A device controller controls an acceleration-related devices and an extraction-related devices of an accelerator for accelerating and extracting a particle beam, in such a way that the controller checks, at a time point when receiving a master clock pulse, that preparation for operating the acceleration-related devices is completed and then commands the acceleration-related devices to operate in accordance with an operation pattern corresponding to a prescribed energy of the particle beam, and commands the acceleration-related devices to operate in accordance with an extracting operation pattern when an extraction enable signal indicating that the particle beam reaches the prescribed energy is turned ON and an extraction-related device setting-status signal indicating that completion of setting the extraction-related devices for the prescribed energy is ON.

In one embodiment of the invention, a method for irradiating a target is disclosed. A proton beam is generated using a cyclotron. A first information is provided to an energy selection system. An energy level for the protons is selected using an energy selection system based on the first information. The first information comprises a depth of said target. The proton beam is routed from the cyclotron through a beam transfer line to a scanning system. A second information is provided to the scanning system. The second information comprises a pair of transversal coordinates. The proton beam is guided to a location on the target determined by the second information using a magnet structure. The target is irradiated with the protons.