[gpaw-users] Funny electronic band structure

Wed Feb 4 18:50:35 CET 2015

Dear Marcin, dear all

Thanks once again for your replies and assistance

Bests,

  Darío
El 04/02/2015 16:35, "Marcin Dulak" <Marcin.Dulak at fysik.dtu.dk> escribió:

>  On 02/04/2015 04:09 PM, Darío Fdez-Pello Lois wrote:
>
>  Dear Jens Jørgen, dear all,
>
>  Yes, the primitive unit cell solved the inconsistency!
>
> please note also that e_f = calc.get_fermi_level() should be taken from
> the first (regular SCF) calculations,
> not the fixdensity one. Another thing is that the old Mo setup (setups={'Mo':
> '6'}) won't produce the correct
> band structure and it should not be used. Another hint: converging
> unoccupied bands is faster with the eigensolver='cg'
> than with the default eigensolver='dav'.
>
> Best regards,
>
> Marcin
>
>
>  Many thanks to you all!!
>
>  Cheers,
>
>     Darío.
>
> 2015-02-04 14:12 GMT+01:00 Jens Jørgen Mortensen <jensj at fysik.dtu.dk>:
>
>> On 02/03/2015 10:59 AM, Darío Fdez-Pello Lois wrote:
>>
>>> Dear all,
>>>
>>>  Thanks for your replies, indeed it should be a colon after 'size', I
>>> mistyped it somehow.
>>>
>>> The requested figures are attached, please let me say that Mo_band.png
>>> comes from the QE and ELK calculations while MoBandstructure.png comes from
>>> GPAW.
>>>
>>
>> It looks like you have a cubic cell with two atoms.  Try with the
>> primitive unit cell:
>>
>> >>> from ase.lattice import bulk
>> >>> mo = bulk('Mo')
>>
>> See here:
>>
>> https://wiki.fysik.dtu.dk/ase/ase/structure.html#ase.lattice.bulk
>>
>> Jens Jørgen
>>
>>
>>> In addition, here are the scripts:
>>> -------SCF
>>> import numpy as NP
>>> from ase.lattice.cubic import BodyCenteredCubic
>>> from gpaw import GPAW,PW,MethfesselPaxton,Mixer
>>>  from ase.io <http://ase.io> import read
>>>
>>> k = 10
>>> ecut = 600
>>> N = 1
>>> configs = read('MoStrain.traj@:')
>>> aa = NP.array([config.cell[0, 0] for config in configs])
>>> a = aa[-1]
>>>
>>> mo = BodyCenteredCubic(size=(N,N,N),symbol='Mo',latticeconstant=a)
>>> mo.calc = GPAW(mode=PW(ecut), xc='PBE', kpts={'size': (k,k,k),'gamma':
>>> True}, setups={'Mo': '6'}, occupations=MethfesselPaxton(0.01),
>>> mixer=Mixer(0.1, 1, 100), txt='bulk.txt')
>>> mo.get_potential_energy()
>>> mo.calc.write('bulk.gpw')
>>>
>>> --------BAND
>>> import numpy as NP
>>>  from ase.io <http://ase.io> import read, write
>>>
>>> from ase.lattice.cubic import BodyCenteredCubic
>>> from ase.dft.kpoints import ibz_points, get_bandpath
>>> from gpaw import GPAW, PW, MethfesselPaxton
>>> import matplotlib
>>> matplotlib.use('Agg')
>>> import matplotlib.pyplot as plt
>>>
>>> num_bands=12
>>>
>>> calc = GPAW('bulk.gpw', fixdensity=True, usesymm=None,
>>> convergence={'bands': num_bands}, maxiter=600, txt='band.txt')
>>> points = ibz_points['bcc']
>>> G = points['Gamma']
>>> H = points['H']
>>> N = points['N']
>>> P = points['P']
>>> kpts, x, X = get_bandpath([G, H, N, G, P], calc.atoms.cell, 200)
>>> calc.set(kpts=kpts)
>>> calc.get_potential_energy()
>>> e_kn = NP.array([calc.get_eigenvalues(k) for k in range(len(kpts))])
>>>
>>> # Plot the band structure
>>>
>>> e_f = calc.get_fermi_level()
>>> e_kn -= e_f
>>> emin = -10 #e_kn.min() - 1.0
>>> emax = 10 #e_kn[:, num_bands].max() + 1.0
>>>
>>> plt.figure(figsize=(5, 6))
