-remove-atom <index>
-rmatom <index>
-rmatom <species>
-rmatom select
This option removes the atom that has the given index, or all atoms of the given species.
Note that if this atom has a shell (in the sense of a core-shell model) and/or auxiliary properties, they are also deleted. In addition, some of the remaining atoms may have a different index after this option is applied.
If a selection was defined (with the option -select) then only selected atoms are removed.
The option -rmatom select removes all selected atoms, no matter their index or their species. It is meant to be used after the option -select, and will not do anything if no selection is defined.
By default no atom is removed.
atomsk initial.cfg -rmatom 1622 final.xsf
This will read the file initial.cfg, remove the atom #1622, and output the result to final.xsf.
atomsk initial.cfg -rmatom Fe final.xyz
This will remove all iron atoms in the system.
atomsk initial.cfg -select in sphere 0.5*box 0.5*box 0.5*box 30 -rmatom Si final.xyz
This will select atoms in a sphere, and delete all silicium atoms that are part of this selection.
atomsk initial.cfg -select in sphere 0.5*box 0.5*box 0.5*box 30 -rmatom select final.xyz
This will select atoms in a sphere, and delete all atoms that are selected.