Merge pull request #535 from RemDelaporteMathurin/dev

Regular merge to main

.gitignore

@@ -102,3 +102,6 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+
+# version file
+**_version.py

festim/__init__.py

@@ -54,6 +54,7 @@
 from .boundary_conditions.fluxes.recombination_flux import RecombinationFlux
 from .boundary_conditions.fluxes.convective_flux import ConvectiveFlux
 from .boundary_conditions.fluxes.flux_custom import CustomFlux
+from .boundary_conditions.fluxes.mass_flux import MassFlux
 
 from .exports.exports import Exports
 from .exports.export import Export

festim/boundary_conditions/fluxes/mass_flux.py

@@ -0,0 +1,30 @@
+from festim import FluxBC, k_B
+import fenics as f
+import sympy as sp
+
+
+class MassFlux(FluxBC):
+    """
+    FluxBC subclass for advective mass flux
+    -D * grad(c) * n = h_mass * (c - c_ext)
+
+    Args:
+        h_mass (float or sp.Expr): mass transfer coefficient (m/s)
+        c_ext (float or sp.Expr): external concentration (1/m3)
+        surfaces (list or int): the surfaces of the BC
+
+    Reference: Bergman, T. L., Bergman, T. L., Incropera, F. P., Dewitt, D. P.,
+    & Lavine, A. S. (2011). Fundamentals of heat and mass transfer. John Wiley & Sons.
+    """
+
+    def __init__(self, h_coeff, c_ext, surfaces) -> None:
+        self.h_coeff = h_coeff
+        self.c_ext = c_ext
+        super().__init__(surfaces=surfaces, field=0)
+
+    def create_form(self, T, solute):
+        h_coeff = f.Expression(sp.printing.ccode(self.h_coeff), t=0, degree=1)
+        c_ext = f.Expression(sp.printing.ccode(self.c_ext), t=0, degree=1)
+
+        self.form = -h_coeff * (solute - c_ext)
+        self.sub_expressions = [h_coeff, c_ext]

festim/concentration/traps/neutron_induced_trap.py

@@ -7,7 +7,7 @@ class NeutronInducedTrap(ExtrinsicTrapBase):
     Class for neutron induced trap creation with annealing.
     The temporal evolution of the trap density is given by
 
-    dn_t/dt = phi*K*(1 - n_t/n_max) + A_0*exp(-E_A/(k_B*T))*n_t
+    dn_t/dt = phi*K*(1 - n_t/n_max) - A_0*exp(-E_A/(k_B*T))*n_t
 
     Args:
         k_0 (float, list): trapping pre-exponential factor (m3 s-1)
@@ -55,6 +55,7 @@ def __init__(
             A_0=A_0,
             E_A=E_A,
             id=id,
+            **kwargs,
         )
 
     def create_form_density(self, dx, dt, T):

pyproject.toml

@@ -2,8 +2,7 @@
 requires = [
     "setuptools >= 45",
     "wheel",
-    "setuptools_scm[toml] >= 6.2",
-    "setuptools_scm_git_archive",
+    "setuptools_scm[toml] >= 7.0.5"
 ]
 build-backend = "setuptools.build_meta"
 

test/unit/test_boundary_conditions.py

@@ -508,6 +508,15 @@ def test_recomb_flux():
     my_BC.create_form(T, c)
 
 
+def test_mass_flux():
+    expr = 2 + festim.x
+    T = fenics.Expression(sp.printing.ccode(expr), degree=1, t=0)
+    c = fenics.Expression(sp.printing.ccode(expr), degree=1, t=0)
+
+    my_BC = festim.MassFlux(surfaces=0, h_coeff=expr, c_ext=expr)
+    my_BC.create_form(T, c)
+
+
 def test_string_for_field_in_dirichletbc():
     """Test catching issue #462"""
     # build

test/unit/test_traps/test_neutron_induced_trap.py

@@ -124,3 +124,48 @@ def test_create_form_density(self):
         print(expected_form)
         print(self.my_trap.form_density)
         assert self.my_trap.form_density.equals(expected_form)
+
+
+class TestNeutronInducedTrapSolverParameters:
+    """
+    Test for NeutronInducedTrap class, with defined ExtrinsicTrapBase
+    solver parameters
+    """
+
+    my_trap = festim.NeutronInducedTrap(
+        1,
+        1,
+        1,
+        1,
+        "mat_name",
+        phi=1,
+        K=2,
+        n_max=3,
+        A_0=4,
+        E_A=5,
+        absolute_tolerance=2.5,
+        relative_tolerance=1.2e-10,
+        maximum_iterations=13,
+        linear_solver="mumps",
+    )
+
+    def test_attributes_from_instanciation(self):
+        """
+        Tests the solver paramters are assigned and ensures that
+        the default values have been updated
+        """
+
+        assert self.my_trap.absolute_tolerance == 2.5
+        assert self.my_trap.relative_tolerance == 1.2e-10
+        assert self.my_trap.maximum_iterations == 13
+        assert self.my_trap.linear_solver == "mumps"
+
+    def test_attributes_change_since_instanciation(self):
+        """
+        Test to ensure values can be updated after instanciation
+        """
+
+        expected_tolerance = 3.6
+        self.my_trap.absolute_tolerance = 3.6
+
+        assert self.my_trap.absolute_tolerance == expected_tolerance