[Pw_forum] Fw: SV: SV: SV: cif2cell enquiry TO NICOLA
Manuel Pérez Jigato
manuel.perez at list.lu
Mon Jun 1 12:12:51 CEST 2015
Dear Nicola
thanks a lot for your comments, your are right, your response was exactly
the same than
that by the author of cif2cell, ie ,the supercell extra symmetries are
disregarded by pwscf
and just the primitive cell symmetries are considered. Certainly, to
compute point defects using
supercells, you usually switch off all symmetries, so, it makes sense to
use the converged conditions
for the supercell and no symmetry at all. However, sometimes you need to
spend some time
doing convergence tests with intermediate size or smaller size supercells,
and that means, usually
working under low quality conditions
>From my point of view, as a newcomer to espresso, I am trying to see
whether certain tests for
convergence can be quickly carried out. Ideally, I would like to see all
the symmetries present so
that I can look at the forces even under low cutoff/small number of k-point
conditions. The reason
I asked this question to the forum is that in case the symmetry limitations
for supercells could be
overcome, this would be helpful for me. At the moment, it looks like the
only way of having zero
forces on certain atoms (in my case) is using converged parameters
Regarding the 5x5x1 set of k-points, this is the smallest set I can think
of, considering the (real space) lattice
parameters I use keep more or less that ratio (inverted), and this set is
certainly not converged...
regards
Manuel
Dr Manuel Pérez Jigato, Chargé de Recherche
Luxembourg Institute of Science and Technology (LIST)
Materials Research and Technology (MRT)
41 rue du Brill
L-4422 BELVAUX
Grand-Duché de Luxembourg
Tel (+352) 47 02 61 - 584
Fax (+352) 47 02 64
e-mail manuel.perez at list.lu
From: Nicola Marzari <nicola.marzari at epfl.ch>
To: PWSCF Forum <pw_forum at pwscf.org>, Manuel Pérez Jigato
<perez at lippmann.lu>,
Date: 31/05/2015 11:51
Subject: Re: [Pw_forum] Fw: SV: SV: SV: cif2cell enquiry TO MKONDRIN
( one file enclosed )
Sent by: pw_forum-bounces at pwscf.org
Dear Manuel,
Torbjörn is saying exactly the same thing I said, re fractional
translations etc...
In my opiinion, f you want to get exactly zero forces on the atoms that
should have zero forces, monitor them as a function of k-point sampling.
Ss you increase the k-points, the ground state charge density should
converge to the symmetric one, even if it has not been symmetrized by
hand by the code.
Also note that 5 5 1 sampling seems to me very inhomogeneous in the
three different directions - why don't you try 2 2 2, 3 3 3, 4 4 4, 8 8
8, ...
and see how it goes (and maybe report?).
Thanks a lot,
nicola
On 30/05/2015 19:03, Manuel Pérez Jigato wrote:
> hi mkondrin
>
> the email below, from the author of cif2cell, explains the reasons for
> having
> zero forces for all copper and chromium atoms on the basis of the CIF
> file site
> symmetries; please find enclosed the cif file
>
> regards
>
> Manuel
> PS the expected forces, qualitatively speaking are shown below (first 6
> lines are oxygen, next three lines are Cr, last 3 lines are copper
> atoms), from a low cutoff, small number of k-points abinit calculation
> (in the espresso calculation some copper and chromium atoms are fixed,
> other copper and chromium atoms move, which means some of the
> copper-copper, chromium-copper and chromium-chromium distances vary, and
> theyshould all be fixed)
>
> cartesian forces (eV/Angstrom) at end:
> 1 0.00000000000000 0.00000000000000 33.52744537217701
> 2 0.00000000000000 0.00000000000000 33.52744537217701
> 3 0.00000000000000 0.00000000000000 33.52744537217700
> 4 0.00000000000000 0.00000000000000 -33.52744537217701
> 5 0.00000000000000 0.00000000000000 -33.52744537217701
> 6 0.00000000000000 0.00000000000000 -33.52744537217700
> 7 0.00000000000000 0.00000000000000 0.00000000000000
> 8 0.00000000000000 0.00000000000000 0.00000000000000
> 9 0.00000000000000 0.00000000000000 0.00000000000000
> 10 0.00000000000000 0.00000000000000 0.00000000000000
> 11 0.00000000000000 0.00000000000000 0.00000000000000
> 12 0.00000000000000 0.00000000000000 0.00000000000000
>
> Dr Manuel Pérez Jigato, Chargé de Recherche
