Welcome to MITgcm’s user manual

Contents:

• 1. Overview
  • 1.1. Introduction
  • 1.2. Illustrations of the model in action
    • 1.2.1. Global atmosphere: ‘Held-Suarez’ benchmark
    • 1.2.2. Ocean gyres
    • 1.2.3. Global ocean circulation
    • 1.2.4. Convection and mixing over topography
    • 1.2.5. Boundary forced internal waves
    • 1.2.6. Parameter sensitivity using the adjoint of MITgcm
    • 1.2.7. Global state estimation of the ocean
    • 1.2.8. Ocean biogeochemical cycles
    • 1.2.9. Simulations of laboratory experiments
  • 1.3. Continuous equations in ‘r’ coordinates
    • 1.3.1. Kinematic Boundary conditions
    • 1.3.2. Atmosphere
    • 1.3.3. Ocean
    • 1.3.4. Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
    • 1.3.5. Solution strategy
    • 1.3.6. Finding the pressure field
    • 1.3.7. Forcing/dissipation
    • 1.3.8. Vector invariant form
    • 1.3.9. Adjoint
  • 1.4. Appendix ATMOSPHERE
    • 1.4.1. Hydrostatic Primitive Equations for the Atmosphere in Pressure Coordinates
  • 1.5. Appendix OCEAN
    • 1.5.1. Equations of Motion for the Ocean
  • 1.6. Appendix OPERATORS
    • 1.6.1. Coordinate systems
• 2. Discretization and Algorithm
  • 2.1. Notation
  • 2.2. Time-stepping
  • 2.3. Pressure method with rigid-lid
  • 2.4. Pressure method with implicit linear free-surface
  • 2.5. Explicit time-stepping: Adams-Bashforth
  • 2.6. Implicit time-stepping: backward method
  • 2.7. Synchronous time-stepping: variables co-located in time
  • 2.8. Staggered baroclinic time-stepping
  • 2.9. Non-hydrostatic formulation
  • 2.10. Variants on the Free Surface
    • 2.10.1. Crank-Nicolson barotropic time stepping
    • 2.10.2. Non-linear free-surface
  • 2.11. Spatial discretization of the dynamical equations
    • 2.11.1. The finite volume method: finite volumes versus finite difference
    • 2.11.2. C grid staggering of variables
    • 2.11.3. Grid initialization and data
    • 2.11.4. Horizontal grid
    • 2.11.5. Vertical grid
    • 2.11.6. Topography: partially filled cells
  • 2.12. Continuity and horizontal pressure gradient term
  • 2.13. Hydrostatic balance
  • 2.14. Flux-form momentum equations
    • 2.14.1. Advection of momentum
    • 2.14.2. Coriolis terms
    • 2.14.3. Curvature metric terms
    • 2.14.4. Non-hydrostatic metric terms
    • 2.14.5. Lateral dissipation
    • 2.14.6. Vertical dissipation
    • 2.14.7. Derivation of discrete energy conservation
    • 2.14.8. Mom Diagnostics
  • 2.15. Vector invariant momentum equations
    • 2.15.1. Relative vorticity
    • 2.15.2. Kinetic energy
    • 2.15.3. Coriolis terms
    • 2.15.4. Shear terms
    • 2.15.5. Gradient of Bernoulli function
    • 2.15.6. Horizontal divergence
    • 2.15.7. Horizontal dissipation
    • 2.15.8. Vertical dissipation
  • 2.16. Tracer equations
    • 2.16.1. Time-stepping of tracers: ABII
  • 2.17. Linear advection schemes
    • 2.17.1. Centered second order advection-diffusion
    • 2.17.2. Third order upwind bias advection
    • 2.17.3. Centered fourth order advection
    • 2.17.4. First order upwind advection
  • 2.18. Non-linear advection schemes
    • 2.18.1. Second order flux limiters
    • 2.18.2. Third order direct space time
    • 2.18.3. Third order direct space time with flux limiting
    • 2.18.4. Multi-dimensional advection
  • 2.19. Comparison of advection schemes
  • 2.20. Shapiro Filter
    • 2.20.1. SHAP Diagnostics
  • 2.21. Nonlinear Viscosities for Large Eddy Simulation
    • 2.21.1. Eddy Viscosity
    • 2.21.2. Mercator, Nondimensional Equations
• 3. Getting Started with MITgcm
  • 3.1. Where to find information
  • 3.2. Obtaining the code
    • 3.2.1. Method 1
    • 3.2.2. Method 2
