Merge pull request #4719 from firedrakeproject/connorjward/merge-release

connorjward · web-flow · commit 7e1d8ad5a6e5 · 2025-11-11T13:30:09.000Z
Merge release into main
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -64,6 +64,8 @@ Cyrus Cheng
 
 Teodoro Fields Collin
 
+Leo Collins
+
 Colin J. Cotter...............<https://www.imperial.ac.uk/people/colin.cotter>
 
 Joshua Coutinho
diff --git a/demos/saddle_point_pc/saddle_point_systems.py.rst b/demos/saddle_point_pc/saddle_point_systems.py.rst
@@ -449,10 +449,10 @@ we then use to solve the problem, we can provide one ourselves.
 Recall that :math:`S` is spectrally a Laplacian only in a
 discontinuous space.  A natural choice is therefore to use an interior
 penalty DG formulation for the Laplacian term on the block of the scalar
-variable. We can provide it as an :class:`~.AuxiliaryOperatorPC` via a python preconditioner. ::
+variable. We can provide it as an :class:`~.AuxiliaryOperatorPC` via a python preconditioner. Note that the ```form``` method in ```AuxiliaryOperatorPC``` takes the test functions as the first argument and the trial functions as the second argument, which is the reverse of the usual convention. ::
 
     class DGLaplacian(AuxiliaryOperatorPC):
-        def form(self, pc, u, v):
+        def form(self, pc, v, u):
             W = u.function_space()
             n = FacetNormal(W.mesh())
             alpha = Constant(4.0)
diff --git a/docs/source/contact.rst b/docs/source/contact.rst
@@ -29,14 +29,3 @@ This is open to all, but you must `request an invite to join
 the channel. Should this not work for whatever reason, please get in
 touch via `GitHub discussions
 <https://github.com/firedrakeproject/firedrake/discussions>`__.
-
-
-Mailing list
-------------
-
-Please join the Firedrake mailing list: firedrake@imperial.ac.uk.  This is a
-very low traffic list but it does carry important announcements, for example
-when we change a user-facing interface. Join the list on `this page
-<mailing_list_>`_.
-
-.. _mailing_list: https://mailman.ic.ac.uk/mailman/listinfo/firedrake
diff --git a/docs/source/images/leocollins.jpeg b/docs/source/images/leocollins.jpeg
diff --git a/docs/source/install.rst b/docs/source/install.rst
@@ -426,6 +426,20 @@ To install Firedrake with SLEPc support you should:
 
    $ pip install --no-binary h5py 'firedrake[check,slepc]'
 
+VTK
+~~~
+
+To install Firedrake with VTK, it should be installed using the ``vtk`` optional
+dependency. For example::
+
+   $ pip install --no-binary h5py 'firedrake[check,vtk]'
+
+.. warning::
+
+   VTK make releases sporadically so will not always support the latest version
+   of Python. This is commonly an issue on macOS where homebrew will use the
+   latest Python very soon after it is released. To fix this you should use
+   an older version of Python (e.g. 3.13 instead of 3.14).
 
