+Improve style compliance in config_src/external code

config_src/external/ODA_hooks/ocean_da_types.F90

@@ -1,90 +1,88 @@
 !> Dummy aata structures and methods for ocean data assimilation.
 module ocean_da_types_mod
 
-  use MOM_time_manager, only : time_type
+use MOM_time_manager, only : time_type
 
-  implicit none
+implicit none ; private
 
-  private
+!> Example type for ocean ensemble DA state
+type, public :: OCEAN_CONTROL_STRUCT
+  integer :: ensemble_size        !< ensemble size
+  real, pointer, dimension(:,:,:)   :: SSH => NULL() !< sea surface height across ensembles [m]
+  real, pointer, dimension(:,:,:,:) :: h => NULL() !< layer thicknesses across ensembles [m or kg m-2]
+  real, pointer, dimension(:,:,:,:) :: T => NULL() !< layer potential temperature across ensembles [degC]
+  real, pointer, dimension(:,:,:,:) :: S => NULL() !< layer salinity across ensembles [ppt]
+  real, pointer, dimension(:,:,:,:) :: U => NULL() !< layer zonal velocity across ensembles [m s-1]
+  real, pointer, dimension(:,:,:,:) :: V => NULL() !< layer meridional velocity across ensembles [m s-1]
+end type OCEAN_CONTROL_STRUCT
 
-  !> Example type for ocean ensemble DA state
-  type, public :: OCEAN_CONTROL_STRUCT
-     integer :: ensemble_size        !< ensemble size
-     real, pointer, dimension(:,:,:)   :: SSH=>NULL() !<sea surface height (m) across ensembles
-     real, pointer, dimension(:,:,:,:) :: h=>NULL() !<layer thicknesses (m or kg) across ensembles
-     real, pointer, dimension(:,:,:,:) :: T=>NULL() !<layer potential temperature (degC) across ensembles
-     real, pointer, dimension(:,:,:,:) :: S=>NULL() !<layer salinity (psu or g kg-1) across ensembles
-     real, pointer, dimension(:,:,:,:) :: U=>NULL() !<layer zonal velocity (m s-1) across ensembles
-     real, pointer, dimension(:,:,:,:) :: V=>NULL() !<layer meridional velocity (m s-1) across ensembles
-  end type OCEAN_CONTROL_STRUCT
+!> Example of a profile type
+type, public :: ocean_profile_type
+  integer :: inst_type !< A numeric code indicating the type of instrument (e.g. ARGO drifter, CTD, ...)
+  logical :: initialized !< a True value indicates that this profile has been allocated for use
+  logical :: colocated !< a True value indicated that the measurements of (num_variables) data are
+                       !! co-located in space-time
+  integer :: ensemble_size !< size of the ensemble of model states used in association with this profile
+  integer :: num_variables !< number of measurement types associated with this profile.
+  integer, pointer, dimension(:) :: var_id !< variable ids are defined by the ocean_types module
+  integer :: platform !< platform types are defined by platform class (e.g. MOORING, DROP, etc.)
+                      !! and instrument type (XBT, CDT, etc.)
+  integer :: levels !< number of levels in the current profile
+  integer :: basin_mask !< 1:Southern Ocean, 2:Atlantic Ocean, 3:Pacific Ocean,
+                        !! 4:Arctic Ocean, 5:Indian Ocean, 6:Mediterranean Sea, 7:Black Sea,
+                        !! 8:Hudson Bay, 9:Baltic Sea, 10:Red Sea, 11:Persian Gulf
+  integer :: profile_flag !< an overall flag for the profile
+  real :: lat      !< latitude [degrees_N]
+  real :: lon      !< longitude [degrees_E]
+  logical :: accepted !< logical flag to disable a profile
+  type(time_type) :: time_window !< The time window associated with this profile
+  real, pointer, dimension(:) :: obs_error  !< The observation error by variable [various units]
+  real  :: loc_dist   !< The impact radius of this observation [m]
+  type(ocean_profile_type), pointer :: next => NULL() !< all profiles are stored as linked list.
+  type(ocean_profile_type), pointer :: prev => NULL() !< previous
+  type(ocean_profile_type), pointer :: cnext => NULL() !< current profiles are stored as linked list.
+  type(ocean_profile_type), pointer :: cprev => NULL() !< previous
+  integer :: nbr_xi !< x nearest neighbor model gridpoint for the profile
+  integer :: nbr_yi !< y nearest neighbor model gridpoint for the profile
+  real :: nbr_dist !< distance to nearest neighbor model gridpoint [m]
+  logical :: compute !< profile is within current compute domain
+  real, dimension(:,:), pointer :: depth => NULL() !< depth of measurement [m]
+  real, dimension(:,:), pointer :: data => NULL() !< data by variable type [various units]
+  integer, dimension(:,:), pointer :: flag => NULL() !< flag by depth and variable type
+  real, dimension(:,:,:), pointer :: forecast => NULL() !< ensemble member first guess
+  real, dimension(:,:,:), pointer :: analysis => NULL() !< ensemble member analysis
+  type(forward_operator_type), pointer :: obs_def => NULL() !< observation forward operator
+  type(time_type) :: time !< profile time type
+  real :: i_index !< model longitude indices respectively
+  real :: j_index !< model latitude indices respectively
+  real, dimension(:,:), pointer :: k_index !< model depth indices
+  type(time_type) :: tdiff !< difference between model time and observation time
+  character(len=128) :: filename !< a filename
+end type ocean_profile_type
 
