Some simulations use “supercells” – larger periodic boundary systems than the primitive unit cell. Here is a walk-through on reducing a large supercell to the primitive unit cell.
Open or import the file with the supercell – here, CaCO3. Note that the space group is unknown, since the file came from VASP, which does not specify a space group with the coordinates.
After perceiving the space group, we see correctly that the system is R -3 c. Now we can reduce the supercell to a primitive cell of CaCO3.
Avogadro provides two algorithms for reducing the unit cell to a primitive or Niggli cell. Here, pick “Primitive.” Note that the volume of this supercell was over 4,000 Å3.
You will need to set a tolerance for the Cartesian coordinates (here, in Å).
After reduction, note that the space group is retained, the lattice is properly Rhombohedral, and the unit cell volume is 36 times smaller.