[gpaw-users] Inaccuracies in phonon dispersion calculation
Jens Jørgen Mortensen
jjmo at dtu.dk
Tue Nov 14 10:54:13 CET 2017
On 11/13/2017 04:09 PM, Holden Parks wrote:
> Hi Jens and Kristen,
>
> Thank you both for your suggestions. Kristen, though I believe my
> structure does converge to ~1meV, I was not specifically setting this
> as a convergence criterion but will do so from now on. I also agree
> that using a cutoff for setting up the dynamical matrix is correct - I
> had just ignored it recently because I believe my problems in getting
> good dispersions were caused by a more serious problem in the original
> force calculations.
>
> Jens, would you please send me your script and/or dispersion curve? I
> would like to run this calculation as well. Thank you!
Attached.
Jens Jørgen
>
> -Holden
>
> On Fri, Nov 10, 2017 at 2:48 AM, Kristen Kaasbjerg
> <kkaa at nanotech.dtu.dk <mailto:kkaa at nanotech.dtu.dk>> wrote:
>
> Good point Jens, it is indeed crucial to crank up the convergence
> criteria in phonon calculations. As the force is the derivative of
> the total energy, I usually converge that one to ~< 1 meV. In this
> respect, you should keep in mind that the criteria you specify for
> the total energy in GPAW is per electron, i.e. you have to convert
> to the total energy of all your supercell electrons.
>
>
> Let me also emphasize that it is important to apply the cutoff to
> the force constant in real space once setting up the dynamical
> matrix. If you don't do that, the interatomic forces will
> have longer range in some directions compared to others, which is
> of course undesirable.
>
>
> Best,
> Kristen
>
>
>
>
>
> ------------------------------------------------------------------------
> *From:* Jens Jørgen Mortensen
> *Sent:* 10 November 2017 07:18
> *To:* Holden Parks
> *Cc:* gpaw-users at listserv.fysik.dtu.dk
> <mailto:gpaw-users at listserv.fysik.dtu.dk>; Kristen Kaasbjerg
> *Subject:* Re: [gpaw-users] Inaccuracies in phonon dispersion
> calculation
> On 11/07/2017 03:20 AM, Holden Parks wrote:
> > Hi Jens,
> >
> > Thank you for the reply. I've tried running the plane-wave
> > calculations with your suggested cutoff but haven't seen an
> > improvement. I've confirmed that inaccuracies in the forces are the
> > cause of the problem in the dispersions, as I've run the same
> > calculation with the Brennan potential (part of the ASAP
> calculator)
> > and the problematic features aren't present (I've attached it
> here).
> > Do you have any thoughts on how I should move forward?
>
> I got a nice looking phonon dispersion with a 7x7x7 cell and these
> parameters:
>
> calc = GPAW(symmetry={'point_group': False},
> mode='lcao',
> basis='szp(dzp)',
> convergence={'density': 1e-7},
> xc='PBE',
> occupations=FermiDirac(0.01))
>
> the important thing being a more tight convergence (I think).
>
> Jens Jørgen
>
> >
> > -Holden
> >
> > On Fri, Nov 3, 2017 at 2:37 AM, Jens Jørgen Mortensen
> <jjmo at dtu.dk <mailto:jjmo at dtu.dk>
> > <mailto:jjmo at dtu.dk>> wrote:
> >
> > On 10/31/2017 11:19 PM, Holden Parks via gpaw-users wrote:
> >
> > Dear GPAW users,
> >
> > I am having a problem calculating the phonon dispersion for
> > bulk diamond silicon. This calculation is performed in ase,
> > and I at first suspected that something was wrong with the
> > implementation. However, the example with aluminum using EMT
> > on the ase manual works perfectly, so I believe my
> problem is
> > that I am incorrectly calculating the force constants
> with my
> > calculator.
> >
> > I've been calculating phonon dispersion curves for silicon
> > with a variety of supercell and k-point sizes, grid spacing
> > values, and displacement (delta) values. I've also tried a
> > using GGA xc functionals rather than LDA, and turned
> > point-group symmetry off. However, there are nonzero (and
> > imaginary frequencies) at the gamma point, and the acoustic
> > dispersion curves don't degenerate where they're expected
> > (between the gamma and W points and between the L and gamma
> > points). I've attached an example dispersion plot and
> the code
> > I used to generate it.
> >
> > Any suggestions at this point would be extremely helpful.
> > Thank you!
> >
> >
> > Try running your calculation in plane-wave mode. Instead of
> > h=0.16, use something like:
> >
> > calc = GPAW(..., mode=PW(300), ...)
> >
> > and remember to do "from gpaw import PW". This should give you
> > better forces.
> >
> > Jens Jørgen
> >
> > -Holden
> >
> > ---------------------
> >
> > from ase.build import bulk
> > from ase.dft.kpoints import ibz_points, bandpath
> > from ase.phonons import Phonons
> > from gpaw import GPAW, FermiDirac
> > import numpy as np
> >
> > # Setup crystal and EMT calculator
> > atoms = bulk('Si', 'diamond', a=5.477)
> > calc = GPAW(kpts=(2, 2, 2),
> > symmetry={'point_group': False},
> > h=0.16,
> > xc='PBE',
> > occupations=FermiDirac(0.01))
> >
> > ph = Phonons(atoms, calc, supercell=(4, 4, 4), delta=0.05)
> > ph.run()
> >
> > # Read forces and assemble the dynamical matrix
> > ph.read(acoustic=True)
> >
> > High-symmetry points in the Brillouin zone
> > G = [0, 0, 0]
> > X = [0.5, 0, 0.5]
> > W = [0.5,0.25,0.75]
> > L = [0.5, 0.5, 0.5]
> >
> > point_names = ['$\Gamma$', 'X', 'W', 'L', '$\Gamma$']
> > path = [G, X, W, L, G]
> >
> > # Band structure in meV
> > freq_conv = 2.41798902*(10**14)
> > path_kc, q, Q = bandpath(path, atoms.cell, 100)
> > omega_kn = freq_conv*ph.band_structure(path_kc)/(10**12)
> >
> >
> > import matplotlib.pyplot as plt
> > plt.figure(1, (8, 6))
> > plt.axes([.1, .07, .67, .85])
> >
> > for n in range(len(omega_kn[0])):
> > omega_n = omega_kn[:, n]
> > plt.plot(q, omega_n, 'k-', lw=2)
> >
> > plt.xticks(Q, point_names, fontsize=18)
> > plt.yticks(fontsize=18)
> > plt.xlim(q[0], q[-1])
> > plt.ylabel("Frequency ($\mathrm{THz}$)", fontsize=22)
> > plt.grid('on')
> >
> > plt.show()
> >
> >
> > _______________________________________________
> > gpaw-users mailing list
> > gpaw-users at listserv.fysik.dtu.dk
> <mailto:gpaw-users at listserv.fysik.dtu.dk>
> > <mailto:gpaw-users at listserv.fysik.dtu.dk
> <mailto:gpaw-users at listserv.fysik.dtu.dk>>
> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
> <https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users>
> >
> <https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
> <https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users>>
> >
> >
> >
>
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: phonon.py
Type: text/x-python
Size: 1249 bytes
Desc: not available
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20171114/c6c61b8a/attachment-0001.py>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: phonons.png
Type: image/png
Size: 56446 bytes
Desc: not available
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20171114/c6c61b8a/attachment-0001.png>
More information about the gpaw-users
mailing list