Add fenicsx and simplified Landlab solvers

wolf-sheep-soil-creep/README.md

@@ -3,7 +3,7 @@ title: Wolf-sheep-grass model with soil creep
 permalink: tutorials-wolf-sheep-soil-creep.html
 aliases:
   - /tutorials-wolf-sheep-soil-creep.html
-keywords: MESA, Landlab, wolf-sheep-grass, soil creep, ABM, agent-based modeling
+keywords: MESA, Landlab, FEniCSx, wolf-sheep-grass, soil creep, ABM, agent-based modeling
 summary: Example of bi-directional ABM-PDE coupling via preCICE.
 ---
 
@@ -31,6 +31,10 @@ Soil-Creep PDE participant:
 
 * Landlab. Numerical modeling of Earth surface dynamics. For more information, have a look at the [Landlab documentation](https://landlab.csdms.io/index.html).
 
+* Standalone reimplementation of the Landlab participant, tailored to this example.
+
+* FEniCSx. For more information, have a look at the [FEniCSx adapter](https://precice.org/adapter-fenicsx.html).
+
 Wolf-Sheep-Grass ABM participant:
 
 * MESA. Agent-based modeling (or ABM) framework. For more information have a look at the [MESA documentation](https://mesa.readthedocs.io/latest/index.html)
@@ -44,6 +48,20 @@ cd soil-creep-landlab
 ./run.sh
 ```
 
+or
+
+```bash
+cd soil-creep-simplified-landlab
+./run.sh
+```
+
+or
+
+```bash
+cd soil-creep-fenicsx
+./run.sh
+```
+
 and
 
 ```bash
@@ -53,7 +71,7 @@ cd wolf-sheep-grass-mesa
 
 ## Post-processing
 
-The soil-creep participant generates Python-based visualizations, which are written to `soil-creep-landlab/output`. The following examples were generated by setting `rng=42` in the `WolfSheepScenario` for the wolf-sheep-grass participant.
+The soil-creep participant generates Python-based visualizations, which are written to `soil-creep-landlab/output` or `soil-creep-fenicsx/output`, depending on which participant is used. The following examples were generated by Landlab with `rng=42` in the `WolfSheepScenario` for the wolf-sheep-grass participant.
 
 ![erosion/deposition patterns](images/tutorials-wolf-sheep-soil-creep-erosion_deposition_patterns.png)
 ![soil thickness](images/tutorials-wolf-sheep-soil-creep-soil_thickness.png)

wolf-sheep-soil-creep/precice-config.xml

@@ -1,69 +1,61 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 <precice-configuration>
+
   <log>
     <sink
       filter="%Severity% > debug"
       format="---[precice] %ColorizedSeverity% %Message%"
       enabled="true" />
   </log>
 
+
   <data:scalar name="Grass" />
   <data:scalar name="Soil" />
 
   <mesh name="Wolf-Sheep-Grass-Mesh" dimensions="2">
     <use-data name="Grass" />
+    <use-data name="Soil" />
   </mesh>
 
   <mesh name="Soil-Creep-Mesh" dimensions="2">
     <use-data name="Grass" />
-  </mesh>
-
-  <mesh name="Soil-Grass-Mesh" dimensions="2">
-    <use-data name="Soil" />
-  </mesh>
-
-  <mesh name="Soil-Depth-Mesh" dimensions="2">
     <use-data name="Soil" />
   </mesh>
 
   <participant name="Wolf-Sheep-Grass">
-    <receive-mesh name="Soil-Depth-Mesh" from="Soil-Creep" />
+    <receive-mesh name="Soil-Creep-Mesh" from="Soil-Creep" />
     <provide-mesh name="Wolf-Sheep-Grass-Mesh" />
-    <provide-mesh name="Soil-Grass-Mesh" />
     <write-data name="Grass" mesh="Wolf-Sheep-Grass-Mesh" />
-    <read-data name="Soil" mesh="Soil-Grass-Mesh" />
+    <read-data name="Soil" mesh="Wolf-Sheep-Grass-Mesh" />
     <mapping:nearest-neighbor
       direction="read"
-      from="Soil-Depth-Mesh"
-      to="Soil-Grass-Mesh"
+      from="Soil-Creep-Mesh"
+      to="Wolf-Sheep-Grass-Mesh"
       constraint="consistent" />
   </participant>
 
