Fluidity advection 2d

.github/workflows/ci.yml

@@ -20,11 +20,12 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install and test
         run: |
           sudo apt-get update
+          sudo apt-get install -y libglu1-mesa
           sudo apt-get install -y python3-pip
           python3 -m pip install --upgrade pip
           python3 -m pip install "$PWD[test]"
@@ -41,7 +42,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install and test
         run: |
@@ -61,7 +62,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install and test
         run: |

.github/workflows/docs.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Build
         run: |
@@ -33,7 +33,7 @@ jobs:
           python3 -m venv .venv-gh-pages
           source .venv-gh-pages/bin/activate
           python3 -m pip install "$PWD"[doc,test]
-          pdoc -t docs/template -o html --math pydrex tests
+          pdoc -t docs/template -o html --math pydrex !pydrex.mesh tests
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
         # If you're changing the branch from main,

README.md

@@ -31,6 +31,10 @@ use `pip install -e "$PWD[dev]"`.
 
 The package metadata and full list of dependencies are specified in [`pyproject.toml`](pyproject.toml).
 
+Optional mesh generation using [gmsh](https://pypi.org/project/gmsh/) is available,
+however the `gmsh` module requires the [`glu`](https://gitlab.freedesktop.org/mesa/glu) library
+(that may not be installed by default on all systems).
+
 ## Test
 
 Some tests can optionally output figures or extended diagnostics when run locally.

examples/fluidity/README.md

@@ -0,0 +1,18 @@
+# Fluidity examples
+
+Most parameters can be set in the relevant makefiles, except for the number of
+grains, which is defined by `(N - 22) / 10` where `N` is the dimension of the
+`CPO_` array in the Fluidity `.flml` file. Timestepping options are also set
+in the `.flml` file.
+
+To run the example contained in `example_directory`,
+ensure that the `envcheck.sh` script is available, and simply run
+`make -f example_directory/Makefile`.
+To clean previous simulation output use the
+`make -f example_directory/Makefile clean` target.
+
+This table lists the corresponding PyDRex tests:
+
+| Fluidity example | PyDRex test |
+| --- | --- |
+| `advection2d` | `test_simple_shear_2d.TestOlivineA.test_dudz_pathline` |

examples/fluidity/advection2d/Makefile

@@ -0,0 +1,63 @@
+# Make options to keep what's left of our sanity.
+.SHELLFLAGS += -u
+.ONESHELL:
+MAKEFLAGS += --warn-undefined-variables
+MAKEFLAGS += --no-builtin-rules
+# Path options, SIM_NAME is the name of the .msh and .py files.
+SIM_NAME := advection2d
+SRC_DIR := advection2d
+OUT_DIR := _out
+# Initial geometry options (in units of metres), passed to `pydrex-mesh`.
+WIDTH := 4e5
+DEPTH := 4e5
+RESOLUTION := 1e3
+# Initial conditions, used to parametrise velocity fields and spawn particles.
+# INIT_HORIZ can be a space-delimited array of values (for multiple particles).
+STRAIN_RATE := 1e-15
+INIT_HORIZ := -1e5
+INIT_VERT := 1e5
+# Recrystallisation parameters.
+STRESS_EXPONENT := 1.5
+DEFORMATION_EXPONENT := 3.5
+GBM_MOBILITY := 10
+GBS_THRESHOLD := 0.3
+NUCLEATION_EFFICIENCY := 5
+
+$(OUT_DIR)/fluidity.log-0: $(OUT_DIR)/$(SIM_NAME).flml $(OUT_DIR)/$(SIM_NAME).msh $(OUT_DIR)/$(SIM_NAME).py $(OUT_DIR)/$(SIM_NAME).ini
+	@echo "********** Running fluidity with verbose logging enabled..."
+	./envcheck.sh -f
+	cd $(OUT_DIR) && fluidity -v2 -l $(SIM_NAME).flml
+
+$(OUT_DIR)/$(SIM_NAME).ini: $(OUT_DIR)/$(SIM_NAME).py
+	@echo "********** Setting up initial conditions and recryst. parameters..."
+	echo "[initial conditions]" > $@
+	echo "WIDTH = $(WIDTH)" >> $@
+	echo "DEPTH = $(DEPTH)" >> $@
+	echo "RESOLUTION = $(RESOLUTION)" >> $@
+	echo "STRAIN_RATE = $(STRAIN_RATE)" >> $@
+	echo "INIT_HORIZ = $(INIT_HORIZ)" >> $@
+	echo "INIT_VERT = $(INIT_VERT)" >> $@
+	echo "STRESS_EXPONENT = $(STRESS_EXPONENT)" >> $@
+	echo "DEFORMATION_EXPONENT = $(DEFORMATION_EXPONENT)" >> $@
+	echo "GBM_MOBILITY = $(GBM_MOBILITY)" >> $@
+	echo "GBS_THRESHOLD = $(GBS_THRESHOLD)" >> $@
+	echo "NUCLEATION_EFFICIENCY = $(NUCLEATION_EFFICIENCY)" >> $@
+
+$(OUT_DIR)/$(SIM_NAME).py: $(SRC_DIR)/$(SIM_NAME).py
+	@echo "********** Copying python velocity callables..."
+	mkdir -p $(@D)
+	cp -f $< $@
+
+$(OUT_DIR)/$(SIM_NAME).flml: $(SRC_DIR)/$(SIM_NAME).flml
+	@echo "********** Copying serial flml file..."
+	mkdir -p $(@D)
+	cp -f $< $@
+
+$(OUT_DIR)/$(SIM_NAME).msh:
+	@echo "********** Building the mesh file..."
+	./envcheck.sh -m
+	pydrex-mesh -k="rectangle" -a xy $(WIDTH),$(DEPTH) $(RESOLUTION) $@
+
+.PHONY: clean
+clean:
+	rm -rf $(OUT_DIR)