We introduce a machine learned surrogate model from high-resolution simulation data to capture the subgrid-scale effects in dry, stratified atmospheric flows. We use deep neural networks (NNs) to model the spatially local state differences between a coarse resolution simulation and a high-resolution simulation. The setup enables the capture of both dissipative and anti-dissipative effects in the state differences. The NN model is able to accurately capture the state differences in offline tests outside the training regime. In online tests intended for production use, the NN coupled coarse simulation has higher accuracy over a significant period of time compared to the coarse-resolution simulation without any correction. We provide evidence to the capability of the NN model to accurately capture high gradient regions in the flow field. With the accumulation of the errors, the NN-coupled simulation becomes computationally unstable after approximately 90 coarse simulation time steps. Insights gained from these surrogate models further pave the way for formulating stable, complex, physics-based spatially local NN models which are driven by traditional subgrid-scale turbulence closure models.