This is the sum total of the views I've gathered from the internet:
Atom is described spherical in shape just for the sake of simplicity. It's very
similar to (not the same as) a group of honey bees (electrons) swarming over a flower (nucleus). The truth is that you can only assign a probability density function for the positions of the electrons around the nucleus, which is in turn based on the solution of the Schrödinger equation for the Coulombic potential under consideration. These give rise to various so-called orbitals which delimit the region in which ##95\%## of an infinite set of measurements of the positions of the electrons is likely to provide.
The "shape" of the atom is determined by this outer boundary.
Now, having precisely defined the meaning of "the shape of an atom", we can rigorously state when an atom is indeed "spherical":
Most atoms, when they are free (and of course most elements are not found as free atoms in nature), are not spherical. The conditions for an atom to be spherical are any of the following:
- The atom has electrons only in the s orbitals.
- The atom has the sub-shell of its largest principal quantum number either half-filled or full-filled (Unsold's Theorem).
That does not, in any way, make it clear why atoms are considered to be spheres in the calculation of packing fractions. I guess it's only because the spherical shape is the simplest and most intuitive model of an atom.
