Here is a list of all modules with brief descriptions:

Nadjustment_initialization	The module configures the model for the geostrophic adjustment test case
Nadvection_test_tracer
Natmos_ocean_fluxes_mod
Nbaroclinic_zone_initialization	Initial conditions for an idealized baroclinic zone
Nbenchmark_initialization
Nbfb_initialization
Nbfb_surface_forcing
Nboundary_impulse_tracer	Implements a boundary impulse response tracer to calculate Green's functions
Ncircle_obcs_initialization	The module configures the model for the "circle_obcs" experiment. circle_obcs = Test of Open Boundary Conditions for an SSH anomaly
Ncoord_adapt	Regrid columns for the adaptive coordinate
Ncoord_hycom	Regrid columns for the HyCOM coordinate
Ncoord_rho	Regrid columns for the continuous isopycnal (rho) coordinate
Ncoord_sigma	Regrid columns for the sigma coordinate
Ncoord_slight	Regrid columns for the SLight coordinate
Ncoord_zlike	Regrid columns for a z-like coordinate (z-star, z-level)
Ncoupler_types_mod
Ncoupler_util
Ndense_water_initialization	Initialization routines for the dense water formation and overflow experiment
Ndome2d_initialization
Ndome_initialization	The module configures the model for the "DOME" experiment. DOME = Dynamics of Overflows and Mixing Experiment
Ndome_tracer
Nexternal_gwave_initialization	The module configures the model for the "external_gwave" experiment. external_gwave = External Gravity Wave
Nideal_age_example
Nisomip_initialization	The module configures the ISOMIP test case
Nisomip_tracer	This module contains the routines used to set up and use a set of (one for now) dynamically passive tracers. For now, just one passive tracer is injected in the sponge layer. Set up and use passive tracers requires the following: (1) register_ISOMIP_tracer (2)
Nkelvin_initialization
Nlock_exchange_initialization	The module configures the model for the "lock_exchange" experiment. lock_exchange = A 2-d density driven hydraulic exchange flow
Nmeso_surface_forcing
Nmidas_vertmap
Nmom	This is the main routine for MOM
Nmom_ale	This module contains the main regridding routines. Regridding comprises two steps: (1) Interpolation and creation of a new grid based on target interface densities (or any other criterion). (2) Remapping of quantities between old grid and new grid. Original module written by Laurent White, 2008.06.09
Nmom_ale_sponge	This module contains the routines used to apply sponge layers when using the ALE mode. Applying sponges requires the following: (1) initialize_ALE_sponge (2) set_up_ALE_sponge_field (tracers) and set_up_ALE_sponge_vel_field (vel) (3) apply_ALE_sponge (4) init_ALE_sponge_diags (not being used for now) (5) ALE_sponge_end (not being used for now)
Nmom_barotropic
Nmom_boundary_update	Controls where open boundary conditions are applied
Nmom_bulk_mixed_layer
Nmom_checksum_packages
Nmom_checksums
Nmom_coms
Nmom_constants
Nmom_continuity	Solve the layer continuity equation
Nmom_continuity_ppm	Solve the layer continuity equation using the PPM method for layer fluxes
Nmom_controlled_forcing	* By Robert Hallberg, July 2011 * This program contains the subroutines that use control-theory * to adjust the surface heat flux and precipitation, based on the * time-mean or periodically (seasonally) varying anomalies from the * observed state. The techniques behind this are described in * Hallberg and Adcroft (2011, in prep.). * Macros written all in capital letters are defined in MOM_memory.h. * A small fragment of the grid is shown below: * j+1 x ^ x ^ x At x: q * j+1 > o > o > At ^: v, tauy * j x ^ x ^ x At >: u, taux * j > o > o > At o: h, fluxes. * j-1 x ^ x ^ x * i-1 i i+1 At x & ^: * i i+1 At > & o: * The boundaries always run through q grid points (x). *
Nmom_coord_initialization	Initializes fixed aspects of the related to its vertical coordinate
