[QE-users] NEB calculation no symmetry found

Wed Feb 13 22:07:32 CET 2019

On Wed, Feb 13, 2019 at 11:53 AM Offermans Willem <willem.offermans at vito.be>
wrote:

If I try to start a calculation, based on the xml input file, I got
> following error
>

It's a long story. A first xml input was implemented years ago but it never
took off. The new xml input is more or less ready but the transition from
"more or less ready" to "done" has still a sizable activation energy. You
can start a calculation from the files pw_1.in, pw_2.in, etc., that the NEB
code creates in the current execution directory. They contain input data
for the starting points on the NEB chain. I did that and got no symmetry,
by the way.

Paolo

$ pw.x -in pd.xml
>
>      Program PWSCF v.6.3 starts on 13Feb2019 at 11:49:38
>
>      This program is part of the open-source Quantum ESPRESSO suite
>      for quantum simulation of materials; please cite
>          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>          "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
>           URL http://www.quantum-espresso.org",
>      in publications or presentations arising from this work. More details
> at
>      http://www.quantum-espresso.org/quote
>
>      Parallel version (MPI & OpenMP), running on      20 processor cores
>      Number of MPI processes:                 1
>      Threads/MPI process:                    20
>
>      MPI processes distributed on     1 nodes
>      Reading xml input from pd.xml
>
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      Error in routine read_input (1):
>      xml input disabled
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
> :
> system msg for write_line failure : Bad file descriptor
>
> So I cannot easily play with the settings.
>
>
> Met vriendelijke groeten,
> Mit freundlichen Grüßen,
> With kind regards,
>
>
> Willem Offermans
> Researcher Electrocatalysis SCT
> VITO NV | Boeretang 200 | 2400 Mol
> Phone:+32(0)14335263 Mobile:+32(0)492182073
>
> Willem.Offermans at Vito.be
>
>
> On 13 Feb 2019, at 11:24, Offermans Willem <willem.offermans at vito.be>
> wrote:
>
> Dear Stefano,
>
>
> No, point symmetry doesn’t depend on units, i.e. squeezing or expanding
> the system equally in all directions doesn’t change symmetry. I agree!
>
> The presence of the inversion symmetry is not to save computational time,
> but to correct for possible dipole interactions.
>
> Anyway, the point is that neb.x is not able to detect and to use the
> symmetry of the involved images. This is weird, since the task of
> optimising/calculating the images
> will be delegated to pw.x, I suppose. And I showed that pw.x detects and
> uses the symmetry. Maybe the keyword ``use_all_frac     = .true.`` is not
> considered for a NEB calculation.
>
>
>
> Met vriendelijke groeten,
> Mit freundlichen Grüßen,
> With kind regards,
>
>
> Willem Offermans
> Researcher Electrocatalysis SCT
> VITO NV | Boeretang 200 | 2400 Mol
> Phone:+32(0)14335263 Mobile:+32(0)492182073
>
> Willem.Offermans at Vito.be
>
> <vito.jpg>
>
> On 13 Feb 2019, at 10:04, Stefano Baroni <baroni at sissa.it> wrote:
>
>
>
> On 13 Feb 2019, at 09:50, Offermans Willem <willem.offermans at vito.be>
> wrote:
>
> Dear Quantum Espresso friends,
>
>
> Dear Wilem:
>
> I made a mistake in my previous e-mail.
> The atom coordinates are not in Angstrom but in Bohr.
>
>
> I have corrected this in my calculations, but still no symmetry found.
>
>
> I would be surprised if you found the contrary. I cannot imagine that the
> point symmetry of any system could depend on units: do you?
>
> $ grep "ymmetr" pd_?/PW.out
> pd_1/PW.out:     No symmetry found
> pd_2/PW.out:     No symmetry found
> pd_3/PW.out:     No symmetry found
> pd_4/PW.out:     No symmetry found
> pd_5/PW.out:     No symmetry found
> pd_6/PW.out:     No symmetry found
> pd_7/PW.out:     No symmetry found
>
> So the question remains. What is the reason that the symmetry cannot be
> detected?
>
> As an extra check I have made a scf calculation on the last image.
>
> $ grep "Sym. Ops." pd.out
>       2 Sym. Ops., with inversion, found ( 1 have fractional translation)
>
> So pw.x can find the symmetry whereas neb.x cannot!
>
>
> Just guessing: maybe for some reasons neb restricts its search to pure
> rotations (no fractional translations involved). Also, I have the
> impression that inversion symmetry does not help save any computer time,
> because in practice it has the same effects as time-reversal symmetry,
> which always holds.
>
> Just my worthless 5 cents …
> SB
>
>
> —
> Stefano Baroni - Trieste —  http://stefano.baroni.me
>
>
>
>
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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