<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><br class=""><blockquote type="cite" class="">On 18 Nov 2015, at 22:55, tomy tunde <<a href="mailto:rskadeniji@yahoo.com" class="">rskadeniji@yahoo.com</a>> wrote:<br class=""><br class="">Dear Giovanni,<br class="">I appreciated your corrections you made for me on what i send.<br class="">Sir, i have used visualization software with xcrysden at 2x2x2 </blockquote><div class=""><br class=""></div><div class="">in which way? I have just opened the input file you have provided in attachment and XcrysDen, after displaying the structure,</div><div class="">gives the following messages:</div><div class="">WARNING: Atom 1 and atom 4 overlap !!! Atom 4 deleted !!!<br class="">WARNING: Atom 1 and atom 7 overlap !!! Atom 7 deleted !!!<br class="">WARNING: Atom 1 and atom 8 overlap !!! Atom 8 deleted !!!<br class="">WARNING: Atom 1 and atom 11 overlap !!! Atom 11 deleted !!!<br class="">WARNING: Atom 1 and atom 14 overlap !!! Atom 14 deleted !!!<br class="">WARNING: Atom 1 and atom 15 overlap !!! Atom 15 deleted !!!<br class="">WARNING: Atom 1 and atom 16 overlap !!! Atom 16 deleted !!!<br class="">WARNING: Atom 1 and atom 17 overlap !!! Atom 17 deleted !!!<br class="">WARNING: Atom 1 and atom 18 overlap !!! Atom 18 deleted !!!<br class="">WARNING: Atom 1 and atom 21 overlap !!! Atom 21 deleted !!!<br class="">….</div><div class="">….</div><div class=""><br class=""></div><div class="">Moreover, if you click on the “translational asymmetric unit” button, that displays the atoms in the primitive unit cell (that is, just those positions you provide in the input), you get the attached image, from which it is clear that while you replicated the positions in a 2x2x2 unit cell, you forgot to provide the corresponding unit cell dimensions (there are atoms out the cell boundaries). </div><div class=""><br class=""></div><div class="">Example (same as I already pointed out in the previous message):</div><div class="">Atom 1</div><div class="">Mg 0.0000000000 0.0000000000 0.0000000000</div><div class="">Atom 4</div><div class="">Mg 0.0000000000 0.0000000000 3.5724606980</div><div class="">Their positions differ by the vector (0., 0., 3.572 A). But the unit cell vector along the c-axis has coordinates (0, 0, c) with c=1.155*5.845*0.529177 A = 3.572 A. Therefore, the positions of atoms 1 and 4 are periodic replicas of each other!!!! The pw.x error message just clearly says that you put two different atoms in the same or equivalent positions, which means that your input is wrong. You must update the cell size and be sure that what you have built is the correct 2x2x2 supercell.</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><blockquote type="cite" class="">but i changed the pseudopotential of Mg </blockquote><div class=""><br class=""></div><div class="">Why? By changing the pseudo potential you’ll never cure an error associated to atomic positions!!!!</div><div class=""><br class=""></div><div class="">Giovanni</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><blockquote type="cite" class="">but it gave me error as shown bel %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</blockquote><blockquote type="cite" class=""> task # 0<br class=""> from check_atoms : error # 1<br class=""> atoms # 1 and # 4 overlap!<br class="">Sir i need further assistance for it with my new scf and xsf file attach<br class="">&control<br class=""> calculation = 'scf'<br class=""> restart_mode='from_scratch'<br class=""> prefix='MgB2',<br class="">pseudo_dir = '/home/adeniji/espresso-5.0/pseudo/', <br class=""> outdir='./'<br class="">/<br class="">&system<br class=""> ibrav=4,<br class=""> celldm(1)=5.845,<br class=""> celldm(3)=1.155,<br class=""> nat=43,<br class=""> ntyp=2, <br class=""> ecutwfc =45.0,<br class=""> ecutrho = 450.0,<br class=""> occupations= 'smearing',<br class=""> degauss= 0.03,<br class=""> smearing= 'cold',<br class=""> /<br class=""> &electrons<br class=""> mixing_beta = 0.7<br class=""> conv_thr = 1.0d-12<br class="">/<br class=""> ATOMIC_SPECIES<br class=""> Mg 24.31 Mg.pbe-sp-rrkjus.UPF<br