[Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3

Wed Aug 19 09:31:30 CEST 2015

I'm glad that helped. If there's only a single lattice parameter and the
cell vectors are the same, I typically just queue up a bunch of static runs
and let them go, then do my own analysis of the optimum, however it does
seem that co-relaxation of ions is important as given in Hammerschmidt *et
al..*

In Hammerschmidt *et al.*, Phys. Status Solidi A 210, No. 1, 131–139 (2013)
there appears to be a lot of variance when using different potentials. It
may be that they mixed in a different proportion of exact exchange or they
generated their pseudos in a different way or QE just behaves fundamentally
different to VASP. You may note however that Fig 4c demonstrates a
'squeezed' crystal that does not exhibit a band gap and similarly the
following type of thing in the following 'expanded' crystal which may
explain the effects you've been seeing. A large amount of discussion on the
relaxation of ions is found on the final page. (I only skimmed it)

It seems like your problem is not an easy one and so I wish you the best.
It seems like your following questions might be outside my expertise.

Cheers,
Jess Vaitkus

On 19 August 2015 at 17:01, Bang C. Huynh <cbh31 at cam.ac.uk> wrote:

> Dear Jesse,
>
> Thank you for your comments. Previously I didn't want to try to do a
> variable-cell relaxation because I thought if I used the lattice constant
> that has also been used to generate the published results (16.95 a.u.)
> things *should* work out fine. They obviously didn't. So currently I am
> trying to do a vc-relax but it's taking a bit long to converge when I start
> with 16.95 a.u. So in the meantime I made a few more nscf runs with other
> lattice constants (e.g. 16.0, 16.5, 16.7) and amazingly I observed a trend
> that when I decreased the lattice constant the band gap at gamma opened up.
> So perhaps what I am going to do now is to start a vc-relax with the
> initial lattice constant of 16.5 maybe, and hope for faster convergence.
>
> What puzzles me though is that these lattice constants that allow for the
> *correct* (or reasonable, at least) band gap at gamma (and probably
> reasonable transport properties?) deviate significantly from that published
> by Pizzi and a few other sources e.g. Hammerschmidt et al., Phys. Status
> Solidi A 210, No. 1, 131–139 (2013). So I'm not sure if this is the problem
> with the pseudopotentials I'm using, or with something else more
> fundamental.
>
>
>
> Regards,
> ---
>
>
> *Bang C. Huynh**Natural Sciences Tripos (Part IB)*
> Peterhouse
> University of Cambridge
> CB2 1RD
> The United Kingdom
>
> On 16-08-2015 06:52, Jesse Vaitkus wrote:
>
> Hello Bang,
>
> you state that you have "calculated with lattice parameter 17.1540 bohr
> (experimental) after the positions of the Sb atoms were relaxed". I think
> you might be slightly misunderstanding what was asked. While it is
> important to optimise the atomic co-ordinates within your box, if you do
> not relax the cell vectors themselves (lattice constant in this case), the
> relaxed ion positions will be meaningless. While it may look fine in
> VESTA, if your atoms positions are out by a scaling factor then they'll
> still look fine. Often the observed lattice constant and that obtained by
> DFT are vastly different.
>
> You should make sure that you output the forces, typically one aims to get
