143 fenics version 0.7.0 --- Hackathon

src/fenicsxconcrete/boundary_conditions/bcs.py

@@ -9,7 +9,7 @@
 from fenicsxconcrete.util import LogMixin
 
 
-def get_boundary_dofs(V: dolfinx.fem.FunctionSpace, marker: Callable) -> np.ndarray:
+def get_boundary_dofs(V: dolfinx.fem.FunctionSpaceBase, marker: Callable) -> np.ndarray:
     """Returns dofs on the boundary specified by geometrical `marker`.
 
     Args:
@@ -78,7 +78,7 @@ def __init__(
     def add_dirichlet_bc(
         self,
         value: (
-            dolfinx.fem.Function | dolfinx.fem.Constant | dolfinx.fem.DirichletBCMetaClass | np.ndarray | Callable
+            dolfinx.fem.Function | dolfinx.fem.Constant | dolfinx.fem.DirichletBC | np.ndarray | Callable
         ),
         boundary: int | np.ndarray | Callable | None = None,
         sub: int = None,
@@ -103,7 +103,7 @@ def add_dirichlet_bc(
                         topologically. Note that `entity_dim` is required if `sub`
                         is not None and `method=geometrical`.
         """
-        if isinstance(value, dolfinx.fem.DirichletBCMetaClass):
+        if isinstance(value, dolfinx.fem.DirichletBC):
             self._bcs.append(value)
         else:
             assert method in ("topological", "geometrical")
@@ -180,7 +180,7 @@ def has_dirichlet(self) -> bool:
         return len(self._bcs) > 0
 
     @property
-    def bcs(self) -> list[dolfinx.fem.DirichletBCMetaClass]:
+    def bcs(self) -> list[dolfinx.fem.DirichletBC]:
         """returns the list of Dirichlet BCs
 
         Returns:

src/fenicsxconcrete/boundary_conditions/boundary.py

@@ -193,7 +193,7 @@ def _show_marked(
     if tdim in (1, 3):
         raise NotImplementedError(f"Not implemented for mesh of topological dimension {tdim=}.")
 
-    V = dolfinx.fem.FunctionSpace(domain, ("Lagrange", 1))
+    V = dolfinx.fem.functionspace(domain, ("Lagrange", 1))
     dofs = dolfinx.fem.locate_dofs_geometrical(V, marker)
     u = dolfinx.fem.Function(V)
     bc = dolfinx.fem.dirichletbc(u, dofs)

src/fenicsxconcrete/experimental_setup/am_multiple_layers.py

@@ -96,7 +96,7 @@ def setup(self) -> None:
         else:
             raise ValueError(f'wrong dimension: {self.p["dim"]} is not implemented for problem setup')
 
-    def create_displacement_boundary(self, V: df.fem.FunctionSpace) -> list[df.fem.bcs.DirichletBCMetaClass]:
+    def create_displacement_boundary(self, V: df.fem.FunctionSpaceBase) -> list[df.fem.bcs.DirichletBC]:
         """defines displacement boundary as fixed at bottom
 
         Args:

src/fenicsxconcrete/experimental_setup/base_experiment.py

@@ -5,8 +5,8 @@
 import pint
 import ufl
 
-from fenicsxconcrete.boundary_conditions.boundary import plane_at, point_at
-from fenicsxconcrete.util import LogMixin, Parameters, QuadratureRule, ureg
+from fenicsxconcrete.boundary_conditions.boundary import plane_at
+from fenicsxconcrete.util import LogMixin, Parameters, QuadratureRule
 
 
 class Experiment(ABC, LogMixin):
@@ -81,7 +81,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
         pass
 
     @abstractmethod
-    def create_displacement_boundary(self, V: df.fem.FunctionSpace) -> list[df.fem.bcs.DirichletBCMetaClass] | None:
+    def create_displacement_boundary(self, V: df.fem.FunctionSpaceBase) -> list[df.fem.bcs.DirichletBC] | None:
         """defines empty displacement boundary conditions (to be done in child)
 
         this function is abstract until there is a need for a material that does not need a displacement boundary

src/fenicsxconcrete/experimental_setup/cantilever_beam.py

@@ -6,7 +6,7 @@
 from petsc4py.PETSc import ScalarType
 
 from fenicsxconcrete.experimental_setup.base_experiment import Experiment
-from fenicsxconcrete.util import Parameters, ureg
+from fenicsxconcrete.util import ureg
 
 
 class CantileverBeam(Experiment):
@@ -81,7 +81,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
 
         return setup_parameters
 
-    def create_displacement_boundary(self, V) -> list:
+    def create_displacement_boundary(self, V: df.fem.FunctionSpaceBase) -> list:
         """defines displacement boundary as fixed at bottom
 