 PyTorch
 ~~~~~~~
diff --git a/docs/source/team.ini b/docs/source/team.ini
@@ -49,6 +49,7 @@ India Marsden: https://www.maths.ox.ac.uk/people/india.marsden
 Daiane I. Dolci: https://www.imperial.ac.uk/people/d.dolci
 Joshua Hope-Collins: https://www.imperial.ac.uk/people/joshua.hope-collins13
 Umberto Zerbinati: https://www.uzerbinati.eu
+Leo Collins:
 
 [inactive-team]
 Lawrence Mitchell: https://www.wence.uk/
diff --git a/firedrake/adjoint_utils/function.py b/firedrake/adjoint_utils/function.py
@@ -278,7 +278,12 @@ def _ad_dot(self, other, options=None):
     def _ad_assign_numpy(dst, src, offset):
         range_begin, range_end = dst.dat.dataset.layout_vec.getOwnershipRange()
         m_a_local = src[offset + range_begin:offset + range_end]
-        dst.dat.data_wo[...] = m_a_local.reshape(dst.dat.data_wo.shape)
+        if dst.function_space().ufl_element().family() == "Real":
+            # Real space keeps a redundant copy of the data on every rank
+            comm = dst.function_space().mesh()._comm
+            dst.dat.data_wo[...] = comm.bcast(m_a_local, root=0)
+        else:
+            dst.dat.data_wo[...] = m_a_local.reshape(dst.dat.data_wo.shape)
         offset += dst.dat.dataset.layout_vec.size
         return dst, offset
 
diff --git a/firedrake/function.py b/firedrake/function.py
@@ -563,8 +563,12 @@ def evaluate(self, coord, mapping, component, index_values):
         # Called by UFL when evaluating expressions at coordinates
         if component or index_values:
             raise NotImplementedError("Unsupported arguments when attempting to evaluate Function.")
+        coord = np.asarray(coord, dtype=utils.ScalarType)
         evaluator = PointEvaluator(self.function_space().mesh(), coord)
-        return evaluator.evaluate(self)
+        result = evaluator.evaluate(self)
+        if len(coord.shape) == 1:
+            result = result.squeeze(axis=0)
+        return result
 
     def at(self, arg, *args, **kwargs):
         warnings.warn(
@@ -827,7 +831,7 @@ def evaluate(self, function: Function) -> np.ndarray | Tuple[np.ndarray, ...]:
         f_at_points = assemble(interpolate(function, P0DG))
         f_at_points_io = Function(P0DG_io).assign(np.nan)
         f_at_points_io.interpolate(f_at_points)
-        result = f_at_points_io.dat.data_ro
+        result = f_at_points_io.dat.data_ro.copy()
 
         # If redundant, all points are now on rank 0, so we broadcast the result
         if self.redundant and self.mesh.comm.size > 1:
diff --git a/firedrake/output/vtk_output.py b/firedrake/output/vtk_output.py
@@ -347,7 +347,7 @@ def get_array(function):
     return array
 
 
-class VTKFile(object):
+class VTKFile:
     _header = (b'<?xml version="1.0" ?>\n'
                b'<VTKFile type="Collection" version="0.1" '
                b'byte_order="LittleEndian">\n'
diff --git a/firedrake/preconditioners/hypre_ads.py b/firedrake/preconditioners/hypre_ads.py
@@ -1,11 +1,12 @@
 from firedrake.preconditioners.base import PCBase
+from firedrake.preconditioners.fdm import tabulate_exterior_derivative
 from firedrake.petsc import PETSc
 from firedrake.function import Function
 from firedrake.ufl_expr import TrialFunction
 from firedrake.dmhooks import get_function_space
 from firedrake.preconditioners.hypre_ams import chop
 from firedrake.interpolation import interpolate
-from finat.ufl import VectorElement
+from finat.ufl import FiniteElement, TensorElement, VectorElement
 from ufl import grad, curl, SpatialCoordinate
 from pyop2.utils import as_tuple
 
@@ -27,16 +28,34 @@ def initialize(self, obj):
         if formdegree != 2 or degree != 1:
             raise ValueError("Hypre ADS requires lowest order RT elements! (not %s of degree %d)" % (family, degree))
 
-        P1 = V.reconstruct(family="Lagrange", degree=1)
-        NC1 = V.reconstruct(family="N1curl" if mesh.ufl_cell().is_simplex else "NCE", degree=1)
+        # Get the auxiliary Nedelec and Lagrange spaces and the coordinate space
+        cell = V.ufl_element().cell
+        NC1_element = FiniteElement("N1curl" if cell.is_simplex else "NCE", cell=cell, degree=1)
