NOC-MSM · b-barton · Sep 17, 2025 · Sep 16, 2025 · Sep 16, 2025 · Sep 16, 2025
diff --git a/docs/grid.md b/docs/grid.md
@@ -95,17 +95,18 @@ Calculate the missing horizontal grid variables and add them to grid.
 @author Ryan Patmore
 @author Anthony Wise
 
-## *class* grid.zgr.Z_Grid(zgr_file, name_map_file, hgr_type, e_dict, logger, dst=1)
+## *class* grid.zgr.Z_Grid(zgr_file, zgr_type, name_map_file, hgr_type, e_dict, logger, dst=1)
 
 > Bases: `object`<br>
 
-### *method* \_\_init\_\_(zgr_file, name_map_file, hgr_type, e_dict, logger, dst=1)
+### *method* \_\_init\_\_(zgr_file, zgr_type, name_map_file, hgr_type, e_dict, logger, dst=1)
 
 Master depth class.
 
 > ### Parameters<br>
 
 > zgr_file (str) : string of file for loading zgr data<br>
+> zgr_type (str) : zgr type from namelist zco, zps or sco<br>
 > name_map_file (str) : string of file for mapping variable names<br>
 > hgr_type (str) : horizontal grid type<br>
 > e_dict (dict) : dictionary of e1 and e2 scale factors<br>
@@ -116,7 +117,7 @@ Master depth class.
 
 > Depth (object) : Depth object<br>
 
-### *method* find_zgrid_type()
+### *method* find_zgrid_type(zgr_type)
 
 Find out what type of vertical grid is provided zco, zps or sigma levels (sco).
 

diff --git a/docs/index.md b/docs/index.md
@@ -59,6 +59,7 @@ The changes relative to the previous version (0.3.0) are:
 - Bug fix for 90 boundaries that meet diagonally to produce a 90 degree corner.
 - Some unit tests have been added and full integration tests.
 - Documentation has been updated and restructured.
+- sn_src_zgr_type and sn_dst_zgr_type are defined in the namelist.bdy
 
 **There is a new library for generating NEMO initial conditions called pyIC.**
 pyIC can be found at: [https://github.com/NOC-MSM/pyIC](https://github.com/NOC-MSM/pyIC)
@@ -198,6 +199,8 @@ Here we will summarise the main variables that will need changing to get started
 
 #### Key Namelist Parameters
 
+- `sn_src_zgr_type`
+- `sn_dst_zgr_type`
 - `sn_src_hgr`
 - `sn_src_zgr`
 - `sn_dst_hgr`
@@ -211,6 +214,11 @@ Here we will summarise the main variables that will need changing to get started
 - `ln_zinterp`
 - `nn_rimwidth`
 
+##### Vertical grid type
+
+- **`sn_src_zgr_type`**: The source vertical coordinate type. This can be 'zco', 'zps' or 'sco'. 'zco' for the z-coordinate full step which are not spatially verying, 'zps' for z-coordinate - partial steps which have some adjustment in height near the seabed and 'sco' for sigma or hybrid z-sigma-coordinates which get thicker or thinner depending on the bathymetry.
+- **`sn_dst_zgr_type`**: Same as `sn_src_zgr_type` but for destination vertical coordinate type.
+
 ##### File Paths
 
