Merge branch 'develop' into black_action

.github/workflows/validation_benchmarks.yml

@@ -0,0 +1,24 @@
+name: Alert validation repository
+on: 
+  release:
+    types:
+      - published
+  push:
+    branches:
+      - develop
+
+jobs:
+  build:
+    name: Dispatch to `pybamm-validation`
+    runs-on: ubuntu-latest
+    steps:
+        - uses: mvasigh/dispatch-action@main
+          with:
+            token: ${{ secrets.BENCHMARKS_ACCESS_TOKEN }}
+            repo: pybamm-validation
+            owner: pybamm-team
+            event_type: ${{ github.event_name }}
+            message: |
+              {
+                "commit_hash": "$GITHUB_SHA"
+              }

.github/workflows/work_precision_sets.yml

@@ -2,7 +2,7 @@ name: Generate work precision sets
 
 on:
   release:
-   types: [created]
+   types: [published]
   workflow_dispatch: 
 
 jobs:

CHANGELOG.md

@@ -1,5 +1,13 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+## Features
+
+-   For experiments, the simulation now automatically checks and skips steps that cannot be performed (e.g. "Charge at 1C until 4.2V" from 100% SOC) ([#2212](https://github.com/pybamm-team/PyBaMM/pull/2212))
+
+## Breaking changes
+
+-   Events must now be defined in such a way that they are positive at the initial conditions (events will be triggered when they become negative, instead of when they change sign in either direction) ([#2212](https://github.com/pybamm-team/PyBaMM/pull/2212))
+
 # [v22.8](https://github.com/pybamm-team/PyBaMM/tree/v22.8) - 2022-08-31
 
 ## Features
@@ -294,7 +302,7 @@ example notebook ([#1602](https://github.com/pybamm-team/PyBaMM/pull/1602))
 ## Breaking changes
 
 -   Refactored the `particle` submodel module, with the models having no size distribution now found in `particle.no_distribution`, and those with a size distribution in `particle.size_distribution`. Renamed submodels to indicate the transport model (Fickian diffusion, polynomial profile) and if they are "x-averaged". E.g., `FickianManyParticles` and `FickianSingleParticle` are now `no_distribution.FickianDiffusion` and `no_distribution.XAveragedFickianDiffusion` ([#1602](https://github.com/pybamm-team/PyBaMM/pull/1602))
--   Changed sensitivity API. Removed `ProcessedSymbolicVariable`, all sensitivity now handled within the solvers and `ProcessedVariable` ()  ([#1552](https://github.com/pybamm-team/PyBaMM/pull/1552))
+-   Changed sensitivity API. Removed `ProcessedSymbolicVariable`, all sensitivity now handled within the solvers and `ProcessedVariable` ([#1552](https://github.com/pybamm-team/PyBaMM/pull/1552),[#2276](https://github.com/pybamm-team/PyBaMM/pull/2276))
 -   The `Yang2017` parameter set has been removed as the complete parameter set is not publicly available in the literature ([#1577](https://github.com/pybamm-team/PyBaMM/pull/1577))
 -   Changed how options are specified for the "loss of active material" and "particle cracking" submodels. "loss of active material" can now be one of "none", "stress-driven", or "reaction-driven", or a 2-tuple for different options in negative and positive electrode. Similarly "particle cracking" (now called "particle mechanics") can now be "none", "swelling only", "swelling and cracking", or a 2-tuple ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
 -   Changed the variable in the full diffusion model from "Electrolyte concentration" to "Porosity times concentration" ([#1476](https://github.com/pybamm-team/PyBaMM/pull/1476))

pybamm/__init__.py

@@ -198,9 +198,8 @@
 #
 # Solver classes
 #
-from .solvers.solution import Solution, make_cycle_solution
+from .solvers.solution import Solution, EmptySolution, make_cycle_solution
 from .solvers.processed_variable import ProcessedVariable
-from .solvers.processed_symbolic_variable import ProcessedSymbolicVariable
 from .solvers.base_solver import BaseSolver
 from .solvers.dummy_solver import DummySolver
 from .solvers.algebraic_solver import AlgebraicSolver

pybamm/expression_tree/exceptions.py

@@ -32,7 +32,8 @@ class SolverError(Exception):
     Solver error: a solution to the model could not be found with the chosen settings
     """
 
