Moved pkg/MOM6_DA_hook to config_src/external

- Removed two git submodules and added bare interfaces to
  config_src/exernal/ODA_hooks/
- Added some missing documentation

.gitmodules

@@ -4,9 +4,3 @@
 [submodule "pkg/GSW-Fortran"]
 	path = pkg/GSW-Fortran
 	url = https://github.com/TEOS-10/GSW-Fortran.git
-[submodule "pkg/MOM6_DA_hooks"]
-	path = pkg/MOM6_DA_hooks
-	url = https://github.com/MJHarrison-GFDL/MOM6_DA_hooks.git
-[submodule "pkg/geoKdTree"]
-	path = pkg/geoKdTree
-	url = https://github.com/travissluka/geoKdTree.git

config_src/external/GFDL_ocean_BGC/README.md

@@ -3,4 +3,4 @@ GFDL_ocean_BGC
 
 These APIs reflect those for the GFDL ocean_BGC available at https://github.com/NOAA-GFDL/ocean_BGC.
 
-The modules in this directory do not do any computations. They simple reflect the APIs of the above package.
+The modules in this directory do not do any computations. They simply reflect the APIs of the above package.

config_src/external/ODA_hooks/README.md

@@ -0,0 +1,9 @@
+ODA_hooks
+=========
+
+These APIs reflect those for the ocean data assimilation hooks similar to https://github.com/MJHarrison-GFDL/MOM6_DA_hooks
+
+The modules in this directory do not do any computations. They simply reflect the APIs of the above package.
+
+- kdtree.f90 - would come from https://github.com/travissluka/geoKdTree
+- ocean_da_core.F90, ocean_da_types.F90, write_ocean_obs.F90 were copied from https://github.com/MJHarrison-GFDL/MOM6_DA_hooks

config_src/external/ODA_hooks/kdtree.f90

@@ -0,0 +1,12 @@
+!> A null version of K-d tree from geoKdTree
+module kdtree
+  implicit none
+  private
+
+  public :: kd_root
+
+  !> A K-d tree tpe
+  type kd_root
+    integer :: dummy !< To stop a compiler from doing nothing
+  end type kd_root
+end module kdtree

config_src/external/ODA_hooks/ocean_da_core.F90

@@ -0,0 +1,90 @@
+!> A set of dummy interfaces for compiling the MOM6 DA driver code.
+module ocean_da_core_mod
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!
+! This module contains a set of dummy interfaces for compiling the MOM6 DA
+! driver code. These interfaces are not finalized and will be replaced by supported
+! interfaces at some later date.
+!
+! 3/22/18
+! [email protected]
+!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  use mpp_domains_mod, only : domain2d
+  use time_manager_mod, only : time_type, set_time, get_date
+  ! ODA_tools modules
+  use ocean_da_types_mod, only : ocean_profile_type, grid_type
+
+
+  implicit none
+  private
+  public :: ocean_da_core_init, open_profile_dataset
+  public :: get_profiles, copy_profiles
+
+contains
+
+  !> Initialize ODA
+  subroutine ocean_da_core_init(Domain, T_grid, Profiles, model_time)
+    type(domain2d), pointer, intent(in) :: Domain !< MOM type for the local domain`
+    type(grid_type), pointer, intent(in) :: T_grid !< MOM grid type for the local domain
+    type(ocean_profile_type), pointer :: Profiles
+    !< This is an unstructured recursive list of profiles
+    !< which are either within the localized domain corresponding
+    !< to the Domain argument, or the global profile list
+    type(time_type), intent(in) :: model_time !< Model time
+
+    Profiles=>NULL()
+    return
+  end subroutine ocean_da_core_init
+
+  !> Open a profile dataset
+  subroutine open_profile_dataset(Profiles, Domain, T_grid, &
+                  filename, time_start, time_end, obs_variable, localize)
+    type(ocean_profile_type), pointer :: Profiles
+    !< This is an unstructured recursive list of profiles
+    !< which are either within the localized domain corresponding
+    !< to the Domain argument, or the global profile list
+    type(domain2d), pointer, intent(in) :: Domain !< MOM type for the local domain
+    type(grid_type), pointer, intent(in) :: T_grid !< MOM grid type for the local domain
+    character(len=*), intent(in) :: filename !< filename containing profile data
+    type(time_type), intent(in) :: time_start, time_end !< start and end times for the analysis
+    integer, intent(in), optional :: obs_variable !< If present, then extract corresponding data
+    !< from file, otherwise, extract all available data which.
+    logical, intent(in), optional :: localize !< Localize the observations to the current computational domain
+
+    return
+
+  end subroutine open_profile_dataset
+
+  !> Get profiles obs relevant to current analysis interval
+  subroutine get_profiles(model_time, Profiles, Current_profiles)
+    type(time_type), intent(in) :: model_time
+    type(ocean_profile_type), pointer :: Profiles
+    type(ocean_profile_type), pointer :: Current_profiles
+
+    Profiles=>NULL()
+    Current_Profiles=>NULL()
+
+    return
+  end subroutine get_profiles
+
+  !> Copy profiles at current analysis step from a linked list to an array
+  !! feasible now since the number of localized current profiles is small
+  subroutine copy_profiles(Current_profiles, Profiles)
+    type(ocean_profile_type), pointer :: Current_profiles
+    type(ocean_profile_type), pointer, dimension(:) :: Profiles
+
+    return
+
+  end subroutine copy_profiles
+
+  !> Copy observations
+  subroutine copy_obs(obs_in, obs_out)
+    type(ocean_profile_type), pointer :: obs_in
+    type(ocean_profile_type), pointer :: obs_out
+
+    return
+  end subroutine copy_obs
+
+end module ocean_da_core_mod