class=""> B 10.81 B.pbe-n-rrkjus.UPF<br class="">ATOMIC_POSITIONS {ANGSTROM}<br class=""> Mg 0.0000000000 0.0000000000 0.0000000000<br class=""> B -0.0000000000 1.7857663930 1.7661255920<br class=""> B 1.5465197830 0.8928986620 1.7661255920<br class=""> Mg 0.0000000000 0.0000000000 3.5724606980<br class=""> B -0.0000000000 1.7857663930 5.3385862900<br class=""> B 1.5465197830 0.8928986620 5.3385862900<br class=""> Mg 0.0000000000 0.0000000000 7.1449213960<br class=""> Mg -1.5465197830 2.6786508380 0.0000000000<br class=""> B -1.5465197830 4.4644172310 1.7661255920<br class=""> B -0.0000000000 3.5715495000 1.7661255920<br class=""> Mg -1.5465197830 2.6786508380 3.5724606980<br class=""> B -1.5465197830 4.4644172310 5.3385862900<br class=""> B -0.0000000000 3.5715495000 5.3385862900<br class=""> Mg -1.5465197830 2.6786508380 7.1449213960<br class=""> Mg -3.0930395660 5.3573016760 0.0000000000<br class=""> Mg -3.0930395660 5.3573016760 3.5724606980<br class=""> Mg -3.0930395660 5.3573016760 7.1449213960<br class=""> Mg 3.0930395650 0.0000000000 0.0000000000<br class=""> B 3.0930395650 1.7857663930 1.7661255920<br class=""> B 4.6395593480 0.8928986620 1.7661255920<br class=""> Mg 3.0930395650 0.0000000000 3.5724606980<br class=""> B 3.0930395650 1.7857663930 5.3385862900<br class=""> B 4.6395593480 0.8928986620 5.3385862900<br class=""> Mg 3.0930395650 0.0000000000 7.1449213960<br class=""> Mg 1.5465197820 2.6786508380 0.0000000000<br class=""> B 1.5465197820 4.4644172310 1.7661255920<br class=""> B 3.0930395650 3.5715495000 1.7661255920<br class=""> Mg 1.5465197820 2.6786508380 3.5724606980<br class=""> B 1.5465197820 4.4644172310 5.3385862900<br class=""> B 3.0930395650 3.5715495000 5.3385862900<br class=""> Mg 1.5465197820 2.6786508380 7.1449213960<br class=""> Mg -0.0000000010 5.3573016760 0.0000000000<br class=""> Mg -0.0000000010 5.3573016760 3.5724606980<br class=""> Mg -0.0000000010 5.3573016760 7.1449213960<br class=""> Mg 6.1860791300 0.0000000000 0.0000000000<br class=""> Mg 6.1860791300 0.0000000000 3.5724606980<br class=""> Mg 6.1860791300 0.0000000000 7.1449213960<br class=""> Mg 4.6395593470 2.6786508380 0.0000000000<br class=""> Mg 4.6395593470 2.6786508380 3.5724606980<br class=""> Mg 4.6395593470 2.6786508380 7.1449213960<br class=""> Mg 3.0930395640 5.3573016760 0.0000000000<br class=""> Mg 3.0930395640 5.3573016760 3.5724606980<br class=""> Mg 3.0930395640 5.3573016760 7.1449213960<br class="">K_POINTS {automatic}<br class="">12 12 6 0 0 0<br class="">Thanks your assistance<br class="">ADENIJI RASAKI IDOWU<br class="">_______________________________________________<br class="">Pw_forum mailing list<br class=""><a href="mailto:Pw_forum@pwscf.org" class="">Pw_forum@pwscf.org</a><br class="">http://pwscf.org/mailman/listinfo/pw_forum<br class=""></blockquote><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><blockquote type="cite" class="">ow<img apple-inline="yes" id="02204C05-89BE-4C7F-9F68-720B138B1059" height="466" width="608" apple-width="yes" apple-height="yes" src="cid:A905BFD1-0841-4DE5-BE7A-F891012504BA" class=""><br class=""></blockquote><br class=""><div class=""><br class="webkit-block-placeholder"></div><div class=""><br class="webkit-block-placeholder"></div><div class=""><br class="webkit-block-placeholder"></div><div class=""><br class="webkit-block-placeholder"></div><div class="">-- <br class=""><br class="">Giovanni Cantele, PhD<br class="">CNR-SPIN<br class="">c/o Dipartimento di Fisica<br class="">Universita' di Napoli "Federico II"<br class="">Complesso Universitario M. S. Angelo - Ed. 6<br class="">Via Cintia, I-80126, Napoli, Italy<br class="">e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" class="">giovanni.cantele@spin.cnr.it</a><br class="">Phone: +39 081 676910<br class="">Skype contact: giocan74<br class=""><br class="">ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" class="">http://www.researcherid.com/rid/A-1951-2009</a><br class="">Web page: <a href="http://people.na.infn.it/~cantele" class="">http://people.na.infn.it/~cantele</a><br class=""></div><br class=""></body></html>