Contents

• Introduction
  • What is GOTM?
  • The idea behind GOTM
  • How to read the documentation
  • Acknowledgements
  
  
• The GOTM main program
  • Introduction
  • GOTM -- the main program
  • Module gotm -- the general framework
  
  
• The mean flow model
  • Introduction
  • Module Mean Flow
  • The vertical grid
  • The Coriolis rotation
  • The U-momentum equation
  • The V-momentum equation
  • The external pressure-gradient
  • The internal pressure-gradient
  • The vertical friction
  • The temperature equation
  • The salinity equation
  • The buoyancy equation
  • Calculation of the vertical shear
  • Calculation of the stratification
  • Convective adjustment
  
  
• The turbulence model
  • Introduction
  • Second-order models
  • Algebraic Models
  • Explicit models for vertical shear and stratification
  • Parameter conversion for other models
  • Numerics
  • Module turbulence: its all in here ...
  • Update turbulence production
  • Update dimensionless alpha's
  • Update time scale ratio
  • The dynamic k-equation
  • The dynamic q2/2-equation
  • The dynamic kb-equation
  • The dynamic q2l-equation
  • The dynamic epsilon-equation
  • The dynamic psi-equation
  • The algebraic k-equation
  • The algebraic kb-equation
  • Some algebraic length-scale relations
  • The algebraic epsilonb-equation
  • The algebraic velocity variances
  • Algebraic length-scale from ISPRAMIX
  • Algebraic length-scale with two master scales
  • The non-local, exact weak-equilibrium stability function
  • The non-local, approximate weak-equilibrium stability function
  • The local, weak-equilibrium stability functions
  • The quasi-equilibrium stability functions
  • The Munk and Anderson (1948) stability function
  • The Schumann and Gerz (1995) stability function
  • Flux Richardson number stability function
  • Calculate c3 from steady-state Richardson number
  • Calculate steady-state Richardson number from c3
  • Update internal wave mixing
  • TKE flux from wave-breaking
  • Module kpp: the KPP-turbulence model
  • Printing GOTM library version
  
  
• Air-Sea interaction
  • Introduction
  • Module airsea -- atmospheric fluxes
  • Module airsea_variables
  • Calculate the humidity
  • Calculate the long-wave back radiation
  • Wrapper for air-sea fluxes calculations
  • Heat and momemtum fluxes according to Kondo
  • Heat and momentum fluxes according to Fairall et al.
  • Calculate the short-wave radiation
  
  
• Working with observed data in GOTM
  • Module observations -- the 'real' world
  
  
• Saving the results
  • Module output -- saving the results
  • Module asciiout -- saving the results in ASCII
  • Module ncdfout -- saving the results in NetCDF
  
  
• Utilities
  • Introduction
  • Module util -- parameters and interfaces for utilities
  • Diffusion schemes -- grid centers
  • Diffusion schemes -- grid faces
  • Advection schemes -- grid centers
  • Lagrangian particle random walk
  • Module mtridiagonal -- solving the system
  • Module eqstate -- the equation of state
  • Interpolate from observation space to model grid
  • Convert between buoyancy fluxes and others
  • Module time -- keep control of time
  • Lagrangian particle random walk
  • General ODE solver
  
  
• Biogeochemical models
  • Mathematical formulation
  • Numerical aspects
  • Computational aspects
  • Module bio -- biological model
  • Module bio_var -- declaration of biological variables
  • Module bio_template -- template bio model
  • Module bio_npzd -- NPZD biogeochemical model
  • Module bio_iow -- IOW biogeochemical model ERGOM
  • Module bio_sed -- simple suspended matter model
  • Module bio_fasham -- Fasham et al. biological model
  • Module bio_rolm -- Yakushev biogeochemical model ROLM
  • Storing the results
  
  
• Extra features
  • Module seagrass -- sea grass dynamics
  
  
• Running GOTM in a GUI
  • Introduction
  • Software required
  
  
• GOTM scenarios
  • Idealised scenarios
  • Shelf sea scenarios
  • Open ocean scenarios
  • Lake scenarios
  • Biogeochemical scenarios
  
  
• Bibliography