We present the framework of the modeling package IonoSeis. This software models Global Navigation Satellite System (GNSS) derived slant total electron content (sTEC) perturbations in the ionosphere due to the interaction of the neutral atmosphere and charged particles in the ionosphere. We use a simplified model to couple the neutral particle momentum into the ionosphere and reconstruct time series of sTEC perturbations that match observed data in both arrival time and perturbation shape. We propagate neutral atmosphere disturbances to ionospheric heights using a three-dimensional ray-tracing code in spherical coordinates called Windy Atmospheric Sonic Propagation (WASP3D), which works for a stationary or non-stationary atmospheric models. The source of the atmosphere perturbation can be an earthquake or volcanic eruption; both couple significant amounts of energy into the atmosphere in the frequency range of a few Millihertz. We demonstrate the output of the code by comparing modeled sTEC perturbation data to the observed perturbation recorded at GNSS station BTNG (Bitung, Indonesia) immediately following the 28 September 2018, Sulawesi-Palu earthquake. With this framework, we provide a software to couple the lithosphere, atmosphere, and ionosphere that can be used to study post-seismic ionospherically-derived signals