I just looked something extra up. I read this on a blog and it seemed to make sense. Here is a slightly edited quote:
some dude on the Internet said:
The microwave emitter is based loosely on an actual military "microwave" weapon. That weapon was capable of very directly focusing itself in terms of direction and distance. If someone walked in front of it, they weren't automatically hit with the force of the weapon the way someone at the designated distance would be. Those standing nearby likewise were unaffected, because of the directional accuracy of the weapon.
It's reasonable that a weapon specifically designed to only vaporize water in a city's water lines would have directional and distance controls. The microwave emissions would be such that they are aimed precisely in a single direction (in the case of BB, downward from the train, toward the ground) and would reach their peak effect at a specific distance -- namely, the distance from the train to the placement of the water lines underground, which the film makes clear run directly beneath the train tracks. Figuring out the distance from inside one of the train cars down to the waterlines, for the entire distance to be traveled in this plot, would require some measurements and maps, but it's actually not all that hard to see how they could figure it out and program the emitter for that specific distance.
So the microwave emissions would thus not affect anything except what it is aimed at -- the water mains directly below, at a specific distance from the train. The controls could easily have been set based on knowledge of how deep underground the water lines were placed, with a bit of leeway (perhaps half a foot above and below, and horizontally from the water lines) to compensate for any bumps or imprecision in the blueprints showing where the lines are (in case of ground settling, or other things that might've shifted the exact location of the lines). This would easily explain why the microwave emitter only affected the water lines without vaporizing water in the air or in people.
Added from comments to his blog:
It's not literal "microwaves" first of all, it's called that because of the comparison to the simple "common" explanation of how microwaves work (exciting the water in stuff).
http://en.wikipedia.org/wiki/Dir...
http://www.onr.navy.mil/en/Media...
I think the wavelength plays a significant role, and if the emitter were designed to use waterlines themselves -- the pipes -- as a sort of parabolic antenna (except all around the water) that concentrates the waves and directs them into the water that way. Yeah, it's a stretch and the details would be left intentionally vague, but the concept of a directed energy weapon focusing energy into pipes to use the pipes as a way of further concentrating the energy around and into water within the pipes, is something I am willing to accept as a vague answer for why the emitter worked on the waterlines but didn't cause people and cats to cook beneath the train.
We could also point out that in the film, there's no shot beneath the train itself, so how do we KNOW whether it boiled anybody or cooked anyone? There might've been a dozen homeless people and graffiti artists and people out for strolls etc under the train track who were all killed by it. The energy is aimed
downward, and directed energy weapons definitely are fully capable of aiming in a specific and narrow direction, so the only question is really whether it happened off-screen since the film merely failed to show what happened beneath the train where any people might've been.
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