Nmom_coriolisadv	Accelerations due to the Coriolis force and momentum advection
Nmom_cpu_clock
Nmom_cvmix_shear	Interface to CVMix interior shear schemes
Nmom_debugging
Nmom_diabatic_aux
Nmom_diabatic_driver	This routine drives the diabatic/dianeutral physics for MOM
Nmom_diag_manager_wrapper	A simple (very thin) wrapper for register_diag_field to avoid a compiler bug with PGI
Nmom_diag_mediator
Nmom_diag_remap	This module is used for runtime remapping of diagnostics to z star, sigma and rho vertical coordinates. It defines the diag_remap_ctrl type which represents a remapping of diagnostics to a particular vertical coordinate. The module is used by the diag mediator module in the following way: 1) _init() is called to initialise a diag_remap_ctrl instance. 2) _configure_axes() is called to read the configuration file and set up the vertical coordinate / axes definitions. 3) _get_axes_info() returns information needed for the diag mediator to define new axes for the remapped diagnostics. 4) _update() is called periodically (whenever h, T or S change) to either create or update the target remapping grids. 5) _do_remap() is called from within a diag post() to do the remapping before the diagnostic is written out
Nmom_diag_to_z
Nmom_diag_vkernels	Provides kernels for single-column interpolation, re-integration (re-mapping of integrated quantities) and intensive-variable remapping in the vertical
Nmom_diagnostics
Nmom_diapyc_energy_req
Nmom_diffconvection
Nmom_document
Nmom_domains
Nmom_dyn_horgrid
Nmom_dynamics_legacy_split
Nmom_dynamics_split_rk2	Time step the adiabatic dynamic core of MOM using RK2 method
Nmom_dynamics_unsplit
Nmom_dynamics_unsplit_rk2
Nmom_energetic_pbl
Nmom_entrain_diffusive
Nmom_eos	Provides subroutines for quantities specific to the equation of state
Nmom_eos_linear
Nmom_eos_nemo
Nmom_eos_teos10
Nmom_eos_unesco
Nmom_eos_wright
Nmom_error_handler
Nmom_file_parser
Nmom_fixed_initialization	Initializes fixed aspects of the model, such as horizontal grid metrics, topography and Coriolis
Nmom_forcing_type	This module implements boundary forcing for MOM6
Nmom_generic_tracer
Nmom_geothermal
Nmom_get_input
Nmom_grid	Provides the ocean grid type
Nmom_grid_initialize
Nmom_hor_index	Defines the horizontal index type (hor_index_type) used for providing index ranges
Nmom_hor_visc
Nmom_ice_shelf	Implements the thermodynamic aspects of ocean / ice-shelf interactions,
Nmom_ice_shelf_initialize
Nmom_int_tide_input
Nmom_interface_heights	The module calculates interface heights, including free surface height
Nmom_internal_tides
Nmom_intrinsic_functions
Nmom_io	This module contains I/O framework code
Nmom_isopycnal_slopes	Calculations of isoneutral slopes and stratification
Nmom_kappa_shear
Nmom_kpp	Provides the K-Profile Parameterization (KPP) of Large et al., 1994, via CVMix
Nmom_lateral_mixing_coeffs	Variable mixing coefficients
Nmom_legacy_barotropic
Nmom_meke	Implements the Mesoscale Eddy Kinetic Energy framework
Nmom_meke_types
Nmom_mixed_layer_restrat	Parameterization of mixed layer restratification by unresolved mixed-layer eddies
Nmom_neutral_diffusion	A column-wise toolbox for implementing neutral diffusion
Nmom_obsolete_diagnostics	Provides a mechanism for recording diagnostic variables that are no longer valid, along with their replacement name if appropriate
Nmom_obsolete_params	Methods for testing for, and list of, obsolete run-time parameters
Nmom_ocmip2_cfc
Nmom_ocmip2_co2calc_mod
Nmom_offline_aux	Contains routines related to offline transport of tracers. These routines are likely to be called from the MOM_offline_main module
Nmom_offline_main	The routines here implement the offline tracer algorithm used in MOM6. These are called from step_offline Some routines called here can be found in the MOM_offline_aux module
Nmom_opacity