-  !> Example of a profile type
-  type, public :: ocean_profile_type
-     integer :: inst_type !< A numeric code indicating the type of instrument (e.g. ARGO drifter, CTD, ...)
-     logical :: initialized !< a True value indicates that this profile has been allocated for use
-     logical :: colocated !< a True value indicated that the measurements of (num_variables) data are
-                          !! co-located in space-time
-     integer :: ensemble_size !< size of the ensemble of model states used in association with this profile
-     integer :: num_variables !< number of measurement types associated with this profile.
-     integer, pointer, dimension(:) :: var_id !< variable ids are defined by the ocean_types module
-     integer :: platform !< platform types are defined by platform class (e.g. MOORING, DROP, etc.)
-                         !! and instrument type (XBT, CDT, etc.)
-     integer :: levels !< number of levels in the current profile
-     integer :: basin_mask !< 1:Southern Ocean, 2:Atlantic Ocean, 3:Pacific Ocean,
-                           !! 4:Arctic Ocean, 5:Indian Ocean, 6:Mediterranean Sea, 7:Black Sea,
-                           !! 8:Hudson Bay, 9:Baltic Sea, 10:Red Sea, 11:Persian Gulf
-     integer :: profile_flag !< an overall flag for the profile
-     real :: lat      !< latitude [degrees_N]
-     real :: lon      !< longitude [degrees_E]
-     logical :: accepted !< logical flag to disable a profile
-     type(time_type) :: time_window !< The time window associated with this profile [s]
-     real, pointer, dimension(:) :: obs_error  !< The observation error by variable
-     real  :: loc_dist   !< The impact radius of this observation (m)
-     type(ocean_profile_type), pointer :: next=>NULL() !< all profiles are stored as linked list.
-     type(ocean_profile_type), pointer :: prev=>NULL() !< previous
-     type(ocean_profile_type), pointer :: cnext=>NULL() !< current profiles are stored as linked list.
-     type(ocean_profile_type), pointer :: cprev=>NULL() !< previous
-     integer :: nbr_xi !< x nearest neighbor model gridpoint for the profile
-     integer :: nbr_yi !< y nearest neighbor model gridpoint for the profile
-     real :: nbr_dist !< distance to nearest neighbor model gridpoint
-     logical :: compute !< profile is within current compute domain
-     real, dimension(:,:), pointer :: depth => NULL() !< depth of measurement [m]
-     real, dimension(:,:), pointer :: data => NULL() !< data by variable type
-     integer, dimension(:,:), pointer :: flag => NULL() !< flag by depth and variable type
-     real, dimension(:,:,:), pointer :: forecast => NULL() !< ensemble member first guess
-     real, dimension(:,:,:), pointer :: analysis => NULL() !< ensemble member analysis
-     type(forward_operator_type), pointer :: obs_def => NULL() !< observation forward operator
-     type(time_type) :: time !< profile time type
-     real :: i_index !< model longitude indices respectively
-     real :: j_index !< model latitude indices respectively
-     real, dimension(:,:), pointer :: k_index !< model depth indices
-     type(time_type) :: tdiff !< difference between model time and observation time
-     character(len=128) :: filename !< a filename
-  end type ocean_profile_type
+!>  Example forward operator type.
+type, public :: forward_operator_type
+  integer :: num                      !< how many?
+  integer, dimension(2) :: state_size !< for
+  integer, dimension(:), pointer :: state_var_index !< for flattened data
+  integer, dimension(:), pointer :: i_index !< i-dimension index
+  integer, dimension(:), pointer :: j_index !< j-dimension index
+  real, dimension(:), pointer :: coef !< coefficient
+end type forward_operator_type
 
