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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
On 01/07/2014 01:18 PM, David Foster wrote:> Dear Users,
Post by David Foster
I used cif2qe.sh shell in PW/tools directory to convert rutile.cif to
It works for me, I get the following output.

How do you run the code, and which version of bash and awk do you have?
Did you change anything in the script?


best regards

&CONTROL
title = 'rutile'
calculation = 'relax'
restart_mode = 'from_scratch'
outdir = './1'
pseudo_dir = '../PP/atompaw'
prefix = 'caz'
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 = 1
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
0.0000000000 .pbe-van_ak.UPF

ATOMIC_POSITIONS crystal
0.000000000000000 0.000000000000000 0.000000000000000
0.305300000000000 0.305300000000000 0.000000000000000
0.500000000000000 0.500000000000000 0.500000000000000
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
--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

-------------- next part --------------
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On 01/07/2014 01:18 PM, David Foster wrote:> Dear Users,
Post by David Foster
I used cif2qe.sh shell in PW/tools directory to convert rutile.cif to
It works for me, I get the following output.

How do you run the code, and which version of bash and awk do you have?
Did you change anything in the script?


best regards

&CONTROL
title = 'rutile'
calculation = 'relax'
restart_mode = 'from_scratch'
outdir = './1'
pseudo_dir = '../PP/atompaw'
prefix = 'caz'
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 = 1
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
0.0000000000 .pbe-van_ak.UPF

ATOMIC_POSITIONS crystal
0.000000000000000 0.000000000000000 0.000000000000000
0.305300000000000 0.305300000000000 0.000000000000000
0.500000000000000 0.500000000000000 0.500000000000000
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
--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

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Dear Lorenzo

Thank you for your reply. I used 5.0.2 version of QE. I didn't change anything. I will download new version and try.

I work on Debian 7.0 which "mwak" has been installed on it. Do I need to install "gawk" on it.


Regards

David Foster

Ph.D. Student of Chemistry

--------------------------------------------
On Tue, 1/7/14, Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr> wrote:

Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Tuesday, January 7, 2014, 5:45 AM

On 01/07/2014 01:18 PM, David Foster
wrote:> Dear Users,
Post by David Foster
I used cif2qe.sh shell in PW/tools directory to convert
rutile.cif to

It works for me, I get the following output.

How do you run the code, and which version of bash and awk
do you have? Did you change anything in the script?


best regards

&CONTROL
? ? ? ? ? ? ? ?
? ? ???title = 'rutile'
? ? ? ? ? ? ?
???calculation = 'relax'
? ? ? ? ? ? ? ?
restart_mode = 'from_scratch'
? ? ? ? ? ? ? ?
? ? ? outdir = './1'
? ? ? ? ? ? ? ?
? pseudo_dir = '../PP/atompaw'
? ? ? ? ? ? ? ?
? ? ? prefix = 'caz'
? ? ? ? ? ? ? ?
? ???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 = 1
? ? ? ? ? ? ? ?
? ???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
? ? ? ???0.0000000000?
.pbe-van_ak.UPF

ATOMIC_POSITIONS crystal
? ? ???0.000000000000000?
???0.000000000000000?
???0.000000000000000
? ? ???0.305300000000000?
???0.305300000000000?
???0.000000000000000
? ? ???0.500000000000000?
???0.500000000000000?
???0.500000000000000
? ? ???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




-- Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris
C?dex 05


-----Inline Attachment Follows-----

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
This is the header of the last version. Note the fourth line:
---
# Version 0.5 Date: 02-Oct-2013
# Version 0.4 Date: 12 Jun 2013
# Version 0.3 Date: 15 Nov 2012
# tested with GNU awk v.4 - may not work with earlier versions
---

