ABINIT Discussion Forums

Posted: **Fri Jun 15, 2018 4:30 pm**

Dear ABINIT developers and users!

How to write in the input file a structure that has two or three atoms of different sort in one crystallographic position (take into account the degree of filling of crystallographic positions).
Cross-reference of the coordinates of each atom leads to an error:

chkinp: ERROR - Atoms number 1 and 2 are located at the same point of the unit cell
(periodic images are taken into account).

Code: Select all

#------------------------------------------------------------------------------
#$Date: 2016-02-18 17:37:37 +0200 (Thu, 18 Feb 2016) $
#$Revision: 176729 $
#$URL: svn://www.crystallography.net/cod/cif/1/00/11/1001155.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
data_1001155
loop_
_publ_author_name
'Bernier, J C'
'Poix, P'
'Michel, A'
_publ_section_title
;
Etude cristallographique et magnetique de deux vanadates mixtes
spinelles
;
_journal_coden_ASTM              BSCFAS
_journal_name_full
;
Bulletin de la Societe Chimique de France (Vol=Year)
;
_journal_page_first              445
_journal_page_last               446
_journal_volume                  1963
_journal_year                    1963
_chemical_formula_structural     'Li Co V O4'
_chemical_formula_sum            'Co Li O4 V'
_chemical_name_systematic        'Lithium cobalt vanadium oxide'
_space_group_IT_number           227
_symmetry_cell_setting           cubic
_symmetry_space_group_name_Hall  'F 4d 2 3 -1d'
_symmetry_space_group_name_H-M   'F d -3 m :1'
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   8.276
_cell_length_b                   8.276
_cell_length_c                   8.276
_cell_volume                     566.8
_cod_original_sg_symbol_H-M      'F d -3 m S'
_cod_database_code               1001155
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
y,z,x
z,x,y
x,z,y
y,x,z
z,y,x
x,-y,-z
y,-z,-x
z,-x,-y
x,-z,-y
y,-x,-z
z,-y,-x
-x,y,-z
-y,z,-x
-z,x,-y
-x,z,-y
-y,x,-z
-z,y,-x
-x,-y,z
-y,-z,x
-z,-x,y
-x,-z,y
-y,-x,z
-z,-y,x
1/4-x,1/4-y,1/4-z
1/4-y,1/4-z,1/4-x
1/4-z,1/4-x,1/4-y
1/4-x,1/4-z,1/4-y
1/4-y,1/4-x,1/4-z
1/4-z,1/4-y,1/4-x
1/4-x,1/4+y,1/4+z
1/4-y,1/4+z,1/4+x
1/4-z,1/4+x,1/4+y
1/4-x,1/4+z,1/4+y
1/4-y,1/4+x,1/4+z
1/4-z,1/4+y,1/4+x
1/4+x,1/4-y,1/4+z
1/4+y,1/4-z,1/4+x
1/4+z,1/4-x,1/4+y
1/4+x,1/4-z,1/4+y
1/4+y,1/4-x,1/4+z
1/4+z,1/4-y,1/4+x
1/4+x,1/4+y,1/4-z
1/4+y,1/4+z,1/4-x
1/4+z,1/4+x,1/4-y
1/4+x,1/4+z,1/4-y
1/4+y,1/4+x,1/4-z
1/4+z,1/4+y,1/4-x
x,1/2+y,1/2+z
1/2+x,y,1/2+z
1/2+x,1/2+y,z
y,1/2+z,1/2+x
1/2+y,z,1/2+x
1/2+y,1/2+z,x
z,1/2+x,1/2+y
1/2+z,x,1/2+y
1/2+z,1/2+x,y
x,1/2+z,1/2+y
