Merge branch 'main' into ensemble-manager-no-op

.gitignore

@@ -90,6 +90,8 @@ gitm_to_netcdf
 netcdf_to_gitm_blocks
 streamflow_obs_diag
 cam_dart_obs_preprocessor
+aether_to_dart
+dart_to_aether
 
 # Observation converter exectutables
 convert_aviso

CHANGELOG.rst

@@ -22,6 +22,18 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**March 12 2024 :: MITgcm/N-BLING with Compressed Staggered Grids. Tag v11.3.0**
+
+- The DART-MITgcm code now supports compressed grids, especially suited for areas like 
+  the Red Sea where land occupies more than 90% of the domain.  
+  Built upon work *contributed by Jiachen Liu*.
+- Allows writing the BGC fields into MITgcm's pickup files.
+- Allows different compression for the regular and staggered grids.
+
+**March 12 2024 :: Aether lat-lon. Tag v11.2.0**
+
+- Aether lat-lon interface added to DART.
+
 **March 11 2024 :: SEIR model for infectious diseases. Tag v11.1.0**
 
 - Added SEIR model which simulates the spread of infectious diseases, for example COVID-19.

assimilation_code/modules/utilities/netcdf_utilities_mod.f90

@@ -63,7 +63,7 @@ module netcdf_utilities_mod
           nc_begin_define_mode,           &
           nc_end_define_mode,             &
           nc_synchronize_file,            &
-          NF90_MAX_NAME, NF90_MAX_VAR_DIMS
+          NF90_MAX_NAME, NF90_MAX_VAR_DIMS, NF90_FILL_REAL
 
 
 ! note here that you only need to distinguish between

assimilation_code/programs/model_mod_check/model_mod_check.f90

@@ -416,7 +416,7 @@ subroutine check_meta_data( iloc )
                                    kind_index=qty_index, &
                                    kind_string=qty_string)
 
-write(string1,'("index ",i11," is i,j,k",3(1x,i4)," and is in domain ",i2)') &
+write(string1,'("index ",i11," is i,j,k",3(1x,i10)," and is in domain ",i2)') &
                   iloc, ix, iy, iz, dom_id
 write(string2,'("is quantity ", I4,", ",A)') var_type, trim(qty_string)//' at location'
 call write_location(0,loc,charstring=string3)
@@ -556,9 +556,12 @@ subroutine check_all_meta_data()
                                    kind_string=qty_string)
 
    ! CLM has (potentially many) columns and needs i7 ish precision
-   write(string1,'(i11,1x,''i,j,k'',3(1x,i7),'' domain '',i2)') &
+!    write(string1,'(i11,1x,''i,j,k'',3(1x,i7),'' domain '',i2)') &
+!                   iloc, ix, iy, iz, dom_id
+   ! EL: integer to short for the new I/O method
+   ! Change to long int to avoid problems
+   write(string1,'(i21,1x,''i,j,k'',3(1x,i21),'' domain '',i2)') &
                   iloc, ix, iy, iz, dom_id
-
    call get_state_meta_data(iloc, loc, var_type)
    metadata_qty_string = trim(get_name_for_quantity(var_type))
 

conf.py

@@ -21,7 +21,7 @@
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '11.1.0'
+release = '11.3.0'
 root_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

index.rst

@@ -439,6 +439,7 @@ References
    :hidden:
 
    models/9var/readme
+   models/aether_lat-lon/readme
    models/am2/readme
    models/bgrid_solo/readme
    models/cam-fv/readme

models/MITgcm_ocean/model_mod.f90

@@ -20,7 +20,7 @@ module model_mod
                                   get_close_state, get_close_obs, set_location, &
                                   VERTISHEIGHT, get_location, is_vertical, &
                                   convert_vertical_obs, convert_vertical_state
-
+! EL use only nc_check was here, deleted for now for testing
 use    utilities_mod,      only : error_handler, E_ERR, E_WARN, E_MSG, &
                                   logfileunit, get_unit, do_output, to_upper, &
                                   find_namelist_in_file, check_namelist_read, &
@@ -56,7 +56,10 @@ module model_mod
                                   get_index_start, get_index_end, &
                                   get_dart_vector_index, get_num_variables, &
                                   get_domain_size, &
-                                  get_io_clamping_minval
+                                  get_io_clamping_minval, get_kind_index
+
+use netcdf_utilities_mod,  only : nc_open_file_readonly, nc_get_variable, & 
+                                  nc_get_dimension_size, nc_close_file
 
 use netcdf
 
@@ -255,9 +258,16 @@ module model_mod
 ! standard MITgcm namelist and filled in here.
 
