Merge remote-tracking branch 'upstream/main' into temperature-as-float

.github/workflows/ci.yml

@@ -13,15 +13,14 @@ jobs:
       uses: conda-incubator/setup-miniconda@v2
       with:
         activate-environment: myenv
-        mamba-version: "*"
+        # mamba-version: "*"
         channels: conda-forge, defaults
 
     - name: Create Conda environment
       shell: bash -l {0}
       run: |
         # conda upgrade --strict-channel-priority -c conda-forge --all
-        conda install -c conda-forge 'conda-libmamba-solver<23.9'
-        mamba install -c conda-forge fenics
+        conda install -c conda-forge fenics numpy=1.24 python=3.10
 
     - name: Install dependencies
       shell: bash -l {0}

docs/source/conf.py

@@ -102,6 +102,24 @@
     "use_edit_page_button": True,
     "repository_branch": "main",
     "path_to_docs": "./docs/source",
+    "icon_links": [
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/FESTIM/",
+            "icon": "https://img.shields.io/pypi/dw/festim",
+            "type": "url",
+        },
+        {
+            "name": "Support Forum",
+            "url": "https://festim.discourse.group/",
+            "icon": "fa-brands fa-discourse",
+        },
+        {
+            "name": "Slack",
+            "url": "https://join.slack.com/t/festim-dev/shared_invite/zt-246hw8d6o-htWASLsbdosUo_2nRKCf9g",
+            "icon": "fa-brands fa-slack",
+        },
+    ],
 }
 
 html_title = "FESTIM Documentation"

docs/source/userguide/export_post_processing.rst

@@ -189,7 +189,7 @@ The data can be accessed in three different ways:
 
     print(flux_surf_3.t)
     print(flux_surf_3.data)
-    print(my_derived_quantities.derived_quantities[2].data)
+    print(my_derived_quantities[2].data)
 
 - export and read from a .csv file:
 

docs/source/userguide/temperature.rst

@@ -76,6 +76,17 @@ For a steady-state problem:
 
 :ref:`Boundary conditions<boundary conditions>` and :ref:`heat sources<sources>` can then be applied to this heat transfer problem.
 
+For transient problems, an initial condition is required:
+
+.. code-block:: python
+
+    model.T = HeatTransferProblem(
+        transient=True,
+        initial_condition=300,
+    )
+
+Initial conditions can be given as float, sympy expressions or a :class:`festim.InitialCondition` instance in order to read from a XDMF file (see :ref:`Initial Conditions<Initial Conditions>` for more details).
+
 ----------------
 From a XDMF file
 ----------------

festim/generic_simulation.py

@@ -269,6 +269,10 @@ def initialise(self):
         # check that dt attribute is None if the sim is steady state
         if not self.settings.transient and self.dt is not None:
             raise AttributeError("dt must be None in steady state simulations")
+        if self.settings.transient and self.settings.final_time is None:
+            raise AttributeError(
+                "final_time argument must be provided to settings in transient simulations"
+            )
         if self.settings.transient and self.dt is None:
             raise AttributeError("dt must be provided in transient simulations")
         if not self.T:
@@ -340,7 +344,7 @@ def initialise(self):
 
         for export in self.exports:
             if isinstance(export, festim.DerivedQuantities):
-                for q in export.derived_quantities:
+                for q in export:
                     if not isinstance(q, tuple(allowed_quantities[self.mesh.type])):
                         warnings.warn(
                             f"{type(q)} may not work as intended for {self.mesh.type} meshes"

festim/temperature/temperature.py

@@ -4,24 +4,26 @@
 
 class Temperature:
     """
-    Description of Temperature
+    Class for Temperature in FESTIM
 
     Args:
         value (sp.Add, int, float, optional): The value of the temperature.
-            Only needed if type is not "expression". Defaults to None.
-        initial_value (sp.Add, int, float, optional): The initial value.
-            Only needed if type is not "expression". Defaults to None.
+            Defaults to None.
 
