MOM6 documentation example?

MOM.rst

MOM module reference

The central module of the MOM6 ocean model

Data Types

MOM_diag_IDs	A structure with diagnostic IDs of the state variables
MOM_control_struct	Control structure for the MOM module, including the variables that describe the state of the ocean.

Functions/Subroutines

step_MOM	This subroutine orchestrates the time stepping of MOM. The adiabatic dynamics are stepped by calls to one of the step_MOM_dyn_...routines. The action of lateral processes on tracers occur in calls to advect_tracer and tracer_hordiff. Vertical mixing and possibly remapping occur inside of diabatic.
step_MOM_dynamics	Time step the ocean dynamics, including the momentum and continuity equations
step_MOM_tracer_dyn	step_MOM_tracer_dyn does tracer advection and lateral diffusion, bringing the tracers up to date with the changes in state due to the dynamics. Surface sources and sinks and remapping are handled via step_MOM_thermo.
step_MOM_thermo	MOM_step_thermo orchestrates the thermodynamic time stepping and vertical remapping, via calls to diabatic (or adiabatic) and ALE_main.
step_offline	step_offline is the main driver for running tracers offline in MOM6. This has been primarily developed with ALE configurations in mind. Some work has been done in isopycnal configuration, but the work is very preliminary. Some more detail about this capability along with some of the subroutines called here can be found in tracers/MOM_offline_control.F90
initialize_MOM	Initialize MOM, including memory allocation, setting up parameters and diagnostics, initializing the ocean state variables, and initializing subsidiary modules
finish_MOM_initialization	Finishes initializing MOM and writes out the initial conditions.
register_diags	Register certain diagnostics
MOM_timing_init	Set up CPU clock IDs for timing various subroutines.
set_restart_fields	Set the fields that are needed for bitwise identical restarting the time stepping scheme. In addition to those specified here directly, there may be fields related to the forcing or to the barotropic solver that are needed; these are specified in sub- routines that are called from this one. This routine should be altered if there are any changes to the time stepping scheme. The CHECK_RESTART facility may be used to confirm that all needed restart fields have been included.
adjust_ssh_for_p_atm	Apply a correction to the sea surface height to compensate for the atmospheric pressure (the inverse barometer).
extract_surface_state	Set the surface (return) properties of the ocean model by setting the appropriate fields in sfc_state. Unused fields are set to NULL or are unallocated.
rotate_initial_state	Rotate initialization fields from input to rotated arrays.
MOM_state_is_synchronized	Return true if all phases of step_MOM are at the same point in time.
get_MOM_state_elements	This subroutine offers access to values or pointers to other types from within the MOM_control_struct, allowing the MOM_control_struct to be opaque.
get_ocean_stocks	Find the global integrals of various quantities.
MOM_end	End of ocean model, including memory deallocation

Detailed Description

namespace mom

Modular Ocean Model (MOM) Version 6.0 (MOM6)

authors Alistair Adcroft, Robert Hallberg, and Stephen Griffies

Additional contributions from:

• Whit Anderson
• Brian Arbic
• Will Cooke
• Anand Gnanadesikan
• Matthew Harrison
• Mehmet Ilicak
• Laura Jackson
• Jasmine John
• John Krasting
• Zhi Liang
• Bonnie Samuels
• Harper Simmons
• Laurent White
• Niki Zadeh

MOM ice-shelf code was developed by * Daniel Goldberg * Robert Hallberg * Chris Little * Olga Sergienko

section section_overview Overview of MOM

This program (MOM) simulates the ocean by numerically solving the hydrostatic primitive equations in generalized Lagrangian vertical coordinates, typically tracking stretched pressure (p*) surfaces or following isopycnals in the ocean's interior, and general orthogonal horizontal coordinates. Unlike earlier versions of MOM, in MOM6 these equations are horizontally discretized on an Arakawa C-grid. (It remains to be seen whether a B-grid dynamic core will be revived in MOM6 at a later date; for now applications requiring a B-grid discretization should use MOM5.1.) MOM6 offers a range of options for the physical parameterizations, from those most appropriate to highly idealized models for geophysical fluid dynamics studies to a rich suite of processes appropriate for realistic ocean simulations. The thermodynamic options typically use conservative temperature and preformed salinity as conservative state variables and a full nonlinear equation of state, but there are also idealized adiabatic configurations of the model that use fixed density layers. Version 6.0 of MOM continues in the long tradition of a commitment to climate-quality ocean simulations embodied in previous versions of MOM, even as it draws extensively on the lessons learned in the development of the Generalized Ocean Layered Dynamics (GOLD) ocean model, which was also primarily developed at NOAA/GFDL. MOM has also benefited tremendously from the FMS infrastructure, which it utilizes and shares with other component models developed at NOAA/GFDL.

When run is isopycnal-coordinate mode, the uppermost few layers

are often used to describe a bulk mixed layer, including the effects of penetrating shortwave radiation. Either a split- explicit time stepping scheme or a non-split scheme may be used for the dynamics, while the time stepping may be split (and use different numbers of steps to cover the same interval) for the forcing, the thermodynamics, and for the dynamics. Most of the numerics are second order accurate in space. MOM can run with an absurdly thin minimum layer thickness. A variety of non-isopycnal vertical coordinate options are under development, but all exploit the advantages of a Lagrangian vertical coordinate, as discussed in detail by Adcroft and Hallberg (Ocean Modelling, 2006).

Details of the numerics and physical parameterizations are

provided in the appropriate source files. All of the available options are selected at run-time by parsing the input files, usually MOM_input and MOM_override, and the options choices are then documented for each run in MOM_param_docs.

MOM6 integrates the equations forward in time in three distinct

phases. In one phase, the dynamic equations for the velocities and layer thicknesses are advanced, capturing the propagation of external and internal inertia-gravity waves, Rossby waves, and other strictly adiabatic processes, including lateral stresses, vertical viscosity and momentum forcing, and interface height diffusion (commonly called Gent-McWilliams diffusion in depth- coordinate models). In the second phase, all tracers are advected and diffused along the layers. The third phase applies diabatic processes, vertical mixing of water properties, and perhaps vertical remapping to cause the layers to track the desired vertical coordinate.

