Merge branch 'develop' into issue-4413-pin-workflows

CHANGELOG.md

@@ -11,6 +11,7 @@
 ## Bug fixes
 
 - Remove internal use of deprecated `set_parameters` function in the `Simulation` class which caused warnings. ([#4638](https://github.com/pybamm-team/PyBaMM/pull/4638))
+- Provide default value for `Symbol.mesh` attribute to avoid errors when adding variables after discretisation. ([#4644](https://github.com/pybamm-team/PyBaMM/pull/4644))
 
 # [v24.11.2](https://github.com/pybamm-team/PyBaMM/tree/v24.11.2) - 2024-11-27
 

docs/source/examples/notebooks/models/pouch-cell-model.ipynb

@@ -301,7 +301,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -311,8 +311,6 @@
     "    pybamm.t,\n",
     "    name=\"voltage_comsol\",\n",
     ")\n",
-    "comsol_voltage.mesh = None\n",
-    "comsol_voltage.secondary_mesh = None\n",
     "comsol_phi_s_cn = get_interp_fun_curr_coll(\"phi_s_cn\")\n",
     "comsol_phi_s_cp = get_interp_fun_curr_coll(\"phi_s_cp\")\n",
     "comsol_current = get_interp_fun_curr_coll(\"current\")\n",

examples/scripts/compare_comsol/compare_comsol_DFN.py

@@ -102,9 +102,6 @@ def get_interp_fun(variable_name, domain):
     comsol_t, np.array(comsol_variables["voltage"]), pybamm.t
 )
 
-comsol_voltage.mesh = None
-comsol_voltage.secondary_mesh = None
-
 # Create comsol model with dictionary of Matrix variables
 comsol_model = pybamm.lithium_ion.BaseModel()
 comsol_model._geometry = pybamm_model.default_geometry

src/pybamm/experiment/step/base_step.py

@@ -1,6 +1,4 @@
-#
-# Private classes and functions for experiment steps
-#
+from __future__ import annotations
 import pybamm
 import numpy as np
 from datetime import datetime
@@ -492,6 +490,10 @@ def set_up(self, new_model, new_parameter_values):
 }
 
 
+def get_unit_from(a_string: str) -> str:
+    return a_string.lstrip("0123456789.-eE ")
+
+
 def _convert_time_to_seconds(time_and_units):
     """Convert a time in seconds, minutes or hours to a time in seconds"""
     if time_and_units is None:
@@ -501,11 +503,10 @@ def _convert_time_to_seconds(time_and_units):
     if isinstance(time_and_units, numbers.Number):
         if time_and_units <= 0:
             raise ValueError("time must be positive")
-        else:
-            return time_and_units
+        return time_and_units
 
     # Split number and units
-    units = time_and_units.lstrip("0123456789.- ")
+    units = get_unit_from(time_and_units)
     time = time_and_units[: -len(units)]
     if units in ["second", "seconds", "s", "sec"]:
         time_in_seconds = float(time)
@@ -528,7 +529,7 @@ def _convert_temperature_to_kelvin(temperature_and_units):
         return temperature_and_units
 
     # Split number and units
-    units = temperature_and_units.lstrip("0123456789.- ")
+    units = get_unit_from(temperature_and_units)
     temperature = temperature_and_units[: -len(units)]
     if units in ["K"]:
         temperature_in_kelvin = float(temperature)
@@ -547,7 +548,7 @@ def _convert_electric(value_string):
         value = 1 / float(value_string[2:])
     else:
         # All other cases e.g. 4 A, 2.5 V, 1.5 Ohm
-        unit = value_string.lstrip("0123456789.- ")
+        unit = get_unit_from(value_string)
         value = float(value_string[: -len(unit)])
         # Catch milli- prefix
         if unit.startswith("m"):

src/pybamm/expression_tree/symbol.py

@@ -236,6 +236,9 @@ def __init__(
         # Set domains (and hence id)
         self.domains = self.read_domain_or_domains(domain, auxiliary_domains, domains)
 
+        # mesh required for solution and processed variables classes
+        self.mesh = None
+
         self._saved_evaluates_on_edges: dict = {}
         self._print_name = None
 

src/pybamm/models/base_model.py

@@ -116,8 +116,6 @@ def generic_deserialise(cls, instance, properties):
             for var in instance._variables.values():
                 if var.domain != []:
                     var.mesh = properties["mesh"][var.domain]
-                else:
-                    var.mesh = None
 
                 if var.domains["secondary"] != []:
                     var.secondary_mesh = properties["mesh"][var.domains["secondary"]]

tests/unit/test_experiments/test_base_step.py

@@ -0,0 +1,17 @@
+import pytest
+import pybamm
+
+
+@pytest.mark.parametrize(
+    "test_string, unit_string",
+    [
+        ("123e-1 W", "W"),
+        ("123K", "K"),
+        ("1A", "A"),
+        ("2.0 mV", "mV"),
+        ("0.5 Ohm", "Ohm"),
+        ("1e0hours", "hours"),
+    ],
+)
+def test_read_units(test_string, unit_string):
+    assert unit_string == pybamm.experiment.step.base_step.get_unit_from(test_string)

tests/unit/test_solvers/test_processed_variable.py

@@ -109,7 +109,6 @@ def test_processed_variable_0D(self, hermite_interp):
         t = pybamm.t
         y = pybamm.StateVector(slice(0, 1))
         var = t * y
-        var.mesh = None
         model = pybamm.BaseModel()
         t_sol = np.linspace(0, 1)
         y_sol = np.array([np.linspace(0, 5)])
@@ -124,7 +123,6 @@ def test_processed_variable_0D(self, hermite_interp):
 
