  Context: With the recent surge of planetary surveys focusing on detecting
Earth-mass planets around M dwarfs, it is becoming more important to understand
chromospheric activity in M dwarfs. Stellar chromospheric calcium emission is
typically measured using the $R'_\mathrm{HK}$ calibrations of Noyes et al.
(1984), which are only valid for $0.44 \le B-V \le 0.82$. Measurements of
calcium emission for cooler dwarfs $B-V \ge 0.82$ are difficult because of
their intrinsic dimness in the blue end of the visible spectrum. Aims: We
measure the absolute Ca II HK and H$\alpha$ flux of a sample of 110 HARPS M
dwarfs and also extend the calibration of $R'_\mathrm{HK}$ to the M dwarf
regime using PHOENIX stellar atmosphere models. Methods: We normalized a
template spectrum with a high signal-to-noise ratio that was obtained by
coadding multiple spectra of the same star to a PHOENIX stellar atmosphere
model to measure the chromospheric Ca II HK and H$\alpha$ flux in physical
units. We used three different $T_\mathrm{eff}$ calibrations and investigated
their effect on Ca II HK and H$\alpha$ activity measurements. We performed
conversions of the Mount Wilson S index to $R'_\mathrm{HK}$ as a function of
effective temperature for the range 2300 K $\le T_\mathrm{eff} \le$ 7200 K.
Last, we calculated continuum luminosity $\chi$ values for Ca II HK and
H$\alpha$ in the same manner as West & Hawley (2008) for $-1.0 \le
\mathrm{Fe/H} \le +1.0$ in steps of $\Delta \mathrm{Fe/H} = 0.5$. Results: We
compare different $T_\mathrm{eff}$ calibrations and find $\Delta T_\mathrm{eff}
\sim$ several 100 K for mid- to late-M dwarfs. Using these different
$T_\mathrm{eff}$ calibrations, we establish a catalog of $\log R'_\mathrm{HK}$
and $\mathcal{F}'_\mathrm{H\alpha}/\mathcal{F}_\mathrm{bol}$ measurements for
110 HARPS M dwarfs. [abridged]