> values lower than 0.01 eV/Ang. If you see values on the order of 1 eV/Ang
> then your system is not relaxed at all. I'm not very well versed in Quantum
> Espresso so I unfortunately cannot tell you the inputs for this.
>
> My apologies if you have already tried this.
>
> Cheers,
> Jesse Vaitkus
>
>
> On 15 August 2015 at 22:44, Bang C. Huynh <cbh31 at cam.ac.uk> wrote:
>
>> Dear Nicki,
>>
>> Thank you very much for your reply. I've checked and indeed there is no
>> direct band gap at gamma. I have tried to recalculate the electronic
>> structure with plane-wave basis sets with different pseudopotentials and
>> different lattice constants, before and after Sb-atom relaxations. However
>> every time the band structure was almost the same, and no band gap could be
>> observed at gamma. An example of this is attached (just from plane waves,
>> no Wannier interpolation), calculated with lattice parameter 17.1540 bohr
>> (experimental) after the positions of the Sb atoms were relaxed, using PBE
>> exchange-correlation functionals (instead of PZ-LDA exch-corr like last
>> time). Here are the full inputs and outputs:
>>
>> https://dl.dropboxusercontent.com/u/21657676/skut5.tar.gz
>>
>> I'm not sure what could have gone wrong... I've checked the crystal
>> structure with VESTA and it appeared fine.
>>
>>
>>
>> Regards,
>> ---
>>
>>
>> *Bang C. Huynh*Peterhouse
>> University of Cambridge
>> CB2 1RD
>> The United Kingdom
>>
>> On 15-08-2015 09:54, Nicki Frank Hinsche wrote:
>>
>> Dear Bang,
>>
>> I think it is rather an „issue" regarding your electronic structure calculation.
>> Your bands only qualitatively agree with published results of Pizzi or e.g. Madsen (Comput. Phys. Commun. 2006 175, 67).
>> You have no fundamental direct bandgap at \Gamma (or at least it is one order of mag. smaller than it should be).
>> This explains your relatively small Seebeck at Ef, too. Maybe you could volume-relax the system, try „strain"
>> (volumes a bit off the equilibrium) or „play" with different functionals to open up the gap.
>>
>> good luck
>> Nicki
>>
>> --------------------------------------------------------
>> Nicki Frank Hinsche, Dr. rer. nat.
>> Institute of physics - Theoretical physics,
>> Martin-Luther-University Halle-Wittenberg,
>> Von-Seckendorff-Platz 1, Room 1.07
>> D-06120 Halle/Saale, Germany
>> Tel.: ++49 345 5525460
>> --------------------------------------------------------
>>
>> Am 15.08.2015 um 02:27 schrieb wannier-request at quantum-espresso.org:
>> Send Wannier mailing list submissions to wannier at quantum-espresso.org To
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>> digest..." Today's Topics: 1. numerical issues with atoms at the center of
>> the unit cell (Aron Szabo) 2. Issue with BoltzWann to calculate
>> thermoelectric properties of skutterudite CoSb3 (Bang C. Huynh)
>> ----------------------------------------------------------------------
>> Message: 1 Date: Fri, 14 Aug 2015 15:09:30 +0200 From: Aron Szabo <
>> szaboa at iis.ee.ethz.ch> To: wannier at quantum-espresso.org Subject:
>> [Wannier] numerical issues with atoms at the center of the unit cell
>> Message-ID: <55CDE88A.8080007 at iis.ee.ethz.ch> Content-Type: text/plain;
>> charset=utf-8; format=flowed Dear Wannier90 users and developers, I have
>> experienced a strange behavior of Wannier90. I was using VASP to do the SCF
>> simulation and generate the initial projections of a system, where I had
