Merge branch 'sox_implimentation_docs' of github.com:jules-lsm/jules-…

…lsm.github.io into sox_implimentation_docs

.github/workflows/build_docs.yml

@@ -0,0 +1,30 @@
+# This workflow ensures that required environment is activated, and ensures
+# that the JULES Sphinx documenation builds correctly.
+
+name: build_docs
+
+# Controls when the action will run
+on: 
+    push:
+    pull_request:
+
+    # Enables manual running from the Actions tab
+    workflow_dispatch:
+
+jobs:
+    build-and-deploy:
+      runs-on: ubuntu-latest
+
+      steps:
+        - name: checkout
+          uses: actions/checkout@v4
+
+        - name: Build documentation
+          run: |
+            conda update conda
+            conda env create -f environment.yml  
+            eval "$(conda shell.bash hook)"
+            conda activate jules-user-guide
+            cd user_guide/doc
+            make html
+

vn7.4/_sources/namelists/jules_vegetation.nml.rst.txt

@@ -554,6 +554,7 @@ This file sets the vegetation options. It contains one namelist called :nml:lst:
       Eqn.11 of that paper, and :ref:`Medlyn et al
       (2012)<References_vegetation>`. Note that as implemented the model uses a
       single parameter (g\ :sub:`1`, assuming that g\ :sub:`0` = 0).
+   3. The SOX model of :ref:`Eller et al. (2020)<References_vegetation>`
 
    .. warning::
 
@@ -940,6 +941,10 @@ This file sets the vegetation options. It contains one namelist called :nml:lst:
   model description – Part 2: Carbon fluxes and vegetation dynamics,
   Geosci. Model Dev., 4, 701-722,
   https://doi.org/10.5194/gmd-4-701-2011
+* Eller et al. (2020), Stomatal optimization based on xylem hydraulics
+  (SOX) improves land surface model simulation of vegetation responses
+  to climate. New Phytologist 226:
+  1622–1637 https://doi.org/10.1111/nph.16419
 * Harman, I.N. & Finnigan, J.J. (2007), A simple unified theory for
   flow in the canopy and roughness sublayer. Boundary-Layer Meteorol.
   123: 339. https://doi.org/10.1007/s10546-006-9145-6

vn7.4/_sources/namelists/pft_params.nml.rst.txt

@@ -337,6 +337,31 @@ ease the direct links to these documents are:
    Only used with the Medlyn model of stomatal conductance (:nml:mem:`JULES_VEGETATION::stomata_model` = 2).
 
 
+.. nml:group:: Only used with the SOX (Eller et al. 2020) model of stomatal conductance (:nml:mem:`JULES_VEGETATION::stomata_model` = 3). A value is required for each PFT.
+
+
+   .. nml:member:: sox_a_io
+
+      :type: real(npft)
+      :default: None
+
+      The shape parameter in the xylem vulnerability curve.
+
+   .. nml:member:: sox_p50_io
+
+      :type: real(npft)
+      :default: None
+
+      Xlem water potential at which xylem hydraulic conductance is half its maximum value (MPa).
+
+   .. nml:member:: sox_rp_min_io
+
+      :type: real(npft)
+      :default: None
+
+      Plant minimum hydraulic resistance (m2 s MPa/mol).
+
+
 .. nml:member:: g_leaf_0_io
 
    :type: real(npft)