I'm running a version of MAUS that was my development branch, merged with changes from the merge branch.
The output of bzr info:
Standalone tree (format: 2a)
Location:
branch root: .

Related branches:
parent branch: /home/celeste/MICE/MAUS/devel
submit branch: bzr+ssh://bazaar.launchpad.net/%2Bbranch/maus/merge/

The output of bzr revision-info:
694 c.e.pidcott@warwick.ac.uk-20140107150557-l0uns23mvurnsnpc

And the version number in the README file is 0.7.7

Also I've just realised that I forgot to set verbose level to 0 for the log, the new log is now attached. The warning now appears for the first time at line 5734 after 356 events have been processed.

This is a sqrt of a negative numpy float type.

When generating a beam, MAUS will generate a new primary; and then check whether the new primary has (total) energy < mass. MAUS will keep throwing new primaries until it finds one with energy > mass. This process can produce the warning you have highlighted, but in fact nothing bad happened.

The relevant lines are src/map/MapPyBeamMaker/beam.py:321

    def make_one_primary(self):
        """ 
        Make a primary particle.

        Returns an dict formatted for insertion into the json tree as a primary.
        See json data tree documentation for further information

        Note that if the dice give us a particle that has "negative" total
        momentum we throw again.
        """ 
        hit = xboa.Hit.Hit.new_from_dict({'pid':-13, "energy":float('nan')})
        while math.isnan(hit["energy"]) or math.isnan(hit["pz"]) or \
              hit["energy"] < hit["mass"]:
            particle_array = self.__process_get_particle_array()
            hit = self.__process_array_to_hit(particle_array,
                                self.reference["pid"], self.momentum_defined_by)
        primary = self.__process_hit_to_primary(hit)
        return primary