P.
Post by David Foster
I will download new version and try.
I work on Debian 7.0 which "mwak" has been installed on it. Do I need to install "gawk" on it.
Regards
David Foster
Ph.D. Student of Chemistry
--------------------------------------------
Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Tuesday, January 7, 2014, 5:45 AM
On 01/07/2014 01:18 PM, David Foster
wrote:> Dear Users,
Post by David Foster
I used cif2qe.sh shell in PW/tools directory to convert
rutile.cif to
It works for me, I get the following output.
How do you run the code, and which version of bash and awk
do you have? Did you change anything in the script?
best regards
&CONTROL
title = 'rutile'
calculation = 'relax'
restart_mode = 'from_scratch'
outdir = './1'
pseudo_dir = '../PP/atompaw'
prefix = 'caz'
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 = 1
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
0.0000000000
.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
0.000000000000000
0.000000000000000
0.000000000000000
0.305300000000000
0.305300000000000
0.000000000000000
0.500000000000000
0.500000000000000
0.500000000000000
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
-- Dr. Lorenzo Paulatto
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris
C?dex 05
-----Inline Attachment Follows-----
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
--
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
And I run as follows:

./cif2qe.sh rutile

without .cif


Regards

David Foster

Ph.D. Student of Chemistry

--------------------------------------------
On Tue, 1/7/14, Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr> wrote:

Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Tuesday, January 7, 2014, 5:45 AM

On 01/07/2014 01:18 PM, David Foster
wrote:> Dear Users,
Post by David Foster
I used cif2qe.sh shell in PW/tools directory to convert
rutile.cif to

It works for me, I get the following output.

How do you run the code, and which version of bash and awk
do you have? Did you change anything in the script?


best regards

&CONTROL
? ? ? ? ? ? ? ?
? ? ???title = 'rutile'
? ? ? ? ? ? ?
???calculation = 'relax'
? ? ? ? ? ? ? ?
restart_mode = 'from_scratch'
? ? ? ? ? ? ? ?
? ? ? outdir = './1'
? ? ? ? ? ? ? ?
? pseudo_dir = '../PP/atompaw'
? ? ? ? ? ? ? ?
? ? ? prefix = 'caz'
? ? ? ? ? ? ? ?
? ???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 = 1
? ? ? ? ? ? ? ?
? ???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
? ? ? ???0.0000000000?
.pbe-van_ak.UPF

ATOMIC_POSITIONS crystal
? ? ???0.000000000000000?
???0.000000000000000?
???0.000000000000000
? ? ???0.305300000000000?
???0.305300000000000?
???0.000000000000000
? ? ???0.500000000000000?
???0.500000000000000?
???0.500000000000000
? ? ???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




-- Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris
C?dex 05


-----Inline Attachment Follows-----

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
Dear Paolo

Thank you for reply. I upgrade the file to 5th version.

I installed gawk 4. Now, I recieve this error:


Error in _Symmetry_equiv_pos_as_xyz. Number of fields !=3: [1]= [2]= [3]=
D:



Regards

David Foster

Ph.D. Student of Chemistry

--------------------------------------------
On Tue, 1/7/14, Paolo Giannozzi <paolo.giannozzi at uniud.it> wrote:

Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
To: pw_forum at pwscf.org
Date: Tuesday, January 7, 2014, 2:11 PM

This is the header of the last
version. Note the fourth line:
---
#? Version 0.5? Date: 02-Oct-2013
#? Version 0.4? Date: 12 Jun 2013
#? Version 0.3? Date: 15 Nov 2012
# tested with GNU awk v.4 - may not work with earlier
versions
---

