[Pw_forum] phonons
lan haiping
lanhaiping at gmail.com
Mon Aug 21 14:43:40 CEST 2006
Dear Stefano :
Thanks for your instructions on science , usage of names and skills
of web communications.
Though i had learned some western customs in my English class years
ago, I think i throwed off most of them back to teachers. I should
appoligize for my naive mistake . En, for Chinese , take my name for
example , in most situations, others would call me ' lan hai-ping' ,
while 'lan' is my family name which means *blue,* and 'hai-ping' is given
name . i think it is the most difference between Chinese and western names
,since our family names are the first names in written and oral usages .
Regards,
Hai-Ping
On 8/20/06, Stefano Baroni <baroni at sissa.it> wrote:
>
>
> On Aug 20, 2006, at 3:15 AM, lan haiping wrote:
>
> Dear Prof Nicola,
>
>
>
> just a note about the "western" usage of names. (I would be glad to hear
> an explanation on how names are used in Chinese!). "Nicola" is the "given"
> name, i.e. it is the name that parents give to the newborn baby. It is
> also called "first" name because in written it is the first name that must
> be used. The other name "Marzari" is the family name which is transmitted
> from one generation to the next in a patrilinear way (a baby gets the
> fathers' family name by default). It is a form of confidentiality to address
> somebody by his/her first name. It is perfect here because: i) it is common
> usage on the web and; ii) it is common practice among scientists
> (particularly in the US). However, addressing somebody by his/her title is
> _very_ formal. Not very appropriate in this forum, but above all kind of
> funny if accompanied by the much more confidential usage of the first name.
> Resuming: "Dear Nicola" is confidential and "Dear Prof. Marzari" is formal -
> both ar OK, the first more appropriate to this forum. "Dear Prof Nicola" is
> just funny! ... I was not joking saying that I am curious about _your_ usage
> of "given", "family", or whatever names. If you have a few spare minutes,
> just let me know ...
>
>
> Science, now!
>
>
> Thanks for your long suggestion.
>
> I may not follow some of your words, would you please clarify ?
> 1, How to relax the ions more ?
>
>
>
>
> The code must have some default threshold for the atomic forces (and,
> maybe, stress too if you also relax the unit cell) such that when forces
> are smaller, it stops. The threshold is usually more than adequate for most
> practical purposes, _but to learn_ What I mean is that it is a good idea to
> practice and to see _with one's own eyes_ how a given property (phonon
> frequencies, in the present case) depend on external parameter and/or
> convergence criteria. As it is possible to vary by hands the values of the
> convergence thresholds, it is a good idea to try a same calculation with
> different values of the relevant thresholds and to see how the frequencies
> depend on them. I have a comment, though. As Nicola said in a previous
> post, it is unlikely (though not impossible) that phonons go soft because
> the structure is poorely optimized. It is worth stopping a while and
> understand carefully why it is both unlikely _and_ possible. It is possible
> because squared phonon frequencies are related to the Hessian (matrix of
> second derivatives) of the energy with respect to the nuclear coordinates.
> It is perfectly possible that, out of equilibrium, one or more of the
> eigenvalues of this matrix are negative. I even believe (but would like not
> to comment on this statement) that the ratio of the configuration space
> corresponding to all positive eigenvalues to the total configuration space
> decreases exponentially with the number of atoms. HOWEVER, phonon
> frequencies only depend on second derivatives of the energy, and not
> directly on first derivatives. So, if you are not too far from the minimum,
> not too good a convergence (i.e. the existence of nonvanishing forces) may
> certainly affect the accuracy of phonon calculations (it would not if the
> crystal were perfectly harmonic), but not the stability of the system (i.e.
> the sign of any of the squared frequencies).
>
> 2, I knew from most refs that ecutwfs 30 Ry for ultrasoft-PP is
> enough in pw calculations , Is it right ?
>
>
>
>
> This statement is meaningless. 30 Ry may be too large or too small a
> cutoff, depending on the PP that you are using. It is true that many US PP
> calculations are done with cutoffs in this range, but whether or not this
> value is appropriate in your case ONLY YOU CAN TELL. i.e. you have to
> perform careful convergence tests in order to be sure that your PW basis set
> is adequate to describe the properties that you want with the accuracy that
> you need (the same holds, of course, for many other devil's details of the
> calculation: k-points, gaussian smearing, etc.)
