[Pw_forum] How to select unit cell for optimization calculation?
Giovanni Cantele
giovanni.cantele at spin.cnr.it
Tue Jul 7 11:33:50 CEST 2015
if you want to optimize the structure (that is, the lattice constant), I would say that you cannot use few atoms.
Convergence of the total energy with respect to the cutoff is a property of the pseudo potentials, so you could check the variations
of the total energy with respect to ecutwfc by considering one atom for each atomic species in a cubic supercell. However, the convergence
of other properties, that are proper of the crystal, e.g. bulk modulus, phonon frequencies, and so on require using the full system.
For the case of alat (lattice parameter) in principle you should relax the system at each value of alat.
Giovanni
> On 07 Jul 2015, at 10:33, max <aquiles011 at gmail.com> wrote:
>
> Thanks for the fast response. definitely need 56 atoms. Thats mean that cannot use few atoms for convergence test and optimize the structure.
>
> If you can, can you suggest me some tricks for convergence test with this lot of atoms?
>
> I need run relax calculation before run scf for ecut and alat convergence test?
>
> On Tue, Jul 7, 2015 at 4:01 AM, Giovanni Cantele <giovanni.cantele at spin.cnr.it <mailto:giovanni.cantele at spin.cnr.it>> wrote:
> 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 <http://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 <mailto: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 <mailto:giovanni.cantele at spin.cnr.it>
> Phone: +39 081 676910 <tel:%2B39%20081%20676910>
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009 <http://www.researcherid.com/rid/A-1951-2009>
> Web page: http://people.na.infn.it/~cantele <http://people.na.infn.it/~cantele>
>
>
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>
>
>
> --
> El éxito solo es para los que se arriesgan por sus objetivos.
>
> Máximo Ramírez Mateo
> Desarrollador de Software
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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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