P.
Post by David Foster
I will download new version and try.
I work on Debian 7.0 which "mwak" has been installed on
it. Do I need to install "gawk" on it.
Post by David Foster
Regards
David Foster
Ph.D. Student of Chemistry
--------------------------------------------
On Tue, 1/7/14, Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr>
? Subject: Re: [Pw_forum] Error in converting CIF
to QE by "cif2qe.sh"
Post by David Foster
? To: "PWSCF Forum" <pw_forum at pwscf.org>
? Date: Tuesday, January 7, 2014, 5:45 AM
?
? On 01/07/2014 01:18 PM, David Foster
? wrote:> Dear Users,
? > I used cif2qe.sh shell in PW/tools directory
to convert
Post by David Foster
? rutile.cif to
?
? It works for me, I get the following output.
?
? How do you run the code, and which version of
bash and awk
Post by David Foster
? do you have? Did you change anything in the
script?
Post by David Foster
?
? best regards
?
? &CONTROL
? ? ? ? ? ? ?
???
Post by David Foster
? ? ? ???title = 'rutile'
? ? ? ? ? ?
???
Post by David Foster
? ???calculation = 'relax'
? ? ? ? ? ? ?
???
Post by David Foster
? restart_mode = 'from_scratch'
? ? ? ? ? ? ?
???
Post by David Foster
? ? ? ? outdir = './1'
? ? ? ? ? ? ?
???
Post by David Foster
? ? pseudo_dir = '../PP/atompaw'
? ? ? ? ? ? ?
???
Post by David Foster
? ? ? ? prefix = 'caz'
? ? ? ? ? ? ?
???
Post by David Foster
? ? ???disk_io = 'none'
? ? ? ? ? ? ?
???
Post by David Foster
? ???verbosity = 'default'
? ? ? ? ? ???
? ???etot_conv_thr = 0.00001
? ? ? ? ? ???
? ???forc_conv_thr = 0.0001
? ? ? ? ? ? ?
???
Post by David Foster
? ? ? ???nstep = 680
? ? ? ? ? ? ?
???
Post by David Foster
? ? ???tstress = .true.
? ? ? ? ? ? ?
???
Post by David Foster
? ? ???tprnfor = .true.
???/
???&SYSTEM
? ? ? ? ? ? ?
???
Post by David Foster
? ? ? ???ibrav = 0
? ? ? ? ? ? ?
???
Post by David Foster
? ? ? ? ???nat = 4
? ? ? ? ? ? ?
???
Post by David Foster
? ? ? ? ? ntyp = 1
? ? ? ? ? ? ?
???
Post by David Foster
? ? ???ecutwfc = 60
? ? ? ? ? ? ?
???
Post by David Foster
? ? ???ecutrho = 600
? !? ? ? ? ? ?
???
Post by David Foster
? ? ? ? london = .true.
???/
???&ELECTRONS
? ? ? ? ? ? ?
electron_maxstep =
Post by David Foster
? 200
? ? ? ? ? ? ?
???
Post by David Foster
? ? ? conv_thr = 1.0D-7
? ? ? ? ? ?
???
Post by David Foster
? diago_thr_init = 1e-4
? ? ? ? ? ?
???
Post by David Foster
? ???startingpot = 'atomic'
? ? ? ? ? ?
???
Post by David Foster
? ???startingwfc = 'atomic'
? ? ? ? ? ?
???
Post by David Foster
? ???mixing_mode = 'plain'
? ? ? ? ? ?
???
Post by David Foster
? ???mixing_beta = 0.5
? ? ? ? ? ?
???
Post by David Foster
? ???mixing_ndim = 8
? ? ? ? ???
? ???diagonalization = 'david'
???/
? &IONS
? ? ? ? ? ? ?
???
Post by David Foster
? ion_dynamics = 'bfgs'
???/
?
? ATOMIC_SPECIES
? ? ? ?
???0.0000000000
Post by David Foster
? .pbe-van_ak.UPF
?
? ATOMIC_POSITIONS crystal
? ? ? ???0.000000000000000
? ???0.000000000000000
? ???0.000000000000000
? ? ? ???0.305300000000000
? ???0.305300000000000
? ???0.000000000000000
? ? ? ???0.500000000000000
? ???0.500000000000000
? ???0.500000000000000
? ? ? ???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
?
? -- Dr. Lorenzo Paulatto
? +33 (0)1 44 275 084 / skype: paulatz
? http://www-int.impmc.upmc.fr/~paulatto/
? 23-24/4?16 Bo?te courrier 115, 4 place Jussieu
75252 Paris
Post by David Foster
? C?dex 05
?
? -----Inline Attachment Follows-----
?
? _______________________________________________
? Pw_forum mailing list
? Pw_forum at pwscf.org
? http://pwscf.org/mailman/listinfo/pw_forum
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
--
Paolo Giannozzi, Dept.
Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
Hi David,
it seems that in the line containing _Symmetry_equiv_pos_as_xyz it does
not recognize the three necessary parameters.
Have a look of the original .cif file and if there is only spaces after
_Symmetry_equiv_pos_as_xyz just delete the line.

