Alphabetical list of page titles

• About this document ...
• Adjoint (1.3.9 )
• Adjoint dump & restart - divided adjoint (DIVA) (5.5 )
• Advection of momentum (2.13.1 )
• Annotated call tree for MITgcm and WRAPPER (4.4.1 )
• Appendix ATMOSPHERE (1.4 )
• Appendix OCEAN (1.5 )
• Appendix:OPERATORS (1.6 )
• Atmosphere (1.3.2 )
• Atmospheric Intermediate Physics: AIM (6.10 )
• Automated testing (3.17.2 )
• Automatic Differentiation (5. )
• Baroclinic Gyre MITgcm Example (3.9 )
• Barotropic Gyre MITgcm Example (3.8 )
• Basic assumptions for the calendar tool (8.3.1 )
• Binary input data (3.14.2 )
• Boundary forced internal waves (1.2.5 )
• Build and run the model (3.14.5 )
• Building/compiling the code elsewhere (3.16.1 )
• Building MITgcm (3.5 )
• Building the AD code (5.2.2 )
• Building with MPI (3.16.3 )
• Bulk Formula Package (6.8 )
• Calendar dates and time intervals (8.3.3 )
• Centennial Time Scale Tracer Injection (3.15 )
• Centered fourth order advection (2.16.3 )
• Centered second order advection-diffusion (2.16.1 )
• C grid staggering of variables (2.10.3 )
• Code configuration (3.14.3 )
• Code Configuration (3.15.4 )
• Code Configuration (3.8.3 )
• Code Configuration (3.9.4 )
• Code configuration (5.3.2 )
• Code configuration (5.4.2 )
• Code description (5.4.1 )
• Communication mechanisms (4.2.5 )
• Communication primitives (4.2.8 )
• Comparison of advection schemes (2.18 )
• Compiling the model and its adjoint (5.3.3 )
• Computational domain, geometry and time-discretization (3.16.5 )
• Configuration (3.14.1 )
• Configuration and setup (3.16.4 )
• Continuity and horizontal pressure gradient terms (2.11 )
• Continuous equations in `r' coordinates (1.3 )
• Controlling communication (4.3.3 )
• Convection and mixing over topography (1.2.4 )
• Coordinate systems (1.6.1 )
• Coriolis terms (2.13.2 )
• Coriolis terms (2.14.3 )
• Coupler for mapping between AIM and ocean (6.13 )
• Coupling interface for Atmospheric Intermediate code (6.12 )
• Crank-Nickelson barotropic time stepping (2.9.1 )
• Curvature metric terms (2.13.3 )
• Customizing MITgcm (3.16 )
• Derivation of discrete energy conservation (2.13.7 )
• Diagnostics and tools (7. )
• DIC Package (6.4 )
• Directory structure of model examples (3.4.2 )
• Discrete Numerical Configuration (3.10.2 )
• Discrete Numerical Configuration (3.11.2 )
• Discrete Numerical Configuration (3.12.2 )
• Discrete numerical configuration (3.13.3 )
• Discrete Numerical Configuration (3.15.3 )
• Discrete Numerical Configuration (3.8.2 )
• Discrete Numerical Configuration (3.9.3 )
• Discretization and Algorithm (2. )
• Distributed memory communication (4.2.7 )
• Do's and Don'ts (6.21.3 )
• Do's and Don'ts (6.4.3 )
• Equation of state (3.16.6 )
• Equations of motion for the ocean (1.5.1 )
• Equations solved (3.13.2 )
• Equations Solved (3.8.1 )
• Equations solved (3.9.2 )
• Estimating Resource Requirements (4.4.3 )
• exch2: Extended Cubed Sphere Topology (6.18 )
• exch2, SIZE.h, and Multiprocessing (6.18.4 )
• Experiment Configuration (3.10.3 )
• Experiment Configuration (3.11.3 )
• Experiment Configuration (3.12.3 )
• Experiment configuration (3.13.5 )
• Explicit time-stepping: Adams-Bashforth (2.4 )
• FFT Filtering Code (6.20 )
• Finding the pressure field (1.3.6 )
• First order upwind advection (2.16.4 )
• Flux-form momentum equations (2.13 )
• Forcing/dissipation (1.3.7 )
• Format of calendar dates (8.3.2 )
• Forward or direct sensitivity (5.1.1 )
• Full list of model examples (3.4.1 )
