[QE-users] NEB calculation no symmetry found
Paolo Giannozzi
p.giannozzi at gmail.com
Thu Feb 14 09:37:13 CET 2019
On Thu, Feb 14, 2019 at 8:34 AM Offermans Willem <willem.offermans at vito.be>
wrote:
>
> Probably you meant to refer to another mail thread. Probably the one
> started by Abdul Shaik.
> http://lists.quantum-espresso.org/pipermail/users/2019-February/042084.html
>
yes, sorry, I cut-and-pasted the wrong address
But can you explicitly make clear why it is not a good idea to have
> symmetry in a NEB calculation?
>
because unlike structural optimization there is no guarantee that the
starting symmetry will be kept during the run. When initial symmetry is
lost, you may end up with more k-points and the code crashes. Of course, if
this does not happen, it is perfectly fine to use symmetry in NEB.
So neb.x is able to detect symmetry. Only in my particular case, it is not
> able to and I wonder why.
the reason has been explained no less than 1001 times: if the code does not
find a symmetry, it's not there, according to the criteria implemented in
the code.
Paolo
On 14 Feb 2019, at 07:55, Paolo Giannozzi <p.giannozzi at gmail.com> wrote:
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
>>
>> <vito.jpg>
>>
>> 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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--
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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