JOREK is a massively parallel fully implicit non-linear extended magneto-hydrodynamic (MHD) code for realistic tokamak X-point plasmas. It has become a widely used versatile simulation code for studying large-scale plasma instabilities and their control and is continuously developed in an international community with strong involvements in the European fusion research programme and ITER organization. This article gives a comprehensive overview of the physics models implemented, numerical methods applied for solving the equations and physics studies performed with the code. A dedicated section highlights some of the verification work done for the code. A hierarchy of different physics models is available including a free boundary and resistive wall extension and hybrid kinetic-fluid models. The code allows for flux-surface aligned iso-parametric finite element grids in single and double X-point plasmas which can be extended to the true physical walls and uses a robust fully implicit time stepping. Particular focus is laid on plasma edge and scrape-off layer (SOL) physics as well as disruption related phenomena. Among the key results obtained with JOREK regarding plasma edge and SOL, are deep insights into the dynamics of edge localized modes (ELMs), ELM cycles, and ELM control by resonant magnetic perturbations, pellet injection, as well as by vertical magnetic kicks. Also ELM free regimes, detachment physics, the generation and transport of impurities during an ELM, and electrostatic turbulence in the pedestal region are investigated. Regarding disruptions, the focus is on the dynamics of the thermal quench (TQ) and current quench triggered by massive gas injection and shattered pellet injection, runaway electron (RE) dynamics as well as the RE interaction with MHD modes, and vertical displacement events. Also the seeding and suppression of tearing modes (TMs), the dynamics of naturally occurring TQs triggered by locked modes, and radiative collapses are being studied.

The interaction of static Resonant Magnetic Perturbations (RMPs) with the plasma flows is modeled in toroidal geometry, using the non-linear resistive MHD code JOREK, which includes the X-point and the scrape-off-layer. Two-fluid diamagnetic effects, the neoclassical poloidal friction and a source of toroidal rotation are introduced in the model to describe realistic plasma flows. RMP penetration is studied taking self-consistently into account the effects of these flows and the radial electric field evolution. JET-like, MAST, and ITER parameters are used in modeling. For JET-like parameters, three regimes of plasma response are found depending on the plasma resistivity and the diamagnetic rotation: at high resistivity and slow rotation, the islands generated by the RMPs at the edge resonant surfaces rotate in the ion diamagnetic direction and their size oscillates. At faster rotation, the generated islands are static and are more screened by the plasma. An intermediate regime with static islands which slightly oscillate is found at lower resistivity. In ITER simulations, the RMPs generate static islands, which forms an ergodic layer at the very edge ($\psi \ge 0.96$ ) characterized by lobe structures near the X-point and results in a small strike point splitting on the divertor targets. In MAST Double Null Divertor geometry, lobes are also found near the X-point and the 3D-deformation of the density and temperature profiles is observed.

For the first time it is experimentally demonstrated on the JET tokamak that a combination of a low impurity concentration bulk plasma and large magnetohydrodynamic instabilities is able to suppress relativistic electron beams without measurable heat loads onto the plasma facing components. Magnetohydrodynamic simulations of the instability and modeling of the postinstability plasma confirm the prompt loss of runaways and the absence of regeneration during the final current collapse. These surprising findings motivate a new approach to dissipate runaway electrons generated during tokamak plasma disruptions.

A possible mechanism of edge localized modes (ELMs) mitigation by resonant magnetic perturbations (RMPs) is proposed based on the results of nonlinear resistive magnetohydrodynamic modeling using the jorek code, realistic JET-like plasma parameters and an RMP spectrum of JET error-field correction coils (EFCC) with a main toroidal number $n=2$ were used in the simulations. Without RMPs, a large ELM relaxation is obtained mainly due to the most unstable medium-$n$ ballooning mode. The externally imposed RMP drives nonlinearly the modes coupled to $n=2$ RMP which produce small multimode relaxations, mitigated ELMs. The modes driven by RMPs exhibit a tearinglike structure and produce additional islands. Mitigated ELMs deposit energy into the divertor mainly in the structures (“footprints”) created by $n=2$ RMPs, however, slightly modulated by other nonlinearly driven even harmonics. The divertor power flux during a ELM phase mitigated by RMPs is reduced almost by a factor of 10. The mechanism of ELM mitigation by RMPs proposed here reproduces generic features of high collisionality RMP experiments, where large ELMs are replaced by small, much more frequent ELMs or magnetic turbulence. Total ELM suppression was also demonstrated in modeling at higher RMP amplitude.