The energy building up is translated by amplifying the magnitude of the vibrations. Physical things will evetually reach a breaking point while fluids will simply heat up.
You will then see how far it is from the HARRP frequency, and doesnt have enough energy to heat that much water over that broad of an area, at that distance.
Sure, let's say they had it emitting microwaves though. Let's say it was a big microwave emitter. It could only work on the atmosphere directly above it. Not anywhere in the world.
The equipment you use determines the frequencies you emit. They couldn't just use it to make a bright light, or emit gamma rays. They experimented with radio waves.