<div dir="ltr"><div>Thanks for your help.<br><br></div>I read in <a href="http://mail-archive.com">mail-archive.com</a> that this spinel work fine with 2 formula units but I cannot found how reducre from 8 formula units to 2 formula units.<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jul 7, 2015 at 5:33 AM, Giovanni Cantele <span dir="ltr"><<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">if you want to optimize the structure (that is, the lattice constant), I would say that you cannot use few atoms.<div><br></div><div>Convergence of the total energy with respect to the cutoff is a property of the pseudo potentials, so you could check the variations</div><div>of the total energy with respect to ecutwfc by considering one atom for each atomic species in a cubic supercell. However, the convergence</div><div>of other properties, that are proper of the crystal, e.g. bulk modulus, phonon frequencies, and so on require using the full system.</div><div><br></div><div>For the case of alat (lattice parameter) in principle you should relax the system at each value of alat.</div><span class="HOEnZb"><font color="#888888"><div><br></div></font></span><div><span class="HOEnZb"><font color="#888888">Giovanni</font></span><div><div class="h5"><br><div><br></div><div><br></div><div><br><div><blockquote type="cite"><div>On 07 Jul 2015, at 10:33, max <<a href="mailto:aquiles011@gmail.com" target="_blank">aquiles011@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><div><div>Thanks for the fast response. <b>definitely need 56 atoms</b>. Thats mean that cannot use few atoms for convergence test and optimize the structure.<br><br></div>If you can, can you suggest me some tricks for convergence test with this lot of atoms?<br><br></div>I need run relax calculation before run scf for ecut and alat convergence test?<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jul 7, 2015 at 4:01 AM, Giovanni Cantele <span dir="ltr"><<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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.<div><br></div><div>The cif file contains only information on the inequivalent atoms, all others can be obtained from the former by applying the</div><div>coordinate transformation of the space group Fd-3m</div><div><br></div><div>A useful way to do that, as specified here:</div><div><br></div><div><a href="http://www.quantum-espresso.org/faq/input-data/#3.2" target="_blank">http://www.quantum-espresso.org/faq/input-data/#3.2</a></div><div><br></div><div>is to run the converter from cif files included in the QE distribution.</div><div><br></div><div><span style="white-space:pre-wrap"> </span>espresso-5.2.0/PW/tools/cif2qe.sh 1513984 > <a href="http://1513984.scf.in/" target="_blank">1513984.scf.in</a></div><div><br></div><div>This produces a file (that you might want to check for correctness and to modify according to your needs) that looks like</div><div><br></div><div><br></div><div>&CONTROL<br> title = '1513984'<br> calculation = 'relax'<br> restart_mode = 'from_scratch'<br> outdir = './1'<br> pseudo_dir = '../PP/atompaw'<br> prefix = '1513984'<br> disk_io = 'none'<br> verbosity = 'default'<br> etot_conv_thr = 0.0001<br> forc_conv_thr = 0.001<br> nstep = 400<br> tstress = .true.<br> tprnfor = .true.