Merge branch 'main' into updt_localization

.gitattributes

@@ -0,0 +1 @@
+*.ipynb linguist-detectable=false

.gitignore

@@ -71,6 +71,9 @@ rttov_test
 rttov_unit_tests
 dart_to_clm
 clm_to_dart
+dart_to_mit
+mit_to_dart
+create_ocean_obs
 
 # Directories to NOT IGNORE ... same as executable names
 # as far as I know, these must be listed after the executables

CHANGELOG.rst

@@ -22,6 +22,12 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**March 31 2022 :: MiTgcm-ocean NBLING. Tag: v9.16.0**
+
+- MITgcm-ocean interface updated to Manhattan.
+- Support for NBLING (ocean biogeochemistry) for MITgcm-ocean.
+- New observation converter for ocean color.
+
 **March 22 2022 :: CLM5-DART Tutorial. Tag: v9.15.0**
 
 - New CLM5-DART tutorial providing new users with 13 steps
@@ -31,7 +37,7 @@ The changes are now listed with the most recent at the top.
   files correctly and provide reproducibility
 
 
-**March 10th 2022 :: Tracer advection model. Tag v9.14.0**
+**March 10 2022 :: Tracer advection model. Tag v9.14.0**
 
 - New model for tracer advection based on Lorenz_96 using a
   Semi-Lagrangian scheme. 

README.rst

@@ -319,6 +319,7 @@ References
    observations/obs_converters/gnd_gps_vtec/README
    observations/obs_converters/gps/gps
    observations/obs_converters/ok_mesonet/ok_mesonet
+   observations/obs_converters/ocean_color/README
    observations/obs_converters/quikscat/QuikSCAT
    observations/obs_converters/even_sphere/README
    observations/obs_converters/obs_error/README
@@ -531,9 +532,7 @@ References
    :caption: non-compiling models
    :hidden:
 
-   models/MITgcm_ocean/trans_pv_sv
    models/MITgcm_ocean/create_ocean_obs
-   models/MITgcm_ocean/trans_sv_pv
    models/NCOMMAS/dart_to_ncommas
    models/NCOMMAS/ncommas_to_dart
 

assimilation_code/modules/observations/default_quantities_mod.f90

@@ -15,6 +15,7 @@
 !   QTY_3D_PARAMETER
 !   QTY_ABSOLUTE_HUMIDITY
 !   QTY_ABSORBED_PAR
+!   QTY_ALKALINITY
 !   QTY_ALTIMETER_TENDENCY
 !   QTY_AMMONIUM_SULPHATE
 !   QTY_AOD
@@ -69,6 +70,11 @@
 !   QTY_CONDENSATIONAL_HEATING
 !   QTY_CWP_PATH
 !   QTY_CWP_PATH_ZERO
+!   QTY_DISSOLVED_INORGANIC_CARBON
+!   QTY_DISSOLVED_INORGANIC_IRON
+!   QTY_DISSOLVED_ORGANIC_NITROGEN
+!   QTY_DISSOLVED_ORGANIC_P
+!   QTY_DISSOLVED_OXYGEN
 !   QTY_DEAD_ROOT_CARBON
 !   QTY_DEAD_ROOT_NITROGEN
 !   QTY_DEAD_STEM_CARBON
@@ -175,6 +181,7 @@
 !   QTY_NEUTRON_INTENSITY
 !   QTY_NEW_VOLCANIC_ASH
 !   QTY_NH3
+!   QTY_NITRATE_CONCENTRATION
 !   QTY_NITROGEN
 !   QTY_NO
 !   QTY_NO2
@@ -188,7 +195,9 @@
 !   QTY_O_N2_COLUMN_DENSITY_RATIO
 !   QTY_PAR_DIFFUSE
 !   QTY_PAR_DIRECT
+!   QTY_PHOSPHATE_CONCENTRATION
 !   QTY_PHOTO_AVAILABLE_RADIATION
+!   QTY_PHYTOPLANKTON_BIOMASS
 !   QTY_POTENTIAL_TEMPERATURE
 !   QTY_POWER_WEIGHTED_FALL_SPEED
 !   QTY_PRECIPITABLE_WATER
@@ -316,6 +325,7 @@
 !   QTY_SULFATE
 !   QTY_SULPHATED_DROPS
 !   QTY_SURFACE_ALBEDO
+!   QTY_SURFACE_CHLOROPHYLL
 !   QTY_SURFACE_ELEVATION
 !   QTY_SURFACE_EMISSIVITY
 !   QTY_SURFACE_HEAD

