Merge pull request #726 from mgharamti/marbl-dart

1D Ocean Column MARBL Interface + Obs Converter

Author: hkershaw-brown

.gitignore

@@ -162,6 +162,8 @@ ssec_satwnd
 gts_to_dart
 littler_tf_dart
 rad_3dvar_to_dart
+bats_to_clim_obs
+bats_to_obs
 L1_AMSUA_to_netcdf
 convert_airs_L2
 convert_amsu_L1

CHANGELOG.rst

@@ -22,6 +22,22 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**September 10 2024:: MARBL_column. Tag 11.8.0**
+
+- Interface for MARBL_column for DART: 
+
+   - state estimation
+   - state and parameter estimation
+   - parameter estimation only
+
+- BATS observation converter, and BATS climatology scripting
+
+*contributed by Robin Armstrong*
+
+Bugfix:
+
+- fix for IO for NetCDF files when only some variables have the unlimited dimension  
+
 **August 29 2024 :: Bug fixes for shortest_time_between_assimilations and get_close_init. Tag 11.7.1**
 
 Bug fixes:

assimilation_code/modules/io/direct_netcdf_mod.f90

@@ -93,7 +93,7 @@ module direct_netcdf_mod
                                  get_index_start, get_index_end , get_num_dims, &
                                  create_diagnostic_structure, &
                                  end_diagnostic_structure, &
-                                 has_unlimited_dim
+                                 has_unlimited_dim, get_io_dim_ids
 
 use io_filenames_mod,     only : get_restart_filename, inherit_copy_units, &
                                  stage_metadata_type, get_file_description, &
@@ -858,16 +858,17 @@ subroutine read_variables(ncfile_in, var_block, start_var, end_var, domain)
    counts(:) = 1
 
    slice_start(:) = 1 ! default to read all dimensions start at 1
-
-   if (has_unlimited_dim(domain)) then
+   
+   ret = nf90_inquire(ncfile_in, unlimitedDimID=unlim_dimID)
+   call nc_check(ret, 'read_variables: nf90_inquire', 'unlimitedDimID')
+   
+   if (has_unlimited_dim(domain) .and. any(get_io_dim_ids(domain, i) ==  unlim_dimID )) then
 
       counts(num_dims) = 1 ! one slice of unlimited dimesion
-      counts(1:num_dims-1) = get_dim_lengths(domain, i) ! the state
+      counts(1:get_num_dims(domain, i)) = get_dim_lengths(domain, i) ! the state
 
       ! read latest time slice - hack to get started with tiegcm
       ! not sure if it will always be the last time slice
-      ret = nf90_inquire(ncfile_in, unlimitedDimID=unlim_dimID)
-      call nc_check(ret, 'read_variables: nf90_inquire', 'unlimitedDimID')
 
       if (unlim_dimID /= -1) then ! unlimited dimension exists
          ret = nf90_inquire_dimension(ncfile_in, unlim_dimID, len=slice_start(num_dims))
@@ -1588,15 +1589,17 @@ subroutine write_variables(ncid, var_block, start_var, end_var, domain, &
       slice_start(:) = 1 ! default to read all dimensions starting at 1
       counts(:) = 1
 
-      if (has_unlimited_dim(domain)) then
+      ret = nf90_inquire(ncid, unlimitedDimID=unlim_dimID)
+      call nc_check(ret, 'read_variables: nf90_inquire', 'unlimitedDimID')
+
+      if (has_unlimited_dim(domain) .and. any(get_io_dim_ids(domain, i) ==  unlim_dimID )) then
 
          counts(num_dims) = 1 ! one slice of unlimited dimesion
          counts(1:get_num_dims(domain, i)) = get_dim_lengths(domain, i)
 
          ! write the latest time slice - HK hack to get started with tiegcm
          ! not sure if it will always be the last time slice
-         ret = nf90_inquire(ncid, unlimitedDimID=unlim_dimID)
-         call nc_check(ret, 'write_variables: nf90_inquire', 'unlimitedDimID')
+         
          if (unlim_dimID /= -1) then ! unlimited dimension exists
             ret = nf90_inquire_dimension(ncid, unlim_dimID, len=slice_start(num_dims))
             call nc_check(ret, 'write_variables: nf90_inquire dimension', 'unlimitedDim length')

assimilation_code/modules/observations/default_quantities_mod.f90

@@ -72,6 +72,8 @@
 !   QTY_CWP_PATH_ZERO
 !   QTY_DISSOLVED_INORGANIC_CARBON
 !   QTY_DISSOLVED_INORGANIC_IRON
+!   QTY_DISSOLVED_INORGANIC_SIO3
+!   QTY_DISSOLVED_ORGANIC_CARBON
 !   QTY_DISSOLVED_ORGANIC_NITROGEN
 !   QTY_DISSOLVED_ORGANIC_P
 !   QTY_DISSOLVED_OXYGEN
@@ -158,6 +160,7 @@
 !   QTY_LANDMASK
 !   QTY_LARGE_SCALE_STATE      desc="state varies with large time/space scale"
 !   QTY_LATENT_HEAT_FLUX
+!   QTY_LAYER_THICKNESS
 !   QTY_LEAF_AREA_INDEX
 !   QTY_LEAF_CARBON
 !   QTY_LEAF_NITROGEN
@@ -167,7 +170,9 @@
 !   QTY_LIVE_STEM_CARBON
 !   QTY_LIVE_STEM_NITROGEN
 !   QTY_MEAN_SOURCE
+!   QTY_MESOZOOPLANKTON_CARBON
 !   QTY_MICROWAVE_BRIGHT_TEMP
+!   QTY_MICROZOOPLANKTON_CARBON
 !   QTY_MINERAL_ACCUM
 !   QTY_MINERAL_COARSE
 !   QTY_MINERAL_NUCLEUS
@@ -382,6 +387,8 @@
 !   QTY_WIND_TURBINE_POWER
 !   QTY_W_CURRENT_COMPONENT
 !   QTY_X_LAMBDA
+!   QTY_COLUMN_DEPTH
+!   QTY_BGC_PARAM
 !
 ! END DART PREPROCESS QUANTITY DEFINITIONS
 

assimilation_code/modules/observations/ocean_quantities_mod.f90

@@ -32,11 +32,17 @@
 !   QTY_PHYTOPLANKTON_BIOMASS
 !   QTY_ALKALINITY
 !   QTY_DISSOLVED_INORGANIC_CARBON
+!   QTY_DISSOLVED_ORGANIC_CARBON
 !   QTY_DISSOLVED_ORGANIC_NITROGEN
 !   QTY_DISSOLVED_ORGANIC_P
 !   QTY_DISSOLVED_INORGANIC_IRON
 !   QTY_SURFACE_CHLOROPHYLL
 !   QTY_LAYER_THICKNESS
+!   QTY_COLUMN_DEPTH
+!   QTY_DISSOLVED_INORGANIC_SIO3
+!   QTY_MESOZOOPLANKTON_CARBON
+!   QTY_MICROZOOPLANKTON_CARBON
+!   QTY_BGC_PARAM
 !
 ! ! fixme - these units are hardcoded in obs_diag and shouldn't be
 !   QTY_U_WIND_COMPONENT

conf.py

@@ -21,7 +21,7 @@
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '11.7.1'
+release = '11.8.0'
 root_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

guide/available-observation-converters.rst

@@ -11,6 +11,7 @@ Each directory has at least one converter:
 -  ``AURA``: See ``DART/observations/obs_converters/AURA``
 -  ``Aviso+/CMEMS``: :doc:`../observations/obs_converters/AVISO/AVISO`
 -  ``Ameriflux``: :doc:`../observations/obs_converters/Ameriflux/level4_to_obs`
+-  ``BATS``: :doc:`../observations/obs_converters/BATS/readme`
 -  ``CHAMP``: :doc:`../observations/obs_converters/CHAMP/work/README`
 -  ``cice``: :doc:`../observations/obs_converters/cice/cice_to_obs`
 -  ``CNOFS``: See ``DART/observations/obs_converters/CNOFS``

index.rst

@@ -361,6 +361,7 @@ References
    observations/obs_converters/Ameriflux/fluxnetfull_to_obs
    observations/obs_converters/Ameriflux/level4_to_obs
    observations/obs_converters/CHAMP/work/README
+   observations/obs_converters/BATS/readme
    observations/obs_converters/cice/cice_to_obs
    observations/obs_converters/CONAGUA/README
    observations/obs_converters/COSMOS/COSMOS_to_obs
@@ -466,6 +467,7 @@ References
    models/lorenz_96_tracer_advection/readme
    models/forced_lorenz_96/readme
    models/MITgcm_ocean/readme
+   models/MARBL_column/readme
    models/MOM6/readme
    models/mpas_atm/readme
    models/mpas_atm/mpas_dart_obs_preprocess