Add fenicsx and simplified Landlab solvers

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/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 ../solver-fenicsx/requirements.txt && pip freeze > pip-installed-packages.log
+    else
+        source .venv/bin/activate
+    fi
+
+fi
+
+mkdir -p output
+python3 ../solver-fenicsx/soil_creep.py
+
+close_log

wolf-sheep-soil-creep/soil-creep-landlab/soil_creep.py

@@ -23,6 +23,8 @@
 
 rmg = RasterModelGrid((width, height))
 
+solver_dt = 0.2 * rmg.dx * rmg.dx / fast_creep
+
 # Create elevation field and have it slope down to the south at 10% gradient
 elev = rmg.add_zeros("topographic__elevation", at="node")
 elev[:] = 0.1 * rmg.y_of_node
@@ -54,24 +56,22 @@
 solver_process_size = 1
 participant = precice.Participant(participant_name, config_file_name, solver_process_index, solver_process_size)
 
-positions = [[x, y] for x in range(width) for y in range(height)]
-vertex_gm_ids = participant.set_mesh_vertices("Soil-Creep-Mesh", positions)
-vertex_soil_ids = participant.set_mesh_vertices("Soil-Depth-Mesh", positions)
+positions = [[x, y] for y in range(height) for x in range(width)]
+vertex_ids = participant.set_mesh_vertices("Soil-Creep-Mesh", positions)
 
 participant.initialize()
 
 while participant.is_coupling_ongoing():
-    solver_dt = 0.2 * rmg.dx * rmg.dx / fast_creep
     precice_dt = participant.get_max_time_step_size()
     dt = np.minimum(solver_dt, precice_dt)
 
-    gm = participant.read_data("Soil-Creep-Mesh", "Grass", vertex_gm_ids, dt)
+    gm = participant.read_data("Soil-Creep-Mesh", "Grass", vertex_ids, dt)
 
     # Assign the higher creep coefficient to cells where the grass has
     # been eaten and not yet recovered; the slower value is assigned to
     # "fully grown" grass patches.
-    creep_coef[gm.flatten() == 1] = fast_creep
-    creep_coef[gm.flatten() == 2] = slow_creep
+    creep_coef[gm == 1] = fast_creep
+    creep_coef[gm == 2] = slow_creep
 
     # Limit the creep coefficient according to the soil-thickness field, so absent soil cannot move.
     creep_coef *= 1.0 - np.exp(-soil / hstar)
@@ -86,7 +86,7 @@
     # Update the soil cover
     soil += elev - prior_elev
 
-    participant.write_data("Soil-Depth-Mesh", "Soil", vertex_soil_ids, soil)
+    participant.write_data("Soil-Creep-Mesh", "Soil", vertex_ids, soil)
 
     participant.advance(dt)
 

wolf-sheep-soil-creep/soil-creep-simplified-landlab/clean.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env sh
+set -e -u
+
+rm -rfv ./output/
+
+. ../../tools/cleaning-tools.sh
+
+clean_precice_logs .
+clean_case_logs .

wolf-sheep-soil-creep/soil-creep-simplified-landlab/requirements.txt

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

wolf-sheep-soil-creep/soil-creep-simplified-landlab/run.sh

@@ -0,0 +1,21 @@
+#!/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 .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