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JSBSim can use its own internal atmosphere, based on the 1976 U.S. Standard Atmosphere, or it can be set at intitialization time to use FlightGear's atmosphere. The property to set this is /environment/params/control-fdm-atmosphere, and it is by default set to "true", meaning FlightGear provides the atmosphere model.
JSBSim has three available turbulence models: Milspec, Tustin and Culp. The default model is Milspec. The turbulence model can be set at startup using the property /environment/params/jsbsim-turbulence-model, using one of the following string values: