Organization of the code

The MOM6 source code is divided into a tree of directories (folders) to group related code (e.g. src/core) or similar modules (e.g. src/parameterizations/vertical).

The highest level of directories are:

src/: Code underneath src/ is always required and compiled.
config_src/: Under config_src are various drivers and memory configuration sources that can only be compiled in limited configurations. See config_src/
pkg/: Packages (source code) from other sources/parties only some of which might be used. We include the entire package as a sub-module but use symbolic-links to extract the parts the MOM6 uses.
docs/: The directory that contains this documentation, namely that beyond the in-code API documentation. Some of the files are configuration files needed for running doxygen and sphinx. Most documentation in this folder is in the form of reStructuredText (.rst) files.
.testing/: A directory for running tests on MOM6. These are some of the smaller/simpler examples that MOM6 can run out of the box, without large netCDF files.

The directory tree is:

MOM6
+-- config_src
|   +-- drivers
|   |   +-- FMS_cap                  # GFDL coupler interface
|   |   +-- ice_solo_driver          # Ice-only standalone
|   |   +-- nuopc_cap                # NUOPC/CESM coupling
|   |   +-- solo_driver              # Ocean-only standalone
|   |   +-- timing_tests             # Performance benchmarks
|   |   +-- unit_tests               # Unit test executables
|   +-- external                     # Null hooks for optional components
|   +-- infra                        # Framework interface (FMS1/FMS2 wrappers)
|   |   +-- FMS1                     # FMS1 wrappers
|   |   +-- FMS2                     # FMS2 wrappers
|   +-- memory
|       +-- dynamic_nonsymmetric
|       +-- dynamic_symmetric
+-- docs
+-- pkg
|   +-- CVMix-src                    # Community Vertical Mixing
|   +-- GSW-Fortran                  # TEOS-10 Gibbs Seawater
+-- src
|   +-- ALE                          # Vertical remapping/regridding
|   +-- core                         # Dynamical core
|   +-- diagnostics                  # Diagnostic calculations
|   +-- equation_of_state            # EOS implementations
|   +-- framework                    # Infrastructure (diagnostics, I/O, parsing, domains)
|   +-- ice_shelf                    # Ice shelf dynamics
|   +-- initialization               # Grid/state initialization
|   +-- ocean_data_assim             # Data assimilation
|   +-- parameterizations
|   |   +-- lateral                  # Lateral parameterizations
|   |   +-- vertical                 # Vertical mixing
|   +-- tracer                       # Tracer transport and specific tracers
|   +-- user                         # Idealized configuration initialization
+-- .testing
    +-- tc0                          # Unit tests
    +-- tc1 / tc1.a / tc1.b          # Benchmark configurations
    +-- tc2 / tc2.a                  # ALE with tides / sigma-coordinate
    +-- tc3                          # Open boundary conditions
    +-- tc4                          # Sponges and I/O initialization

config_src/

memory/dynamic_nonsymmetric/, memory/dynamic_symmetric/: One or none of config_src/memory/dynamic_nonsymmetric/ or config_src/memory/dynamic_symmetric/ can be included at compile time. If neither is used then a MOM_memory.h file specific to the model configuration must be present - this is known as a “static” compile with fixed layout and domain shape.
external/: Contains “null” modules providing the API to optional components to use with MOM6. Currently available are ocean data assimilation (ODA_hooks) and the GFDL ocean bio-geochemistry model (GFDL_ocean_BGC). When building MOM6 in stand-alone ocean-only mode these modules should be compiled in. To use the actual ODA or BGC, add the appropriate source to the search paths .
infra/: Contains MOM6-specific thin wrappers to all of the FMS types and routines that are used by MOM6. The code in this directory should only be called by the infrastructure-agnostic code in src/framework.
drivers/ice_solo_driver/: This driver produces a stand-alone ice-shelf executable that steps the ice-shelf model without any ocean dynamics.
drivers/solo_driver/: This driver produces an ocean-only executable with no other coupled components (no sea-ice, no atmosphere, etc.). It is the simplest configuration and fastest to compile and thus used for a lot of testing.
drivers/FMS_cap/: This driver provides an interface for the GFDL coupler to call. It requires compiling MOM6 along with at least a sea-ice model and possibly all other components in a coupled model.
drivers/nuopc_cap/: This driver provides a NUOPC-compliant interface for coupling MOM6 within CESM or other NUOPC-based coupled systems.
drivers/unit_tests/: Unit test executables for testing individual MOM6 components in isolation.
drivers/timing_tests/: Performance benchmark executables for profiling MOM6 routines.

src/

core/: The dynamical core modules (except for the ALE remapping/regridding).
ALE/: Functions for remapping from between arbitrary vertical grids and generating grids.
diagnostics/: Some diagnostic calculations
equation_of_state/: Various equations of state (linear; Wright, 1997; TEOS-10; …).
framework/: Low-level wrappers for communication, diagnostics management, parsing of input parameters, time management, CPU clocks.
ice_shelf/: Ice shelf dynamics and thermodynamics.
initialization/: Initialization of the horizontal grid, vertical coordinate, and the state.
ocean_data_assim/: Data assimilation interfaces.
parameterizations/lateral: Sub-grid scale parameterization with fluxes primarily oriented in the lateral direction.
parameterizations/vertical: Sub-grid scale parameterization with fluxes primarily oriented in the vertical direction, including the top and bottom boundary layer schemes.
tracer/: Everything to do with tracers, including advection and isopycnal stirring.
user/: Initialization and forcing for specific (coded) configurations.