The present file (MOM.F90) orchestrates the main time stepping

loops. One time integration option for the dynamics uses a split explicit time stepping scheme to rapidly step the barotropic pressure and velocity fields. The barotropic velocities are averaged over the baroclinic time step before they are used to advect thickness and determine the baroclinic accelerations. As described in Hallberg and Adcroft (2009), a barotropic correction is applied to the time-mean layer velocities to ensure that the sum of the layer transports agrees with the time-mean barotropic transport, thereby ensuring that the estimates of the free surface from the sum of the layer thicknesses agrees with the final free surface height as calculated by the barotropic solver. The barotropic and baroclinic velocities are kept consistent by recalculating the barotropic velocities from the baroclinic transports each time step. This scheme is described in Hallberg, 1997, J. Comp. Phys. 135, 54-65 and in Hallberg and Adcroft, 2009, Ocean Modelling, 29, 15-26.

The other time integration options use non-split time stepping

schemes based on the 3-step third order Runge-Kutta scheme described in Matsuno, 1966, J. Met. Soc. Japan, 44, 85-88, or on a two-step quasi-2nd order Runge-Kutta scheme. These are much slower than the split time-stepping scheme, but they are useful for providing a more robust solution for debugging cases where the more complicated split time-stepping scheme may be giving suspect solutions.

There are a range of closure options available. Horizontal

velocities are subject to a combination of horizontal biharmonic and Laplacian friction (based on a stress tensor formalism) and a vertical Fickian viscosity (perhaps using the kinematic viscosity of water). The horizontal viscosities may be constant, spatially varying or may be dynamically calculated using Smagorinsky's approach. A diapycnal diffusion of density and thermodynamic quantities is also allowed, but not required, as is horizontal diffusion of interface heights (akin to the Gent-McWilliams closure of geopotential coordinate models). The diapycnal mixing may use a fixed diffusivity or it may use the shear Richardson number dependent closure, like that described in Jackson et al. (JPO, 2008). When there is diapycnal diffusion, it applies to momentum as well. As this is in addition to the vertical viscosity, the vertical Prandtl always exceeds 1. A refined bulk-mixed layer is often used to describe the planetary boundary layer in realistic ocean simulations.

MOM has a number of noteworthy debugging capabilities.

Excessively large velocities are truncated and MOM will stop itself after a number of such instances to keep the model from crashing altogether. This is useful in diagnosing failures, or (by accepting some truncations) it may be useful for getting the model past the adjustment from an ill-balanced initial condition. In addition, all of the accelerations in the columns with excessively large velocities may be directed to a text file. Parallelization errors may be diagnosed using the DEBUG option, which causes extensive checksums to be written out along with comments indicating where in the algorithm the sums originate and what variable is being summed. The point where these checksums differ between runs is usually a good indication of where in the code the problem lies. All of the test cases provided with MOM are routinely tested to ensure that they give bitwise identical results regardless of the domain decomposition, or whether they use static or dynamic memory allocation.

section section_structure Structure of MOM

About 115 other files of source code and 4 header files comprise the MOM code, although there are several hundred more files that make up the FMS infrastructure upon which MOM is built. Each of the MOM files contains comments documenting what it does, and most of the file names are fairly self-evident. In addition, all subroutines and data types are referenced via a module use, only statement, and the module names are consistent with the file names, so it is not too hard to find the source file for a subroutine.

The typical MOM directory tree is as follows:

verbatim

../MOM |-- config_src | |-- coupled_driver | |-- dynamic | `-- solo_driver |-- examples | |-- CM2G | |-- ... | `-- torus_advection_test `-- src

|-- core |-- diagnostics |-- equation_of_state |-- framework |-- ice_shelf |-- initialization |-- parameterizations | |-- lateral | `-- vertical |-- tracer `-- user

endverbatim

Rather than describing each file here, each directory contents will be described to give a broad overview of the MOM code structure.

The directories under config_src contain files that are used for

configuring the code, for instance for coupled or ocean-only runs. Only one or two of these directories are used in compiling any, particular run.

• config_src/coupled_driver: The files here are used to couple MOM as a component in a larger run driven by the FMS coupler. This includes code that converts various forcing fields into the code structures and flux and unit conventions used by MOM, and converts the MOM surface fields back to the forms used by other FMS components.

• config_src/dynamic: The only file here is the version of MOM_memory.h that is used for dynamic memory configurations of MOM.

• config_src/solo_driver: The files here are include the _main driver that is used when MOM is configured as an ocean-only model, as well as the files that specify the surface forcing in this configuration.

  The directories under examples provide a large number of working

configurations of MOM, along with reference solutions for several different compilers on GFDL's latest large computer. The versions of MOM_memory.h in these directories need not be used if dynamic memory allocation is desired, and the answers should be unchanged.

The directories under src contain most of the MOM files. These

files are used in every configuration using MOM.

• src/core: The files here constitute the MOM dynamic core. This directory also includes files with the types that describe the model's lateral grid and have defined types that are shared across various MOM modules to allow for more succinct and flexible subroutine argument lists.
• src/diagnostics: The files here calculate various diagnostics that are anciliary to the model itself. While most of these diagnostics do not directly affect the model's solution, there are some, like the calculation of the deformation radius, that are used in some of the process parameterizations.
• src/equation_of_state: These files describe the physical properties of sea-water, including both the equation of state and when it freezes.
• src/framework: These files provide infrastructure utilities for MOM. Many are simply wrappers for capabilities provided by FMS, although others provide capabilities (like the file_parser) that are unique to MOM. When MOM is adapted to use a modeling infrastructure distinct from FMS, most of the required changes are in this directory.
• src/initialization: These are the files that are used to initialize the MOM grid or provide the initial physical state for MOM. These files are not intended to be modified, but provide a means for calling user-specific initialization code like the examples in src/user.
• src/parameterizations/lateral: These files implement a number of quasi-lateral (along-layer) process parameterizations, including lateral viscosities, parameterizations of eddy effects, and the calculation of tidal forcing.
• src/parameterizations/vertical: These files implement a number of vertical mixing or diabatic processes, including the effects of vertical viscosity and code to parameterize the planetary boundary layer. There is a separate driver that orchestrates this portion of the algorithm, and there is a diversity of parameterizations to be found here.
• src/tracer: These files handle the lateral transport and diffusion of tracers, or are the code to implement various passive tracer packages. Additional tracer packages are readily accommodated.
• src/user: These are either stub routines that a user could use to change the model's initial conditions or forcing, or are examples that implement specific test cases. These files can easily be hand edited to create new analytically specified configurations.

