The microscopic origin of glass transition, when liquid viscosity changes continuously by more than ten orders of magnitude, is challenging to explain from first principles. Here we describe the detailed derivation and implementation of a Markovian Network model to calculate the shear viscosity of deeply supercooled liquids based on numerical sampling of an atomistic energy landscape, which sheds some light on this transition. Shear stress relaxation is calculated from a master-equation description in which the system follows a transition-state pathway trajectory of hopping among local energy minima separated by activation barriers, which is in turn sampled by a metadynamics-based algorithm. Quantitative connection is established between the temperature variation of the calculated viscosity and the underlying potential energy and inherent stress landscape, showing a different landscape topography or “terrain” is needed for low-temperature viscosity (of order 10[superscript 7] Pa·s) from that associated with high-temperature viscosity (10[superscript −5] Pa·s). Within this range our results clearly indicate the crossover from an essentially Arrhenius scaling behavior at high temperatures to a low-temperature behavior that is clearly super-Arrhenius (fragile) for a Kob-Andersen model of binary liquid. Experimentally the manifestation of this crossover in atomic dynamics continues to raise questions concerning its fundamental origin. In this context this work explicitly demonstrates that a temperature-dependent “terrain” characterizing different parts of the same potential energy surface is sufficient to explain the signature behavior of vitrification, at the same time the notion of a temperature-dependent effective activation barrier is quantified.