POP Reference Manual

• 1. Cover
• 2. Introduction
• 3. The Primitive Equations in General Coordinates
• 4. Spatial Discretization
  • 4.1. Discrete Horizontal and Vertical Grids
  • 4.2. Finite-difference operators
  • 4.3. Discrete Tracer Transport Equations
    • 4.3.1. Tracer Advection
    • 4.3.2. Horizontal Tracer Diffusion
    • 4.3.3. Vertical Tracer Diffusion
  • 4.4. Discrete Momentum Equations.
    • 4.4.1. Momentum Advection
    • 4.4.2. Metric Terms
    • 4.4.3. Horizontal Friction
    • 4.4.4. Vertical Friction
  • 4.5. Energetic Consistency
• 5. Time Discretization
  • 5.1. Filtering Timesteps
  • 5.2. Tracer Transport Equations
    • 5.2.1. Tracer Acceleration
    • 5.2.2. Implicit Vertical Diffusion
    • 5.2.3. Tridiagonal Solver
  • 5.3. Splitting of Barotropic and Baroclinic Modes
  • 5.4. Baroclinic Momentum Equations
    • 5.4.1. Pressure Averaging
    • 5.4.2. Semi-Implicit Treatment of Coriolis and Vertical Friction Terms
  • 5.5. Barotropic Equations
    • 5.5.1. Linear Free Surface Model
    • 5.5.2. Time Discretization of the Barotropic Equations
    • 5.5.3. Conjugate Gradient Algorithm
• 6. Grids
  • 6.1. Global Orthogonal Grids
    • 6.1.1. Dipole Grids
    • 6.1.2. Tripole Grids
  • 6.2. Vertical Grid Variants
    • 6.2.1. Variable-Thickness Surface Layer
    • 6.2.2. Partial Bottom Cells
• 7. Advection
  • 7.1. Third-Order Upwind Advection
  • 7.2. Flux-Limited Lax-Wendroff Algorithm
• 8. Sub-grid Scale Mixing Parameterizations
  • 8.1. Horizontal Tracer Diffusion
    • 8.1.1. Laplacian Horizontal Diffusivity
    • 8.1.2. Biharmonic Horizontal Diffusivity
    • 8.1.3. The Gent-McWilliams Parameterization
    • 8.1.4. Parameterization of Mixed Layer Eddies
  • 8.2. Horizontal Viscosity
    • 8.2.1. Laplacian Horizontal Viscosity
    • 8.2.2. Biharmonic Horizontal Viscosity
    • 8.2.3. Anisotropic Horizontal Viscosity
  • 8.3. Vertical Mixing
    • 8.3.1. Convection
    • 8.3.2. Constant Vertical Viscosity
    • 8.3.3. Richardson Number Dependent Mixing
    • 8.3.4. The KPP Boundary-Layer Parameterization
    • 8.3.5. Tidally Driven Mixing
• 9. Other Model Physics
  • 9.1. Equation of State
    • 9.1.1. Boussinesq Correction
    • 9.1.2. Hydrostatic Pressure
    • 9.1.3. Expansion Diagnostic
  • 9.2. Sea-Ice Formation and Melting
  • 9.3. Freshwater Balancing over Marginal Seas
  • 9.4. Overflow Parameterization
    • 9.4.1. Calculation of Overflow Properties
    • 9.4.2. Model Modifications
  • 9.5. Passive Tracers
    • 9.5.1. Ideal Age
    • 9.5.2. Chlorofluorocarbons
• 10. Forcing
  • 10.1. Penetration of Solar Radiation
    • 10.1.1. Jerlov Water Type
    • 10.1.2. Absorption Based on Chlorophyll
    • 10.1.3. Diurnal Cycle
  • 10.2. Ice Runoff
  • 10.3. Tracer Fluxes and Averaging Time Steps
• 11. Parallel Implementation
  • 11.1. Domain Decomposition
    • 11.1.1. Cartesian Distribution
    • 11.1.2. Rake Distribution
    • 11.1.3. Space-filling Curve Distribution
  • 11.2. Parallel I/O
• 12. References