config_src/external/ODA_hooks/ocean_da_types.F90

@@ -0,0 +1,126 @@
+!> This module contains a set of data structures and interfaces for compiling the MOM6 DA
+!! driver code.
+module ocean_da_types_mod
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!
+! This module contains a set of data structures and interfaces for compiling the MOM6 DA
+! driver code. This code is not yet finalized and will be replaced by supported
+! software at some later date.
+!
+! 3/22/18
+! [email protected]
+!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+#ifndef MAX_LEVS_FILE_
+#define MAX_LEVS_FILE_ 50
+#endif
+
+#ifndef MAX_LINKS_
+#define MAX_LINKS_ 100
+#endif
+
+!============================================================
+! This module contains type declarations and default values
+! for oda modules.
+!============================================================
+
+! Contact: [email protected] and [email protected]
+
+  use time_manager_mod, only : time_type
+  !use obs_tools_mod, only : obs_def_type
+  !use mpp_domains_mod, only : domain2d
+
+  implicit none
+
+  private
+
+  integer, parameter, public :: MAX_LEVELS_FILE = MAX_LEVS_FILE_ !< Controls record length for optimal storage
+  integer, parameter, public :: MAX_LINKS = MAX_LINKS_ !< Maximum number of records per profile for storage for profiles
+  integer, parameter, public :: UNKNOWN = 0
+
+  integer, save, public :: TEMP_ID = 1
+  integer, save, public :: SALT_ID = 2
+  real, parameter, public :: MISSING_VALUE = -1.e10
+
+  !> Type for ocean state in DA space (same decomposition and vertical grid)
+  type, public :: OCEAN_CONTROL_STRUCT
+     integer :: 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
+     integer, dimension(:), pointer :: id_t=>NULL(), id_s=>NULL()  !< diagnostic IDs for temperature and salinity
+     integer, dimension(:), pointer :: id_u=>NULL(), id_v=>NULL()     !< diagnostic IDs for zonal and meridional velocity
+     integer, dimension(:), pointer :: id_ssh=>NULL()  !< diagnostic IDs for SSH
+  end type OCEAN_CONTROL_STRUCT
+
+  !> Profile
+  type, public :: ocean_profile_type
+     integer :: variable !< variable ids are defined by the ocean_types module (e.g. TEMP_ID, SALT_ID)
+     integer :: inst_type !< instrument types are defined by platform class (e.g. MOORING, DROP, etc.) and instrument type (XBT, CDT, etc.)
+     integer :: nvar !< number of observations types associated with the current profile
+     real    :: project !< e.g. FGGE, COARE, ACCE, ...
+     real    :: probe !< MBT, XBT, drifting buoy
+     real    :: ref_inst !< instrument (thermograph, hull sensor, ...)
+     integer :: wod_cast_num !< NODC world ocean dataset unique id
+     real    :: fix_depth !< adjust profile depths (for XBT drop rate corrections)
+     real    :: ocn_vehicle !< ocean vehicle type
+     real    :: database_id !< a unique profile id
+     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
+     integer :: profile_flag_s !< an overall flag for the profile salinity
+     real :: lat, lon !< latitude and longitude (degrees E and N)
+     logical :: accepted !< logical flag to disable a profile
+     integer :: nlinks !< number of links used to construct the profile (when reading from disk)
+     type(ocean_profile_type), pointer :: next=>NULL() !< all profiles are stored as linked list.
+     type(ocean_profile_type), pointer :: prev=>NULL()
+     type(ocean_profile_type), pointer :: cnext=>NULL() ! current profiles are stored as linked list.
+     type(ocean_profile_type), pointer :: cprev=>NULL()
+     integer :: nbr_xi, nbr_yi ! nearest neighbor model gridpoint for the profile
+     real :: nbr_dist ! distance to nearest neighbor model gridpoint
+     real, dimension(:), pointer :: depth
+     real, dimension(:), pointer :: data_t => NULL(), data_s => NULL()
+     real, dimension(:), pointer :: data
+     !integer, dimension(:), pointer :: flag_t
+     !integer, dimension(:), pointer :: flag_s ! level-by-level flags for salinity
+     !::sdu:: For now ECDA use flag as a logical, will likely change in future releases.
+     logical, dimension(:), pointer :: flag
+     real    :: temp_err, salt_err ! measurement error
+     !real, dimension(:), pointer :: ms_t ! ms temperature by level
+     !real, dimension(:), pointer :: ms_s ! ms salinity by level
+     real, dimension(:), pointer :: ms_inv => NULL()
+     real, dimension(:), pointer :: ms => NULL()
+!     type(obs_def_type), dimension(:), pointer :: obs_def => NULL()
+     type(time_type) :: time
+     integer         :: yyyy
+     integer         :: mmdd
+     !type(time_type), pointer :: Model_time ! each profile can be associated with a first-guess field with an associated time and grid
+     !type(grid_type), pointer :: Model_grid
+     real :: i_index, j_index ! model longitude and latitude indices respectively
+     real, dimension(:), pointer :: k_index ! model depth indices
+     type(time_type) :: tdiff      ! positive difference between model time and observation time
+  end type ocean_profile_type
+
+  !> Grid information for ODA purposes, including arrays of
+  !! lat, lon, depth, thickness, basin and land mask
+  type, public :: grid_type
+     real, pointer, dimension(:,:) :: x=>NULL(), y=>NULL()
+     !real, pointer, dimension(:,:) :: x_bound=>NULL(), y_bound=>NULL()
+     !real, pointer, dimension(:,:) :: dx=>NULL(), dy=>NULL()
+     real, pointer, dimension(:,:,:) :: z=>NULL()
+     real, pointer, dimension(:,:,:) :: h=>NULL()
+     !real, pointer, dimension(:) :: z_bound=>NULL()
+     !real, pointer, dimension(:) :: dz => NULL()
+     real, pointer, dimension(:,:) :: basin_mask => NULL()
+     real, pointer, dimension(:,:,:) :: mask => NULL()
+     !type(domain2d), pointer :: Dom ! FMS domain type
+     !logical :: cyclic
+     integer :: ni, nj, nk
+  end type grid_type
+
+end module ocean_da_types_mod

