisfactory. I am very much grateful to you.
Furthermore, I wish to carried out simulations with 3x3x2 and 4x4x2
supercell for SCF and NSCF (i.e. DOS) calculation. For these supercells,
simulation scf energy does not converge and shows a statement "End of
self-consistent calculation, convergence NOT achieved after 200
iterations: stopping ". I am running these simulations over HPC with 24
processors. Can you suggest to me which command I need to modify to ensure
proper convergence of energy?
I will be very grateful to you.
Warm regards
SUNIL
&CONTROL
calculation = "scf"
max_seconds = 8.64000e+04
outdir = "./outdir"
prefix = "espresso"
pseudo_dir = '/home/pseudopot'
wf_collect = .TRUE.
wfcdir = "./wfcdir"
/
&SYSTEM
a = 1.68262e+01
c = 3.36859e+01
degauss = 1.00000e-02
ecutrho = 2.25000e+02
ecutwfc = 2.50000e+01
ibrav = 4
nat = 128
ntyp = 2
occupations = "smearing"
smearing = "gaussian"
/
&ELECTRONS
conv_thr = 1.00000e-06
electron_maxstep = 200
mixing_beta = 7.00000e-01
startingpot = "atomic"
startingwfc = "atomic+random"
/
K_POINTS {automatic}
8 8 1 0 0 0
ATOMIC_SPECIES
Cd 112.41100 Cd.pbe-n-van.UPF
S 32.06600 S.pbe-van_bm.UPF
ATOMIC_POSITIONS {angstrom}
Cd 0.000000 2.428644 0.960104
Cd 2.103268 1.214322 4.381568
S 0.000000 2.428644 3.537739
S 2.103268 1.214322 6.959204
Cd 0.000000 2.428644 7.803033
Cd 2.103268 1.214322 11.224497
S 0.000000 2.428644 10.380668
S 2.103268 1.214322 13.802133
Cd -2.103270 6.071615 0.960104
Cd -0.000002 4.857293 4.381568
S -2.103270 6.071615 3.537739
S -0.000002 4.857293 6.959204
Cd -2.103270 6.071615 7.803033
Cd -0.000002 4.857293 11.224497
S -2.103270 6.071615 10.380668
S -0.000002 4.857293 13.802133
Cd -4.206540 9.714585 0.960104
Cd -2.103272 8.500263 4.381568
S -4.206540 9.714585 3.537739
S -2.103272 8.500263 6.959204
Cd -4.206540 9.714585 7.803033
Cd -2.103272 8.500263 11.224497
S -4.206540 9.714585 10.380668
S -2.103272 8.500263 13.802133
Cd -6.309810 13.357556 0.960104
Cd -4.206542 12.143234 4.381568
S -6.309810 13.357556 3.537739
S -4.206542 12.143234 6.959204
Cd -6.309810 13.357556 7.803033
Cd -4.206542 12.143234 11.224497
S -6.309810 13.357556 10.380668
S -4.206542 12.143234 13.802133
Cd 4.206540 2.428644 0.960104
Cd 6.309808 1.214322 4.381568
S 4.206540 2.428644 3.537739
S 6.309808 1.214322 6.959204
Cd 4.206540 2.428644 7.803033
Cd 6.309808 1.214322 11.224497
S 4.206540 2.428644 10.380668
S 6.309808 1.214322 13.802133
Cd 2.103270 6.071615 0.960104
Cd 4.206538 4.857293 4.381568
S 2.103270 6.071615 3.537739
S 4.206538 4.857293 6.959204
Cd 2.103270 6.071615 7.803033
Cd 4.206538 4.857293 11.224497
S 2.103270 6.071615 10.380668
S 4.206538 4.857293 13.802133
Cd 0.000000 9.714585 0.960104
Cd 2.103268 8.500263 4.381568
S 0.000000 9.714585 3.537739
S 2.103268 8.500263 6.959204
Cd 0.000000 9.714585 7.803033
Cd 2.103268 8.500263 11.224497
S 0.000000 9.714585 10.380668