-  !>  Example forward operator type.
-  type, public :: forward_operator_type
-     integer :: num                      !< how many?
-     integer, dimension(2) :: state_size !< for
-     integer, dimension(:), pointer :: state_var_index !< for flattened data
-     integer, dimension(:), pointer :: i_index !< i-dimension index
-     integer, dimension(:), pointer :: j_index !< j-dimension index
-     real, dimension(:), pointer :: coef !< coefficient
-  end type forward_operator_type
-
-  !> Grid type for DA
-  type, public :: grid_type
-     real, pointer, dimension(:,:) :: x=>NULL()    !< x
-     real, pointer, dimension(:,:) :: y=>NULL()    !< y
-     real, pointer, dimension(:,:,:) :: z=>NULL()  !< z
-     real, pointer, dimension(:,:,:) :: h=>NULL()  !< h
-     real, pointer, dimension(:,:) :: basin_mask => NULL() !< basin mask
-     real, pointer, dimension(:,:,:) :: mask => NULL()     !< land mask?
-     real, pointer, dimension(:,:) :: bathyT => NULL()     !< bathymetry at T points
-     logical :: tripolar_N    !< True for tripolar grids
-     integer :: ni !< ni
-     integer :: nj !< nj
-     integer :: nk !< nk
-  end type grid_type
+!> Grid type for DA
+type, public :: grid_type
+  real, pointer, dimension(:,:) :: x => NULL()    !< x
+  real, pointer, dimension(:,:) :: y => NULL()    !< y
+  real, pointer, dimension(:,:,:) :: z => NULL()  !< z
+  real, pointer, dimension(:,:,:) :: h => NULL()  !< h
+  real, pointer, dimension(:,:) :: basin_mask => NULL() !< basin mask
+  real, pointer, dimension(:,:,:) :: mask => NULL()     !< land mask?
+  real, pointer, dimension(:,:) :: bathyT => NULL()     !< bathymetry at T points [m]
+  logical :: tripolar_N    !< True for tripolar grids
+  integer :: ni !< ni
+  integer :: nj !< nj
+  integer :: nk !< nk
+end type grid_type
 
 end module ocean_da_types_mod

config_src/external/ODA_hooks/write_ocean_obs.F90

@@ -1,16 +1,12 @@
 !> Dummy interfaces for writing ODA data
 module write_ocean_obs_mod
 
+use ocean_da_types_mod, only : ocean_profile_type
+use MOM_time_manager, only : time_type, get_time, set_date
 
- use ocean_da_types_mod, only : ocean_profile_type
- use MOM_time_manager, only : time_type, get_time, set_date
+implicit none ; private
 
