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JOREK Wiki
Information for New JOREK Users
Compiling and Running
Obtain the Source Code
Compilation and Libraries
Compile
Build System
Hard-Coded Parameters
Preprocessor Flags
Compile with 64-bit Integers
Compile MUMPS
Compile without Intel MKL
Example SCOTCH Configuration
Example PaStiX Configuration
HPC & PC Configurations
Leonardo-CPU
Leonardo with GNU OpenMPI
Leonardo with Intel oneAPI
Leonardo with Raven Libraries
LUMI-CPU
Pitagora-CPU
Pitagora-GPU
IPP Garching
TOK-I Cluster
TOK Cluster
Raven
Viper
ITER Cluster
EUROfusion Gateway
TGCC-CEA
macOS
Run
List of input parameters
Code Development
Coding Guidelines
Development Workflow
Regression Tests
NRT preparation with rsync
Plot memory usage
Physics Models
Notation Conventions
Normalization
Vector Identities
Coordinate Systems
Base Fluid Models
Reduced MHD models
RMHD Model
Expressions and Derivations
Magnetic Vector Potential
Current Expression
Vorticity Expression
Stream Function and Electric Potential Expression
The j x B Term Expression
The v x B Term Expression
The Continuity Equation Expression
The Poloidal Flux Equation Expression
The Diamagnetic Vorticity Expression
Derivation of the Parallel Momentum Equation
Parallel Electric Field in RMHD
Helicity Conservation
Tokamak Full MHD
Stellarator Reduced MHD
Weak-Form Resistive Term in Full MHD
Kinetic Particle Module
Energetic Ion
Known issues
Neutrals and Impurities
Gas Puffing
Impurity Collisions
Atomic Processes
Coupling Scheme
Neutral neutral collisions
Introduction to the particle wall_actions
Run with kinetic neutrals and impurities
Particle types
Particle pushers
Kinetic Runaway Electrons
Running with Kinetic Runaway Electrons
Kinetic timestepping
Model Extensions
Free Boundary Extension (STARWALL, CARIDDI)
Free-boundary references
real_space2bezier (Guido's notes)
JOREK-STARWALL tutorial: resistive-wall tearing mode
Running JOREK in free-boundary mode
Running and setting up STARWALL
Running and setting up CARIDDI
Free-boundary diagnostics and tools
Compress the Response Matrices
Impurities
Atomic physics in with_neutrals and with_impurities models
Impurities — Fluid Model
Impurities — Marker Model
ADAS Atomic Data
Neutrals
Neutrals — Fluid Model
Runaway Electrons
REs — Fluid Model
Numerics and Tools
Spatial Discretization
Introduction to Bezier surfaces
Introduction to spatial discretization
Poloidal discretization
Spatial discretization and mesh
Spatial Discretization
Introduction to Bezier surfaces
Introduction to spatial discretization
Poloidal discretization
Spatial discretization and mesh
Grids
Double X-point Grid Construction
Grad-Shafranov Tutorial
Gn-continuous Grid Construction
Wall-extended Grid Construction
Alternative Wall-extended Grid Construction
X-point Grid Construction
Time Integration
Element Matrix FFT
Solver and Preconditioner
Sparse Matrix Format
Random-Number Generators
HDF5 Tools
Diagnostics and post-processing
Diagnostics and Scripts
Check Energy Conservation
Assess Fluid Loads on 3D Walls
Plot Equation Terms in VTK
JOREK-IMAS
Macroscopic_vars.dat
Howto
First Steps
Get Started with JOREK
Get Started with JOREK-STARWALL
Get Started with JOREK-CARIDDI
Get Started with JOREK Diagnostics
Paraview plugin
Grid and Equilibrium
Set Up a JOREK Simulation Grid
Create an X-Point Plasma from a Limiter Plasma
Physics Options
Boundary Conditions
Choose Boundary Conditions
Run with Sheath Heat-Flux BC
Vpar smoothing at grazing angles
Plasma Functions and Coefficients
Get D_perp and ZK_perp for Stationary Profiles
Set Up Resistivity
Set Up Parallel Heat Conduction (ZKpar)
Activation of Physical Terms
Run with Diamagnetic Drift
Include Diamagnetic Drift in Viscosity
Run with Neoclassical Effects
Run with Ohmic Heating
Activate the Inward Pinch Term
Controllers and Actuators
Use the Controller Module
Run with RMPs
Numerics and Stabilization
Run with Taylor-Galerkin Stabilization
Correct Negative Densities / Temperatures
Run with Mode Groups in Preconditioner
Use Shock Capturing Features
Variable MultiScale (VMS) Stabilization
Run with Non-Linear Time-Stepping (Newton)
Impurities, Neutrals and Fuelling
Run an MGI Simulation
Run an SPI Simulation
Run with Kinetic Neutrals and Impurities
Run Particle Simulations with Neutral Collisions
Kinetic Particles
Use Phase Space Projections
Assess Particle Wall Loads with Particle Tracker
Generate Poincaré Plots with Particle Tracker
Runaway Electron Physics in Particle Tracker
Compile and Run the Particle Fast Camera
Post-processing
Reconstruct Namelist Input Parameter Changes
Stellarator
Run Stellarator Simulations
Run Stellarator Model with Divertor Region
Machines
ITER
JET
JET ELM tutorial
KB5 bolometer
ASDEX Upgrade
Active controller model for vertical stabilization
PF coils
Contributing to the Docs
FAQ
Publication Rules
JOREK Logo
Code License
Community Governance Rules
JOREK Website
Howto
Physics Options
Activation of Physical Terms
Activation of Physical Terms
Instructions for enabling optional physical terms in the JOREK equations.
Table of contents
Run with Diamagnetic Drift
Include Diamagnetic Drift in Viscosity
Run with Neoclassical Effects
Run with Ohmic Heating
Activate the Inward Pinch Term