1/2+x,z,1/2+y
1/2+x,1/2+z,y
y,1/2+x,1/2+z
1/2+y,x,1/2+z
1/2+y,1/2+x,z
z,1/2+y,1/2+x
1/2+z,y,1/2+x
1/2+z,1/2+y,x
x,1/2-y,1/2-z
1/2+x,-y,1/2-z
1/2+x,1/2-y,-z
y,1/2-z,1/2-x
1/2+y,-z,1/2-x
1/2+y,1/2-z,-x
z,1/2-x,1/2-y
1/2+z,-x,1/2-y
1/2+z,1/2-x,-y
x,1/2-z,1/2-y
1/2+x,-z,1/2-y
1/2+x,1/2-z,-y
y,1/2-x,1/2-z
1/2+y,-x,1/2-z
1/2+y,1/2-x,-z
z,1/2-y,1/2-x
1/2+z,-y,1/2-x
1/2+z,1/2-y,-x
-x,1/2+y,1/2-z
1/2-x,y,1/2-z
1/2-x,1/2+y,-z
-y,1/2+z,1/2-x
1/2-y,z,1/2-x
1/2-y,1/2+z,-x
-z,1/2+x,1/2-y
1/2-z,x,1/2-y
1/2-z,1/2+x,-y
-x,1/2+z,1/2-y
1/2-x,z,1/2-y
1/2-x,1/2+z,-y
-y,1/2+x,1/2-z
1/2-y,x,1/2-z
1/2-y,1/2+x,-z
-z,1/2+y,1/2-x
1/2-z,y,1/2-x
1/2-z,1/2+y,-x
-x,1/2-y,1/2+z
1/2-x,-y,1/2+z
1/2-x,1/2-y,z
-y,1/2-z,1/2+x
1/2-y,-z,1/2+x
1/2-y,1/2-z,x
-z,1/2-x,1/2+y
1/2-z,-x,1/2+y
1/2-z,1/2-x,y
-x,1/2-z,1/2+y
1/2-x,-z,1/2+y
1/2-x,1/2-z,y
-y,1/2-x,1/2+z
1/2-y,-x,1/2+z
1/2-y,1/2-x,z
-z,1/2-y,1/2+x
1/2-z,-y,1/2+x
1/2-z,1/2-y,x
1/4-x,3/4-y,3/4-z
3/4-x,1/4-y,3/4-z
3/4-x,3/4-y,1/4-z
1/4-y,3/4-z,3/4-x
3/4-y,1/4-z,3/4-x
3/4-y,3/4-z,1/4-x
1/4-z,3/4-x,3/4-y
3/4-z,1/4-x,3/4-y
3/4-z,3/4-x,1/4-y
1/4-x,3/4-z,3/4-y
3/4-x,1/4-z,3/4-y
3/4-x,3/4-z,1/4-y
1/4-y,3/4-x,3/4-z
3/4-y,1/4-x,3/4-z
3/4-y,3/4-x,1/4-z
1/4-z,3/4-y,3/4-x
3/4-z,1/4-y,3/4-x
3/4-z,3/4-y,1/4-x
1/4-x,3/4+y,3/4+z
3/4-x,1/4+y,3/4+z
3/4-x,3/4+y,1/4+z
1/4-y,3/4+z,3/4+x
3/4-y,1/4+z,3/4+x
3/4-y,3/4+z,1/4+x
1/4-z,3/4+x,3/4+y
3/4-z,1/4+x,3/4+y
3/4-z,3/4+x,1/4+y
1/4-x,3/4+z,3/4+y
3/4-x,1/4+z,3/4+y
3/4-x,3/4+z,1/4+y
1/4-y,3/4+x,3/4+z
3/4-y,1/4+x,3/4+z
3/4-y,3/4+x,1/4+z
1/4-z,3/4+y,3/4+x
3/4-z,1/4+y,3/4+x
3/4-z,3/4+y,1/4+x
1/4+x,3/4-y,3/4+z
3/4+x,1/4-y,3/4+z
3/4+x,3/4-y,1/4+z
1/4+y,3/4-z,3/4+x
3/4+y,1/4-z,3/4+x
3/4+y,3/4-z,1/4+x
1/4+z,3/4-x,3/4+y
3/4+z,1/4-x,3/4+y
3/4+z,3/4-x,1/4+y
1/4+x,3/4-z,3/4+y
3/4+x,1/4-z,3/4+y
3/4+x,3/4-z,1/4+y
1/4+y,3/4-x,3/4+z
3/4+y,1/4-x,3/4+z
3/4+y,3/4-x,1/4+z
1/4+z,3/4-y,3/4+x
3/4+z,1/4-y,3/4+x
3/4+z,3/4-y,1/4+x
1/4+x,3/4+y,3/4-z
3/4+x,1/4+y,3/4-z
3/4+x,3/4+y,1/4-z
1/4+y,3/4+z,3/4-x
3/4+y,1/4+z,3/4-x
3/4+y,3/4+z,1/4-x
1/4+z,3/4+x,3/4-y
3/4+z,1/4+x,3/4-y
3/4+z,3/4+x,1/4-y
1/4+x,3/4+z,3/4-y
3/4+x,1/4+z,3/4-y
3/4+x,3/4+z,1/4-y
1/4+y,3/4+x,3/4-z
3/4+y,1/4+x,3/4-z
3/4+y,3/4+x,1/4-z
1/4+z,3/4+y,3/4-x
3/4+z,1/4+y,3/4-x
3/4+z,3/4+y,1/4-x
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_attached_hydrogens
_atom_site_calc_flag
Li1 Li1+ 16 d 0.625 0.625 0.625 0.5 0 d
Co1 Co2+ 16 d 0.625 0.625 0.625 0.35 0 d
Co2 Co2+ 8 a 0. 0. 0. 0.3 0 d
V1 V5+ 8 a 0. 0. 0. 0.7 0 d
V2 V5+ 16 d 0.625 0.625 0.625 0.15 0 d
O1 O2- 32 e 0.375 0.375 0.375 1. 0 d
loop_
_atom_type_symbol
_atom_type_oxidation_number
Li1+ 1.000
Co2+ 2.000
V5+ 5.000
O2- -2.000