   <participant name="Soil-Creep">
     <receive-mesh name="Wolf-Sheep-Grass-Mesh" from="Wolf-Sheep-Grass" />
     <provide-mesh name="Soil-Creep-Mesh" />
-    <provide-mesh name="Soil-Depth-Mesh" />
     <read-data name="Grass" mesh="Soil-Creep-Mesh" />
-    <write-data name="Soil" mesh="Soil-Depth-Mesh" />
+    <write-data name="Soil" mesh="Soil-Creep-Mesh" />
     <mapping:nearest-neighbor
       direction="read"
       from="Wolf-Sheep-Grass-Mesh"
       to="Soil-Creep-Mesh"
       constraint="consistent" />
   </participant>
 
+
   <m2n:sockets acceptor="Wolf-Sheep-Grass" connector="Soil-Creep" exchange-directory=".." />
 
+
   <coupling-scheme:serial-explicit>
     <participants first="Soil-Creep" second="Wolf-Sheep-Grass" />
     <time-window-size value="2" />
     <max-time value="100" />
-    <exchange
-      data="Grass"
-      mesh="Wolf-Sheep-Grass-Mesh"
-      from="Wolf-Sheep-Grass"
-      to="Soil-Creep"
-      initialize="true" />
-    <exchange data="Soil" mesh="Soil-Depth-Mesh" from="Soil-Creep" to="Wolf-Sheep-Grass" />
+    <exchange data="Grass" mesh="Wolf-Sheep-Grass-Mesh" from="Wolf-Sheep-Grass" to="Soil-Creep" initialize="true"/>
+    <exchange data="Soil" mesh="Soil-Creep-Mesh" from="Soil-Creep" to="Wolf-Sheep-Grass" />
   </coupling-scheme:serial-explicit>
+
 </precice-configuration>

wolf-sheep-soil-creep/soil-creep-fenicsx/clean.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env sh
+set -e -u
+
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+cd "$SCRIPT_DIR"
+
+rm -rfv ./output/
+
+. ../../tools/cleaning-tools.sh
+
+clean_fenicsx .

wolf-sheep-soil-creep/soil-creep-fenicsx/precice-adapter-config.json

@@ -0,0 +1,19 @@
+{
+  "participant_name": "Soil-Creep",
+  "precice_config_file_path": "../precice-config.xml",
+  "interfaces": [
+    {
+      "mesh_name": "Soil-Creep-Mesh",
+      "write_data": [
+        {
+          "name": "Soil"
+        }
+      ],
+      "read_data": [
+        {
+          "name": "Grass"
+        }
+      ]
+    }
+  ]
+}

wolf-sheep-soil-creep/soil-creep-fenicsx/requirements.txt

@@ -0,0 +1,4 @@
+numpy >1, <2
+fenicsxprecice~=1.0
+matplotlib>=3,<4
+pyprecice~=3.0

wolf-sheep-soil-creep/soil-creep-fenicsx/run.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+set -e -u
+
+. ../../tools/log.sh
+
+exec > >(tee --append "$LOGFILE") 2>&1
+
+if [ ! -v PRECICE_TUTORIALS_NO_VENV ]; then
+
+    if [ ! -d ".venv" ]; then
+        python3 -m venv --system-site-packages .venv
+        source .venv/bin/activate
+        pip install -r requirements.txt && pip freeze > pip-installed-packages.log
+    else
+        source .venv/bin/activate
+    fi
+
+fi
+
+mkdir -p output
+python3 soil_creep.py
+
+close_log