[Pw_forum] How to select unit cell for optimization calculation?
Giovanni Cantele
giovanni.cantele at spin.cnr.it
Tue Jul 7 10:01:56 CEST 2015
As far as I understand, the LiMn2O4 has 8 formula units in one unit cell, so you definitely need 56 atoms in the unit cell.
The cif file contains only information on the inequivalent atoms, all others can be obtained from the former by applying the
coordinate transformation of the space group Fd-3m
A useful way to do that, as specified here:
http://www.quantum-espresso.org/faq/input-data/#3.2 <http://www.quantum-espresso.org/faq/input-data/#3.2>
is to run the converter from cif files included in the QE distribution.
espresso-5.2.0/PW/tools/cif2qe.sh 1513984 > 1513984.scf.in
This produces a file (that you might want to check for correctness and to modify according to your needs) that looks like
&CONTROL
title = '1513984'
calculation = 'relax'
restart_mode = 'from_scratch'
outdir = './1'
pseudo_dir = '../PP/atompaw'
prefix = '1513984'
disk_io = 'none'
verbosity = 'default'
etot_conv_thr = 0.0001
forc_conv_thr = 0.001
nstep = 400
tstress = .true.
tprnfor = .true.
/
&SYSTEM
ibrav = 0
nat = 56
ntyp = 3
ecutwfc = 60
ecutrho = 480
vdw_corr = 'xdm'
xdm_a1 = 1.2153
xdm_a2 = 2.3704
/
&ELECTRONS
electron_maxstep = 200
conv_thr = 1.0D-7
diago_thr_init = 1e-4
startingpot = 'atomic'
startingwfc = 'atomic'
mixing_mode = 'plain'
mixing_beta = 0.5
mixing_ndim = 8
diagonalization = 'david'
/
&IONS
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
Li1+ 0.0000000000 Li1+.pw86pbe-n-kjpaw_psl.1.0.0.UPF
Mn3.5+ 0.0000000000 Mn3.5+.pw86pbe-n-kjpaw_psl.1.0.0.UPF
O2- 0.0000000000 O2-.pw86pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
Li1+ 0.87500000000000 0.87500000000000 0.87500000000000
Li1+ 0.12500000000000 0.12500000000000 0.12500000000000
Li1+ 0.87500000000000 0.37500000000000 0.37500000000000
Li1+ 0.37500000000000 0.87500000000000 0.37500000000000
Li1+ 0.37500000000000 0.37500000000000 0.87500000000000
Li1+ 0.12500000000000 0.62500000000000 0.62500000000000
Li1+ 0.62500000000000 0.12500000000000 0.62500000000000
Li1+ 0.62500000000000 0.62500000000000 0.12500000000000
Mn3.5+ 0.50000000000000 0.25000000000000 0.25000000000000
Mn3.5+ 0.25000000000000 0.50000000000000 0.25000000000000
Mn3.5+ 0.25000000000000 0.25000000000000 0.50000000000000
Mn3.5+ 0.50000000000000 0.50000000000000 0.50000000000000
Mn3.5+ 0.50000000000000 0.75000000000000 0.75000000000000
Mn3.5+ 0.75000000000000 0.50000000000000 0.75000000000000
Mn3.5+ 0.75000000000000 0.75000000000000 0.50000000000000
Mn3.5+ 0.00000000000000 0.25000000000000 0.75000000000000
Mn3.5+ 0.00000000000000 0.75000000000000 0.25000000000000
Mn3.5+ 0.25000000000000 0.00000000000000 0.75000000000000
Mn3.5+ 0.75000000000000 0.00000000000000 0.25000000000000
Mn3.5+ 0.25000000000000 0.75000000000000 0.00000000000000
Mn3.5+ 0.75000000000000 0.25000000000000 0.00000000000000
Mn3.5+ 0.50000000000000 0.00000000000000 0.00000000000000
Mn3.5+ 0.00000000000000 0.50000000000000 0.00000000000000
Mn3.5+ 0.00000000000000 0.00000000000000 0.50000000000000
O2- 0.73730000000000 0.01270000000000 0.01270000000000
O2- 0.01270000000000 0.73730000000000 0.01270000000000
O2- 0.01270000000000 0.01270000000000 0.73730000000000
O2- 0.73730000000000 0.73730000000000 0.73730000000000
O2- 0.26270000000000 0.98730000000000 0.98730000000000
O2- 0.98730000000000 0.26270000000000 0.98730000000000
O2- 0.98730000000000 0.98730000000000 0.26270000000000
O2- 0.26270000000000 0.26270000000000 0.26270000000000
O2- 0.73730000000000 0.51270000000000 0.51270000000000
O2- 0.23730000000000 0.01270000000000 0.51270000000000
O2- 0.23730000000000 0.51270000000000 0.01270000000000
O2- 0.01270000000000 0.23730000000000 0.51270000000000
O2- 0.51270000000000 0.73730000000000 0.51270000000000
O2- 0.51270000000000 0.23730000000000 0.01270000000000
O2- 0.01270000000000 0.51270000000000 0.23730000000000
O2- 0.51270000000000 0.01270000000000 0.23730000000000
O2- 0.51270000000000 0.51270000000000 0.73730000000000
O2- 0.73730000000000 0.23730000000000 0.23730000000000
O2- 0.23730000000000 0.73730000000000 0.23730000000000
O2- 0.23730000000000 0.23730000000000 0.73730000000000
O2- 0.26270000000000 0.48730000000000 0.48730000000000
O2- 0.76270000000000 0.98730000000000 0.48730000000000
O2- 0.76270000000000 0.48730000000000 0.98730000000000
O2- 0.98730000000000 0.76270000000000 0.48730000000000
O2- 0.48730000000000 0.26270000000000 0.48730000000000
O2- 0.48730000000000 0.76270000000000 0.98730000000000
O2- 0.98730000000000 0.48730000000000 0.76270000000000
O2- 0.48730000000000 0.98730000000000 0.76270000000000
O2- 0.48730000000000 0.48730000000000 0.26270000000000
O2- 0.26270000000000 0.76270000000000 0.76270000000000
O2- 0.76270000000000 0.26270000000000 0.76270000000000
O2- 0.76270000000000 0.76270000000000 0.26270000000000
K_POINTS automatic
2 2 2 0 0 0
CELL_PARAMETERS
15.57115429380366 0.00000000000000 0.00000000000000
0.00000000000000 15.57115429380366 0.00000000000000
0.00000000000000 0.00000000000000 15.57115429380366
Giovanni
> On 06 Jul 2015, at 20:51, max <aquiles011 at gmail.com> wrote:
>
> Hello,
>
> I'm confusing, I need to do some convergence test, but I don't know if I need primitive or one unit cell and how to select it.
