<font color='black' size='2' face='arial'><font face="arial" size="2" color="black">I may be missing something, but when I opened your structure with the XCrysden there were many warning messages, including many messages of atoms overlapped. I don't have Jmole to re-check, but it seems to me that your structure is too much compressed.<br>
<br>
<br>
Fabio Negreiros Ribeiro<br>
Laboratorio de Fisica de Superficies da Universidade Federal de Minas Gerais, Brasil<br>
<br>
<br>
<div style="font-family: arial,helvetica; font-size: 10pt; color: black;">-----Original Message-----<br>
From: Payam Norouzzadeh <payam.norouzzadeh@gmail.com><br>
To: pw_forum@pwscf.org<br>
Sent: Wed, Jun 16, 2010 5:29 pm<br>
Subject: [Pw_forum] overlap of atoms<br>
<br>
<div id="AOLMsgPart_3_41152735-7674-438a-9112-d7b322c5108b">
<div dir="ltr">Hello Espresso users
<div>I have checked the structure I want to relax it by Xcrysden and Jmole and there was no overlap between atoms but Espresso leave</div>
<div>an error message like : overlap between atoms 1 and 5, 2 and 6 ,....</div>
<div>Could someone please have a look to my input file and let me know how can I fix it?</div>
<div><br>
</div>
<div>Best regards,Payam Norouzzadeh</div>
<div><br>
</div>
<div><br>
</div>
<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) = 11.6, </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>
</div>
<!-- end of AOLMsgPart_3_41152735-7674-438a-9112-d7b322c5108b -->
<div id="AOLMsgPart_4_41152735-7674-438a-9112-d7b322c5108b" style="margin: 0px; font-family: Tahoma,Verdana,Arial,Sans-Serif; font-size: 12px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<pre style="font-size: 9pt;"><tt>_______________________________________________<br>
Pw_forum mailing list<br>
<a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
<a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
</tt></pre>
</div>
<!-- end of AOLMsgPart_4_41152735-7674-438a-9112-d7b322c5108b -->
</div>
</font></font>