user_initialization logical logical user_initialization::first_call first_call = .true. A module variable that should not be used. TodoMove this module variable into a control structure. user_init_temperature_salinity user_initialize_sponges user_initialize_thickness user_initialize_topography user_initialize_velocity user_set_coord user_set_obc_data user_set_rotation write_user_log subroutine, public subroutine, public user_initialization::user_set_coord (Rlay, g_prime, GV, US, param_file, eqn_of_state) user_set_coord Rlay Rlay g_prime g_prime GV GV US US param_file param_file eqn_of_state eqn_of_state Set vertical coordinates. gv The ocean's vertical grid structure rlay Layer potential density [R ~> kg m-3]. g_prime The reduced gravity at each interface [L2 Z-1 T-2 ~> m s-2]. us A dimensional unit scaling type param_file A structure indicating the open file to parse for model parameter values. eqn_of_state Equation of state structure first_call mom_error_handler::mom_error write_user_log mom_coord_initialization::mom_initialize_coord subroutine, public subroutine, public user_initialization::user_initialize_topography (D, G, param_file, max_depth, US) user_initialize_topography D D G G param_file param_file max_depth max_depth US US Initialize topography. g The dynamic horizontal grid type d Ocean bottom depth in m or Z if US is present param_file Parameter file structure max_depth Maximum model depth in the units of D us A dimensional unit scaling type first_call mom_error_handler::mom_error write_user_log mom_fixed_initialization::mom_initialize_topography subroutine, public subroutine, public user_initialization::user_initialize_thickness (h, G, GV, param_file, just_read_params) user_initialize_thickness h h G G GV GV param_file param_file just_read_params just_read_params initialize thicknesses. g The ocean's grid structure. gv The ocean's vertical grid structure. h The thicknesses being initialized [H ~> m or kg m-2]. param_file A structure indicating the open file to parse for model parameter values. just_read_params If present and true, this call will only read parameters without changing h. first_call mom_error_handler::mom_error write_user_log subroutine, public subroutine, public user_initialization::user_initialize_velocity (u, v, G, US, param_file, just_read_params) user_initialize_velocity u u v v G G US US param_file param_file just_read_params just_read_params initialize velocities. g Ocean grid structure. u i-component of velocity [L T-1 ~> m s-1] v j-component of velocity [L T-1 ~> m s-1] us A dimensional unit scaling type param_file A structure indicating the open file to parse for model parameter values. just_read_params If present and true, this call will only read parameters without changing h. first_call mom_error_handler::mom_error write_user_log subroutine, public subroutine, public user_initialization::user_init_temperature_salinity (T, S, G, param_file, eqn_of_state, just_read_params) user_init_temperature_salinity T T S S G G param_file param_file eqn_of_state eqn_of_state just_read_params just_read_params This function puts the initial layer temperatures and salinities into T(:,:,:) and S(:,:,:). g Ocean grid structure. t Potential temperature [degC]. s Salinity [ppt]. param_file A structure indicating the open file to parse for model parameter values. eqn_of_state Equation of state structure just_read_params If present and true, this call will only read parameters without changing T & S. first_call mom_error_handler::mom_error write_user_log subroutine, public subroutine, public user_initialization::user_initialize_sponges (G, GV, use_temp, tv, param_file, CSp, h) user_initialize_sponges G G GV GV use_temp use_temp tv tv param_file param_file CSp CSp h h Set up the sponges. g Ocean grid structure. gv The ocean's vertical grid structure. use_temp If true, temperature and salinity are state variables. tv A structure containing pointers to any available thermodynamic fields, potential temperature and salinity or mixed layer density. Absent fields have NULL ptrs. param_file A structure indicating the open file to parse for model parameter values. csp A pointer to the sponge control structure. h Layer thicknesses [H ~> m or kg m-2]. first_call mom_error_handler::mom_error write_user_log mom_state_initialization::mom_initialize_state subroutine, public subroutine, public user_initialization::user_set_obc_data (OBC, tv, G, param_file, tr_Reg) user_set_obc_data OBC OBC tv tv G G param_file param_file tr_Reg tr_Reg This subroutine sets the properties of flow at open boundary conditions. obc This open boundary condition type specifies whether, where, and what open boundary conditions are used. tv A structure containing pointers to any available thermodynamic fields, including potential temperature and salinity or mixed layer density. Absent fields have NULL ptrs. g The ocean's grid structure. param_file A structure indicating the open file to parse for model parameter values. tr_reg Tracer registry. first_call write_user_log subroutine, public subroutine, public user_initialization::user_set_rotation (G, param_file) user_set_rotation G G param_file param_file g The ocean's grid structure param_file A structure to parse for run-time parameters first_call mom_error_handler::mom_error write_user_log subroutine subroutine user_initialization::write_user_log (param_file) write_user_log param_file param_file Write output about the parameter values being used. param_file A structure indicating the open file to parse for model parameter values. first_call user_init_temperature_salinity user_initialize_sponges user_initialize_thickness user_initialize_topography user_initialize_velocity user_set_coord user_set_obc_data user_set_rotation A template of a user to code up customized initial conditions. 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 might be initialized here are: u - Zonal velocity [Z T-1 ~> m s-1]. v - Meridional velocity [Z T-1 ~> m s-1]. h - Layer thickness [H ~> m or kg m-2]. (Must be positive.) GbathyT - Basin depth [Z ~> m]. (Must be positive.) GCoriolisBu - The Coriolis parameter [T-1 ~> s-1]. GVg_prime - The reduced gravity at each interface [L2 Z-1 T-2 ~> m s-2]. GVRlay - Layer potential density (coordinate variable) [R ~> kg m-3]. If ENABLE_THERMODYNAMICS is defined: T - Temperature [degC]. S - Salinity [psu]. If BULKMIXEDLAYER is defined: Rml - Mixed layer and buffer layer potential densities [R ~> 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. 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.