Merge pull request #523 from RemDelaporteMathurin/dev

Bugfixes
festim-dev · Sep 14, 2022 · c753f25 · c753f25
2 parents 33937d0 + 71ccb00
commit c753f25
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Showing 20 changed files with 125 additions and 97 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -10,21 +10,21 @@ jobs:
       - run:
           name: Run Unit tests
           command: |
-            python3 -m pytest test/unit/ --cov FESTIM --cov-report xml --cov-report term
+            python3 -m pytest test/unit/ --cov festim --cov-report xml --cov-report term
       - run:
           name: Run HTransportProblem tests
           command: |
-            python3 -m pytest test/h_transport_problem/ --cov FESTIM --cov-append --cov-report xml --cov-report term
+            python3 -m pytest test/h_transport_problem/ --cov festim --cov-append --cov-report xml --cov-report term
       - run:
           name: Run HeatTransferProblem tests
           command: |
-            python3 -m pytest test/heat_transfer_problem/ --cov FESTIM --cov-append --cov-report xml --cov-report term
+            python3 -m pytest test/heat_transfer_problem/ --cov festim --cov-append --cov-report xml --cov-report term
       - run:
           name: Run Simulation tests
           command: |
-            python3 -m pytest test/simulation/ --cov FESTIM --cov-append --cov-report xml --cov-report term
+            python3 -m pytest test/simulation/ --cov festim --cov-append --cov-report xml --cov-report term
       - run:
           name: Run System tests
           command: |
-            python3 -m pytest test/system/ --cov FESTIM --cov-append --cov-report xml --cov-report term
-            bash <(curl -s https://codecov.io/bash) -t cf160fda-091b-4d7f-a22d-a9509c36720c
+            python3 -m pytest test/system/ --cov festim --cov-append --cov-report xml --cov-report term
+            bash <(curl -s https://codecov.io/bash)
diff --git a/demos/demo_Ogorodnikova.ipynb b/demos/demo_Ogorodnikova.ipynb
@@ -232,7 +232,7 @@
    "outputs": [],
    "source": [
     "my_model.boundary_conditions = [\n",
-    "    F.DirichletBC(surfaces=[1, 2], value=0)\n",
+    "    F.DirichletBC(surfaces=[1, 2], value=0, field=0)\n",
     "]"
    ]
   },

diff --git a/demos/demo_derived_quantities.ipynb b/demos/demo_derived_quantities.ipynb
@@ -189,11 +189,13 @@
     "my_model.boundary_conditions = [\n",
     "    F.DirichletBC(\n",
     "        surfaces=1,\n",
-    "        value=1e15\n",
+    "        value=1e15,\n",
+    "        field=0\n",
     "    ),\n",
     "    F.DirichletBC(\n",
     "        surfaces=2,\n",
-    "        value=0\n",
+    "        value=0,\n",
+    "        field=0\n",
     "    )\n",
     "]"
    ]
@@ -645,7 +647,7 @@
  "metadata": {
   "file_extension": ".py",
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3.6.9 64-bit",
    "language": "python",
    "name": "python3"
   },
@@ -665,7 +667,12 @@
   "name": "python",
   "npconvert_exporter": "python",
   "pygments_lexer": "ipython3",
-  "version": 3
+  "version": 3,
+  "vscode": {
+   "interpreter": {
+    "hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
+   }
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2

diff --git a/demos/demo_multi_materials.ipynb b/demos/demo_multi_materials.ipynb
@@ -221,7 +221,8 @@
    "source": [
     "left_bc = F.DirichletBC(\n",
     "    surfaces=1,\n",
-    "    value=1e20\n",
+    "    value=1e20,\n",
+    "    field=0\n",
     "    )\n",
     "\n",
     "right_bc = F.RecombinationFlux(\n",

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
@@ -10,7 +10,7 @@ Installing FEniCS
 
 FESTIM requires FEniCS to run.
 
