[Pw_forum] local and global minimums in relaxation
btw, where are old posts archived, I wanted to post these comments on Linked In Computational chemistry group to explain my reaction to a post someone else made there earlier ( see link to water model below).? > From: marchywka at hotmail.com > To: pw_forum at pwscf.org > Date: Thu, 27 Dec 2012 11:44:44 -0500 > Subject: Re: [Pw_forum] local and global minimums in relaxation > > > > > > > Date: Mon, 24 Dec 2012 23:20:34 -0500 > > From: correlation at tut.by > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] local and global minimums in relaxation > > > > I see.. > > Thank you! > > Well as I understand the situation, normally you have a molecule that you > want to > optimize and hope your original structure is close enough that the "forces" > the minimizer > sees get it to the right answer. Most molecules are not in some global > minimum configuration > of atoms right? You could take atoms infinitely far apart I guess and see > what you get. > > Personally though I did have a related question and that is what is neglected > by trying to > find a static ground state and ignoring any fluctuations? This is probably > not yet > relevant compared to errors in getting static result but curious if anyone > wanted to comment. > This was just posted on the linked in Computational Chemistry group, showing importance of fluctuation in understanding water, thought it was relevant to my earlier comment LOL http://www.rsc.org/chemistryworld/2013/02/water-structure-tetrahedral-controversy-xas-xafs > > > > > > > Sergey > > > > On 12/21/2012 3:47 PM, Paolo Giannozzi wrote: > > > On Dec 21, 2012, at 20:01 , Sergey wrote: > > > > > >> when I do relaxation (using bfgs algorithm), I end up with the > > >> system in > > >> one of the minimums. It can be local one or it can be global one. And > > >> there is probably several other possible local minimums in the system. > > >> How can I publish such a result? As I see in the papers no one usually > > >> describe this issue. Usually it is just - 'we performed structural > > >> optimization (relaxation) and here is the result.' > > >> > > >> How to deal with this matter? > > > if you find a better way to deal with this matter, your future career is > > > guaranteed. It is a well-known problem. That's way smart people > > > have invented simulating annealing, genetic algorithms, > > > metadynamics, ... > > > > > > P. > > > --- > > > Paolo Giannozzi, Dept of Chemistry, > > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > > > > ___ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] phonon density of states calculation of a mono-clinic crystal
On Thu, 2013-02-14 at 10:35 +0100, Giovanni Pizzi wrote:
> I think it should be possible to fix the problem directly in the
> matdyn files, without rerunning pw and ph.
for sure it is not needed to re-run the entire calculation,
but it may be needed to comment out some overzealous check
from q2r.f90 or related routines
P.
> On 02/14/2013 12:40 AM, Matthijs Mentink wrote:
>
> > Dear all,
> >
> > I'm trying to calculate the phonon density of states as a function
> > of energy of a mono-clinic crystal. I use ibrav = 0 and define
> > lattice vectors using 'CELL_PARAMETERS {bohr]'.
> >
> > This allows me to do a self-consistent calculation (pw.x) and phonon
> > dispersion calculations (ph.x) but I run into trouble when I try to
> > use q2r.x. This is the error message that I get:
> >
> > Error in routine read_file (1):
> > wrong celldm
> >
> >
> > In the pwscf input file I don't define celldm, because I use ibrav =
> > 0, but q2r seems to have a problem with that.
> >
> > Is there any way to fix this? Would it work if I start from scratch
> > (not a very appealing option) and use ibrav = 12?
