Merge pull request festim-dev#764 from RemDelaporteMathurin/update-do…

…lfinx-0.8

Update dolfinx 0.8

.github/workflows/ci_conda.yml

@@ -14,13 +14,13 @@ jobs:
       with:
         activate-environment: myenv
         miniforge-version: latest
-        use-mamba: true
+        # use-mamba: true
         channels: conda-forge
 
     - name: Create Conda environment
       shell: bash -l {0}
       run: |
-        mamba install -c conda-forge fenics-dolfinx=0.7.2
+        conda install -c conda-forge fenics-dolfinx=0.8.0
 
     - name: Install local package and dependencies
       shell: bash -l {0}

.github/workflows/ci_docker.yml

@@ -3,9 +3,12 @@ on: [pull_request, push]
 
 jobs:
   run-tests:
-      runs-on: ubuntu-latest
-      container: dolfinx/dolfinx:v0.7.2
-      steps:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        container_version: [v0.8.0, nightly]
+    container: dolfinx/dolfinx:${{ matrix.container_version }}
+    steps:
         - name: Checkout code
           uses: actions/checkout@v2
 

festim/boundary_conditions/dirichlet_bc.py

@@ -127,7 +127,7 @@ def temperature_dependent(self):
             return False
 
     def create_value(
-        self, mesh, function_space: fem.FunctionSpaceBase, temperature, t: fem.Constant
+        self, mesh, function_space: fem.FunctionSpace, temperature, t: fem.Constant
     ):
         """Creates the value of the boundary condition as a fenics object and sets it to
         self.value_fenics.
@@ -138,7 +138,7 @@ def create_value(
 
         Args:
             mesh (dolfinx.mesh.Mesh) : the mesh
-            function_space (dolfinx.fem.FunctionSpaceBase): the function space
+            function_space (dolfinx.fem.FunctionSpace): the function space
             temperature (float): the temperature
             t (dolfinx.fem.Constant): the time
         """

test/system_tests/test_1_mobile_1_trap.py

@@ -31,8 +31,7 @@ def v_exact(mod):
     trapped_analytical_ufl = v_exact(ufl)
     trapped_analytical_np = v_exact(np)
 
-    elements = ufl.FiniteElement("P", test_mesh_1d.mesh.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_1d.mesh, elements)
+    V = fem.functionspace(test_mesh_1d.mesh, ("Lagrange", 1))
     T = fem.Function(V)
     f = fem.Function(V)
     g = fem.Function(V)
@@ -132,8 +131,7 @@ def u_exact_alt(mod):
     H_analytical_ufl = u_exact(ufl)
     H_analytical_np = u_exact_alt(np)
 
-    elements = ufl.FiniteElement("P", test_mesh_1d.mesh.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_1d.mesh, elements)
+    V = fem.functionspace(test_mesh_1d.mesh, ("Lagrange", 1))
     T = fem.Function(V)
 
     D_0 = 1
@@ -197,8 +195,7 @@ def v_exact(mod):
     trapped_analytical_ufl = v_exact(ufl)
     trapped_analytical_np = v_exact(np)
 
-    elements = ufl.FiniteElement("P", test_mesh_3d.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_3d, elements)
+    V = fem.functionspace(test_mesh_3d, ("Lagrange", 1))
     T = fem.Function(V)
     f = fem.Function(V)
     g = fem.Function(V)
@@ -311,8 +308,7 @@ def v_exact(mod):
     trapped_analytical_ufl = v_exact(ufl)
     trapped_analytical_np = v_exact(np)
 
-    elements = ufl.FiniteElement("P", test_mesh_2d.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_2d, elements)
+    V = fem.functionspace(test_mesh_2d, ("Lagrange", 1))
     T = fem.Function(V)
     f = fem.Function(V)
     g = fem.Function(V)

test/system_tests/test_1_mobile_species.py

@@ -25,8 +25,7 @@ def u_exact(mod):
     H_analytical_ufl = u_exact(ufl)
     H_analytical_np = u_exact(np)
 
-    elements = ufl.FiniteElement("CG", test_mesh_1d.mesh.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_1d.mesh, elements)
+    V = fem.functionspace(test_mesh_1d.mesh, ("Lagrange", 1))
     T = fem.Function(V)
 
