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Hi,
Yes, you can specify externality costs by pollutant. Ensuring that Costs are enabled in Basic Params, look at Basic Params: Costing and enable "Environmental externality costs".
This will add an Effects branch under Key Assumptions in your tree, under which you may add pollutants of your choice. Each of these new branches will have an 'Externality Cost' variable, which allows you to assign costs per unit of emissions anywhere they may occur in your model. These costs will form a separate category in LEAP's cost-benefit summary view, or when you view Costs: Social Costs in the Results view, displayed using all social cost categories.
Best,
Taylor
UPDATE: I've just found that externality costs are not treated as a separate cost category in the latest version of LEAP (2015.0.4.0 at the time of writing). Apologies for not pointing this out earlier - we're looking into it and will make a change in a subsequent version of LEAP.
UPDATE 10/12/2015: This problem has been resolved in the latest version of LEAP, 2015.0.7.0 at the time of writing.