This depends so much on the engine! The emissions depend on so many factors that effective prediction is going to be very difficult, and will vary greatly with working conditions, load, speed, fuel type, valve timing, injection timing, injection efficacy, engine temperature and so forth. Please make sure that you are tackling a solvable problem!
Mass of exhaust gas can be found using mass of air and mass of fuel is the simplest way. The mass of exhaust gas can be found even by using the amount the carbon present in the fuel.If you want to find the individual constituents of exhaust gas and the percentage of its, then using the combustion equations theoretically we can calculate Gravimetric analysis or volumetric analysis. Check in the Books FUEL and COMBUSTION by Samir Sarkar or any thermal engineering books for caluculations.
in addition to the factors affect on exhaust emission in diesel engine which indicated above. prediction of the exhaust emission in diesel engine based on: techiques which applied in internal combustion engine, state of parts in fuel system such as injectors,... and design of exhaust system,
You can very well predict emissions with air-fuel ratio, though it might require some additional tricks in doing so.
You can start with splitting your diesel emission into major fundamental constituents such as soot, NOx, CO and such. There are very well established phenomological models available for the prediction of the constituents to good accuracy.
However, in addition to air/fuel ratio you would require additional combustion parameters such as injection timing, incylinder pressure and temperature, combustion bowl shape, fuel quality, Injection and air turbulence,etc., This is because in Direct Injection, we have to consider the local air-fuel ratios. Because near the fuel spray cone, the region is rich leading to high Soot formation and near the walls where the spray is lean, leading to HC formation.
For example, at a constant engine speed, injection timing, rail pressure and air-fuel ratio, we can obtain higher or lower HC,CO,soot emissions by varying the air swirl.
So the emission modeling must consider these factors for accurate prediction.
As pointed out by Tony Maine, this is a very difficult problem! The overall air fuel ratio doesn't tell you much about the actual combustion. In a diffusion flame, as in the diesel, the combustion is always occurring near stoichiometric conditions, which in some respects simplifies things. There are some methods based on this, for example, Egnell from Lund University has some fairly simple methods for NOx emissions based on stoichiometric combustion assumptions. But you still need to know what happens during combustion. Smoke/particulate emissions are very difficult, and as far as I know, still need a fair amount of empiricism. HC and CO emissions are also difficult, but not that important for diesels compared to NOx and particulates. But in all likelihood, you will need to go to CFD methods, and even there, it is really difficult. In short, overall fuel air ratio is not enough, you need more information.