#TOC Entry            REPLACE               PATTERN
#The following are used to preformat the table of contents
Installation          _INSTALL_             CMIREDIR:getting_started_with_mitgcm:
 Download             _DOWNLOAD_            CMIREDIR:obtainingCode:
 Compilation          _COMPILATION_         CMIREDIR:buildingCode:
 Running the model    _RUNNING_             CMIREDIR:runModel:
 Customization        _CUSTOMIZATION_       CMIREDIR:customizing_mitgcm:
Tutorials             _TUTORIALS_           CMIREDIR:eg-baro:
 Barotropic Gyre      _BAROTROPIC_          CMIREDIR:eg-baro:
 Baroclinic Gyre      _BAROCLINIC_          CMIREDIR:eg-fourlayer:
 Global Ocean         _GLOBAL_              CMIREDIR:eg-global:
 Held Suarez Atmosphe _HELD_                CMIREDIR:eg-hs:
 Open Ocean Convectio _OPEN_                CMIREDIR:eg-bconv:
 Shelf Convection     _SHELF_               CMIREDIR:eg-gravityplume:
 Tracer injection     _TRACERINJ_           CMIREDIR:eg-simple-tracer:
# Parallel Global Ocea _PARALLEL_            ^<TITLE>5. Tutorial II - Parallelism
 Tracer Sensitivity   _TRACER_              CMIREDIR:eg-simple-tracer:
Documentation         _DOCUMENTATION_       ^<TITLE>1. Overview of MITgcm
 MITgcm in Action     _MITGCM_              ^<TITLE>1.* Introduction
 Continuous formulati _CONTINUOUS_          ^<TITLE>1.* Continuous
 Numerical Algorithm  _NUMERICAL_           ^<TITLE>2. Discretization and Algorithm
 Software Architectur _SOFTWARE_            ^<TITLE>4. Software Architecture
 Automatic Differenti _AUTOMATIC_           ^<TITLE>5. Automatic Differentiation
 Optional Packages    _OPTIONAL_            ^<TITLE>6. Physical
 Diagnostics          _DIAGNOSTICS_         CMIREDIR:processing_tools:
 Interface to ECCO    _INTERFACE_           ^<TITLE>8. Interface with ECCO
#The following are used to preformat the front_page
Atmosphere            _ATMOSPHERE_          CMIREDIR:atmospheric_example:
Oceanic               _OCEANIC_              ^<TITLE>1.* Global ocean circulation
Non-Hydrostatic       _NONHYDROSTATIC_       ^<TITLE>1.* Convection and mixing over topography
Horizontal Orthogonal _HORIZONTAL_           ^<TITLE>2.* Vector invariant momentum equations
Finite Volume         _FINITE_               fig:finite-volumes
Physical Parameteriz  _PHYSICAL_             ^<TITLE>6. Physical
Tangent Linear        _TANGENT_              ^<TITLE>1.* Parameter sensitivity using the adjoint of MITgcm
Domain Decomposition  _DOMAIN_               The three level domain decomposition
#Documentation - see above
#Download - see above
#Tutorials see above
#Browse Code - see above
#The following are used to preformat the Quicklinks menu
AD                    _AD_                   ^<TITLE>5. Automatic Differentiation
Adjoint               _ADJOINT_              ^<TITLE>5.1.2 Reverse or adjoint sensitivity
Atmospheric           _ATMOSPHERIC_          ^<TITLE>1.4.1 Hydrostatic
CVS                   _CVS_                 ^<TITLE>3.2 Obtaining the code
Flux-form             _FLUX_                 ^<TITLE>2.13 Flux-form momentum equations
GM/Redi               _GM_                   CMIREDIR:gmredi:
KPP                   _KPP_                  CMIREDIR:package_kpp:
Linear Advection      _LINEAR_               ^<TITLE>2.16 Linear advection schemes
MATLAB                _MATLAB_               ^<TITLE>7.1.2 utils/matlab
Nonlinear Advection   _NONLINEAR_            ^<TITLE>2.17 Non-linear advection schemes
Ocean Equations       _OCEANEQ_              ^<TITLE>1.5.1 Equations of motion for the ocean
Operators             _OPERATORS_            ^<TITLE>1.6 Appendix:OPERATORS
#Runtime Diagnostics  _DIAGNOSTICS           ^<TITLE>7. Diagnostics and tools
Starting/Restarting   _STARTING_             CMIREDIR:runModel:
Tangent-linear        _TANGENT_              ^<TITLE>5.1.1 Forward or direct
Time-stepping         _TIMESTEP_             ^<TITLE>2.1 Time-stepping
MPI                   _MPI_                  ^<TITLE>4.2.7 Distributed memory
Threads               _THREADS_              ^<TITLE>4.2.6 Shared memory
Vector Invariant      _VECTOR_               ^<TITLE>2.14 Vector invariant momentum equations
WRAPPER               _WRAPPER_              ^<TITLE>4.2 WRAPPER