Calculation with super cells behave just like common unit cell under the periodic continuation approximation. They have a super-cell flag in their .txt description that tells jems not to duplicate atoms with either x, y or z coordinates equals to 0.

Super-cells can contain have several thousands atoms.

A super-cell model (9304 atoms), Pt octahedra crystal surrounded with oxygen atoms and supported by amorphous carbon film is shown in (Fig. 1).

HRTEM or HRSTEM dynamical calculations are only possible with thin slices. It is this necessary to cut the crystal inito slices (Fig. 2). The slice description is show below.

Dynamical calculations can still be performed using the multilice method. The projected potential of each slice as well as WPOA, HAADF and dynamical SAED are calculated considering super-cells as an ordinary unit-cell (periodic continuation).

The .txt file of the atoms in slice 0016 are provided below. It contains 153 atoms. Note that the slice is triclinic P1 and its superCell flag set to true. The lattice parameters (a, b, c) are (6, 6, 0.1997295) [nm]. Using the multislice calculation sampling 0.01 nm images dimension will be (1024, 1024). With 0.02 a (512, 512) calculation of the whole super-cell can be performed in less tan 2 minutes on Apple M1 MacBook Pro.

After each slice the wave-function can be saved and resused by the HRTEM imager (Fig. 6)

  file|/Users/pierrestadelmann/jemsNetBeansV5/jemsData/SuperCell/PtOctahedron/PtOct_0016.txt
  name|PtOct_0016
  creator|pierrestadelmann
  date|Thu Feb 01 13:46:42 CET 2024
  system|triclinic
  superCell|true
  HMSymbol|1|1|0|0|0| P  1      
  rps|0|x    ,   y    ,   z
  lattice|0|6.0
  lattice|1|6.0
  lattice|2|0.1997295
  lattice|3|90.0
  lattice|4|90.0
  lattice|5|90.0
  atom|0|O ,_,0.261900,0.671200,0.947996,0.0050,1.0000,0.1000,Def,0
  atom|1|O ,_,0.470400,0.126000,0.923996,0.0050,1.0000,0.1000,Def,0
  atom|2|Pt,_,0.719900,0.644700,0.919996,0.0050,1.0000,0.1000,Def,0
  atom|3|O ,_,0.343100,0.349900,0.911996,0.0050,1.0000,0.1000,Def,0
  atom|4|O ,_,0.617100,0.240000,0.887996,0.0050,1.0000,0.1000,Def,0
  atom|5|O ,_,0.613800,0.789700,0.875996,0.0050,1.0000,0.1000,Def,0
  atom|6|Pt,_,0.606900,0.752600,0.855996,0.0050,1.0000,0.1000,Def,0
  atom|7|O ,_,0.453800,0.823400,0.831997,0.0050,1.0000,0.1000,Def,0
  atom|8|Pt,_,0.310600,0.762800,0.799997,0.0050,1.0000,0.1000,Def,0
  atom|9|Pt,_,0.811800,0.497300,0.795997,0.0050,1.0000,0.1000,Def,0
  atom|10|Pt,_,0.530300,0.824000,0.767997,0.0050,1.0000,0.1000,Def,0
  atom|11|O ,_,0.321700,0.675300,0.759997,0.0050,1.0000,0.1000,Def,0
  atom|12|O ,_,0.550200,0.826200,0.739998,0.0050,1.0000,0.1000,Def,0
  atom|13|O ,_,0.666100,0.306500,0.727998,0.0050,1.0000,0.1000,Def,0
  atom|14|Pt,_,0.285300,0.324800,0.723998,0.0050,1.0000,0.1000,Def,0
  atom|15|O ,_,0.641000,0.224500,0.691998,0.0050,1.0000,0.1000,Def,0
  atom|16|O ,_,0.785000,0.519300,0.683998,0.0050,1.0000,0.1000,Def,0
  atom|17|O ,_,0.154400,0.420500,0.679998,0.0050,1.0000,0.1000,Def,0
  atom|18|O ,_,0.690400,0.201800,0.671998,0.0050,1.0000,0.1000,Def,0
  atom|19|Pt,_,0.530700,0.827200,0.667998,0.0050,1.0000,0.1000,Def,0
  atom|20|O ,_,0.491800,0.212100,0.663998,0.0050,1.0000,0.1000,Def,0
  atom|21|Pt,_,0.284700,0.667200,0.659998,0.0050,1.0000,0.1000,Def,0
  atom|22|Pt,_,0.402600,0.680600,0.651999,0.0050,1.0000,0.1000,Def,0
  atom|23|Pt,_,0.348900,0.721700,0.635999,0.0050,1.0000,0.1000,Def,0
  atom|24|Pt,_,0.323000,0.341400,0.627999,0.0050,1.0000,0.1000,Def,0
  atom|25|O ,_,0.725700,0.417800,0.607999,0.0050,1.0000,0.1000,Def,0
  atom|26|O ,_,0.632700,0.218900,0.571999,0.0050,1.0000,0.1000,Def,0
  atom|27|O ,_,0.752800,0.363000,0.555999,0.0050,1.0000,0.1000,Def,0
  atom|28|O ,_,0.654200,0.763100,0.548000,0.0050,1.0000,0.1000,Def,0
  atom|29|Pt,_,0.270200,0.566500,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|30|Pt,_,0.368200,0.664500,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|31|Pt,_,0.466200,0.762500,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|32|Pt,_,0.498800,0.795100,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|33|Pt,_,0.433500,0.729800,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|34|Pt,_,0.400800,0.697100,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|35|Pt,_,0.204900,0.501200,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|36|Pt,_,0.335500,0.631800,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|37|Pt,_,0.237500,0.533800,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|38|Pt,_,0.302900,0.599200,0.544000,0.0050,1.0000,0.1000,Def,0