Most simulations can be set up by modifying only the files MOM_input, and possibly one or two of the files in src/user. In addition, the diag_table (MOM_diag_table) will commonly be modified to tailor the output to the needs of the question at hand. The FMS utility mkmf works with a file called path_names to build an appropriate makefile, and path_names should be edited to reflect the actual location of the desired source code.

There are 3 publicly visible subroutines in this file (MOM.F90). * step_MOM steps MOM over a specified interval of time. * MOM_initialize calls initialize and does other initialization

that does not warrant user modification.

• extract_surface_state determines the surface (bulk mixed layer if traditional isoycnal vertical coordinate) properties of the current model state and packages pointers to these fields into an exported structure.

  The remaining subroutines in this file (src/core/MOM.F90) are:

• find_total_transport determines the barotropic mass transport.

• register_diags registers many diagnostic fields for the dynamic solver, or of the main model variables.

• MOM_timing_init initializes various CPU time clocks.

• write_static_fields writes out various time-invariant fields.

• set_restart_fields is used to specify those fields that are written to and read from the restart file.

section section_heat_budget Diagnosing MOM heat budget

Here are some example heat budgets for the ALE version of MOM6.

subsection subsection_2d_heat_budget Depth integrated heat budget

Depth integrated heat budget diagnostic for MOM.

• OPOTTEMPTEND_2d = T_ADVECTION_XY_2d + OPOTTEMPPMDIFF_2d + HFDS + HFGEOU

• T_ADVECTION_XY_2d = horizontal advection

• OPOTTEMPPMDIFF_2d = neutral diffusion

• HFDS = net surface boundary heat flux

• HFGEOU = geothermal heat flux

• HFDS = net surface boundary heat flux entering the ocean

  = rsntds + rlntds + hfls + hfss + heat_pme + hfsifrazil

• More heat flux cross-checks * hfds = net_heat_coupler + hfsifrazil + heat_pme * heat_pme = heat_content_surfwater

  = heat_content_massin + heat_content_massout = heat_content_fprec + heat_content_cond + heat_content_vprec

  • hfrunoffds + hfevapds + hfrainds

subsection subsection_3d_heat_budget Depth integrated heat budget

Here is an example 3d heat budget diagnostic for MOM.

• OPOTTEMPTEND = T_ADVECTION_XY + TH_TENDENCY_VERT_REMAP + OPOTTEMPDIFF + OPOTTEMPPMDIFF

  • BOUNDARY_FORCING_HEAT_TENDENCY + FRAZIL_HEAT_TENDENCY

• OPOTTEMPTEND = net tendency of heat as diagnosed in MOM.F90
• T_ADVECTION_XY = heating of a cell from lateral advection
• TH_TENDENCY_VERT_REMAP = heating of a cell from vertical remapping
• OPOTTEMPDIFF = heating of a cell from diabatic diffusion
• OPOTTEMPPMDIFF = heating of a cell from neutral diffusion
• BOUNDARY_FORCING_HEAT_TENDENCY = heating of cell from boundary fluxes
• FRAZIL_HEAT_TENDENCY = heating of cell from frazil
• TH_TENDENCY_VERT_REMAP has zero vertical sum, as it redistributes heat in vertical.
• OPOTTEMPDIFF has zero vertical sum, as it redistributes heat in the vertical.
• BOUNDARY_FORCING_HEAT_TENDENCY generally has 3d structure, with k > 1 contributions from penetrative shortwave, and from other fluxes for the case when layers are tiny, in which case MOM6 partitions tendencies into k > 1 layers.
• FRAZIL_HEAT_TENDENCY generally has 3d structure, since MOM6 frazil calculation checks the full ocean column.
• FRAZIL_HEAT_TENDENCY[k=@sum] = HFSIFRAZIL = column integrated frazil heating.
• HFDS = FRAZIL_HEAT_TENDENCY[k=@sum] + BOUNDARY_FORCING_HEAT_TENDENCY[k=@sum]

Here is an example 2d heat budget (depth summed) diagnostic for MOM.

• OPOTTEMPTEND_2d = T_ADVECTION_XY_2d + OPOTTEMPPMDIFF_2d + HFDS

Here is an example 3d salt budget diagnostic for MOM.

• OSALTTEND = S_ADVECTION_XY + SH_TENDENCY_VERT_REMAP + OSALTDIFF + OSALTPMDIFF

  • BOUNDARY_FORCING_SALT_TENDENCY

• OSALTTEND = net tendency of salt as diagnosed in MOM.F90
• S_ADVECTION_XY = salt convergence to cell from lateral advection
• SH_TENDENCY_VERT_REMAP = salt convergence to cell from vertical remapping
• OSALTDIFF = salt convergence to cell from diabatic diffusion
• OSALTPMDIFF = salt convergence to cell from neutral diffusion
• BOUNDARY_FORCING_SALT_TENDENCY = salt convergence to cell from boundary fluxes
• SH_TENDENCY_VERT_REMAP has zero vertical sum, as it redistributes salt in vertical.
• OSALTDIFF has zero vertical sum, as it redistributes salt in the vertical.
• BOUNDARY_FORCING_SALT_TENDENCY generally has 3d structure, with k > 1 contributions from the case when layers are tiny, in which case MOM6 partitions tendencies into k > 1 layers.
• SFDSI = BOUNDARY_FORCING_SALT_TENDENCY[k=@sum]

Here is an example 2d salt budget (depth summed) diagnostic for MOM.

• OSALTTEND_2d = S_ADVECTION_XY_2d + OSALTPMDIFF_2d + SFDSI (+ SALT_FLUX_RESTORE)

!!

Type Documentation

type MOM_diag_IDs

A structure with diagnostic IDs of the state variables

Parameters

• id_u :: 3-d state field diagnostic IDs
• id_v :: 3-d state field diagnostic IDs
• id_h :: 3-d state field diagnostic IDs

type , public :: MOM_control_struct

Control structure for the MOM module, including the variables that describe the state of the ocean.

