Deprecate MeshFromRefinements

docs/source/api/meshing.rst

@@ -15,10 +15,6 @@ Meshing
     :members:
     :show-inheritance:
 
-.. autoclass:: MeshFromRefinements
-    :members:
-    :show-inheritance:
-
 .. autoclass:: MeshFromXDMF
     :members:
     :show-inheritance:

festim/__init__.py

@@ -31,7 +31,6 @@
 
 from .meshing.mesh import Mesh
 from .meshing.mesh_1d import Mesh1D
-from .meshing.mesh_from_refinements import MeshFromRefinements
 from .meshing.mesh_from_vertices import MeshFromVertices
 from .meshing.mesh_from_xdmf import MeshFromXDMF
 

test/heat_transfer_problem/test_solving.py

@@ -1,6 +1,7 @@
 import festim
 import pytest
 import fenics as f
+import numpy as np
 
 
 @pytest.mark.parametrize("preconditioner", ["default", "icc"])
@@ -13,7 +14,7 @@ def test_create_functions_linear_solver_gmres(preconditioner):
         preconditioner (str): the preconditioning method
     """
 
-    mesh = festim.MeshFromRefinements(10, size=0.1)
+    mesh = festim.MeshFromVertices(np.linspace(0, 0.1, num=11))
 
     materials = festim.Materials([festim.Material(id=1, D_0=1, E_D=0, thermal_cond=1)])
     mesh.define_measures(materials)
@@ -60,7 +61,7 @@ def sim(self):
 
     def test_custom_solver(self):
         """Solves the system using the built-in solver and using the f.NewtonSolver"""
-        mesh = festim.MeshFromRefinements(10, size=0.1)
+        mesh = festim.MeshFromVertices(np.linspace(0, 0.1, num=11))
         materials = festim.Materials(
             [festim.Material(id=1, D_0=1, E_D=0, thermal_cond=1)]
         )

test/simulation/test_postprocessing_integration.py

@@ -12,7 +12,7 @@ def my_sim(self):
         """A pytest fixture defining the festim.Simulation object"""
         my_sim = festim.Simulation({})
         my_sim.t = 0
-        my_sim.mesh = festim.MeshFromRefinements(10, 1)
+        my_sim.mesh = festim.MeshFromVertices(np.linspace(0, 1, num=11))
         my_sim.settings = festim.Settings(None, None, final_time=10)
         mat1 = festim.Material(1, D_0=1, E_D=1)
         my_sim.materials = festim.Materials([mat1])
@@ -120,10 +120,12 @@ def test_pure_diffusion(self, my_sim):
             my_sim.run_post_processing()
             data = derived_quantities.data
 
+            print(data)
+
             assert len(data) == i + 1
             assert data[i][0] == t
-            assert data[i][1] == 10
-            assert data[i][2] == 20
+            assert data[i][1] == pytest.approx(10)
+            assert data[i][2] == pytest.approx(20)
             assert data[i][3] == pytest.approx(11)
             assert data[i][4] == pytest.approx(11)
 
@@ -259,7 +261,7 @@ def test_surface_kinetics(self):
         """
         my_sim = festim.Simulation({})
         my_sim.t = 0
-        my_sim.mesh = festim.MeshFromRefinements(10, 1)
+        my_sim.mesh = festim.MeshFromVertices(np.linspace(0, 1, num=11))
         my_sim.settings = festim.Settings(None, None, final_time=10)
         mat1 = festim.Material(1, D_0=1, E_D=1)
         my_sim.materials = festim.Materials([mat1])

test/system/test_chemical_potential.py

@@ -71,7 +71,7 @@ def run(h):
             festim.InitialCondition(field=0, value=u),
         ]
 
