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The Import CIF window allows to select a crystal structure among multiple .cif files. The
window shows by default the [0,0,1] projection of the selected structure (Fig. 1).
The atoms can be labelled and projections [1,0,0] or [0,1,0] selected (Figures 2a,
2b).
A maximum of 50 different .cif files can be loaded at once (BiFeO3).

Figure 1 Import CIF with 50 .cif structures.
The toolbar contains tool buttons allowing for:
The popup menu attached to the drawing allows for displaying HAADF, WPOA, SAED images and to change
the projection direction.
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Figure 2a Drawing popup menu. |
Figure 2b Projection [1,0,0]. |
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Figure 3a HAADF [001]. |
Figure 3b WPOAD [001, temperature color LUT. |
A typical .cif file saved by jems as the following structure (andalusite.cif) where:
- data_ should be on the first line.
- # first character of the line indicates a comment (except for #End of data).
- _space_group_crystal_system describes the crystal system.
- _space_group_IT_number the space-group number (International Tables).
- _symmetry_space_group_name_H-M the Hermann-Mauguin symbol.
- loop_ starts the loop on the RPS code.
- _cell_length_ a, b, c and alpha, beta, gamma provides the unit cell parameters (Å and °.)
- loop_ starts the loop on the _atom_type_symbol and _atom_type_oxidation_number.
- loop_ starts the loop on the the atoms of the unit cell.
- #End of data marks the end of the cif description of the crystal.
Note that each atom is followed by a sequence number starting at 0 for the first atom of the loop_.
Many crystal data can be put on the same .cif file. Any crystal data just have to start with data_name1 and
end with #End of data_name.
Since jems uses mainly .txt crystal file format for the simulations, it is necessary to save the loaded .cif
crystal structure in .txt format. It is recommended to check the RPS code and/or space-group before saving the
structure in jems .txt format.
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data_Andalusite
# jems Export CIF Andalusite
_database_code_ICSD ''
_chemical_formula_analytical 'no chemical formula analytical'
_chemical_formula_structural 'no chemical formula structural'
_audit_creation_date 'Tue-Feb-06-21:21:44-CET-2024'
_space_group_crystal_system 'orthorhombic'
_space_group_IT_number 58
_symmetry_space_group_name_H-M 'P n n m'
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
0 'x , y , z'
1 '-x , -y , z'
2 '1/2 - x ,1/2 + y ,1/2 - z'
3 '1/2 + x ,1/2 - y ,1/2 - z'
4 '-x , -y , -z'
5 'x , y , -z'
6 '1/2 + x ,1/2 - y ,1/2 + z'
7 '1/2 - x ,1/2 + y ,1/2 + z'
_cell_length_a 7.679000
_cell_length_b 7.749600
_cell_length_c 5.679800
_cell_angle_alpha 90.000000
_cell_angle_beta 90.000000
_cell_angle_gamma 90.000000
loop_
_atom_type_symbol
_atom_type_oxidation_number
Al3+ 3.
Si4+ 4.
O2- -2.
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_absorption
Al0 Al3+ e 0.000000 0.000000 0.247700 0.000000 1.000000 0.034000
Al1 Al3+ g 0.361000 0.138900 0.500000 0.000000 1.000000 0.034000
Si2 Si4+ g 0.230500 0.253800 0.000000 0.000000 1.000000 0.035000
O3 O2- g 0.457400 0.350800 0.500000 0.000000 1.000000 0.029000
O4 O2- g 0.413200 0.370600 0.000000 0.000000 1.000000 0.029000
O5 O2- g 0.093700 0.410900 0.000000 0.000000 1.000000 0.029000
O6 O2- h 0.224300 0.136000 0.241300 0.000000 1.000000 0.029000
#End of data_Andalusite