>> scandium over MoS2. I was using Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as
>> projections. And when running wannier90, most of the Wannier functions had
>> reasonably small (2-3 A^2) spreads even at the first step, except those
>> that were corresponding to the l=2 (d orbital) projections of the 3rd and
>> 9th Sc atoms (>100 A^2), and they remained large during the minimization.
>> It was suspicious that those atoms had direct z coordinates very close to
>> 0.5, and I thought this error might have been related to this fact. So I
>> have shifted all the atoms with 0.025 in the z direction, and calculated
>> everything again, and now the spreads were as small for those orbitals as
>> for every other, while the system itself was in fact the same, since a
>> shift does not change anything in a periodic system. So it seems like there
>> is some numerical instability when atom coordinates are very close to the
>> half of a lattice vector. I don't know if it is related to VASP or
>> wannier90. I can circumvent it easily now that I know it. I was just
>> wondering if anyone else has experienced the same, or maybe have any guess
>> where this error could originate from. I can provide additional details if
>> anyone is interested. The original POSCAR file is below. Best regards, Aron
>> Szabo POSCAR: MoS2+Sc 3.18300000000000 1.0 0.0 0.0 0.0 1.73205080757 0.0
>> 0.0 0.0 9.5617407071622829 Sc Mo S 12 2 4 Direct 0.0000000000000000
>> -0.0000000000000000 0.3265600783327190 0.0 0.3333332999999996
>> 0.4146745116137508 0.0000000000000000 -0.0000000000000000
>> 0.5006405198480147 0.0 0.3333332999999996 0.5867734775290360
>> 0.0000000000000000 -0.0000000000000000 0.6736668439773074 0.0
>> 0.3333332999999996 0.7587831003021329 0.5000000000000000 0.5000000000000000
>> 0.3265600783327190 0.5 0.8333332999999996 0.4146745116137508 0.5
>> 0.5000000000000000 0.5006405198480147 0.5 0.8333332999999996
>> 0.5867734775290360 0.5 0.5000000000000000 0.6736668439773074 0.5
>> 0.8333332999999996 0.7587831003021329 -0.0000000000000000
>> -0.0000000000000000 0.2132268304255010 0.5000000000000000
>> 0.5000000000000000 0.2132268304255010 0.0 0.3333332999999996
>> 0.2689120454016644 0.0 0.3333332999999996 0.1626395725698760 0.5
>> 0.8333332999999996 0.2689120454016644 0.5 0.8333332999999996
>> 0.1626395725698760 ------------------------------ Message: 2 Date: Sat, 15
>> Aug 2015 02:27:36 +0200 From: "Bang C. Huynh" <cbh31 at cam.ac.uk> To:
>> wannier at quantum-espresso.org Subject: [Wannier] Issue with BoltzWann to
>> calculate thermoelectric properties of skutterudite CoSb3 Message-ID: <
>> ca836a00462f123174c6d3aaed3bcfee at cam.ac.uk> Content-Type: text/plain;
>> charset="us-ascii" Dear all, I have recently tried to use Quantum ESPRESSO,
>> Wannier90 and BoltzWann to calculate the thermoelectric properties of
>> CoSb3. However my results aren't quite as expected in the sense that they
>> don't seem to agree well with those published in D. Volja et al., Phys.
>> Rev. B 85, 245211 (2012) and G. Pizzi et al., Comp. Phys. Comm. 185,
>> 422-429 (2014). For instance please see the attached plot for the
>> seebeck_xx coefficient. I have checked out this thread in the mail archive (
>> http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html
>> [1]) and tried to use the same lattice parameters as reported in G. Pizzi