• GCHEM Package (6.21 )
• General features (8.4.1 )
• General setup (5.2.1 )
• Generating Topology Files for exch2 (6.18.3 )
• Generic Advection/Diffusion (6.9 )
• Gent/McWiliams/Redi SGS Eddy parameterization (6.3 )
• Getting Started with MITgcm (3. )
• Global atmosphere: `Held-Suarez' benchmark (1.2.1 )
• Global ocean circulation (1.2.3 )
• Global Ocean MITgcm Exmaple (3.10 )
• Global state estimation of the ocean (1.2.7 )
• GM parameterization (6.3.2 )
• Gradient of Bernoulli function (2.14.5 )
• Gravity Plume On a Continental Slope (3.14 )
• Grid initialization and data (2.10.4 )
• Griffies Skew Flux (6.3.3 )
• Held-Suarez Atmosphere MITgcm Example (3.12 )
• Horizontal dissipation (2.14.6 )
• Horizontal dissipation (2.14.7 )
• Horizontal grid (2.10.5 )
• Hydrographic constraints (8.1.2 )
• Hydrostatic balance (2.12 )
• Hydrostatic Primitive Equations for the Atmosphere in pressurecoordinates (1.4.1 )
• Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic andNon-hydrostatic forms (1.3.4 )
• Illustrations of the model in action (1.2 )
• Implicit time-stepping: backward method (2.5 )
• Interface with ECCO (8. )
• Introduction (1.1 )
• Introduction (3.15.1 )
• Introduction (5.5.1 )
• Introduction (6.18.1 )
• Introduction (6.19.1 )
• Introduction (6.21.1 )
• Introduction (6.4.1 )
• Introduction (6.9.1 )
• Invoking exch2 (6.18.2 )
• Key Routines (6.18.6 )
• Key subroutines and parameters (6.21.2 )
• Key subroutines and parameters (6.4.2 )
• Key subroutines, parameters and files (6.10.1 )
• Key subroutines, parameters and files (6.12.1 )
• Key subroutines, parameters and files (6.13.1 )
• Key subroutines, parameters and files (6.14.1 )
• Key subroutines, parameters and files (6.17.1 )
• Key subroutines, parameters and files (6.20.1 )
• Key subroutines, parameters and files (6.9.2 )
• Key Variables (6.18.5 )
• Kinematic Boundary conditions (1.3.1 )
• Kinetic energy (2.14.2 )
• Land package (6.11 )
• Lateral dissipation (2.13.5 )
• Linear advection schemes (2.16 )
• Looking at the output (3.6.2 )
• Machine model parallelism (4.2.4 )
• MDSIO (6.16 )
• Measuring and Characterizing Performance (4.4.2 )
• Memory architecture (4.2.9 )
• Method 1 - Checkout from CVS (3.2.1 )
• Method 2 - Tar file download (3.2.2 )
• MITgcm Example Experiments (3.4 )
• MITgcm execution under WRAPPER (4.4 )
• MNC Internals (6.15.2 )
• Model and directory structure (3.3 )
• Model parameters (3.14.4 )
• Model Uses (9. )
• Momentum equations (3.16.7 )
• Multi-dimensional advection (2.17.4 )
• NetCDF I/O Integration: MNC (6.15 )
• Non-hydrostatic formulation (2.8 )
• Non-hydrostatic metric terms (2.13.4 )
• Non-linear advection schemes (2.17 )
• Non-linear free-surface (2.9.2 )
• Notation (2.10.1 )
• Number of iterations vs. number of simulations (8.4.3 )
• Numerical stability criteria and other considerations (3.13.4 )
• Obtaining the code (3.2 )
• Ocean (1.3.3 )
• Ocean biogeochemical cycles (1.2.8 )
• Ocean gyres (1.2.2 )
• Ocean vertical mixing - the nonlocal K-profile parameterization scheme KPP (6.5 )
• Output files (3.6.1 )
• Overall architectural goals (4.1 )
• Overview (3.10.1 )
• Overview (3.11.1 )
• Overview (3.12.1 )
• Overview (3.13.1 )
• Overview (3.15.2 )
• Overview (3.9.1 )
• Overview of MITgcm (1. )
• Overview of the experiment (5.3.1 )
• Package Activation (6.1.2 )
• Package Coding Standards (6.2 )
• Package Inclusion/Exclusion (6.1.1 )
• Package Reference (6.3.8 )
• Packages are Not Libraries (6.2.1 )