  atom|39|Pt,_,0.184900,0.582700,0.528000,0.0050,1.0000,0.1000,Def,0
  atom|40|Pt,_,0.734100,0.527700,0.524000,0.0050,1.0000,0.1000,Def,0
  atom|41|Pt,_,0.302900,0.533900,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|42|Pt,_,0.335500,0.566500,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|43|Pt,_,0.270200,0.501200,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|44|Pt,_,0.368200,0.599200,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|45|Pt,_,0.466100,0.697100,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|46|Pt,_,0.433500,0.664500,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|47|Pt,_,0.498800,0.729800,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|48|Pt,_,0.237500,0.468500,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|49|Pt,_,0.531500,0.762500,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|50|Pt,_,0.400800,0.631800,0.520000,0.0050,1.0000,0.1000,Def,0
  atom|51|Pt,_,0.400800,0.566500,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|52|Pt,_,0.531500,0.697100,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|53|Pt,_,0.433500,0.599200,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|54|Pt,_,0.564100,0.729800,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|55|Pt,_,0.335500,0.501200,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|56|Pt,_,0.270200,0.435900,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|57|Pt,_,0.368200,0.533900,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|58|Pt,_,0.302900,0.468500,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|59|Pt,_,0.498800,0.664500,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|60|Pt,_,0.466100,0.631800,0.496000,0.0050,1.0000,0.1000,Def,0
  atom|61|Pt,_,0.469900,0.137600,0.492000,0.0050,1.0000,0.1000,Def,0
  atom|62|Pt,_,0.302800,0.403200,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|63|Pt,_,0.498800,0.599200,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|64|Pt,_,0.335500,0.435900,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|65|Pt,_,0.564100,0.664500,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|66|Pt,_,0.531500,0.631800,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|67|Pt,_,0.466100,0.566500,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|68|Pt,_,0.368200,0.468500,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|69|Pt,_,0.400800,0.501200,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|70|Pt,_,0.433500,0.533900,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|71|Pt,_,0.596800,0.697200,0.472000,0.0050,1.0000,0.1000,Def,0
  atom|72|O ,_,0.913900,0.583000,0.456000,0.0050,1.0000,0.1000,Def,0
  atom|73|Pt,_,0.400800,0.435900,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|74|Pt,_,0.564100,0.599200,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|75|Pt,_,0.531500,0.566500,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|76|Pt,_,0.335500,0.370600,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|77|Pt,_,0.433500,0.468500,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|78|Pt,_,0.498800,0.533900,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|79|Pt,_,0.629400,0.664500,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|80|Pt,_,0.368200,0.403200,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|81|Pt,_,0.466100,0.501200,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|82|Pt,_,0.596800,0.631800,0.448001,0.0050,1.0000,0.1000,Def,0
  atom|83|O ,_,0.242600,0.357500,0.436001,0.0050,1.0000,0.1000,Def,0
  atom|84|Pt,_,0.629400,0.599200,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|85|Pt,_,0.400800,0.370600,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|86|Pt,_,0.596800,0.566500,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|87|Pt,_,0.433500,0.403200,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|88|Pt,_,0.498800,0.468600,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|89|Pt,_,0.564100,0.533900,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|90|Pt,_,0.368200,0.337900,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|91|Pt,_,0.662100,0.631800,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|92|Pt,_,0.531400,0.501200,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|93|Pt,_,0.466100,0.435900,0.420001,0.0050,1.0000,0.1000,Def,0
  atom|94|Pt,_,0.790900,0.487700,0.416001,0.0050,1.0000,0.1000,Def,0