Parameters

• h :: layer thickness [H ~> m or kg m-2]
• T :: potential temperature [degC]
• S :: salinity [ppt]
• u :: zonal velocity component [L T-1 ~> m s-1]
• uh :: uh = u * h * dy at u grid points [H L2 T-1 ~> m3 s-1 or kg s-1]
• uhtr :: accumulated zonal thickness fluxes to advect tracers [H L2 ~> m3 or kg]
• v :: meridional velocity [L T-1 ~> m s-1]
• vh :: vh = v * h * dx at v grid points [H L2 T-1 ~> m3 s-1 or kg s-1]
• vhtr :: accumulated meridional thickness fluxes to advect tracers [H L2 ~> m3 or kg]
• ssh_rint :: A running time integral of the sea surface height [T m ~> s m].
• ave_ssh_ibc :: time-averaged (over a forcing time step) sea surface height with a correction for the inverse barometer [m]
• eta_av_bc :: free surface height or column mass time averaged over the last baroclinic dynamics time step [H ~> m or kg m-2]
• Hml :: active mixed layer depth [Z ~> m]
• time_in_cycle :: The running time of the current time-stepping cycle in calls that step the dynamics, and also the length of the time integral of ssh_rint [T ~> s].
• time_in_thermo_cycle :: The running time of the current time-stepping cycle in calls that step the thermodynamics [T ~> s].
• G_in :: Input grid metric
• G :: Model grid metric
• rotate_index :: True if index map is rotated
• GV :: structure containing vertical grid info
• US :: structure containing various unit conversion factors
• tv :: structure containing pointers to available thermodynamic fields
• t_dyn_rel_adv :: The time of the dynamics relative to tracer advection and lateral mixing [T ~> s], or equivalently the elapsed time since advectively updating the tracers. t_dyn_rel_adv is invariably positive and may span multiple coupling timesteps.
• t_dyn_rel_thermo :: The time of the dynamics relative to diabatic processes and remapping [T ~> s]. t_dyn_rel_thermo can be negative or positive depending on whether the diabatic processes are applied before or after the dynamics and may span multiple coupling timesteps.
• t_dyn_rel_diag :: The time of the diagnostics relative to diabatic processes and remapping [T ~> s]. t_dyn_rel_diag is always positive, since the diagnostics must lag.
• preadv_h_stored :: If true, the thicknesses from before the advective cycle have been stored for use in diagnostics.
• diag :: structure to regulate diagnostic output timing
• visc :: structure containing vertical viscosities, bottom drag viscosities, and related fields
• MEKE :: structure containing fields related to the Mesoscale Eddy Kinetic Energy
• adiabatic :: If true, there are no diapycnal mass fluxes, and no calls to routines to calculate or apply diapycnal fluxes.
• diabatic_first :: If true, apply diabatic and thermodynamic processes before time stepping the dynamics.
• use_ALE_algorithm :: If true, use the ALE algorithm rather than layered isopycnal/stacked shallow water mode. This logical is set by calling the function useRegridding() from the MOM_regridding module.
• offline_tracer_mode :: If true, step_offline() is called instead of step_MOM(). This is intended for running MOM6 in offline tracer mode
• Time :: pointer to the ocean clock
• dt :: (baroclinic) dynamics time step [T ~> s]
• dt_therm :: thermodynamics time step [T ~> s]
• thermo_spans_coupling :: If true, thermodynamic and tracer time steps can span multiple coupled time steps.
• nstep_tot :: The total number of dynamic timesteps tcaaken so far in this run segment
• count_calls :: If true, count the calls to step_MOM, rather than the number of dynamics steps in nstep_tot
• debug :: If true, write verbose checksums for debugging purposes.
• ntrunc :: number u,v truncations since last call to write_energy
• cont_stencil :: The stencil for thickness from the continuity solver.
• do_dynamics :: If false, does not call step_MOM_dyn_*. This is an undocumented run-time flag that is fragile.
• split :: If true, use the split time stepping scheme.
• use_RK2 :: If true, use RK2 instead of RK3 in unsplit mode (i.e., no split between barotropic and baroclinic).
• thickness_diffuse :: If true, diffuse interface height w/ a diffusivity KHTH.
• thickness_diffuse_first :: If true, diffuse thickness before dynamics.
• mixedlayer_restrat :: If true, use submesoscale mixed layer restratifying scheme.
• useMEKE :: If true, call the MEKE parameterization.
• useWaves :: If true, update Stokes drift
• use_p_surf_in_EOS :: If true, always include the surface pressure contributions in equation of state calculations.
• dtbt_reset_period :: The time interval between dynamic recalculation of the barotropic time step [s]. If this is negative dtbt is never calculated, and if it is 0, dtbt is calculated every step.
• dtbt_reset_interval :: A time_time representation of dtbt_reset_period.
• dtbt_reset_time :: The next time DTBT should be calculated.
• h_pre_dyn :: The thickness before the transports [H ~> m or kg m-2].
• T_pre_dyn :: Temperature before the transports [degC].
• S_pre_dyn :: Salinity before the transports [ppt].
• ADp :: structure containing pointers to accelerations, for derived diagnostics (e.g., energy budgets)
• CDp :: structure containing pointers to continuity equation terms, for derived diagnostics (e.g., energy budgets)
• u_prev :: previous value of u stored for diagnostics [L T-1 ~> m s-1]
• v_prev :: previous value of v stored for diagnostics [L T-1 ~> m s-1]
• interp_p_surf :: If true, linearly interpolate surface pressure over the coupling time step, using specified value at the end of the coupling step. False by default.
• p_surf_prev_set :: If true, p_surf_prev has been properly set from a previous time-step or the ocean restart file. This is only valid when interp_p_surf is true.
• p_surf_prev :: surface pressure [R L2 T-2 ~> Pa] at end previous call to step_MOM
• p_surf_begin :: surface pressure [R L2 T-2 ~> Pa] at start of step_MOM_dyn_...
• p_surf_end :: surface pressure [R L2 T-2 ~> Pa] at end of step_MOM_dyn_...
• write_IC :: If true, then the initial conditions will be written to file
• IC_file :: A file into which the initial conditions are written in a new run if SAVE_INITIAL_CONDS is true.
• calc_rho_for_sea_lev :: If true, calculate rho to convert pressure to sea level
• Hmix :: Diagnostic mixed layer thickness over which to average surface tracer properties when a bulk mixed layer is not used [Z ~> m], or a negative value if a bulk mixed layer is being used.
• HFrz :: If HFrz > 0, the nominal depth over which melt potential is computed [Z ~> m]. The actual depth over which melt potential is computed is min(HFrz, OBLD), where OBLD is the boundary layer depth. If HFrz <= 0 (default), melt potential will not be computed.
• Hmix_UV :: Depth scale over which to average surface flow to feedback to the coupler/driver [Z ~> m] when bulk mixed layer is not used, or a negative value if a bulk mixed layer is being used.
• check_bad_sfc_vals :: If true, scan surface state for ridiculous values.
• bad_val_ssh_max :: Maximum SSH before triggering bad value message [Z ~> m]
• bad_val_sst_max :: Maximum SST before triggering bad value message [degC]
• bad_val_sst_min :: Minimum SST before triggering bad value message [degC]
• bad_val_sss_max :: Maximum SSS before triggering bad value message [ppt]
• bad_val_col_thick :: Minimum column thickness before triggering bad value message [Z ~> m]
• answers_2018 :: If true, use expressions for the surface properties that recover the answers from the end of 2018. Otherwise, use more appropriate expressions that differ at roundoff for non-Boussinsq cases.
• IDs :: Handles used for diagnostics.
• transport_IDs :: Handles used for transport diagnostics.
• sfc_IDs :: Handles used for surface diagnostics.
• diag_pre_sync :: The grid (thicknesses) before remapping
• diag_pre_dyn :: The grid (thicknesses) before dynamics
• dyn_unsplit_CSp :: Pointer to the control structure used for the unsplit dynamics
• dyn_unsplit_RK2_CSp :: Pointer to the control structure used for the unsplit RK2 dynamics
• dyn_split_RK2_CSp :: Pointer to the control structure used for the mode-split RK2 dynamics
• thickness_diffuse_CSp :: Pointer to the control structure used for the isopycnal height diffusive transport. This is also common referred to as Gent-McWilliams diffusion
• mixedlayer_restrat_CSp :: Pointer to the control structure used for the mixed layer restratification
• set_visc_CSp :: Pointer to the control structure used to set viscosities
• diabatic_CSp :: Pointer to the control structure for the diabatic driver
• MEKE_CSp :: Pointer to the control structure for the MEKE updates
• VarMix :: Pointer to the control structure for the variable mixing module
• Barotropic_CSp :: Pointer to the control structure for the barotropic module
• tracer_Reg :: Pointer to the MOM tracer registry
• tracer_adv_CSp :: Pointer to the MOM tracer advection control structure
• tracer_diff_CSp :: Pointer to the MOM along-isopycnal tracer diffusion control structure
• tracer_flow_CSp :: Pointer to the control structure that orchestrates the calling of tracer packages
• update_OBC_CSp :: Pointer to the control structure for updating open boundary condition properties
• OBC :: Pointer to the MOM open boundary condition type
• sponge_CSp :: Pointer to the layered-mode sponge control structure
• ALE_sponge_CSp :: Pointer to the ALE-mode sponge control structure
• ALE_CSp :: Pointer to the Arbitrary Lagrangian Eulerian (ALE) vertical coordinate control structure
• sum_output_CSp :: Pointer to the globally summed output control structure
• diagnostics_CSp :: Pointer to the MOM diagnostics control structure
• offline_CSp :: Pointer to the offline tracer transport control structure
• ensemble_ocean :: if true, this run is part of a larger ensemble for the purpose of data assimilation or statistical analysis.
• odaCS :: a pointer to the control structure for handling ensemble model state vectors and data assimilation increments and priors

