Talking in detail about my procedure, I opened the following input file (which is for equlibrium lattice parameter of CaO) which has two atomic positions in X-crysden. Then it showed me a structure with 27 atoms whose co-ordinates (read by atoms info) are as follows: Ca 0.5 0.5 0.0 Ca 0.0 0.0 0.0 Ca 0.5 0.0 0.5 Ca 0.0 0.5 0.5 O 0.0 0.0 0.5 O 0.5 0.5 0.5 O 0.0 0.5 0.0 O 0.5 0.0 0.0 Ca 0.5 0.5 1.0 Ca 0.0 0.0 1.0 O 0.0 0.5 1.0 O 0.5 0.0 1.0 Ca 0.0 1.0 0.0 Ca 0.5 1.0 0.5 O 0.0 1.0 0.5 O 0.5 1.0 0.0 Ca 0.0 1.0 1.0 O 0.5 1.0 1.0 Ca 1.0 0.0 0.0 Ca 1.0 0.5 0.5 O 1.0 0.0 0.5 O 1.0 0.5 0.0 Ca 1.0 0.0 1.0 O 1.0 0.5 1.0 Ca 1.0 1.0 0.0 O 1.0 1.0 0.5 Ca 1.0 1.0 1.0 So, don't I have to include all this atomic positions while calculating energy due to vacancy?
On Wed, Dec 25, 2019 at 11:31 AM Pooja Vyas <[email protected]> wrote: > For instance, I tried calculation for Si-Ge alloy with the following > script, but there was no such error faced here. > > &control > calculation = 'scf', > prefix = 'sige' > tstress= .true. > tprnfor= .true. > outdir = '/home/userpooja/cao.oct/' > pseudo_dir = '/home/userpooja/cao.oct/pseudo/' > / > &system > ibrav = 0, > celldm(1) = 5.4492, > nat = 16, > ntyp = 2, > ecutwfc = 100, > / > &electrons > mixing_beta = 0.7 > / > > ATOMIC_SPECIES > > Si 28.0855 Si.pz-vbc.UPF > Ge 72.64 Ge.pz-bhs.UPF > > ATOMIC_POSITIONS > Si 0.0 0.0 0.0 > Si 0.5 0.5 0.0 > Si 0.5 0.0 0.5 > Ge 0.0 0.5 0.5 > Ge 0.25 0.25 0.25 > Ge 0.75 0.75 0.25 > Ge 0.75 0.25 0.75 > Ge 0.25 0.75 0.75 > Si 1.0 0.5 0.5 > Si 1.0 1.0 0.0 > Ge 1.25 0.25 0.25 > Ge 1.5 0.0 0.5 > Ge 1.5 0.5 0.0 > Si 1.75 0.75 0.25 > Si 1.75 0.25 0.75 > Si 1.25 0.75 0.75 > > CELL_PARAMETERS > 2.0 0.0 0.0 > 0.0 1.0 0.0 > 0.0 0.0 1.0 > > K_POINTS (automatic) > 11 11 11 1 1 1 > > On Wed, Dec 25, 2019 at 11:28 AM Pooja Vyas <[email protected]> > wrote: > >> Respected Sir/Madam, >> I want to calculate the energy due to vacancy in CaO. I need to create a >> supercell. So for that, don't I need all the above atomic positions of CaO >> in input file? Are only two atomic positions (0,0,0) and (0.5,0.5,0.5) >> enough? If yes, how can I create vacancy with just two atomic positions? I >> searched for a query similar to mine, but couldn't get any. >> >> On Tue, Dec 17, 2019 at 6:23 PM Offermans Willem < >> [email protected]> wrote: >> >>> Please explain why you are asking for another forum for Quantum Espresso >>> users. >>> >>> So even if there are other fora, to my opinion 1 forum is just fine and >>> preferable. >>> >>> >>> Met vriendelijke groeten, >>> Mit freundlichen Grüßen, >>> With kind regards, >>> >>> >>> Willem Offermans >>> Researcher Electrocatalysis SCT >>> VITO NV | Boeretang 200 | 2400 Mol >>> Phone:+32(0)14335263 Mobile:+32(0)492182073 >>> >>> [email protected] >>> >>> >>> On 17 Dec 2019, at 11:25, Pooja Vyas <[email protected]> wrote: >>> >>> Is there any other forum available where discussions regarding Quantum >>> Espresso can be done with other Quantum Espresso users? >>> >>> On Tue, Dec 17, 2019 at 3:34 PM