-It can be installed using Docker::
+It can be installed using `Docker <https://www.docker.com/>`_::
 
     docker run -ti -v $(pwd):/home/fenics/shared quay.io/fenicsproject/stable:latest
 

diff --git a/festim/boundary_conditions/boundary_condition.py b/festim/boundary_conditions/boundary_condition.py
@@ -1,15 +1,22 @@
-import festim
-import fenics as f
-import sympy as sp
+class BoundaryCondition:
+    """Base BoundaryCondition class
 
+    Args:
+        surfaces (list or int): the surfaces of the BC
+        field (int or str): the field the boundary condition is
+            applied to. 0 and "solute" stand for the mobile
+            concentration, "T" for temperature
+    """
 
-class BoundaryCondition:
-    def __init__(self, surfaces, field=0) -> None:
+    def __init__(self, surfaces, field) -> None:
 
         if not isinstance(surfaces, list):
             surfaces = [surfaces]
         self.surfaces = surfaces
 
-        self.field = field
+        if field == "solute":
+            self.field = 0
+        else:
+            self.field = field
         self.expression = None
         self.sub_expressions = []
diff --git a/festim/boundary_conditions/dirichlets/custom_dc.py b/festim/boundary_conditions/dirichlets/custom_dc.py
@@ -28,7 +28,7 @@ def fun(T, solute, param1):
 
     def __init__(self, surfaces, function, field=0, **prms) -> None:
 
-        super().__init__(surfaces, field=field)
+        super().__init__(surfaces, field=field, value=None)
         self.function = function
         self.prms = prms
         self.convert_prms()

diff --git a/festim/boundary_conditions/dirichlets/dc_imp.py b/festim/boundary_conditions/dirichlets/dc_imp.py
@@ -35,7 +35,7 @@ class ImplantationDirichlet(DirichletBC):
     """
 
     def __init__(self, surfaces, phi, R_p, D_0, E_D, Kr_0=None, E_Kr=None) -> None:
-        super().__init__(surfaces, field=0)
+        super().__init__(surfaces, field=0, value=None)
         self.phi = phi
         self.R_p = R_p
         self.D_0 = D_0

diff --git a/festim/boundary_conditions/dirichlets/dirichlet_bc.py b/festim/boundary_conditions/dirichlets/dirichlet_bc.py
@@ -8,13 +8,14 @@ class DirichletBC(BoundaryCondition):
 
     Args:
         surfaces (list or int): the surfaces of the BC
-        value (float or sp.Expr, optional): the value of the boundary
-            condition. Defaults to None.
-        field (int, optional): the field the boundary condition is
-            applied to. Defaults to 0.
+        value (float or sp.Expr): the value of the boundary
+            condition.
+        field (int or str): the field the boundary condition is
+            applied to. 0 and "solute" stand for the mobile
+            concentration, "T" for temperature
     """
 
-    def __init__(self, surfaces, value=None, field=0) -> None:
+    def __init__(self, surfaces, value, field) -> None:
         super().__init__(surfaces, field=field)
         self.value = value
         self.dirichlet_bc = []

diff --git a/festim/boundary_conditions/dirichlets/henrys_bc.py b/festim/boundary_conditions/dirichlets/henrys_bc.py
@@ -19,7 +19,7 @@ class HenrysBC(DirichletBC):
     """
 
     def __init__(self, surfaces, H_0, E_H, pressure) -> None:
-        super().__init__(surfaces, field=0)
+        super().__init__(surfaces, field=0, value=None)
         self.H_0 = H_0
         self.E_H = E_H
         self.pressure = pressure

diff --git a/festim/boundary_conditions/dirichlets/sieverts_bc.py b/festim/boundary_conditions/dirichlets/sieverts_bc.py
@@ -19,7 +19,7 @@ class SievertsBC(DirichletBC):
     """
 
     def __init__(self, surfaces, S_0, E_S, pressure) -> None:
-        super().__init__(surfaces, field=0)
+        super().__init__(surfaces, field=0, value=None)
         self.S_0 = S_0
         self.E_S = E_S
         self.pressure = pressure

diff --git a/festim/boundary_conditions/fluxes/recombination_flux.py b/festim/boundary_conditions/fluxes/recombination_flux.py
@@ -21,7 +21,7 @@ def __init__(self, Kr_0, E_Kr, order, surfaces) -> None:
         self.Kr_0 = Kr_0
         self.E_Kr = E_Kr
         self.order = order
-        super().__init__(surfaces=surfaces)
+        super().__init__(surfaces=surfaces, field=0)
 
     def create_form(self, T, solute):
         Kr_0_expr = f.Expression(sp.printing.ccode(self.Kr_0), t=0, degree=1)

diff --git a/festim/concentration/traps/trap.py b/festim/concentration/traps/trap.py
@@ -1,4 +1,4 @@
-from festim import Concentration, k_B, Material
+from festim import Concentration, k_B, Material, Theta
 from fenics import *
 import sympy as sp
 import numpy as np
@@ -107,7 +107,7 @@ def make_density(self, densities):
                         )
                     )
 
