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module DoxyGenization in the MOM6/src/core directory #817

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Jul 12, 2018
Merged

module DoxyGenization in the MOM6/src/core directory #817

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0da8297
Module dOxyGenization for MOM_variables & vertGrid
Hallberg-NOAA Jul 11, 2018
c621b54
Module dOxyGenization for MOM
Hallberg-NOAA Jul 11, 2018
f3b818b
Module dOxyGenization for MOM_checksum_packages
Hallberg-NOAA Jul 11, 2018
0431fd7
Module dOxyGenization for MOM_dynamics_unsplit
Hallberg-NOAA Jul 11, 2018
de13a2c
Module dOxyGenization for MOM_transribe_grid
Hallberg-NOAA Jul 11, 2018
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25 changes: 14 additions & 11 deletions src/core/MOM.F90
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
!> The central module of the MOM6 ocean model
module MOM

! This file is part of MOM6. See LICENSE.md for the license.
Expand All @@ -9,7 +10,6 @@ module MOM
use MOM_cpu_clock, only : cpu_clock_id, cpu_clock_begin, cpu_clock_end
use MOM_cpu_clock, only : CLOCK_COMPONENT, CLOCK_SUBCOMPONENT
use MOM_cpu_clock, only : CLOCK_MODULE_DRIVER, CLOCK_MODULE, CLOCK_ROUTINE
use MOM_coord_initialization, only : MOM_initialize_coord
use MOM_diag_mediator, only : diag_mediator_init, enable_averaging
use MOM_diag_mediator, only : diag_mediator_infrastructure_init
use MOM_diag_mediator, only : diag_set_state_ptrs, diag_update_remap_grids
Expand All @@ -30,7 +30,6 @@ module MOM
use MOM_error_handler, only : MOM_set_verbosity, callTree_showQuery
use MOM_error_handler, only : callTree_enter, callTree_leave, callTree_waypoint
use MOM_file_parser, only : read_param, get_param, log_version, param_file_type
use MOM_fixed_initialization, only : MOM_initialize_fixed
use MOM_forcing_type, only : forcing, mech_forcing
use MOM_forcing_type, only : MOM_forcing_chksum, MOM_mech_forcing_chksum
use MOM_get_input, only : Get_MOM_Input, directories
Expand All @@ -40,7 +39,6 @@ module MOM
use MOM_restart, only : register_restart_field, query_initialized, save_restart
use MOM_restart, only : restart_init, is_new_run, MOM_restart_CS
use MOM_spatial_means, only : global_mass_integral
use MOM_state_initialization, only : MOM_initialize_state
use MOM_time_manager, only : time_type, set_time, time_type_to_real, operator(+)
use MOM_time_manager, only : operator(-), operator(>), operator(*), operator(/)
use MOM_time_manager, only : operator(>=), increment_date
Expand All @@ -52,6 +50,7 @@ module MOM
use MOM_ALE, only : ALE_getCoordinate, ALE_getCoordinateUnits, ALE_writeCoordinateFile
use MOM_ALE, only : ALE_updateVerticalGridType, ALE_remap_init_conds, ALE_register_diags
use MOM_boundary_update, only : call_OBC_register, OBC_register_end, update_OBC_CS
use MOM_coord_initialization, only : MOM_initialize_coord
use MOM_diabatic_driver, only : diabatic, diabatic_driver_init, diabatic_CS
use MOM_diabatic_driver, only : adiabatic, adiabatic_driver_init, diabatic_driver_end
use MOM_diabatic_driver, only : legacy_diabatic
Expand All @@ -72,8 +71,9 @@ module MOM
use MOM_dynamics_unsplit_RK2, only : initialize_dyn_unsplit_RK2, end_dyn_unsplit_RK2
use MOM_dynamics_unsplit_RK2, only : MOM_dyn_unsplit_RK2_CS
use MOM_dyn_horgrid, only : dyn_horgrid_type, create_dyn_horgrid, destroy_dyn_horgrid
use MOM_EOS, only : EOS_init, calculate_density
use MOM_debugging, only : check_redundant
use MOM_EOS, only : EOS_init, calculate_density
use MOM_fixed_initialization, only : MOM_initialize_fixed
use MOM_grid, only : ocean_grid_type, set_first_direction
use MOM_grid, only : MOM_grid_init, MOM_grid_end
use MOM_hor_index, only : hor_index_type, hor_index_init
Expand All @@ -91,6 +91,7 @@ module MOM
use MOM_set_visc, only : set_viscous_BBL, set_viscous_ML, set_visc_init
use MOM_set_visc, only : set_visc_register_restarts, set_visc_CS
use MOM_sponge, only : init_sponge_diags, sponge_CS
use MOM_state_initialization, only : MOM_initialize_state
use MOM_sum_output, only : write_energy, accumulate_net_input
use MOM_sum_output, only : MOM_sum_output_init, sum_output_CS
use MOM_ALE_sponge, only : init_ALE_sponge_diags, ALE_sponge_CS
Expand Down Expand Up @@ -860,6 +861,7 @@ subroutine step_MOM(forces, fluxes, sfc_state, Time_start, time_interval, CS, &

