<div dir="ltr"><pre class="gmail-tw-data-text gmail-tw-text-large gmail-XcVN5d gmail-tw-ta" id="gmail-tw-target-text" dir="ltr" style="unicode-bidi:isolate;line-height:36px;background-color:rgb(248,249,250);border:none;padding:2px 0.14em 2px 0px;font-family:inherit;overflow:hidden;width:277.017px;white-space:pre-wrap"><span lang="en" style="">Dear Michel, thanks for your tips.
Wonderful! I was successful. </span></pre><pre class="gmail-tw-data-text gmail-tw-text-large gmail-XcVN5d gmail-tw-ta" id="gmail-tw-target-text" dir="ltr" style="unicode-bidi:isolate;line-height:36px;background-color:rgb(248,249,250);border:none;padding:2px 0.14em 2px 0px;font-family:inherit;overflow:hidden;width:277.017px;white-space:pre-wrap"><span lang="en" style="">Thank you very much. </span></pre></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Em ter., 28 de jul. de 2020 às 16:34, <<a href="mailto:michel@if.usp.br">michel@if.usp.br</a>> escreveu:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br>
Dear Regina,<br>
<br>
What about the directory of the flag outdir, do you have write <br>
permission there? Try to set the outdir to the folder you are running <br>
dist.x<br>
<br>
Michel Marcondes<br>
Postdoctoral Research Scientist<br>
Universidade de Sao Paulo<br>
Departamento de Fisica dos Materiais<br>
Instituto de Fisica<br>
Sao Paulo, SP<br>
<a href="http://lattes.cnpq.br/9541158390223884" rel="noreferrer" target="_blank">http://lattes.cnpq.br/9541158390223884</a><br>
<br>
Quoting Regina Lelis de Sousa <<a href="mailto:rlsousa@mail.uft.edu.br" target="_blank">rlsousa@mail.uft.edu.br</a>>:<br>
<br>
> Dear Michel, thanks for your tips. I tried to run "dist.x" again using the<br>
> input file pw.x, but the following error message is displayed:<br>
> "<br>
> ...<br>
> Current dimensions of program PWSCF are:<br>
> Max number of different atomic species (ntypx) = 10<br>
> Max number of k-points (npk) = 40000<br>
> Max angular momentum in pseudopotentials (lmaxx) = 3<br>
><br>
> mkdir fail: [2] No such file or directory<br>
><br>
> <br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> Error in routine check_tempdir (1):<br>
> tmp_dir cannot be opened<br>
> <br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
><br>
> stopping ...<br>
> --------------------------------------------------------------------------<br>
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD<br>
> with errorcode 1.<br>
><br>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
> You may or may not see output from other processes, depending on<br>
> exactly when Open MPI kills them.<br>
> --------------------------------------------------------------------------<br>
> "<br>
><br>
> I wonder if you had a problem similar to this. I don't understand what's<br>
> going on, because I'm running "dist.x" in a directory with permissions to<br>
> read and write data.<br>
> Thanks in advance.<br>
><br>
> Em seg., 27 de jul. de 2020 às 19:04, <<a href="mailto:michel@if.usp.br" target="_blank">michel@if.usp.br</a>> escreveu:<br>
><br>
>><br>
>> Hi Regina,<br>
>><br>
>> Dist.x can read the standard pw.x input. Just use the same input file<br>
>> you used in the pw.x calculation and it should work.<br>
>><br>
>> Best regards,<br>
>><br>
>> Michel Marcondes<br>
>> Postdoctoral Research Scientist<br>
>> Universidade de Sao Paulo<br>
>> Departamento de Fisica dos Materiais<br>
>> Instituto de Fisica<br>
>> Sao Paulo, SP<br>
>> <a href="http://lattes.cnpq.br/9541158390223884" rel="noreferrer" target="_blank">http://lattes.cnpq.br/9541158390223884</a><br>
>><br>
>> Quoting Regina Lelis de Sousa <<a href="mailto:rlsousa@mail.uft.edu.br" target="_blank">rlsousa@mail.uft.edu.br</a>>:<br>
>><br>
>> > Dear users,<br>
>> > I am trying to use the “dist.x” tool, but I am not being successful. I<br>
>> made<br>
>> > the input following the instructions that were in the header of the<br>
>> > pwtools/dist.f file:<br>
>> > "4 4 8.1373549243 0.0 4.64457064033418 0. 0. 0.<br>
>> > ATOMIC_POSITIONS {angstrom}<br>
>> > Cd 0.000000000 2.471758676 2.929708140<br>
>> > Se 0.000000000 -0.003943951 2.578112496<br>
>> > Cd 0.000000 2.471759 6.429708<br>
>> > Se 0.000000 -0.003944 6.078112"<br>
>> ><br>
>> > The crystal is hexagonal and we have 4 atoms at the base. However, when I<br>
>> > run “dist.x”, I get the following error message:<br>
>> > " Parallel version (MPI), running on 1 processors<br>
>> ><br>
>> > MPI processes distributed on 1 nodes<br>
>> > Waiting for input...<br>
>> > Reading input from standard input<br>
>> ><br>
>> ><br>
>> ><br>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
>> > Error in routine read_namelists (1):<br>
>> > bad line in namelist &control: "Se 0.000000 -0.003944<br>
>> > 6.078112" (error could be in the previous line)<br>
>> ><br>
>> ><br>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