Functions/Subroutine Documentation

subroutine step_MOM ( forces_in , fluxes_in , sfc_state , Time_start , time_int_in , CS , Waves , do_dynamics , do_thermodynamics , start_cycle , end_cycle , cycle_length , reset_therm )

This subroutine orchestrates the time stepping of MOM. The adiabatic dynamics are stepped by calls to one of the step_MOM_dyn_...routines. The action of lateral processes on tracers occur in calls to advect_tracer and tracer_hordiff. Vertical mixing and possibly remapping occur inside of diabatic.

Parameters

• forces_in :: [inout] A structure with the driving mechanical forces
• fluxes_in :: [inout] A structure with pointers to themodynamic, tracer and mass exchange forcing fields
• sfc_state :: [inout] surface ocean state
• Time_start :: [in] starting time of a segment, as a time type
• time_int_in :: [in] time interval covered by this run segment [s].
• CS :: control structure from initialize_MOM
• Waves :: An optional pointer to a wave property CS
• do_dynamics :: [in] Present and false, do not do updates due to the dynamics.
• do_thermodynamics :: [in] Present and false, do not do updates due to the thermodynamics or remapping.
• start_cycle :: [in] This indicates whether this call is to be treated as the first call to step_MOM in a time-stepping cycle; missing is like true.
• end_cycle :: [in] This indicates whether this call is to be treated as the last call to step_MOM in a time-stepping cycle; missing is like true.
• cycle_length :: [in] The amount of time in a coupled time stepping cycle [s].
• reset_therm :: [in] This indicates whether the running sums of thermodynamic quantities should be reset. If missing, this is like start_cycle.

Calls into

|disable_averaging|_ |find_eta|_ |allocate_mech_forcing|_ |rotate_forcing|_ |calculate_diagnostic_fields|_ |MOM_state_chksum|_ |rotate_surface_state|_ |deallocate_forcing_type|_ MOM_state_is_synchronized |MOM_mech_forcing_chksum|_ step_MOM_thermo |MOM_error|_ adjust_ssh_for_p_atm |callTree_showQuery|_ |post_tracer_diagnostics|_ |do_group_pass|_ |create_group_pass|_ |allocate_forcing_type|_ |oda|_ |cpu_clock_end|_ |set_prior_tracer|_ |calc_depth_function|_ |post_data|_ |set_analysis_time|_ |accumulate_net_input|_ |check_redundant|_ |diag_update_remap_grids|_ |cpu_clock_begin|_ |real_to_time|_ extract_surface_state |callTree_enter|_ |callTree_waypoint|_ |deallocate_mech_forcing|_ |complete_group_pass|_ |rotate_mech_forcing|_ |Update_Stokes_Drift|_ |pass_var|_ step_MOM_dynamics |post_surface_thermo_diags|_ |write_energy|_ |diag_copy_diag_to_storage|_ |start_group_pass|_ |enable_averages|_ |calc_resoln_function|_ |post_surface_dyn_diags|_ step_MOM_tracer_dyn |callTree_leave|_

subroutine step_MOM_dynamics ( forces , p_surf_begin , p_surf_end , dt , dt_thermo , bbl_time_int , CS , Time_local , Waves )