> Luxembourg Institute of Science and Technology (LIST)
> Materials Research and Technology (MRT)
> 41 rue du Brill
> L-4422 BELVAUX
> Grand-Duché de Luxembourg
> Tel (+352) 47 02 61 - 584
> Fax (+352) 47 02 64
> e-mail manuel.perez at list.lu
>
> -----Forwarded by Manuel Pérez Jigato/LIST on 05/30/2015 06:35PM -----
> To: Manuel Pérez Jigato <manuel.perez at list.lu>
> From: Björkman Torbjörn <torbjorn.bjorkman at aalto.fi>
> Date: 05/29/2015 02:04PM
> Subject: SV: SV: SV: cif2cell enquiry
>
> Well, whether or not it is explicitly used for symmetrization, the
> symmetry is of course still there. So if by symmetry the forces should
> be zero, then they should be zero. In your case I can see from the CIF
> that the forces should indeed be zero, since they are 3a and 3b Wyckoff
> positions, which have no free parameters. If they are not, then there is
> some form of numerical problem, how bad it is of course depends on how
> large the forces are. The manual mentioned that the fourier mesh might
> not having the symmetry of the lattice in all cases, it may be that it
> is possible to get that in order by selecting them as multiples of 3 for
> a trigonal lattice. That's all I can say, I don't know anything specific
> about QE.
>
> Cheers,
> Torbjörn
>
> ---
> Torbjörn Björkman, PhD
> COMP, Aalto University School of Science
> Espoo, Finland
>
> ------------------------------------------------------------------------
> *Från:* Manuel Pérez Jigato [manuel.perez at list.lu]
> *Skickat:* den 29 maj 2015 14:42
> *Till:* Björkman Torbjörn
> *Ämne:* Re: SV: SV: cif2cell enquiry
>
> thanks a lot Bjorkman, it is very kind of you
> my only worry would be the possible implications for the forces
> I will ask to the pwscf mailing list
> regards
> Manuel
>
> Inactive hide details for Björkman Torbjörn ---29/05/2015
> 12:08:34---Dear Manuel, I can find nothing that looks wrong in the
> ciBjörkman Torbjörn ---29/05/2015 12:08:34---Dear Manuel, I can find
> nothing that looks wrong in the cif2cell output, but a quick look in the
"Tr
>
> From: Björkman Torbjörn <torbjorn.bjorkman at aalto.fi>
> To: Manuel Pérez Jigato <manuel.perez at list.lu>,
> Date: 29/05/2015 12:08
> Subject: SV: SV: cif2cell enquiry
>
> ------------------------------------------------------------------------
>
>
>
> Dear Manuel,
>
> I can find nothing that looks wrong in the cif2cell output, but a quick
> look in the "Troubleshooting" section of the QE manual seems to provide
> the most likely answer:
>
> pw.x does not find all the symmetries you expected
>
>
> ...
>
> * a fractional translation, without rotation, is a symmetry operation
> of the system. This means that the cell is actually a supercell. In
> this case, all symmetry operations containing fractional
> translations are disabled. The reason is that in this rather exotic
> case there is no simple way to select those symmetry operations
> forming a true group, in the mathematical sense of the term.
>
>
> What they say is that QE in cases like these will just say "this is a
> supercell" and throw the fractional translations away, which gives you
> 12 symmetries instead of 36, just as it should. I have no idea if you
> can bypass this behaviour in QE though, better ask on their mailing list.
>
> Hope this helps,
> Torbjörn
>
> ---
> Torbjörn Björkman, PhD
> COMP, Aalto University School of Science
> Espoo, Finland
>
> ------------------------------------------------------------------------
>
> *Från:* Manuel Pérez Jigato [manuel.perez at list.lu]*
> Skickat:* den 29 maj 2015 12:37*
> Till:* Björkman Torbjörn*
> Ämne:* Re: SV: cif2cell enquiry
>
> Dear Bjorkman
>
> thanks for your prompt reply
> please find enclosed the files/(See attached file: esta.cif)(See
> attached file: QE_NOREDUCE_esta.in)(See attached file: second.in)(See
> attached file: second.out)(See attached file: output_noreduce.txt)/
>
> Manuel
> PS the different between the two .in files is that one of them is the
> direct output from cif2cell, whilst the other is produced by
> adding a few options by hand, before running quantum-espresso (whose
> output you can see as well)
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, EPFL
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