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You can try the R package eixport, with wrf_put # example # Read the array emissions, CO <- wrf_get(file = "Path_to_WRFCHEMI", name = "E_CO") # Change the values, here you should use your data CO[] = rnorm(length(CO)) # Inyect your emissions into the wrfchemi wrf_put(file = "Path_to_WRFCHEMI", name = "E_CO", POL = CO) How to deal with the speciation (...