In any cases, Lorenzo succeed in using the conversion, so maybe it is
again a problem related with your version og awk. Preferabily please use
gawk (gnu awk).

Regards,
Carlo
Post by David Foster
Dear Paolo
Thank you for reply. I upgrade the file to 5th version.
Error in _Symmetry_equiv_pos_as_xyz. Number of fields !=3: [1]= [2]= [3]=
Regards
David Foster
Ph.D. Student of Chemistry
--------------------------------------------
Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
To: pw_forum at pwscf.org
Date: Tuesday, January 7, 2014, 2:11 PM
This is the header of the last
---
# Version 0.5 Date: 02-Oct-2013
# Version 0.4 Date: 12 Jun 2013
# Version 0.3 Date: 15 Nov 2012
# tested with GNU awk v.4 - may not work with earlier
versions
---
P.
Post by David Foster
I will download new version and try.
I work on Debian 7.0 which "mwak" has been installed on
it. Do I need to install "gawk" on it.
Post by David Foster
Regards
David Foster
Ph.D. Student of Chemistry
--------------------------------------------
On Tue, 1/7/14, Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr>
Subject: Re: [Pw_forum] Error in converting CIF
to QE by "cif2qe.sh"
Post by David Foster
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Tuesday, January 7, 2014, 5:45 AM
On 01/07/2014 01:18 PM, David Foster
wrote:> Dear Users,
Post by David Foster
I used cif2qe.sh shell in PW/tools directory
to convert
Post by David Foster
rutile.cif to
It works for me, I get the following output.
How do you run the code, and which version of
bash and awk
Post by David Foster
do you have? Did you change anything in the
script?
Post by David Foster
best regards
&CONTROL
title = 'rutile'
calculation = 'relax'
restart_mode = 'from_scratch'
outdir = './1'
pseudo_dir = '../PP/atompaw'
prefix = 'caz'
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 = 1
ecutwfc = 60
ecutrho = 600
!
london = .true.
/
&ELECTRONS
electron_maxstep =
Post by David Foster
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
0.0000000000
Post by David Foster
.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
0.000000000000000
0.000000000000000
0.000000000000000
0.305300000000000
0.305300000000000
0.000000000000000
0.500000000000000
0.500000000000000
0.500000000000000
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
-- Dr. Lorenzo Paulatto
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu
75252 Paris
Post by David Foster
C?dex 05
-----Inline Attachment Follows-----
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
--
Paolo Giannozzi, Dept.
Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
--
------------------------------------------------------------
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/
Thank you very much, Carlo.

I delete the line

The problem solved.

Thank you very much.


Regards

David Foster

Ph.D. Student of Chemistry

--------------------------------------------
On Wed, 1/8/14, Carlo Nervi <carlo.nervi at unito.it> wrote:

Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
To: pw_forum at pwscf.org
Date: Wednesday, January 8, 2014, 3:44 AM

Hi David,
it seems that in the line containing
_Symmetry_equiv_pos_as_xyz it does
not recognize the three necessary parameters.
Have a look of the original .cif file and if there is only
spaces after
_Symmetry_equiv_pos_as_xyz just delete the line.

In any cases, Lorenzo succeed in using the conversion, so
maybe it is
again a problem related with your version og awk.
Preferabily please use
gawk (gnu awk).