+        P1_element = FiniteElement("Lagrange", cell=cell, degree=1)
+        coords_element = VectorElement(P1_element, dim=mesh.geometric_dimension)
+        if V.shape:
+            NC1_element = TensorElement(NC1_element, shape=V.shape)
+            P1_element = TensorElement(P1_element, shape=V.shape)
+
+        NC1 = V.reconstruct(element=NC1_element)
+        P1 = V.reconstruct(element=P1_element)
+        VectorP1 = V.reconstruct(element=coords_element)
+
         G_callback = appctx.get("get_gradient", None)
         if G_callback is None:
-            G = chop(assemble(interpolate(grad(TrialFunction(P1)), NC1)).petscmat)
+            try:
+                G = chop(assemble(interpolate(grad(TrialFunction(P1)), NC1)).petscmat)
+            except NotImplementedError:
+                # dual evaluation not yet implemented see https://github.com/firedrakeproject/fiat/issues/109
+                G = tabulate_exterior_derivative(P1, NC1)
         else:
             G = G_callback(P1, NC1)
         C_callback = appctx.get("get_curl", None)
         if C_callback is None:
-            C = chop(assemble(interpolate(curl(TrialFunction(NC1)), V)).petscmat)
+            try:
+                C = chop(assemble(interpolate(curl(TrialFunction(NC1)), V)).petscmat)
+            except NotImplementedError:
+                C = tabulate_exterior_derivative(NC1, V)
         else:
             C = C_callback(NC1, V)
 
@@ -50,7 +69,6 @@ def initialize(self, obj):
         pc.setHYPREDiscreteGradient(G)
         pc.setHYPREDiscreteCurl(C)
 
-        VectorP1 = P1.reconstruct(element=VectorElement(P1.ufl_element()))
         coords = Function(VectorP1).interpolate(SpatialCoordinate(mesh))
         pc.setCoordinates(coords.dat.data_ro.copy())
 
diff --git a/firedrake/preconditioners/hypre_ams.py b/firedrake/preconditioners/hypre_ams.py
@@ -1,13 +1,14 @@
 import petsctools
 from firedrake.preconditioners.base import PCBase
+from firedrake.preconditioners.fdm import tabulate_exterior_derivative
 from firedrake.petsc import PETSc
 from firedrake.function import Function
 from firedrake.ufl_expr import TrialFunction
 from firedrake.dmhooks import get_function_space
 from firedrake.utils import complex_mode
 from firedrake.interpolation import interpolate
 from ufl import grad, SpatialCoordinate
-from finat.ufl import VectorElement
+from finat.ufl import FiniteElement, TensorElement, VectorElement
 from pyop2.utils import as_tuple
 
 __all__ = ("HypreAMS",)
@@ -48,10 +49,21 @@ def initialize(self, obj):
         if formdegree != 1 or degree != 1:
             raise ValueError("Hypre AMS requires lowest order Nedelec elements! (not %s of degree %d)" % (family, degree))
 
-        P1 = V.reconstruct(family="Lagrange", degree=1)
+        # Get the auxiliary Lagrange space and the coordinate space
+        P1_element = FiniteElement("Lagrange", degree=1)
+        coords_element = VectorElement(P1_element, dim=mesh.geometric_dimension)
+        if V.shape:
+            P1_element = TensorElement(P1_element, shape=V.shape)
+        P1 = V.reconstruct(element=P1_element)
+        VectorP1 = V.reconstruct(element=coords_element)
+
         G_callback = appctx.get("get_gradient", None)
         if G_callback is None:
-            G = chop(assemble(interpolate(grad(TrialFunction(P1)), V)).petscmat)
+            try:
+                G = chop(assemble(interpolate(grad(TrialFunction(P1)), V)).petscmat)
+            except NotImplementedError:
+                # dual evaluation not yet implemented see https://github.com/firedrakeproject/fiat/issues/109
+                G = tabulate_exterior_derivative(P1, V)
         else:
             G = G_callback(P1, V)
 
@@ -68,7 +80,6 @@ def initialize(self, obj):
         if zero_beta:
             pc.setHYPRESetBetaPoissonMatrix(None)
 
-        VectorP1 = P1.reconstruct(element=VectorElement(P1.ufl_element()))
         coords = Function(VectorP1).interpolate(SpatialCoordinate(mesh))
         pc.setCoordinates(coords.dat.data_ro.copy())
         pc.setFromOptions()
diff --git a/pyproject.toml b/pyproject.toml