Time step the ocean dynamics, including the momentum and continuity equations

Parameters

• forces :: [in] A structure with the driving mechanical forces
• p_surf_begin :: A pointer (perhaps NULL) to the surface pressure at the beginning of this dynamic step, intent in [R L2 T-2 ~> Pa].
• p_surf_end :: A pointer (perhaps NULL) to the surface pressure at the end of this dynamic step, intent in [R L2 T-2 ~> Pa].
• dt :: [in] time interval covered by this call [T ~> s].
• dt_thermo :: [in] time interval covered by any updates that may span multiple dynamics steps [T ~> s].
• bbl_time_int :: [in] time interval over which updates to the bottom boundary layer properties will apply [T ~> s], or zero not to update the properties.
• CS :: control structure from initialize_MOM
• Time_local :: [in] End time of a segment, as a time type
• Waves :: Container for wave related parameters; the fields in Waves are intent in here.

Calls into

|disable_averaging|_ |set_viscous_BBL|_ |callTree_showQuery|_ |uvchksum|_ |step_MOM_dyn_unsplit_RK2|_ |calc_slope_functions|_ |cpu_clock_end|_ |hchksum|_ |step_MOM_dyn_unsplit|_ |post_data|_ |diag_update_remap_grids|_ |step_forward_MEKE|_ |cpu_clock_begin|_ |real_to_time|_ |callTree_waypoint|_ |pass_var|_ |step_MOM_dyn_split_RK2|_ |enable_averages|_ |thickness_diffuse|_ |mixedlayer_restrat|_

Called by

step_MOM

subroutine step_MOM_tracer_dyn ( CS , G , GV , US , h , Time_local )

step_MOM_tracer_dyn does tracer advection and lateral diffusion, bringing the tracers up to date with the changes in state due to the dynamics. Surface sources and sinks and remapping are handled via step_MOM_thermo.

Parameters

• CS :: [inout] control structure
• G :: [inout] ocean grid structure
• GV :: [in] ocean vertical grid structure
• US :: [in] A dimensional unit scaling type
• h :: [in] layer thicknesses after the transports [H ~> m or kg m-2]
• Time_local :: [in] The model time at the end of the time step.

Calls into

|disable_averaging|_ |advect_tracer|_ |create_group_pass|_ |do_group_pass|_ |enable_averages|_ |uvchksum|_ |diag_update_remap_grids|_ |cpu_clock_begin|_ |update_segment_tracer_reservoirs|_ |cpu_clock_end|_ |callTree_waypoint|_ |tracer_hordiff|_ |hchksum|_ |callTree_showQuery|_ |post_transport_diagnostics|_

Called by

step_MOM

subroutine step_MOM_thermo ( CS , G , GV , US , u , v , h , tv , fluxes , dtdia , Time_end_thermo , update_BBL , Waves )

MOM_step_thermo orchestrates the thermodynamic time stepping and vertical remapping, via calls to diabatic (or adiabatic) and ALE_main.

Parameters

• CS :: [inout] Master MOM control structure
• G :: [inout] ocean grid structure
• GV :: [inout] ocean vertical grid structure
• US :: [in] A dimensional unit scaling type
• u :: [inout] zonal velocity [L T-1 ~> m s-1]
• v :: [inout] meridional velocity [L T-1 ~> m s-1]
• h :: [inout] layer thickness [H ~> m or kg m-2]
• tv :: [inout] A structure pointing to various thermodynamic variables
• fluxes :: [inout] pointers to forcing fields
• dtdia :: [in] The time interval over which to advance [T ~> s]
• Time_end_thermo :: [in] End of averaging interval for thermo diags
• update_BBL :: [in] If true, calculate the bottom boundary layer properties.
• Waves :: Container for wave related parameters the fields in Waves are intent in here.

Calls into

|disable_averaging|_ |set_viscous_BBL|_ |MOM_state_chksum|_ |adiabatic|_ |callTree_showQuery|_ |uvchksum|_ |do_group_pass|_ |create_group_pass|_ |MOM_forcing_chksum|_ |apply_oda_tracer_increments|_ |postALE_tracer_diagnostics|_ |preAle_tracer_diagnostics|_ |diabatic|_ |cpu_clock_end|_ |hchksum|_ |check_redundant|_ |diag_update_remap_grids|_ |cpu_clock_begin|_ |callTree_enter|_ |callTree_wayPoint|_ |enable_averages|_ |MOM_thermo_chksum|_ |callTree_leave|_ |ALE_main|_

Called by

step_MOM

subroutine step_offline ( forces , fluxes , sfc_state , Time_start , time_interval , CS )

step_offline is the main driver for running tracers offline in MOM6. This has been primarily developed with ALE configurations in mind. Some work has been done in isopycnal configuration, but the work is very preliminary. Some more detail about this capability along with some of the subroutines called here can be found in tracers/MOM_offline_control.F90

Parameters

• forces :: [in] A structure with the driving mechanical forces
• fluxes :: [inout] pointers to forcing fields
• sfc_state :: [inout] surface ocean state
• Time_start :: [in] starting time of a segment, as a time type
• time_interval :: [in] time interval
• CS :: control structure from initialize_MOM
• first_iter :: True if this is the first time step_offline has been called in a given interval
• last_iter :: True if this is the last time step_tracer is to be called in an offline interval
• do_vertical :: If enough time has elapsed, do the diabatic tracer sources/sinks
• adv_converged :: True if all the horizontal fluxes have been used

