Altitude definitions

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hMSL
gps.hmsl is height in mm above mean sea level (height above geoid)
gps altitude
gps.lla_pos.alt is height in mm above WGS84 reference ellipsoid
ground alt
ground altitude (above hMSL) defined by flightplan


JSBsim uses GEOCENTRIC instead of GEODETIC latitude and altitude see FlightGear CoordinateSystem

For a proper explanation of the differences see this.