     D_0 = 1
@@ -86,8 +85,7 @@ def u_exact_alt(mod):
     H_analytical_ufl = u_exact(ufl)
     H_analytical_np = u_exact_alt(np)
 
-    elements = ufl.FiniteElement("P", test_mesh_1d.mesh.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_1d.mesh, elements)
+    V = fem.functionspace(test_mesh_1d.mesh, ("Lagrange", 1))
     T = fem.Function(V)
 
     D_0 = 1
@@ -146,8 +144,7 @@ def u_exact(mod):
     H_analytical_ufl = u_exact(ufl)
     H_analytical_np = u_exact(np)
 
-    elements = ufl.FiniteElement("CG", test_mesh_2d.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_2d, elements)
+    V = fem.functionspace(test_mesh_2d, ("Lagrange", 1))
     T = fem.Function(V)
 
     D_0 = 1
@@ -212,8 +209,7 @@ def u_exact(mod):
     H_analytical_ufl = u_exact(ufl)
     H_analytical_np = u_exact(np)
 
-    elements = ufl.FiniteElement("CG", test_mesh_3d.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_3d, elements)
+    V = fem.functionspace(test_mesh_3d, ("Lagrange", 1))
     T = fem.Function(V)
 
     D_0 = 1

test/system_tests/test_fluxes.py

@@ -15,8 +15,7 @@ def test_flux_bc_1_mobile_MMS_steady_state():
 
     u_exact = lambda x: 1 + 2 * x[0] ** 2
 
-    elements = ufl.FiniteElement("CG", test_mesh_1d.mesh.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_1d.mesh, elements)
+    V = fem.functionspace(test_mesh_1d.mesh, ("Lagrange", 1))
     T = fem.Function(V)
 
     D_0 = 1
@@ -65,10 +64,6 @@ def test_flux_bc_heat_transfer_steady_state():
 
     u_exact = lambda x: 1 + 2 * x[0] ** 2
 
-    elements = ufl.FiniteElement("CG", test_mesh_1d.mesh.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_1d.mesh, elements)
-    T = fem.Function(V)
-
     thermal_cond = 2.3
 
     my_model = F.HeatTransferProblem()

test/system_tests/test_heat_transfer.py

@@ -19,8 +19,7 @@ def u_exact(mod):
     T_analytical_ufl = u_exact(ufl)
     T_analytical_np = u_exact(np)
 
-    elements = ufl.FiniteElement("CG", test_mesh_1d.mesh.ufl_cell(), 1)
-    V = fem.FunctionSpace(test_mesh_1d.mesh, elements)
+    V = fem.functionspace(test_mesh_1d.mesh, ("Lagrange", 1))
     T_solution = fem.Function(V)
     T_solution.interpolate(lambda x: 1 + np.sin(2 * np.pi * x[0]))
 

test/system_tests/tools.py

@@ -6,10 +6,10 @@
 
 def error_L2(u_computed, u_exact, degree_raise=3):
     # Create higher order function space
-    degree = u_computed.function_space.ufl_element().degree()
-    family = u_computed.function_space.ufl_element().family()
+    degree = u_computed.function_space.ufl_element().degree
+    family = u_computed.function_space.ufl_element().family_name
     mesh = u_computed.function_space.mesh
-    W = fem.FunctionSpace(mesh, (family, degree + degree_raise))
+    W = fem.functionspace(mesh, (family, degree + degree_raise))
     # Interpolate approximate solution
     u_W = fem.Function(W)
     u_W.interpolate(u_computed)

test/test_dirichlet_bc.py

@@ -76,7 +76,7 @@ def test_callable_for_value():
     assert isinstance(bc.value_fenics, fem.Function)
 
     # check the initial value of the boundary condition
-    assert bc.value_fenics.vector.array[-1] == float(
+    assert bc.value_fenics.x.petsc_vec.array[-1] == float(
         value(x=np.array([subdomain.x]), t=0.0)
     )
 
