FESOM2 documentation

Authors

Sergey Danilov, Dmitry Sidorenko, Nikolay Koldunov, Patrick Scholz, Qiang Wang, Thomas Rackow, Helge Goessling and Lorenzo Zampieri

Contents:

• Getting Started with FESOM2
  • TL;DR version for supported HPC systems
  • Detailed steps of compiling and runing the code
  • Other things you need to know earlier on
  • Troubleshooting
  • Docker based installation
  • Necessary Ubuntu packages
• General configuration (namelist.config)
  • Sections of the namelist
• Ocean configuration (namelist.oce)
  • Sections of the namelist
• Forcing configuration (namelist.forcing)
  • Sections of the namelist
• Standard sea ice configuration (namelist.ice)
  • Sections of the namelist
• Icepack sea ice configuration
  • General information
  • Implementation
  • Compilation
  • Running the model
  • Code structure
  • Frequently asked questions
• Data pre/post processing
  • netCDF files for initial conditions
  • Interpolate initial conditions from existing run
  • Convert grid to netCDF that CDO understands
• Geometry
  • The placement of variables
  • Notation
  • Earth sphericity
  • Bottom representation
  • Partial cells
• Meshes
  • Mesh files
  • Mesh arrays
  • Auxiliary mesh arrays
  • Modularity
• Main equations
  • Main equations
• Vertical discretization: Layer thicknesses and layer equations
• Temporal discretization: Asynchronous time stepping
  • Thickness and tracers
  • Elevation
  • Momentum equation
  • Momentum equation in form eq_mom_fl
  • Current options for the vertical coordinate
  • Implicit vertical diffusion
• Spatial discretization of equations (mostly in horizontal directions)
  • Finite-volume basics
  • Horizontal operators
  • Momentum advection
  • Vector-invariant form
  • Horizontal viscosity operators
  • ‘Canonical’ operators
  • Selection of viscosity coefficient
  • Numerical viscosities (viscosity filters)
  • Transport of scalar quantities. Horizontal part
  • Vertical advection of scalars
  • Compact scheme (also the Parabolic Spline Method
  • GM and isoneutral operators
• Time stepping for the transport \(\mathbf{U}=h\mathbf{u}\) instead of velocity
• Subcycling instead of solver
• Isoneutral diffusion on triangular prisms
• References

Proposed structure:

Introduction
Getting started
    TL;DR version for supported HPC systems
    Detailed steps of compiling and runing the code
    Ubuntu based Docker container (to get first impression of the model)
    Troubleshooting
Looking at the results
    Notebooks that comes with the model
    pyfesom2 (short description with link to documentation)
Tutorials
    Build model on Ubuntu (Video)
    Add new output variable (Video)
    First look at model output (Video)
General configuration (namelist.configure)
    Time stepping
    Restarts
    ALE options
    Mesh geometry and partitioning
Ocean configuration (namelist.oce)
    Ocean dynamics
    Ocean tracers
    Adding a new tracer
    Initial conditions
Sea ice configuration (namelist.ice)
    Ice dynamics
    Ice thermodynamics
Atmospheric forcing (namelist.forcing)
Output (namelist.io)
    Adding new output variable
Meshes
    Mesh format
    Mesh generation?
Partitioning
    MESSY
    Hierarchical partitioning
Data pre/post processing
    Initial conditions
    Convert grid to netCDF that CDO understands
Discretizations and Algorithms
Coupling interfaces
    To atmosphere
    To ocean biogeochemistry?
Example experiments
FAQ
History

Indices and tables

• Index

• Module Index

• Search Page