Nmom_open_boundary	Controls where open boundary conditions are applied
Nmom_pointaccel
Nmom_pressureforce	A thin wrapper for Boussinesq/non-Boussinesq forms of the pressure force calculation
Nmom_pressureforce_afv	Analytically integrated finite volume pressure gradient
Nmom_pressureforce_mont	Provides the Montgomery potential form of pressure gradient
Nmom_regridding	Generates vertical grids as part of the ALE algorithm
Nmom_regularize_layers
Nmom_remapping	Provides column-wise vertical remapping functions
Nmom_restart
Nmom_safe_alloc
Nmom_set_diffusivity
Nmom_set_visc
Nmom_shared_initialization	Code that initializes fixed aspects of the model grid, such as horizontal grid metrics, topography and Coriolis, and can be shared between components
Nmom_shortwave_abs
Nmom_spatial_means
Nmom_sponge
Nmom_state_initialization	Initialize state variables, u, v, h, T and S
Nmom_string_functions
Nmom_sum_output
Nmom_surface_forcing
Nmom_tfreeze
Nmom_thickness_diffuse	Thickness diffusion (or Gent McWilliams)
Nmom_tidal_forcing
Nmom_time_manager
Nmom_tracer_advect	This program contains the subroutines that advect tracers along coordinate surfaces
Nmom_tracer_diabatic	This module contains routines that implement physical fluxes of tracers (e.g. due to surface fluxes or mixing). These are intended to be called from call_tracer_column_fns in the MOM_tracer_flow_control module
Nmom_tracer_flow_control
Nmom_tracer_hor_diff	Main routine for lateral (along surface or neutral) diffusion of tracers
Nmom_tracer_registry	This module contains the tracer_registry_type and the subroutines that handle registration of tracers and related subroutines. The primary subroutine, register_tracer, is called to indicate the tracers advected and diffused
Nmom_tracer_z_init
Nmom_transcribe_grid
Nmom_unit_tests	Invokes unit tests in all modules that have them
Nmom_variables
Nmom_vert_friction	Implements vertical viscosity (vertvisc)
Nmom_verticalgrid
Nmom_wave_speed	Routines for calculating baroclinic wave speeds
Nmom_wave_structure
Nmom_write_cputime
Nocean_model_mod
Noil_tracer
Np1m_functions
Np3m_functions
Npcm_functions
Nphillips_initialization	By Robert Hallberg, April 1994 - June 2002 * This subroutine initializes the fields for the simulations. * The one argument passed to initialize, Time, is set to the * current time of the simulation. The fields which are initialized * here are: * u - Zonal velocity in m s-1. * v - Meridional velocity in m s-1. * h - Layer thickness in m. (Must be positive.) * D - Basin depth in m. (Must be positive.) * f - The Coriolis parameter, in s-1. * g - The reduced gravity at each interface, in m s-2. * Rlay - Layer potential density (coordinate variable) in kg m-3. * If ENABLE_THERMODYNAMICS is defined: * T - Temperature in C. * S - Salinity in psu. * If SPONGE is defined: * A series of subroutine calls are made to set up the damping * rates and reference profiles for all variables that are damped * in the sponge. * Any user provided tracer code is also first linked through this * subroutine. * Forcing-related fields (taux, tauy, buoy, ustar, etc.) are set * in MOM_surface_forcing.F90. * These variables are all set in the set of subroutines (in this * file) Phillips_initialize_thickness, Phillips_initialize_velocity, * Phillips_initialize_topography and Phillips_initialize_sponges * that seet up fields that are specific to the Phillips instability * test case. * Macros written all in capital letters are defined in MOM_memory.h. * A small fragment of the grid is shown below: * j+1 x ^ x ^ x At x: q, f * j+1 > o > o > At ^: v, tauy * j x ^ x ^ x At >: u, taux * j > o > o > At o: h, D, buoy, tr, T, S, ustar * j-1 x ^ x ^ x * i-1 i i+1 At x & ^: * i i+1 At > & o: * The boundaries always run through q grid points (x). *
Nplm_functions
Npolynomial_functions