     Attributes:
         T (fenics.Function): the function attributed with temperature
         T_n (fenics.Function): the previous function
         value (sp.Add, int, float): the expression of temperature
         expression (fenics.Expression): the expression of temperature as a
             fenics object
+
+    Usage:
+        >>> import festim as F
+        >>> my_model = F.Simulation(...)
+        >>> my_model.T = F.Temperature(300 + 10 * F.x + F.t)
     """
 
     def __init__(self, value=None) -> None:
-        # self.type = type
         self.T = None
         self.T_n = None
         self.value = value

festim/temperature/temperature_solver.py

@@ -8,7 +8,7 @@ class HeatTransferProblem(festim.Temperature):
     Args:
         transient (bool, optional): If True, a transient simulation will
             be run. Defaults to True.
-        initial_condition (festim.InitialCondition, optional): The initial condition.
+        initial_condition (int, float, sp.Expr, festim.InitialCondition, optional): The initial condition.
             Only needed if transient is True.
         absolute_tolerance (float, optional): the absolute tolerance of the newton
             solver. Defaults to 1e-03
@@ -56,6 +56,17 @@ def __init__(
         self.boundary_conditions = []
         self.sub_expressions = []
 
+    @property
+    def initial_condition(self):
+        return self._initial_condition
+
+    @initial_condition.setter
+    def initial_condition(self, value):
+        if isinstance(value, (int, float, sp.Expr)):
+            self._initial_condition = festim.InitialCondition(field="T", value=value)
+        else:
+            self._initial_condition = value
+
     # TODO rename initialise?
     def create_functions(self, materials, mesh, dt=None):
         """Creates functions self.T, self.T_n and test function self.v_T.
@@ -73,7 +84,10 @@ def create_functions(self, materials, mesh, dt=None):
         self.T = f.Function(V, name="T")
         self.T_n = f.Function(V, name="T_n")
         self.v_T = f.TestFunction(V)
-
+        if self.transient and self.initial_condition is None:
+            raise AttributeError(
+                "Initial condition is required for transient heat transfer simulations"
+            )
         if self.transient and self.initial_condition:
             if isinstance(self.initial_condition.value, str):
                 if self.initial_condition.value.endswith(".xdmf"):

test/simulation/test_initialise.py

@@ -220,3 +220,29 @@ def test_wrong_type_temperature(value):
         match="accepted types for T attribute are int, float, sympy.Expr or festim.Temperature",
     ):
         my_model.T = value
+
+
+def test_error_raised_when_no_final_time():
+    """
+    Creates a Simulation object and checks that a AttributeError is raised
+    when .initialise() is called without a final_time argument
+    """
+
+    my_model = F.Simulation()
+
+    my_model.mesh = F.MeshFromVertices([0, 1, 2, 3])
+
+    my_model.materials = F.Material(D_0=1, E_D=0, id=1)
+
+    my_model.T = F.Temperature(500)
+
+    my_model.settings = F.Settings(
+        absolute_tolerance=1e-10,
+        relative_tolerance=1e-10,
+        transient=True,
+    )
+
+    my_model.dt = F.Stepsize(1)
+
+    with pytest.raises(AttributeError, match="final_time argument must be provided"):
+        my_model.initialise()

test/simulation/test_postprocessing_integration.py

@@ -174,6 +174,7 @@ def test_fluxes(self, my_sim):
         assert np.isclose(data[1][3], -1 * grad_T * lambda_x_0)
         assert np.isclose(data[1][4], -1 * grad_T * lambda_x_1 * -1)
 
+    @pytest.mark.filterwarnings("ignore:in 1D")
     def test_performance_xdmf_export_every_N_iterations(self, my_sim, tmpdir):
         """Runs run_post_processing several times with different export.mode
         values and checks that the xdmf
@@ -215,6 +216,7 @@ def test_performance_xdmf_export_every_N_iterations(self, my_sim, tmpdir):
                 for t_expected, t in zip(expected_times, times):
                     assert t_expected == pytest.approx(float(t))
 
+    @pytest.mark.filterwarnings("ignore:in 1D")
     def test_xdmf_export_only_last_timestep(self, my_sim, tmpdir):
         """Runs run_post_processing with mode="last":
         - when the time is not the final time and checks that nothing has been

test/system/test_misc.py

@@ -76,6 +76,7 @@ def test_error_transient_without_stepsize():
         transient=True,
         absolute_tolerance=1e-10,
         relative_tolerance=1e-10,
+        final_time=10,
     )
 
     my_model.dt = None
@@ -330,3 +331,23 @@ def test_materials_setter():
     test_materials = F.Materials([])
     my_model.materials = test_materials
     assert my_model.materials is test_materials
+
+
+def test_error_raised_when_no_IC_heat_transfer():
+    """
+    Checks that an error is raised when no initial condition is provided for
+    transient heat transfer simulations
+    """
+    my_model = F.Simulation()
+
+    my_model.T = F.HeatTransferProblem(transient=True, initial_condition=None)
+    my_model.mesh = F.MeshFromVertices(np.linspace(0, 1, 10))
+    my_model.materials = F.Material(1, 1, 0.1)
+    my_model.settings = F.Settings(1e-10, 1e-10, final_time=1e-7)
+    my_model.dt = F.Stepsize(1e-9)
+
+    with pytest.raises(
+        AttributeError,
+        match="Initial condition is required for transient heat transfer simulations",
+    ):
+        my_model.initialise()

