Merge branch 'release' into pbrubeck/morley-tet

Author: pbrubeck

.github/workflows/core.yml

@@ -144,7 +144,7 @@ jobs:
             $(python3 ./firedrake-repo/scripts/firedrake-configure --arch ${{ matrix.arch }} --show-system-packages)
           apt-get -y install python3-venv
           : # Dependencies needed to run the test suite
-          apt-get -y install parallel
+          apt-get -y install fonts-dejavu graphviz graphviz-dev parallel poppler-utils
 
       - name: Install PETSc
         run: |
@@ -234,7 +234,7 @@ jobs:
           : # Use pytest-xdist here so we can have a single collated output (not possible
           : # for parallel tests)
           firedrake-run-split-tests 1 1 -n 8 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/tsfc
-        timeout-minutes: 60
+        timeout-minutes: 10
 
       - name: Run PyOP2 tests
         if: inputs.run_tests && (success() || steps.install.conclusion == 'success')
@@ -246,7 +246,7 @@ jobs:
           firedrake-run-split-tests 2 4 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
           firedrake-run-split-tests 3 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
           firedrake-run-split-tests 4 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
-        timeout-minutes: 15
+        timeout-minutes: 10
 
 
       - name: Run Firedrake tests (nprocs = 1)
@@ -256,14 +256,14 @@ jobs:
           : # Use pytest-xdist here so we can have a single collated output (not possible
           : # for parallel tests)
           firedrake-run-split-tests 1 1 -n 8 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
-        timeout-minutes: 60
+        timeout-minutes: 90
 
       - name: Run tests (nprocs = 2)
         if: inputs.run_tests && (success() || steps.install.conclusion == 'success')
         run: |
           . venv/bin/activate
           firedrake-run-split-tests 2 4 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
-        timeout-minutes: 30
+        timeout-minutes: 60
 
       - name: Run tests (nprocs = 3)
         if: inputs.run_tests && (success() || steps.install.conclusion == 'success')
@@ -422,6 +422,8 @@ jobs:
             echo Error: there are untracked files in the repository
             echo The output from 'git status' is:
             git status
+            echo The output from 'git diff' is:
+            git diff
             exit 1
           fi
 

.gitignore

@@ -15,10 +15,12 @@ __pycache__/
 /demos/immersed_fem/immersed_domain.msh
 /docs/build/
 /docs/notebooks/.ipynb_checkpoints/
+/docs/notebooks/tape.pdf
 /docs/source/apt_deps.txt
 /docs/source/firedrake.rst
 /docs/source/firedrake.*.rst
 /docs/source/homebrew_deps.txt
+/docs/source/minimal_apt_deps.txt
 /docs/source/obtaining_pyop2.rst
 /docs/source/petsc_configure_options.txt
 /docs/source/team.rst

AUTHORS.rst

@@ -122,7 +122,7 @@ Geordie McBain
 
 Andrew T. T. McRae
 
-Oliver Meister................<https://www5.in.tum.de/wiki/index.php/Dipl.-Inf._Oliver_Meister>
+Oliver Meister
 
 Lawrence Mitchell.............<https://www.wence.uk/>
 

Makefile

@@ -88,33 +88,6 @@ clean:
 	@echo "    RM tinyasm/*.so"
 	-@rm -f tinyasm/*.so > /dev/null 2>&1
 
-# Do verbose checking if running on CI and always set no:cacheprovider because
-# we don't want to generate any cache files in $VIRTUAL_ENV/lib/.../firedrake/_check
-check_flags =
-ifeq ($(FIREDRAKE_CI), 1)
-	check_flags = --verbose -p no:cacheprovider
-else
-	check_flags = --quiet -p no:cacheprovider
-endif
-
-CHECK_PYTEST_ARGS =
-
-.PHONY: check
-check:
-	@echo "    Running serial smoke tests"
-	@python3 -m pytest $(check_flags) $(CHECK_PYTEST_ARGS) \
-		tests/firedrake/regression/test_stokes_mini.py::test_stokes_mini \
-		tests/firedrake/regression/test_locate_cell.py  `# spatialindex` \
-		tests/firedrake/supermesh/test_assemble_mixed_mass_matrix.py::test_assemble_mixed_mass_matrix[2-CG-CG-0-0]  `# supermesh` \
-		tests/firedrake/regression/test_matrix_free.py::test_fieldsplitting[parameters3-cofunc_rhs-variational]  `# fieldsplit` \
-		tests/firedrake/regression/test_nullspace.py::test_near_nullspace  `# near nullspace`
-	@echo "    Serial tests passed"
-	@echo "    Running parallel smoke tests"
-	@mpiexec -n 3 python3 -m pytest $(check_flags) $(CHECK_PYTEST_ARGS) -m parallel[3] \
-		tests/firedrake/regression/test_dg_advection.py::test_dg_advection_icosahedral_sphere \
-		tests/firedrake/regression/test_interpolate_cross_mesh.py::test_interpolate_cross_mesh_parallel[extrudedcube]  `# vertex-only mesh`
-	@echo "    Parallel tests passed"
-
 .PHONY: durations
 durations:
 	@echo "    Generate timings to optimise pytest-split"

demos/boussinesq/boussinesq.py.rst

@@ -160,43 +160,46 @@ cannot always be sure that the linear solver at hand is correctly utilising the
 To directly eliminate the nullspace we introduce a class :code:`FixAtPointBC` which
 implements a boundary condition that fixes a field at a single point. ::
 