-    def create_form(self, mobile, materials, T, dx, dt=None, chemical_pot=False):
+    def create_form(self, mobile, materials, T, dx, dt=None):
         """Creates the general form associated with the trap
         d ct/ dt = k c_m (n - c_t) - p c_t + S
 
@@ -118,17 +118,13 @@ def create_form(self, mobile, materials, T, dx, dt=None, chemical_pot=False):
             dx (fenics.Measure): the dx measure of the sim
             dt (festim.Stepsize, optional): If None assuming steady state.
                 Defaults to None.
-            chemical_pot (bool, optional): If True, continuity of chemical
-                potential is assumed. Defaults to False.
         """
         self.F = 0
-        self.create_trapping_form(mobile, materials, T, dx, dt, chemical_pot)
+        self.create_trapping_form(mobile, materials, T, dx, dt)
         if self.sources is not None:
             self.create_source_form(dx)
 
-    def create_trapping_form(
-        self, mobile, materials, T, dx, dt=None, chemical_pot=False
-    ):
+    def create_trapping_form(self, mobile, materials, T, dx, dt=None):
         """d ct/ dt = k c_m (n - c_t) - p c_t
 
         Args:
@@ -138,8 +134,6 @@ def create_trapping_form(
             dx (fenics.Measure): the dx measure of the sim
             dt (festim.Stepsize, optional): If None assuming steady state.
                 Defaults to None.
-            chemical_pot (bool, optional): If True, continuity of chemical
-                potential is assumed. Defaults to False.
         """
         solution = self.solution
         prev_solution = self.previous_solution
@@ -148,11 +142,6 @@ def create_trapping_form(
         if not all(isinstance(mat, Material) for mat in self.materials):
             self.make_materials(materials)
 
-        T = T.T
-        c_0 = mobile.solution
-        if chemical_pot:
-            theta = c_0
-
         expressions_trap = []
         F_trapping = 0  # initialise the form
 
@@ -185,24 +174,24 @@ def create_trapping_form(
             # expressions to be updated
             expressions_trap.append(density)
 
-            if chemical_pot:
-                # TODO this needs changing for Henry
-                # change of variable
-                S_0 = mat.S_0
-                E_S = mat.E_S
-                c_0 = theta * S_0 * exp(-E_S / k_B / T)
+            if isinstance(mobile, Theta) and mat.solubility_law == "henry":
+                raise NotImplementedError(
+                    "Henry law of solubility is not implemented with traps"
+                )
+
+            c_0, c_0_n = mobile.get_concentration_for_a_given_material(mat, T)
 
             # k(T)*c_m*(n - c_t) - p(T)*c_t
             F_trapping += (
                 -k_0
-                * exp(-E_k / k_B / T)
+                * exp(-E_k / k_B / T.T)
                 * c_0
                 * (density - solution)
                 * test_function
                 * dx(mat.id)
             )
             F_trapping += (
-                p_0 * exp(-E_p / k_B / T) * solution * test_function * dx(mat.id)
+                p_0 * exp(-E_p / k_B / T.T) * solution * test_function * dx(mat.id)
             )
 
         self.F_trapping = F_trapping

diff --git a/festim/concentration/traps/traps.py b/festim/concentration/traps/traps.py
@@ -31,10 +31,10 @@ def make_traps_materials(self, materials):
         for trap in self.traps:
             trap.make_materials(materials)
 
-    def create_forms(self, mobile, materials, T, dx, dt=None, chemical_pot=False):
+    def create_forms(self, mobile, materials, T, dx, dt=None):
         self.F = 0
         for trap in self.traps:
-            trap.create_form(mobile, materials, T, dx, dt=dt, chemical_pot=chemical_pot)
+            trap.create_form(mobile, materials, T, dx, dt=dt)
             self.F += trap.F
             self.sub_expressions += trap.sub_expressions
 

diff --git a/festim/h_transport_problem.py b/festim/h_transport_problem.py
@@ -195,9 +195,7 @@ def define_variational_problem(self, materials, mesh, dt=None):
         expressions += self.mobile.sub_expressions
 
         # Add traps
-        self.traps.create_forms(
-            self.mobile, materials, self.T, mesh.dx, dt, self.settings.chemical_pot
-        )
+        self.traps.create_forms(self.mobile, materials, self.T, mesh.dx, dt)
         F += self.traps.F
         expressions += self.traps.sub_expressions
         self.F = F