When the average density for a planet is stated does it incorporate the mass of the atmosphere, when a planet has an atmosphere, or is the mass of the atmosphere ignored?
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Whether of not you include the mass of the atmosphere doesn't matter much. For instance, the mass of Earth's atmosphere is roughly $10^{-6}$ of Earth's mass, corresponding to the uncertainty in the gravitational constant $G$ used to calculate the mass in the first place.
But the volume that you use for calculating the average density could potentially matter, depending on your definition of the height of the atmosphere. For Earth, the lowest-orbiting satellites are at a height of $\sim100\,\mathrm{km}$, so if you include that, your volume will be 5% larger. This number can be much lower if you define the height of the atmosphere to be the scale height (0.3%), or much higher if you include the thermosphere (1600%).
Because the height of the atmosphere is quite arbitrary, this is rarely if ever included in the average density of a (rocky) planet.
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$\begingroup$ For gas giants the gaseous component obviously has to be included both for the mass and the volume. So I believe that for reasons of consistency, this will be done too, for the rocky planets. A common convention is to take as radius the radius of the 1 bar level of atmospheric pressure, which will yield comparative radii for most planets and moons with atmospheres, and those without. $\endgroup$ Commented Feb 5, 2020 at 23:48
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$\begingroup$ @AtmosphericPrisonEscape You're probably right. I know about the "1 bar" rule, but I don't know whether or not the part above this arbitrary height is included in the mass. But it would make sense if it were. $\endgroup$– pelaCommented Feb 7, 2020 at 15:03