[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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