JSV  ...how to create octahedra

 

JSV supports only tetrahedra and octahedra. I hope to improve that in future releases.

Note: if you specified an octahedron in the input file for one cell (1x1x1) this might not give octahedra for other numbers of unit cells (eg:2x2x2). That's because the individual atom numbers might not be the same. This depends on the space group routines, which generate the atom positions. So you should first choose the numbers of unit cells, then specify your octahedron and then activate the changes by selecting from the menu [Cells] the number of unit cells you have chosen (eg. [2x2x2]). Then you can write a SDF file so that you changes are permanently saved. Using [File] [reload cell] is equivalent to [Cells] [1x1x1]

Step 1)  
Display the cells (here 2x2x2) with NO polyhedra specified in the input file and switch to [mode] [numbers] .  You may also create bonds first (menu [Bonds][make single bonds]), to make the relations more clear.   

Step 2)  
Select the numbers of atoms forming ONE octahedron as its vertices (eg.: 3 4 7 32 16 7 2 )  
 
Step 3)  
Edit the input file by adding a value for [npoly] and in the line after [poly] add the number of vertices and the atoms you selected (eg.: 6 3 4 32 16 7 2) Below an example file is given for 2x2x2 cells and the changed lines in the input file are highlightened. 
  
asymmetric_unit_cell
[cell] 3.848 3.848 3.848 90 90 90
[natom] 3 
[nbond] 0 
[npoly] 1 
[space_group] 221 1
[title] Ca-Ti-O3 (perovskite)
[atoms] 
Ca 20 0.0 0.0 0.0
Ti 22 0.5 0.5 0.5
O 8 0.5 0.5 0.0
[bonds]
[poly]
 6 4 3 16 32 7 2      2x2x2 cells
Step 4)  
Select menu [Cells] [2x2x2] to make JSV calculate the polyhedra for 2x2x2 cells.