Merge pull request festim-dev#1008 from RemDelaporteMathurin/dokken/test-updates

test fixes

Author: RemDelaporteMathurin

test/system_tests/test_io.py

@@ -136,8 +136,8 @@ def test_VTXExport_times_added_to_milestones(tmpdir):
     ]
     my_model.temperature = 100
     my_model.settings = F.Settings(
-        atol=1e0,
-        rtol=1e0,
+        atol=0.999,
+        rtol=0.999,
         final_time=4,
         transient=True,
         stepsize=F.Stepsize(initial_value=3),

test/test_coupled_heat_hydrogen_problem.py

@@ -79,14 +79,14 @@ def test_initial_dt_values_are_the_same():
     test_heat_problem = F.HeatTransferProblem(
         mesh=test_mesh,
         subdomains=test_subdomains,
-        settings=F.Settings(atol=1, rtol=1, transient=True, stepsize=0.5, final_time=5),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=True, stepsize=0.5, final_time=5),
     )
 
     test_hydrogen_problem = F.HydrogenTransportProblem(
         mesh=test_mesh,
         subdomains=test_subdomains,
         species=[test_H],
-        settings=F.Settings(atol=1, rtol=1, transient=True, stepsize=1.5, final_time=5),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=True, stepsize=1.5, final_time=5),
     )
 
     test_coupled_problem = F.CoupledTransientHeatTransferHydrogenTransport(
@@ -112,7 +112,7 @@ def test_dts_always_the_same():
     test_heat_problem = F.HeatTransferProblem(
         mesh=test_mesh,
         subdomains=test_subdomains,
-        settings=F.Settings(atol=1, rtol=1, transient=True, stepsize=dt, final_time=1),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=True, stepsize=dt, final_time=1),
         initial_condition=F.InitialTemperature(500),
     )
 
@@ -121,7 +121,7 @@ def test_dts_always_the_same():
         subdomains=test_subdomains,
         species=[test_H],
         initial_conditions=[F.InitialCondition(value=10, species=test_H)],
-        settings=F.Settings(atol=1, rtol=1, transient=True, stepsize=0.1, final_time=1),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=True, stepsize=0.1, final_time=1),
     )
 
     test_coupled_problem = F.CoupledTransientHeatTransferHydrogenTransport(
@@ -145,14 +145,14 @@ def test_error_raised_when_final_times_not_the_same():
     test_heat_problem = F.HeatTransferProblem(
         mesh=test_mesh,
         subdomains=test_subdomains,
-        settings=F.Settings(atol=1, rtol=1, transient=True, stepsize=1, final_time=10),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=True, stepsize=1, final_time=10),
     )
 
     test_hydrogen_problem = F.HydrogenTransportProblem(
         mesh=test_mesh,
         subdomains=test_subdomains,
         species=[test_H],
-        settings=F.Settings(atol=1, rtol=1, transient=True, stepsize=1, final_time=5),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=True, stepsize=1, final_time=5),
     )
 
     test_coupled_problem = F.CoupledTransientHeatTransferHydrogenTransport(
@@ -173,11 +173,11 @@ def test_error_raised_when_both_problems_not_transient():
     set to transient"""
 
     test_heat_problem = F.HeatTransferProblem(
-        settings=F.Settings(atol=1, rtol=1, transient=False),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=False),
     )
 
     test_hydrogen_problem = F.HydrogenTransportProblem(
-        settings=F.Settings(atol=1, rtol=1, transient=True, stepsize=1, final_time=4),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=True, stepsize=1, final_time=4),
     )
 
     with pytest.raises(

test/test_h_transport_problem.py

@@ -6,7 +6,7 @@
 import tqdm.autonotebook
 import ufl
 from dolfinx import default_scalar_type, fem, nls
-
+from packaging.version import Version
 import festim as F
 
 test_mesh = F.Mesh1D(vertices=np.array([0.0, 1.0, 2.0, 3.0, 4.0]))
@@ -161,8 +161,13 @@ def test_iterate():
         my_model.u - my_model.u_n
     ) / my_model.dt * v * ufl.dx - source_value * v * ufl.dx
 
