The Faraday cup is a conductive cup used to measure a beam current. The charged particles are collected in the cup (sometimes trapped by a magnetic field from permanent magnets) and after they hit the metallic interior body of the cup, a net charge is gained. Measuring the net charge flow over time will result in a current measurement.
A centered Faraday cup in the EBL Raith 100 looks like the image below. If the Faraday isn't centered correctly all beam current measurements will be off. Center the Faraday cup by moving the stage with the joystick on the desk.