Calls into

|disable_averaging|_ |increment_date|_ |MOM_mesg|_ |tracer_hordiff|_ |update_offline_fields|_ adjust_ssh_for_p_atm |MOM_error|_ |offline_fw_fluxes_into_ocean|_ |offline_redistribute_residual|_ |extract_offline_main|_ |offline_advection_ale|_ |calc_slope_functions|_ |cpu_clock_end|_ |calc_depth_function|_ |post_offline_convergence_diags|_ |cpu_clock_begin|_ |real_to_time|_ extract_surface_state |offline_diabatic_ale|_ |offline_fw_fluxes_out_ocean|_ |enable_averaging|_ |pass_var|_ |ALE_offline_tracer_final|_ |calc_resoln_function|_ |offline_advection_layer|_

subroutine initialize_MOM ( Time , Time_init , param_file , dirs , CS , restart_CSp , Time_in , offline_tracer_mode , input_restart_file , diag_ptr , count_calls , tracer_flow_CSp )

Initialize MOM, including memory allocation, setting up parameters and diagnostics, initializing the ocean state variables, and initializing subsidiary modules

Parameters

• Time :: [inout] model time, set in this routine
• Time_init :: [in] The start time for the coupled model's calendar
• param_file :: [out] structure indicating parameter file to parse
• dirs :: [out] structure with directory paths
• CS :: pointer set in this routine to MOM control structure
• restart_CSp :: pointer set in this routine to the restart control structure that will be used for MOM.
• Time_in :: [in] time passed to MOM_initialize_state when model is not being started from a restart file
• offline_tracer_mode :: [out] True is returned if tracers are being run offline
• input_restart_file :: [in] If present, name of restart file to read
• diag_ptr :: A pointer set in this routine to the diagnostic regulatory structure
• tracer_flow_CSp :: A pointer set in this routine to the tracer flow control structure.
• count_calls :: [in] If true, nstep_tot counts the number of calls to step_MOM instead of the number of dynamics timesteps.

Calls into

|lock_tracer_registry|_ |find_eta|_ |register_surface_diags|_ |ALE_remap_init_conds|_ |register_obsolete_diagnostics|_ |rotate_hor_index|_ |SZJ_|_ |MOM_initialize_coord|_ |MOM_error|_ |rotate_OBC_init|_ |get_param|_ |offline_transport_init|_ |set_visc_register_restarts|_ MOM_timing_init |call_OBC_register|_ |register_temp_salt_segments|_ |get_MOM_input|_ |rotate_dyngrid|_ |destroy_dyn_horgrid|_ |EOS_init|_ |query_initialized|_ |file_exists|_ |real_to_time|_ |register_cell_measure|_ |MOM_domains_init|_ |MOM_set_verbosity|_ |diag_copy_diag_to_storage|_ |VarMix_init|_ |var_desc|_ |copy_MOM_grid_to_dyngrid|_ |update_ALE_sponge_field|_ |init_ALE_sponge_diags|_ |diag_mediator_init|_ |unit_tests|_ |tracer_advect_init|_ |init_oda|_ |uvchksum|_ |tracer_registry_init|_ |init_sponge_diags|_ |create_group_pass|_ |tracer_hor_diff_init|_ |read_param|_ |initialize_dyn_unsplit|_ |register_restarts_dyn_unsplit_RK2|_ |set_first_direction|_ rotate_initial_state |thickness_diffuse_init|_ |create_dyn_horgrid|_ |rotate_OBC_config|_ |register_transport_diags|_ |MEKE_alloc_register_restart|_ |MOM_read_data|_ |MOM_diagnostics_init|_ |MOM_io_init|_ |ALE_init|_ |num_PEs|_ |restart_init|_ |adjustGridForIntegrity|_ |diag_mediator_infrastructure_init|_ |call_tracer_register|_ |set_axes_info|_ |MOM_sum_output_init|_ |verticalGridInit|_ |MOM_initialize_state|_ |copy_dyngrid_to_MOM_grid|_ |write_static_fields|_ |MEKE_init|_ |MOM_grid_init|_ |diag_grid_storage_init|_ |set_visc_init|_ |diag_masks_set|_ |register_diags_offline_transport|_ |MOM_initialize_fixed|_ |log_version|_ |initialize_dyn_split_RK2|_ |register_tracer|_ |callTree_enter|_ |callTree_waypoint|_ |cpu_clock_id|_ |set_masks_for_axes|_ |diag_set_state_ptrs|_ |tracer_flow_control_init|_ |clone_MOM_domain|_ |ALE_register_diags|_ |mixedlayer_restrat_register_restarts|_ |slasher|_ |insert_offline_main|_ |initialize_dyn_unsplit_RK2|_ register_diags |do_group_pass|_ |get_tr_flux_units|_ |mixedlayer_restrat_init|_ |adiabatic_driver_init|_ |safe_alloc_ptr|_ |cpu_clock_end|_ |ALE_updateVerticalGridType|_ |hchksum|_ |register_restarts_dyn_unsplit|_ |register_restarts_dyn_split_RK2|_ set_restart_fields |diag_update_remap_grids|_ |find_obsolete_params|_ |cpu_clock_begin|_ |ALE_writeCoordinateFile|_ |MOM_debugging_init|_ |SZI_|_ |pass_var|_ |is_new_run|_ |MOM_grid_end|_ |open_boundary_register_restarts|_ |register_tracer_diagnostics|_ |hor_index_init|_ |unit_scaling_init|_ |rotate_ALE_sponge|_ |callTree_leave|_ |ALE_main|_ |diabatic_driver_init|_

subroutine finish_MOM_initialization ( Time , dirs , CS , restart_CSp )

Finishes initializing MOM and writes out the initial conditions.

Parameters

• Time :: [in] model time, used in this routine
• dirs :: [in] structure with directory paths
• CS :: pointer to MOM control structure
• restart_CSp :: pointer to the restart control structure that will be used for MOM.

Calls into

|write_energy|_ |find_eta|_ |fix_restart_unit_scaling|_ |cpu_clock_begin|_ |fix_restart_scaling|_ |register_restart_field|_ |save_restart|_ |SZK_|_ |cpu_clock_end|_ |SZI_|_ |callTree_enter|_ |callTree_leave|_ |SZJ_|_

subroutine register_diags ( Time , G , GV , US , IDs , diag )

Register certain diagnostics

Parameters

• Time :: [in] current model time
• G :: [in] ocean grid structure
• GV :: [in] ocean vertical grid structure
• US :: [inout] A dimensional unit scaling type
• IDs :: [inout] A structure with the diagnostic IDs.
• diag :: [inout] regulates diagnostic output

Calls into

|register_diag_field|_ |get_thickness_units|_

Called by

initialize_MOM

subroutine MOM_timing_init ( CS )

Set up CPU clock IDs for timing various subroutines.