-    problem = fem.petsc.NonlinearProblem(form, my_model.u, bcs=[])
-    my_model.solver = nls.petsc.NewtonSolver(MPI.COMM_WORLD, problem)
+
+    if Version(dolfinx.__version__) == Version("0.9.0"):
+        problem = fem.petsc.NonlinearProblem(form, my_model.u, bcs=[])
+        my_model.solver = nls.petsc.NewtonSolver(MPI.COMM_WORLD, problem)
+    elif Version(dolfinx.__version__) > Version("0.9.0"):
+        problem = fem.petsc.NonlinearProblem(form, my_model.u, bcs=[])
+        my_model.solver = problem
 
     my_model.t = fem.Constant(mesh, 0.0)
 
@@ -818,7 +823,7 @@ def test_create_initial_conditions_ValueError_raised_when_not_transient():
         subdomains=[my_vol],
         species=[H],
         initial_conditions=[F.InitialCondition(value=1.0, species=H)],
-        settings=F.Settings(atol=1, rtol=1, transient=False),
+        settings=F.Settings(atol=1, rtol=0.9999, transient=False),
     )
 
     with pytest.raises(
@@ -851,7 +856,7 @@ def test_create_initial_conditions_expr_fenics(input_value, expected_value):
         subdomains=[vol_subdomain],
         species=[H],
         initial_conditions=[F.InitialCondition(value=input_value, species=H)],
-        settings=F.Settings(atol=1, rtol=1, final_time=2, stepsize=1),
+        settings=F.Settings(atol=1, rtol=0.9999, final_time=2, stepsize=1),
     )
 
     # RUN
@@ -881,7 +886,7 @@ def test_create_species_from_trap():
         n=1,
         volume=my_vol,
     )
-    my_settings = F.Settings(atol=1, rtol=1, transient=False)
+    my_settings = F.Settings(atol=1, rtol=0.9999, transient=False)
     my_model = F.HydrogenTransportProblem(
         mesh=test_mesh,
         subdomains=[my_vol],
@@ -932,7 +937,7 @@ def test_create_initial_conditions_value_fenics_multispecies(
             F.InitialCondition(value=input_value_2, species=D),
             F.InitialCondition(value=input_value_1, species=H),
         ],
-        settings=F.Settings(atol=1, rtol=1, final_time=2, stepsize=1),
+        settings=F.Settings(atol=1, rtol=0.9999, final_time=2, stepsize=1),
     )
 
     # RUN

test/test_multispecies_problem.py

@@ -3,9 +3,9 @@
 import numpy as np
 from dolfinx.fem import Constant
 from ufl import exp
-
+from packaging.version import Version
 import festim as F
-
+import dolfinx
 
 def relative_error_computed_to_analytical(
     D, permeability, computed_flux, L, times, P_up
@@ -113,15 +113,26 @@ def test_multispecies_permeation_problem():
     ]
     my_model.initialise()
 
-    my_model.solver.convergence_criterion = "incremental"
-    ksp = my_model.solver.krylov_solver
-    opts = PETSc.Options()
-    option_prefix = ksp.getOptionsPrefix()
-    opts[f"{option_prefix}ksp_type"] = "cg"
-    opts[f"{option_prefix}pc_type"] = "gamg"
-    opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
-    ksp.setFromOptions()
-
+    if Version(dolfinx.__version__) == Version("0.9.0"):
+        my_model.solver.convergence_criterion = "incremental"
+        ksp = my_model.solver.krylov_solver
+        opts = PETSc.Options()
+        option_prefix = ksp.getOptionsPrefix()
+        opts[f"{option_prefix}ksp_type"] = "cg"
+        opts[f"{option_prefix}pc_type"] = "gamg"
+        opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
+        ksp.setFromOptions()
+    elif Version(dolfinx.__version__) > Version("0.9.0"):
+        snes = my_model.solver.solver
+        opts = PETSc.Options()
+        option_prefix = snes.getOptionsPrefix()
+        opts[f"{option_prefix}snes_atol"] = 0
+        opts[f"{option_prefix}snes_rtol"] = 0
+        opts[f"{option_prefix}snes_stol"] = 1e-8
+        opts[f"{option_prefix}ksp_type"] = "cg"
+        opts[f"{option_prefix}pc_type"] = "gamg"
+        opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
+        snes.setFromOptions()
     my_model.run()
 