Regards,
??? Carlo
Post by David Foster
Dear Paolo
Thank you for reply. I upgrade the file to 5th
version.
Post by David Foster
Error in _Symmetry_equiv_pos_as_xyz. Number of fields
!=3: [1]= [2]= [3]=
Post by David Foster
Regards
David Foster
Ph.D. Student of Chemistry
--------------------------------------------
On Tue, 1/7/14, Paolo Giannozzi <paolo.giannozzi at uniud.it>
???Subject: Re: [Pw_forum] Error in
converting CIF to QE by "cif2qe.sh"
Post by David Foster
???To: pw_forum at pwscf.org
???Date: Tuesday, January 7, 2014, 2:11
PM
Post by David Foster
???This is the header of the last
???---
02-Oct-2013
Post by David Foster
???#? Version 0.4? Date: 12 Jun
2013
Post by David Foster
???#? Version 0.3? Date: 15 Nov
2012
Post by David Foster
???# tested with GNU awk v.4 - may not
work with earlier
Post by David Foster
???versions
???---
???P.
???On Tue, 2014-01-07 at 07:08 -0800,
???> I will download new version and
try.
Post by David Foster
???>
???> I work on Debian 7.0 which "mwak"
has been installed on
Post by David Foster
???it. Do I need to install "gawk" on
it.
Post by David Foster
???>
???>
???> Regards
???>
???> David Foster
???>
???> Ph.D. Student of Chemistry
???>
???>
--------------------------------------------
Post by David Foster
???> On Tue, 1/7/14, Lorenzo Paulatto
<lorenzo.paulatto at impmc.upmc.fr>
Post by David Foster
???>
???>? Subject: Re: [Pw_forum]
Error in converting CIF
Post by David Foster
???to QE by "cif2qe.sh"
???>? To: "PWSCF Forum" <pw_forum at pwscf.org>
???>? Date: Tuesday, January 7,
2014, 5:45 AM
Post by David Foster
???>
???>? On 01/07/2014 01:18 PM,
David Foster
Post by David Foster
???>? wrote:> Dear Users,
???>? > I used cif2qe.sh shell
in PW/tools directory
Post by David Foster
???to convert
???>? rutile.cif to
???>
???>? It works for me, I get the
following output.
Post by David Foster
???>
???>? How do you run the code,
and which version of
Post by David Foster
???bash and awk
???>? do you have? Did you change
anything in the
Post by David Foster
???script?
???>
???>
???>? best regards
???>
???>? &CONTROL
???>
???>? ? ?
???title = 'rutile'
Post by David Foster
???>
???>?
???calculation = 'relax'
Post by David Foster
???>
???>? restart_mode =
'from_scratch'
Post by David Foster
???>
???>? ? ? ? outdir
= './1'
Post by David Foster
???>
???>? ? pseudo_dir =
'../PP/atompaw'
Post by David Foster
???>
???>? ? ? ? prefix
= 'caz'
Post by David Foster
???>
???>? ?
???disk_io = 'none'
Post by David Foster
???>
???>? ???verbosity
= 'default'
Post by David Foster
???>
???>?
???etot_conv_thr = 0.00001
Post by David Foster
???>
???>?
???forc_conv_thr = 0.0001
Post by David Foster
???>
???>? ? ?
???nstep = 680
Post by David Foster
???>
???>? ?
???tstress = .true.
Post by David Foster
???>
???>? ?
???tprnfor = .true.
Post by David Foster
???>???/
???>???&SYSTEM
???>
???>? ? ?
???ibrav = 0
Post by David Foster
???>
???>? ? ? ?
???nat = 4
Post by David Foster
???>
???>? ? ? ? ?
ntyp = 1
Post by David Foster
???>
???>? ?
???ecutwfc = 60
Post by David Foster
???>
???>? ?
???ecutrho = 600
Post by David Foster
???>? !
???>? ? ? ? london
= .true.
Post by David Foster
???>???/
???>???&ELECTRONS
???>
???electron_maxstep =
???>? 200
???>
???>? ? ? conv_thr =
1.0D-7
Post by David Foster
???>
???>? diago_thr_init = 1e-4
???>
???>?
???startingpot = 'atomic'
Post by David Foster
???>
???>?
???startingwfc = 'atomic'
Post by David Foster
???>
???>?
???mixing_mode = 'plain'
Post by David Foster
???>
???>?
???mixing_beta = 0.5
Post by David Foster
???>
???>?
???mixing_ndim = 8
Post by David Foster
???>
???>?
???diagonalization = 'david'
Post by David Foster
???>???/
???>? &IONS
???>
???>? ion_dynamics = 'bfgs'
???>???/
???>
???>
???>? ATOMIC_SPECIES
???>
? ? ? 0.0000000000
???>? .pbe-van_ak.UPF
???>
???>? ATOMIC_POSITIONS crystal
???>? ? ?
???0.000000000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>? ? ?
???0.305300000000000
Post by David Foster
???>?
???0.305300000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>? ? ?
???0.500000000000000
Post by David Foster
???>?
???0.500000000000000
Post by David Foster
???>?
???0.500000000000000
Post by David Foster
???>? ? ?
???0.805300000000000
Post by David Foster
???>?
???0.194700000000000
Post by David Foster
???>?
???0.500000000000000
Post by David Foster
???>
???>? K_POINTS automatic
???>? 5? 5?
8???0 0 0
Post by David Foster
???>
???>
???>? CELL_PARAMETERS
???>? ? ?
8.680891628420765
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>? ? ?
0.000000000000001
Post by David Foster
???>?
???8.680891628420765
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>? ? ?
0.000000000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>?
???5.590036668211679
Post by David Foster
???>
???>
???>
???>
???>? -- Dr. Lorenzo Paulatto
Universit? Paris 6
Post by David Foster
???>? +33 (0)1 44 275 084 /
skype: paulatz
Post by David Foster
???>? http://www-int.impmc.upmc.fr/~paulatto/
???>? 23-24/4?16 Bo?te courrier
115, 4 place Jussieu
Post by David Foster
???75252 Paris
???>? C?dex 05
???>
???>
???>? -----Inline Attachment
Follows-----
Post by David Foster
???>
???>?
_______________________________________________
Post by David Foster
???>? Pw_forum mailing list
???>? Pw_forum at pwscf.org
???>? http://pwscf.org/mailman/listinfo/pw_forum
???>
???>
_______________________________________________
Post by David Foster
???> Pw_forum mailing list
???> Pw_forum at pwscf.org
???> http://pwscf.org/mailman/listinfo/pw_forum
???--
???Paolo Giannozzi, Dept.
???Chemistry&Physics&Environment,
???Univ. Udine, via delle Scienze 208,
33100 Udine, Italy
Post by David Foster
???Phone +39-0432-558216, fax
+39-0432-558222
Post by David Foster
???_______________________________________________
???Pw_forum mailing list
???Pw_forum at pwscf.org
???http://pwscf.org/mailman/listinfo/pw_forum
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
--
------------------------------------------------------------
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/
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
Sorry, but I have new problems. I have numbered the output to clearly

