added a new system test in/out + collapse post-processing solution + …

…new sub_function attribute

src/festim/exports/vtx.py

@@ -109,7 +109,7 @@ def get_functions(self) -> list[_Function]:
                 legacy_output = True
                 break
         if legacy_output:
-            return [field.post_processing_solution for field in self._field]
+            return [field.sub_function for field in self._field]
         else:
             if self._subdomain is None:
                 raise ValueError("Subdomain must be specified")

src/festim/hydrogen_transport_problem.py

@@ -523,6 +523,7 @@ def assign_functions_to_species(self):
             sub_test_functions = [ufl.TestFunction(self.function_space)]
             self.species[0].sub_function_space = self.function_space
             self.species[0].post_processing_solution = self.u
+            self.species[0].sub_function = self.u
         else:
             sub_solutions = list(ufl.split(self.u))
             sub_prev_solution = list(ufl.split(self.u_n))

src/festim/species.py

@@ -75,6 +75,7 @@ def __init__(self, name: str = None, mobile=True, subdomains=None) -> None:
         self.sub_function_space = None
         self.post_processing_solution = None
         self.collapsed_function_space = None
+        self.sub_function = None
 
         self.subdomains = subdomains
         self.subdomain_to_solution = {}

test/system_tests/test_io.py

@@ -4,7 +4,7 @@
 import mpi4py.MPI as MPI
 
 
-def test():
+def test_out_in():
     mesh = dolfinx.mesh.create_unit_square(
         MPI.COMM_WORLD, nx=10, ny=10, cell_type=dolfinx.cpp.mesh.CellType.quadrilateral
     )
@@ -13,7 +13,7 @@ def test():
 
     my_mat = F.Material(name="mat", D_0=1, E_D=0)
     vol = F.VolumeSubdomain(id=0, material=my_mat)
-    surf = F.SurfaceSubdomain(id=0)
+    surf = F.SurfaceSubdomain(id=1)
     my_model.subdomains = [vol, surf]
 
     H = F.Species("H")
@@ -32,44 +32,63 @@ def test():
     ]
 
     my_model.settings = F.Settings(
-        atol=1e-12, rtol=1e-12, transient=True, final_time=100
+        atol=1e-12, rtol=1e-12, transient=True, final_time=10
     )
     my_model.settings.stepsize = F.Stepsize(1)
 
     my_model.exports = [
         F.VTXSpeciesExport(
-            filename="H.bp",
-            field=[H],
+            filename="out_checkpoint.bp",
+            field=[H, D],
             checkpoint=True,
         ),
+        F.VTXSpeciesExport(
+            filename="model_1_out_h.bp",
+            field=[H],
+        ),
     ]
 
     my_model.initialise()
     my_model.run()
 
     my_model2 = F.HydrogenTransportProblem()
     my_model2.mesh = F.Mesh(mesh)
-    my_model.subdomains = [vol, surf]
+    my_model2.subdomains = [vol, surf]
 
     H = F.Species("H")
     D = F.Species("D")
-    my_model.species = [H, D]
+    my_model2.species = [H, D]
 
-    my_model.temperature = 500
+    my_model2.temperature = 500
 
-    my_model.initial_conditions = [
+    my_model2.initial_conditions = [
+        F.InitialConcentrationFromFile(
+            filename="out_checkpoint.bp", species=H, name="H", timestamp=10
+        ),
         F.InitialConcentrationFromFile(
-            filename="H.bp", species=H, name="H", timestamp=100
+            filename="out_checkpoint.bp", species=D, name="D", timestamp=10
         ),
-        # F.InitialConcentrationFromFile(
-        #     filename="H.bp", species=D, name="D", timestamp=100
-        # ),
     ]
 
-    my_model.settings = F.Settings(
-        atol=1e-12, rtol=1e-12, transient=True, final_time=100
+    my_model2.settings = F.Settings(
+        atol=1e-10, rtol=1e-10, transient=True, final_time=10
     )
-    my_model.settings.stepsize = F.Stepsize(1)
+    my_model2.settings.stepsize = F.Stepsize(0.1)
 
-    my_model.initialise()
-    my_model.run()
+    my_model2.exports = [
+        F.VTXSpeciesExport(
+            filename="model_2_out_h.bp",
+            field=[H],
+        ),
+    ]
+
+    my_model2.initialise()
+    my_model2.run()
+
+    import numpy as np
+
+    np.testing.assert_allclose(
+        H.post_processing_solution.x.array,
+        1.5,
+        atol=1e-10,
+    )

test/test_vtx.py

@@ -14,7 +14,7 @@ def test_vtx_export_one_function(tmpdir):
     """Test can add one function to a vtx export"""
     u = dolfinx.fem.Function(V)
     sp = F.Species("H")
-    sp.post_processing_solution = u
+    sp.sub_function = u
     filename = str(tmpdir.join("my_export.bp"))
     my_export = F.VTXSpeciesExport(filename, field=sp)
 
@@ -30,8 +30,8 @@ def test_vtx_export_two_functions(tmpdir):
 
     sp1 = F.Species("1")
     sp2 = F.Species("2")
-    sp1.post_processing_solution = u
-    sp2.post_processing_solution = v
+    sp1.sub_function = u
+    sp2.sub_function = v
     filename = str(tmpdir.join("my_export.bp"))
     my_export = F.VTXSpeciesExport(filename, field=[sp1, sp2])