<div dir="ltr"><div>Talking in detail about my procedure,</div><div>I opened the following input file (which is for equlibrium lattice parameter of CaO) which has two atomic positions in X-crysden. Then it showed me a structure with 27 atoms whose co-ordinates (read by atoms info) are as follows:</div><div>Ca 0.5 0.5 0.0<br>Ca 0.0 0.0 0.0<br>Ca 0.5 0.0 0.5<br>Ca 0.0 0.5 0.5<br>O 0.0 0.0 0.5<br>O 0.5 0.5 0.5<br>O 0.0 0.5 0.0<br>O 0.5 0.0 0.0<br>Ca 0.5 0.5 1.0<br>Ca 0.0 0.0 1.0<br>O 0.0 0.5 1.0<br>O 0.5 0.0 1.0<br>Ca 0.0 1.0 0.0<br>Ca 0.5 1.0 0.5<br>O 0.0 1.0 0.5<br>O 0.5 1.0 0.0<br>Ca 0.0 1.0 1.0<br>O 0.5 1.0 1.0<br>Ca 1.0 0.0 0.0<br>Ca 1.0 0.5 0.5<br>O 1.0 0.0 0.5<br>O 1.0 0.5 0.0<br>Ca 1.0 0.0 1.0<br>O 1.0 0.5 1.0<br>Ca 1.0 1.0 0.0<br>O 1.0 1.0 0.5<br>Ca 1.0 1.0 1.0</div><div>So, don't I have to include all this atomic positions while calculating energy due to vacancy?<br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Dec 25, 2019 at 11:31 AM Pooja Vyas <<a href="mailto:poojavyas1251995@gmail.com">poojavyas1251995@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>For instance, I tried calculation for Si-Ge alloy with the following script, but there was no such error faced here.</div><div><br></div><div>&control<br> calculation = 'scf',<br> prefix = 'sige'<br> tstress= .true.<br> tprnfor= .true.<br> outdir = '/home/userpooja/cao.oct/'<br> pseudo_dir = '/home/userpooja/cao.oct/pseudo/'<br> /<br> &system<br> ibrav = 0,<br> celldm(1) = 5.4492,<br> nat = 16,<br> ntyp = 2,<br> ecutwfc = 100,<br>/<br>&electrons<br> mixing_beta = 0.7<br> /<br><br>ATOMIC_SPECIES<br><br>Si 28.0855 Si.pz-vbc.UPF<br>Ge 72.64 Ge.pz-bhs.UPF<br><br>ATOMIC_POSITIONS<br>Si 0.0 0.0 0.0<br>Si 0.5 0.5 0.0<br>Si 0.5 0.0 0.5<br>Ge 0.0 0.5 0.5<br>Ge 0.25 0.25 0.25<br>Ge 0.75 0.75 0.25<br>Ge 0.75 0.25 0.75<br>Ge 0.25 0.75 0.75<br>Si 1.0 0.5 0.5<br>Si 1.0 1.0 0.0<br>Ge 1.25 0.25 0.25<br>Ge 1.5 0.0 0.5<br>Ge 1.5 0.5 0.0<br>Si 1.75 0.75 0.25<br>Si 1.75 0.25 0.75<br>Si 1.25 0.75 0.75<br><br>CELL_PARAMETERS<br>2.0 0.0 0.0<br>0.0 1.0 0.0<br>0.0 0.0 1.0<br><br>K_POINTS (automatic)<br> 11 11 11 1 1 1<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Dec 25, 2019 at 11:28 AM Pooja Vyas <<a href="mailto:poojavyas1251995@gmail.com" target="_blank">poojavyas1251995@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Respected Sir/Madam,</div><div>I want to calculate the energy due to vacancy in CaO. I need to create a supercell. So for that, don't I need all the above atomic positions of CaO in input file? Are only two atomic positions (0,0,0) and (0.5,0.5,0.5) enough? If yes, how can I create vacancy with just two atomic positions? I searched for a query similar to mine, but couldn't get any. <br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Dec 17, 2019 at 6:23 PM Offermans Willem <<a href="mailto:willem.offermans@vito.be" target="_blank">willem.offermans@vito.be</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>Please explain why you are asking for another forum for Quantum Espresso users.</div>
<div><br>
</div>
<div>So even if there are other fora, to my opinion 1 forum is just fine and preferable.</div>
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<blockquote type="cite">
<div>On 17 Dec 2019, at 11:25, Pooja Vyas <<a href="mailto:poojavyas1251995@gmail.com" target="_blank">poojavyas1251995@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Is there any other forum available where discussions regarding Quantum Espresso can be done with other Quantum Espresso users?<br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Dec 17, 2019 at 3:34 PM Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>sorry, at some point of my message I (or the automatic correction) wrote
<div>CaO has a cubic bcc lattice</div>
<div>that instead was meant</div>
<div><span>CaO has a cubic fcc lattice</span></div>
<div><font><span><br>
</span></font></div>
<div><font><span>Giovanni<br>
</span></font>
<div><br>
<blockquote type="cite">
<div>On 17 Dec 2019, at 10:47, Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>> wrote:</div>
