Merge 6de9a13 into 44398b9

.github/workflows/test_on_push.yml

@@ -83,10 +83,10 @@ jobs:
       run: tox -e examples
 
     - name: Install and run coverage
-      if: success() && (matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7)
+      if: success() && (matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9)
       run: tox -e coverage
 
     - name: Upload coverage report
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
       uses: codecov/codecov-action@v1
 

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+-   `Solution` objects can now be created by stepping *different* models ([#1408](https://github.com/pybamm-team/PyBaMM/pull/1408))
 -   Added support for Python 3.9 and dropped support for Python 3.6. Python 3.6 may still work but is now untested ([#1370](https://github.com/pybamm-team/PyBaMM/pull/1370))
 -   Added the electrolyte overpotential and Ohmic losses for full conductivity, including surface form ([#1350](https://github.com/pybamm-team/PyBaMM/pull/1350))
 -   Added functionality to `Citations` to print formatted citations ([#1340](https://github.com/pybamm-team/PyBaMM/pull/1340))
@@ -22,6 +23,7 @@
 
 ## Optimizations
 
+-   Improved the way an `Experiment` is simulated to reduce solve time (at the cost of slightly higher set-up time) ([#1408](https://github.com/pybamm-team/PyBaMM/pull/1408))
 -   Add script and workflow to automatically update parameter_sets.py docstrings ([#1371](https://github.com/pybamm-team/PyBaMM/pull/1371))
 -   Add URLs checker in workflows ([#1347](https://github.com/pybamm-team/PyBaMM/pull/1347))
 -   The `Solution` class now only creates the concatenated `y` when the user asks for it. This is an optimization step as the concatenation can be slow, especially with larger experiments ([#1331](https://github.com/pybamm-team/PyBaMM/pull/1331))

examples/scripts/DFN.py

@@ -15,8 +15,8 @@
 
 # load parameter values and process model and geometry
 param = model.default_parameter_values
-param.process_model(model)
 param.process_geometry(geometry)
+param.process_model(model)
 
 # set mesh
 var = pybamm.standard_spatial_vars

examples/scripts/experimental_protocols/cccv.py

@@ -15,7 +15,7 @@
             "Rest for 1 hour",
         ),
     ]
-    * 3
+    * 3,
 )
 model = pybamm.lithium_ion.DFN()
 sim = pybamm.Simulation(model, experiment=experiment, solver=pybamm.CasadiSolver())

examples/scripts/experimental_protocols/gitt.py

@@ -5,7 +5,7 @@
 
 pybamm.set_logging_level("INFO")
 experiment = pybamm.Experiment(
-    [("Discharge at C/20 for 1 hour", "Rest for 1 hour")] * 20
+    [("Discharge at C/20 for 1 hour", "Rest for 1 hour")] * 20,
 )
 model = pybamm.lithium_ion.DFN()
 sim = pybamm.Simulation(model, experiment=experiment, solver=pybamm.CasadiSolver())

pybamm/experiments/experiment.py

@@ -40,10 +40,18 @@ class Experiment:
     period : string, optional
         Period (1/frequency) at which to record outputs. Default is 1 minute. Can be
         overwritten by individual operating conditions.
-
+    use_simulation_setup_type : str
+        Whether to use the "new" (default) or "old" simulation set-up type. "new" is
+        faster at simulating individual steps but has higher set-up overhead
     """
 
-    def __init__(self, operating_conditions, parameters=None, period="1 minute"):
+    def __init__(
+        self,
+        operating_conditions,
+        parameters=None,
+        period="1 minute",
+        use_simulation_setup_type="new",
+    ):
         self.period = self.convert_time_to_seconds(period.split())
         operating_conditions_cycles = []
         for cycle in operating_conditions:
@@ -84,6 +92,8 @@ def __init__(self, operating_conditions, parameters=None, period="1 minute"):
         else:
             raise TypeError("experimental parameters should be a dictionary")
 
+        self.use_simulation_setup_type = use_simulation_setup_type
+
     def __str__(self):
         return str(self.operating_conditions_strings)
 

pybamm/models/base_model.py

@@ -93,7 +93,7 @@ def __init__(self, name="Unnamed model"):
         self._algebraic = {}
         self._initial_conditions = {}
         self._boundary_conditions = {}
-        self._variables = {}
+        self._variables = pybamm.FuzzyDict({})
         self._events = []
         self._concatenated_rhs = None
         self._concatenated_algebraic = None
@@ -382,13 +382,25 @@ def set_initial_conditions_from(self, solution, inplace=True):
         else:
             model = self.new_copy()
 
+        if isinstance(solution, pybamm.Solution):
+            solution = solution.last_state
+        else:
+            solution = pybamm.FuzzyDict(solution)
         for var, equation in model.initial_conditions.items():
             if isinstance(var, pybamm.Variable):
-                final_state = solution[var.name]
+                try:
+                    final_state = solution[var.name]
+                except KeyError as e:
+                    raise pybamm.ModelError(
+                        "To update a model from a solution, each variable in "
+                        "model.initial_conditions must appear in the solution with "
+                        "the same key as the variable name. In the solution provided, "
+                        f"{e.args[0]}"
+                    )
                 if isinstance(solution, pybamm.Solution):
                     final_state = final_state.data
                 if final_state.ndim == 1:
-                    final_state_eval = np.array([final_state[-1]])
+                    final_state_eval = final_state[-1:]
                 elif final_state.ndim == 2:
                     final_state_eval = final_state[:, -1]
                 elif final_state.ndim == 3:
@@ -399,7 +411,15 @@ def set_initial_conditions_from(self, solution, inplace=True):
             elif isinstance(var, pybamm.Concatenation):
                 children = []
                 for child in var.orphans:
-                    final_state = solution[child.name]
+                    try:
+                        final_state = solution[child.name]
+                    except KeyError as e:
+                        raise pybamm.ModelError(
+                            "To update a model from a solution, each variable in "
+                            "model.initial_conditions must appear in the solution with "
+                            "the same key as the variable name. In the solution "
+                            f"provided, {e.args[0]}"
+                        )
                     if isinstance(solution, pybamm.Solution):
                         final_state = final_state.data
                     if final_state.ndim == 2:

pybamm/models/standard_variables.py

@@ -265,18 +265,18 @@
 
 # SEI variables
 L_inner_av = pybamm.Variable(
-    "X-averaged inner SEI thickness", domain="current collector"
+    "X-averaged inner negative electrode SEI thickness", domain="current collector"
 )
 L_inner = pybamm.Variable(
-    "Inner SEI thickness",
+    "Inner negative electrode SEI thickness",
     domain=["negative electrode"],
     auxiliary_domains={"secondary": "current collector"},
 )
 L_outer_av = pybamm.Variable(
-    "X-averaged outer SEI thickness", domain="current collector"
+    "X-averaged outer negative electrode SEI thickness", domain="current collector"
 )
 L_outer = pybamm.Variable(
-    "Outer SEI thickness",
+    "Outer negative electrode SEI thickness",
     domain=["negative electrode"],
     auxiliary_domains={"secondary": "current collector"},
 )

pybamm/models/submodels/interface/kinetics/base_kinetics.py

@@ -37,7 +37,7 @@ def get_fundamental_variables(self):
             j = pybamm.Variable(
                 "Total "
                 + self.domain.lower()
-                + " electrode interfacial current density",
+                + " electrode interfacial current density variable",
                 domain=self.domain.lower() + " electrode",
                 auxiliary_domains={"secondary": "current collector"},
             )

pybamm/plotting/quick_plot.py

@@ -7,7 +7,8 @@
 
 
 class LoopList(list):
-    """A list which loops over itself when accessing an index so that it never runs out
+    """
+    A list which loops over itself when accessing an index so that it never runs out
     """
 
     def __getitem__(self, i):
@@ -114,7 +115,7 @@ def __init__(
                 # attribute
                 solutions[idx] = sol.solution
 
-        models = [solution.model for solution in solutions]
+        models = [solution.all_models[0] for solution in solutions]
 
         # Set labels
         if labels is None: