An atomic magnetometer is a magnetic field sensor. Like any other sensor, it can be used for any number of applications and in any number of industries. How can someone justify trying to patent just the use of an older patented technology in an entire industry without inventing anything at all. Basically all that is claimed in the application is that the "inventors" will incorporate magnetometers in their traditional surveying instrumentation to sense magnetic field, that's it. Don't you at least have to pretend to invent something first before trying to patent an invention?
This has not yet resulted in a granted patent. It is a patent application only. The U.S. counterpart is 2010/0225313. It has just been given a "final" rejection by the USPTO in Jan. of 2013.
I do not know the field, but there is nothing fundamentally wrong about a patent involving a known sensor applied in a new way. But it does have to be new and useful and not obvious - no requirement for being earth-shattering. The claims do seem to be limited to subterranean applications and some claims further limit it to boreholes.