[Pw_forum] cif2qe conversion failure

[Carlo Nervi]

Hello,
the problem is related to your cif input file.
Instead of "_atom_site_label" you should have "_atom_site_type_symbol"
because the label could be any strings...

HTH,
Carlo


2016-04-13 18:14 GMT+02:00 Tsung-Lung Li <quantum at mail.ncyu.edu.tw>:

> Dear QE Users:
>
> I try to use cif2qe to convert the structure of gypsum with command
>
> cif2qe -i filename > filename.in
>
> but the resultant file contains an empty section of ATOMIC_POSITIONS. I
> wonder this problem can be fixed.  Thank you in advance.
>
> Listed below is the cif downloaded from American Mineralogist Crystal
> Structure Database.
>
>
> data_global
> _chemical_name_mineral 'Gypsum'
> loop_
> _publ_author_name
> 'Comodi P'
> 'Nazzareni S'
> 'Zanazzi P F'
> 'Speziale S'
> _journal_name_full 'American Mineralogist'
> _journal_volume 93
> _journal_year 2008
> _journal_page_first 1530
> _journal_page_last 1537
> _publ_section_title
> ;
>   High-pressure behavior of gypsum: A single-crystal X-ray study
>   Note: P = 0.0001 GPa
> ;
> _database_code_amcsd 0004651
> _chemical_compound_source 'Valle di Caramanico, Abruzzo, Italy'
> _chemical_formula_sum 'Ca S O6 H4'
> _cell_length_a 6.277
> _cell_length_b 15.181
> _cell_length_c 5.672
> _cell_angle_alpha 90
> _cell_angle_beta 114.11
> _cell_angle_gamma 90
> _cell_volume 493.340
> _exptl_crystal_density_diffrn      2.318
> _symmetry_space_group_name_H-M 'C 1 2/c 1'
> loop_
> _space_group_symop_operation_xyz
>    'x,y,z'
>    '1/2+x,1/2+y,z'
>    'x,-y,1/2+z'
>    '1/2+x,1/2-y,1/2+z'
>    '-x,y,1/2-z'
>    '1/2-x,1/2+y,1/2-z'
>    '-x,-y,-z'
>    '1/2-x,1/2-y,-z'
> loop_
> _atom_site_label
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> _atom_site_U_iso_or_equiv
> Ca   0.00000   0.17050   0.25000   0.01170
> S   0.00000   0.32727   0.75000   0.00990
> O   0.08319   0.27218   0.59103   0.01690
> O   0.19997   0.38195   0.91298   0.01690
> O  -0.20823   0.06826  -0.07831   0.02410
> H  -0.25800   0.08700  -0.23400   0.03300
> H  -0.24400   0.02000  -0.07700   0.04400
>
>
>
>
>
> Listed below is the resultant QE file
>
> ! Generated by using cif2qe Version 1.2 - Date: Wed Apr 13 21:35:09 CST
> 2016
> !   _symmetry_space_group_name_H-M =
> !   _symmetry_Int_Tables_number =
> !   _symmetry_cell_setting =
> ! a=6.277  b=15.181  c=5.672  alpha=90  beta=114.11  gamma=90
> ! Found by cif2qe: lattice = monoclinic    Space group =    ibrav = 0
> !
> !
> ! Symmetry found:
> !   1                          x,y,z    [x]  [y]  [z]
> !   2                  1/2+x,1/2+y,z    [1/2+x]  [1/2+y]  [z]
> !   3                     x,-y,1/2+z    [x]  [-y]  [1/2+z]
> !   4              1/2+x,1/2-y,1/2+z    [1/2+x]  [1/2-y]  [1/2+z]
> !   5                     -x,y,1/2-z    [-x]  [y]  [1/2-z]
> !   6              1/2-x,1/2+y,1/2-z    [1/2-x]  [1/2+y]  [1/2-z]
> !   7                       -x,-y,-z    [-x]  [-y]  [-z]
> !   8                 1/2-x,1/2-y,-z    [1/2-x]  [1/2-y]  [-z]
> &CONTROL
>                         title = 'AMS_DATA-0.0001GPa'
>                   calculation = 'relax'
>                  restart_mode = 'from_scratch'
>                        outdir = './1'
>                    pseudo_dir = '../PP/atompaw'
>                        prefix = 'AMS_DATA-0.0001GPa'
>                       disk_io = 'none'
>                     verbosity = 'default'
>                 etot_conv_thr = 0.0001
>                 forc_conv_thr = 0.001
>                         nstep = 400
>                       tstress = .true.
>                       tprnfor = .true.
>   /
>   &SYSTEM
>                         ibrav = 0
>                           nat = 0
>                          ntyp = 0
>                       ecutwfc = 60
>                       ecutrho = 480
>                      vdw_corr = 'xdm'
>                        xdm_a1 = 1.2153
>                        xdm_a2 = 2.3704
>   /
>   &ELECTRONS
>              electron_maxstep = 200
>                      conv_thr = 1.0D-7
>                diago_thr_init = 1e-4
>                   startingpot = 'atomic'
>                   startingwfc = 'atomic'
>                   mixing_mode = 'plain'
>                   mixing_beta = 0.5
>                   mixing_ndim = 8
>               diagonalization = 'david'
>   /
> &IONS
>                  ion_dynamics = 'bfgs'
>   /
>
> ATOMIC_SPECIES
>
> ATOMIC_POSITIONS crystal
>
> K_POINTS automatic
> 2  1  3   0 0 0
>
>
>
> --
> Tsung-Lung Li, Ph. D.
> Professor
> Department of Electrophysics
> National Chia-Yi University
> 300 Hsueh-Fu Road, Chiayi 60004, Taiwan
> Phone: 886-5-2717904.  FAX: 886-5-2717909.
> E-mail:quantum at mail.ncyu.edu.tw
>
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>



-- 

------------------------------------------------------------
Prof. Carlo Nervi carlo.nervi at unito.it  Tel:+39 0116707507/8
Fax: +39 0116707855      -      Dipartimento di Chimica, via
P. Giuria 7, 10125 Torino, Italy.    http://lem.ch.unito.it/
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