         Args:

src/fenicsxconcrete/experimental_setup/compression_cylinder.py

@@ -184,7 +184,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
 
         return default_parameters
 
-    def create_displacement_boundary(self, V: df.fem.FunctionSpace) -> list[df.fem.bcs.DirichletBCMetaClass]:
+    def create_displacement_boundary(self, V: df.fem.FunctionSpaceBase) -> list[df.fem.bcs.DirichletBC]:
         """Defines the displacement boundary conditions
 
         Args:

src/fenicsxconcrete/experimental_setup/simple_beam.py

@@ -87,7 +87,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
 
         return setup_parameters
 
-    def create_displacement_boundary(self, V) -> list:
+    def create_displacement_boundary(self, V: df.fem.FunctionSpaceBase) -> list[df.fem.bcs.DirichletBC]:
         """defines displacement boundary as fixed at bottom
 
         Args:

src/fenicsxconcrete/experimental_setup/simple_cube.py

@@ -98,7 +98,7 @@ def setup(self) -> None:
         self.use_body_force = False
         self.temperature_bc = df.fem.Constant(domain=self.mesh, c=self.p["T_bc"])
 
-    def create_displacement_boundary(self, V: df.fem.FunctionSpace) -> list[df.fem.bcs.DirichletBCMetaClass]:
+    def create_displacement_boundary(self, V: df.fem.FunctionSpaceBase) -> list[df.fem.bcs.DirichletBC]:
         """Defines the displacement boundary conditions
 
         Args:
@@ -192,7 +192,7 @@ def apply_temp_bc(self, T_bc: pint.Quantity | float) -> None:
     def apply_body_force(self) -> None:
         self.use_body_force = True
 
-    def create_temperature_bcs(self, V: df.fem.FunctionSpace) -> list[df.fem.bcs.DirichletBCMetaClass]:
+    def create_temperature_bcs(self, V: df.fem.FunctionSpaceBase) -> list[df.fem.bcs.DirichletBC]:
         """defines empty temperature boundary conditions (to be done in child)
 
         this function is abstract until there is a need for a material that does need a temperature boundary

src/fenicsxconcrete/experimental_setup/tensile_beam.py

@@ -82,7 +82,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
 
         return setup_parameters
 
-    def create_displacement_boundary(self, V) -> list:
+    def create_displacement_boundary(self, V: df.fem.FunctionSpaceBase) -> list[df.fem.bcs.DirichletBC]:
         """Defines the displacement boundary conditions
 
         Args:

src/fenicsxconcrete/finite_element_problem/concrete_am.py

@@ -143,7 +143,7 @@ def setup(self) -> None:
 
         self.rule = QuadratureRule(cell_type=self.mesh.ufl_cell(), degree=self.p["q_degree"])
         # displacement space (name V required for sensors!)
-        self.V = df.fem.VectorFunctionSpace(self.mesh, ("CG", self.p["degree"]))
+        self.V = df.fem.functionspace(self.mesh, ("CG", self.p["degree"], (self.mesh.geometry.dim,)))
         self.strain_stress_space = self.rule.create_quadrature_tensor_space(self.mesh, (self.p["dim"], self.p["dim"]))
 
         # global variables for all AM problems relevant
@@ -243,12 +243,14 @@ def pv_plot(self) -> None:
         # write further fields
         sigma_plot = project(
             self.mechanics_problem.sigma(self.fields.displacement),
-            df.fem.TensorFunctionSpace(self.mesh, self.q_fields.plot_space_type),
+            df.fem.functionspace(
+                self.mesh, self.q_fields.plot_space_type + (self.q_fields.stress.ufl_element().value_shape(), True)
+            ),
             self.rule.dx,
         )
 
