Procedures and results on hardware level detector calibration in Super-Kamiokande (SK) are presented in this paper. In particular, we report improvements made in our calibration methods for the experimental phase IV in which new readout electronics have been operating since 2008. The topics are separated into two parts. The first part describes the determination of constants needed to interpret the digitized output of our electronics so that we can obtain physical numbers such as photon counts and their arrival times for each photomultiplier tube (PMT). In this context, we developed an in-situ procedure to determine high-voltage settings for PMTs in large detectors like SK, as well as a new method for measuring PMT quantum efficiency and gain in such a detector. The second part describes the modeling of the detector in our Monte Carlo simulation, including in particular the optical properties of its water target and their variability over time. Detailed studies on the water quality are also presented. As a result of this work, we achieved a precision sufficient for physics analysis over a wide energy range (from a few MeV to above a TeV). For example, the charge determination was understood at the 1% level, and the timing resolution was 2.1 nsec at the one-photoelectron charge level and 0.5 nsec at the 100-photoelectron charge level.
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