add a link to reference for modflow coupling

Author: SarahAlidoost

docs/notebooks/bmi_MODFLOW_coupling.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# STEMMUS_SCOPE & MODFLOW 6 BMI coupling\n",
     "\n",
-    "This Python notebook shows a simple example of BMI coupling between the STEMMUS_SCOPE model and the MODFLOW 6 model. The example is prepared for one of the PLUMBER2 dataset (https://researchdata.edu.au/plumber2-forcing-evaluation-surface-models/1656048): the LooBos site, the Netherlands (NL-Loo). To run this notebook, the following are required:\n",
+    "This Python notebook shows a simple example of BMI coupling between the STEMMUS_SCOPE model and the MODFLOW 6 model, based on research carried by \"M. Daoud\", as a part of [EcoExtreML](https://research-software-directory.org/projects/ecoextreml) project, for more info see [this reference](https://research.utwente.nl/en/publications/investigating-the-role-of-groundwater-in-mitigating-vegetation-wa). The example is prepared for one of the PLUMBER2 dataset (https://researchdata.edu.au/plumber2-forcing-evaluation-surface-models/1656048): the LooBos site, the Netherlands (NL-Loo). To run this notebook, the following are required:\n",
     "- Install the related packages:\n",
     "    - pyStemmusScope package (https://pystemmusscope.readthedocs.io/en/latest/).\n",
     "    - modflowapi Python package (https://github.com/MODFLOW-USGS/modflowapi?tab=readme-ov-file#installation).\n",
@@ -124,11 +124,11 @@
     }
    ],
    "source": [
-    "# Add the matlab runtime compiler locations: \n",
+    "# Add the matlab runtime compiler locations:\n",
     "matlab_version = 'R2023a'\n",
-    "matlab_path = '/opt/matlab/MATLAB_Runtime/' + matlab_version \n",
-    " \n",
-    "os.environ['LD_LIBRARY_PATH'] = (   \n",
+    "matlab_path = '/opt/matlab/MATLAB_Runtime/' + matlab_version\n",
+    "\n",
+    "os.environ['LD_LIBRARY_PATH'] = (\n",
     "    f\"{matlab_path}/runtime/glnxa64:\"\n",
     "    f\"{matlab_path}/bin/glnxa64:\"\n",
     "    f\"{matlab_path}/sys/os/glnxa64:\"\n",
@@ -262,7 +262,7 @@
    ],
    "source": [
     "sim = ApiSimulation.load(modflow)\n",
-    "gwf_name = sim.model_names[0] # groundwater flow model \n",
+    "gwf_name = sim.model_names[0] # groundwater flow model\n",
     "gwe_name = sim.model_names[1] # groundwater energy (heat) model\n",
     "gwf_name, gwe_name"
    ]
@@ -399,7 +399,7 @@
    "source": [
     "stemmus_scope.set_value(\"groundwater_elevation_top_aquifer\", top_elev)\n",
     "stemmus_scope.set_value(\"groundwater_head_bottom_layer\", gwhead_init)\n",
-    "stemmus_scope.set_value(\"groundwater_temperature\", gwtemp_init) "
+    "stemmus_scope.set_value(\"groundwater_temperature\", gwtemp_init)"
    ]
   },
   {
@@ -6650,9 +6650,9 @@
    ],
    "source": [
     "while modflow.get_current_time() < modflow.get_end_time():\n",
-    "    while stemmus_scope.get_current_time() < stemmus_scope.get_end_time(): \n",
-    "        \n",
-    "        # Get STEMMUS_SCOPE variables (soil moisture, soil temperature, groundwater recharge)  \n",
+    "    while stemmus_scope.get_current_time() < stemmus_scope.get_end_time():\n",
+    "\n",
+    "        # Get STEMMUS_SCOPE variables (soil moisture, soil temperature, groundwater recharge)\n",
     "        stemmus_scope.get_value(\"soil_moisture\", soil_moisture[i])\n",
     "        stemmus_scope.get_value(\"soil_temperature\", soil_temperature[i])\n",
     "        stemmus_scope.get_value(\"groundwater_recharge\", gw_recharge)\n",
@@ -6669,19 +6669,19 @@
     "        # Set STEMMUS_SCOPE variables (groundwater head, groundwater temperature)\n",
     "        stemmus_scope.set_value(\"groundwater_head_bottom_layer\", gwhead)\n",
     "        stemmus_scope.set_value(\"groundwater_temperature\", gwtemp)\n",
-    "        \n",
+    "\n",
     "        # Set MODFLOW 6 variables (groundwater recharge)\n",
-    "        kstp, kper = sim.kstp, sim.kper     \n",
+    "        kstp, kper = sim.kstp, sim.kper\n",
     "        if kstp == nstp - 1:\n",
-    "            # groundwater recharge per stress period = sum of groundwater recharge per time step \n",
+    "            # groundwater recharge per stress period = sum of groundwater recharge per time step\n",
     "            gw_recharge_nper = np.array([-1 * np.sum(gw_recharge_nstp) / 100]) # multiply by -1 due to different signs of both models\n",
     "            modflow.set_value(rch_tag, gw_recharge_nper)\n",
-    "            gw_recharge_nstp = np.array([]) \n",
-    "             \n",
-    "        # Track the simulation time of MODFLOW 6  \n",
+    "            gw_recharge_nstp = np.array([])\n",
+    "\n",
+    "        # Track the simulation time of MODFLOW 6\n",
     "        print('Updating MODFLOW Stress period ' + str(kper + 1) + ', time step ' + str(kstp + 1))\n",
     "        # print(kper  + 1, kstp + 1, gwhead, gwtemp)\n",
-    "       \n",
+    "\n",
     "        # Update models\n",
     "        stemmus_scope.update()\n",
     "        modflow.update()"