Parameters

• CS :: [in] control structure set up by initialize_MOM.

Calls into

|cpu_clock_id|_

Called by

initialize_MOM

subroutine set_restart_fields ( GV , US , param_file , CS , restart_CSp )

Set the fields that are needed for bitwise identical restarting the time stepping scheme. In addition to those specified here directly, there may be fields related to the forcing or to the barotropic solver that are needed; these are specified in sub- routines that are called from this one. This routine should be altered if there are any changes to the time stepping scheme. The CHECK_RESTART facility may be used to confirm that all needed restart fields have been included.

Parameters

• GV :: [inout] ocean vertical grid structure
• US :: [inout] A dimensional unit scaling type
• param_file :: [in] opened file for parsing to get parameters
• CS :: [in] control structure set up by initialize_MOM
• restart_CSp :: pointer to the restart control structure that will be used for MOM.

Calls into

|get_thickness_units|_ |get_flux_units|_ |var_desc|_ |register_restart_field|_ |get_param|_ |register_restart_pair|_

Called by

initialize_MOM

subroutine adjust_ssh_for_p_atm ( tv , G , GV , US , ssh , p_atm , use_EOS )

Apply a correction to the sea surface height to compensate for the atmospheric pressure (the inverse barometer).

Parameters

• tv :: [in] A structure pointing to various thermodynamic variables
• G :: [in] ocean grid structure
• GV :: [in] ocean vertical grid structure
• US :: [in] A dimensional unit scaling type
• ssh :: [inout] time mean surface height [m]
• p_atm :: Ocean surface pressure [R L2 T-2 ~> Pa]
• use_EOS :: [in] If true, calculate the density for the SSH correction using the equation of state.

Calls into

|EOS_domain|_ |calculate_density|_

Called by

step_MOM step_offline

subroutine extract_surface_state ( CS , sfc_state_in )

Set the surface (return) properties of the ocean model by setting the appropriate fields in sfc_state. Unused fields are set to NULL or are unallocated.

Parameters

• CS :: Master MOM control structure
• sfc_state_in :: [inout] transparent ocean surface state structure shared with the calling routine data in this structure is intent out.
• G :: pointer to a structure containing metrics and related information
• G_in :: Input grid metric
• GV :: structure containing vertical grid info
• US :: structure containing various unit conversion factors
• h :: h : layer thickness [H ~> m or kg m-2]
• depth :: Distance from the surface in depth units [Z ~> m] or [H ~> m or kg m-2]
• depth_ml :: Depth over which to average to determine mixed layer properties [Z ~> m] or [H ~> m or kg m-2]
• dh :: Thickness of a layer within the mixed layer [Z ~> m] or [H ~> m or kg m-2]
• mass :: Mass per unit area of a layer [R Z ~> kg m-2]
• T_freeze :: freezing temperature [degC]
• I_depth :: The inverse of depth [Z-1 ~> m-1] or [H-1 ~> m-1 or m2 kg-1]
• missing_depth :: The portion of depth_ml that can not be found in a column [H ~> m or kg m-2]
• H_rescale :: A conversion factor from thickness units to the units used in the calculation of properties of the uppermost ocean [nondim] or [Z H-1 ~> 1 or m3 kg-1]
• delT :: Depth integral of T-T_freeze [Z degC ~> m degC]
• use_temperature :: If true, temp and saln used as state variables.

Calls into

|rotate_surface_state|_ |call_tracer_surface_state|_ |sum_across_PEs|_ |calculate_TFreeze|_ |MOM_surface_chksum|_ |allocate_surface_state|_ |deallocate_surface_state|_ |callTree_enter|_ |callTree_leave|_ |MOM_error|_

Called by

step_MOM step_offline

subroutine rotate_initial_state ( u_in , v_in , h_in , T_in , S_in , use_temperature , turns , u , v , h , T , S )

Rotate initialization fields from input to rotated arrays.

Parameters

Calls into

|rotate_array|_ |rotate_vector|_

Called by

initialize_MOM

function MOM_state_is_synchronized ( CS , adv_dyn ) result ( in_synch )

Return true if all phases of step_MOM are at the same point in time.

Parameters

• CS :: MOM control structure
• adv_dyn :: [in] If present and true, only check whether the advection is up-to-date with the dynamics.
• in_synch :: True if all phases of the update are synchronized.

Called by

step_MOM

subroutine get_MOM_state_elements ( CS , G , GV , US , C_p , C_p_scaled , use_temp )

This subroutine offers access to values or pointers to other types from within the MOM_control_struct, allowing the MOM_control_struct to be opaque.

Parameters

• CS :: MOM control structure
• G :: structure containing metrics and grid info
• GV :: structure containing vertical grid info
• US :: A dimensional unit scaling type
• C_p :: [out] The heat capacity [J kg degC-1]
• C_p_scaled :: [out] The heat capacity in scaled units [Q degC-1 ~> J kg degC-1]
• use_temp :: [out] True if temperature is a state variable

subroutine get_ocean_stocks ( CS , mass , heat , salt , on_PE_only )

Find the global integrals of various quantities.

Parameters

• CS :: MOM control structure
• heat :: [out] The globally integrated integrated ocean heat [J].
• salt :: [out] The globally integrated integrated ocean salt [kg].
• mass :: [out] The globally integrated integrated ocean mass [kg].
• on_PE_only :: [in] If present and true, only sum on the local PE.

Calls into

|global_mass_integral|_

subroutine MOM_end ( CS )

End of ocean model, including memory deallocation

Parameters

• CS :: MOM control structure

Calls into

|OBC_register_end|_ |end_dyn_split_RK2|_ |MOM_grid_end|_ |tracer_registry_end|_ |end_dyn_unsplit|_ |unit_scaling_end|_ |end_dyn_unsplit_RK2|_ |verticalGridEnd|_ |tracer_hor_diff_end|_ |tracer_advect_end|_ |offline_transport_end|_ |tracer_flow_control_end|_ |ALE_end|_ |diabatic_driver_end|_