[QE-users] X-CrysDen atomic position error

Pooja Vyas poojavyas1251995 at gmail.com
Wed Dec 25 07:18:33 CET 2019 

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 <poojavyas1251995 at gmail.com>
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 <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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