         E_plot = project(
-            self.mechanics_problem.q_E, df.fem.FunctionSpace(self.mesh, self.q_fields.plot_space_type), self.rule.dx
+            self.mechanics_problem.q_E, df.fem.functionspace(self.mesh, self.q_fields.plot_space_type), self.rule.dx
         )
 
         E_plot.name = "Youngs_Modulus"

src/fenicsxconcrete/finite_element_problem/linear_elasticity.py

@@ -6,7 +6,7 @@
 
 from fenicsxconcrete.experimental_setup import CantileverBeam, Experiment
 from fenicsxconcrete.finite_element_problem.base_material import MaterialProblem, QuadratureFields, SolutionFields
-from fenicsxconcrete.util import Parameters, ureg
+from fenicsxconcrete.util import ureg
 
 
 class LinearElasticity(MaterialProblem):
@@ -44,8 +44,8 @@ def setup(self) -> None:
             )
 
         # define function space ets.
-        self.V = df.fem.VectorFunctionSpace(self.mesh, ("Lagrange", self.p["degree"]))  # 2 for quadratic elements
-        self.V_scalar = df.fem.FunctionSpace(self.mesh, ("Lagrange", self.p["degree"]))
+        self.V = df.fem.functionspace(self.mesh, ("Lagrange", self.p["degree"], (self.mesh.geometry.dim,)))  # 2 for quadratic elements
+        self.V_scalar = df.fem.functionspace(self.mesh, ("Lagrange", self.p["degree"], (1,)))
 
         # Define variational problem
         self.u_trial = ufl.TrialFunction(self.V)
@@ -100,7 +100,6 @@ def parameter_description() -> dict[str, str]:
             "nu": "Poissons Ratio",
             "stress_state": "for 2D plain stress or plane strain",
             "degree": "Polynomial degree for the FEM model",
-            "dt": "time step",
         }
 
         return description
@@ -134,7 +133,7 @@ def sigma(self, u: ufl.argument.Argument) -> ufl.core.expr.Expr:
 
     def solve(self) -> None:
         self.update_time()
-        self.logger.info(f"solving t={self.time}")
+        self.logger.info("solving t=%s", self.time)
         self.weak_form_problem.solve()
 
         # TODO Defined as abstractmethod. Should it depend on sensor instead of material?

src/fenicsxconcrete/sensor_definition/displacement_sensor.py

@@ -34,11 +34,11 @@ def measure(self, problem: MaterialProblem) -> None:
             t : time of measurement for time dependent problems, default is 1
         """
         # get displacements
-        bb_tree = df.geometry.BoundingBoxTree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
+        bb_tree = df.geometry.bb_tree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
         cells = []
 
         # Find cells whose bounding-box collide with the points
-        cell_candidates = df.geometry.compute_collisions(bb_tree, [self.where])
+        cell_candidates = df.geometry.compute_collisions_points(bb_tree, [self.where])
 
         # Choose one of the cells that contains the point
         colliding_cells = df.geometry.compute_colliding_cells(problem.experiment.mesh, cell_candidates, [self.where])

src/fenicsxconcrete/sensor_definition/doh_sensor.py

@@ -48,11 +48,11 @@ def measure(self, problem: MaterialProblem) -> None:
         # project stress onto visualization space
 
         # finding the cells corresponding to the point
-        bb_tree = df.geometry.BoundingBoxTree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
+        bb_tree = df.geometry.bb_tree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
         cells = []
 
         # Find cells whose bounding-box collide with the points
-        cell_candidates = df.geometry.compute_collisions(bb_tree, [self.where])
+        cell_candidates = df.geometry.compute_collisions_points(bb_tree, [self.where])
 
         # Choose one of the cells that contains the point
         colliding_cells = df.geometry.compute_colliding_cells(problem.experiment.mesh, cell_candidates, [self.where])

src/fenicsxconcrete/sensor_definition/strain_sensor.py

@@ -42,17 +42,17 @@ def measure(self, problem: MaterialProblem) -> None:
 
         strain_function = project(
             strain,  # stress fct from problem
-            df.fem.TensorFunctionSpace(problem.experiment.mesh, problem.q_fields.plot_space_type),  # tensor space
+            df.fem.functionspace(problem.experiment.mesh, problem.q_fields.plot_space_type),  # tensor space
             problem.q_fields.measure,
         )
         # project stress onto visualization space
 