>
> I'm using this structure http://www.crystallography.net/cod/1513984.html <http://www.crystallography.net/cod/1513984.html>
>
> I extracted the crystallographic translation. The cell formula units are 8, has 56 atoms. See ATOMIC_POSITIONS bellow.
>
> One unit cell of LiMn2O4 (spinel) has 7 atoms.
>
> I have the following questions:
>
> Do I need to put 7 atoms in the primitive cell or how many?
>
> How can I select the atoms position for primitive or one unit cell?
>
> ATOMIC_POSITIONS alat
> Li 0.125000000 0.125000000 0.125000000
> Li -0.125000000 0.875000000 0.875000000
> Li 0.875000000 -0.125000000 0.875000000
> Li 0.875000000 0.875000000 -0.125000000
> Li -0.125000000 -0.125000000 -0.125000000
> Li -0.125000000 0.375000000 0.375000000
> Li 0.375000000 0.875000000 0.375000000
> Li 0.875000000 0.375000000 0.375000000
> Mn 0.500000000 0.500000000 0.500000000
> Mn -0.500000000 1.250000000 1.250000000
> Mn 1.250000000 -0.500000000 1.250000000
> Mn 1.250000000 1.250000000 -0.500000000
> Mn -0.500000000 -0.500000000 -0.500000000
> Mn 0.500000000 -0.250000000 -0.250000000
> Mn -0.250000000 0.500000000 -0.250000000
> Mn -0.250000000 -0.250000000 0.500000000
> Mn -0.500000000 0.750000000 0.750000000
> Mn 0.000000000 1.250000000 0.750000000
> Mn 0.000000000 0.750000000 1.250000000
> Mn 1.250000000 0.000000000 0.750000000
> Mn 0.750000000 -0.500000000 0.750000000
> Mn 0.750000000 0.000000000 1.250000000
> Mn 1.250000000 0.750000000 0.000000000
> Mn 0.750000000 1.250000000 0.000000000
> O -0.262700000 1.012700000 1.012700000
> O 1.012700000 -0.262700000 1.012700000
> O 1.012700000 1.012700000 -0.262700000
> O -0.262700000 -0.262700000 -0.262700000
> O 0.262700000 -0.012700000 -0.012700000
> O -0.012700000 0.262700000 -0.012700000
> O -0.012700000 -0.012700000 0.262700000
> O 0.262700000 0.262700000 0.262700000
> O -0.262700000 0.512700000 0.512700000
> O 0.237300000 1.012700000 0.512700000
> O 0.237300000 0.512700000 1.012700000
> O 1.012700000 0.237300000 0.512700000
> O 0.512700000 -0.262700000 0.512700000
> O 0.512700000 0.237300000 1.012700000
> O 1.012700000 0.512700000 0.237300000
> O 0.512700000 1.012700000 0.237300000
> O 0.512700000 0.512700000 -0.262700000
> O -0.262700000 0.237300000 0.237300000
> O 0.237300000 -0.262700000 0.237300000
> O 0.237300000 0.237300000 -0.262700000
> O 0.262700000 0.487300000 0.487300000
> O 0.762700000 -0.012700000 0.487300000
> O 0.762700000 0.487300000 -0.012700000
> O -0.012700000 0.762700000 0.487300000
> O 0.487300000 0.262700000 0.487300000
> O 0.487300000 0.762700000 -0.012700000
> O -0.012700000 0.487300000 0.762700000
> O 0.487300000 -0.012700000 0.762700000
> O 0.487300000 0.487300000 0.262700000
> O 0.262700000 0.762700000 0.762700000
> O 0.762700000 0.262700000 0.762700000
> O 0.762700000 0.762700000 0.262700000
>
> --
> Máximo Ramírez
> Physics Degree
> Universidad Autónoma de Santo Domingo
> _______________________________________________
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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
Phone: +39 081 676910
Skype contact: giocan74
ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
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