-    pass
+    def __init__(self, *args):
+        self.message = args[0]
 
 
 class SolverWarning(UserWarning):

pybamm/models/full_battery_models/base_battery_model.py

@@ -578,15 +578,19 @@ def __init__(self, extra_options):
 
         super().__init__(options.items())
 
-    def phase_number_to_names(self, number):
-        """
-        Converts number of phases to a list ["primary", "secondary", ...]
-        """
-        number = int(number)
-        phases = ["primary"]
-        if number >= 2:
-            phases.append("secondary")
-        return phases
+    @property
+    def phases(self):
+        try:
+            return self._phases
+        except AttributeError:
+            self._phases = {}
+            for domain in ["negative", "positive"]:
+                number = int(getattr(self, domain)["particle phases"])
+                phases = ["primary"]
+                if number >= 2:
+                    phases.append("secondary")
+                self._phases[domain] = phases
+            return self._phases
 
     def print_options(self):
         """
@@ -1340,7 +1344,7 @@ def x_not_zero(x):
         self.events.append(
             pybamm.Event(
                 "Maximum voltage",
-                V - self.param.voltage_high_cut,
+                self.param.voltage_high_cut - V,
                 pybamm.EventType.TERMINATION,
             )
         )

pybamm/models/full_battery_models/lead_acid/basic_full.py

@@ -231,13 +231,13 @@ def __init__(self, name="Basic full model"):
                     "Zero negative electrode porosity cut-off", pybamm.min(eps_n)
                 ),
                 pybamm.Event(
-                    "Max negative electrode porosity cut-off", pybamm.max(eps_n) - 1
+                    "Max negative electrode porosity cut-off", 1 - pybamm.max(eps_n)
                 ),
                 pybamm.Event(
                     "Zero positive electrode porosity cut-off", pybamm.min(eps_p)
                 ),
                 pybamm.Event(
-                    "Max positive electrode porosity cut-off", pybamm.max(eps_p) - 1
+                    "Max positive electrode porosity cut-off", 1 - pybamm.max(eps_p)
                 ),
             ]
         )
@@ -294,6 +294,6 @@ def __init__(self, name="Basic full model"):
         self.events.extend(
             [
                 pybamm.Event("Minimum voltage", voltage - param.voltage_low_cut),
-                pybamm.Event("Maximum voltage", voltage - param.voltage_high_cut),
+                pybamm.Event("Maximum voltage", param.voltage_high_cut - voltage),
             ]
         )

pybamm/models/full_battery_models/lithium_ion/base_lithium_ion_model.py

@@ -46,11 +46,9 @@ def __init__(self, options=None, name="Unnamed lithium-ion model", build=False):
             )
 
         # Add relevant secondary length scales
-        phases_p = int(getattr(self.options, "positive")["particle phases"])
-        if phases_p >= 2:
+        if len(self.options.phases["positive"]) >= 2:
             self._length_scales["positive secondary particle"] = self.param.p.sec.R_typ
-        phases_n = int(getattr(self.options, "negative")["particle phases"])
-        if not self.half_cell and phases_n >= 2:
+        if not self.half_cell and len(self.options.phases["negative"]) >= 2:
             self._length_scales["negative secondary particle"] = self.param.n.sec.R_typ
 
         self.set_standard_output_variables()
@@ -134,14 +132,11 @@ def set_degradation_variables(self):
         else:
             domains = ["negative", "positive"]
         for domain in domains:
-            phases = self.options.phase_number_to_names(
-                getattr(self.options, domain)["particle phases"]
-            )
             self.variables[f"Total lithium in {domain} electrode [mol]"] = sum(
                 self.variables[
                     f"Total lithium in {phase} phase in {domain} electrode [mol]"
                 ]
-                for phase in phases
+                for phase in self.options.phases[domain]
             )
 
