From June 1957 to December 1961, Allen was assigned to Kirtland Air Force Base, New Mexico, as the science adviser to the Physics Division of the Air Force Special Weapons Center. ("Special weapons" is a euphemism for nuclear and thermonuclear bombs.) Allen specialized in the military effects of high altitude nuclear explosions and participated in several nuclear weapons test series. He was scientific director of a major experiment that utilized a large series of high altitude rockets to measure the characteristics of electrons trapped in the geomagnetic field after an exoatmospheric nuclear burst.