[QE-users] NEB calculation no symmetry found
Paolo Giannozzi
p.giannozzi at gmail.com
Thu Feb 14 07:55:27 CET 2019
On Wed, Feb 13, 2019 at 10:07 PM Paolo Giannozzi <p.giannozzi at gmail.com>
wrote:
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.
>
and, by the way, this recent thread explains why it is not a good thing to
have symmetry in NEB images:
http://lists.quantum-espresso.org/pipermail/users/2019-February/042111.html
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
>
>
--
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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