-        my_mesh = festim.MeshFromRefinements(round(size / h), size)
+        my_mesh = festim.MeshFromVertices(np.linspace(0, size, round(size / h) + 1))
 
         my_bcs = [
             festim.DirichletBC(surfaces=[1, 2], value=u, field=0),

test/system/test_extrinsic_traps.py

@@ -1,10 +1,11 @@
 import festim as F
+import numpy as np
 
 
 def test_extrinsic_trap():
     """Runs a festim sim with an extrinsic trap"""
     my_materials = F.Materials([F.Material(id=1, D_0=2, E_D=1, name="mat")])
-    my_mesh = F.MeshFromRefinements(10, 1)
+    my_mesh = F.MeshFromVertices(np.linspace(0, 1, 11))
 
     my_traps = F.ExtrinsicTrap(
         k_0=1,

test/system/test_misc.py

@@ -45,7 +45,7 @@ def test_convective_flux(tmpdir):
 def test_error_steady_state_with_stepsize():
     """Checks that an error is raised when a stepsize is given for a steady state simulation"""
     my_model = F.Simulation()
-    my_model.mesh = F.MeshFromRefinements(1000, size=1)
+    my_model.mesh = F.MeshFromVertices(np.linspace(0, 1, num=1001))
 
     my_model.materials = F.Materials([F.Material(D_0=1, E_D=0, id=1)])
 
@@ -67,7 +67,7 @@ def test_error_steady_state_with_stepsize():
 def test_error_transient_without_stepsize():
     """Checks that an error is raised when a stepsize is not given for a transient simulation"""
     my_model = F.Simulation()
-    my_model.mesh = F.MeshFromRefinements(1000, size=1)
+    my_model.mesh = F.MeshFromVertices(np.linspace(0, 1, num=100))
 
     my_model.materials = F.Materials([F.Material(D_0=1, E_D=0, id=1)])
 

test/system/test_system.py

@@ -45,7 +45,7 @@ def test_run_temperature_stationary(tmpdir):
 
     my_materials = [festim.Material(id=1, D_0=4.1e-7, E_D=0.39, thermal_cond=1)]
 
-    my_mesh = festim.MeshFromRefinements(200, size=size)
+    my_mesh = festim.MeshFromVertices(np.linspace(0, size, num=200))
     my_boundary_conditions = [
         festim.DirichletBC(value=1, field=0, surfaces=[1]),
         festim.DirichletBC(value=u, field="T", surfaces=[1, 2]),
@@ -115,7 +115,7 @@ def test_run_temperature_transient(tmpdir):
             )
         ]
     )
-    my_mesh = festim.MeshFromRefinements(200, size)
+    my_mesh = festim.MeshFromVertices(np.linspace(0, size, num=200))
 
     my_bcs = [
         festim.DirichletBC(surfaces=[1], value=1, field=0),
@@ -216,7 +216,7 @@ def run(h):
             festim.InitialCondition(field=1, value=v),
         ]
 
-        my_mesh = festim.MeshFromRefinements(round(size / h), size)
+        my_mesh = festim.MeshFromVertices(np.linspace(0, size, num=round(size / h) + 1))
 
         my_bcs = [
             festim.DirichletBC(surfaces=[1, 2], value=u, field=0),
@@ -342,7 +342,7 @@ def run(h):
             festim.InitialCondition(field=1, value=v),
         ]
 
-        my_mesh = festim.MeshFromRefinements(round(size / h), size)
+        my_mesh = festim.MeshFromVertices(np.linspace(0, size, num=round(size / h) + 1))
 
         my_bcs = [
             festim.DirichletBC(surfaces=[1, 2], value=u, field=0),
@@ -442,7 +442,7 @@ def test_run_chemical_pot_mass_balance(tmpdir):
         festim.InitialCondition(field=0, value=1),
     ]
 
-    my_mesh = festim.MeshFromRefinements(5, 1)
+    my_mesh = festim.MeshFromVertices(np.linspace(0, 1, num=6))
 
     my_temp = festim.Temperature(700 + 210 * festim.t)
 
