[QE-users] Error in routine latgen (13): wrong celldm(3)
Mauro Sgroi
maurofrancesco.sgroi at gmail.com
Fri May 29 15:41:34 CEST 2020
Dear Paolo,
Thanks a lot for the clarification.
Best regards,
Mauro.
Il ven 29 mag 2020, 15:14 Paolo Giannozzi <p.giannozzi at gmail.com> ha
scritto:
> On Fri, May 29, 2020 at 1:56 PM Mauro Sgroi <
> maurofrancesco.sgroi at gmail.com> wrote:
>
>>
>> My space group is 15. I've the coordinates of the not equivalent atoms
>> from a cif experimental file.
>> Those Wyckoff positions are referred to the non-primitive conventional
>> cell with 48 atoms.
>> [...] I imagine that pw.x automatically understands that those are
>> referred to the conventional cell and transforms them in the equivalent
>> positions in the primitive (24-atoms) cell.
>> Is this correct?
>>
>
> I think that the code generates all atomic positions by applying all
> symmetry operations to the provided Wyckoff positions. Then, it throws away
> atoms that, modulo lattice translations, overlap. The code always assumes
> the smallest (primitive) unit cell.
>
> Or should I transform manually the coordinates referring them to the
>> primitive monoclinic axes?
>>
>
> I don't think you need to do anything (unless you don't get the correct
> number of atoms, of course): the code expects Wyckoff positions as they are
> defined in big crystallography books, produces atomic positions in the
> primitive unit cells as they are internally used.
>
> Paolo
>
> Thanks a lot and best regards,
>> Mauro Sgroi.
>>
>>
>> Il dom 17 mag 2020, 19:03 Paolo Giannozzi <p.giannozzi at gmail.com> ha
>> scritto:
>>
>>> On Sat, May 16, 2020 at 10:23 PM Mauro Sgroi <
>>> maurofrancesco.sgroi at gmail.com> wrote:
>>>
>>>
>>>> Checking the output of ph.x I found that the celldm parameters are
>>>> changed with respect to the initial scf calculation (and also the number of
>>>> atoms in the cell pass from 24 to 30).
>>>>
>>>
>>> With your input and the latest development version, the self-consistent
>>> calculation also produces 30 atoms from your Wyckoff positions. I get
>>> exactly the same lattice parameters in the phonon and in the scf code. I
>>> also get this interesting message:
>>> BEWARE: axis for ibrav=-13 changed, see documentation!
>>> related to this change I did some time ago upon suggestion by don't
>>> remember who:
>>>
>>> https://gitlab.com/QEF/q-e/-/commit/962a723a9d1e79244c8a2d7468937ab9f29982f4
>>> Are you by any chance running different version of the scf and phonon
>>> code?
>>>
>>> Paolo
>>>
>>> Could you please help me to solve this problem?
>>>> Below I'm attaching the input of pw.x, ph.x and the initial output of
>>>> ph.x.
>>>> Thanks a lot in advance and best regards,
>>>> Mauro Sgroi.
>>>>
>>>> SCF
>>>> &CONTROL
>>>> title = 'Li2TiS3_monoclinic'
>>>> pseudo_dir =
>>>> '/workhpc/FCA/FCA_CRF_STRUT/sgroi/DATABASE/ESPRESSO'
>>>> prefix = 'LTS_mono'
>>>> outdir =
>>>> '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/LTS_mono_low_kpt_cell'
>>>> calculation = 'scf'
>>>> verbosity = 'high'
>>>> /
>>>> &SYSTEM
>>>> space_group = 15
>>>> uniqueb = .true.