>> (2014). I have also tried to relax the Sb atoms but to no avail. The band
>> structure however agrees pretty well with that shown in G. Pizzi (2014).
>> Below are my inputs. Please also see the additional output files here:
>> https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [2
>> <https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz>].
>> The Fermi energy is 8.1265 eV using the pseudopotentials as specified in
>> the nscf input file. I'm pretty much new to using these packages so any
>> help would be greatly appreciated. Thank you very much. My apology if this
>> issue seems repeated. Regards, -- BANG C. HUYNH Natural Sciences (Part IB)
>> Peterhouse University of Cambridge CB2 1RD The United Kingdom ======
>> skut6.nscf ====== &CONTROL title = skutterudite , calculation = 'nscf' ,
>> outdir = '/home/bang/Desktop/skutterudite/skut6/' , wfcdir =
>> '/home/bang/Desktop/skutterudite/skut6/' , pseudo_dir =
>> '/home/bang/Desktop/skutterudite/pseudo/' , prefix = 'skut6' , / &SYSTEM
>> ibrav = 3, celldm(1) = 16.95, nat = 16, ntyp = 2, ecutwfc = 30 , ecutrho =
>> 240 , nbnd = 100, occupations = 'smearing' , starting_spin_angle = .false.
>> , degauss = 0.06 , smearing = 'gaussian' , / &ELECTRONS / &IONS /
>> ATOMIC_SPECIES Co 58.93000 Co.pz-nd-rrkjus.UPF Sb 121.76000 Sb.pz-bhs.UPF
>> ATOMIC_POSITIONS (alat) Co 0.250000000 0.250000000 0.250000000 0 0 0 Co
>> 0.250000000 0.750000000 0.750000000 0 0 0 Co 0.750000000 0.250000000
>> 0.750000000 0 0 0 Co 0.750000000 0.750000000 0.250000000 0 0 0 Sb
>> 0.000000000 0.336000000 0.159000000 Sb -0.159000000 0.000000000 0.336000000
>> Sb 0.000000000 -0.336000000 -0.159000000 Sb 0.159000000 0.000000000
>> -0.336000000 Sb -0.000000000 0.336000000 -0.159000000 Sb 0.336000000
>> 0.159000000 0.000000000 Sb 0.000000000 -0.336000000 0.159000000 Sb
>> -0.336000000 -0.159000000 0.000000000 Sb 0.159000000 -0.000000000
>> 0.336000000 Sb 0.336000000 -0.159000000 0.000000000 Sb -0.159000000
>> 0.000000000 -0.336000000 Sb -0.336000000 0.159000000 0.000000000 K_POINTS
>> crystal 64 0.00000000 0.00000000 0.00000000 1.562500e-02 0.00000000
>> 0.00000000 0.25000000 1.562500e-02 0.00000000 0.00000000 0.50000000
>> 1.562500e-02 0.00000000 0.00000000 0.75000000 1.562500e-02 0.00000000
>> 0.25000000 0.00000000 1.562500e-02 0.00000000 0.25000000 0.25000000
>> 1.562500e-02 0.00000000 0.25000000 0.50000000 1.562500e-02 0.00000000
>> 0.25000000 0.75000000 1.562500e-02 0.00000000 0.50000000 0.00000000
>> 1.562500e-02 0.00000000 0.50000000 0.25000000 1.562500e-02 0.00000000
>> 0.50000000 0.50000000 1.562500e-02 0.00000000 0.50000000 0.75000000
>> 1.562500e-02 0.00000000 0.75000000 0.00000000 1.562500e-02 0.00000000
>> 0.75000000 0.25000000 1.562500e-02 0.00000000 0.75000000 0.50000000
>> 1.562500e-02 0.00000000 0.75000000 0.75000000 1.562500e-02 0.25000000
>> 0.00000000 0.00000000 1.562500e-02 0.25000000 0.00000000 0.25000000
>> 1.562500e-02 0.25000000 0.00000000 0.50000000 1.562500e-02 0.25000000
>> 0.00000000 0.75000000 1.562500e-02 0.25000000 0.25000000 0.00000000
>> 1.562500e-02 0.25000000 0.25000000 0.25000000 1.562500e-02 0.25000000
>> 0.25000000 0.50000000 1.562500e-02 0.25000000 0.25000000 0.75000000
>> 1.562500e-02 0.25000000 0.50000000 0.00000000 1.562500e-02 0.25000000
>> 0.50000000 0.25000000 1.562500e-02 0.25000000 0.50000000 0.50000000
>> 1.562500e-02 0.25000000 0.50000000 0.75000000 1.562500e-02 0.25000000
>> 0.75000000 0.00000000 1.562500e-02 0.25000000 0.75000000 0.25000000
