  We develop a large scale quantum master equation approach to describe
dynamical processes of practical open quantum systems driven by both coherent
and stochastic interactions by including more than one thousand true states of
the systems, motivated by the development of highly bright and fully coherent
lasers in the X-ray wavelength regime. The method combines the processes of
coherent dynamics induced by the X-ray laser and incoherent relaxations due to
spontaneous emissions, Auger decays, and electronic collisions. As examples,
theoretical investigation of {\it real} coherent dynamics of inner-shell
electrons of a neon gas, irradiated by a high-intensity X-ray laser with a full
temporal coherence, is carried out with the approach. In contrast to the rate
equation treatment, we find that coherence can suppress the multiphoton
absorptions of a neon gas in the ultra-intense X-ray pulse, due to
coherence-induced Rabi oscillations and power broadening effects. We study the
influence of coherence on ionization processes of neon, and directly prove that
sequential single-photon processes for both outer- and inner-shell electrons
dominate the ionizations for the recently typical experiments with a laser
intensity of $\approx10^{18}$ ${\rm W/cm^2}$. We discuss possible experimental
implementations such as signatures for coherent evolution of inner-shell
electrons via resonance fluorescence processes. The approach can also be
applied to many different practical open quantum systems in atomic, quantum
optical, and cold matter systems, which are treated qualitatively by a
few-level master equation model before.
