Modeling aerosol injection in the atmosphere is important for several applications including predicting the climatological affects of volcanic eruptions and assessing outcomes of various climate engineering and climate change mitigation strategies. Aerosol injection modeling is computationally challenging since it activates physical pathways where aerosol species interact, modify the optical properties of the atmosphere, and ultimately affect global temperatures over a months-years-long time-scale. We present the CLDERA-tools software toolkit that enables in-situ analysis of physical pathways in the Department of Energy’s Energy Exascale Earth System Model (E3SM). CLDERA-tools non-invasively constructs representations of physical pathways concurrent with model runs to enable real-time discovery of physical pathways and avoid expensive post-processing of data. We present results using CLDERA-tools to compute physical pathways from simulations of the E3SM model atmosphere using a modified Held-Suarez configuration supporting various aerosol and chemistry options.