Code: Select all

Co     4.138000     4.138000     0.000000
Co     4.138000     0.000000     4.138000
Co     0.000000     4.138000     4.138000
Co     1.034500     1.034500     5.172500
Co     1.034500     5.172500     1.034500
Co     5.172500     1.034500     1.034500
 V     1.034500     1.034500     5.172500
 V     1.034500     5.172500     1.034500
 V     5.172500     1.034500     1.034500
 V     4.138000     4.138000     0.000000
 V     4.138000     0.000000     4.138000
 V     0.000000     4.138000     4.138000
 O     7.241500     7.241500     3.103500
 O     7.241500     3.103500     7.241500
 O     3.103500     7.241500     7.241500
Li     1.034500     1.034500     5.172500
Li     1.034500     5.172500     1.034500
Li     5.172500     1.034500     1.034500
Li     3.103500     7.241500     1.034500
Li     7.241500     3.103500     1.034500
Li     3.103500     1.034500     7.241500
Li     7.241500     1.034500     3.103500
Li     1.034500     3.103500     7.241500
Li     1.034500     7.241500     3.103500
 O     1.034500     1.034500     3.103500
 O     1.034500     5.172500     7.241500
 O     5.172500     1.034500     7.241500
 O     7.241500     1.034500     5.172500
 O     7.241500     5.172500     1.034500
 O     3.103500     1.034500     1.034500
 O     1.034500     7.241500     5.172500
 O     1.034500     3.103500     1.034500
 O     5.172500     7.241500     1.034500
 O     3.103500     3.103500     7.241500
 O     3.103500     7.241500     3.103500
 O     7.241500     3.103500     3.103500
 O     1.034500     1.034500     7.241500
 O     1.034500     5.172500     3.103500
 O     5.172500     1.034500     3.103500
 O     1.034500     3.103500     5.172500
 O     1.034500     7.241500     1.034500
 O     5.172500     3.103500     1.034500
 O     3.103500     1.034500     5.172500
 O     3.103500     5.172500     1.034500
 O     7.241500     1.034500     1.034500
 V     6.207000     6.207000     2.069000
 V     6.207000     2.069000     6.207000
 V     2.069000     6.207000     6.207000
 V     3.103500     7.241500     1.034500
 V     7.241500     3.103500     1.034500
 V     3.103500     1.034500     7.241500
 V     7.241500     1.034500     3.103500
 V     1.034500     3.103500     7.241500
 V     1.034500     7.241500     3.103500
Co     3.103500     7.241500     1.034500
Co     7.241500     3.103500     1.034500
Co     3.103500     1.034500     7.241500
Co     7.241500     1.034500     3.103500
Co     1.034500     3.103500     7.241500
Co     1.034500     7.241500     3.103500
Co     6.207000     6.207000     2.069000
Co     6.207000     2.069000     6.207000
Co     2.069000     6.207000     6.207000
Co     2.069000     2.069000     2.069000
Co     5.172500     7.241500     7.241500
Co     7.241500     5.172500     7.241500
Co     7.241500     7.241500     5.172500
Co     3.103500     5.172500     3.103500
Co     5.172500     3.103500     3.103500
Co     3.103500     3.103500     5.172500
 V     5.172500     7.241500     7.241500
 V     7.241500     5.172500     7.241500
 V     7.241500     7.241500     5.172500
 V     3.103500     5.172500     3.103500
 V     5.172500     3.103500     3.103500
 V     3.103500     3.103500     5.172500
 V     2.069000     2.069000     2.069000
 O     7.241500     5.172500     5.172500
 O     5.172500     7.241500     5.172500
 O     5.172500     5.172500     7.241500
 O     7.241500     7.241500     7.241500
 O     5.172500     3.103500     5.172500
 O     3.103500     5.172500     5.172500
 O     5.172500     5.172500     3.103500
Li     5.172500     7.241500     7.241500
Li     7.241500     5.172500     7.241500
Li     7.241500     7.241500     5.172500
Li     3.103500     5.172500     3.103500
Li     5.172500     3.103500     3.103500
Li     3.103500     3.103500     5.172500
Li     5.172500     5.172500     5.172500
 O     3.103500     3.103500     3.103500
 V     0.000000     0.000000     0.000000
 V     5.172500     5.172500     5.172500
Co     5.172500     5.172500     5.172500
Co     0.000000     0.000000     0.000000

Posted: **Sat Jun 16, 2018 4:00 pm**

So you're saying you have partial occupancy of sites (chemical disorder). Generally this is handled by creating a supercell, with the equivalent site occupied by different atom types in different cells. In abinit, and other DFT codes, a site can be occupied by one and only one atom at a time.

ABINIT Discussion Forums

Write a structure to the input file

Write a structure to the input file

Re: Write a structure to the input file