Yeah, templates stink for mathhammer. As mentioned, you're just going to have to put some assumptions in your parameters. You're already used to doing this (like assuming your opponent has cover, and of a certain type, or not), but somehow, it feels ickier here.
There are a few guiding principles, though. One of them is displacement. A 40k mini sits on a 20mm (roughly .4" in radius) base, and can be displaced up to 2" apart and still maintain coherency.
This means that it is possible for your opponent to spread out in such a way where they will only take a single hit per shot of a small blast template weapon, as the 1.5" radius of a small blast template is (much) less than the potential 2.4" of maximum displacement. However, a large blast template has a radius of 2.5", which means it's impossible for a large blast template hitting in the middle of a unit to score fewer than 3 hits.
From there, you can look at other bases. For example, at maximum displacement, anything on a 40mm base will cause a large blast to hit only one model, and, of course, a monstrous creature will only ever take one hit, and the like.
From here, you can mess with your parameters, as it's theoretically possible to hit what, 25 models with a single large blast, or something like that? Of course, with any of these assumptions, you have to start questioning how likely it is that you will be in those circumstances.
One way to get around this is with ranges. For example, I like to assume that a small blast template will hit between 1 and 3 models most of the time you shoot it, and 3-5 for large blasts. Of course, I also like to be conservative here, because I cannot guarantee that I'm going to be up against an opponent who doesn't know what displacement means. When that does happen, I'll just have to be pleasantly surprised.
Another thing to consider here is the scatter+BS subtraction over target size. This actually makes calculating blast weapons versus vehicles not THAT difficult (depending on how big of a vehicle you're shooting at), at least to get a ballpark figure. With infantry it's a lot tougher, as it depends much more on what other units are near the target unit (in what displacement) that the template could scatter over onto.
As for flamer templates, it's a crap-shoot. More than blast template weapons, I take into consideration how those templates are getting there. A pinpoint deepstrike squad, like sternguard in a drop pod, or iconed CSM, or even stormtroopers with airborne assault, I can pretty safely assume something like 5-8 hits per shot. In a unit that will be used solely as a counter-assault role, I like to move it up to more like 8 and less like 5. In an offensive role, or for general use, I generally don't calculate higher than 3. Personal experience has taught me not to expect more than this.
It's all rather subjective, though, as each different person is going to bring their own initial assumptions to the calculation. The best thing you can do, I guess, is to just be transparent about your assumptions.
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