  atom|95|Pt,_,0.531400,0.435900,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|96|Pt,_,0.466100,0.370600,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|97|Pt,_,0.498800,0.403200,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|98|Pt,_,0.662100,0.566500,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|99|Pt,_,0.400800,0.305300,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|100|Pt,_,0.564100,0.468600,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|101|Pt,_,0.694700,0.599200,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|102|Pt,_,0.629400,0.533900,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|103|Pt,_,0.433500,0.337900,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|104|Pt,_,0.596800,0.501200,0.396001,0.0050,1.0000,0.1000,Def,0
  atom|105|Pt,_,0.629400,0.468600,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|106|Pt,_,0.498800,0.337900,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|107|Pt,_,0.662100,0.501200,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|108|Pt,_,0.596800,0.435900,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|109|Pt,_,0.694700,0.533900,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|110|Pt,_,0.466100,0.305300,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|111|Pt,_,0.727400,0.566500,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|112|Pt,_,0.433500,0.272600,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|113|Pt,_,0.564100,0.403200,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|114|Pt,_,0.926500,0.564500,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|115|Pt,_,0.531400,0.370600,0.372001,0.0050,1.0000,0.1000,Def,0
  atom|116|Pt,_,0.760000,0.533900,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|117|Pt,_,0.629400,0.403300,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|118|Pt,_,0.727400,0.501200,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|119|Pt,_,0.694700,0.468600,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|120|Pt,_,0.596700,0.370600,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|121|Pt,_,0.466100,0.240000,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|122|Pt,_,0.662100,0.435900,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|123|Pt,_,0.498800,0.272600,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|124|Pt,_,0.531400,0.305300,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|125|Pt,_,0.564100,0.337900,0.348002,0.0050,1.0000,0.1000,Def,0
  atom|126|Pt,_,0.596700,0.305300,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|127|Pt,_,0.727400,0.435900,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|128|Pt,_,0.498800,0.207300,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|129|Pt,_,0.760000,0.468600,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|130|Pt,_,0.792700,0.501200,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|131|Pt,_,0.564100,0.272600,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|132|Pt,_,0.694700,0.403300,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|133|Pt,_,0.531400,0.240000,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|134|Pt,_,0.629400,0.337900,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|135|Pt,_,0.662100,0.370600,0.324002,0.0050,1.0000,0.1000,Def,0
  atom|136|O ,_,0.803500,0.392600,0.320002,0.0050,1.0000,0.1000,Def,0
  atom|137|O ,_,0.466800,0.711100,0.288002,0.0050,1.0000,0.1000,Def,0
  atom|138|O ,_,0.227000,0.585500,0.260002,0.0050,1.0000,0.1000,Def,0
  atom|139|O ,_,0.320200,0.291100,0.256002,0.0050,1.0000,0.1000,Def,0
  atom|140|O ,_,0.399800,0.236300,0.256002,0.0050,1.0000,0.1000,Def,0
  atom|141|O ,_,0.167200,0.525400,0.232003,0.0050,1.0000,0.1000,Def,0
  atom|142|O ,_,0.620000,0.756400,0.220003,0.0050,1.0000,0.1000,Def,0
  atom|143|Pt,_,0.231700,0.593300,0.216003,0.0050,1.0000,0.1000,Def,0
  atom|144|O ,_,0.482300,0.823000,0.212003,0.0050,1.0000,0.1000,Def,0
  atom|145|O ,_,0.606900,0.768900,0.192003,0.0050,1.0000,0.1000,Def,0
  atom|146|O ,_,0.662400,0.202000,0.180003,0.0050,1.0000,0.1000,Def,0
  atom|147|O ,_,0.781900,0.410700,0.116004,0.0050,1.0000,0.1000,Def,0
  atom|148|Pt,_,0.559700,0.747500,0.096004,0.0050,1.0000,0.1000,Def,0
  atom|149|O ,_,0.676200,0.688800,0.096004,0.0050,1.0000,0.1000,Def,0
  atom|150|O ,_,0.728000,0.682000,0.076004,0.0050,1.0000,0.1000,Def,0
  atom|151|O ,_,0.698800,0.680800,0.040005,0.0050,1.0000,0.1000,Def,0
  atom|152|O ,_,0.383800,0.648700,0.016005,0.0050,1.0000,0.1000,Def,0
  

PtOct_0016 Atoms of Slice 0016.