 Directory paths in bdy file can be relative or absolute.
@@ -448,6 +456,10 @@ Summary of minimum requirements:
 "e3uw" = * vertical scale factor distance between w-levels on u-grid (dims [t, z, y, x])
 "e3vw" = * vertical scale factor distance between w-levels on v-grid (dims [t, z, y, x])
 "e3fw" = * vertical scale factor distance between w-levels on f-grid (dims [t, z, y, x])
+
+"ln_zco" = * flag for zco vertical coordinates 1 for true, 0 for false often provided in domain_cfg.nc
+"ln_zps" = * flag for zps vertical coordinates 1 for true, 0 for false often provided in domain_cfg.nc
+"ln_sco" = * flag for sco vertical coordinates 1 for true, 0 for false often provided in domain_cfg.nc
 ```
 
 ### Step 5: Running pyBDY
@@ -473,6 +485,19 @@ The example child (destination) here is a regional NEMO model that covers the In
 
 Below is excerpts from an example *namelist.bdy*.
 
+This sections tells pybdy the vertical coordinate type of the parent (src) and child (dst). In this case the the parent is on constant z-levels and the child is on spatially varying sigma-levels.
+
+```
+!------------------------------------------------------------------------------
+!   vertical coordinate
+!------------------------------------------------------------------------------
+   sn_src_zgr_type = 'zco' ! vertical coordinate type: 'zco', 'zps' or 'sco'
+   sn_dst_zgr_type = 'sco' ! vertical coordinate type: 'zco', 'zps' or 'sco'
+                           ! 'zco' is z-coordinate - full    steps
+                           ! 'zps' is z-coordinate - partial steps
+                           ! 'sco' is s- or hybrid z-s-coordinate
+```
+
 Here the file paths are set. These can be absolute (i.e. starting with "/") or relative (i.e. starting with "./"). For help with what variables are needed in these files see [How to use pyBDY :student:](#how-to-use-pybdy-student). In the example case, the bathmetry file needed to be calculated before running pybdy. It may also be the case that you need to calculate variables like gdept for the sn_src_zgr file fore running pybdy. For setting up the grid_name_map.json see the JSON file example section below.
 
 ```
@@ -637,7 +662,10 @@ This is an example .json file: *grid_name_map.json*. It specifise the names of v
     "e3f": "e3f",
     "e3uw": "e3uw",
     "e3vw": "e3vw",
-    "e3fw": "e3fw"
+    "e3fw": "e3fw",
+    "ln_zco": "ln_zco",
+    "ln_zps": "ln_zps",
+    "ln_sco": "ln_sco"
   },
   "dst_variable_map": {
     "nav_lon": "nav_lon",
@@ -674,7 +702,10 @@ This is an example .json file: *grid_name_map.json*. It specifise the names of v
     "e3f": "e3f_0",
     "e3uw": "e3uw_0",
     "e3vw": "e3vw_0",
-    "e3fw": "e3fw"
+    "e3fw": "e3fw",
+    "ln_zco": "ln_zco",
+    "ln_zps": "ln_zps",
+    "ln_sco": "ln_sco"
   }
 }
 ```

diff --git a/docs/pybdy.gui.md b/docs/pybdy.gui.md
@@ -17,24 +17,24 @@ Initialise an APLpyNormalize instance.
 > Optional Keyword Parametersument<br>
 
 > *vmin*: [ None | float ]<br>
-> : Minimum pixel value to use for the scaling.<br>
+> :   Minimum pixel value to use for the scaling.<br>
 
 > *vmax*: [ None | float ]<br>
-> : Maximum pixel value to use for the scaling.<br>
+> :   Maximum pixel value to use for the scaling.<br>
 
 > *stretch*: [ ‘linear’ | ‘log’ | ‘sqrt’ | ‘arcsinh’ | ‘power’ ]<br>
-> : The stretch function to use (default is ‘linear’).<br>
+> :   The stretch function to use (default is ‘linear’).<br>
 
 > *vmid*: [ None | float ]<br>
-> : Mid-pixel value used for the log and arcsinh stretches. If<br>
-> set to None, a default value is picked.<br>
+> :   Mid-pixel value used for the log and arcsinh stretches. If<br>
+>     set to None, a default value is picked.<br>
 
 > *exponent*: [ float ]<br>
-> : if self.stretch is set to ‘power’, this is the exponent to use.<br>
+> :   if self.stretch is set to ‘power’, this is the exponent to use.<br>
 
 > *clip*: [ True | False ]<br>
-> : If clip is True and the given value falls outside the range,<br>
-> the returned value will be 0 or 1, whichever is closer.<br>
+> :   If clip is True and the given value falls outside the range,<br>
+>     the returned value will be 0 or 1, whichever is closer.<br>
 
 ### *method* inverse(value)
 
@@ -45,7 +45,7 @@ data value.
 
 value
 
-> : Normalized value.<br>
+> \: Normalized value.<br>
 
 # pybdy.gui.nemo_bdy_input_window module
 
@@ -286,7 +286,7 @@ Run callback for the dropdown in the settings.
 
 Run callback when the True/False dropdown for the settings,
 
-> : which has a boolean value, is changed.<br>
+> \: which has a boolean value, is changed.<br>
 
 ### *method* init_ui()
 
@@ -494,7 +494,7 @@ Refresh the canvas.
 
 This method looks at the list of points available and depending on the number of points
 
-> : in the list creates a point or line or a polygon and draws them.<br>
+> \: in the list creates a point or line or a polygon and draws them.<br>
 
 ### *method* reset()
 

diff --git a/docs/pybdy.md b/docs/pybdy.md
@@ -445,7 +445,7 @@ Interpolate source data onto destination vertical levels.
 > sc_bdy (np.array) : souce data [nz_sc, nbdy, 9]<br>
 > dst_dep (np.array) : the depth of the destination grid chunk [nz, nbdy]<br>
 > bdy_bathy (np.array): the destination grid bdy points bathymetry<br>
-> z_ind (np.array) : the indices of the sc depth above and below bdy<br>
+> z_ind (np.array) : the indices of the sc depth above and below bdy point<br>
 > z_dist (np.array) : the distance weights of the selected points<br>
 > num_bdy (int) : number of boundary points in chunk<br>
 > zinterp (bool) : vertical interpolation flag<br>
@@ -498,8 +498,8 @@ weightings for vector quantities.
 > DstCoord (obj) : destination grid information<br>
 > Grid (dict) : containing grid type ‘t’, ‘u’, ‘v’ and source time<br>
 > var_name (list) : netcdf file variable names (str)<br>
-> years (list) : years to extract (default [1979])<br>
-> months (list) : months to extract (default [11])<br>
+> grd (str) : grid to process ‘t’, ‘u’, ‘v’<br>
+> pair (str) : None or ‘uv’<br>
 
 > ### Returns<br>
 

diff --git a/docs/pybdy.tide.md b/docs/pybdy.tide.md
@@ -71,15 +71,15 @@ Convert the input contituents to index in the tidal constituents.
 > ### Parameters<br>
 
 > constituents: The list of constituents available from the source data<br>
-> : e.g. TPXO: [‘m2’, ‘s2’, ‘n2’, ‘k2’, ‘k1’, ‘o1’, ‘p1’, ‘q1’, ‘mf’, ‘mm’, ‘m4’, ‘ms4’, ‘mn4’]<br>