     times = outgassing_flux_spe_1.t

test/test_permeation_problem.py

@@ -4,6 +4,8 @@
 
 import numpy as np
 from dolfinx.fem import Constant
+from packaging.version import Version
+import dolfinx
 from ufl import exp
 
 import festim as F
@@ -92,13 +94,26 @@ def test_permeation_problem(mesh_size=1001):
     my_model.initialise()
 
     my_model.solver.convergence_criterion = "incremental"
-    ksp = my_model.solver.krylov_solver
-    opts = PETSc.Options()
-    option_prefix = ksp.getOptionsPrefix()
-    opts[f"{option_prefix}ksp_type"] = "cg"
-    opts[f"{option_prefix}pc_type"] = "gamg"
-    opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
-    ksp.setFromOptions()
+    if Version(dolfinx.__version__) == Version("0.9.0"):
+        ksp = my_model.solver.krylov_solver
+        opts = PETSc.Options()
+        option_prefix = ksp.getOptionsPrefix()
+        opts[f"{option_prefix}ksp_type"] = "cg"
+        opts[f"{option_prefix}pc_type"] = "gamg"
+        opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
+        ksp.setFromOptions()
+    elif Version(dolfinx.__version__) > Version("0.9.0"):
+        snes = my_model.solver.solver
+        opts = PETSc.Options()
+        option_prefix = snes.getOptionsPrefix()
+        opts[f"{option_prefix}snes_atol"] = 0
+        opts[f"{option_prefix}snes_rtol"] = 0
+        opts[f"{option_prefix}snes_stol"] = 1e-8
+        opts[f"{option_prefix}ksp_type"] = "cg"
+        opts[f"{option_prefix}pc_type"] = "gamg"
+        opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
+        snes.setFromOptions()
+
 
     my_model.run()
 
@@ -193,15 +208,27 @@ def test_permeation_problem_multi_volume(tmp_path):
 
     my_model.initialise()
 
-    my_model.solver.convergence_criterion = "incremental"
-    ksp = my_model.solver.krylov_solver
-    opts = PETSc.Options()
-    option_prefix = ksp.getOptionsPrefix()
-    opts[f"{option_prefix}ksp_type"] = "cg"
-    opts[f"{option_prefix}pc_type"] = "gamg"
-    opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
-    ksp.setFromOptions()
-
+    if Version(dolfinx.__version__) == Version("0.9.0"):
+        ksp = my_model.solver.krylov_solver
+        opts = PETSc.Options()
+        option_prefix = ksp.getOptionsPrefix()
+        opts[f"{option_prefix}ksp_type"] = "cg"
+        opts[f"{option_prefix}pc_type"] = "gamg"
+        opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
+        ksp.setFromOptions()
+    elif Version(dolfinx.__version__) > Version("0.9.0"):
+        snes = my_model.solver.solver
+        opts = PETSc.Options()
+        option_prefix = snes.getOptionsPrefix()
+        opts[f"{option_prefix}snes_atol"] = 0
+        opts[f"{option_prefix}snes_rtol"] = 0
+        opts[f"{option_prefix}snes_stol"] = 1e-8
+        opts[f"{option_prefix}ksp_type"] = "cg"
+        opts[f"{option_prefix}pc_type"] = "gamg"
+        opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
+        snes.setFromOptions()
+
+    
     my_model.run()
 
     times = outgassing_flux.t