[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"

[Carlo Nervi]

Il 07/01/2014 13.18, David Foster ha scritto:
> Dear Users,
> I used cif2qe.sh shell in PW/tools directory to convert rutile.cif to
>
> QE input. I got following errors:
>
> awk: 29: unexpected character '&'
> awk: line 75: syntax error at or near [
> awk: line 99: syntax error at or near [
> awk: line 101: syntax error at or near [
> awk: line 105: syntax error at or near [
>
> ===================================
> This is rutile cif:
> ================================
>
> # Part of the Crystallography Open Database
> # All data on this site have been placed in the public domain by the
> # contributors.
> #------------------------------------------------------------------------------
> #$Date: 2010-06-10 15:11:07 +0000 (Thu, 10 Jun 2010) $
> #$Revision: 1210 $
> #$URL: svn://cod.ibt.lt/cod/cif/9/9009083.cif $
> #------------------------------------------------------------------------------
> #
> # This file is available in the Crystallography Open Database (COD),
> # http://www.crystallography.net/. The original data for this entry
> # were provided the American Mineralogist Crystal Structure Database,
> # http://rruff.geo.arizona.edu/AMS/amcsd.php
> #
> # The file may be used within the scientific community so long as
> # proper attribution is given to the journal article from which the
> # data were obtained.
> #
> data_9009083
> loop_
> _publ_author_name
> 'Wyckoff, R. W. G.'
> _publ_section_title
> ;
>   Second edition. Interscience Publishers, New York, New York
> ;
> _journal_name_full               'Crystal Structures'
> _journal_page_first              239
> _journal_page_last               444
> _journal_volume                  1
> _journal_year                    1963
> _chemical_formula_sum            'O2 Ti'
> _chemical_name_mineral           Rutile
> _space_group_IT_number           136
> _symmetry_space_group_name_Hall  '-P 4n 2n'
> _symmetry_space_group_name_H-M   'P 42/m n m'
> _cell_angle_alpha                90
> _cell_angle_beta                 90
> _cell_angle_gamma                90
> _cell_length_a                   4.59373
> _cell_length_b                   4.59373
> _cell_length_c                   2.95812
> _cell_volume                     62.423
> _exptl_crystal_density_diffrn    4.250
> _[local]_cod_chemical_formula_sum_orig 'Ti O2'
> _cod_database_code               9009083
> _amcsd_database_code             AMCSD#0011415
> loop_
> _symmetry_equiv_pos_as_xyz
> x,y,z
> -y,-x,z
> y,x,-z
> 1/2+y,1/2-x,1/2-z
> 1/2-y,1/2+x,1/2+z
> 1/2+x,1/2-y,1/2+z
> 1/2-x,1/2+y,1/2-z
> x,y,-z
> -x,-y,z
> y,x,z
> -y,-x,-z
> 1/2-y,1/2+x,1/2-z
> 1/2+y,1/2-x,1/2+z
> 1/2-x,1/2+y,1/2+z
> 1/2+x,1/2-y,1/2-z
> -x,-y,-z
> loop_
> _atom_site_label
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> Ti 0.00000 0.00000 0.00000
> O 0.30530 0.30530 0.00000
>
> anybody can help?
>
> Regards
>
> David Foster
>
> Ph.D. Student of Chemistry
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>

Hello,
it seems that the .cif file is not fully standard.
Try this in sequence:
1) rename "_atom_site_label" to "_atom_site_type_symbol"
2) try to separate each _loop putting a blank line at the end of its own 
block. For example before each _loop line

I do not understand what you deleted in the file, but do not delete the 
line containing "_symmetry_equiv_pos_as_xyz": it is necessary to define 
the symmetry! I was meaning to keep that line but to delete any blank 
line in between.

I did it and the results is:

&CONTROL
                        title = 'rutile'
                  calculation = 'relax'
                 restart_mode = 'from_scratch'
                       outdir = './1'
                   pseudo_dir = '../PP/atompaw'
                       prefix = 'rutile'
                      disk_io = 'none'
                    verbosity = 'default'
                etot_conv_thr = 0.00001
                forc_conv_thr = 0.0001
                        nstep = 680
                      tstress = .true.
                      tprnfor = .true.
  /
  &SYSTEM
                        ibrav = 0
                          nat = 4
                         ntyp = 2
                      ecutwfc = 60
                      ecutrho = 600
!                      london = .true.
  /
  &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
    Ti   47.8670000000  Ti.pbe-van_ak.UPF
     O   15.9994000000  O.pbe-van_ak.UPF

ATOMIC_POSITIONS crystal
Ti     0.000000000000000     0.000000000000000     0.000000000000000
  O     0.305300000000000     0.305300000000000     0.000000000000000
Ti     0.500000000000000     0.500000000000000     0.500000000000000
  O     0.805300000000000     0.194700000000000     0.500000000000000

K_POINTS automatic
5  5  8   0 0 0


CELL_PARAMETERS
     8.680891628420765     0.000000000000000     0.000000000000000
     0.000000000000001     8.680891628420765     0.000000000000000
     0.000000000000000     0.000000000000000     5.590036668211679


HTH,
	Carlo

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