+> :   e.g. TPXO: [‘m2’, ‘s2’, ‘n2’, ‘k2’, ‘k1’, ‘o1’, ‘p1’, ‘q1’, ‘mf’, ‘mm’, ‘m4’, ‘ms4’, ‘mn4’]<br>
 
 > inputcons: The dictionary of constituents from the namelist with their numbers<br>
-> : e.g. {‘1’: “‘M2’”, ‘3’: “‘K2’”, ‘2’: “‘S2’”, ‘4’: “‘M4’”}<br>
+> :   e.g. {‘1’: “‘M2’”, ‘3’: “‘K2’”, ‘2’: “‘S2’”, ‘4’: “‘M4’”}<br>
 
 > ### Returns<br>
 
 > retindx: The indices (relative to the source data list) of the dictionary items from the namelist<br>
-> : e.g. [ 0. 3. 1. 10.]<br>
+> :   e.g. [ 0. 3. 1. 10.]<br>
 
 ## pybdy.tide.nemo_bdy_tide3.nemo_bdy_tide_rot(setup, DstCoord, Grid_T, Grid_U, Grid_V, comp)
 
@@ -140,7 +140,7 @@ TPXO9v5 only carries the bathymetry variable
 > return: mask dataarray.<br>
 
 > Useage:<br>
-> : self.grid[mask_name] = generate_landmask(bathy_name)<br>
+> :   self.grid[mask_name] = generate_landmask(bathy_name)<br>
 
 ### *method* interpolate_constituents(nc_dataset, real_var_name, img_var_name, lon_var_name, lat_var_name, lon, lat, height_data=None, maskname=None)
 

diff --git a/inputs/grid_name_map.json b/inputs/grid_name_map.json
@@ -40,7 +40,10 @@
             "e3f": "e3f",
             "e3uw": "e3uw",
             "e3vw": "e3vw",
-            "e3fw": "e3fw"
+            "e3fw": "e3fw",
+            "ln_zco": "ln_zco",
+            "ln_zps": "ln_zps",
+            "ln_sco": "ln_sco"
     },
     "dst_variable_map": {
             "nav_lon": "nav_lon",
@@ -77,6 +80,9 @@
             "e3f": "e3f",
             "e3uw": "e3uw",
             "e3vw": "e3vw",
-            "e3fw": "e3fw"
+            "e3fw": "e3fw",
+            "ln_zco": "ln_zco",
+            "ln_zps": "ln_zps",
+            "ln_sco": "ln_sco"
     }
 }
diff --git a/inputs/grid_name_map_readme.txt b/inputs/grid_name_map_readme.txt
@@ -75,3 +75,7 @@ In all cases "t" should be size 1. Pybdy does not deal with time varying grids.
 "e3uw" = * vertical scale factor distance between w-levels on u-grid (dims [t, z, y, x])
 "e3vw" = * vertical scale factor distance between w-levels on v-grid (dims [t, z, y, x])
 "e3fw" = * vertical scale factor distance between w-levels on f-grid (dims [t, z, y, x])
+
+"ln_zco" = * flag for zco vertical coordinates 1 for true, 0 for false often provided in domain_cfg.nc
+"ln_zps" = * flag for zps vertical coordinates 1 for true, 0 for false often provided in domain_cfg.nc
+"ln_sco" = * flag for sco vertical coordinates 1 for true, 0 for false often provided in domain_cfg.nc
diff --git a/inputs/namelist_local.bdy b/inputs/namelist_local.bdy
@@ -9,6 +9,15 @@
 !!
 !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
+!------------------------------------------------------------------------------
+!   vertical coordinate
+!------------------------------------------------------------------------------
+   sn_src_zgr_type = 'zps' ! vertical coordinate type: 'zco', 'zps' or 'sco'
+   sn_dst_zgr_type = 'zps' ! vertical coordinate type: 'zco', 'zps' or 'sco'
+                           ! 'zco' is z-coordinate - full    steps
+                           ! 'zps' is z-coordinate - partial steps
+                           ! 'sco' is s- or hybrid z-s-coordinate
+
 !------------------------------------------------------------------------------
 !  grid information
 !------------------------------------------------------------------------------

diff --git a/inputs/namelist_remote.bdy b/inputs/namelist_remote.bdy
@@ -9,6 +9,15 @@
 !!
 !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
+!------------------------------------------------------------------------------
+!   vertical coordinate
+!------------------------------------------------------------------------------
+   sn_src_zgr_type = 'sco' ! vertical coordinate type: 'zco', 'zps' or 'sco'
+   sn_dst_zgr_type = 'sco' ! vertical coordinate type: 'zco', 'zps' or 'sco'
+                           ! 'zco' is z-coordinate - full    steps
+                           ! 'zps' is z-coordinate - partial steps
+                           ! 'sco' is s- or hybrid z-s-coordinate
+
 !------------------------------------------------------------------------------
 !  grid information
 !------------------------------------------------------------------------------