assimilation_code/modules/observations/ocean_quantities_mod.f90

@@ -26,6 +26,16 @@
 !   QTY_SEA_SURFACE_PRESSURE
 !   QTY_SEA_SURFACE_HEIGHT
 !   QTY_SEA_SURFACE_ANOMALY
+!   QTY_NITRATE_CONCENTRATION
+!   QTY_PHOSPHATE_CONCENTRATION
+!   QTY_DISSOLVED_OXYGEN
+!   QTY_PHYTOPLANKTON_BIOMASS
+!   QTY_ALKALINITY
+!   QTY_DISSOLVED_INORGANIC_CARBON
+!   QTY_DISSOLVED_ORGANIC_NITROGEN
+!   QTY_DISSOLVED_ORGANIC_P
+!   QTY_DISSOLVED_INORGANIC_IRON
+!   QTY_SURFACE_CHLOROPHYLL
 !
 ! ! 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 = '9.15.0'
+release = '9.16.0'
 master_doc = 'README'
 
 # -- General configuration ---------------------------------------------------

models/MITgcm_ocean/create_ocean_obs.f90

@@ -1,8 +1,6 @@
 ! DART software - Copyright UCAR. This open source software is provided
 ! by UCAR, "as is", without charge, subject to all terms of use at
 ! http://www.image.ucar.edu/DAReS/DART/DART_download
-!
-! $Id$
 
 program create_ocean_obs
 
@@ -12,24 +10,27 @@ program create_ocean_obs
 ! redefined to occur at NOON on the day they were observed.
 
 use         types_mod, only : r8, deg2rad, PI
+
 use  obs_sequence_mod, only : obs_sequence_type, write_obs_seq, &
                               static_init_obs_sequence, destroy_obs_sequence 
+
 use dart_MITocean_mod, only : real_obs_sequence
+
 use     utilities_mod, only : initialize_utilities, register_module, &
                               do_output, logfileunit, &
                               error_handler, finalize_utilities, E_ERR, E_MSG, &
                               find_namelist_in_file, check_namelist_read
+
 use  time_manager_mod, only : time_type, set_date, set_time, print_date, &
                               operator(+), set_calendar_type, GREGORIAN
 
 
 implicit none
 
 ! version controlled file description for error handling, do not edit
-character(len=256), parameter :: source   = &
-   "$URL$"
-character(len=32 ), parameter :: revision = "$Revision$"
-character(len=128), parameter :: revdate  = "$Date$"
+character(len=*), parameter :: source   = 'create_ocean_obs.f90'
+character(len=*), parameter :: revision = ''
+character(len=*), parameter :: revdate  = ''
 
 type(obs_sequence_type) :: seq
 
@@ -42,8 +43,8 @@ program create_ocean_obs
 
 integer :: year = 1996, month = 1, day = 1, tot_days = 31
 integer :: max_num = 800000
-character(len = 129) :: fname = 'raw_ocean_obs.txt'
-character(len = 129) :: output_name = 'raw_ocean_obs_seq.out'
+character(len=256) :: fname = 'raw_ocean_obs.txt'
+character(len=256) :: output_name = 'raw_ocean_obs_seq.out'
 logical :: hfradar = .false.
 
 real(r8) :: lon1 =   0.0_r8,  &   !  lower longitude bound
@@ -95,8 +96,3 @@ program create_ocean_obs
 
 end program create_ocean_obs
 
-! <next few lines under version control, do not edit>
-! $URL$
-! $Id$
-! $Revision$
-! $Date$

models/MITgcm_ocean/create_ocean_obs.rst

@@ -1,12 +1,6 @@
 PROGRAM ``create_ocean_obs``
 ============================
 
-.. attention::
-
-   ``MITgcm_ocean`` works with versions of DART *before* Manhattan (9.x.x) and has yet to be updated. If you are interested in
-   using ``MITgcm_ocean`` with more recent versions of DART, contact DAReS staff to assess the feasibility of an update.
-   Until that time, you should consider this documentation as out-of-date.
-
 
 ``create_ocean_obs`` is responsible for converting an interim ASCII file of ocean observations into a DART observation
 sequence file. The interim ASCII file is a simple 'whitespace separated' table where each row is an observation and each