Hello everyone,
Does anyone know about a software that I could use to read a given microstate or configuration (the file can be in whatever format, let’s say), superimpose some arbitrary, fancy polyhedron shape (things like rhombic dodecahedron) and then export only the coordinates of the atoms/beads that lie in the inside of my polyhedron (without any additional criteria let’s say)?
You can build complex selection geometries with LAMMPS by combining multiple region primitives as unions or intersections. simple polyhedra, for example can be constructed from the intersection of multiple plane regions. Just requires a bit of vector algebra 
In LAMMPS you can then do group selections based on regions and delete atoms in a group.
Yes, I am aware… with Ovito I realized I could also do it as well as I was exploring the “Slice” “functionality” earlier… I guess when I wrote this message I was with my feet out of the floor, dreaming about something where I would simply need to press enter and the rhombic dodecahedron I have in my mind would appear before my eyes :""D
In any case it wouldnt be a good idea to be lazy and do this braindeadlessly since I want my dodecahedron to be such that the crystal structure ends with specific crystallographic planes in the facets.
Anyways… thanks for the help ^^