-substitute <sp1> <sp2>
This option substitutes all atoms of species <sp1> by atoms of species <sp2>.
The <sp1> and <sp2> can be entered as atomic number or species names.
If a selection was defined (with the option -select) then only selected atoms are substituted.
By default no atom is substituted.
atomsk sto.cfg -substitute 38 56 bto.xsf
This will read the file sto.cfg, replace all strontium atoms (atomic number=38) by barium atoms (atomic number=56), and output the final system into bto.xsf.
atomsk initial.cfg -sub Fe W final.xyz
This will read initial.cfg, substitute iron (Fe) by tungsten (W) and write the result into final.xyz.
atomsk initial.lmc -sub 1 Si -sub 2 C final.xyz
This option can also be useful when reading file formats containing "atom types" (1, 2, 3...) instead of actual atomic numbers, like the LAMMPS custom format (lmc). The command above will replace all atoms of type 1 by silicon (Si), and those of type 2 by carbon (C).