mom mom::mom_control_struct mom::mom_diag_ids integer integer mom::id_clock_ocean id_clock_ocean CPU time clock IDs. mom_timing_init step_mom integer integer mom::id_clock_dynamics id_clock_dynamics CPU time clock IDs. mom_timing_init step_mom step_mom_dynamics integer integer mom::id_clock_thermo id_clock_thermo CPU time clock IDs. mom_timing_init step_mom_thermo step_mom_tracer_dyn integer integer mom::id_clock_tracer id_clock_tracer CPU time clock IDs. mom_timing_init step_mom_tracer_dyn integer integer mom::id_clock_diabatic id_clock_diabatic CPU time clock IDs. mom_timing_init step_mom_thermo integer integer mom::id_clock_adiabatic id_clock_adiabatic CPU time clock IDs. mom_timing_init step_mom_thermo integer integer mom::id_clock_continuity id_clock_continuity CPU time clock IDs. mom_timing_init integer integer mom::id_clock_thick_diff id_clock_thick_diff CPU time clock IDs. mom_timing_init step_mom_dynamics integer integer mom::id_clock_bbl_visc id_clock_bbl_visc CPU time clock IDs. mom_timing_init step_mom_dynamics step_mom_thermo integer integer mom::id_clock_ml_restrat id_clock_ml_restrat CPU time clock IDs. mom_timing_init step_mom_dynamics integer integer mom::id_clock_diagnostics id_clock_diagnostics CPU time clock IDs. mom_timing_init step_mom step_mom_dynamics step_mom_tracer_dyn integer integer mom::id_clock_z_diag id_clock_z_diag CPU time clock IDs. mom_timing_init integer integer mom::id_clock_init id_clock_init CPU time clock IDs. finish_mom_initialization initialize_mom integer integer mom::id_clock_mom_init id_clock_mom_init CPU time clock IDs. initialize_mom mom_timing_init integer integer mom::id_clock_pass id_clock_pass CPU time clock IDs. mom_timing_init step_mom step_mom_dynamics step_mom_thermo step_mom_tracer_dyn integer integer mom::id_clock_pass_init id_clock_pass_init CPU time clock IDs. initialize_mom mom_timing_init integer integer mom::id_clock_ale id_clock_ale CPU time clock IDs. mom_timing_init step_mom_thermo step_offline integer integer mom::id_clock_other id_clock_other CPU time clock IDs. mom_timing_init step_mom step_mom_dynamics step_mom_tracer_dyn integer integer mom::id_clock_offline_tracer id_clock_offline_tracer CPU time clock IDs. mom_timing_init step_offline integer integer mom::id_clock_unit_tests id_clock_unit_tests CPU time clock IDs. initialize_mom subroutine, public subroutine, public mom::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) step_mom forces_in forces_in fluxes_in fluxes_in sfc_state sfc_state Time_start Time_start time_int_in time_int_in CS CS Waves Waves do_dynamics do_dynamics do_thermodynamics do_thermodynamics start_cycle start_cycle end_cycle end_cycle cycle_length cycle_length reset_therm 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. forces_in A structure with the driving mechanical forces fluxes_in A structure with pointers to themodynamic, tracer and mass exchange forcing fields sfc_state surface ocean state time_start starting time of a segment, as a time type time_int_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 Present and false, do not do updates due to the dynamics. do_thermodynamics Present and false, do not do updates due to the thermodynamics or remapping. start_cycle 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 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 The amount of time in a coupled time stepping cycle [s]. reset_therm This indicates whether the running sums of thermodynamic quantities should be reset. If missing, this is like start_cycle. adjust_ssh_for_p_atm mom_lateral_mixing_coeffs::calc_depth_function mom_lateral_mixing_coeffs::calc_resoln_function mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint mom_domains::complete_group_pass mom_diag_mediator::diag_copy_diag_to_storage extract_surface_state id_clock_diagnostics id_clock_dynamics id_clock_ocean id_clock_other id_clock_pass mom_state_is_synchronized mom_forcing_type::rotate_forcing mom_forcing_type::rotate_mech_forcing mom_variables::rotate_surface_state mom_oda_driver_mod::set_analysis_time mom_oda_driver_mod::set_prior_tracer mom_domains::start_group_pass step_mom_dynamics step_mom_thermo step_mom_tracer_dyn mom_wave_interface::update_stokes_drift mom_main subroutine subroutine mom::step_mom_dynamics (forces, p_surf_begin, p_surf_end, dt, dt_thermo, bbl_time_int, CS, Time_local, Waves) step_mom_dynamics forces forces p_surf_begin p_surf_begin p_surf_end p_surf_end dt dt dt_thermo dt_thermo bbl_time_int bbl_time_int CS CS Time_local Time_local Waves Waves Time step the ocean dynamics, including the momentum and continuity equations. forces 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 time interval covered by this call [T ~> s]. dt_thermo time interval covered by any updates that may span multiple dynamics steps [T ~> s]. bbl_time_int 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 End time of a segment, as a time type waves Container for wave related parameters; the mom_error_handler::calltree_waypoint id_clock_bbl_visc id_clock_diagnostics id_clock_dynamics id_clock_ml_restrat id_clock_other id_clock_pass id_clock_thick_diff mom_meke::step_forward_meke mom_thickness_diffuse::thickness_diffuse step_mom subroutine subroutine mom::step_mom_tracer_dyn (CS, G, GV, US, h, Time_local) step_mom_tracer_dyn CS CS G G GV GV US US h h Time_local 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. cs control structure g ocean grid structure gv ocean vertical grid structure us A dimensional unit scaling type h layer thicknesses after the transports [H ~> m or kg m-2] time_local The model time at the end of the time step. mom_error_handler::calltree_waypoint id_clock_diagnostics id_clock_other id_clock_pass id_clock_thermo id_clock_tracer step_mom subroutine subroutine mom::step_mom_thermo (CS, G, GV, US, u, v, h, tv, fluxes, dtdia, Time_end_thermo, update_BBL, Waves) step_mom_thermo CS CS G G GV GV US US u u v v h h tv tv fluxes fluxes dtdia dtdia Time_end_thermo Time_end_thermo update_BBL update_BBL Waves Waves MOM_step_thermo orchestrates the thermodynamic time stepping and vertical remapping, via calls to diabatic (or adiabatic) and ALE_main. cs Master MOM control structure g ocean grid structure gv ocean vertical grid structure us A dimensional unit scaling type u zonal velocity [L T-1 ~> m s-1] v meridional velocity [L T-1 ~> m s-1] h layer thickness [H ~> m or kg m-2] tv A structure pointing to various thermodynamic variables fluxes pointers to forcing fields dtdia The time interval over which to advance [T ~> s] time_end_thermo End of averaging interval for thermo diags update_bbl If true, calculate the bottom boundary layer properties. waves Container for wave related parameters mom_diabatic_driver::adiabatic mom_oda_driver_mod::apply_oda_tracer_increments mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint id_clock_adiabatic id_clock_ale id_clock_bbl_visc id_clock_diabatic id_clock_pass id_clock_thermo step_mom subroutine, public subroutine, public mom::step_offline (forces, fluxes, sfc_state, Time_start, time_interval, CS) step_offline forces forces fluxes fluxes sfc_state sfc_state Time_start Time_start time_interval time_interval CS 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 forces A structure with the driving mechanical forces fluxes pointers to forcing fields sfc_state surface ocean state time_start starting time of a segment, as a time type time_interval time interval cs control structure from initialize_MOM adjust_ssh_for_p_atm mom_ale::ale_offline_tracer_final mom_lateral_mixing_coeffs::calc_depth_function mom_lateral_mixing_coeffs::calc_resoln_function extract_surface_state id_clock_ale id_clock_offline_tracer mom_offline_main::offline_advection_layer mom_main ocean_model_mod::update_ocean_model subroutine, public subroutine, public mom::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 Time Time Time_init Time_init param_file param_file dirs dirs CS CS restart_CSp restart_CSp Time_in Time_in offline_tracer_mode offline_tracer_mode input_restart_file input_restart_file diag_ptr diag_ptr count_calls count_calls tracer_flow_CSp tracer_flow_CSp Initialize MOM, including memory allocation, setting up parameters and diagnostics, initializing the ocean state variables, and initializing subsidiary modules. time model time, set in this routine time_init The start time for the coupled model's calendar param_file structure indicating parameter file to parse dirs 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 time passed to MOM_initialize_state when model is not being started from a restart file offline_tracer_mode True is returned if tracers are being run offline input_restart_file 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 count_calls If true, nstep_tot counts the number of calls to step_MOM instead of the number of dynamics timesteps. mom_diabatic_driver::adiabatic_driver_init mom_boundary_update::call_obc_register mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint mom_dyn_horgrid::create_dyn_horgrid mom_dyn_horgrid::destroy_dyn_horgrid mom_diag_mediator::diag_copy_diag_to_storage mom_eos::eos_init mom_obsolete_params::find_obsolete_params mom_get_input::get_mom_input mom_verticalgrid::get_tr_flux_units id_clock_init id_clock_mom_init id_clock_pass_init id_clock_unit_tests mom_ale_sponge::init_ale_sponge_diags mom_sponge::init_sponge_diags mom_restart::is_new_run mom_tracer_registry::lock_tracer_registry mom_meke::meke_alloc_register_restart mom_meke::meke_init mom_mixed_layer_restrat::mixedlayer_restrat_register_restarts mom_coord_initialization::mom_initialize_coord mom_fixed_initialization::mom_initialize_fixed mom_state_initialization::mom_initialize_state mom_sum_output::mom_sum_output_init mom_timing_init register_diags mom_obsolete_diagnostics::register_obsolete_diagnostics mom_restart::restart_init mom_transcribe_grid::rotate_dyngrid mom_hor_index::rotate_hor_index rotate_initial_state mom_open_boundary::rotate_obc_config mom_open_boundary::rotate_obc_init mom_grid::set_first_direction set_restart_fields mom_set_visc::set_visc_register_restarts mom_thickness_diffuse::thickness_diffuse_init mom_unit_tests::unit_tests mom_main subroutine, public subroutine, public mom::finish_mom_initialization (Time, dirs, CS, restart_CSp) finish_mom_initialization Time Time dirs dirs CS CS restart_CSp restart_CSp Finishes initializing MOM and writes out the initial conditions. time model time, used in this routine dirs structure with directory paths cs pointer to MOM control structure restart_csp pointer to the restart control structure that will be used for MOM. mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_unit_scaling::fix_restart_unit_scaling id_clock_init mom_main subroutine subroutine mom::register_diags (Time, G, GV, US, IDs, diag) register_diags Time Time G G GV GV US US IDs IDs diag diag Register certain diagnostics. time current model time g ocean grid structure gv ocean vertical grid structure us A dimensional unit scaling type ids A structure with the diagnostic IDs. diag regulates diagnostic output mom_verticalgrid::get_thickness_units initialize_mom subroutine subroutine mom::mom_timing_init (CS) mom_timing_init CS CS Set up CPU clock IDs for timing various subroutines. cs control structure set up by initialize_MOM. id_clock_adiabatic id_clock_ale id_clock_bbl_visc id_clock_continuity id_clock_diabatic id_clock_diagnostics id_clock_dynamics id_clock_ml_restrat id_clock_mom_init id_clock_ocean id_clock_offline_tracer id_clock_other id_clock_pass id_clock_pass_init id_clock_thermo id_clock_thick_diff id_clock_tracer id_clock_z_diag initialize_mom subroutine subroutine mom::set_restart_fields (GV, US, param_file, CS, restart_CSp) set_restart_fields GV GV US US param_file param_file CS CS restart_CSp 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. gv ocean vertical grid structure us A dimensional unit scaling type param_file opened file for parsing to get parameters cs control structure set up by initialize_MOM restart_csp pointer to the restart