 integer :: Nx=-1, Ny=-1, Nz=-1    ! grid counts for each field
+integer :: comp2d = -1, comp3d=-1, comp3dU = -1, comp3dV = -1 ! size of commpressed variables
 
 ! locations of cell centers (C) and edges (G) for each axis.
 real(r8), allocatable :: XC(:), XG(:), YC(:), YG(:), ZC(:), ZG(:)
+real(r4), allocatable :: XC_sq(:), YC_sq(:), XG_sq(:), YG_sq(:)
+real(r8), allocatable :: ZC_sq(:)
+
+integer, allocatable :: Xc_Ti(:), Yc_Ti(:), Zc_Ti(:)
+integer, allocatable :: Xc_Ui(:), Yc_Ui(:), Zc_Ui(:)
+integer, allocatable :: Xc_Vi(:), Yc_Vi(:), Zc_Vi(:) 
 
 real(r8)        :: ocean_dynamics_timestep = 900.0_r4
 integer         :: timestepcount = 0
@@ -277,7 +287,6 @@ module model_mod
 integer, parameter :: NUM_STATE_TABLE_COLUMNS = 5
 character(len=vtablenamelength) :: mitgcm_variables(NUM_STATE_TABLE_COLUMNS, MAX_STATE_VARIABLES ) = ' '
 
-
 character(len=256) :: model_shape_file = ' '
 integer  :: assimilation_period_days = 7
 integer  :: assimilation_period_seconds = 0
@@ -292,8 +301,9 @@ module model_mod
 logical :: go_to_dart    = .false.
 logical :: do_bgc        = .false.
 logical :: log_transform = .false.
+logical :: compress      = .false.
 
-namelist /trans_mitdart_nml/ go_to_dart, do_bgc, log_transform
+namelist /trans_mitdart_nml/ go_to_dart, do_bgc, log_transform, compress
 
 ! /pkg/mdsio/mdsio_write_meta.F writes the .meta files 
 type MIT_meta_type
@@ -327,6 +337,7 @@ subroutine static_init_model()
 
 integer :: i, iunit, io
 integer :: ss, dd
+integer :: ncid ! for reading compressed coordinates
 
 ! The Plan:
 !
@@ -528,13 +539,62 @@ subroutine static_init_model()
 domain_id = add_domain(model_shape_file, nvars, &
                     var_names, quantity_list, clamp_vals, update_list )
 
+if (compress) then ! read in compressed coordinates
+
+   ncid    = nc_open_file_readonly(model_shape_file)
+   comp2d  = nc_get_dimension_size(ncid, 'comp2d' , 'static_init_model', model_shape_file)
+   comp3d  = nc_get_dimension_size(ncid, 'comp3d' , 'static_init_model', model_shape_file)
+   comp3dU = nc_get_dimension_size(ncid, 'comp3dU', 'static_init_model', model_shape_file)
+   comp3dV = nc_get_dimension_size(ncid, 'comp3dV', 'static_init_model', model_shape_file)
+
+   allocate(XC_sq(comp3d))
+   allocate(YC_sq(comp3d))
+   allocate(ZC_sq(comp3d))  ! ZC is r8
+
+   allocate(XG_sq(comp3d))
+   allocate(YG_sq(comp3d))
+
+   allocate(Xc_Ti(comp3d))
+   allocate(Yc_Ti(comp3d))
+   allocate(Zc_Ti(comp3d))
+
+   allocate(Xc_Ui(comp3dU))
+   allocate(Yc_Ui(comp3dU))
+   allocate(Zc_Ui(comp3dU))
+
+   allocate(Xc_Vi(comp3dV))
+   allocate(Yc_Vi(comp3dV))
+   allocate(Zc_Vi(comp3dV))
+
+   call nc_get_variable(ncid, 'XCcomp', XC_sq)
+   call nc_get_variable(ncid, 'YCcomp', YC_sq)
+   call nc_get_variable(ncid, 'ZCcomp', ZC_sq)
+
+   call nc_get_variable(ncid, 'XGcomp', XG_sq)
+   call nc_get_variable(ncid, 'YGcomp', YG_sq)
+
+   call nc_get_variable(ncid, 'Xcomp_ind', Xc_Ti)
+   call nc_get_variable(ncid, 'Ycomp_ind', Yc_Ti)
+   call nc_get_variable(ncid, 'Zcomp_ind', Zc_Ti)
+
+   call nc_get_variable(ncid, 'Xcomp_indU', Xc_Ui)
+   call nc_get_variable(ncid, 'Ycomp_indU', Yc_Ui)
+   call nc_get_variable(ncid, 'Zcomp_indU', Zc_Ui)
+
+   call nc_get_variable(ncid, 'Xcomp_indV', Xc_Vi)
+   call nc_get_variable(ncid, 'Ycomp_indV', Yc_Vi)
+   call nc_get_variable(ncid, 'Zcomp_indV', Zc_Vi)
+
+   call nc_close_file(ncid)
+
+endif
+
 model_size = get_domain_size(domain_id)
 
