Changelog

Changelog#

Full refactoring of dolfinx.fem.petsc.NonlinearProblem, which now uses the PETSc SNES backend. See the non-linear poisson demo for details.
dolfinx.fem.petsc.LinearProblem now requires an additional argument, petsc_options_prefix. This should be a unique string identifier for each LinearProblem that is created.
Change how one reads in GMSH data with gmshio. See the membrane code for more details.
dolfinx.fem.FiniteElement.interpolation_points() -> dolfinx.fem.FiniteElement.interpolation_points.
dolfinx.io.gmshio has been renamed to dolfinx.io.gmsh
Input to dolfinx.fem.petsc.create_vector() has changed. One should now call dolfinx.fem.extract_function_spaces() on the input form first.

scale in apply_lifting has been renamed to alpha
Use dolfinx.fem.Function.x.petsc_vec as opposed to dolfinx.fem.Function.vector

Replace all ufl.FiniteElement and ufl.VectorElement with the appropriate basix.ufl.element()
Replace dolfinx.fem.FunctionSpace with dolfinx.fem.functionspace()

No API changes, release due to various bug-fixes from the 0.7.0 release, see: FEniCS/dolfinx for more information

Renamed dolfinx.graph.create_adjacencylist to dolfinx.graph.adjacencylist()
Renamed dolfinx.plot.create_vtk_mesh to dolfinx.plot.vtk_mesh()
Initialization of dolfinx.geometry.BoundingBoxTree has been changed to dolfinx.geometry.bb_tree()
create_mesh with Meshio has been modified. Note that you now need to pass dtype np.int32 to the cell_data.
Update dolfinx petsc API. Now one needs to explicitly import dolfinx.fem.petsc and dolfinx.fem.nls, as PETSc is no longer a strict requirement. Replace petsc4py.PETSc.ScalarType with dolfinx.default_scalar_type in demos where we do not use petsc4py explicitly.

Remove ipygany and pythreejs as plotting backends. Using panel.
Add gif-output to [chapter2/diffusion_code] and [chapter2/hyperelasticity].
Replace dolfinx.fem.Function.geometric_dimension with len(dolfinx.fem.Function)
Improve [chapter2/ns_code2] to have better splitting scheme and density.
Improve mesh quality in [chapter3/em].
jit_params and form_compiler_params renamed to *_options.

Using new GMSH interface in DOLFINx (dolfinx.io.gmshio) in all demos using GMSH
Added a section on custom Newton-solvers, see [chapter4/newton-solver].
Various minor DOLFINx API updates. dolfinx.mesh.compute_boundary_facets -> dolfinx.mesh.exterior_facet_indices() with slightly different functionality. Use dolfinx.mesh.MeshTagsMetaClass.find instead of mt.indices[mt.values==value].
Various numpy updates, use np.full_like.
Change all notebooks to use jupytext to automatically sync .ipynb with .py files.
Add example of how to use DOLFINx in complex mode, see [chapter1/complex_mode].

All pyvista plotting has been rewritten to use ipygany and pythreejs as well as using a cleaner interface.
dolfinx.plot.create_vtk_topology has been renamed to dolfinx.plot.create_vtk_mesh and can now be directly used as input to pyvista.UnstructuredGrid.
dolfinx.fem.Function.compute_point_values has been deprecated. Interpolation into a CG-1 is now the way of getting vertex values.
Instead of initializing class with Form, use form.
Instead of initializing class with DirichletBC use dirichletbc.
Updates on error computations in Error control: Computing convergence rates.
Added tutorial on interpolation of ufl.core.expr.Expr in Deflection of a membrane.
Added tutorial on how to apply constant-valued Dirichlet conditions in Deflection of a membrane.
Various API changes relating to the import structure of DOLFINx

Major improvements in Form compiler parameters, using pandas and seaborn for visualization of speed-ups gained using form compiler parameters.
API change: dolfinx.cpp.la.scatter_forward(u.x) -> u.x.scatter_forward
Various plotting updates due to new version of pyvista.
Updating of the Hyperelasticity demo, now using DOLFINx wrappers to create the non-linear problem
Internal updates due to bumping of jupyter-book versions
Various typos and capitalizations fixed by @mscroggs in PR 35.