I think vacuum can be modeled in ANSYS fluent also by taking air as a medium and changing its properties (e.g. Thermal conductivity, density, etc.) you can refer to the following research article.

Article CFD modeling of a thermal energy storage based heat pipe eva...

Hope this helps.

This will depend on the Knudsen number in your case, please calculate this. For Kn < 0.1 Navier-Stokes can be used (with care), for higher values of the Knudsen number you need to use different computational methods (such as DSMC or lattice Boltzmann). See also: https://en.wikipedia.org/wiki/Knudsen_number

TransCalc is a network-based computational simulation software package for the design of vacuum systems. TransCalc is based upon duct-flow prediction techniques which provide a solution across all pressure ranges.

Pascal is a smart simulation tool enables the engineering of a flow-optimisation pump system using empirical data gained from existing pumps, which is coupled with data from the components required to complete the vacuum system, and then through simulation allows the study of three-dimensional molecular flow through the whole unit.

VacSim is a PC-based software simulation package which uses the hermetic capture of a vacuum system and is able to predict/calculate how the system pressure varies with time, throughput volumes, pump speed and oil back-streaming. VacSim is able to produce pump-down curves, show the impact of bakeout regimes, illustrate the impact of (construction) material and demonstrate what difference a pump change will make.

COMSOL can trace its development from 1986 at the Royal Institute of Technology in Stockholm, Sweden. It is used for vacuum system simulation including those used in semi-conductor processing, particle acceleration and mass spectrometers.