         # LAM
@@ -255,10 +250,7 @@ def set_summary_variables(self):
     def set_open_circuit_potential_submodel(self):
         for domain in ["negative", "positive"]:
             domain_options = getattr(self.options, domain)
-            phases = self.options.phase_number_to_names(
-                domain_options["particle phases"]
-            )
-            for phase in phases:
+            for phase in self.options.phases[domain]:
                 ocp_option = getattr(domain_options, phase)["open circuit potential"]
                 ocp_submodels = pybamm.open_circuit_potential
                 if ocp_option == "single":
@@ -345,9 +337,7 @@ def set_crack_submodel(self):
     def set_active_material_submodel(self):
         for domain in ["negative", "positive"]:
             lam = getattr(self.options, domain)["loss of active material"]
-            phases = self.options.phase_number_to_names(
-                getattr(self.options, domain)["particle phases"]
-            )
+            phases = self.options.phases[domain]
             for phase in phases:
                 if lam == "none":
                     submod = pybamm.active_material.Constant(

pybamm/models/full_battery_models/lithium_ion/basic_dfn.py

@@ -270,5 +270,5 @@ def __init__(self, name="Doyle-Fuller-Newman model"):
         # Events specify points at which a solution should terminate
         self.events += [
             pybamm.Event("Minimum voltage", voltage - param.voltage_low_cut),
-            pybamm.Event("Maximum voltage", voltage - param.voltage_high_cut),
+            pybamm.Event("Maximum voltage", param.voltage_high_cut - voltage),
         ]

pybamm/models/full_battery_models/lithium_ion/basic_dfn_half_cell.py

@@ -295,7 +295,7 @@ def __init__(self, options=None, name="Doyle-Fuller-Newman half cell model"):
         self.events.append(
             pybamm.Event(
                 "Maximum voltage",
-                voltage_dim - self.param.voltage_high_cut_dimensional,
+                self.param.voltage_high_cut_dimensional - voltage_dim,
                 pybamm.EventType.TERMINATION,
             )
         )

pybamm/models/full_battery_models/lithium_ion/basic_spm.py

@@ -179,5 +179,5 @@ def __init__(self, name="Single Particle Model"):
         }
         self.events += [
             pybamm.Event("Minimum voltage", V - param.voltage_low_cut),
-            pybamm.Event("Maximum voltage", V - param.voltage_high_cut),
+            pybamm.Event("Maximum voltage", param.voltage_high_cut - V),
         ]

pybamm/models/full_battery_models/lithium_ion/dfn.py

@@ -57,22 +57,12 @@ def set_convection_submodel(self):
         ] = pybamm.convection.through_cell.NoConvection(self.param, self.options)
 
     def set_intercalation_kinetics_submodel(self):
-        for domain in ["Negative", "Positive"]:
+        for domain in ["negative", "positive"]:
             intercalation_kinetics = self.get_intercalation_kinetics(domain)
-            phases = self.options.phase_number_to_names(
-                getattr(self.options, domain.lower())["particle phases"]
-            )
-            for phase in ["primary", "secondary"]:
-                # Add kinetics for each phase included in the options
-                # If a phase is not included, add "NoReaction"
-                if phase in phases:
-                    submod = intercalation_kinetics(
-                        self.param, domain, "lithium-ion main", self.options, phase
-                    )
-                else:
-                    submod = pybamm.kinetics.NoReaction(
-                        self.param, domain, "lithium-ion main", self.options, phase
-                    )
+            for phase in self.options.phases[domain]:
+                submod = intercalation_kinetics(
+                    self.param, domain, "lithium-ion main", self.options, phase
+                )
                 self.submodels[f"{domain.lower()} {phase} interface"] = submod
 
             self.submodels[
@@ -84,10 +74,7 @@ def set_intercalation_kinetics_submodel(self):
     def set_particle_submodel(self):
         for domain in ["negative", "positive"]:
             particle = getattr(self.options, domain)["particle"]
-            phases = self.options.phase_number_to_names(
-                getattr(self.options, domain)["particle phases"]
-            )
-            for phase in phases:
+            for phase in self.options.phases[domain]:
                 if particle == "Fickian diffusion":
                     submod = pybamm.particle.FickianDiffusion(
                         self.param, domain, self.options, phase=phase, x_average=False

