[Pw_forum] anatase errors

Safa Alzaim safa.alzaim at gmail.com
Sun Nov 8 00:55:24 CET 2015


Thanks a lot, Paolo! I appreciate it.

On Sat, Nov 7, 2015 at 7:12 PM, Paolo Giannozzi <p.giannozzi at gmail.com>
wrote:

> If I remember correctly anatase has 12 atoms in a simple tetragonal unit
> cell. This is an example of input data I found in my disk.
>
> Note that HGH pseudopotentials are 1) very hard: 40 Ry for wavefunctions
> is way too small, and 2) norm-conserving: increasing the ratio between
> ecutrho and ecutwfc beyond its standard value 4 is not justified,
>
> Paolo
>
> On Sat, Nov 7, 2015 at 12:16 AM, Safa Alzaim <safa.alzaim at gmail.com>
> wrote:
>
>> Many thanks, Giovanni, for your explanation. Unfortunately, I am still
>> getting errors. What could be the issue with the code below? I've checked
>> all the values.
>> Thanks,
>> Safa
>>
>> &CONTROL
>>                        title = anatase1 ,
>>                  calculation = 'scf' ,
>>                 restart_mode = 'from_scratch' ,
>>                   wf_collect = .true. ,
>>                       outdir = '/home/osboxes/qe/PWgui-5.2.1/' ,
>>                       wfcdir = '/home/osboxes/qe/PWgui-5.2.1/' ,
>>                   pseudo_dir = '/home/osboxes/qe/mypseudo/' ,
>>                       prefix = 'anatasetry1' ,
>>  /
>>  &SYSTEM
>>                        ibrav = 7,
>>                            A = 3.73 ,
>>                            C = 9.37 ,
>>                          nat = 6,
>>                         ntyp = 2,
>>                      ecutwfc = 40 ,
>>                      ecutrho = 320 ,
>>  /
>>  &ELECTRONS
>>               conv_thr = 1.0d-8 ,
>>                  mixing_mode = 'plain' ,
>>              diagonalization = 'david' ,
>>  /
>> ATOMIC_SPECIES
>>    Ti   46.86700  Ti.blyp-sp-hgh.UPF
>>     O   15.99400  O.blyp-hgh.UPF
>> ATOMIC_POSITIONS crystal
>>    Ti      0.000000000    0.000000000    0.000000000
>>    Ti      0.000000000    0.500000000    0.250000000
>>     O      0.000000000    0.000000000    0.208000000
>>     O       0.000000000    0.000000000   -0.208000000
>>     O       0.000000000      0.500000000    0.458000000
>>     O         0.000000000    0.500000000    0.292000000
>> K_POINTS automatic
>>   2  2  1   1 1 1
>>
>>
>>
>>
>>
>>
>>
>> On Thu, Nov 5, 2015 at 9:00 AM, Giovanni Cantele <
>> giovanni.cantele at spin.cnr.it> wrote:
>>
>>> Dear Safa,
>>>
>>> the errors you get is because you input the TiO2 anatase primitive unit
>>> cell, but include also periodic replicas of some atoms, that means that as
>>> the scf cycle starts, some atoms overlap and it will never converge!
>>>
>>> For example:
>>>     Ti      0.000000000    0.000000000    0.000000000
>>> and
>>>     Ti      3.730000000    0.000000000    0.000000000
>>> are obtained one from the other through a lattice translation (a,0,0)
>>> and so they cannot be included both in the ATOMIC_POSITIONS card if the A
>>> and C parameters specify the crystal primitive cell.
>>>
>>> If you want to use the cif file with VESTA, before exporting the xyz
>>> coordinates you must be sure that only the atoms in the primitive cell are
>>> shown. However, you can also look through lot of papers published
>>> on TiO2 anatase and related systems. If you do so, you discover that the
>>> unit cell contains two TiO units with Ti ions at 0,0,0 and (0, 1/2 , 1/4)
>>> and O ions at (0,0,u), (0,0,-u), (0,1/2 ,u+1/4 ) and (0,1/2 , 1/2-u) with
>>> u=0.208.
>>> This coordinates are in crystal units.
>>>
>>>
>>> Giovanni
>>>
>>> --
>>>
>>> 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
>>> Phone: +39 081 676910
>>> Skype contact: giocan74
>>>
>>> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
>>> Web page: http://people.na.infn.it/~cantele
>>>
>>> > On 05 Nov 2015, at 02:43, Safa Alzaim <safa.alzaim at gmail.com> wrote:
