Molecular kinetic simulations are typically used to accurately describe the tenuous regions of the upper atmospheres on planetary bodies. These simulations track the motion of particles representing real atmospheric atoms and/or molecules subject to collisions, the objects gravity, and external influences. Because particles can end up in very large ballistic orbits, upper boundary conditions (UBC) are typically used to limit the domain size thereby reducing the time for the atmosphere to reach steady-state. In the absence of a clear altitude at which all molecules are removed, such as a Hill sphere, an often used condition is to choose an altitude at which collisions become infrequent so that particles on escape trajectories are removed. The remainder are then either specularly reflected back into the simulation domain or their ballistic trajectories are calculated analytically or explicitly tracked so they eventually re-enter the domain. Here we examine the effect of the choice of the UBC on the escape rate and the structure of the atmosphere near the nominal exobase in the convenient and frequently used 1D spherically symmetric approximation. Using Callisto as the example body, we show that the commonly used specular reflection UBC can lead to significant uncertainties when simulating a species with a lifetime comparable to or longer than a dynamical time scale, such as an overestimation of escape rates and an inflated exosphere. Therefore, although specular reflection is convenient, the molecular lifetimes and bodys dynamical time scales need to be considered even when implementing the convenient 1D spherically symmetric simulations in order to accurately estimate the escape rate and the density and temperature structure in the transition regime.
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