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Q: Which unit is attached to 'number of particles per volume' (e.g. of the atmosphere)? The questions focuses on the 'number of' and not on the 'volume'.

The units [#/m3], [particles/m3] and [1/m3] are used in publications. Neither [#/m3] nor [particles/m3] are SI compliant. However, [1/m3] would be SI compliant but it looks ... incomplete.

edit 1: The particles are of different size and composition. Converting the number of particles into another unit is not reasonable for my application.

daniel.heydebreck
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In my experience $[m^{-3}]$ or $[cm^{-3}]$ as number density is very well understood throughout the communities of both earth, solar-system as well as exoplanetary scientists.

Take for example the recently published The atmosphere of Pluto as observed by New Horizons which in fig. 3 shows the derived atmospheric composition of Pluto from occultation measurments in $[cm^{-3}]$ with some model curves:

enter image description here (Property of G. R. Gladstone et. al 2016 and the New Horizons Science team)

The density in this unit is just a very natural and convenient outcome of the used occultation-inversion techniques. Thus of course the units are sometimes simply the result of the context in which a work is done, and as other commentators stated, a mole could be used. However I'd argue that $[cm^{-3}]$ is sufficiently simple to be understood in any context and adding moles just makes things unnecessary confusing as it suggests numbers to have a unit, which they don't.
It just physically makes no sense.