Giovanni Cantele < >>> [email protected]> wrote: >>> >>>> sorry, at some point of my message I (or the automatic correction) >>>> wrote >>>> CaO has a cubic bcc lattice >>>> that instead was meant >>>> CaO has a cubic fcc lattice >>>> >>>> Giovanni >>>> >>>> On 17 Dec 2019, at 10:47, Giovanni Cantele < >>>> [email protected]> wrote: >>>> >>>> You’re using ibrav=2, which corresponds to a cubic F (fcc). The atomic >>>> positions are in alat units. As such, as clearly stated by the error >>>> message, >>>> atoms 1 and 2 are equivalent. Indeed, their positions are: >>>> #1 --> a/2 a/2 0 >>>> #2 —> 0 0 0 >>>> >>>> Atom #1 lies at the center of a face, its position for a cubic bcc >>>> lattice is obtained by translating the lattice site at the origin (where >>>> atom #2 lies) >>>> by a direct lattice vector. >>>> >>>> You must specify *ONLY* inequivalent atoms, their periodic replicas >>>> cannot be included in the list of atoms. There are many other similar >>>> overlapping atoms, such as >>>> Ca —> 0 0 0 with Ca —> 1 1 0 or Ca —> 0 0 1. >>>> >>>> Actually, to be honest, you should probably remove *ALL ATOMS BUT TWO*. >>>> Indeed, as far as I remember, CaO has a cubic bcc lattice >>>> with on Ca atom in 0 0 0 and on O atom in a/2 a/2 a/2 (but please >>>> check!). >>>> >>>> Provided that, in my opinion, any question is welcome, my suggestion is >>>> that you try to give a solution to error messages by yourself before >>>> asking people, because what you learn if you “try to solve” is >>>> priceless if compared to what you learn if you “ask to solve”. In this >>>> respect, >>>> Quantum-ESPRESSO is an exceptional lab to make experience, since >>>> especially (but not only) for the easiest tasks (such as build the band >>>> structure of >>>> simple solids) many error messages are self-explanatory and >>>> user-friendly! ;-) >>>> >>>> Giovanni >>>> >>>> >>>> >>>> On 17 Dec 2019, at 10:25, Pooja Vyas <[email protected]> >>>> wrote: >>>> >>>> Following is my input file. I obtained the atomic position using >>>> X-CrysDen. But when I run the file it shows me an error message. >>>> >>>> Input file: >>>> &control >>>> calculation = 'scf', >>>> prefix = '9.1334' >>>> tstress= .true. >>>> tprnfor= .true. >>>> outdir = '/home/userpooja/cao.oct/' >>>> pseudo_dir = '/home/userpooja/cao.oct/pseudo/' >>>> / >>>> &system >>>> ibrav = 2, >>>> celldm(1) = 9.1334, >>>> nat = 27, >>>> ntyp = 2, >>>> ecutwfc = 100, >>>> / >>>> &electrons >>>> mixing_beta = 0.7 >>>> / >>>> >>>> ATOMIC_SPECIES >>>> >>>> Ca 40.078 Ca.pbe-nsp-van.UPF >>>> O 15.999 O.pbe-van_ak.UPF >>>> >>>> ATOMIC_POSITIONS (alat) >>>> Ca 0.5 0.5 0.0 >>>> Ca 0.0 0.0 0.0 >>>> Ca 0.5 0.0 0.5 >>>> Ca 0.0 0.5 0.5 >>>> O 0.0 0.0 0.5 >>>> O 0.5 0.5 0.5 >>>> O 0.0 0.5 0.0 >>>> O 0.5 0.0 0.0 >>>> Ca 0.5 0.5 1.0 >>>> Ca 0.0 0.0 1.0 >>>> O 0.0 0.5 1.0 >>>> O 0.5 0.0 1.0 >>>> Ca 0.0 1.0 0.0 >>>> Ca 0.5 1.0 0.5 >>>> O 0.0 1.0 0.5 >>>> O 0.5 1.0 0.0 >>>> Ca 0.0 1.0 1.0 >>>> O 0.5 1.0 1.0 >>>> Ca 1.0 0.0 0.0 >>>> Ca 1.0 0.5 0.5 >>>> O 1.0 0.0 0.5 >>>> O 1.0 0.5 0.0 >>>> Ca 1.0 0.0 1.0 >>>> O 1.0 0.5 1.0 >>>> Ca 1.0 1.0 0.0 >>>> O 1.0 1.0 0.5 >>>> Ca 1.0 1.0 1.0 >>>> K_POINTS (automatic) >>>> 11 11 11 1 1 1 >>>> >>>> Error: >>>> >>>> >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> task # 17 >>>> from check_atoms : error # 1 >>>> atoms # 1 and # 2 differ by lattice vector (-1, 1, 0) in >>>> crystal axis >>>> >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> _______________________________________________ >>>> Quantum ESPRESSO is supported by MaX ( >>>> www.max-centre.eu/quantum-espresso) >>>> users mailing list [email protected] >>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>> >>>> >>>> -- >>>> >>>> Giovanni Cantele, PhD >>>> >>>> CNR-SPIN >>>> c/o Dipartimento di Fisica >>>> Universita' di Napoli "Federico II" >>>> Complesso Universitario M. S. Angelo - Ed. 6 >>>> Via Cintia, I-80126, Napoli, Italy >>>> >>>> e-mail: [email protected] <[email protected]> >>>> [email protected] >>>> Phone: +39 081 676910 >>>> Skype contact: giocan74 >>>> Web page: https://sites.google.com/view/giovanni-cantele >>>> >>>> _______________________________________________ >>>> Quantum ESPRESSO is supported by MaX ( >>>> www.max-centre.eu/quantum-espresso) >>>> users mailing list [email protected] >>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>> >>>> >>>> -- >>>> >>>> Giovanni Cantele, PhD >>>> >>>> CNR-SPIN >>>> c/o Dipartimento di Fisica >>>> Universita' di Napoli "Federico II" >>>> Complesso Universitario M. S. Angelo - Ed. 6 >>>> Via Cintia, I-80126, Napoli, Italy >>>> >>>> e-mail: [email protected] <[email protected]> >>>> [email protected] >>>> Phone: +39 081 676910 >>>> Skype contact: giocan74 >>>> Web page: https://sites.google.com/view/giovanni-cantele >>>> >>>> _______________________________________________ >>>> Quantum ESPRESSO is supported by MaX ( >>>> www.max-centre.eu/quantum-espresso) >>>> users mailing list [email protected] >>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>> >>> _______________________________________________ >>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso >>> ) >>> users mailing list [email protected] >>> https://lists.quantum-espresso.org/mailman/listinfo/users >>> >>> >>> Indien u VITO Mol bezoekt, hou aub er dan rekening mee dat de >>> hoofdingang voortaan enkel bereikbaar is vanuit de richting Dessel-Retie, >>> niet vanuit richting Mol, zie vito.be/route. <http://www.vito.be/route> >>> If you plan to visit VITO at Mol, then please note that the main >>> entrance can only be reached coming from Dessel-Retie and no longer coming >>> from Mol, see vito.be/en/contact/locations. >>> <http://www.vito.be/en/contact/locations> >>> VITO Disclaimer: http://www.vito.be/e-maildisclaimer >>> _______________________________________________ >>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso >>> ) >>> users mailing list [email protected] >>> https://lists.quantum-espresso.org/mailman/listinfo/users >> >>
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