talk about it:


1&CONTROL
2 title = 'rutile1'
3 calculation = 'relax'
4 restart_mode = 'from_scratch'
5 outdir = './1'
6 pseudo_dir = '../PP/atompaw'
7 prefix = 'rutile1'
8 disk_io = 'none'
9 verbosity = 'default'
10 etot_conv_thr = 0.00001
11 forc_conv_thr = 0.0001
12 nstep = 680
13 tstress = .true.
14 tprnfor = .true.
15 /
16 &SYSTEM
17 ibrav = 0
18 nat = 0
19 ntyp = 1
20 ecutwfc = 60
21 ecutrho = 600
22! london = .true.
23 /
24 &ELECTRONS
25 electron_maxstep = 200
26 conv_thr = 1.0D-7
27 diago_thr_init = 1e-4
28 startingpot = 'atomic'
29 startingwfc = 'atomic'
30 mixing_mode = 'plain'
31 mixing_beta = 0.5
32 mixing_ndim = 8
33 diagonalization = 'david'
34 /
35&IONS
36 ion_dynamics = 'bfgs'
37 /
38
39
40 ATOMIC_SPECIES
41 0.0000000000 .pbe-van_ak.UPF
42
43 ATOMIC_POSITIONS crystal
44
45 K_POINTS automatic
46 5 5 8 0 0 0
47
48
49 CELL_PARAMETERS
50 8.680891628420765 0.000000000000000 0.000000000000000
51 0.000000000000001 8.680891628420765 0.000000000000000
52 0.000000000000000 0.000000000000000 5.590036668211679


1- at line 41 atomic symbols have not been shown (similar to lorenzo's
output)

2- at line 44, positions have not been printed (contrary to lorenzo's
output)

3- I think in rutile, we should have 6 atoms in cell, but lorenzo's
output has 4 atoms without symbols.



