If you are using the TOUGH2 simulators packaged with PetraSim, you will need to use a very large volume element to represent the atmosphere (see the "Extra Cells" section in the PetraSim manual). There is also a section in the manual on Time-Dependent Essential (Direchlet) Boundary Conditions, starting on page 69. You will need to use a sink or source to increase/decrease the pressure and temperature in the cell.
You also may find the exercise titled "Time Dependent Multi-Phase Boundary Conditions" useful. It is posted on the RockWare website: https://www.rockware.com/petrasim-example-problems/
Note that there is a "TIMBC" boundary condition available in TOUGH3 and iTOUGH2. If you are using TOUGH3 with PetraSim, you might consider modifying your input file to include this type of boundary condition, which is not yet supported in the PetraSim interface.
Also, please note that you can direct PetraSim-specific questions to the PetraSim support forum hosted by RockWare: https://www.rockware.com/forum/index.php?/forum/5-toughpetrasim-forum/