- implicit none
-
- private
-
- public :: open_profile_file, write_profile, close_profile_file, &
-            write_ocean_obs_init
+public :: open_profile_file, write_profile, close_profile_file, write_ocean_obs_init
 
 contains
 

config_src/external/drifters/MOM_particles.F90

@@ -1,26 +1,28 @@
 !> A set of dummy interfaces for compiling the MOM6 drifters code
 module MOM_particles_mod
 
+! This file is part of MOM6. See LICENSE.md for the license.
+
 use MOM_grid,         only : ocean_grid_type
 use MOM_time_manager, only : time_type, get_date, operator(-)
 use MOM_variables,    only : thermo_var_ptrs
+use particles_types_mod, only : particles, particles_gridded
 
+implicit none ; private
 
-use particles_types_mod, only: particles, particles_gridded
-
-public particles_run, particles_init, particles_save_restart, particles_end
+public particles, particles_run, particles_init, particles_save_restart, particles_end
 
 contains
 
 !> Initializes particles container "parts"
 subroutine particles_init(parts, Grid, Time, dt, u, v)
   ! Arguments
- type(particles), pointer, intent(out) :: parts !< Container for all types and memory
- type(ocean_grid_type), target, intent(in) :: Grid !< Grid type from parent model
- type(time_type), intent(in) :: Time !< Time type from parent model
- real, intent(in)            :: dt !< particle timestep in seconds
- real, dimension(:,:,:),intent(in)      :: u !< Zonal velocity field
- real, dimension(:,:,:),intent(in)      :: v !< Meridional velocity field
+  type(particles), pointer, intent(out) :: parts !< Container for all types and memory
+  type(ocean_grid_type), target, intent(in) :: Grid !< Grid type from parent model
+  type(time_type), intent(in) :: Time !< Time type from parent model
+  real, intent(in)            :: dt   !< particle timestep [s]
+  real, dimension(:,:,:), intent(in)    :: u !< Zonal velocity field [m s-1]
+  real, dimension(:,:,:), intent(in)    :: v !< Meridional velocity field [m s-1]
 
 end subroutine particles_init
 
@@ -29,30 +31,30 @@ subroutine particles_run(parts, time, uo, vo, ho, tv, stagger)
   ! Arguments
   type(particles), pointer :: parts !< Container for all types and memory
   type(time_type), intent(in) :: time !< Model time
-  real, dimension(:,:,:),intent(in) :: uo !< Ocean zonal velocity (m/s)
-  real, dimension(:,:,:),intent(in) :: vo !< Ocean meridional velocity (m/s)
-  real, dimension(:,:,:),intent(in) :: ho !< Ocean layer thickness [H ~> m or kg m-2]
-  type(thermo_var_ptrs), intent(in) :: tv !< structure containing pointers to available thermodynamic fields
+  real, dimension(:,:,:), intent(in) :: uo !< Ocean zonal velocity [m s-1]
+  real, dimension(:,:,:), intent(in) :: vo !< Ocean meridional velocity [m s-1]
+  real, dimension(:,:,:), intent(in) :: ho !< Ocean layer thickness [H ~> m or kg m-2]
+  type(thermo_var_ptrs),  intent(in) :: tv !< structure containing pointers to available thermodynamic fields
   integer, optional, intent(in) :: stagger !< Flag for whether velocities are staggered
 
 end subroutine particles_run
 
 
 !>Save particle locations (and sometimes other vars) to restart file
-subroutine particles_save_restart(parts,temp,salt)
-! Arguments
-type(particles), pointer :: parts !< Container for all types and memory
-real,dimension(:,:,:),optional,intent(in) :: temp !< Optional container for temperature
-real,dimension(:,:,:),optional,intent(in) ::  salt !< Optional container for salinity
+subroutine particles_save_restart(parts, temp, salt)
+  ! Arguments
+  type(particles), pointer :: parts !< Container for all types and memory
+  real, dimension(:,:,:), optional, intent(in) :: temp !< Optional container for temperature
+  real, dimension(:,:,:), optional, intent(in) :: salt !< Optional container for salinity
 
