Merge branch 'fenicsx' into time_as_Constant

.github/workflows/ci.yml

@@ -2,40 +2,40 @@ name: CI
 on: [pull_request, push]
 
 jobs:
-  run-on-conda:
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
-    - name: Set up Conda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: myenv
-        mamba-version: "*"
-        channels: conda-forge, defaults
-
-    - name: Create Conda environment
-      shell: bash -l {0}
-      run: |
-        mamba install -c conda-forge fenics-dolfinx
-
-    - name: Install local package and dependencies
-      shell: bash -l {0}
-      run: |
-        pip install .[test]
-
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest test/ --cov festim --cov-report xml --cov-report term
+  # run-on-conda:
+  #   runs-on: ubuntu-latest
+
+  #   steps:
+  #   - name: Checkout code
+  #     uses: actions/checkout@v2
+
+  #   - name: Set up Conda
+  #     uses: conda-incubator/setup-miniconda@v2
+  #     with:
+  #       activate-environment: myenv
+  #       mamba-version: "*"
+  #       channels: conda-forge, defaults
+
+  #   - name: Create Conda environment
+  #     shell: bash -l {0}
+  #     run: |
+  #       mamba install -c conda-forge fenics-dolfinx
+
+  #   - name: Install local package and dependencies
+  #     shell: bash -l {0}
+  #     run: |
+  #       pip install .[test]
+
+  #   - name: Run tests
+  #     shell: bash -l {0}
+  #     run: |
+  #       pytest test/ --cov festim --cov-report xml --cov-report term
 
-    - name: Upload to codecov
-      uses: codecov/codecov-action@v3
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        files: ./coverage.xml
+  #   - name: Upload to codecov
+  #     uses: codecov/codecov-action@v3
+  #     with:
+  #       token: ${{ secrets.CODECOV_TOKEN }}
+  #       files: ./coverage.xml
 
   run-on-docker:
     runs-on: ubuntu-latest

festim/hydrogen_transport_problem.py

@@ -292,12 +292,10 @@ def run(self, final_time: float):
             mobile_xdmf.write_function(self.u, float(self.t))
 
             cm = self.species[0].solution
-            # TODO this should be a property of Mesh
-            n = FacetNormal(self.mesh.mesh)
             D = self.subdomains[0].material.get_diffusion_coefficient(
                 self.mesh.mesh, self.temperature
             )
-            surface_flux = form(D * dot(grad(cm), n) * self.ds(2))
+            surface_flux = form(D * dot(grad(cm), self.mesh.n) * self.ds(2))
             flux = assemble_scalar(surface_flux)
             flux_values.append(flux)
             times.append(float(self.t))

festim/mesh/mesh.py

@@ -1,3 +1,6 @@
+import ufl
+
+
 class Mesh:
     """
     Mesh class
@@ -9,6 +12,7 @@ class Mesh:
         mesh (dolfinx.mesh.Mesh): the mesh
         vdim (int): the dimension of the mesh cells
         fdim (int): the dimension of the mesh facets
+        n (ufl.FacetNormal): the normal vector to the facets
     """
 
     def __init__(self, mesh=None):
@@ -32,3 +36,7 @@ def vdim(self):
     @property
     def fdim(self):
         return self.mesh.topology.dim - 1
+
+    @property
+    def n(self):
+        return ufl.FacetNormal(self.mesh)