>>>> celldm(1) = 11.552652
>>>> celldm(2) = 1.73103
>>>> celldm(3) = 1.952171
>>>> celldm(5) = -0.172475
>>>> nat = 8
>>>> ntyp = 8
>>>> ecutwfc = 52
>>>> ecutrho = 575
>>>> nbnd = 120
>>>> occupations = 'smearing'
>>>> degauss = 0.005
>>>> smearing = 'cold'
>>>> /
>>>> &ELECTRONS
>>>> electron_maxstep = 200
>>>> conv_thr = 1.0D-12
>>>> /
>>>>
>>>>
>>>> ATOMIC_SPECIES
>>>> Li1 6.941 Li.pbe-sl-kjpaw_psl.1.0.0.UPF
>>>> Li2 6.941 Li.pbe-sl-kjpaw_psl.1.0.0.UPF
>>>> Li3 6.941 Li.pbe-sl-kjpaw_psl.1.0.0.UPF
>>>> Ti1 47.867 Ti.pbe-spn-kjpaw_psl.1.0.0.UPF
>>>> Ti2 47.867 Ti.pbe-spn-kjpaw_psl.1.0.0.UPF
>>>> S1 32.06 S.pbe-nl-kjpaw_psl.1.0.0.UPF
>>>> S2 32.06 S.pbe-nl-kjpaw_psl.1.0.0.UPF
>>>> S3 32.06 S.pbe-nl-kjpaw_psl.1.0.0.UPF
>>>>
>>>> ATOMIC_POSITIONS {crystal_sg}
>>>> Li1 0.3368954 0.8267566 0.9998022
>>>> Li2 0.4164759 0.4164759 0.2500000
>>>> Li3 0.5000000 0.0000000 0.5000000
>>>> Ti1 0.0836168 0.0836168 0.2500000
>>>> Ti2 0.7514196 0.7514196 0.2500000
>>>> S1 0.1929125 0.9744265 0.6332331
>>>> S2 0.3771191 0.1029193 0.1331970
>>>> S3 0.4557540 0.7282681 0.3676504
>>>>
>>>> K_POINTS automatic
>>>> 6 3 3 0 0 0
>>>>
>>>> PHonon
>>>> Normal modes for LTS
>>>> &inputph
>>>> prefix='LTS_mono'
>>>> outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/LTS_mono_low_kpt_cell'
>>>> tr2_ph=1.0d-14
>>>> amass(1)=6.941
>>>> amass(2)=6.941
>>>> amass(3)=6.941
>>>> amass(4)=47.867
>>>> amass(5)=47.867
>>>> amass(6)=32.06
>>>> amass(7)=32.06
>>>> amass(8)=32.06
>>>> epsil=.false.
>>>> !lraman=.true.
>>>> trans=.true.
>>>> asr=.true.
>>>> fildyn='dmat.lts'
>>>> /
>>>> 0.0 0.0 0.0
>>>>
>>>> Part of Phonon output
>>>> bravais-lattice index = 13
>>>> lattice parameter (alat) = 11.5527 a.u.
>>>> unit-cell volume = 2566.1373 (a.u.)^3
>>>> number of atoms/cell = 30
>>>> number of atomic types = 8
>>>> kinetic-energy cut-off = 52.0000 Ry
>>>> charge density cut-off = 575.0000 Ry
>>>> convergence threshold = 1.0E-14
>>>> beta = 0.7000
>>>> number of iterations used = 4
>>>> Exchange-correlation = PBE ( 1 4 3 4 0 0)
>>>>
>>>>
>>>> celldm(1)= 11.55265 celldm(2)= 0.99956 celldm(3)= 0.00000
>>>> celldm(4)= -0.50022 celldm(5)= 0.00000 celldm(6)= 0.00000
>>>>
>>>> crystal axes: (cart. coord. in units of alat)
>>>> a(1) = ( 0.5000 0.8655 0.0000 )
>>>> a(2) = ( -0.5000 0.8655 0.0000 )
>>>> a(3) = ( -0.3367 0.0000 1.9229 )
>>>>
>>>> reciprocal axes: (cart. coord. in units 2 pi/alat)
>>>> b(1) = ( 1.0000 0.5777 0.1751 )
>>>> b(2) = ( -1.0000 0.5777 -0.1751 )
>>>> b(3) = ( 0.0000 -0.0000 0.5200 )
>>>>
>>>>
>>>> Atoms inside the unit cell:
>>>>
>>>> Cartesian axes
>>>>
>>>> site n. atom mass positions (alat units)
>>>> 1 Li1 6.9410 tau( 1) = ( -0.49974 0.56563
>>>> 1.92254 )
>>>> 2 Li1 6.9410 tau( 2) = ( -0.00531 0.56563
>>>> 0.96184 )
>>>> 3 Li1 6.9410 tau( 3) = ( 0.16304 1.16540
>>>> 0.00038 )
>>>> 4 Li1 6.9410 tau( 4) = ( -0.33139 1.16540
>>>> 0.96108 )
>>>> 5 Li2 6.9410 tau( 5) = ( 0.33230 0.72093
>>>> 0.48073 )
>>>> 6 Li2 6.9410 tau( 6) = ( -0.50065 0.72093
>>>> 0.48073 )
>>>> 7 Li2 6.9410 tau( 7) = ( -0.16900 0.14458
>>>> 1.44219 )
>>>> 8 Li2 6.9410 tau( 8) = ( -0.33605 0.14458
>>>> 1.44219 )
>>>> 9 Li3 6.9410 tau( 9) = ( -0.16835 0.86552
>>>> 0.96146 )
>>>> 10 Li3 6.9410 tau( 10) = ( 0.00000 0.86552
>>>> 0.00000 )
>>>> 11 Ti1 47.8670 tau( 11) = ( -0.00056 0.14474
>>>> 0.48073 )
>>>> 12 Ti1 47.8670 tau( 12) = ( -0.16779 0.14474
>>>> 0.48073 )
>>>> 13 Ti1 47.8670 tau( 13) = ( 0.16386 0.72077
>>>> 1.44219 )
>>>> 14 Ti1 47.8670 tau( 14) = ( -0.66891 0.72077
>>>> 1.44219 )
>>>> 15 Ti2 47.8670 tau( 15) = ( 0.16724 0.43521
>>>> 0.48073 )
>>>> 16 Ti2 47.8670 tau( 16) = ( -0.33559 0.43521
>>>> 0.48073 )
>>>> 17 Ti2 47.8670 tau( 17) = ( -0.00395 0.43030
>>>> 1.44219 )
>>>> 18 Ti2 47.8670 tau( 18) = ( -0.50111 0.43030
>>>> 1.44219 )
>>>> 19 S1 32.0600 tau( 19) = ( -0.52030 0.82125
>>>> 1.21765 )
>>>> 20 S1 32.0600 tau( 20) = ( 0.01525 0.82125
>>>> 1.66672 )
>>>> 21 S1 32.0600 tau( 21) = ( 0.18360 0.90978
>>>> 0.70526 )
>>>> 22 S1 32.0600 tau( 22) = ( -0.35195 0.90978
>>>> 0.25620 )
>>>> 23 S2 32.0600 tau( 23) = ( -0.16773 1.04367
>>>> 0.25613 )
>>>> 24 S2 32.0600 tau( 24) = ( -0.00062 1.04367
>>>> 0.70533 )
>>>> 25 S2 32.0600 tau( 25) = ( -0.16897 0.68736
>>>> 1.66679 )
>>>> 26 S2 32.0600 tau( 26) = ( -0.33608 0.68736
>>>> 1.21758 )
>>>> 27 S3 32.0600 tau( 27) = ( -0.16803 0.39514
>>>> 0.70696 )
>>>> 28 S3 32.0600 tau( 28) = ( -0.00032 0.39514
>>>> 0.25450 )
>>>> 29 S3 32.0600 tau( 29) = ( -0.16867 1.33589
>>>> 1.21595 )
>>>> 30 S3 32.0600 tau( 30) = ( -0.33638 1.33589
>>>> 1.66842 )
>>>>
>>>>
>>>> _______________________________________________
>>>> Quantum ESPRESSO is supported by MaX (
>>>> www.max-centre.eu/quantum-espresso)
>>>> users mailing list users at lists.quantum-espresso.org
>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>>
>>>
>>> --
>>> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> Phone +39-0432-558216, fax +39-0432-558222
>>>
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
>>> )
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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