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Import CIF

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).

Figure1

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.

Figure2a Figure2b

Figure 2a Drawing popup menu.

Figure 2b Projection [1,0,0].

Figure3a Figure3b

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:

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