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Export

Export allows for exporting jems .txt crystal strutures in 3 format:

Figure2

Figure 1 Export structure as a .cif file.


Andalusite show a typical .cif file exported by jems (see Import CIF for more details). jems uses only a small subset of the tags of the Crystallographic Information Framework.


  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

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Export .xyz

Figure2

Figure 2 Export structure as a .xyz file.

Only Primitive crystals (space-group P1) and described in a orthorhombic cell can be saved.

  ;Andalusite_P1.xyz::Andalusite_P1::xyz crystal file created by jems
0  0.767900  0.774960  0.567980 90.000000 90.000000 90.000000
Al  0.000000  0.000000  0.247700  1.000000  0.000000  0.034000
Al  0.000000  0.000000  0.752300  1.000000  0.000000  0.034000
Al  0.500000  0.500000  0.252300  1.000000  0.000000  0.034000
Al  0.500000  0.500000  0.747700  1.000000  0.000000  0.034000
Al  0.361000  0.138900  0.500000  1.000000  0.000000  0.034000
Al  0.639000  0.861100  0.500000  1.000000  0.000000  0.034000
Al  0.139000  0.638900  0.000000  1.000000  0.000000  0.034000
Al  0.861000  0.361100  0.000000  1.000000  0.000000  0.034000
Si  0.230500  0.253800  0.000000  1.000000  0.000000  0.035000
Si  0.769500  0.746200  0.000000  1.000000  0.000000  0.035000
Si  0.269500  0.753800  0.500000  1.000000  0.000000  0.035000
Si  0.730500  0.246200  0.500000  1.000000  0.000000  0.035000
O   0.457400  0.350800  0.500000  1.000000  0.000000  0.029000
O   0.542600  0.649200  0.500000  1.000000  0.000000  0.029000
O   0.042600  0.850800  0.000000  1.000000  0.000000  0.029000
O   0.957400  0.149200  0.000000  1.000000  0.000000  0.029000
O   0.413200  0.370600  0.000000  1.000000  0.000000  0.029000
O   0.586800  0.629400  0.000000  1.000000  0.000000  0.029000
O   0.086800  0.870600  0.500000  1.000000  0.000000  0.029000
O   0.913200  0.129400  0.500000  1.000000  0.000000  0.029000
O   0.093700  0.410900  0.000000  1.000000  0.000000  0.029000
O   0.906300  0.589100  0.000000  1.000000  0.000000  0.029000
O   0.406300  0.910900  0.500000  1.000000  0.000000  0.029000
O   0.593700  0.089100  0.500000  1.000000  0.000000  0.029000
O   0.224300  0.136000  0.241300  1.000000  0.000000  0.029000
O   0.775700  0.864000  0.758700  1.000000  0.000000  0.029000
O   0.775700  0.864000  0.241300  1.000000  0.000000  0.029000
O   0.224300  0.136000  0.758700  1.000000  0.000000  0.029000
O   0.275700  0.636000  0.258700  1.000000  0.000000  0.029000
O   0.724300  0.364000  0.741300  1.000000  0.000000  0.029000
O   0.724300  0.364000  0.258700  1.000000  0.000000  0.029000
O   0.275700  0.636000  0.741300  1.000000  0.000000  0.029000

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Export .inp

Figure3

Figure 3 Export structure as a .inp file.

Create a batch file to be piped to old EMS crystal builder (bu1). This feature is no more supported. The old EMS system written F77, C and C++ is still available (mainly for windows OS).

The lines below are the bu1 input to create the Si data structure used by the EMS.


  Si/b
  Si/Crystal file created by jems
  1
  0.54309,0.54309,0.54309,90.0,90.0,90.0
  n
  F
  z,  x,  y
  y,  z,  x
  x,  z,  y
  y,  x,  z
  z,  y,  x
  x, -y, -z
  z, -x, -y
  y, -z, -x
  x, -z, -y
  y, -x, -z
  z, -y, -x
  -x,  y, -z
  -z,  x, -y
  -y,  z, -x
  -x,  z, -y
  -y,  x, -z
  -z,  y, -x
  -x, -y,  z
  -z, -x,  y
  -y, -z,  x
  -x, -z,  y
  -y, -x,  z
  -z, -y,  x
  1/4 - x, 1/4 - y, 1/4 - z
  1/4 - z, 1/4 - x, 1/4 - y
  1/4 - y, 1/4 - z, 1/4 - x
  1/4 - x, 1/4 + y, 1/4 + z
  1/4 - z, 1/4 + x, 1/4 + y
  1/4 - y, 1/4 + z, 1/4 + x
  1/4 + x, 1/4 - y, 1/4 + z
  1/4 + z, 1/4 - x, 1/4 + y
  1/4 + y, 1/4 - z, 1/4 + x
  1/4 + x, 1/4 + y, 1/4 - z
  1/4 + z, 1/4 + x, 1/4 - y
  1/4 + y, 1/4 + z, 1/4 - x
  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 + 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 - 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 + z, 1/4 - y
  1/4 + y, 1/4 + x, 1/4 - z
  1/4 + z, 1/4 + y, 1/4 - x
  *
  Si,0.000000,0.000000,0.000000,0.0053,1.0000,0.0290
  *
  300.0
  6,6,6
  *