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.matti...@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" <suniliit...@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.matti...@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" <suniliit...@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 < > suniliit...@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.matti...@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 <tkarp...@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 > >> >>> > <suniliit...@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@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@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.matti...@ism.cnr.it> > >> >>> > >> >>> _______________________________________________ > >> >>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > >> >>> users mailing list users@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.matti...@ism.cnr.it> > >> > >> _______________________________________________ > >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > >> users mailing list users@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.matti...@ism.cnr.it> > > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users >
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