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Yeah, kilogram is considered for some weird reasons (supposedly, related to the French revolution and French linguistics, gram sounded similar to a noble title) the fundamental unit in the SI system, breaking the whole consistency. But still the prefixes are added to gram and not to kilogram. There is no micro-kilogram, there is miligram.

On the other hand, the unit megatonne is used – to measure the power of explosives (1 Mt explosive is the one which causes similar damage to 1 Mt of TNT). Generally, the SI prefixes find use also outside the SI system, currently the most popular of those cases (and also inconsistent) are the digital data units.

Traditionally, for digital data, those prefixes used to mean multiplying by 1024 and not by 1000 – because when converted to the binary system, 1024 was a nice, round number (10 000 000 000 in binary) while 1000 not. Although it wasn't always true as often for marketing reasons it made more sense to multiply by 1000 (as it gives larger numbers), so e.g. the capacities of drives were usually indicated in units multiplied by 1000 and not 1024. The manufacturers were arguing that according to the SI system, those prefixes mean multiplying by 1000, so they could also do so for bits and bytes, although it was kind of against the industry standard.

Later some institutions tried to standardize that and they decided that multiplying by 1000 should be represented by the SI prefixes, while multiplying by 1024 by new prefixes: kibi-, mebi-, gibi- etc, written as Ki, Mi etc. (e.g. KiB, MiB, GiB instead of kB, MB, GB – by the way, the kilobytes acronym was often misspelled, at least according to the SI system, as KB). And some software, especially from the open source range, respects that but it's still rather rare.
 

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Lord Kelvin
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Well...actually, a kilogram is a special case since it's the standard unit in itself, rather than the gram, even though it already has a prefix in its name. Which means that it's more correct to write 10^3 kg for a tonne, rather than 10^6 g for a tonne. In physics you almost always use the kilogram as a unit of mass, rather than the gram.
It depends on which physics. Astrophysicists commonly use gram, although it's counterintuitive: cgs system simplifies a lot of equations in electromagnetism and spherical trigonometry.
 
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