>>> >
>>> > Hello All,
>>> >     I am new at QE, so please excuse the simplicity of my questions. I
>>> am working with bulk TiO2 anatase. I downloaded a cif, and then used Vesta
>>> to convert the data to xyz coordinates. However, I get the 31 atom unit
>>> cell instead of the primitive cell. In any case, I entered A and C values.
>>> I keep getting errors when I try to run the file. If anybody could help,
>>> I'd really appreciate it.
>>> > Thanks!
>>> > Safa
>>> >
>>> >
>>> > &CONTROL
>>> >                        title = anatase1 ,
>>> >                  calculation = 'scf' ,
>>> >                 restart_mode = 'from_scratch' ,
>>> >                   wf_collect = .true. ,
>>> >                       outdir = '/home/osboxes/qe/PWgui-5.2.1/' ,
>>> >                       wfcdir = '/home/osboxes/qe/PWgui-5.2.1/' ,
>>> >                   pseudo_dir = '/home/osboxes/qe/mypseudo/' ,
>>> >                       prefix = 'anatasetry1' ,
>>> >  /
>>> >  &SYSTEM
>>> >                        ibrav = 7,
>>> >                            A = 3.73 ,
>>> >                            C = 9.37 ,
>>> >                          nat = 31,
>>> >                         ntyp = 2,
>>> >                      ecutwfc = 40 ,
>>> >                      ecutrho = 320 ,
>>> >  /
>>> >  &ELECTRONS
>>> >               conv_thr = 1.0d-8 ,
>>> >                  mixing_mode = 'plain' ,
>>> >              diagonalization = 'david' ,
>>> >  /
>>> > ATOMIC_SPECIES
>>> >    Ti   46.86700  Ti.blyp-sp-hgh.UPF
>>> >     O   15.99400  O.blyp-hgh.UPF
>>> > ATOMIC_POSITIONS angstrom
>>> >    Ti      0.000000000    0.000000000    0.000000000
>>> >    Ti      0.000000000    0.000000000    9.370000000
>>> >    Ti      0.000000000    3.730000000    0.000000000
>>> >    Ti      0.000000000    3.730000000    9.370000000
>>> >    Ti      3.730000000    0.000000000    0.000000000
>>> >    Ti      3.730000000    0.000000000    9.370000000
>>> >    Ti      3.730000000    3.730000000    0.000000000
>>> >    Ti      3.730000000    3.730000000    9.370000000
>>> >    Ti      1.865000000    1.865000000    4.685000000
>>> >    Ti      0.000000000    1.865000000    2.342500000
>>> >    Ti      3.730000000    1.865000000    2.342500000
>>> >    Ti      1.865000000    0.000000000    7.027500000
>>> >    Ti      1.865000000    3.730000000    7.027500000
>>> >     O      0.000000000    0.000000000    1.874000000
>>> >     O      0.000000000    3.730000000    1.874000000
>>> >     O      3.730000000    0.000000000    1.874000000
>>> >     O      3.730000000    3.730000000    1.874000000
>>> >     O      1.865000000    1.865000000    6.559000000
>>> >     O      0.000000000    1.865000000    4.216500000
>>> >     O      3.730000000    1.865000000    4.216500000
>>> >     O      1.865000000    0.000000000    8.901500000
>>> >     O      1.865000000    3.730000000    8.901500000
>>> >     O      1.865000000    0.000000000    5.153500000
>>> >     O      1.865000000    3.730000000    5.153500000
>>> >     O      0.000000000    1.865000000    0.468500000
>>> >     O      3.730000000    1.865000000    0.468500000
>>> >     O      1.865000000    1.865000000    2.811000000
>>> >     O      0.000000000    0.000000000    7.496000000
>>> >     O      0.000000000    3.730000000    7.496000000
>>> >     O      3.730000000    0.000000000    7.496000000
>>> >     O      3.730000000    3.730000000    7.496000000
>>> > K_POINTS automatic
>>> >   2  2  1   1 1 1
>>> >
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>>>
>>>
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>>
>>
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>
>
>
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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>
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