Regards

David Foster

Ph.D. Student of Chemistry

--------------------------------------------
On Wed, 1/8/14, Carlo Nervi <carlo.nervi at unito.it> wrote:

Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
To: pw_forum at pwscf.org
Date: Wednesday, January 8, 2014, 3:44 AM

Hi David,
it seems that in the line containing
_Symmetry_equiv_pos_as_xyz it does
not recognize the three necessary parameters.
Have a look of the original .cif file and if there is only
spaces after
_Symmetry_equiv_pos_as_xyz just delete the line.

In any cases, Lorenzo succeed in using the conversion, so
maybe it is
again a problem related with your version og awk.
Preferabily please use
gawk (gnu awk).

Regards,
??? Carlo
Post by David Foster
Dear Paolo
Thank you for reply. I upgrade the file to 5th
version.
Post by David Foster
Error in _Symmetry_equiv_pos_as_xyz. Number of fields
!=3: [1]= [2]= [3]=
Post by David Foster
Regards
David Foster
Ph.D. Student of Chemistry
--------------------------------------------
On Tue, 1/7/14, Paolo Giannozzi <paolo.giannozzi at uniud.it>
???Subject: Re: [Pw_forum] Error in
converting CIF to QE by "cif2qe.sh"
Post by David Foster
???To: pw_forum at pwscf.org
???Date: Tuesday, January 7, 2014, 2:11
PM
Post by David Foster
???This is the header of the last
???---
02-Oct-2013
Post by David Foster
???#? Version 0.4? Date: 12 Jun
2013
Post by David Foster
???#? Version 0.3? Date: 15 Nov
2012
Post by David Foster
???# tested with GNU awk v.4 - may not
work with earlier
Post by David Foster
???versions
???---
???P.
???On Tue, 2014-01-07 at 07:08 -0800,
???> I will download new version and
try.
Post by David Foster
???>
???> I work on Debian 7.0 which "mwak"
has been installed on
Post by David Foster
???it. Do I need to install "gawk" on
it.
Post by David Foster
???>
???>
???> Regards
???>
???> David Foster
???>
???> Ph.D. Student of Chemistry
???>
???>
--------------------------------------------
Post by David Foster
???> On Tue, 1/7/14, Lorenzo Paulatto
<lorenzo.paulatto at impmc.upmc.fr>
Post by David Foster
???>
???>? Subject: Re: [Pw_forum]
Error in converting CIF
Post by David Foster
???to QE by "cif2qe.sh"
???>? To: "PWSCF Forum" <pw_forum at pwscf.org>
???>? Date: Tuesday, January 7,
2014, 5:45 AM
Post by David Foster
???>
???>? On 01/07/2014 01:18 PM,
David Foster
Post by David Foster
???>? wrote:> Dear Users,
???>? > I used cif2qe.sh shell
in PW/tools directory
Post by David Foster
???to convert
???>? rutile.cif to
???>
???>? It works for me, I get the
following output.
Post by David Foster
???>
???>? How do you run the code,
and which version of
Post by David Foster
???bash and awk
???>? do you have? Did you change
anything in the
Post by David Foster
???script?
???>
???>
???>? best regards
???>
???>? &CONTROL
???>
???>? ? ?
???title = 'rutile'
Post by David Foster
???>
???>?
???calculation = 'relax'
Post by David Foster
???>
???>? restart_mode =
'from_scratch'
Post by David Foster
???>
???>? ? ? ? outdir
= './1'
Post by David Foster
???>
???>? ? pseudo_dir =
'../PP/atompaw'
Post by David Foster
???>
???>? ? ? ? prefix
= 'caz'
Post by David Foster
???>
???>? ?
???disk_io = 'none'
Post by David Foster
???>
???>? ???verbosity
= 'default'
Post by David Foster
???>
???>?
???etot_conv_thr = 0.00001
Post by David Foster
???>
???>?
???forc_conv_thr = 0.0001
Post by David Foster
???>
???>? ? ?
???nstep = 680
Post by David Foster
???>
???>? ?
???tstress = .true.
Post by David Foster
???>
???>? ?
???tprnfor = .true.
Post by David Foster
???>???/
