[QE-users] X-CrysDen atomic position error

Pooja Vyas poojavyas1251995 at gmail.com
Wed Dec 25 06:58:32 CET 2019 

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 <willem.offermans at vito.be>
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
>
> Willem.Offermans at Vito.be
>
>
> On 17 Dec 2019, at 11:25, Pooja Vyas <poojavyas1251995 at gmail.com> 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 <
> giovanni.cantele at spin.cnr.it> 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 <giovanni.cantele at spin.cnr.it>
>> 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 <poojavyas1251995 at gmail.com> 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)
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>>
>> --
>>
>> 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: giovanni.cantele at spin.cnr.it <giovanni.cantele at spin.cnr.it>
>>             gcantele at gmail.com
>> 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 users at lists.quantum-espresso.org
>> 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: giovanni.cantele at spin.cnr.it <giovanni.cantele at spin.cnr.it>
>>             gcantele at gmail.com
>> 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 users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
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