[QE-users] X-CrysDen atomic position error

Pooja Vyas poojavyas1251995 at gmail.com
Wed Dec 25 07:01:28 CET 2019 

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 <poojavyas1251995 at gmail.com>
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 <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
>>> )
>>> 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
>>>
>>>
>>> --
>>>
>>> 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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