 if (do_output()) write(*,*) 'model_size = ', model_size
 
 end subroutine static_init_model
 
-
 function get_model_size()
 !------------------------------------------------------------------
 !
@@ -954,6 +1014,63 @@ function lon_dist(lon1, lon2)
 end function lon_dist
 
 
+function get_compressed_dart_vector_index(iloc, jloc, kloc, dom_id, var_id)
+!=======================================================================
+!
+
+! returns the dart vector index for the compressed state
+
+integer, intent(in) :: iloc, jloc, kloc
+integer, intent(in) :: dom_id, var_id
+integer(i8)         :: get_compressed_dart_vector_index
+
+integer     :: i    ! loop counter
+integer     :: qty
+integer(i8) :: offset
+
+offset = get_index_start(dom_id, var_id)
+
+qty = get_kind_index(dom_id, var_id)
+
+get_compressed_dart_vector_index = -1
+
+! MEG: Using the already established compressed indices
+!
+! 2D compressed variables
+if (qty == QTY_SEA_SURFACE_HEIGHT .or. qty == QTY_SURFACE_CHLOROPHYLL ) then
+   do i = 1, comp2d
+      if (Xc_Ti(i) == iloc .and. Yc_Ti(i) == jloc .and. Zc_Ti(i) == 1) then
+         get_compressed_dart_vector_index = offset + i - 1
+      endif
+   enddo
+   return
+endif
+
+! 3D compressed variables
+if (qty == QTY_U_CURRENT_COMPONENT) then 
+   do i = 1, comp3dU
+      if (Xc_Ui(i) == iloc .and. Yc_Ui(i) == jloc .and. Zc_Ui(i) == kloc) then 
+         get_compressed_dart_vector_index = offset + i - 1
+      endif  
+   enddo
+elseif (qty == QTY_V_CURRENT_COMPONENT) then
+   do i = 1, comp3dV
+      if (Xc_Vi(i) == iloc .and. Yc_Vi(i) == jloc .and. Zc_Vi(i) == kloc) then 
+         get_compressed_dart_vector_index = offset + i - 1
+      endif  
+   enddo
+else
+   do i = 1, comp3d
+      if (Xc_Ti(i) == iloc .and. Yc_Ti(i) == jloc .and. Zc_Ti(i) == kloc) then 
+         get_compressed_dart_vector_index = offset + i - 1
+      endif  
+   enddo
+endif
+
+
+end function get_compressed_dart_vector_index
+
+
 function get_val(lon_index, lat_index, level, var_id, state_handle,ens_size, masked)
 !=======================================================================
 !
@@ -971,24 +1088,28 @@ function get_val(lon_index, lat_index, level, var_id, state_handle,ens_size, mas
 
 if ( .not. module_initialized ) call static_init_model
 
-state_index = get_dart_vector_index(lon_index, lat_index, level, domain_id, var_id)
-get_val = get_state(state_index,state_handle)
+masked = .false.
 
