Merge pull request #201 from seismic-anisotropy/effective-viscosity

Add pydrex.viscosity module

examples/fluidity/advection2d/Makefile

@@ -23,7 +23,7 @@ GBM_MOBILITY := 10
 GBS_THRESHOLD := 0.3
 NUCLEATION_EFFICIENCY := 5
 
-$(OUT_DIR)/fluidity.log-0: $(OUT_DIR)/$(SIM_NAME).flml \
+all: $(OUT_DIR)/$(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
@@ -56,6 +56,6 @@ $(OUT_DIR)/$(SIM_NAME).msh:
 	./envcheck.sh -m
 	pydrex-mesh -k="rectangle" -a xy $(WIDTH),$(DEPTH) -r G:$(RESOLUTION) $@
 
-.PHONY: clean
+.PHONY: all clean
 clean:
 	rm -rf $(OUT_DIR)

examples/fluidity/corner2d/Makefile

@@ -27,7 +27,7 @@ GBM_MOBILITY := 10
 GBS_THRESHOLD := 0.3
 NUCLEATION_EFFICIENCY := 5
 
-$(OUT_DIR)/fluidity.log-0: $(OUT_DIR)/$(SIM_NAME).flml \
+all: $(OUT_DIR)/$(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
@@ -61,6 +61,6 @@ $(OUT_DIR)/$(SIM_NAME).msh:
 	pydrex-mesh -k="rectangle" -a xy $(WIDTH),$(DEPTH) \
 		-c $(HALF_WIDTH),-$(HALF_DEPTH) -r NW:$(RESOLUTION_HI),SE:$(RESOLUTION_LO) $@
 
-.PHONY: clean
+.PHONY: all clean
 clean:
 	rm -rf $(OUT_DIR)

examples/fluidity/ridge2d/Makefile

@@ -0,0 +1,94 @@
+# 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 := ridge2d
+SRC_DIR := ridge2d
+OUT_DIR := _out
+# Number of processors to use for parallelisation.
+NPROCS := 4
+# Initial geometry options (in units of metres), passed to `pydrex-mesh`.
+# Negative depth value makes z-values negative.
+WIDTH := 1e6
+DEPTH := -4e5
+HALF_WIDTH := $(shell python3 -c 'print($(WIDTH)/2)')
+HALF_DEPTH := $(shell python3 -c 'print($(DEPTH)/2)')
+RESOLUTION_HI := 5e2
+RESOLUTION_LO := 1e4
+RESOLUTION_MED := 1e3
+# Initial options for temperature field.
+SURFACE_TEMP := 273
+DIFF_TEMP := 1350
+THERM_DIFFUSIVITY := 2.23e-6
+THERM_FIT := "Standard"
+MIN_AGE := 1
+# Initial conditions, used to parametrise velocity fields and spawn particles.
+# INIT_HORIZ can be a space-delimited array of values (for multiple particles).
+# NOTE: PLATE_SPEED is in cm/yr here.
+PLATE_SPEED := 2.0
+# INIT_HORIZ := 3.13e4 9.74e4 2.02e5 3.97e5
+# INIT_DEPTH := 2e5
+# # Recrystallisation parameters.
+# STRESS_EXPONENT := 1.5
+# DEFORMATION_EXPONENT := 3.5
+# GBM_MOBILITY := 10
+# GBS_THRESHOLD := 0.3
+# NUCLEATION_EFFICIENCY := 5
+
+all: $(OUT_DIR)/$(SIM_NAME)_P$(NPROCS).flml
+	@echo "********** Running fluidity in parallel with verbose logging enabled..."
+	cd $(OUT_DIR) && mpiexec -np $(NPROCS) fluidity -v2 -l $<
+
+$(OUT_DIR)/$(SIM_NAME)_P$(NPROCS).flml: $(OUT_DIR)/$(SIM_NAME).flml \
+	$(OUT_DIR)/$(SIM_NAME).msh $(OUT_DIR)/$(SIM_NAME).py $(OUT_DIR)/$(SIM_NAME).ini
+	@echo "********** Creating parallel flml file using flredecomp..."
+	./envcheck.sh -f
+	cd $(OUT_DIR) && mpiexec -np $(NPROCS) flredecomp -i 1 -o $(NPROCS) $(SIM_NAME) $(SIM_NAME)_P$(NPROCS)
+
+$(OUT_DIR)/$(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 "HALF_WIDTH = $(HALF_WIDTH)" >> $@
+	echo "HALF_DEPTH = $(HALF_DEPTH)" >> $@
+	echo "RESOLUTION_HI = $(RESOLUTION_HI)" >> $@
+	echo "RESOLUTION_LO = $(RESOLUTION_LO)" >> $@
+	echo "RESOLUTION_MED = $(RESOLUTION_MED)" >> $@
+	echo "SURFACE_TEMP = $(SURFACE_TEMP)" >> $@
+	echo "DIFF_TEMP = $(DIFF_TEMP)" >> $@
+	echo "THERM_DIFFUSIVITY = $(THERM_DIFFUSIVITY)" >> $@
+	echo "THERM_FIT = $(THERM_FIT)" >> $@
+	echo "MIN_AGE = $(MIN_AGE)" >> $@
+	echo "PLATE_SPEED = $(PLATE_SPEED)" >> $@
+
+$(OUT_DIR)/$(SIM_NAME).msh: $(OUT_DIR)/$(SIM_NAME).geo
+	@echo "********** Building the mesh file..."
+	./envcheck.sh -m
+	gmsh -2 -o $@ $<
+
+$(OUT_DIR)/$(SIM_NAME).py: $(SRC_DIR)/$(SIM_NAME).py
+	@echo "********** Copying python field setters..."
+	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).geo: $(SRC_DIR)/$(SIM_NAME).geo
+	@echo "********* Copying the .geo file..."
+	mkdir -p $(@D)
+	sed -i "s/width = .*;/width = $(WIDTH);/" $<
+	sed -i "s/depth = .*;/depth = $(DEPTH);/" $<
+	sed -i "s/res_hi = .*;/res_hi = $(RESOLUTION_HI);/" $<
+	sed -i "s/res_lo = .*;/res_lo = $(RESOLUTION_LO);/" $<
+	sed -i "s/res_med = .*;/res_med = $(RESOLUTION_MED);/" $<
+	cp -f $< $@
+
+.PHONY: all clean
+clean:
+	rm -rf $(OUT_DIR)