         # finding the cells corresponding to the point
-        bb_tree = df.geometry.BoundingBoxTree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
+        bb_tree = df.geometry.bb_tree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
         cells = []
 
         # Find cells whose bounding-box collide with the points
-        cell_candidates = df.geometry.compute_collisions(bb_tree, [self.where])
+        cell_candidates = df.geometry.compute_collisions_points(bb_tree, [self.where])
 
         # Choose one of the cells that contains the point
         colliding_cells = df.geometry.compute_colliding_cells(problem.experiment.mesh, cell_candidates, [self.where])

src/fenicsxconcrete/sensor_definition/stress_sensor.py

@@ -42,16 +42,16 @@ def measure(self, problem: MaterialProblem) -> None:
 
         stress_function = project(
             stress,  # stress fct from problem
-            df.fem.TensorFunctionSpace(problem.experiment.mesh, problem.q_fields.plot_space_type),  # tensor space
+            df.fem.functionspace(problem.experiment.mesh, problem.q_fields.plot_space_type),  # tensor space
             problem.q_fields.measure,
         )
 
         # finding the cells corresponding to the point
-        bb_tree = df.geometry.BoundingBoxTree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
+        bb_tree = df.geometry.bb_tree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
         cells = []
 
         # Find cells whose bounding-box collide with the points
-        cell_candidates = df.geometry.compute_collisions(bb_tree, [self.where])
+        cell_candidates = df.geometry.compute_collisions_points(bb_tree, [self.where])
 
         # Choose one of the cells that contains the point
         colliding_cells = df.geometry.compute_colliding_cells(problem.experiment.mesh, cell_candidates, [self.where])

src/fenicsxconcrete/sensor_definition/temperature_sensor.py

@@ -34,11 +34,11 @@ def measure(self, problem: MaterialProblem) -> None:
             t : time of measurement for time dependent problems, default is 1
         """
         # get displacements
-        bb_tree = df.geometry.BoundingBoxTree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
+        bb_tree = df.geometry.bb_tree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
         cells = []
 
         # Find cells whose bounding-box collide with the points
-        cell_candidates = df.geometry.compute_collisions(bb_tree, [self.where])
+        cell_candidates = df.geometry.compute_collisions_points(bb_tree, [self.where])
 
         # Choose one of the cells that contains the point
         colliding_cells = df.geometry.compute_colliding_cells(problem.experiment.mesh, cell_candidates, [self.where])

src/fenicsxconcrete/sensor_definition/youngs_modulus_sensor.py

@@ -48,11 +48,11 @@ def measure(self, problem: MaterialProblem) -> None:
         # project stress onto visualization space
 
         # finding the cells corresponding to the point
-        bb_tree = df.geometry.BoundingBoxTree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
+        bb_tree = df.geometry.bb_tree(problem.experiment.mesh, problem.experiment.mesh.topology.dim)
         cells = []
 
         # Find cells whose bounding-box collide with the points
-        cell_candidates = df.geometry.compute_collisions(bb_tree, [self.where])
+        cell_candidates = df.geometry.compute_collisions_points(bb_tree, [self.where])
 
         # Choose one of the cells that contains the point
         colliding_cells = df.geometry.compute_colliding_cells(problem.experiment.mesh, cell_candidates, [self.where])

tests/boundary_conditions/test_bcs_get_boundary_dofs.py

@@ -3,6 +3,7 @@
 import dolfinx
 import numpy as np
 from mpi4py import MPI
+from basix.ufl import element
 
 from fenicsxconcrete.boundary_conditions.bcs import BoundaryConditions, get_boundary_dofs
 from fenicsxconcrete.boundary_conditions.boundary import plane_at
@@ -44,7 +45,8 @@ def test_whole_boundary() -> None:
     dim = 2
 
     domain = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, n, n, dolfinx.mesh.CellType.quadrilateral)
-    V = dolfinx.fem.VectorFunctionSpace(domain, ("Lagrange", degree), dim=dim)
+    el = element("Lagrange", domain.basix_cell(), degree, shape=(dim,))
+    V = dolfinx.fem.functionspace(domain, el)
 