• Parameter sensitivity using the adjoint of MITgcm (1.2.6 )
• P coordinate Global Ocean MITgcm Example (3.11 )
• Physical Parameterization and Packages (6. )
• Pre-processing software (7.2 )
• Pressure method with implicit linear free-surface (2.3 )
• Pressure method with rigid-lid (2.2 )
• Recipe 1: single processor (5.5.2 )
• Recipe 2: multi processor (MPI) (5.5.3 )
• Redi scheme: Isopycnal diffusion (6.3.1 )
• Reference Material (6.21.4 )
• Reference Material (6.4.4 )
• Relative vorticity (2.14.1 )
• Reverse or adjoint sensitivity (5.1.2 )
• Running MITgcm (3.6 )
• Running the example (3.13.6 )
• Running The Example (3.9.5 )
• RW Basic binary I/O utilities (6.19 )
• Sea Ice Package: ``seaice'' (6.7 )
• Sea surface height from TOPEX/Poseidon and ERS-1/2 altimetry (8.1.1 )
• Second order flux limiters (2.17.1 )
• Sensitivity of Air-Sea Exchange to Tracer Injection Site (5.3 )
• Shapiro Filter (2.19 )
• Shared memory communication (4.2.6 )
• Shear terms (2.14.4 )
• Short routine description (8.3.6 )
• Simulation controls (3.16.9 )
• Simulations of laboratory experiments (1.2.9 )
• Simulation state monitoring toolkit (6.17 )
• Software Architecture (4. )
• Solution strategy (1.3.5 )
• Some basic algebra (5.1 )
• Spatial discretization of the dynamical equations (2.10 )
• Specifying a domain decomposition (4.3.1 )
• Staggered baroclinic time-stepping (2.7 )
• Starting the code (4.3.2 )
• Storing vs. recomputation in reverse mode (5.1.3 )
• Summary (4.2.10 )
• Summary (8.2.1 )
• Supporting hardware neutrality (4.2.2 )
• Surface Driven Convection (3.13 )
• Synchronous time-stepping: variables co-located in time (2.6 )
• Tapering and stability (6.3.5 )
• Tapering: Danabasoglu and McWilliams, J. Clim. 1995 (6.3.6 )
• Tapering: Large, Danabasoglu and Doney, JPO 1997 (6.3.7 )
• Target hardware (4.2.1 )
• Testing (3.17 )
• The AD build process in detail (5.2.3 )
• The calendar package cal (8.3 )
• The control variables (independent variables) (5.2.5 )
• The cost function (dependent variable) (5.2.4 )
• The ECCO state estimation cost function DRAFT!!! (8.1 )
• The external forcing package exf (8.2 )
• The finite volume method: finite volumes versus finite difference (2.10.2 )
• The gradient check package (5.4 )
• The individual calendars (8.3.5 )
• The line search optimisation algorithm (8.4 )
• The online vs. offline version (8.4.2 )
• Thermodynamic Sea Ice Package: ``thsice'' (6.6 )
• Third order direct space time (2.17.2 )
• Third order direct space time with flux limiting (2.17.3 )
• Third order upwind bias advection (2.16.2 )
• Time-stepping (2.1 )
• Time-stepping of tracers: ABII (2.15.1 )
• TLM and ADM generation in general (5.2 )
• Toolkit for building couplers (6.14 )
• Topography: partially filled cells (2.10.7 )
• Tracer equations (2.15 )
• Tracer equations (3.16.8 )
• Tutorials (3.7 )
• Using genmake2 (3.16.2 )
• Using MITgcm Packages (6.1 )
• Using MNC (6.15.1 )
• Using testreport (3.17.1 )
• Using the calendar together with MITgcm (8.3.4 )
• Using the WRAPPER (4.3 )
• Utilities supplied with the model (7.1 )
• utils/matlab (7.1.2 )
• utils/scripts (7.1.1 )
• Variable (6.3.4 )
• Variants on the Free Surface (2.9 )
• Vector invariant form (1.3.8 )
• Vector invariant momentum equations (2.14 )
• Vertical dissipation (2.13.6 )
• Vertical dissipation (2.14.8 )
• Vertical grid (2.10.6 )
• Where to find information (3.1 )
• WRAPPER (4.2 )
• WRAPPER machine model (4.2.3 )

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