[QE-users] NEB calculation no symmetry found

Thu Feb 14 08:33:44 CET 2019

Dear Paolo,

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
The one you are actually referring to, is the one we are in right now.

But can you explicitly make clear why it is not a good idea to have symmetry in a NEB calculation?
I’m not convinced right now.

The model I choose has S2 symmetry and only prevents phenomena to occur, which might break this symmetry.
I don’t expect any problem with that.

Moreover, I don’t think it is on purpose that neb.x cannot detect the symmetry. As the mail thread, started by Abdul Shaik, showed that it was even possible to change the number of k-points for one of the images during the NEB calculation. So neb.x is able to detect symmetry. Only in my particular case, it is not able to and I wonder why.

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<mailto:Willem.Offermans at Vito.be>

[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]

On 14 Feb 2019, at 07:55, Paolo Giannozzi <p.giannozzi at gmail.com<mailto:p.giannozzi at gmail.com>> wrote:

On Wed, Feb 13, 2019 at 10:07 PM Paolo Giannozzi <p.giannozzi at gmail.com<mailto:p.giannozzi at gmail.com>> wrote:

You can start a calculation from the files pw_1.in<http://pw_1.in/>, pw_2.in<http://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<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<mailto:Willem.Offermans at Vito.be>

<vito.jpg>

On 13 Feb 2019, at 11:24, Offermans Willem <willem.offermans at vito.be<mailto: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<mailto:Willem.Offermans at Vito.be>

<vito.jpg>

On 13 Feb 2019, at 10:04, Stefano Baroni <baroni at sissa.it<mailto:baroni at sissa.it>> wrote:

On 13 Feb 2019, at 09:50, Offermans Willem <willem.offermans at vito.be<mailto: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<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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