<div dir="ltr">Hello Espresso users<div><br><div>I want to relax the given structure in below that is a Clathrate with BCC structure and 54 atoms. I am getting errors about overlap of atoms.</div><div>As Dr.<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Lorenzo Paulatto mentioned if I apply the </span><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">basis vector a/2*(1,1,1) </span><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">of the bcc lattice I notice that some atoms overlap each other (1 and 5,2 and 6 ,....).</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">I am sure that the positions are correct and I used other softwares like ABINIT and VASP and got relaxed structures without trouble. Likely I should </span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">stop checking the </span><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">symmetry</span><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "> of structure.Does any one know how can I do that?</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">This is my input file:</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><div>
&CONTROL</div><div> title = Ba ,</div><div> calculation = 'relax' ,</div><div> restart_mode = 'from_scratch' ,</div><div> wf_collect = .true. ,</div>
<div> outdir = '/lustre/work/pnorouzz/espresso//Ba/relax' ,</div><div> wfcdir = '/lustre/work/pnorouzz/espresso/Ba/relax' ,</div><div> pseudo_dir = '/lustre/work/pnorouzz/espresso//Ba/relax' ,</div>
<div> dt = 20 ,</div><div> /</div><div> &SYSTEM</div><div> ibrav = 3, </div><div> celldm(1) = 22, </div><div> nat = 54,</div><div> ntyp = 3,</div>
<div> ecutwfc = 50 ,</div><div> ecutrho = 500 ,</div><div> /</div><div> &ELECTRONS</div><div> conv_thr = 1.D-8 ,</div><div> mixing_beta = 0.5D0 ,</div>
<div> /</div><div> &IONS</div><div> ion_dynamics = 'damp' ,</div><div> pot_extrapolation = 'second_order' ,</div><div> wfc_extrapolation = 'second_order' ,</div>
<div> upscale = 100 ,</div><div> /</div><div>ATOMIC_SPECIES</div><div> Ba 137.327 Ba.pw91-nsp-van.UPF</div><div> Sn 118.710 Sn.pw91-n-van.UPF</div><div> Ga 71.0843639 Ga.pw91-n-van.UPF </div>
<div>ATOMIC_POSITIONS </div><div>Ba<span class="Apple-tab-span" style="white-space:pre"> </span>0.186<span class="Apple-tab-span" style="white-space:pre"> </span>0.186<span class="Apple-tab-span" style="white-space:pre"> </span>0.186</div>
<div>Ba<span class="Apple-tab-span" style="white-space:pre"> </span>0.814<span class="Apple-tab-span" style="white-space:pre"> </span>0.814<span class="Apple-tab-span" style="white-space:pre"> </span>0.186</div><div>Ba<span class="Apple-tab-span" style="white-space:pre"> </span>0.814<span class="Apple-tab-span" style="white-space:pre"> </span>0.186<span class="Apple-tab-span" style="white-space:pre"> </span>0.814</div>
<div>Ba<span class="Apple-tab-span" style="white-space:pre"> </span>0.186<span class="Apple-tab-span" style="white-space:pre"> </span>0.814<span class="Apple-tab-span" style="white-space:pre"> </span>0.814</div><div>Ba<span class="Apple-tab-span" style="white-space:pre"> </span>0.686<span class="Apple-tab-span" style="white-space:pre"> </span>0.686<span class="Apple-tab-span" style="white-space:pre"> </span>0.686</div>
<div>Ba<span class="Apple-tab-span" style="white-space:pre"> </span>0.314<span class="Apple-tab-span" style="white-space:pre"> </span>0.314<span class="Apple-tab-span" style="white-space:pre"> </span>0.686</div><div>Ba<span class="Apple-tab-span" style="white-space:pre"> </span>0.314<span class="Apple-tab-span" style="white-space:pre"> </span>0.686<span class="Apple-tab-span" style="white-space:pre"> </span>0.314</div>
<div>Ba<span class="Apple-tab-span" style="white-space:pre"> </span>0.686<span class="Apple-tab-span" style="white-space:pre"> </span>0.314<span class="Apple-tab-span" style="white-space:pre"> </span>0.314</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0.5</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.6348<span class="Apple-tab-span" style="white-space:pre"> </span>0.6348<span class="Apple-tab-span" style="white-space:pre"> </span>0.3652</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.3652<span class="Apple-tab-span" style="white-space:pre"> </span>0.6348<span class="Apple-tab-span" style="white-space:pre"> </span>0.6348</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.1348<span class="Apple-tab-span" style="white-space:pre"> </span>0.1348<span class="Apple-tab-span" style="white-space:pre"> </span>0.8652</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.8652<span class="Apple-tab-span" style="white-space:pre"> </span>0.1348<span class="Apple-tab-span" style="white-space:pre"> </span>0.1348</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596<span class="Apple-tab-span" style="white-space:pre"> </span>0.1441</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404<span class="Apple-tab-span" style="white-space:pre"> </span>0.1441</div><div>
Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596<span class="Apple-tab-span" style="white-space:pre"> </span>0.8559</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404<span class="Apple-tab-span" style="white-space:pre"> </span>0.8559</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.1441<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596</div><div>
Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.8559<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596<span class="Apple-tab-span" style="white-space:pre"> </span>0.1441<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404<span class="Apple-tab-span" style="white-space:pre"> </span>0.1441<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404</div><div>
Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596<span class="Apple-tab-span" style="white-space:pre"> </span>0.6441</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404<span class="Apple-tab-span" style="white-space:pre"> </span>0.6441</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596<span class="Apple-tab-span" style="white-space:pre"> </span>0.3559</div><div>
Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404<span class="Apple-tab-span" style="white-space:pre"> </span>0.3559</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.6441<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.3559<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404</div><div>
Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596<span class="Apple-tab-span" style="white-space:pre"> </span>0.6441<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404<span class="Apple-tab-span" style="white-space:pre"> </span>0.6441<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596<span class="Apple-tab-span" style="white-space:pre"> </span>0.3559<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404</div><div>
Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404<span class="Apple-tab-span" style="white-space:pre"> </span>0.3559<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0.25<span class="Apple-tab-span" style="white-space:pre"> </span>0.5</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0.75<span class="Apple-tab-span" style="white-space:pre"> </span>0.5</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0.25</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0.75</div><div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0.25</div>
<div>Sn<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0.75</div><div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.3652<span class="Apple-tab-span" style="white-space:pre"> </span>0.3652<span class="Apple-tab-span" style="white-space:pre"> </span>0.3652</div>
<div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.6348<span class="Apple-tab-span" style="white-space:pre"> </span>0.3652<span class="Apple-tab-span" style="white-space:pre"> </span>0.6348</div><div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.8652<span class="Apple-tab-span" style="white-space:pre"> </span>0.8652<span class="Apple-tab-span" style="white-space:pre"> </span>0.8652</div>
<div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.1348<span class="Apple-tab-span" style="white-space:pre"> </span>0.8652<span class="Apple-tab-span" style="white-space:pre"> </span>0.1348</div><div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.1441<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404</div>
<div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.8559<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596</div><div>
Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596<span class="Apple-tab-span" style="white-space:pre"> </span>0.8559<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404</div><div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.58404<span class="Apple-tab-span" style="white-space:pre"> </span>0.8559<span class="Apple-tab-span" style="white-space:pre"> </span>0.41596</div>
<div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.6441<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404</div><div>
Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.3559<span class="Apple-tab-span" style="white-space:pre"> </span>0.08404<span class="Apple-tab-span" style="white-space:pre"> </span>0.91596</div><div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.25<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0</div>
<div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.75<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0.25<span class="Apple-tab-span" style="white-space:pre"> </span>0</div>
<div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.5<span class="Apple-tab-span" style="white-space:pre"> </span>0.75<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.25<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0.5</div>
<div>Ga<span class="Apple-tab-span" style="white-space:pre"> </span>0.75<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>0.5</div><div>K_POINTS automatic </div>
<div>4 4 4 0 0 0 </div><div><br></div></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Best regards,Payam Norouzzadeh</span></div><div>
<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><br></div></div></div>