[Pw_forum] Symmetry recognition
Pascal Boulet
pascal.boulet at univ-amu.fr
Fri Feb 24 18:07:06 CET 2017
Hello,
Here is a simple example with Al2O3 of the problem I am facing.
The initial 'vc-relax' calculation is performed with the input file (partial informations here):
&SYSTEM
ibrav = 5,
a = 5.12,
b = 5.12,
c = 5.12,
cosac = 0.56956647,
space_group = 167,
nat = 2,
ntyp = 2,
…
/
ATOMIC_POSITIONS crystal_sg
Al 0.355 0.355 0.355
O 0.553 -0.053 0.25
The output file shows:
bravais-lattice index = 5
lattice parameter (alat) = 9.6754 a.u.
unit-cell volume = 905.7461 (a.u.)^3
number of atoms/cell = 10
…
celldm(1)= 9.675398 celldm(2)= 1.000000 celldm(3)= 1.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 0.707107 -0.408248 0.577350 )
a(2) = ( 0.000000 0.816497 0.577350 )
a(3) = ( -0.707107 -0.408248 0.577350 )
…
12 Sym. Ops., with inversion, found ( 6 have fractional translation)
…
point group D_3d (-3m)
…
Crystallographic axes
site n. atom positions (cryst. coord.)
1 Al tau( 1) = ( 0.3550000 0.3550000 0.3550000 )
2 Al tau( 2) = ( 0.1450000 0.1450000 0.1450000 )
3 Al tau( 3) = ( 0.6450000 0.6450000 0.6450000 )
4 Al tau( 4) = ( 0.8550000 0.8550000 0.8550000 )
5 O tau( 5) = ( 0.2500000 0.5530000 0.9470000 )
6 O tau( 6) = ( 0.5530000 0.9470000 0.2500000 )
7 O tau( 7) = ( 0.9470000 0.2500000 0.5530000 )
8 O tau( 8) = ( 0.7500000 0.4470000 0.0530000 )
9 O tau( 9) = ( 0.4470000 0.0530000 0.7500000 )
10 O tau( 10) = ( 0.0530000 0.7500000 0.4470000 )
number of k points= 60
I make the calculation intentionally fail to restart it. In the restart input file I change restart_mode = ‘from_scratch’, by restart_mode = ‘restart’.
I also have to add startingpot = ‘atomic’, and startingwfc = 'atomic+random’ … the wfc files are not present for some reasons… I have to find why is this.
The new output file shows:
Atomic positions and unit cell read from directory:
./al2o3.save/
…
bravais-lattice index = 5
lattice parameter (alat) = 9.6754 a.u.
unit-cell volume = 905.7461 (a.u.)^3
number of atoms/cell = 10
…
celldm(1)= 9.675398 celldm(2)= 1.000000 celldm(3)= 1.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 0.707107 -0.408248 0.577350 )
a(2) = ( 0.000000 0.816497 0.577350 )
a(3) = ( -0.707107 -0.408248 0.577350 )
…
3 Sym. Ops. (no inversion) found
…
point group C_3 (3)
…
Crystallographic axes
site n. atom positions (cryst. coord.)
1 Al tau( 1) = ( 0.3798376 0.3798376 0.3798376 )
2 Al tau( 2) = ( 0.1201624 0.1201624 0.1201624 )
3 Al tau( 3) = ( 0.7202472 0.7202472 0.7202472 )
4 Al tau( 4) = ( 1.0218300 1.0218300 1.0218300 )
5 O tau( 5) = ( 0.4065635 0.6450760 0.9807839 )
6 O tau( 6) = ( 0.6450760 0.9807839 0.4065635 )
7 O tau( 7) = ( 0.9807839 0.4065635 0.6450760 )
8 O tau( 8) = ( 0.7548213 0.5163088 0.1806009 )
9 O tau( 9) = ( 0.5163088 0.1806009 0.7548213 )
10 O tau( 10) = ( 0.1806009 0.7548213 0.5163088 )
number of k points= 88
Is it numerical or am I doing something wrong?
I join a tarball file with all the data if useful.
Thank you for your help,
Pascal
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Le 23 févr. 2017 à 21:45, Paolo Giannozzi <p.giannozzi at gmail.com> a écrit :
> Of course there is a reason, but not necessarily a good one. If you
> are "restarting from an incomplete calculation", I guess that the code
> overwrites the input coordinates with the current ones. The symmetry
> should be the same, but sometimes numerical noise breaks the symmetry.
> It is impossible to say more without an example.
>
> Paolo
>
> On Thu, Feb 23, 2017 at 8:56 AM, Pascal Boulet
> <pascal.boulet at univ-amu.fr> wrote:
>> Dear all,
>>
>> I am running a structural optimization with QE 6.0. The structure is
>> orthorhombic, ibrav=8, with 8 symmetry elements. The first run did not
>> converge so I have to restart it. But as I restart it, the number of
>> symmetry is now 4, there is a descent of symmetry. I shall say that I use
>> the space_group option with COORDINATES crystal_sg. But the problem remains
>> if I put all the coordinates (unsurprisingly).
>>
>> Is there a reason for this, and can I avoid this?
>>
>> Thank you
>> Best regards
>> Pascal
>>
>> -
>> Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE
>> Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen -
>> 13013 Marseille
>> Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50
>> Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire - Email :
>> pascal.boulet at univ-amu.fr
>>
>>
>>
>>
>>
>> _______________________________________________
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>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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