<br> /<br> &SYSTEM<br> ibrav = 0<br> nat = 56<br> ntyp = 3<br> ecutwfc = 60<br> ecutrho = 480<br> vdw_corr = 'xdm'<br> xdm_a1 = 1.2153<br> xdm_a2 = 2.3704<br> /<br> &ELECTRONS<br> electron_maxstep = 200<br> conv_thr = 1.0D-7<br> diago_thr_init = 1e-4<br> startingpot = 'atomic'<br> startingwfc = 'atomic'<br> mixing_mode = 'plain'<br> mixing_beta = 0.5<br> mixing_ndim = 8<br> diagonalization = 'david'<br> /<br>&IONS<br> ion_dynamics = 'bfgs'<br> /<br><br>ATOMIC_SPECIES<br> Li1+ 0.0000000000 Li1+.pw86pbe-n-kjpaw_psl.1.0.0.UPF<br> Mn3.5+ 0.0000000000 Mn3.5+.pw86pbe-n-kjpaw_psl.1.0.0.UPF<br> O2- 0.0000000000 O2-.pw86pbe-n-kjpaw_psl.1.0.0.UPF<br><br>ATOMIC_POSITIONS crystal<br>Li1+ 0.87500000000000 0.87500000000000 0.87500000000000<br>Li1+ 0.12500000000000 0.12500000000000 0.12500000000000<br>Li1+ 0.87500000000000 0.37500000000000 0.37500000000000<br>Li1+ 0.37500000000000 0.87500000000000 0.37500000000000<br>Li1+ 0.37500000000000 0.37500000000000 0.87500000000000<br>Li1+ 0.12500000000000 0.62500000000000 0.62500000000000<br>Li1+ 0.62500000000000 0.12500000000000 0.62500000000000<br>Li1+ 0.62500000000000 0.62500000000000 0.12500000000000<br>Mn3.5+ 0.50000000000000 0.25000000000000 0.25000000000000<br>Mn3.5+ 0.25000000000000 0.50000000000000 0.25000000000000<br>Mn3.5+ 0.25000000000000 0.25000000000000 0.50000000000000<br>Mn3.5+ 0.50000000000000 0.50000000000000 0.50000000000000<br>Mn3.5+ 0.50000000000000 0.75000000000000 0.75000000000000<br>Mn3.5+ 0.75000000000000 0.50000000000000 0.75000000000000<br>Mn3.5+ 0.75000000000000 0.75000000000000 0.50000000000000<br>Mn3.5+ 0.00000000000000 0.25000000000000 0.75000000000000<br>Mn3.5+ 0.00000000000000 0.75000000000000 0.25000000000000<br>Mn3.5+ 0.25000000000000 0.00000000000000 0.75000000000000<br>Mn3.5+ 0.75000000000000 0.00000000000000 0.25000000000000<br>Mn3.5+ 0.25000000000000 0.75000000000000 0.00000000000000<br>Mn3.5+ 0.75000000000000 0.25000000000000 0.00000000000000<br>Mn3.5+ 0.50000000000000 0.00000000000000 0.00000000000000<br>Mn3.5+ 0.00000000000000 0.50000000000000 0.00000000000000<br>Mn3.5+ 0.00000000000000 0.00000000000000 0.50000000000000<br>O2- 0.73730000000000 0.01270000000000 0.01270000000000<br>O2- 0.01270000000000 0.73730000000000 0.01270000000000<br>O2- 0.01270000000000 0.01270000000000 0.73730000000000<br>O2- 0.73730000000000 0.73730000000000 0.73730000000000<br>O2- 0.26270000000000 0.98730000000000 0.98730000000000<br>O2- 0.98730000000000 0.26270000000000 0.98730000000000<br>O2- 0.98730000000000 0.98730000000000 0.26270000000000<br>O2- 0.26270000000000 0.26270000000000 0.26270000000000<br>O2- 0.73730000000000 0.51270000000000 0.51270000000000<br>O2- 0.23730000000000 0.01270000000000 0.51270000000000<br>O2- 0.23730000000000 0.51270000000000 0.01270000000000<br>O2- 0.01270000000000 0.23730000000000 0.51270000000000<br>O2- 0.51270000000000 0.73730000000000 0.51270000000000<br>O2- 0.51270000000000 0.23730000000000 0.01270000000000<br>O2- 0.01270000000000 0.51270000000000 0.23730000000000<br>O2- 0.51270000000000 0.01270000000000 0.23730000000000<br>O2- 0.51270000000000 0.51270000000000 0.73730000000000<br>O2- 0.73730000000000 0.23730000000000 0.23730000000000<br>O2- 0.23730000000000 0.73730000000000 0.23730000000000<br>O2- 0.23730000000000 0.23730000000000 0.73730000000000<br>O2- 0.26270000000000 0.48730000000000 0.48730000000000<br>O2- 0.76270000000000 0.98730000000000 0.48730000000000<br>O2- 0.76270000000000 0.48730000000000 0.98730000000000<br>O2- 0.98730000000000 0.76270000000000 0.48730000000000<br>O2- 0.48730000000000 0.26270000000000 0.48730000000000<br>O2- 