baroni at sissa.it
Sun Aug 20 10:26:59 CEST 2006
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 ...
> 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
> 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
> 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).
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 .
> On 8/20/06, Nicola Marzari <marzari at mit.edu> wrote:
> Dear Haiping,
> there are two possibilities that lead to negative phonon
> frequencies at
> 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
> duals much higher than anything you are used to (to give you an
> for an ultrasoft C for diamond, you need 100 Ry in the wavefunction
> 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
> (after enforcing said rules) the convergence of the low frequency
> 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).
> >> 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
> >> 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
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
[+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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