[QE-users] Error in routine latgen (13): wrong celldm(3)
Mauro Sgroi
maurofrancesco.sgroi at gmail.com
Tue Jun 2 20:07:22 CEST 2020
Dear Paolo,
sorry for bothering you again.
Now I fixed the version of pw.x and ph.x (I'm using for both version 6.5)
and checked the atomic positions in the input file.
I'm able to use dynmat.x only if I use cif2cell to generate the input,
ibrav=0 and explicitly the cell vectors.
If I use spgroup and A, B, C, cos(beta) or celldm(1), celldm(2), etc, ph.x
writes celldm(i) values different than those generated by pw.x.
Here is my new input file:
&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'
calculation = 'scf'
verbosity = 'high'
/
&SYSTEM
space_group = 15
uniqueb = .true.
A = 6.1839
B = 10.70446
C = 12.1280935
cosAC = -0.17166
nat = 8
ntyp = 3
ecutwfc = 52
ecutrho = 575
nbnd = 120
occupations = 'smearing'
degauss = 0.005
smearing = 'cold'
/
&ELECTRONS
electron_maxstep = 200
conv_thr = 1.0D-12
/
ATOMIC_SPECIES
Li 6.941 Li.pbe-sl-kjpaw_psl.1.0.0.UPF
Ti 47.867 Ti.pbe-spn-kjpaw_psl.1.0.0.UPF
S 32.06 S.pbe-nl-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal_sg}
Li 0.24488 0.08177 0.00019
Li 0.00000 0.08323 0.25000
Li 0.25000 0.25000 0.50000
Ti 0.00000 0.41656 0.25000
Ti 0.00000 0.74871 0.25000
S 0.39073 0.08366 0.36679
S 0.13716 0.25993 0.13331
S 0.13628 0.09205 0.63225
K_POINTS automatic
6 3 3 0 0 0
And for ph.x
Normal modes for LTS
&inputph
prefix='LTS_mono'
outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/LTS_mono'
tr2_ph=1.0d-14
amass(1)=6.941
amass(2)=47.867
amass(3)=32.06
epsil=.false.
!lraman=.true.
trans=.true.
asr=.true.
fildyn='LTS.dmat'
/
0.0 0.0 0.0
Part of the pw.x output file:
Title:
Li2TiS3_monoclinic
bravais-lattice index = -13
lattice parameter (alat) = 11.6859 a.u.
unit-cell volume = 2668.6492 (a.u.)^3
number of atoms/cell = 24
number of atomic types = 3
number of electrons = 144.00
number of Kohn-Sham states= 120
kinetic-energy cutoff = 52.0000 Ry
charge density cutoff = 575.0000 Ry
convergence threshold = 1.0E-12
mixing beta = 0.7000
number of iterations used = 8 plain mixing
Exchange-correlation= SLA PW PBX PBC
( 1 4 3 4 0 0 0)
celldm(1)= 11.685877 celldm(2)= 1.731021 celldm(3)= 1.961237
celldm(4)= 0.000000 celldm(5)= -0.171660 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 0.500000 0.865510 0.000000 )
a(2) = ( -0.500000 0.865510 0.000000 )
a(3) = ( -0.336666 0.000000 1.932125 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.000000 0.577694 0.174246 )
b(2) = ( -1.000000 0.577694 -0.174246 )
b(3) = ( 0.000000 -0.000000 0.517565 )
Part of the ph.x output:
Normal modes for LTS
bravais-lattice index = 13
lattice parameter (alat) = 11.6859 a.u.
unit-cell volume = 2668.6492 (a.u.)^3
number of atoms/cell = 24
number of atomic types = 3
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 0)
celldm(1)= 11.68588 celldm(2)= 0.99955 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 1.9321 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.0000 0.5777 0.1742 )
b(2) = ( -1.0000 0.5777 -0.1742 )
b(3) = ( 0.0000 -0.0000 0.5176 )
The celldm(i) values are different so when I run dynmat.x I get
Reading Dynamical Matrix from file LTS.dmat
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine latgen (13):
wrong celldm(3)
Could you please help me to solve the problem?
Thanks a lot in advance and best regards,
Mauro Sgroi.
Il giorno ven 29 mag 2020 alle ore 15:41 Mauro Sgroi <
maurofrancesco.sgroi at gmail.com> ha scritto:
> 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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