> >
> > thanks in advance,
> >
> > Matthias Mentink
> > PhD candidate
> > Superconducting magnet group,
> > Lawrence Berkeley National Laboratory,
> > Berkeley, CA
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
> Giovanni Pizzi
> Post-doctoral Research Scientist
> EPFL STI IMX THEOS
> MXC 340 (B?timent MXC)
> Station 12
> CH-1015 Lausanne (Switzerland)
> Phone: +41 21 69 31124
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] symmetry not recognized
This error usually indicates that ph.x has some difficulty to recognize the symmetries in your system. You can skip this check and continue the phonon calculation as in previous versions of the code by using the flag search_sym=.false., but often the phonons are wrong in these cases, so it would be better to understand if the symmetry group found by pw.x and by ph.x is correct or not. HTH, Andrea On Wed, 2013-02-13 at 13:33 -0500, Jennifer Wohlwend wrote: > My goal is to use epw.x but when I was trying to first complete the > ph.x calculation I kept running into this error: > % > % > from tipo_sym : error # 1 > symmetry not recognized > % > % > stopping ... > I checked the forum concerning this error but as expected the > misplaced parenthesis had been fixed in the 4.0.3 version (only using > such an old version b/c epw.x requires it). After encountering this > error while testing an epw.x example I tried a pwscf example02 that > utilizes ph.x (from version 4.0.3; The example shows how to use pw.x > and ph.x to calculate phonon frequencies at Gamma and X for Si and C > in the diamond structure and for fcc-Ni.) and I received the same > error. > Any help would be much appreciated! > Thank you, > J. Wohlwend > > Universal Technology Corporation > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Andrea Dal CorsoTel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it
[Pw_forum] phonon density of states calculation of a mono-clinic crystal
Hi,
there was such a problem in earlier versions but it should have been
fixed in recent ones. Which version of quantum espresso are you using?
Could you also post the first few lines of your prefix-matdyn1 file, and
your pw and ph input/output files? For the future it is better to run
with new versions, but I think it should be possible to fix the problem
directly in the matdyn files, without rerunning pw and ph.
Best,
Giovanni Pizzi
On 02/14/2013 12:40 AM, Matthijs Mentink wrote:
> Dear all,
>
> I'm trying to calculate the phonon density of states as a function of
> energy of a mono-clinic crystal. I use ibrav = 0 and define lattice
> vectors using 'CELL_PARAMETERS {bohr]'.
>
> This allows me to do a self-consistent calculation (pw.x) and phonon
> dispersion calculations (ph.x) but I run into trouble when I try to
> use q2r.x. This is the error message that I get:
>
> /Error in routine read_file (1):
> wrong celldm/
>
> In the pwscf input file I don't define celldm, because I use ibrav =
> 0, but q2r seems to have a problem with that.
>
> Is there any way to fix this? Would it work if I start from scratch
> (not a very appealing option) and use ibrav = 12?
>
> thanks in advance,
>
> Matthias Mentink
> PhD candidate
> Superconducting magnet group,
> Lawrence Berkeley National Laboratory,
> Berkeley, CA
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124
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[Pw_forum] symmetry not recognized
Thank you Andrea, I will include that flag. This error showed up consistently through each system in the given example as well as the epw.x examples so that leads me to believe there is an issue with the code (I'm assuming...with trepidation). Since this is an older version I was wondering if it was a known issue that might have been resolved in the newer version, if that is the case then hopefully I will be able to find the issue while comparing the two versions. If, instead, this is a operator error (mine) and I'm totally barking up the wrong tree please let me know :) Thank you again, JW UTC > From: dalcorso at sissa.it > To: pw_forum at pwscf.org > Date: Thu, 14 Feb 2013 10:44:40 +0100 > Subject: Re: [Pw_forum] symmetry not recognized > > This error usually indicates that ph.x has some difficulty to recognize > the symmetries in your system. You can skip this check and continue the > phonon calculation as in previous versions of the code by > using the flag search_sym=.false., but often the phonons are wrong in > these cases, so it would be better to understand if the symmetry group > found by pw.x and by ph.x is correct or not. > > HTH, > > Andrea > > On Wed, 2013-02-13 at 13:33 -0500, Jennifer Wohlwend wrote: > > My goal is to use epw.x but when I was trying to first complete the > > ph.x calculation I kept running into this error: > > % > > % > > from tipo_sym : error # 1 > > symmetry not recognized > > % > > % > > stopping ... > > I checked the forum concerning this error but as expected the > > misplaced parenthesis had been fixed in the 4.0.3 version (only using > > such an old version b/c epw.x requires it). After encountering this > > error while testing an epw.x example I tried a pwscf example02 that > > utilizes ph.x (from version 4.0.3; The example shows how to use pw.x > > and ph.x to calculate phonon frequencies at Gamma and X for Si and C > > in the diamond structure and for fcc-Ni.) and I received the same > > error. > > Any help would be much appreciated! > > Thank you, > > J. Wohlwend > > > > Universal Technology Corporation > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > -- > Andrea Dal Corso Tel. 0039-040-3787428 > SISSA, Via Bonomea 265 Fax. 0039-040-3787249 > I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130214/6d97accc/attachment.html
