When I read the manual of lammps, it mentioned compute stress/atom does NOT include contributions due to fixes. Is that meaning if I apply fix indent command, the stress doen’t include the effect of indent? If not, how should I do if I’d like to see the stress field due to the indent?
The fixes the manual is talking about are shake and fix rigid
which impose internal constraints that do make a virial
contribution (just not for per-atom stress yet).
An indenter is an external force, so it's forces aren't added
to the global pressure or per-atom stress. However, the
indenter deforms the atoms, so that atom-atom interactions
are changed. Those do change the global pressure and
per-atom stress, which is probably what you want.