0.48730000000000 0.76270000000000 0.98730000000000<br>O2- 0.98730000000000 0.48730000000000 0.76270000000000<br>O2- 0.48730000000000 0.98730000000000 0.76270000000000<br>O2- 0.48730000000000 0.48730000000000 0.26270000000000<br>O2- 0.26270000000000 0.76270000000000 0.76270000000000<br>O2- 0.76270000000000 0.26270000000000 0.76270000000000<br>O2- 0.76270000000000 0.76270000000000 0.26270000000000<br><br>K_POINTS automatic<br>2 2 2 0 0 0<br><br>CELL_PARAMETERS<br> 15.57115429380366 0.00000000000000 0.00000000000000<br> 0.00000000000000 15.57115429380366 0.00000000000000<br> 0.00000000000000 0.00000000000000 15.57115429380366<br><br></div><div><br></div><div><br></div><div>Giovanni</div><div><br></div><div><br></div><div><br><div><blockquote type="cite"><div><div><div>On 06 Jul 2015, at 20:51, max <<a href="mailto:aquiles011@gmail.com" target="_blank">aquiles011@gmail.com</a>> wrote:</div><br></div></div><div><div><div><div dir="ltr"><div><div><div><div><div>Hello,<br><br></div>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.<br><br></div>I'm using this structure <a href="http://www.crystallography.net/cod/1513984.html" target="_blank">http://www.crystallography.net/cod/1513984.html</a><br><br></div>I extracted the crystallographic translation. The cell formula units are 8, has 56 atoms. See ATOMIC_POSITIONS bellow.<br><br>One unit cell of LiMn2O4 (spinel) has 7 atoms.<br></div><b><br></b></div>I have the following questions:<b><br></b><div><div><br><b><b>Do I need to put 7 atoms in the primitive cell or how many?<br><br></b>How can I select the atoms position for primitive or one unit cell?</b><br><br>ATOMIC_POSITIONS alat <br> Li 0.125000000 0.125000000 0.125000000 <br> Li -0.125000000 0.875000000 0.875000000 <br> Li 0.875000000 -0.125000000 0.875000000 <br> Li 0.875000000 0.875000000 -0.125000000 <br> Li -0.125000000 -0.125000000 -0.125000000 <br> Li -0.125000000 0.375000000 0.375000000 <br> Li 0.375000000 0.875000000 0.375000000 <br> Li 0.875000000 0.375000000 0.375000000 <br> Mn 0.500000000 0.500000000 0.500000000 <br> Mn -0.500000000 1.250000000 1.250000000 <br> Mn 1.250000000 -0.500000000 1.250000000 <br> Mn 1.250000000 1.250000000 -0.500000000 <br> Mn -0.500000000 -0.500000000 -0.500000000 <br> Mn 0.500000000 -0.250000000 -0.250000000 <br> Mn -0.250000000 0.500000000 -0.250000000 <br> Mn -0.250000000 -0.250000000 0.500000000 <br> Mn -0.500000000 0.750000000 0.750000000 <br> Mn 0.000000000 1.250000000 0.750000000 <br> Mn 0.000000000 0.750000000 1.250000000 <br> Mn 1.250000000 0.000000000 0.750000000 <br> Mn 0.750000000 -0.500000000 0.750000000 <br> Mn 0.750000000 0.000000000 1.250000000 <br> Mn 1.250000000 0.750000000 0.000000000 <br> Mn 0.750000000 1.250000000 0.000000000 <br> O -0.262700000 1.012700000 1.012700000 <br> O 1.012700000 -0.262700000 1.012700000 <br> O 1.012700000 1.012700000 -0.262700000 <br> O -0.262700000 -0.262700000 -0.262700000 <br> O 0.262700000 -0.012700000 -0.012700000 <br> O -0.012700000 0.262700000 -0.012700000 <br> O -0.012700000 -0.012700000 0.262700000 <br> O 0.262700000 0.262700000 0.262700000 <br> O -0.262700000 0.512700000 0.512700000 <br> O 0.237300000 1.012700000 0.512700000 <br> O 0.237300000 0.512700000 1.012700000 <br> O 1.012700000 0.237300000 0.512700000 <br> O 0.512700000 -0.262700000 0.512700000 <br> O 0.512700000 0.237300000 1.012700000 <br> O 1.012700000 0.512700000 0.237300000 <br> O 0.512700000 1.012700000 0.237300000 <br> O 