>>> for n in range(num_bands):
>>>     plt.plot(x, e_kn[:, n])
>>> for p in X:
>>>     plt.plot([p, p], [emin, emax], 'k-')
>>> plt.plot([0, X[-1]], [0, 0], 'k-')
>>> plt.xticks(X, ['$%s$' % n for n in ['\Gamma', 'H', 'N', '\Gamma', 'P']])
>>> plt.axis(xmin=0, xmax=X[-1], ymin=emin, ymax=emax)
>>> plt.xlabel('k-vector')
>>> plt.ylabel('E - E$_F$ (eV)')
>>> plt.title('Bandstructure of Mo')
>>> plt.savefig('MoBandstructure.png')
>>>
>>> --------------------
>>> END of scripts
>>>
>>>
>>> Best regards,
>>>
>>>    Darío
>>>
>>>
>>>  2015-02-03 8:19 GMT+01:00 Jussi Enkovaara <jussi.enkovaara at csc.fi
>>> <mailto:jussi.enkovaara at csc.fi>>:
>>>
>>>
>>>     Hi Dario,
>>>     could you be a bit more specific what's wrong with the band
>>>     stucture (preferrably with a picture of correct / incorrect one),
>>>     e.g are some bands fine but others not?
>>>
>>>     In principle, your script below looks fine, but could you also
>>>     provide the full scripts for SCF and band structure calculations?
>>>
>>>     Best regards,
>>>     Jussi Enkovaara
>>>
>>>
>>>     On 2015-02-03 00:38, Darío Fdez-Pello Lois wrote:
>>>
>>>         Dear all,
>>>
>>>         My question is related to the calculation of the electronic
>>>         band structure
>>>         of molybdenum, which I was successfully able to reproduce both
>>>         using a full
>>>         potential code (ELK) and a plane wave one (Quantum Espesso).
>>>         Unfortunately,
>>>         the same doesn't happen when I use GPAW (with PW mode)
>>>         resulting a quite
>>>         different structure.
>>>         Here are the relevant (I guess) lines, of course the
>>>         obligatory parameter's
>>>         convergence were peviouslly done:
>>>
>>>         [ ... ]
>>>         mo=BodyCenteredCubic(size(N,N,N),symbol='Mo',latticeconstant=a)
>>>         mo.calc = GPAW(mode=PW(ecut),
>>>                xc='PBE',
>>>                kpts={'size'(k,k,k),'gamma': True},
>>>                setups={'Mo': '6'},
>>>                occupations=MethfesselPaxton(0.01),
>>>                mixer=Mixer(0.1, 1, 100),
>>>                txt='bulk.txt')
>>>         [ ... ]
>>>
>>>         thereafter I run the band structure script similar to the one
>>>         given in the
>>>         tutorial (with obvious changes: bcc instead of fcc, etc.)
>>>
>>>         I am very confused at this point and I hope some of you would
>>>         kindly give
>>>         me some insight.
>>>
>>>         Best,
>>>
>>>            Darío.
>>>
>>>
>>>
>>>
>>>         _______________________________________________
>>>         gpaw-users mailing list
>>>         gpaw-users at listserv.fysik.dtu.dk
>>>          <mailto:gpaw-users at listserv.fysik.dtu.dk>
>>>         https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>>>
>>>
>>>     _______________________________________________
>>>     gpaw-users mailing list
>>>     gpaw-users at listserv.fysik.dtu.dk
>>>      <mailto:gpaw-users at listserv.fysik.dtu.dk>
>>>     https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>>
>>
>
>
> _______________________________________________
> gpaw-users mailing listgpaw-users at listserv.fysik.dtu.dkhttps://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20150204/8aba0a2d/attachment.html>