[QE-users] Dist.x

Tue Jul 28 22:24:16 CEST 2020

Dear Michel, thanks for your tips.
Wonderful! I was successful.

Thank you very much.

Em ter., 28 de jul. de 2020 às 16:34, <michel at if.usp.br> escreveu:

>
> Dear Regina,
>
> What about the directory of the flag outdir, do you have write
> permission there? Try to set the outdir to the folder you are running
> dist.x
>
> Michel Marcondes
> Postdoctoral Research Scientist
> Universidade de Sao Paulo
> Departamento de Fisica dos Materiais
> Instituto de Fisica
> Sao Paulo, SP
> http://lattes.cnpq.br/9541158390223884
>
> Quoting Regina Lelis de Sousa <rlsousa at mail.uft.edu.br>:
>
> > Dear Michel, thanks for your tips. I tried to run "dist.x" again using
> the
> > input file pw.x, but the following error message is displayed:
> >  "
> > ...
> >     Current dimensions of program PWSCF are:
> >      Max number of different atomic species (ntypx) = 10
> >      Max number of k-points (npk) =  40000
> >      Max angular momentum in pseudopotentials (lmaxx) =  3
> >
> > mkdir fail: [2] No such file or directory
> >
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >      Error in routine check_tempdir (1):
> >      tmp_dir cannot be opened
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >      stopping ...
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> > "
> >
> > I wonder if you had a problem similar to this. I don't understand what's
> > going on, because I'm running "dist.x" in a directory with permissions to
> > read and write data.
> > Thanks in advance.
> >
> > Em seg., 27 de jul. de 2020 às 19:04, <michel at if.usp.br> escreveu:
> >
> >>
> >> Hi Regina,
> >>
> >> Dist.x can read the standard pw.x input. Just use the same input file
> >> you used in the pw.x calculation and it should work.
> >>
> >> Best regards,
> >>
> >> Michel Marcondes
> >> Postdoctoral Research Scientist
> >> Universidade de Sao Paulo
> >> Departamento de Fisica dos Materiais
> >> Instituto de Fisica
> >> Sao Paulo, SP
> >> http://lattes.cnpq.br/9541158390223884
> >>
> >> Quoting Regina Lelis de Sousa <rlsousa at mail.uft.edu.br>:
> >>
> >> > Dear users,
> >> > I am trying to use the “dist.x” tool, but I am not being successful. I
> >> made
> >> > the input following the instructions that were in the header of the
> >> > pwtools/dist.f file:
> >> > "4 4 8.1373549243 0.0 4.64457064033418 0. 0. 0.
> >> > ATOMIC_POSITIONS {angstrom}
> >> > Cd       0.000000000   2.471758676   2.929708140
> >> > Se       0.000000000  -0.003943951   2.578112496
> >> > Cd 0.000000 2.471759 6.429708
> >> > Se 0.000000 -0.003944 6.078112"
> >> >
> >> > The crystal is hexagonal and we have 4 atoms at the base. However,
> when I
> >> > run “dist.x”, I get the following error message:
> >> > "     Parallel version (MPI), running on     1 processors
> >> >
> >> >      MPI processes distributed on     1 nodes
> >> >      Waiting for input...
> >> >      Reading input from standard input
> >> >
> >> >
> >> >
> >>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >> >      Error in routine  read_namelists (1):
> >> >       bad line in namelist &control: "Se        0.000000
> -0.003944
> >> >     6.078112" (error could be in the previous line)
> >> >
> >> >
> >>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >> > ".
> >> >
> >> > In addition, I found on the link: "
> >> > https://www.quantum-espresso.org/Doc/pw_user_guide/node6.html" the
> >> > following description: "dist.x symbolic link to pw.x: reads input data
> >> for
> >> > PWscf, calculates distances and angles between atoms in a cell, taking
> >> into
> >> > account periodicity ". Therefore, I have doubts whether or not I am
> using
> >> > the correct input.
> >> >
> >> > If anyone can help me solve this problem, I would be grateful.
> >> > Thanks in advance.
> >> >
> >> > --
> >> > Tenha uma ótima semana,
> >> >
> >> > Atenciosamente,
> >> >
> >> >
> >> > *Dra. Regina Lélis de Sousa*
> >> >
> >> > Professora do Curso de Licenciatura em Física e do MNPEF. Pesquisadora
> >> do L
> >> > ABMADE.
> >> > <http://www.uft.edu.br/yyyy>
> >> >
> >> > www.uft.edu.br/ <http://www.uft.edu.br/yyyy> | +55 63 3416-5683 |
> +55 63
> >> > 3416-5625
> >> > "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).
> >>
> >>
> >>
> >>
> >
> > --
> > Tenha uma ótima semana,
> >
> > Atenciosamente,
> >
> >
> > *Dra. Regina Lélis de Sousa*
> >
> > Professora do Curso de Licenciatura em Física e do MNPEF. Pesquisadora
> do L
> > ABMADE.
> > <http://www.uft.edu.br/yyyy>
> >
> > www.uft.edu.br/ <http://www.uft.edu.br/yyyy> | +55 63 3416-5683 | +55 63
> > 3416-5625
> > "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).
>
>
>
>

-- 
Tenha uma ótima semana,

Atenciosamente,

*Dra. Regina Lélis de Sousa*

Professora do Curso de Licenciatura em Física e do MNPEF. Pesquisadora do L
ABMADE.
<http://www.uft.edu.br/yyyy>

www.uft.edu.br/ <http://www.uft.edu.br/yyyy> | +55 63 3416-5683 | +55 63
3416-5625
"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).
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