From d1c0f4f776f0b1d027296c67abf3d6f0be82cffc Mon Sep 17 00:00:00 2001
From: Helen Kershaw <20047007+hkershaw-brown@users.noreply.github.com>
Date: Tue, 6 Jan 2026 14:40:53 -0500
Subject: [PATCH] feat: add clamping variables to MOM6

fixes #1028
---
 models/MOM6/model_mod.f90  |  8 ++++----
 models/MOM6/readme.rst     | 21 +++++++++++++++------
 models/MOM6/work/input.nml | 10 +++++-----
 3 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/models/MOM6/model_mod.f90 b/models/MOM6/model_mod.f90
index 7121b5402..a2f3f6668 100644
--- a/models/MOM6/model_mod.f90
+++ b/models/MOM6/model_mod.f90
@@ -60,8 +60,8 @@ module model_mod
                               init_time => fail_init_time, &
                               init_conditions => fail_init_conditions, &
                               convert_vertical_obs, adv_1step, &
-                              parse_variables, &
-                              MAX_STATE_VARIABLE_FIELDS
+                              parse_variables_clamp, &
+                              MAX_STATE_VARIABLE_FIELDS_CLAMP
 
 implicit none
 private
@@ -127,7 +127,7 @@ module model_mod
 character(len=256) :: ocean_geometry = 'ocean_geometry.nc'
 integer  :: assimilation_period_days      = 1
 integer  :: assimilation_period_seconds   = 0
-character(len=vtablenamelength) :: model_state_variables(MAX_STATE_VARIABLE_FIELDS) = ' '
+character(len=vtablenamelength) :: model_state_variables(MAX_STATE_VARIABLE_FIELDS_CLAMP) = ' '
 character(len=NF90_MAX_NAME) :: layer_name = 'Layer'
 logical :: use_pseudo_depth = .false. ! use pseudo depth instead of sum(layer thickness) for vertical location
 
@@ -178,7 +178,7 @@ subroutine static_init_model()
 ! parse_variables converts the character table that was read in from
 ! model_nml:model_state_variables to a state_var_type that can be passed
 ! to add_domain
-dom_id = add_domain(template_file, parse_variables(model_state_variables))
+dom_id = add_domain(template_file, parse_variables_clamp(model_state_variables))
 
 model_size = get_domain_size(dom_id)
 
diff --git a/models/MOM6/readme.rst b/models/MOM6/readme.rst
index e8bc5d6a5..144c29a6e 100644
--- a/models/MOM6/readme.rst
+++ b/models/MOM6/readme.rst
@@ -74,12 +74,12 @@ The namelist options for DART-MOM6 are as follows:
     &model_nml
        template_file = 'mom6.r.nc',
        ocean_geometry = 'ocean_geometry.nc',
-       static_file = 'c.e22.GMOM.T62_g16.nuopc.001.mom6.static.nc',
-       model_state_variables        = 'Salt ', 'QTY_SALINITY             ', 'UPDATE',
-                                      'Temp ', 'QTY_POTENTIAL_TEMPERATURE', 'UPDATE',
-                                      'u    ', 'QTY_U_CURRENT_COMPONENT  ', 'UPDATE',
-                                      'v    ', 'QTY_V_CURRENT_COMPONENT  ', 'UPDATE',
-                                      'h    ', 'QTY_LAYER_THICKNESS      ', 'UPDATE',
+       static_file = 'static.nc',
+       model_state_variables        = 'Salt ', 'QTY_SALINITY             ', 'NA', 'NA', 'UPDATE',
+                                      'Temp ', 'QTY_POTENTIAL_TEMPERATURE', 'NA', 'NA', 'UPDATE',
+                                      'u    ', 'QTY_U_CURRENT_COMPONENT  ', 'NA', 'NA', 'UPDATE',
+                                      'v    ', 'QTY_V_CURRENT_COMPONENT  ', 'NA', 'NA', 'UPDATE',
+                                      'h    ', 'QTY_LAYER_THICKNESS      ', 'NA', 'NA', 'UPDATE',
        assimilation_period_days     = 1
        assimilation_period_seconds  = 0
        use_pseudo_depth = .false. ! use pseudo depth instead of sum(layer thickness) for vertical location
@@ -104,6 +104,15 @@ The namelist options for DART-MOM6 are as follows:
          geolat_v(:,:) Latitude of meridional velocity (Cv) point
 
 
+* ``model_state_variables`` defines the list of model variables from the MOM6 restart file that will be included in the DART state. Each row in the table should have the following fields:
+
+    - **NetCDF variable name**: Name of the variable in the MOM6 restart file (e.g., 'Salt').
+    - **DART Quantity**: The DART quantity associated with the variable (e.g., 'QTY_SALINITY').
+    - **Clamping lower bound**: Minimum allowed value for the variable when writing out restarts (use 'NA' for no bound).
+    - **Clamping upper bound**: Maximum allowed value for the variable when writing out restarts (use 'NA' for no bound).
+    - **UPDATE or NO_COPY_BACK**: Use 'UPDATE' to allow DART to update this variable during assimilation, or 'NO_COPY_BACK' to prevent updates (variable will be read but not written back).
+
+
 Vertical Coordinate
 -------------------
 
diff --git a/models/MOM6/work/input.nml b/models/MOM6/work/input.nml
index 875e70cc5..7c6c32700 100644
--- a/models/MOM6/work/input.nml
+++ b/models/MOM6/work/input.nml
@@ -142,11 +142,11 @@
    template_file = 'mom6.r.nc', 
    static_file = 'mom6.static.nc',
    ocean_geometry = 'ocean_geometry.nc',
-   model_state_variables        = 'Salt ', 'QTY_SALINITY             ', 'UPDATE',
-                                  'Temp ', 'QTY_POTENTIAL_TEMPERATURE', 'UPDATE',
-                                  'u    ', 'QTY_U_CURRENT_COMPONENT  ', 'UPDATE',
-                                  'v    ', 'QTY_V_CURRENT_COMPONENT  ', 'UPDATE',
-                                  'h    ', 'QTY_LAYER_THICKNESS      ', 'UPDATE',
+   model_state_variables        = 'Salt ', 'QTY_SALINITY             ', 'NA', 'NA', 'UPDATE',
+                                  'Temp ', 'QTY_POTENTIAL_TEMPERATURE', 'NA', 'NA', 'UPDATE',
+                                  'u    ', 'QTY_U_CURRENT_COMPONENT  ', 'NA', 'NA', 'UPDATE',
+                                  'v    ', 'QTY_V_CURRENT_COMPONENT  ', 'NA', 'NA', 'UPDATE',
+                                  'h    ', 'QTY_LAYER_THICKNESS      ', 'NA', 'NA', 'UPDATE',
    /
 
 &utilities_nml