`main_density_calc` works on a single bead, passing all bead information to it leads to high memory usage

[omgol411]

main_density_calc in main.py takes coords, radius, and mass.
These are for all beads while the function works on a single bead.
Similarly, a single BeadDensity class instance should be common to all beads and outside main_density_calc.

[omgol411]

fixed in #47