end subroutine step_MOM

!> Time step the ocean dynamics, including the momentum and continuity equations
subroutine step_MOM_dynamics(forces, p_surf_begin, p_surf_end, dt, dt_thermo, &
bbl_time_int, CS, Time_local, Waves)
type(mech_forcing), intent(in) :: forces !< A structure with the driving mechanical forces
Expand Down Expand Up @@ -1478,7 +1480,8 @@ subroutine step_offline(forces, fluxes, sfc_state, Time_start, time_interval, CS

end subroutine step_offline

!> This subroutine initializes MOM.
!> Initialize MOM, including memory allocation, setting up parameters and diagnostics,
!! initializing the ocean state variables, and initializing subsidiary modules
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)
Expand Down Expand Up @@ -2444,7 +2447,7 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &

end subroutine initialize_MOM

!> This subroutine finishes initializing MOM and writes out the initial conditions.
!> Finishe initializing MOM and writes out the initial conditions.
subroutine finish_MOM_initialization(Time, dirs, CS, restart_CSp)
type(time_type), intent(in) :: Time !< model time, used in this routine
type(directories), intent(in) :: dirs !< structure with directory paths
Expand Down Expand Up @@ -2518,7 +2521,7 @@ subroutine register_diags(Time, G, GV, IDs, diag)
Time, 'Instantaneous Sea Surface Height', 'm')
end subroutine register_diags

!> This subroutine sets up clock IDs for timing various subroutines.
!> Set up CPU clock IDs for timing various subroutines.
subroutine MOM_timing_init(CS)
type(MOM_control_struct), intent(in) :: CS !< control structure set up by initialize_MOM.

Expand Down Expand Up @@ -2609,7 +2612,7 @@ subroutine set_restart_fields(GV, param_file, CS, restart_CSp)

end subroutine set_restart_fields

!> This subroutine applies a correction to the sea surface height to compensate
!> Apply a correction to the sea surface height to compensate
!! for the atmospheric pressure (the inverse barometer).
subroutine adjust_ssh_for_p_atm(tv, G, GV, ssh, p_atm, use_EOS)
type(thermo_var_ptrs), intent(in) :: tv !< A structure pointing to various thermodynamic variables
Expand Down Expand Up @@ -2646,8 +2649,8 @@ subroutine adjust_ssh_for_p_atm(tv, G, GV, ssh, p_atm, use_EOS)

end subroutine adjust_ssh_for_p_atm

!> This subroutine sets the surface (return) properties of the ocean
!! model by setting the appropriate fields in sfc_state. Unused fields
!> 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.
subroutine extract_surface_state(CS, sfc_state)
type(MOM_control_struct), pointer :: CS !< Master MOM control structure
Expand Down Expand Up @@ -2991,7 +2994,7 @@ subroutine get_ocean_stocks(CS, mass, heat, salt, on_PE_only)

end subroutine get_ocean_stocks

!> End of model
!> End of ocean model, including memory deallocation
subroutine MOM_end(CS)
type(MOM_control_struct), pointer :: CS !< MOM control structure

Expand Down
8 changes: 3 additions & 5 deletions src/core/MOM_checksum_packages.F90
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
!> Provides routines that do checksums of groups of MOM variables
module MOM_checksum_packages

! This file is part of MOM6. See LICENSE.md for the license.

! This module provdes a several routines that do check-sums of groups
! This module provides several routines that do check-sums of groups
! of variables in the various dynamic solver routines.

use MOM_debugging, only : hchksum, uvchksum
Expand Down Expand Up @@ -110,10 +111,7 @@ subroutine MOM_thermo_chksum(mesg, tv, G, haloshift)
!! thermodynamic variables.
type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure.
integer, optional, intent(in) :: haloshift !< The width of halos to check (default 0).
! Arguments: mesg - A message that appears on the chksum lines.
! (in) tv - A structure containing pointers to any thermodynamic
! fields that are in use.
! (in) G - The ocean's grid structure.

integer :: is, ie, js, je, nz, hs
is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = G%ke
hs=1; if (present(haloshift)) hs=haloshift
Expand Down
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