test/unit/test_exports/test_derived_quantities/test_surface_quantity.py

@@ -1,4 +1,3 @@
-from nis import match
 import festim as F
 import pytest
 

test/unit/test_exports/test_derived_quantities/test_volume_quantity.py

@@ -1,4 +1,3 @@
-from nis import match
 import festim as F
 import pytest
 

test/unit/test_exports/test_trap_density_xdmf_export.py

@@ -3,6 +3,7 @@
 import sympy as sp
 from pathlib import Path
 import numpy as np
+import pytest
 
 
 def test_trap_density_xdmf_export_intergration_with_simultion(tmpdir):
@@ -96,6 +97,7 @@ def test_trap_density_xdmf_export_write(tmpdir):
     assert error_L2 < 1e-10
 
 
+@pytest.mark.filterwarnings("ignore:in 1D")
 def test_trap_density_xdmf_export_traps_materials_mixed(tmpdir):
     """Integration test for TrapDensityXDMF.write() with a trap material given
     as a string. Creates a festim simulation and exports the trap density as an

test/unit/test_exports/test_xdmf_export.py

@@ -10,7 +10,7 @@ def folder(tmpdir):
 
 
 def test_define_file_upon_construction(folder):
-    mesh = f.UnitIntervalMesh(10)
+    mesh = f.UnitSquareMesh(8, 8)
     filename = "{}/my_filename.xdmf".format(folder)
     my_xdmf = XDMFExport("solute", label="solute_label", filename=filename)
 
@@ -30,7 +30,7 @@ def test_default_filename():
 
 
 class TestDefineFile:
-    mesh = f.UnitIntervalMesh(10)
+    mesh = f.UnitSquareMesh(8, 8)
     my_xdmf = XDMFExport("solute", "my_label", filename="my_filename.xdmf")
 
     def test_file_exists(self, folder):
@@ -44,7 +44,7 @@ def test_file_exists(self, folder):
 
 
 class TestWrite:
-    mesh = f.UnitIntervalMesh(10)
+    mesh = f.UnitSquareMesh(8, 8)
     V = f.FunctionSpace(mesh, "P", 1)
     u = f.Function(V)
     label_to_function = {"solute": u}

test/unit/test_temperature.py

@@ -69,9 +69,7 @@ def thermal_cond(a):
     bc1 = festim.DirichletBC(surfaces=[1], value=u, field="T")
     bc2 = festim.FluxBC(surfaces=[2], value=2, field="T")
 
-    my_temp = festim.HeatTransferProblem(
-        transient=True, initial_condition=festim.InitialCondition(field="T", value=0)
-    )
+    my_temp = festim.HeatTransferProblem(transient=True, initial_condition=0)
     my_temp.boundary_conditions = [bc1, bc2]
     my_temp.sources = [festim.Source(-4, volume=[1], field="T")]
     my_temp.create_functions(my_mats, my_mesh, dt=dt)
@@ -133,6 +131,30 @@ class is created from this file and the error norm between the written and
     assert error_L2 < 1e-9
 
 
+def test_temperature_with_expr():
+    """
+    Test for the InitialCondition.create_functions() with a sympy expression
+    and checks that the error norm between the expected and computed
+    functions is below a certain threshold.
+    """
+    # create function to be comapared
+    mesh = fenics.UnitSquareMesh(10, 10)
+    # TempFromXDMF needs a festim mesh
+    my_mesh = festim.Mesh()
+    my_mesh.dx = fenics.dx
+    my_mesh.ds = fenics.ds
+    my_mesh.mesh = mesh
+    my_mats = festim.Materials(
+        [festim.Material(id=1, D_0=1, E_D=0, thermal_cond=1, heat_capacity=1, rho=1)]
+    )
+    my_T = festim.HeatTransferProblem(transient=True, initial_condition=300 + festim.x)
+    my_T.create_functions(mesh=my_mesh, materials=my_mats, dt=festim.Stepsize(2))
+
+    expected_expr = fenics.Expression("300 + x[0]", degree=2)
+    error_L2 = fenics.errornorm(expected_expr, my_T.T_n, "L2")
+    assert error_L2 < 1e-9
+
+
 def test_temperature_from_xdmf_create_functions(tmpdir):
     """Test for the TemperatureFromXDMF.create_functions().
     Creates a function, writes it to an XDMF file, then a TemperatureFromXDMF