-! Masked returns false if the value is masked
-! A grid variable is assumed to be masked if its value is FVAL. 
-! Just to maintain legacy, we also assume that A grid variable is assumed 
-! to be masked if its value is exactly 0.
-! See discussion in lat_lon_interpolate.
+if (compress) then
 
-! MEG CAUTION: THE ABOVE STATEMENT IS INCORRECT
-! trans_mitdart already looks for 0.0 and makes them FVAL
-! So, in the condition below we don't need to check for zeros
-! The only mask is FVAL
-masked = .false.
-do i=1,ens_size
-!   if(get_val(i) == FVAL .or. get_val(i) == 0.0_r8 ) masked = .true.
-    if(get_val(i) == FVAL) masked = .true.
-enddo
+   state_index = get_compressed_dart_vector_index(lon_index, lat_index, level, domain_id, var_id)
+
+   if (state_index .ne. -1) then
+      get_val = get_state(state_index,state_handle)
+   else
+      masked = .true.
+   endif
+
+else
+
+   state_index = get_dart_vector_index(lon_index, lat_index, level, domain_id, var_id)
+   get_val = get_state(state_index,state_handle)
+
+   do i=1,ens_size  ! HK this is checking the whole ensemble, can you have different masks for each ensemble member?
+       if(get_val(i) == FVAL) masked = .true.
+   enddo
+
+endif
 
 end function get_val
 
@@ -1079,16 +1200,28 @@ subroutine get_state_meta_data(index_in, location, qty)
 
 call get_model_variable_indices(index_in, iloc, jloc, kloc, kind_index = qty)
 
-lon   = XC(iloc)
-lat   = YC(jloc)
-depth = ZC(kloc)
+if (compress) then ! all variables ae 1D
+   lon   = XC_sq(iloc)
+   lat   = YC_sq(iloc)
+   depth = ZC_sq(iloc)
+   ! Acounting for variables those on staggered grids
+   if (qty == QTY_U_CURRENT_COMPONENT) lon   = XG_sq(iloc)
+   if (qty == QTY_V_CURRENT_COMPONENT) lat   = YG_sq(iloc)
+else
+
+   lon   = XC(iloc)
+   lat   = YC(jloc)
+   depth = ZC(kloc)
+
+   ! Acounting for variables those on staggered grids
+   if (qty == QTY_U_CURRENT_COMPONENT) lon   = XG(iloc)
+   if (qty == QTY_V_CURRENT_COMPONENT) lat   = YG(jloc)
+
+endif
 
-! Acounting for surface variables and those on staggered grids
 ! MEG: check chl's depth here
 if (qty == QTY_SEA_SURFACE_HEIGHT .or. &
     qty == QTY_SURFACE_CHLOROPHYLL) depth = 0.0_r8
-if (qty == QTY_U_CURRENT_COMPONENT) lon   = XG(iloc)
-if (qty == QTY_V_CURRENT_COMPONENT) lat   = YG(jloc)  
 
 location = set_location(lon, lat, depth, VERTISHEIGHT)
 
@@ -1297,6 +1430,8 @@ end subroutine nc_write_model_atts
 !------------------------------------------------------------------
 ! Create an ensemble of states from a single state.
 
+! Note if you perturb a compressed state, this will not be bitwise
+! with perturbing a non-compressed state.
 subroutine pert_model_copies(state_ens_handle, ens_size, pert_amp, interf_provided)
 
 type(ensemble_type), intent(inout) :: state_ens_handle

models/MITgcm_ocean/model_mod.nml

@@ -2,5 +2,6 @@
    assimilation_period_days     = 7
    assimilation_period_seconds  = 0
    model_perturbation_amplitude = 0.2
+   model_shape_file             = 'mem01_reduced.nc'
   /
 

models/MITgcm_ocean/readme.rst

@@ -34,8 +34,14 @@ can be set in the ``&trans_mitdart_nml`` namelist in ``input.nml``.
    &trans_mitdart_nml
      do_bgc = .false.         ! change to .true. if doing bio-geo-chemistry
      log_transform = .false.  ! change to .true. if using log_transform
+     compress = .false.       ! change to .true. to compress the state vector
    /
 
+``compress = .true.`` can be used to generate netcdf files for use with DART which has missing values (land) removed.
+For some datasets this reduces the state vector size significantly. For example, the state vector size is
+reduced by approximately 90% for the Red Sea. The program ``expand_netcdf`` can be used to uncompress the netcdf
+file to view the data in a convenient form.
+
 
 .. Warning::