S 2.103268 8.500263 13.802133
Cd -2.103270 13.357556 0.960104
Cd -0.000002 12.143234 4.381568
S -2.103270 13.357556 3.537739
S -0.000002 12.143234 6.959204
Cd -2.103270 13.357556 7.803033
Cd -0.000002 12.143234 11.224497
S -2.103270 13.357556 10.380668
S -0.000002 12.143234 13.802133
Cd 8.413080 2.428644 0.960104
Cd 10.516348 1.214322 4.381568
S 8.413080 2.428644 3.537739
S 10.516348 1.214322 6.959204
Cd 8.413080 2.428644 7.803033
Cd 10.516348 1.214322 11.224497
S 8.413080 2.428644 10.380668
S 10.516348 1.214322 13.802133
Cd 6.309810 6.071615 0.960104
Cd 8.413078 4.857293 4.381568
S 6.309810 6.071615 3.537739
S 8.413078 4.857293 6.959204
Cd 6.309810 6.071615 7.803033
Cd 8.413078 4.857293 11.224497
S 6.309810 6.071615 10.380668
S 8.413078 4.857293 13.802133
Cd 4.206540 9.714585 0.960104
Cd 6.309808 8.500263 4.381568
S 4.206540 9.714585 3.537739
S 6.309808 8.500263 6.959204
Cd 4.206540 9.714585 7.803033
Cd 6.309808 8.500263 11.224497
S 4.206540 9.714585 10.380668
S 6.309808 8.500263 13.802133
Cd 2.103270 13.357556 0.960104
Cd 4.206538 12.143234 4.381568
S 2.103270 13.357556 3.537739
S 4.206538 12.143234 6.959204
Cd 2.103270 13.357556 7.803033
Cd 4.206538 12.143234 11.224497
S 2.103270 13.357556 10.380668
S 4.206538 12.143234 13.802133
Cd 12.619620 2.428644 0.960104
Cd 14.722888 1.214322 4.381568
S 12.619620 2.428644 3.537739
S 14.722888 1.214322 6.959204
Cd 12.619620 2.428644 7.803033
Cd 14.722888 1.214322 11.224497
S 12.619620 2.428644 10.380668
S 14.722888 1.214322 13.802133
Cd 10.516350 6.071615 0.960104
Cd 12.619618 4.857293 4.381568
S 10.516350 6.071615 3.537739
S 12.619618 4.857293 6.959204
Cd 10.516350 6.071615 7.803033
Cd 12.619618 4.857293 11.224497
S 10.516350 6.071615 10.380668
S 12.619618 4.857293 13.802133
Cd 8.413080 9.714585 0.960104
Cd 10.516348 8.500263 4.381568
S 8.413080 9.714585 3.537739
S 10.516348 8.500263 6.959204
Cd 8.413080 9.714585 7.803033
Cd 10.516348 8.500263 11.224497
S 8.413080 9.714585 10.380668
S 10.516348 8.500263 13.802133
Cd 6.309810 13.357556 0.960104
Cd 8.413078 12.143234 4.381568
S 6.309810 13.357556 3.537739
S 8.413078 12.143234 6.959204
Cd 6.309810 13.357556 7.803033
Cd 8.413078 12.143234 11.224497
S 6.309810 13.357556 10.380668
S 8.413078 12.143234 13.802133
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 11:19 PM Giuseppe Mattioli <
giuseppe.mattioli at ism.cnr.it> wrote:
>
> 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)
> >> >>> >> users mailing list users at lists.quantum-espresso.org
> >> >>> >> https://lists.quantum-espresso.org/mailman/listinfo/users
> >> >>> > _______________________________________________
> >> >>> > 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>
> >>
> >> _______________________________________________
> >> 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
>
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