A comprehensive approach to modeling open quantum systems consistent with thermodynamics is presented. The theory of open quantum systems is employed to define system bath partitions. The Markovian master equation defines an isothermal partition between the system and bath. Two methods to derive the quantum master equation are described: the weak coupling limit and the repeated collision model. The role of the eigenoperators of the free system dynamics is highlighted, in particular, for driven systems. The thermodynamical relations are pointed out. Models that lead to loss of coherence, i.e., dephasing are described. The implication of the laws of thermodynamics to simulating transport and spectroscopy is described. The indications for self-averaging in large quantum systems and thus its importance in modeling are described. Basic modeling by the surrogate Hamiltonian is described, as well as thermal boundary conditions using the repeated collision model and their use in the stochastic surrogate Hamiltonian. The problem of modeling with explicitly time dependent driving is analyzed. Finally, the use of the stochastic surrogate Hamiltonian for modeling ultrafast spectroscopy and quantum control is reviewed.