@@ -44,7 +44,6 @@ dependencies = [
   "scipy",
   "sympy",
   "islpy>=2025.1.5; sys_platform == 'darwin'",
-  "vtk",
 ]
 classifiers = [
   "Development Status :: 5 - Production/Stable",
@@ -87,6 +86,7 @@ docs = [
   "sphinxcontrib-svg2pdfconverter",
   "sphinxcontrib-youtube",
   "sphinx-copybutton",
+  "vtk",  # needed to resolve API
 ]
 jax = [
   "jax",
@@ -102,6 +102,9 @@ slepc = [
 torch = [  # requires passing '--extra-index-url' to work
   "torch",
 ]
+vtk = [
+  "vtk",
+]
 
 # Dependencies needed to run the full test suite
 ci = [
@@ -123,6 +126,7 @@ ci = [
   # TODO RELEASE
   # "slepc4py==3.24.0",
   "torch",  # requires passing '--extra-index-url' to work
+  "vtk",
 ]
 docker = [  # Used in firedrake-vanilla container
   "ipympl",  # needed for notebook testing
@@ -139,6 +143,7 @@ docker = [  # Used in firedrake-vanilla container
   "pytest-xdist",
   # TODO RELEASE
   # "slepc4py==3.24.0",
+  "vtk",
 ]
 
 [build-system]
diff --git a/tests/firedrake/adjoint/test_reduced_functional.py b/tests/firedrake/adjoint/test_reduced_functional.py
@@ -2,6 +2,7 @@
 
 from firedrake import *
 from firedrake.adjoint import *
+from pytest_mpi.parallel_assert import parallel_assert
 
 from numpy.random import rand
 
@@ -251,3 +252,34 @@ def test_interpolate_mixed():
     h.subfunctions[0].dat.data[:] = 5
     h.subfunctions[1].dat.data[:] = 6
     assert taylor_test(Jhat, f, h) > 1.9
+
+
+@pytest.mark.skipcomplex
+@pytest.mark.parallel(2)
+def test_real_space_assign_numpy():
+    """Check that Function._ad_assign_numpy correctly handles
+    zero length arrays on some ranks for Real space in parallel.
+    """
+    mesh = UnitSquareMesh(1, 1)
+    R = FunctionSpace(mesh, "R", 0)
+    dst = Function(R)
+    src = dst.dat.dataset.layout_vec.array_r.copy()
+    data = 1 + np.arange(src.shape[0])
+    src[:] = data
+    dst._ad_assign_numpy(dst, src, offset=0)
+    parallel_assert(np.allclose(dst.dat.data_ro, data))
+
+
+@pytest.mark.skipcomplex
+@pytest.mark.parallel(2)
+def test_real_space_parallel():
+    """Check that scipy.optimize works for Real space in parallel
+    despite dat.data array having zero length on some ranks.
+    """
+    mesh = UnitSquareMesh(1, 1)
+    R = FunctionSpace(mesh, "R", 0)
+    m = Function(R)
+    J = assemble((m-1)**2*dx)
+    Jhat = ReducedFunctional(J, Control(m))
+    opt = minimize(Jhat)
+    parallel_assert(np.allclose(opt.dat.data_ro, 1))
diff --git a/tests/firedrake/conftest.py b/tests/firedrake/conftest.py
@@ -68,6 +68,14 @@ def _skip_test_dependency(dependency):
         except ImportError:
             return skip
 
+    elif dependency == "vtk":
+        try:
+            import vtk  # noqa: F401
+            del vtk
+            return not skip
+        except ImportError:
+            return skip
+
     elif dependency in ("mumps", "hypre"):
         return dependency not in get_external_packages()
 
@@ -83,6 +91,8 @@ def _skip_test_dependency(dependency):
     ("jax", "skipjax", "JAX is not installed"),
     ("matplotlib", "skipplot", "Matplotlib is not installed"),
     ("netgen", "skipnetgen", "Netgen and ngsPETSc are not installed"),
+    ("vtk", "skipvtk", "VTK is not installed"),
+
 )
 
 
@@ -118,6 +128,10 @@ def pytest_configure(config):
         "markers",
         "skipslepc: mark as skipped if slepc4py is not installed"
     )
+    config.addinivalue_line(
+        "markers",
+        "skipvtk: mark as skipped if vtk is not installed"
+    )
     config.addinivalue_line(
         "markers",
         "skiptorch: mark as skipped if PyTorch is not installed"
diff --git a/tests/firedrake/output/test_pvd_output.py b/tests/firedrake/output/test_pvd_output.py
diff --git a/tests/firedrake/regression/test_hypre_ads.py b/tests/firedrake/regression/test_hypre_ads.py
diff --git a/tests/firedrake/regression/test_hypre_ams.py b/tests/firedrake/regression/test_hypre_ams.py
diff --git a/tests/firedrake/regression/test_point_eval_api.py b/tests/firedrake/regression/test_point_eval_api.py
diff --git a/tests/firedrake/regression/test_point_eval_fs.py b/tests/firedrake/regression/test_point_eval_fs.py