@@ -85,7 +85,7 @@ def test_callable_for_value():
         t.value = i
         bc.update(float(t))
         expected_value = float(value(x=np.array([subdomain.x]), t=float(t)))
-        computed_value = bc.value_fenics.vector.array[-1]
+        computed_value = bc.value_fenics.x.petsc_vec.array[-1]
         assert np.isclose(computed_value, expected_value)
 
 
@@ -115,7 +115,7 @@ def test_value_callable_x_t_T():
 
     # check the initial value of the boundary condition
     assert np.isclose(
-        bc.value_fenics.vector.array[-1],
+        bc.value_fenics.x.petsc_vec.array[-1],
         float(value(x=np.array([subdomain.x]), t=float(t), T=float(T))),
     )
 
@@ -126,7 +126,7 @@ def test_value_callable_x_t_T():
         bc.update(float(t))
 
         expected_value = float(value(x=np.array([subdomain.x]), t=float(t), T=float(T)))
-        computed_value = bc.value_fenics.vector.array[-1]
+        computed_value = bc.value_fenics.x.petsc_vec.array[-1]
         assert np.isclose(computed_value, expected_value)
 
 
@@ -203,7 +203,7 @@ def test_callable_x_only():
 
     # check the initial value of the boundary condition
     assert np.isclose(
-        bc.value_fenics.vector.array[-1],
+        bc.value_fenics.x.petsc_vec.array[-1],
         float(value(x=np.array([subdomain.x]))),
     )
 
@@ -212,7 +212,7 @@ def test_callable_x_only():
         t.value = i
         bc.update(float(t))
         expected_value = float(value(x=np.array([subdomain.x])))
-        computed_value = bc.value_fenics.vector.array[-1]
+        computed_value = bc.value_fenics.x.petsc_vec.array[-1]
         assert np.isclose(computed_value, expected_value)
 
 
@@ -265,13 +265,13 @@ def test_integration_with_HTransportProblem(value):
         arguments = value.__code__.co_varnames
         if "x" in arguments and "t" in arguments and "T" in arguments:
             expected_value = value(x=np.array([subdomain.x]), t=2.0, T=550.0)
-            computed_value = my_bc.value_fenics.vector.array[-1]
+            computed_value = my_bc.value_fenics.x.petsc_vec.array[-1]
         elif "x" in arguments and "t" in arguments:
             expected_value = value(x=np.array([subdomain.x]), t=2.0)
-            computed_value = my_bc.value_fenics.vector.array[-1]
+            computed_value = my_bc.value_fenics.x.petsc_vec.array[-1]
         elif "x" in arguments:
             expected_value = value(x=np.array([subdomain.x]))
-            computed_value = my_bc.value_fenics.vector.array[-1]
+            computed_value = my_bc.value_fenics.x.petsc_vec.array[-1]
         elif "t" in arguments:
             expected_value = value(t=2.0)
             computed_value = float(my_bc.value_fenics)
@@ -387,13 +387,13 @@ def test_integration_with_a_multispecies_HTransportProblem(value_A, value_B):
         arguments = value_B.__code__.co_varnames
         if "x" in arguments and "t" in arguments and "T" in arguments:
             expected_value = value_B(x=np.array([subdomain_B.x]), t=2.0, T=550.0)
-            computed_value = my_bc_B.value_fenics.vector.array[-1]
+            computed_value = my_bc_B.value_fenics.x.petsc_vec.array[-1]
         elif "x" in arguments and "t" in arguments:
             expected_value = value_B(x=np.array([subdomain_B.x]), t=2.0)
-            computed_value = my_bc_B.value_fenics.vector.array[-1]
+            computed_value = my_bc_B.value_fenics.x.petsc_vec.array[-1]
         elif "x" in arguments:
             expected_value = value_B(x=np.array([subdomain_B.x]))
-            computed_value = my_bc_B.value_fenics.vector.array[-1]
+            computed_value = my_bc_B.value_fenics.x.petsc_vec.array[-1]
         elif "t" in arguments:
             expected_value = value_B(t=2.0)
             computed_value = float(my_bc_B.value_fenics)

test/test_h_transport_problem.py

@@ -804,7 +804,7 @@ def test_create_initial_conditions_expr_fenics(input_value, expected_value):
     my_model.initialise()
 