         # scalar value
         var = y
-        var.mesh = None
         t_sol = np.array([0])
         y_sol = np.array([1])[:, np.newaxis]
         yp_sol = np.array([1])[:, np.newaxis]
@@ -180,7 +178,6 @@ def test_processed_variable_0D_discrete_data(self, hermite_interp):
         data = pybamm.DiscreteTimeData(data_t, data_v, "test_data")
         var = (y - data) ** order
         expected_entries = (y_sol - data_v) ** order
-        var.mesh = None
         model = pybamm.BaseModel()
         var_casadi = to_casadi(var, y_sol)
         processed_var = pybamm.process_variable(
@@ -206,7 +203,6 @@ def test_processed_variable_0D_discrete_data(self, hermite_interp):
         var = (y - data) ** order
         expected = (y_sol_interp - data_v) ** order
         expected_entries = (y_sol - data_v_interp) ** order
-        var.mesh = None
         model = pybamm.BaseModel()
         var_casadi = to_casadi(var, y_sol)
         processed_var = pybamm.process_variable(
@@ -227,7 +223,6 @@ def test_processed_variable_0D_no_sensitivity(self, hermite_interp):
         t = pybamm.t
         y = pybamm.StateVector(slice(0, 1))
         var = t * y
-        var.mesh = None
         t_sol = np.linspace(0, 1)
         y_sol = np.array([np.linspace(0, 5)])
         yp_sol = self._get_yps(y_sol, hermite_interp)
@@ -246,7 +241,6 @@ def test_processed_variable_0D_no_sensitivity(self, hermite_interp):
         y = pybamm.StateVector(slice(0, 1))
         a = pybamm.InputParameter("a")
         var = t * y * a
-        var.mesh = None
         t_sol = np.linspace(0, 1)
         y_sol = np.array([np.linspace(0, 5)])
         inputs = {"a": np.array([1.0])}
@@ -593,8 +587,6 @@ def test_processed_var_0D_interpolation(self, hermite_interp):
         y = pybamm.StateVector(slice(0, 1))
         var = y
         eqn = t * y
-        var.mesh = None
-        eqn.mesh = None
 
         t_sol = np.linspace(0, 1, 1000)
         y_sol = np.array([5 * t_sol])
@@ -631,10 +623,7 @@ def test_processed_var_0D_interpolation(self, hermite_interp):
     @pytest.mark.parametrize("hermite_interp", _hermite_args)
     def test_processed_var_0D_fixed_t_interpolation(self, hermite_interp):
         y = pybamm.StateVector(slice(0, 1))
-        var = y
         eqn = 2 * y
-        var.mesh = None
-        eqn.mesh = None
 
         t_sol = np.array([10])
         y_sol = np.array([[100]])
@@ -1191,7 +1180,6 @@ def test_process_spatial_variable_names(self):
         t = pybamm.t
         y = pybamm.StateVector(slice(0, 1))
         var = t * y
-        var.mesh = None
         t_sol = np.linspace(0, 1)
         y_sol = np.array([np.linspace(0, 5)])
         var_casadi = to_casadi(var, y_sol)
@@ -1235,12 +1223,8 @@ def solution_setup(t_sol, sign):
             return sol
 
         # without spatial dependence
-        t = pybamm.t
         y = pybamm.StateVector(slice(0, 1))
         var = y
-        eqn = t * y
-        var.mesh = None
-        eqn.mesh = None
 
         sign1 = +1
         t_sol1 = np.linspace(0, 1, 100)

tests/unit/test_solvers/test_processed_variable_computed.py

@@ -72,7 +72,6 @@ def test_processed_variable_0D(self):
         # without space
         y = pybamm.StateVector(slice(0, 1))
         var = y
-        var.mesh = None
         t_sol = np.array([0])
         y_sol = np.array([1])[:, np.newaxis]
         var_casadi = to_casadi(var, y_sol)
@@ -117,7 +116,6 @@ def test_processed_variable_0D_no_sensitivity(self):
         t = pybamm.t
         y = pybamm.StateVector(slice(0, 1))
         var = t * y
-        var.mesh = None
         t_sol = np.linspace(0, 1)
         y_sol = np.array([np.linspace(0, 5)])
         var_casadi = to_casadi(var, y_sol)
@@ -136,7 +134,6 @@ def test_processed_variable_0D_no_sensitivity(self):
         y = pybamm.StateVector(slice(0, 1))
         a = pybamm.InputParameter("a")
         var = t * y * a
-        var.mesh = None
         t_sol = np.linspace(0, 1)
         y_sol = np.array([np.linspace(0, 5)])
         inputs = {"a": np.array([1.0])}