0.512700000 0.512700000 -0.262700000 <br> O -0.262700000 0.237300000 0.237300000 <br> O 0.237300000 -0.262700000 0.237300000 <br> O 0.237300000 0.237300000 -0.262700000 <br> O 0.262700000 0.487300000 0.487300000 <br> O 0.762700000 -0.012700000 0.487300000 <br> O 0.762700000 0.487300000 -0.012700000 <br> O -0.012700000 0.762700000 0.487300000 <br> O 0.487300000 0.262700000 0.487300000 <br> O 0.487300000 0.762700000 -0.012700000 <br> O -0.012700000 0.487300000 0.762700000 <br> O 0.487300000 -0.012700000 0.762700000 <br> O 0.487300000 0.487300000 0.262700000 <br> O 0.262700000 0.762700000 0.762700000 <br> O 0.762700000 0.262700000 0.762700000 <br> O 0.762700000 0.762700000 0.262700000<br clear="all"><div><div><div><div><br>-- <br><div><div>Máximo Ramírez<br></div><div>Physics Degree<br></div><div>Universidad Autónoma de Santo Domingo<br></div></div>
</div></div></div></div></div></div></div></div></div>
_______________________________________________<br>Pw_forum mailing list<br><a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br><a href="http://pwscf.org/mailman/listinfo/pw_forum" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a></div></blockquote></div><br><div>
-- <br><br>Giovanni Cantele, PhD<br>CNR-SPIN<br>c/o Dipartimento di Fisica<br>Universita' di Napoli "Federico II"<br>Complesso Universitario M. S. Angelo - Ed. 6<br>Via Cintia, I-80126, Napoli, Italy<br>e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a><br>Phone: <a href="tel:%2B39%20081%20676910" value="+39081676910" target="_blank">+39 081 676910</a><br>Skype contact: giocan74<br><br>ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a><br>Web page: <a href="http://people.na.infn.it/~cantele" target="_blank">http://people.na.infn.it/~cantele</a><br>
</div>
<br></div></div><br>_______________________________________________<br>
Pw_forum mailing list<br>
<a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
<a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br></blockquote></div><br><br clear="all"><br>-- <br><div><div dir="ltr"><div>El éxito solo es para los que se arriesgan por sus objetivos.<br><br> Máximo Ramírez Mateo<br></div> Desarrollador de Software<br></div></div>
</div>
_______________________________________________<br>Pw_forum mailing list<br><a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br><a href="http://pwscf.org/mailman/listinfo/pw_forum" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a></div></blockquote></div><br><div>
-- <br><br>Giovanni Cantele, PhD<br>CNR-SPIN<br>c/o Dipartimento di Fisica<br>Universita' di Napoli "Federico II"<br>Complesso Universitario M. S. Angelo - Ed. 6<br>Via Cintia, I-80126, Napoli, Italy<br>e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a><br>Phone: <a href="tel:%2B39%20081%20676910" value="+39081676910" target="_blank">+39 081 676910</a><br>Skype contact: giocan74<br><br>ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a><br>Web page: <a href="http://people.na.infn.it/~cantele" target="_blank">http://people.na.infn.it/~cantele</a><br>
</div>
<br></div></div></div></div></div><br>_______________________________________________<br>
Pw_forum mailing list<br>
<a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
<a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><div>El éxito solo es para los que se arriesgan por sus objetivos.<br><br> Máximo Ramírez Mateo<br></div> Desarrollador de Software<br></div></div>
</div>