-    import firedrake.utils as firedrake_utils
-
-    class FixAtPointBC(firedrake.DirichletBC):
-        r'''A special BC object for pinning a function at a point.
-
-        :arg V: the :class:`.FunctionSpace` on which the boundary condition should be applied.
-        :arg g: the boundary condition value.
-        :arg bc_point: the point at which to pin the function.
-            The location of the finite element DOF nearest to bc_point is actually used.
-        '''
-        def __init__(self, V, g, bc_point):
-            super(FixAtPointBC, self).__init__(V, g, bc_point)
-            if isinstance(bc_point, tuple):
-                bc_point = as_vector(bc_point)
-            self.bc_point = bc_point
-
-        @firedrake_utils.cached_property
-        def nodes(self):
-            V = self.function_space()
-            x = firedrake.SpatialCoordinate(V.mesh())
-            xdist = x - self.bc_point
-
-            test = firedrake.TestFunction(V)
-            trial = firedrake.TrialFunction(V)
-            xphi = firedrake.assemble(ufl.inner(xdist * test, xdist * trial) * ufl.dx, diagonal=True)
-            phi = firedrake.assemble(ufl.inner(test, trial) * ufl.dx, diagonal=True)
-            with xphi.dat.vec as xu, phi.dat.vec as u:
-                xu.pointwiseDivide(xu, u)
-                min_index, min_value = xu.min()     # Find the index of the DOF closest to bc_point
-
-            nodes = V.dof_dset.lgmap.applyInverse([min_index])
-            nodes = nodes[nodes >= 0]
-            return nodes
-
+    import functools
+
+    class FixAtPointBC(DirichletBC):
+       r'''A special BC object for pinning a function at a point.
+
+       :arg V: the :class:`.FunctionSpace` on which the boundary condition should be applied.
+       :arg g: the boundary condition value.
+       :arg bc_point: the point at which to pin the function.
+           The location of the finite element DOF nearest to bc_point is actually used.
+       '''
+       def __init__(self, V, g, bc_point):
+           super().__init__(V, g, bc_point)
+
+       @functools.cached_property
+       def nodes(self):
+           V = self.function_space()
+           if V.mesh().ufl_coordinate_element().degree() != 1:
+               # Ensure a P1 mesh
+               coordinates = V.mesh().coordinates
+               P1 = coordinates.function_space().reconstruct(degree=1)
+               P1_mesh = Mesh(Function(P1).interpolate(coordinates))
+               V = V.reconstruct(mesh=P1_mesh)
+
+           point = [tuple(self.sub_domain)]
+           vom = VertexOnlyMesh(V.mesh(), point)
+           P0 = FunctionSpace(vom, "DG", 0)
+           Fvom = Cofunction(P0.dual()).assign(1)
+
+           # Take the basis function with the largest abs value at bc_point
+           v = TestFunction(V)
+           F = assemble(Interpolate(inner(v, v), Fvom))
+           with F.dat.vec as Fvec:
+               max_index, _ = Fvec.max()
+           nodes = V.dof_dset.lgmap.applyInverse([max_index])
+           nodes = nodes[nodes >= 0]
+           return nodes
+ 
 We use this to fix the pressure and auxiliary temperature at the origin::
 
-    aux_bcs = [FixAtPointBC(Z.sub(1), 0, as_vector([0, 0])), 
+    aux_bcs = [FixAtPointBC(Z.sub(1), 0, (0, 0)), 
                FixAtPointBC(Z.sub(2), 0, as_vector([0, 0]))]
 
 :code:`FixAtPointBC` takes three arguments: the function space to fix, the value with which it

demos/demo_references.bib

@@ -34,6 +34,14 @@ @Book{2006:SV
   year =         2006
 }
 
+@book{Perry:2007,
+	title =        {Perry’s Chemical Engineers’ Handbook},
+	edition =      {8th},
+	author =       {Green, Don W. and Perry, Robert H.},
+	year =         2007,
+	publisher =   {McGraw Hill Professional}
+}
+
 @InBook{2015:lmscup,
   author =       {O. Bokhove and A. Kalogirou},
   title =        {Lectures on the Theory of Water Waves},
@@ -309,6 +317,25 @@ @article{Ricker:1953
   doi={https://doi.org/10.1190/1.1437843}
 }
 
+@article{Krishna:1997,
+	title={The {M}axwell--{S}tefan approach to mass transfer},
+	author={Krishna, Rajamani and Wesselingh, Johannes A},
+	journal={Chemical Engineering Science},
+	volume={52},
+  number={6},
+	pages={861--911},
+	year={1997},
+  publisher={Elsevier},
+	doi={10.1016/S0009-2509(96)00458-7}
+}
+
+@article{BaierReinio:2025,
+	title={High-order finite element methods for three-dimensional multicomponent convection-diffusion},
+  author={Baier-Reinio, Aaron and Farrell, Patrick E},
+  journal={arXiv preprint arXiv:2408.17390},
+  year={2025}
+}
+
 @article{Brubeck2022,
   author        = {Brubeck, Pablo D. and Farrell, Patrick E.},
   doi           = {10.1137/21M1444187},