     # option (a)
     bc_handler = BoundaryConditions(domain, V)
@@ -70,7 +72,8 @@ def test_xy_plane() -> None:
     dim = 3
 
     domain = dolfinx.mesh.create_unit_cube(MPI.COMM_WORLD, n, n, n, dolfinx.mesh.CellType.hexahedron)
-    V = dolfinx.fem.VectorFunctionSpace(domain, ("Lagrange", degree), dim=dim)
+    el = element("Lagrange", domain.basix_cell(), degree, shape=(dim,))
+    V = dolfinx.fem.functionspace(domain, el)
     xy_plane = plane_at(0.0, "z")
 
     # option (a)

tests/boundary_conditions/test_boundary_line_at.py

@@ -11,7 +11,7 @@
 def test_cube() -> None:
     n = 4
     domain = dolfinx.mesh.create_unit_cube(MPI.COMM_WORLD, n, n, n, dolfinx.mesh.CellType.hexahedron)
-    V = dolfinx.fem.FunctionSpace(domain, ("Lagrange", 1))
+    V = dolfinx.fem.functionspace(domain, ("Lagrange", 1))
 
     x_axis = line_at([0, 0], ["z", "y"])
     y_axis = line_at([0, 0], ["z", "x"])

tests/boundary_conditions/test_boundary_plane_at.py

@@ -10,7 +10,7 @@
 
 def test_square() -> None:
     domain = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 8, 8, dolfinx.mesh.CellType.quadrilateral)
-    V = dolfinx.fem.FunctionSpace(domain, ("Lagrange", 1))
+    V = dolfinx.fem.functionspace(domain, ("Lagrange", 1))
 
     bottom = plane_at(0.0, "y")
     top = plane_at(1.0, "y")
@@ -56,7 +56,7 @@ def l_shaped_boundary(x):
 def test_cube() -> None:
     nx, ny, nz = 4, 4, 4
     domain = dolfinx.mesh.create_unit_cube(MPI.COMM_WORLD, nx, ny, nz, dolfinx.mesh.CellType.hexahedron)
-    V = dolfinx.fem.FunctionSpace(domain, ("Lagrange", 1))
+    V = dolfinx.fem.functionspace(domain, ("Lagrange", 1))
 
     xy_plane = plane_at(0.0, "z")
     dofs = dolfinx.fem.locate_dofs_geometrical(V, xy_plane)

tests/boundary_conditions/test_boundary_point_at.py

@@ -4,6 +4,7 @@
 import numpy as np
 from mpi4py import MPI
 from petsc4py.PETSc import ScalarType
+from basix.ufl import element
 
 from fenicsxconcrete.boundary_conditions.boundary import point_at
 
@@ -12,7 +13,7 @@ def test_type_error() -> None:
     """test TypeError in conversion to float"""
     n = 10
     domain = dolfinx.mesh.create_interval(MPI.COMM_WORLD, n, [0.0, 10.0])
-    V = dolfinx.fem.FunctionSpace(domain, ("Lagrange", 1))
+    V = dolfinx.fem.functionspace(domain, ("Lagrange", 1))
     x = point_at(5)
     dofs = dolfinx.fem.locate_dofs_geometrical(V, x)
     nodal_value = 42
@@ -25,7 +26,7 @@ def test_type_error() -> None:
 def test_function_space() -> None:
     n = 101
     domain = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, n, n, dolfinx.mesh.CellType.quadrilateral)
-    V = dolfinx.fem.FunctionSpace(domain, ("Lagrange", 2))
+    V = dolfinx.fem.functionspace(domain, ("Lagrange", 2))
 
     h = 1.0 / n
     my_point = point_at(np.array([h * 2, h * 5]))
@@ -40,7 +41,9 @@ def test_function_space() -> None:
 def test_vector_function_space() -> None:
     n = 101
     domain = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, n, n, dolfinx.mesh.CellType.quadrilateral)
-    V = dolfinx.fem.VectorFunctionSpace(domain, ("Lagrange", 2))
+    degree = 2
+    ve = element("Lagrange", domain.basix_cell(), degree, shape=(2,))
+    V = dolfinx.fem.functionspace(domain, ve)
 
     # note the inconsistency in specifying the coordinates
     # this is handled by `to_floats`