update model notebooks towards release 0.1

ben1post · Jul 21, 2023 · 994ec57 · 994ec57
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diff --git a/notebooks/1_NP_Chemostat_ModelApplication.ipynb b/notebooks/1_NP_Chemostat_ModelApplication.ipynb
@@ -302,7 +302,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "23e697e2cba340188adfecdbfdee7f25",
+       "model_id": "36def5daea86469f849d58d29687e939",
        "version_major": 2,
        "version_minor": 0
       },
@@ -372,7 +372,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x107fed8a0>"
+       "<matplotlib.legend.Legend at 0x177cdfa60>"
       ]
      },
      "execution_count": 10,
@@ -407,7 +407,7 @@
     {
      "data": {
       "text/plain": [
-       "[<matplotlib.lines.Line2D at 0x14177dcc0>]"
+       "[<matplotlib.lines.Line2D at 0x178f55d80>]"
       ]
      },
      "execution_count": 11,
@@ -466,7 +466,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x15de9c610>"
+       "<matplotlib.legend.Legend at 0x179531000>"
       ]
      },
      "execution_count": 13,

diff --git a/notebooks/2_NPZD_Slab_ModelApplication.ipynb b/notebooks/2_NPZD_Slab_ModelApplication.ipynb
diff --git a/notebooks/3_NPxZx_SizeBased_ModelApplication.ipynb b/notebooks/3_NPxZx_SizeBased_ModelApplication.ipynb
diff --git a/notebooks/README.md b/notebooks/README.md
@@ -2,12 +2,17 @@
 
 Here the first models included within the library are presented in interactive Jupyter notebooks. 
 
-The notebooks show all steps from creating the _model setup_ object to analyzing model output and provide a template for further exploration and experimentation with the provided plankton community models.
+The notebooks show all steps from creating the _model setup_ object to analyzing model output and provide a template for further exploration and experimentation with the provided plankton community models. More detailed descriptions of the methods are given the manuscript accompanying the release.
 
 ## Model applications
 
 The following model applications are included in the Phydra library. All models are embedded in 0-dimensional physical settings.:
 
 - A simple NP (Nutrient-Phytoplankton) model in a chemostat setting.
 - A fully configured NPZD (Nutrient-Phytoplankton-Zooplankton-Detritus) model.
-- A complex size-structured NPZ model in a simplified physical setting.
+- A complex size-structured NPZ model in a simplified physical setting.
+
+
+## The framework
+
+Xarray-simlab-ODE extends [Xarray-simlab](https://xarray-simlab.readthedocs.io/en/latest/) to allow the modular construction, setup and execution of models based on ordinary differential equations, in an interactive workflow fully compatible with the Python scientific ecosystem through the [Xarray](https://docs.xarray.dev/en/stable/) data framework. You can read more about Xarray-simlab-ODE in the [XSO Documentation on ReadTheDocs](https://xarray-simlab-ode.readthedocs.io/en/latest/index.html).
diff --git a/phydra/models/__init__.py b/phydra/models/__init__.py
@@ -1,5 +1,5 @@
 from .chemostat import NPChemostat, NPChemostat_sinu
 
-from .slabocean import NPZDSlabOcean, NPZDSlabOcean_smith
+from .slabocean import NPZDSlabOcean, NPZDSlabOcean_3layer
 
 from .sizebased import NPxZxSizeBased
diff --git a/phydra/models/slabocean/__init__.py b/phydra/models/slabocean/__init__.py
@@ -1 +1 @@
-from ._models import NPZDSlabOcean, NPZDSlabOcean_smith
+from ._models import NPZDSlabOcean, NPZDSlabOcean_3layer
diff --git a/phydra/models/slabocean/_models.py b/phydra/models/slabocean/_models.py
@@ -30,7 +30,7 @@
     # Growth
     'Growth': EMPOWER_Growth_ML,
     'Nut_lim': EMPOWER_Monod_ML,
-    'Light_lim': EMPOWER_Smith_Anderson3Layer_ML,
+    'Light_lim': EMPOWER_Smith_LambertBeer_ML,
     'Temp_lim': EMPOWER_Eppley_ML,
 
     # Grazing
@@ -49,4 +49,4 @@
     'Forcings': StationForcingFromFile,
 })
 
-NPZDSlabOcean_smith = NPZDSlabOcean.update_processes({'Light_lim': EMPOWER_Smith_LambertBeer_ML})
+NPZDSlabOcean_3layer = NPZDSlabOcean.update_processes({'Light_lim': EMPOWER_Smith_Anderson3Layer_ML})