[QE-users] Error in routine latgen (13): wrong celldm(3)
Mauro Sgroi
maurofrancesco.sgroi at gmail.com
Fri May 29 13:55:22 CEST 2020
Dear Paolo,
Thanks a lot.
I verified with our HPC management and effectively there was a mismatch
between the versions of pw.x and ph.x.
Now it runs properly.
On the other hand I would need a clarification on how the input of
coordinates with crystal_sg works.
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 noticed that if I use those positions in the input the coordinates are
transformed. I imagnine 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?
Or should I transform manually the coordinates referring them to the
primitive monoclinic axes?
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 )
>>
>>
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>
>
>
> --
> 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)
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> https://lists.quantum-espresso.org/mailman/listinfo/users
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