Nppm_functions	Provides functions used with the Piecewise-Parabolic-Method in the vertical ALE algorithm
Npqm_functions
Npseudo_salt_tracer
Nregional_dyes
Nregrid_consts	Contains constants for interpreting input parameters that control regridding
Nregrid_defs
Nregrid_edge_slopes
Nregrid_edge_values
Nregrid_interp
Nregrid_solvers
Nrossby_front_2d_initialization	Initial conditions for the 2D Rossby front test
Nscm_cvmix_tests	Initial conditions and forcing for the single column model (SCM) CVmix test set
Nscm_idealized_hurricane	Initial conditions and forcing for the single column model (SCM) idealized hurricane example
Nseamount_initialization	The module configures the model for the idealized seamount test case
Nshelf_triangular_festuff
Nshelfwave_initialization	The module configures the model for the idealized shelfwave test case
Nsloshing_initialization	The module configures the model for the non-rotating sloshing test case
Nsoliton_initialization	Initial conditions for the Equatorial Rossby soliton test (Boyd)
Nsupercritical_initialization	The module configures the model for the "supercritical" experiment. https://marine.rutgers.edu/po/index.php?model=test-problems&title=supercritical
Ntidal_bay_initialization	The module configures the model for the "tidal_bay" experiment. tidal_bay = Tidally resonant bay from Zygmunt Kowalik's class on tides
Nuser_change_diffusivity	By Robert Hallberg, May 2012
Nuser_initialization	By Robert Hallberg, April 1994 - June 2002 * This subroutine initializes the fields for the simulations. * The one argument passed to initialize, Time, is set to the * current time of the simulation. The fields which are initialized * here are: * u - Zonal velocity in m s-1. * v - Meridional velocity in m s-1. * h - Layer thickness in m. (Must be positive.) * GbathyT - Basin depth in m. (Must be positive.) * GCoriolisBu - The Coriolis parameter, in s-1. * GVg_prime - The reduced gravity at each interface, in m s-2. * GVRlay - Layer potential density (coordinate variable), kg m-3. * If ENABLE_THERMODYNAMICS is defined: * T - Temperature in C. * S - Salinity in psu. * If BULKMIXEDLAYER is defined: * Rml - Mixed layer and buffer layer potential densities in * units of kg m-3. * If SPONGE is defined: * A series of subroutine calls are made to set up the damping * rates and reference profiles for all variables that are damped * in the sponge. * Any user provided tracer code is also first linked through this * subroutine. * Forcing-related fields (taux, tauy, buoy, ustar, etc.) are set * in MOM_surface_forcing.F90. * These variables are all set in the set of subroutines (in this * file) USER_initialize_bottom_depth, USER_initialize_thickness, * USER_initialize_velocity, USER_initialize_temperature_salinity, * USER_initialize_mixed_layer_density, USER_initialize_sponges, * USER_set_coord, and USER_set_ref_profile. * The names of these subroutines should be self-explanatory. They * start with "USER_" to indicate that they will likely have to be * modified for each simulation to set the initial conditions and * boundary conditions. Most of these take two arguments: an integer * argument specifying whether the fields are to be calculated * internally or read from a NetCDF file; and a string giving the * path to that file. If the field is initialized internally, the * path is ignored. * Macros written all in capital letters are defined in MOM_memory.h. * A small fragment of the grid is shown below: * j+1 x ^ x ^ x At x: q, CoriolisBu * j+1 > o > o > At ^: v, tauy * j x ^ x ^ x At >: u, taux * j > o > o > At o: h, bathyT, buoy, tr, T, S, Rml, ustar * j-1 x ^ x ^ x * i-1 i i+1 At x & ^: * i i+1 At > & o: * The boundaries always run through q grid points (x). *
Nuser_revise_forcing
Nuser_shelf_init
Nuser_surface_forcing
Nuser_tracer_example