[Wien] Cif File
Gavin Abo
gsabo at crimson.ua.edu
Sat Apr 24 15:17:32 CEST 2021
For example, in the cif file below you see the lattice parameters (in
the hexagonal setting) and spacegroup:
_cell_length_a 3.35
_cell_length_b 3.35
_cell_length_c 16.53
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 120
...
_symmetry_space_group_name_H-M 'R-3m'
_symmetry_Int_Tables_number 166
So in StructGen of w2web, select "Lattice parameters in A" and put
a=3.35, b=3.35, and c=16.53 for the lattice constants. For Lattice,
select "166_R-3m".
You will also need to put the lattice angles and atom coordinates into
StructGen.
Keep in mind for the atom coordinates that since the above is for a R
lattice spacegroup, those need to be in the rhombohedral setting as
mentioned in the posts at the following three links:
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05554.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11017.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18489.html
If you are a beginner, it is usually best to use runsp_lapw (and not
runafm_lapw) as described at:
http://susi.theochem.tuwien.ac.at/reg_user/faq/afm.html
As seen in StructGen (or the case.struct file), the atom coordinates are
for the 'inequivalent' atomic positions.
So if end up with Yb having only 1 inequivalent atomic position in
StructGen. You wouldn't be able to specify an AFM configuration later
with instgen_lapw during init_lapw as you can only specify a single up
or down (ferromagnet configuration).
If that is the case, you will need to create a supercell (change the
spacegroup) by using special labels to make some or all of the
'equivalent' atomic positions into inequivalent ones so that you can
specify your AFM configuration during instgen_lapw.
Some guidance on making supercells can be found at:
http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html
Other guidance on making supercells can be found in past posts in the
mailing list archive.
I think there used to be a good presentation on calculating different
magnetic configurations, but I haven't been able to find it again. I
think the website that was hosting it did not put it up again when that
website seemed to have gone down from a transition to a new server.
It might have been the "Magnetic and charge order phase transition in
YBaFe2O5" presentation mentioned in the post at:
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20603.html
Since it looked like that was Prof. Blaha's presentation, you might be
able to request a copy of it from him.
username at computername:~/Desktop/cif$ cat sd_1006604\ \(2\).cif
##CIF_1.1
data_sm_global
#Used dictionaries
loop_
_audit_conform_dict_name
_audit_conform_dict_version
_audit_conform_dict_location
cif_core.dic 2.4.2 .
cif_pd.dic 1.0.1 .
cif_sm.dic 0.1 'redaktion.landolt-boernstein(at)springer.com'
#About this content and reference
_sm_credits_copyright
;PAULING FILE Multinaries Edition - 2012. SpringerMaterials Release 2014.
http://www.paulingfile.com
Unique LPF ID Number SD1006604
Project Coordinator: Shuichi Iwata
Section-Editors: Karin Cenzual (Crystal Structures), Hiroaki Okamoto (Phase
Diagrams), Fritz Hulliger (Physical Properties)
(c) Springer & Material Phases Data System (MPDS), Switzerland & National
Institute for Materials Science (NIMS), Japan 2014.
(Data generated pre-2002: (c) Springer & MPDS & NIMS;
post-2001: (c) Springer & MPDS)
All Rights Reserved. Version 2014.06.
;
_audit_creation_method
;This data have been compiled from the crystallographic datasheet for
"NaYbO2 Crystal Structure"
taken from SpringerMaterials (sm_isp_sd_1006604).
;
_publ_section_references
;Brüesch P., Schüler C.: <i>Raman and Infrared Spectra of
Crystals with α-NaFeO<sub>2</sub> Structure</i>. Journal of
Physics and Chemistry of Solids <b>32</b> (1971) 1025-1038.
;
#Phase classification
_sm_phase_labels 'NaYbO2'
_chemical_name_mineral ''
_sm_chemical_compound_class 'oxide'
_sm_phase_prototype 'NaFeO2 '
_sm_pearson_symbol 'hR12'
_symmetry_Int_Tables_number 166
_sm_sample_details
;sample prepared from Yb<sub>2</sub>O<sub>3</sub>,
Na<sub>2</sub>O<sub>2</sub>
;
_sm_measurement_details
;
;
_sm_interpretation_details
;complete structure determined
;
data_sm_isp_SD1006604-standardized_unitcell
#Cell Parameters
_cell_length_a 3.35
_cell_length_b 3.35
_cell_length_c 16.53
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 120
_sm_length_ratio_ab 1.000
_sm_length_ratio_bc 0.203
_sm_length_ratio_ca 4.934
_cell_volume 160.7
_symmetry_space_group_name_H-M 'R-3m'
_symmetry_Int_Tables_number 166
_cell_formula_units_Z 3
_sm_cell_transformation
;origin shift 0 0 1/2
;
#Atom Coordinates
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_Wyckoff_symbol
_sm_site_symmetry
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_sm_coordination_number
_sm_atomic_environment_type
O 'O' .6c .3m 0 0 0.24 1 6 'octahedron, Yb<sub>3</sub>Na<sub>3</sub>'
Yb 'Yb' .3b .-3m 0 0 0.5 1 6 'octahedron, O<sub>6</sub>'
Na 'Na' .3a .-3m 0 0 0 1 6 'octahedron, O<sub>6</sub>'
_sm_atom_site_transformation
;origin shift 0 0 1/2
;
data_sm_isp_SD1006604-published_cell
#Cell Parameters
_cell_length_a 3.35
_cell_length_b 3.35
_cell_length_c 16.53
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 120
_sm_length_ratio_ab 1.000
_sm_length_ratio_bc 0.203
_sm_length_ratio_ca 4.934
_cell_volume 160.65
_symmetry_space_group_name_H-M 'R-3m'
_symmetry_Int_Tables_number 166
_cell_formula_units_Z 3
#Atom Coordinates
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_Wyckoff_symbol
_sm_site_symmetry
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_sm_coordination_number
_sm_atomic_environment_type
Yb 'Yb' .3a .-3m 0 0 0 1 ? '?'
Na 'Na' .3b .-3m 0 0 0.5 1 ? '?'
O 'O' .6c .3m 0 0 0.26 1 ? '?'
data_sm_isp_SD1006604-niggli_reduced_cell
#Cell Parameters
_cell_length_a 3.35
_cell_length_b 3.35
_cell_length_c 5.8396
_cell_angle_alpha 73.331
_cell_angle_beta 73.331
_cell_angle_gamma 60
_sm_length_ratio_ab 1.000
_sm_length_ratio_bc 0.574
_sm_length_ratio_ca 1.743
_cell_volume 53.55
_symmetry_space_group_name_H-M ''
_symmetry_Int_Tables_number ?
_cell_formula_units_Z 3
#Atom Coordinates
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_Wyckoff_symbol
_sm_site_symmetry
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_sm_coordination_number
_sm_atomic_environment_type
? ? ? ? ? ? ? ? ? ?
On 4/24/2021 5:21 AM, 413119008 at nitt.edu wrote:
>
> sir
>
>
> I am using wien2k in my ubuntu system and Iam not able to open this
> cif file into structgen.when i click use this file iam getting an
> error in error files such that "this cif file cannot be acccessed.Also
> i want to know how can i make this as an input file for AFM
> calculation for Yb ions.
>
>
> with regards
>
> Narayanan Namboodirir P
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