@@ -512,7 +512,7 @@ def run(h):
         ]
 
         size = 0.1
-        my_mesh = festim.MeshFromRefinements(round(size / h), size)
+        my_mesh = festim.MeshFromVertices(np.linspace(0, size, num=round(size / h) + 1))
 
         my_source = festim.Source(f, 1, "solute")
 
@@ -624,7 +624,7 @@ def run(h):
         ]
 
         size = 0.1
-        my_mesh = festim.MeshFromRefinements(round(size / h), size)
+        my_mesh = festim.MeshFromVertices(np.linspace(0, size, num=round(size / h) + 1))
 
         my_sources = [festim.Source(f, 1, "solute"), festim.Source(g, 1, "1")]
 
@@ -718,7 +718,7 @@ def test_chemical_pot_T_solve_stationary(tmpdir):
     my_materials = festim.Materials(
         [festim.Material(id=1, D_0=1, E_D=0.1, S_0=2, E_S=0.2, thermal_cond=1)]
     )
-    my_mesh = festim.MeshFromRefinements(10, 1)
+    my_mesh = festim.MeshFromVertices(np.linspace(0, 1, num=11))
 
     my_temp = festim.HeatTransferProblem(transient=False)
     my_bcs = [
@@ -772,7 +772,7 @@ def test_export_particle_flux_with_chemical_pot(tmpdir):
     my_materials = festim.Materials(
         [festim.Material(id=1, D_0=2, E_D=1, S_0=2, E_S=1, thermal_cond=2)]
     )
-    my_mesh = festim.MeshFromRefinements(10, 1)
+    my_mesh = festim.MeshFromVertices(np.linspace(0, 1, num=11))
 
     my_temp = festim.Temperature(300)
 
@@ -885,7 +885,7 @@ def test_steady_state_traps_not_everywhere():
         ]
     )
 
-    my_mesh = festim.MeshFromRefinements(100, 1)
+    my_mesh = festim.MeshFromVertices(np.linspace(0, 1, num=101))
 
     my_trap = festim.Trap(1, 0, 1, 0, ["mat_1", "mat_3"], 1)
 
@@ -922,7 +922,7 @@ def test_no_jacobian_update():
     mat = festim.Material(id=1, D_0=1, E_D=0)
     my_materials = festim.Materials([mat])
 
-    my_mesh = festim.MeshFromRefinements(10, 1)
+    my_mesh = festim.MeshFromVertices(np.linspace(0, 1, num=100))
 
     my_trap = festim.Trap(1, 0, 1, 0, [mat], 1)
 
@@ -959,7 +959,7 @@ def test_nb_iterations_bewteen_derived_quantities_compute():
 
     def init_sim(nb_it_compute):
         my_materials = festim.Materials([festim.Material(id=1, D_0=1, E_D=0)])
-        my_mesh = festim.MeshFromRefinements(10, 1)
+        my_mesh = festim.MeshFromVertices(np.linspace(0, 1, num=11))
 
         my_temp = festim.Temperature(300)
 
@@ -1011,7 +1011,7 @@ def test_error_steady_state_diverges():
         ]
     )
 
-    my_mesh = festim.MeshFromRefinements(10, 1)
+    my_mesh = festim.MeshFromVertices(np.linspace(0, 1, num=11))
 
     my_temp = festim.Temperature(-1)
 
@@ -1037,7 +1037,7 @@ def test_error_steady_state_diverges():
 def test_completion_tone():
     """Checks that when a completion tone is enabled, sim is not affected"""
     my_model = festim.Simulation(log_level=20)
-    my_model.mesh = festim.MeshFromRefinements(10, size=1)
+    my_model.mesh = festim.MeshFromVertices(np.linspace(0, 1, num=11))
     my_model.materials = festim.Materials([festim.Material(id=1, D_0=1, E_D=0)])
     my_model.T = festim.Temperature(100)
     my_model.boundary_conditions = [