>> 1.562500e-02 0.25000000 0.75000000 0.50000000 1.562500e-02 0.25000000
>> 0.75000000 0.75000000 1.562500e-02 0.50000000 0.00000000 0.00000000
>> 1.562500e-02 0.50000000 0.00000000 0.25000000 1.562500e-02 0.50000000
>> 0.00000000 0.50000000 1.562500e-02 0.50000000 0.00000000 0.75000000
>> 1.562500e-02 0.50000000 0.25000000 0.00000000 1.562500e-02 0.50000000
>> 0.25000000 0.25000000 1.562500e-02 0.50000000 0.25000000 0.50000000
>> 1.562500e-02 0.50000000 0.25000000 0.75000000 1.562500e-02 0.50000000
>> 0.50000000 0.00000000 1.562500e-02 0.50000000 0.50000000 0.25000000
>> 1.562500e-02 0.50000000 0.50000000 0.50000000 1.562500e-02 0.50000000
>> 0.50000000 0.75000000 1.562500e-02 0.50000000 0.75000000 0.00000000
>> 1.562500e-02 0.50000000 0.75000000 0.25000000 1.562500e-02 0.50000000
>> 0.75000000 0.50000000 1.562500e-02 0.50000000 0.75000000 0.75000000
>> 1.562500e-02 0.75000000 0.00000000 0.00000000 1.562500e-02 0.75000000
>> 0.00000000 0.25000000 1.562500e-02 0.75000000 0.00000000 0.50000000
>> 1.562500e-02 0.75000000 0.00000000 0.75000000 1.562500e-02 0.75000000
>> 0.25000000 0.00000000 1.562500e-02 0.75000000 0.25000000 0.25000000
>> 1.562500e-02 0.75000000 0.25000000 0.50000000 1.562500e-02 0.75000000
>> 0.25000000 0.75000000 1.562500e-02 0.75000000 0.50000000 0.00000000
>> 1.562500e-02 0.75000000 0.50000000 0.25000000 1.562500e-02 0.75000000
>> 0.50000000 0.50000000 1.562500e-02 0.75000000 0.50000000 0.75000000
>> 1.562500e-02 0.75000000 0.75000000 0.00000000 1.562500e-02 0.75000000
>> 0.75000000 0.25000000 1.562500e-02 0.75000000 0.75000000 0.50000000
>> 1.562500e-02 0.75000000 0.75000000 0.75000000 1.562500e-02 ====== skut6.win
>> ====== #restart = plot #wannier_plot = true #bands_plot = true
>> #bands_plot_format = xmgr num_bands = 100 num_wann = 56 dis_win_max = 20.d0
>> dis_win_min = 2.d0 dis_froz_max = 8.1265 !Fermi energy dis_num_iter = 1200
>> dis_mix_ratio = 1.d0 num_iter = 300 #num_print_cycles = 50 begin
>> unit_cell_cart !body-centered cubic bohr 8.475 8.475 8.475 -8.475 8.475
>> 8.475 -8.475 -8.475 8.475 end unit_cell_cart begin atoms_cart bohr Co
>> 4.237500000 4.237500000 4.237500000 Co 4.237500000 12.712500000
>> 12.712500000 Co 12.712500000 4.237500000 12.712500000 Co 12.712500000
>> 12.712500000 4.237500000 Sb 0.000000000 5.695200000 2.695050000 Sb
>> -2.695050000 0.000000000 5.695200000 Sb 0.000000000 -5.695200000
>> -2.695050000 Sb 2.695050000 0.000000000 -5.695200000 Sb 0.000000000
>> 5.695200000 -2.695050000 Sb 5.695200000 2.695050000 0.000000000 Sb
>> 0.000000000 -5.695200000 2.695050000 Sb -5.695200000 -2.695050000
>> 0.000000000 Sb 2.695050000 0.000000000 5.695200000 Sb 5.695200000
>> -2.695050000 0.000000000 Sb -2.695050000 0.000000000 -5.695200000 Sb
>> -5.695200000 2.695050000 0.000000000 End atoms_cart begin projections
>> Co:l=2:r=5 Sb:l=1:r=3 end projections begin kpoint_path G 0.00000 0.00000
>> 0.00000 H 0.50000 -0.50000 -0.50000 H 0.50000 -0.50000 -0.50000 P 0.75000
>> 0.25000 -0.25000 P 0.75000 0.25000 -0.25000 N 0.50000 0.00000 0.00000 N
>> 0.50000 0.00000 0.00000 G 0.00000 0.00000 0.00000 end kpoint_path mp_grid =
>> 4 4 4 begin kpoints 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
>> 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000
>> 0.75000000 0.00000000 0.25000000 0.00000000 0.00000000 0.25000000
>> 0.25000000 0.00000000 0.25000000 0.50000000 0.00000000 0.25000000