>> > ".<br>
>> ><br>
>> > In addition, I found on the link: "<br>
>> > <a href="https://www.quantum-espresso.org/Doc/pw_user_guide/node6.html" rel="noreferrer" target="_blank">https://www.quantum-espresso.org/Doc/pw_user_guide/node6.html</a>" the<br>
>> > following description: "dist.x symbolic link to pw.x: reads input data<br>
>> for<br>
>> > PWscf, calculates distances and angles between atoms in a cell, taking<br>
>> into<br>
>> > account periodicity ". Therefore, I have doubts whether or not I am using<br>
>> > the correct input.<br>
>> ><br>
>> > If anyone can help me solve this problem, I would be grateful.<br>
>> > Thanks in advance.<br>
>> ><br>
>> > --<br>
>> > Tenha uma ótima semana,<br>
>> ><br>
>> > Atenciosamente,<br>
>> ><br>
>> ><br>
>> > *Dra. Regina Lélis de Sousa*<br>
>> ><br>
>> > Professora do Curso de Licenciatura em Física e do MNPEF. Pesquisadora<br>
>> do L<br>
>> > ABMADE.<br>
>> > <<a href="http://www.uft.edu.br/yyyy" rel="noreferrer" target="_blank">http://www.uft.edu.br/yyyy</a>><br>
>> ><br>
>> > <a href="http://www.uft.edu.br/" rel="noreferrer" target="_blank">www.uft.edu.br/</a> <<a href="http://www.uft.edu.br/yyyy" rel="noreferrer" target="_blank">http://www.uft.edu.br/yyyy</a>> | +55 63 3416-5683 | +55 63<br>
>> > 3416-5625<br>
>> > "Success is knowing that you have done your best and have exploited your<br>
>> > God-given or gene-given abilities to the next maximum extent. More than<br>
>> > this, no one can do...". (Alan Graham MacDiarmid).<br>
>><br>
>><br>
>><br>
>><br>
><br>
> --<br>
> Tenha uma ótima semana,<br>
><br>
> Atenciosamente,<br>
><br>
><br>
> *Dra. Regina Lélis de Sousa*<br>
><br>
> Professora do Curso de Licenciatura em Física e do MNPEF. Pesquisadora do L<br>
> ABMADE.<br>
> <<a href="http://www.uft.edu.br/yyyy" rel="noreferrer" target="_blank">http://www.uft.edu.br/yyyy</a>><br>
><br>
> <a href="http://www.uft.edu.br/" rel="noreferrer" target="_blank">www.uft.edu.br/</a> <<a href="http://www.uft.edu.br/yyyy" rel="noreferrer" target="_blank">http://www.uft.edu.br/yyyy</a>> | +55 63 3416-5683 | +55 63<br>
> 3416-5625<br>
> "Success is knowing that you have done your best and have exploited your<br>
> God-given or gene-given abilities to the next maximum extent. More than<br>
> this, no one can do...". (Alan Graham MacDiarmid).<br>
<br>
<br>
<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">
<span style="font-family:verdana,sans-serif">Tenha uma ótima semana,<br><br>Atenciosamente,<br><br></span><br><span style="font-family:verdana,sans-serif">
</span><span></span><span></span><table width="576" cellspacing="0" cellpadding="7">
<colgroup><col width="78">
<col width="470">
</colgroup><tbody><tr>
<td style="border-color:currentcolor rgb(0,0,10) currentcolor currentcolor;border-style:none solid none none;border-width:medium 1px medium medium;padding:0in 0.08in 0in 0in" width="78"><img src="https://docs.google.com/uc?export=download&id=0B23jiEfYVPV3VF9ycGU0WS0wa0k&revid=0B23jiEfYVPV3YktlNEJVMm5tcmpDVEgyblkzZkxHMlV1bWFrPQ" width="96" height="81"><p align="center"></p>
</td>
<td style="border-color:currentcolor currentcolor currentcolor rgb(0,0,10);border-style:none none none solid;border-width:medium medium medium 1px;padding:0in 0in 0in 0.08in" width="470">
<p style="margin-bottom:0in"><font face="Arial, serif"><font style="font-size:10pt" size="2"><b>Dra.
Regina Lélis de Sousa</b></font></font></p>
<p><font face="Arial, serif"><font style="font-size:10pt" size="2">Professora do Curso
de Licenciatura em Física e do MNPEF. Pesquisadora do L</font></font><font face="Arial, serif"><font style="font-size:10pt" size="2">ABMADE.<a href="http://www.uft.edu.br/yyyy" target="_blank"><br></a></font></font></p><p><font face="Arial, serif"><font style="font-size:10pt" size="2"><a href="http://www.uft.edu.br/yyyy" target="_blank">www.uft.edu.br/</a>
| +55 63 </font></font><font face="Arial, serif"><font style="font-size:10pt" size="2">3416</font></font><font face="Arial, serif"><font style="font-size:10pt" size="2">-56</font></font><font face="Arial, serif"><font style="font-size:10pt" size="2">83</font></font><font face="Arial, serif"><font style="font-size:10pt" size="2">
| +55 63 </font></font><span><font face="Arial, serif"><font style="font-size:10pt" size="2">3416</font></font><font face="Arial, serif"><font style="font-size:10pt" size="2">-56</font></font></span><font face="Arial, serif"><font style="font-size:10pt" size="2">25</font></font></p>
</td>
</tr>
</tbody></table>
<span style="font-family:verdana,sans-serif">"Success is knowing that you have done your best and have exploited your God-given or gene-given abilities to the next maximum extent. More than this, no one can do...". (Alan Graham MacDiarmid).<br></span><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>