This was explained very well by Noyes et al. 1984 (Rotation, Convection, and Magnetic Activity in Lower Main-Sequence Stars). Magnetic fields form at the base of the convective zone. There, differential rotation causes ionized material to exhibit helical behavior. These magnetic fields experience turbulence in their rise through the convective zone, which creates stress. These stresses are carried up into the chromosphere, heating the chromosphere and causing distinct emission lines in the cores of the Ca II absorption features. The stronger the emission, the stronger the magnetic fields that generated the stress-heating. Likewise, the shorter the rotation period, the more differential rotation, and the stronger the helical motion is that causes the magnetic fields.
It would be interesting to see how much of this heating is actually coming from the magnetic fields by examining another indicator of magnetic fields (maybe x-ray luminosity?). It is amazing however, that this complex process seems to produce such a tight relation between chromospheric Ca II flux and rotation period.
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