     assert np.isclose(
-        my_model.species[0].prev_solution.vector.array[-1],
+        my_model.species[0].prev_solution.x.petsc_vec.array[-1],
         expected_value,
     )
 

test/test_heat_transfer_problem.py

@@ -34,10 +34,10 @@ def source_from_exact_solution(
 
 def error_L2(u_computed, u_exact, degree_raise=3):
     # Create higher order function space
-    degree = u_computed.function_space.ufl_element().degree()
-    family = u_computed.function_space.ufl_element().family()
+    degree = u_computed.function_space.ufl_element().degree
+    family = u_computed.function_space.ufl_element().family_name
     mesh = u_computed.function_space.mesh
-    W = fem.FunctionSpace(mesh, (family, degree + degree_raise))
+    W = fem.functionspace(mesh, (family, degree + degree_raise))
     # Interpolate approximate solution
     u_W = fem.Function(W)
     u_W.interpolate(u_computed)
@@ -388,6 +388,9 @@ def test_meshtags_from_xdmf(tmp_path, mesh):
         facet_tag = np.full(len(facet_indices[i]), idx + 1, dtype=np.int32)
         facet_tags.append(facet_tag)
 
+    facet_tags = np.array(facet_tags).flatten()
+    facet_indices = np.array(facet_indices).flatten()
+
     facet_meshtags = dolfinx.mesh.meshtags(mesh, fdim, facet_indices, facet_tags)
 
     # create volume meshtags

test/test_initial_condition.py

@@ -78,7 +78,7 @@ def test_warning_raised_when_giving_time_as_arg_initial_temperature():
     """Test that a warning is raised if the value is given with t in its arguments"""
 
     # give function to species
-    V = fem.FunctionSpace(test_mesh.mesh, ("CG", 1))
+    V = fem.functionspace(test_mesh.mesh, ("Lagrange", 1))
     my_species = F.Species("test")
     my_species.prev_solution = fem.Function(V)
 
@@ -107,7 +107,7 @@ def test_create_value_fenics_initial_temperature(input_value, expected_type):
     # BUILD
 
     # give function to species
-    V = fem.FunctionSpace(test_mesh.mesh, ("CG", 1))
+    V = fem.functionspace(test_mesh.mesh, ("Lagrange", 1))
     c = fem.Function(V)
 
     my_species = F.Species("test")

test/test_mesh.py

@@ -82,6 +82,9 @@ def test_meshtags_from_xdmf(tmp_path, mesh):
         facet_tag = np.full(len(facet_indices[i]), idx + 1, dtype=np.int32)
         facet_tags.append(facet_tag)
 
+    facet_tags = np.array(facet_tags).flatten()
+    facet_indices = np.array(facet_indices).flatten()
+
     facet_meshtags = fenics_mesh.meshtags(mesh, fdim, facet_indices, facet_tags)
 
     # create volume meshtags

test/test_surface_quantity.py

@@ -20,16 +20,16 @@ def test_surface_flux_export_compute():
     facet_indices = np.array(
         dummy_surface.locate_boundary_facet_indices(my_mesh.mesh),
         dtype=np.int32,
-    )
+    ).flatten()
     tags_facets = np.array(
         [1],
         dtype=np.int32,
-    )
+    ).flatten()
     facet_meshtags = meshtags(my_mesh.mesh, 0, facet_indices, tags_facets)
     ds = ufl.Measure("ds", domain=my_mesh.mesh, subdomain_data=facet_meshtags)
 
     # give function to species
-    V = fem.functionspace(my_mesh.mesh, ("CG", 1))
+    V = fem.functionspace(my_mesh.mesh, ("Lagrange", 1))
     c = fem.Function(V)
     c.interpolate(lambda x: 2 * x[0] ** 2 + 1)
 

test/test_total_volume.py

@@ -22,7 +22,7 @@ def test_total_volume_export_compute():
     dx = ufl.Measure("dx", domain=my_mesh.mesh, subdomain_data=cell_meshtags)
 
     # give function to species
-    V = fem.functionspace(my_mesh.mesh, ("CG", 1))
+    V = fem.functionspace(my_mesh.mesh, ("Lagrange", 1))
     c = fem.Function(V)
     c.interpolate(lambda x: 2 * x[0] ** 2 + 1)