  • 3.3. Updating the code
  • 3.4. Model and directory structure
  • 3.5. Building the code
    • 3.5.1. Building/compiling the code elsewhere
    • 3.5.2. Using genmake2
    • 3.5.3. Building with MPI
  • 3.6. Running the model
    • 3.6.1. Running with MPI
    • 3.6.2. Output files
    • 3.6.3. Looking at the output
  • 3.7. Customizing the model configuration
    • 3.7.1. Parameters: Computational Domain, Geometry and Time-Discretization
    • 3.7.2. Parameters: Equation of State
    • 3.7.3. Parameters: Momentum Equations
    • 3.7.4. Parameters: Tracer Equations
    • 3.7.5. Parameters: Simulation Controls
    • 3.7.6. Parameters: Default Values
• 4. MITgcm Tutorial Example Experiments
  • 4.1. Barotropic Gyre MITgcm Example
    • 4.1.1. Equations Solved
    • 4.1.2. Discrete Numerical Configuration
    • 4.1.3. Code Configuration
  • 4.2. A Rotating Tank in Cylindrical Coordinates
    • 4.2.1. Equations Solved
    • 4.2.2. Discrete Numerical Configuration
    • 4.2.3. Code Configuration
• 5. Contributing to the MITgcm
  • 5.1. Bugs and feature requests
  • 5.2. Using Git and Github
    • 5.2.1. Quickstart Guide
    • 5.2.2. Detailed guide for those less familiar with Git and GitHub
  • 5.3. Coding style guide
    • 5.3.1. Automatic testing with Travis-CI
  • 5.4. Contributing to the manual
    • 5.4.1. Section headings
    • 5.4.2. Internal document references
    • 5.4.3. Other embedded links
    • 5.4.4. Symbolic Notation
    • 5.4.5. Figures
    • 5.4.6. Tables
    • 5.4.7. Other text blocks
    • 5.4.8. Other style conventions
    • 5.4.9. Building the manual
  • 5.5. Reviewing pull requests
• 6. Software Architecture
• 7. Automatic Differentiation
• 8. Packages I - Physical Parameterizations
  • 8.1. Overview
    • 8.1.1. Using MITgcm Packages
  • 8.2. Packages Related to Hydrodynamical Kernel
    • 8.2.1. Generic Advection/Diffusion
    • 8.2.2. Shapiro Filter
    • 8.2.3. FFT Filtering Code
    • 8.2.4. exch2: Extended Cubed Sphere Topology
    • 8.2.5. Gridalt - Alternate Grid Package
  • 8.3. General purpose numerical infrastructure packages
    • 8.3.1. OBCS: Open boundary conditions for regional modeling
    • 8.3.2. RBCS Package
    • 8.3.3. PTRACERS Package
  • 8.4. Ocean Packages
    • 8.4.1. GMREDI: Gent-McWilliams/Redi SGS Eddy Parameterization
    • 8.4.2. KPP: Nonlocal K-Profile Parameterization for Vertical Mixing
    • 8.4.3. GGL90: a TKE vertical mixing scheme
    • 8.4.4. OPPS: Ocean Penetrative Plume Scheme
    • 8.4.5. KL10: Vertical Mixing Due to Breaking Internal Waves
    • 8.4.6. BULK_FORCE: Bulk Formula Package
    • 8.4.7. EXF: The external forcing package
    • 8.4.8. CAL: The calendar package
  • 8.5. Atmosphere Packages
    • 8.5.1. Atmospheric Intermediate Physics: AIM
    • 8.5.2. Land package
    • 8.5.3. Fizhi: High-end Atmospheric Physics
  • 8.6. Sea Ice Packages
    • 8.6.1. THSICE: The Thermodynamic Sea Ice Package
    • 8.6.2. SEAICE Package
• 9. Packages II - Diagnostics and I/O
• 10. Ocean State Estimation Packages
  • 10.1. ECCO: model-data comparisons using gridded data sets
    • 10.1.1. Generic Cost Function
    • 10.1.2. Generic Integral Function
    • 10.1.3. Custom Cost Functions
    • 10.1.4. Key Routines
    • 10.1.5. Compile Options
  • 10.2. PROFILES: model-data comparisons at observed locations
  • 10.3. CTRL: Model Parameter Adjustment Capability
  • 10.4. SMOOTH: Smoothing And Covariance Model
  • 10.5. The line search optimisation algorithm
    • 10.5.1. General features
    • 10.5.2. The online vs. offline version
    • 10.5.3. Number of iterations vs. number of simulations
• 11. Under Development
• 12. Previous Applications of MITgcm
• 13. References