<br>
<div>
<div>You’re using ibrav=2, which corresponds to a cubic F (fcc). The atomic positions are in alat units. As such, as clearly stated by the error message,
<div>atoms 1 and 2 are equivalent. Indeed, their positions are:</div>
<div>#1 --> a/2 a/2 0</div>
<div>#2 —> 0 0 0</div>
<div><br>
</div>
<div>Atom #1 lies at the center of a face, its position for a cubic bcc lattice is obtained by translating the lattice site at the origin (where atom #2 lies)</div>
<div>by a direct lattice vector. </div>
<div><br>
</div>
<div>You must specify *ONLY* inequivalent atoms, their periodic replicas cannot be included in the list of atoms. There are many other similar</div>
<div>overlapping atoms, such as</div>
<div>Ca —> 0 0 0 with Ca —> 1 1 0 or Ca —> 0 0 1.</div>
<div><br>
</div>
<div>Actually, to be honest, you should probably remove *ALL ATOMS BUT TWO*. Indeed, as far as I remember, CaO has a cubic bcc lattice</div>
<div>with on Ca atom in 0 0 0 and on O atom in a/2 a/2 a/2 (but please check!).</div>
<div><br>
</div>
<div>Provided that, in my opinion, any question is welcome, my suggestion is that you try to give a solution to error messages by yourself before</div>
<div>asking people, because what you learn if you “try to solve” is priceless if compared to what you learn if you “ask to solve”. In this respect,</div>
<div>Quantum-ESPRESSO is an exceptional lab to make experience, since especially (but not only) for the easiest tasks (such as build the band structure of</div>
<div>simple solids) many error messages are self-explanatory and user-friendly! ;-)</div>
<div><br>
</div>
<div>Giovanni</div>
<div><br>
</div>
<div><br>
<div><br>
<blockquote type="cite">
<div>On 17 Dec 2019, at 10:25, Pooja Vyas <<a href="mailto:poojavyas1251995@gmail.com" target="_blank">poojavyas1251995@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">
<div>Following is my input file. I obtained the atomic position using X-CrysDen. But when I run the file it shows me an error message.</div>
<div><br>
</div>
<div>Input file:</div>
<div>&control<br>
calculation = 'scf',<br>
prefix = '9.1334'<br>
tstress= .true.<br>
tprnfor= .true.<br>
outdir = '/home/userpooja/cao.oct/'<br>
pseudo_dir = '/home/userpooja/cao.oct/pseudo/'<br>
/<br>
&system<br>
ibrav = 2,<br>
celldm(1) = 9.1334,<br>
nat = 27,<br>
ntyp = 2,<br>
ecutwfc = 100,<br>
/<br>
&electrons<br>
mixing_beta = 0.7<br>
/<br>
<br>
ATOMIC_SPECIES<br>
<br>
Ca 40.078 Ca.pbe-nsp-van.UPF<br>
O 15.999 O.pbe-van_ak.UPF<br>
<br>
ATOMIC_POSITIONS (alat)<br>
Ca 0.5 0.5 0.0<br>
Ca 0.0 0.0 0.0<br>
Ca 0.5 0.0 0.5<br>
Ca 0.0 0.5 0.5<br>
O 0.0 0.0 0.5<br>
O 0.5 0.5 0.5<br>
O 0.0 0.5 0.0<br>
O 0.5 0.0 0.0<br>
Ca 0.5 0.5 1.0<br>
Ca 0.0 0.0 1.0<br>
O 0.0 0.5 1.0<br>
O 0.5 0.0 1.0<br>
Ca 0.0 1.0 0.0<br>
Ca 0.5 1.0 0.5<br>
O 0.0 1.0 0.5<br>
O 0.5 1.0 0.0<br>
Ca 0.0 1.0 1.0<br>
O 0.5 1.0 1.0<br>
Ca 1.0 0.0 0.0<br>
Ca 1.0 0.5 0.5<br>
O 1.0 0.0 0.5<br>
O 1.0 0.5 0.0<br>
Ca 1.0 0.0 1.0<br>
O 1.0 0.5 1.0<br>
Ca 1.0 1.0 0.0<br>
O 1.0 1.0 0.5<br>
Ca 1.0 1.0 1.0<br>
K_POINTS (automatic)<br>
11 11 11 1 1 1</div>
<div><br>
</div>
<div>Error: <br>
</div>
<div><br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
task # 17<br>
from check_atoms : error # 1<br>
atoms # 1 and # 2 differ by lattice vector (-1, 1, 0) in crystal axis<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
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<div style="text-align:start;text-indent:0px"><span style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px">-- <br>
<br>
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<div style="text-align:start;text-indent:0px"><span style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px">-- <br>
<br>
Giovanni Cantele, PhD</span></div>
<div style="text-align:start;text-indent:0px"><span style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px"><br>
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Via Cintia, I-80126, Napoli, Italy</span></div>
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