>
> But i donot have much idear about ecutwfs in ph calculations .
>
>
>
>
> By and large, (squared) phonon frequencies are second derivatives of the
> crystal energy for a given kinetic-energy cutoff. If a cutoff is OK for
> geometry optimization, it is also so for phonon calculation (see below)
>
>
> Would you please give me some refs of more detail settings about PH
> calculations ?
>
>
>
> S. Baroni, A. Dal Corso, S. de Gironcoli, and P. Giannozzi, Rev. Mod.
> Phys. 73, 515 (2001).
>
>
> Enjoy!
>
>
> Stefano B.
>
>
> PS: for us, it is considered polite to sign with our first name, or with
> the first name followed by the family name. It would be unpolite (except for
> formal business correspondence) to prepend the title to the signature -
> "Stefano" or "Stefano B.": confidential, OK; "Stefano Baroni" a bit less
> confidential, also OK in most cases; "Prof. Stefano Baroni": very formal and
> kind of assuming and not-so-polite in many cases - OK in a few
>
>
>
> I am trying to find more problems related to this wrong result following
> your suggestion.
> Thank you again, it really helps me much.
>
> p.s. It is nice for me listening your lectures in Beijing , i really
> learn much from your 3 lectures .
>
>
> Regards,
>
> Hai-Ping
>
>
> On 8/20/06, Nicola Marzari <marzari at mit.edu> wrote:
> >
> >
> >
> >
> > Dear Haiping,
> >
> >
> > there are two possibilities that lead to negative phonon frequencies at
> > gamma.
> >
> > The first one is less likely:
> >
> > 1) you have not carefully relaxed the *internal* degrees of freedom -
> > i.e. the ionic coodinates. Then, the phonon code discovers that moving
> > the atoms along a certain pattern (an "eigenvector" of the dynamical
> > matrix at gamma) the energy goes down. Perfect - just relax the ions
> > more. Relaxation of the unit cell has nothing to do with this
> >
> > The second one is more likely:
> >
> > 2) the calculation is not converged with respect
> > to the plane wave cutoff needed, and the number of k-points needed,
> > for the small or zero frequencies at gamma. Obtaining an accurate,
> > faithful description of low energy modes requires cutoffs and especially
> > duals much higher than anything you are used to (to give you an example,
> > for an ultrasoft C for diamond, you need 100 Ry in the wavefunction and
> > 2800 Ry in the charge density to get a convergence, at gamma,
> > of the zero modes down to the last cm-1). Does it mean you need
> > to use 100/2800 Ry for diamond ? No ! By enforcing the translation sum
> > rules that the interatomic force constants must satisfy, you can monitor
> > (after enforcing said rules) the convergence of the low frequency modes,
> >
> > and discover you can use much more reasonable cutoffs.
> >
> > Still, even more than a regular calculations, phonons require a
> > through control on the parameters that define your calculation.
> >
> > Note that, as a warm-up, it is easier to converge LDA calculations
> > than GGA calculations (the exchange-correlation terms, calculated in
> > real space, introduce very high frequencies in reciprocal space).
> >
> > nicola
> >
> >
> > >> Dear All,
> > >> I also have calculated gamma phonon frequencies of anatase TiO2 .
> > >> I run ph.x caculation after relaxing the structure, but 9 of 18
> > frequencies
> > >> are minus.
> > >>
> > >> Would you please give me some hints and help?
> > >>
> > >> input settings are below, thank you in advance !
> > >>
> > >> *phonons of TiO2 at Gamma
> > >> &inputph
> > >> tr2_ph=1.0d-14,
> > >> recover=.true.,
> > >> epsil=.true.,
> > >> prefix='tio2',
> > >> fildyn='TiO2-gamma.dyn ',
> > >> outdir='/home/haiping/tmp/'
> > >> /
> > >> 0.0 0.0 0.0*
> >
> >
> > ---------------------------------------------------------------------
> > Prof Nicola Marzari Department of Materials Science and Engineering
> > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA
> > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
> ---
> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste
> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
>
>
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