[Pw_forum] How to select unit cell for optimization calculation?
max
aquiles011 at gmail.com
Tue Jul 7 19:23:04 CEST 2015
Thanks for your help.
I read in mail-archive.com that this spinel work fine with 2 formula units
but I cannot found how reducre from 8 formula units to 2 formula units.
On Tue, Jul 7, 2015 at 5:33 AM, Giovanni Cantele <
giovanni.cantele at spin.cnr.it> wrote:
> 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> 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
>>
>> 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
>>
>> 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
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
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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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>>
>
>
>
> --
> El éxito solo es para los que se arriesgan por sus objetivos.
>
> Máximo Ramírez Mateo
> Desarrollador de Software
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
>
> 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
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
El éxito solo es para los que se arriesgan por sus objetivos.
Máximo Ramírez Mateo
Desarrollador de Software
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