[ase-users] reading cif files
Ingo Opahle
ingo.opahle at rub.de
Thu Sep 15 16:48:35 CEST 2011
Hallo,
I have problems reading the attached cif file (ase revision 2303).
The error message I get is
Traceback (most recent call last):
File "cifview.py", line 2, in <module>
casi=read('1001067.cif')
File "/home/users/opahlivs/ase/ase/io/__init__.py", line 173, in read
return read_cif(filename, index)
File "/home/users/opahlivs/ase/ase/io/cif.py", line 267, in read_cif
return tags2atoms(tags, **kwargs)
File "/home/users/opahlivs/ase/ase/io/cif.py", line 228, in tags2atoms
sitesym=sitesym)
File "/home/users/opahlivs/ase/ase/lattice/spacegroup/spacegroup.py", line 679, in spacegroup_from_data
spg._rotations, spg._translations = parse_sitesym(sitesym)
File "/home/users/opahlivs/ase/ase/lattice/spacegroup/spacegroup.py", line 650, in parse_sitesym
'invalid site symmetry: %s' % sym)
ase.lattice.spacegroup.spacegroup.SpacegroupValueError: invalid site symmetry: -x, y, 0.5-z
The problem seems to be that ase expects 1/2 instead of 0.5 (which is frequently used in the cif files),
I think this could be fixed by modifying line 639 in spacegroup.py from
while n < len(s) and (s[n].isdigit() or s[n] == '/'):
to
while n < len(s) and ((s[n].isdigit()) or (s[n] == '.') or (s[n] == '/')):
Best regards
Ingo
---------------------------------
Dr. Ingo Opahle
ICAMS
Ruhr-Universität Bochum
Stiepeler Straße 129
44801 Bochum
Tel. +49 234 32 29316
email: ingo.opahle at rub.de
---------------------------------
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##############################################################################
# #
# Ca-Si # Ca5Si3 # 1001067 #
# #
##############################################################################
# #
# Copyright (c) 2008 ASM International & Material Phases Data System. #
# All rights reserved. #
# This copy of Pearson's Crystal Data is licensed to: #
# ICAMS Ruhr Universitaet Bochum #
# #
##############################################################################
data_1001067
_audit_creation_date 2010-02-25
_audit_creation_method
;
Pearson's Crystal Data browser
;
#_database_code_PCD 1001067
# Entry summary
_chemical_formula_structural Ca5Si3
_chemical_formula_sum Ca5Si3
_chemical_name_mineral ?
_chemical_compound_source ?
_chemical_name_structure_type Cr5B3,tI32,140
_chemical_formula_weight 284.7
_chemical_melting_point ?
# Bibliographic data
_publ_section_title
;
Hydrogen Impurity Effects. A5Tt3 Intermetallic Compounds between A= Ca, Sr, Ba, Eu and Tt= Si, Ge, Sn with Cr5B3-like Structures that are Stable Both as Binary and as Ternary Hydride and Fluoride Phases
;
_journal_coden_ASTM JSSCBI
_journal_year 2001
_journal_volume 159
_journal_page_first 149
_journal_page_last 162
_journal_language English
loop_
_publ_author_name
_publ_author_address
'Leon Escamilla E.A.'
;
Iowa State University
Department of Chemistry
Ames
U.S.A. Iowa
;
'Corbett J.D.'
;
Iowa State University
Department of Chemistry
Ames
U.S.A. Iowa
;
# Standardized crystallographic data
_cell_length_a 7.6495
_cell_length_b 7.6495
_cell_length_c 14.835
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 868.1
_cell_formula_units_Z 4
_symmetry_Int_Tables_number 140
_symmetry_space_group_name_H-M I4/mcm
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
2 '-x, -y, -z'
3 '-x, -y, z'
4 '-x, y, 0.5-z'
5 '-x, y, 0.5+z'
6 '-y, -x, 0.5-z'
7 '-y, -x, 0.5+z'
8 '-y, x, -z'
9 '-y, x, z'
10 'x, -y, 0.5-z'
11 'x, -y, 0.5+z'
12 'x, y, -z'
13 'y, -x, -z'
14 'y, -x, z'
15 'y, x, 0.5-z'
16 'y, x, 0.5+z'
17 '0.5+x, 0.5+y, 0.5+z'
18 '0.5-x, 0.5-y, 0.5-z'
19 '0.5-x, 0.5-y, 0.5+z'
20 '0.5-x, 0.5+y, 1-z'
21 '0.5-x, 0.5+y, 1+z'
22 '0.5-y, 0.5-x, 1-z'
23 '0.5-y, 0.5-x, 1+z'
24 '0.5-y, 0.5+x, 0.5-z'
25 '0.5-y, 0.5+x, 0.5+z'
26 '0.5+x, 0.5-y, 1-z'
27 '0.5+x, 0.5-y, 1+z'
28 '0.5+x, 0.5+y, 0.5-z'
29 '0.5+y, 0.5-x, 0.5-z'
30 '0.5+y, 0.5-x, 0.5+z'
31 '0.5+y, 0.5+x, 1-z'
32 '0.5+y, 0.5+x, 1+z'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_Wyckoff_symbol
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Ca2 Ca l 16 0.17978 0.67978 0.13986 1
Si2 Si h 8 0.61307 0.11307 0 1
Ca1 Ca c 4 0 0 0 1
Si1 Si a 4 0 0 0.25 1
_exptl_crystal_colour ?
_exptl_crystal_density_meas ?
_cell_measurement_temperature ?
_cell_measurement_radiation 'X-rays, Cu Ka1'
_cell_measurement_wavelength 1.54056
_cell_measurement_reflns_used ?
_diffrn_ambient_temperature ?
_diffrn_measurement_device 'automatic diffractometer'
_diffrn_measurement_device_type 'Enraf-Nonius CAD4'
_diffrn_radiation_type X-rays
_diffrn_reflns_number 2182
_exptl_absorpt_coefficient_mu 3.33
_exptl_absorpt_correction_type empirical
_computing_structure_solution 'starting values from the literature'
_refine_ls_number_parameters 16
_refine_ls_number_reflns 275
_refine_ls_R_factor_all 0.015
_refine_ls_wR_factor_all 0.019
_computing_structure_refinement 'DIFABS; TEXSAN package'
# End of data set 1001067
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