config_src/external/ODA_hooks/write_ocean_obs.F90

@@ -0,0 +1,60 @@
+!> Dummy interfaces for writing ODA data
+module write_ocean_obs_mod
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!
+! This module contains a set of dummy interfaces for compiling the MOM6 DA
+! driver code. These interfaces are not finalized and will be replaced by supported
+! interfaces at some later date.
+!
+! 3/22/18
+! [email protected]
+!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+ use ocean_da_types_mod, only : ocean_profile_type
+ use time_manager_mod, only : time_type, get_time, set_date, operator ( - )
+
+ implicit none
+
+ private
+
+ public :: open_profile_file, write_profile, close_profile_file, &
+      write_ocean_obs_init
+
+contains
+
+!> Open a profile file
+integer function open_profile_file(name, nvar, grid_lon, grid_lat,thread,fset)
+  character(len=*), intent(in) :: name !< File name
+  integer, intent(in), optional :: nvar !< Number of variables
+  real, dimension(:), optional, intent(in) :: grid_lon !< Longitude [degreeE]
+  real, dimension(:), optional, intent(in) :: grid_lat !< Latitude [degreeN]
+  integer, intent(in), optional :: thread !< Thread
+  integer, intent(in), optional :: fset !< File set 
+
+  open_profile_file=-1
+end function open_profile_file
+
+!> Write a profile
+subroutine write_profile(unit,profile)
+  integer, intent(in) :: unit !< File unit
+  type(ocean_profile_type), intent(in) :: profile !< Profile
+
+  return
+end subroutine write_profile
+
+!> Close a profile file
+subroutine close_profile_file(unit)
+  integer, intent(in) :: unit !< File unit
+
+  return
+end subroutine close_profile_file
+
+!> Initialize write_ocean_obs module
+subroutine write_ocean_obs_init()
+
+  return
+end subroutine write_ocean_obs_init
+
+end module write_ocean_obs_mod