control structure that will be used for MOM. mom_verticalgrid::get_flux_units mom_verticalgrid::get_thickness_units initialize_mom subroutine subroutine mom::adjust_ssh_for_p_atm (tv, G, GV, US, ssh, p_atm, use_EOS) adjust_ssh_for_p_atm tv tv G G GV GV US US ssh ssh p_atm p_atm use_EOS use_EOS Apply a correction to the sea surface height to compensate for the atmospheric pressure (the inverse barometer). tv A structure pointing to various thermodynamic variables g ocean grid structure gv ocean vertical grid structure us A dimensional unit scaling type ssh time mean surface height [m] p_atm Ocean surface pressure [R L2 T-2 ~> Pa] use_eos If true, calculate the density for the SSH correction using the equation of state. mom_eos::eos_domain step_mom step_offline subroutine, public subroutine, public mom::extract_surface_state (CS, sfc_state_in) extract_surface_state CS CS sfc_state_in 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. cs Master MOM control structure sfc_state_in transparent ocean surface state structure shared with the calling routine data in this structure is intent out. mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_checksum_packages::mom_surface_chksum mom_variables::rotate_surface_state mom_main step_mom step_offline subroutine subroutine mom::rotate_initial_state (u_in, v_in, h_in, T_in, S_in, use_temperature, turns, u, v, h, T, S) rotate_initial_state u_in u_in v_in v_in h_in h_in T_in T_in S_in S_in use_temperature use_temperature turns turns u u v v h h T T S S Rotate initialization fields from input to rotated arrays. initialize_mom logical function, public logical function, public mom::mom_state_is_synchronized (CS, adv_dyn) mom_state_is_synchronized CS CS adv_dyn adv_dyn Return true if all phases of step_MOM are at the same point in time. cs MOM control structure adv_dyn If present and true, only check whether the advection is up-to-date with the dynamics. True if all phases of the update are synchronized. mom_main step_mom subroutine, public subroutine, public mom::get_mom_state_elements (CS, G, GV, US, C_p, C_p_scaled, use_temp) get_mom_state_elements CS CS G G GV GV US US C_p C_p C_p_scaled C_p_scaled use_temp 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. 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 The heat capacity [J kg degC-1] c_p_scaled The heat capacity in scaled units [Q degC-1 ~> J kg degC-1] use_temp True if temperature is a state variable mom_main subroutine, public subroutine, public mom::get_ocean_stocks (CS, mass, heat, salt, on_PE_only) get_ocean_stocks CS CS mass mass heat heat salt salt on_PE_only on_PE_only Find the global integrals of various quantities. cs MOM control structure heat The globally integrated integrated ocean heat [J]. salt The globally integrated integrated ocean salt [kg]. mass The globally integrated integrated ocean mass [kg]. on_pe_only If present and true, only sum on the local PE. mom_spatial_means::global_mass_integral ocean_model_mod::ocean_stock_pe subroutine, public subroutine, public mom::mom_end (CS) mom_end CS CS End of ocean model, including memory deallocation. cs MOM control structure mom_diabatic_driver::diabatic_driver_end mom_boundary_update::obc_register_end mom_offline_main::offline_transport_end mom_tracer_advect::tracer_advect_end mom_tracer_flow_control::tracer_flow_control_end mom_tracer_hor_diff::tracer_hor_diff_end mom_tracer_registry::tracer_registry_end mom_unit_scaling::unit_scaling_end mom_main The central module of the MOM6 ocean model. Modular Ocean Model (MOM) Version 6.0 (MOM6) 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 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. 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: ../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 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. Here are some example heat budgets for the ALE version of MOM6. 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 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)