???>???&SYSTEM
???>
???>? ? ?
???ibrav = 0
Post by David Foster
???>
???>? ? ? ?
???nat = 4
Post by David Foster
???>
???>? ? ? ? ?
ntyp = 1
Post by David Foster
???>
???>? ?
???ecutwfc = 60
Post by David Foster
???>
???>? ?
???ecutrho = 600
Post by David Foster
???>? !
???>? ? ? ? london
= .true.
Post by David Foster
???>???/
???>???&ELECTRONS
???>
???electron_maxstep =
???>? 200
???>
???>? ? ? conv_thr =
1.0D-7
Post by David Foster
???>
???>? diago_thr_init = 1e-4
???>
???>?
???startingpot = 'atomic'
Post by David Foster
???>
???>?
???startingwfc = 'atomic'
Post by David Foster
???>
???>?
???mixing_mode = 'plain'
Post by David Foster
???>
???>?
???mixing_beta = 0.5
Post by David Foster
???>
???>?
???mixing_ndim = 8
Post by David Foster
???>
???>?
???diagonalization = 'david'
Post by David Foster
???>???/
???>? &IONS
???>
???>? ion_dynamics = 'bfgs'
???>???/
???>
???>
???>? ATOMIC_SPECIES
???>
? ? ? 0.0000000000
???>? .pbe-van_ak.UPF
???>
???>? ATOMIC_POSITIONS crystal
???>? ? ?
???0.000000000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>? ? ?
???0.305300000000000
Post by David Foster
???>?
???0.305300000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>? ? ?
???0.500000000000000
Post by David Foster
???>?
???0.500000000000000
Post by David Foster
???>?
???0.500000000000000
Post by David Foster
???>? ? ?
???0.805300000000000
Post by David Foster
???>?
???0.194700000000000
Post by David Foster
???>?
???0.500000000000000
Post by David Foster
???>
???>? K_POINTS automatic
???>? 5? 5?
8???0 0 0
Post by David Foster
???>
???>
???>? CELL_PARAMETERS
???>? ? ?
8.680891628420765
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>? ? ?
0.000000000000001
Post by David Foster
???>?
???8.680891628420765
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>? ? ?
0.000000000000000
Post by David Foster
???>?
???0.000000000000000
Post by David Foster
???>?
???5.590036668211679
Post by David Foster
???>
???>
???>
???>
???>? -- Dr. Lorenzo Paulatto
Universit? Paris 6
Post by David Foster
???>? +33 (0)1 44 275 084 /
skype: paulatz
Post by David Foster
???>? http://www-int.impmc.upmc.fr/~paulatto/
???>? 23-24/4?16 Bo?te courrier
115, 4 place Jussieu
Post by David Foster
???75252 Paris
???>? C?dex 05
???>
???>
???>? -----Inline Attachment
Follows-----
Post by David Foster
???>
???>?
_______________________________________________
Post by David Foster
???>? Pw_forum mailing list
???>? Pw_forum at pwscf.org
???>? http://pwscf.org/mailman/listinfo/pw_forum
???>
???>
_______________________________________________
Post by David Foster
???> Pw_forum mailing list
???> Pw_forum at pwscf.org
???> http://pwscf.org/mailman/listinfo/pw_forum
???--
???Paolo Giannozzi, Dept.
???Chemistry&Physics&Environment,
???Univ. Udine, via delle Scienze 208,
33100 Udine, Italy
Post by David Foster
???Phone +39-0432-558216, fax
+39-0432-558222
Post by David Foster
???_______________________________________________
???Pw_forum mailing list
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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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Post by David Foster
Dear Users,
I used cif2qe.sh shell in PW/tools directory to convert rutile.cif to
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 [
===================================
================================
# 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
--
------------------------------------------------------------
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/