 end subroutine particles_save_restart
 
 !> Deallocate all memory and disassociated pointer
-subroutine particles_end(parts,temp,salt)
-! Arguments
-type(particles), pointer :: parts !< Container for all types and memory
-real,dimension(:,:,:),optional,intent(in) :: temp !< Optional container for temperature
-real,dimension(:,:,:),optional,intent(in) :: salt !< Optional container for salinity
+subroutine particles_end(parts, temp, salt)
+  ! Arguments
+  type(particles), pointer :: parts !< Container for all types and memory
+  real, dimension(:,:,:), optional, intent(in) :: temp !< Optional container for temperature
+  real, dimension(:,:,:), optional, intent(in) :: salt !< Optional container for salinity
 
 end subroutine particles_end
 

config_src/external/drifters/MOM_particles_types.F90

@@ -1,12 +1,15 @@
 !> Dummy data structures and methods for drifters package
 module particles_types_mod
 
+! This file is part of MOM6. See LICENSE.md for the license.
+
 use MOM_grid, only : ocean_grid_type
-use mpp_domains_mod, only: domain2D
+use MOM_domains, only: domain2D
 
+implicit none ; private
 
 !> Container for gridded fields
-type :: particles_gridded
+type, public :: particles_gridded
   type(domain2D), pointer :: domain !< MPP parallel domain
   integer :: halo !< Nominal halo width
   integer :: isc !< Start i-index of computational domain
@@ -60,7 +63,7 @@ module particles_types_mod
 
 
 !>xyt is a data structure containing particle position and velocity fields.
-type :: xyt
+type, public :: xyt
   real :: lon !< Longitude of particle (degree N or unit of grid coordinate)
   real :: lat !< Latitude of particle (degree N or unit of grid coordinate)
   real :: day      !< Day of this record (days)
@@ -77,7 +80,7 @@ module particles_types_mod
 end type xyt
 
 !>particle types are data structures describing a tracked particle
-type :: particle
+type, public :: particle
   type(particle), pointer :: prev=>null() !< Previous link in list
   type(particle), pointer :: next=>null() !< Next link in list
 ! State variables (specific to the particles, needed for restarts)
@@ -109,19 +112,19 @@ module particles_types_mod
 
 
 !>A buffer structure for message passing
-type :: buffer
+type, public :: buffer
   integer :: size=0 !< Size of buffer
   real, dimension(:,:), pointer :: data !< Buffer memory
 end type buffer
 
 !> A wrapper for the particle linked list (since an array of pointers is not allowed)
-type :: linked_list
+type, public :: linked_list
   type(particle), pointer :: first=>null() !< Pointer to the beginning of a linked list of parts
 end type linked_list
 
 
 !> A grand data structure for the particles in the local MOM domain
-type :: particles !; private
+type, public :: particles !; private
   type(particles_gridded) :: grd !< Container with all gridded data
   type(linked_list), dimension(:,:), allocatable :: list !< Linked list of particles
   type(xyt), pointer :: trajectories=>null() !< A linked list for detached segments of trajectories

config_src/external/stochastic_physics/get_stochy_pattern.F90

@@ -0,0 +1,22 @@
+! The are stubs for ocean stochastic physics
+! the fully functional code is available at
+! https://github.com/noaa-psd/stochastic_physics
+module get_stochy_pattern_mod
+
+! This file is part of MOM6. See LICENSE.md for the license.
+
+implicit none ; private
+
+public  :: write_stoch_restart_ocn
+
+contains
+
+!> Write the restart file for the stochastic physics perturbations.
+subroutine write_stoch_restart_ocn(sfile)
+  character(len=*) :: sfile   !< name of restart file
+
+  ! This stub function does not actually do anything.
+  return
+end subroutine write_stoch_restart_ocn
+
+end module get_stochy_pattern_mod