The mass is the combined masses of the protons and neutrons in the nucleus. Electrons are usually ignored because their mass is actually 1840 times smaller than a proton!
Density can be used as a measure of how dense the bulk material is (a number of atoms). Or as a descriptor of how densely located an atoms electrons are to its nucleus.
Their density is not so well defined. Density is mass divided by volume, and the volume of an atom is a bit nebulous, because the electrons in the surrounding electron cloud (which is part of the atom) are quantum mechanical particles and don’t have a well-defined position. So it would be difficult to specify the density of a single atom. (The *average* density of an atom in a pure solid or liquid must be equal to the density of the solid or liquid; it is a standard feature of quantum mechanics that averages are better defined than individual measurements.)
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