>> 0.75000000 0.00000000 0.50000000 0.00000000 0.00000000 0.50000000
>> 0.25000000 0.00000000 0.50000000 0.50000000 0.00000000 0.50000000
>> 0.75000000 0.00000000 0.75000000 0.00000000 0.00000000 0.75000000
>> 0.25000000 0.00000000 0.75000000 0.50000000 0.00000000 0.75000000
>> 0.75000000 0.25000000 0.00000000 0.00000000 0.25000000 0.00000000
>> 0.25000000 0.25000000 0.00000000 0.50000000 0.25000000 0.00000000
>> 0.75000000 0.25000000 0.25000000 0.00000000 0.25000000 0.25000000
>> 0.25000000 0.25000000 0.25000000 0.50000000 0.25000000 0.25000000
>> 0.75000000 0.25000000 0.50000000 0.00000000 0.25000000 0.50000000
>> 0.25000000 0.25000000 0.50000000 0.50000000 0.25000000 0.50000000
>> 0.75000000 0.25000000 0.75000000 0.00000000 0.25000000 0.75000000
>> 0.25000000 0.25000000 0.75000000 0.50000000 0.25000000 0.75000000
>> 0.75000000 0.50000000 0.00000000 0.00000000 0.50000000 0.00000000
>> 0.25000000 0.50000000 0.00000000 0.50000000 0.50000000 0.00000000
>> 0.75000000 0.50000000 0.25000000 0.00000000 0.50000000 0.25000000
>> 0.25000000 0.50000000 0.25000000 0.50000000 0.50000000 0.25000000
>> 0.75000000 0.50000000 0.50000000 0.00000000 0.50000000 0.50000000
>> 0.25000000 0.50000000 0.50000000 0.50000000 0.50000000 0.50000000
>> 0.75000000 0.50000000 0.75000000 0.00000000 0.50000000 0.75000000
>> 0.25000000 0.50000000 0.75000000 0.50000000 0.50000000 0.75000000
>> 0.75000000 0.75000000 0.00000000 0.00000000 0.75000000 0.00000000
>> 0.25000000 0.75000000 0.00000000 0.50000000 0.75000000 0.00000000
>> 0.75000000 0.75000000 0.25000000 0.00000000 0.75000000 0.25000000
>> 0.25000000 0.75000000 0.25000000 0.50000000 0.75000000 0.25000000
>> 0.75000000 0.75000000 0.50000000 0.00000000 0.75000000 0.50000000
>> 0.25000000 0.75000000 0.50000000 0.50000000 0.75000000 0.50000000
>> 0.75000000 0.75000000 0.75000000 0.00000000 0.75000000 0.75000000
>> 0.25000000 0.75000000 0.75000000 0.50000000 0.75000000 0.75000000
>> 0.75000000 end kpoints !!! -- Begin of BoltzWann input -- !!! boltzwann =
>> true boltz_calc_also_dos = true boltz_dos_energy_step = 0.01 smr_type =
>> gauss boltz_dos_adpt_smr = false boltz_dos_smr_fixed_en_width = 0.03 kmesh
>> = 60 boltz_mu_min = 6. boltz_mu_max = 10. boltz_mu_step = 0.01
>> boltz_temp_min = 300. boltz_temp_max = 300. boltz_temp_step = 50
>> boltz_relax_time = 10. !! Next variable is commented because 2 is its
>> default value !num_elec_per_state = 2 !!! --- End of BoltzWann input ---
>> !!! Links: ------ [1]
>> http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html
>> [2] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz
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>
>
> --
>
> ————————————————————————————————
> Mr. Jesse Vaitkus MAIP
> BAppSc(Phys) Hons, BAppSc(Nano)
>
> PhD candidate
> Room 14.6.02
>
> Chemical and Quantum Physics
> School of Applied Sciences
> RMIT University
> Victoria 3001
> Australia
>
> jesse.vaitkus at rmit.edu.au
> ————————————————————————————————
>
>
> _______________________________________________
> Wannier mailing list
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>

-- 

————————————————————————————————
Mr. Jesse Vaitkus MAIP
BAppSc(Phys) Hons, BAppSc(Nano)

PhD candidate
Room 14.6.02

Chemical and Quantum Physics
School of Applied Sciences
RMIT University
Victoria 3001
Australia

jesse.vaitkus at rmit.edu.au
————————————————————————————————
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