[QE-users] Error in routine latgen (13): wrong celldm(3)
Paolo Giannozzi
p.giannozzi at gmail.com
Fri May 29 15:13:31 CEST 2020
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
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