pybamm/models/full_battery_models/lithium_ion/newman_tobias.py

@@ -59,10 +59,7 @@ def __init__(self, options=None, name="Newman-Tobias model", build=True):
     def set_particle_submodel(self):
         for domain in ["negative", "positive"]:
             particle = getattr(self.options, domain)["particle"]
-            phases = self.options.phase_number_to_names(
-                getattr(self.options, domain)["particle phases"]
-            )
-            for phase in phases:
+            for phase in self.options.phases[domain]:
                 if particle == "Fickian diffusion":
                     submod = pybamm.particle.FickianDiffusion(
                         self.param, domain, self.options, phase=phase, x_average=True

pybamm/models/full_battery_models/lithium_ion/spm.py

@@ -95,20 +95,10 @@ def set_intercalation_kinetics_submodel(self):
                 )
             else:
                 intercalation_kinetics = self.get_intercalation_kinetics(domain)
-                phases = self.options.phase_number_to_names(
-                    getattr(self.options, domain)["particle phases"]
-                )
-                for phase in ["primary", "secondary"]:
-                    # Add kinetics for each phase included in the options
-                    # If a phase is not included, add "NoReaction"
-                    if phase in phases:
-                        submod = intercalation_kinetics(
-                            self.param, domain, "lithium-ion main", self.options, phase
-                        )
-                    else:
-                        submod = pybamm.kinetics.NoReaction(
-                            self.param, domain, "lithium-ion main", self.options, phase
-                        )
+                for phase in self.options.phases[domain]:
+                    submod = intercalation_kinetics(
+                        self.param, domain, "lithium-ion main", self.options, phase
+                    )
                     self.submodels[f"{domain} {phase} interface"] = submod
                 self.submodels[
                     f"total {domain} interface"
@@ -119,10 +109,7 @@ def set_intercalation_kinetics_submodel(self):
     def set_particle_submodel(self):
         for domain in ["negative", "positive"]:
             particle = getattr(self.options, domain)["particle"]
-            phases = self.options.phase_number_to_names(
-                getattr(self.options, domain)["particle phases"]
-            )
-            for phase in phases:
+            for phase in self.options.phases[domain]:
                 if particle == "Fickian diffusion":
                     submod = pybamm.particle.FickianDiffusion(
                         self.param, domain, self.options, phase=phase, x_average=True

pybamm/models/submodels/active_material/total_active_material.py

@@ -28,9 +28,7 @@ def get_coupled_variables(self, variables):
         Domain = self.domain
         domain = Domain.lower()
 
-        phases = self.options.phase_number_to_names(
-            getattr(self.options, domain)["particle phases"]
-        )
+        phases = self.options.phases[domain]
         eps_solid = sum(
             variables[f"{Domain} electrode {phase} active material volume fraction"]
             for phase in phases

pybamm/models/submodels/base_submodel.py

@@ -96,23 +96,20 @@ def __init__(
         # Error checks for phase and domain
         self.set_phase(phase)
 
-    def set_phase(self, phase, check_phases=True):
+    def set_phase(self, phase):
         if phase is not None:
             if self.domain is None:
                 raise ValueError("Phase must be None if domain is None")
             options_phase = getattr(self.options, self.domain.lower())[
                 "particle phases"
             ]
-            if check_phases:
-                if options_phase == "1" and phase != "primary":
-                    raise ValueError(
-                        "Phase must be 'primary' if there is only one phase"
-                    )
-                elif options_phase == "2" and phase not in ["primary", "secondary"]:
-                    raise ValueError(
-                        "Phase must be either 'primary' or 'secondary' "
-                        "if there are two phases"
-                    )
+            if options_phase == "1" and phase != "primary":
+                raise ValueError("Phase must be 'primary' if there is only one phase")
+            elif options_phase == "2" and phase not in ["primary", "secondary"]:
+                raise ValueError(
+                    "Phase must be either 'primary' or 'secondary' "
+                    "if there are two phases"
+                )
 
             if options_phase == "1" and phase == "primary":
                 # Only one phase, no need to distinguish between

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

@@ -34,12 +34,6 @@ def __init__(self, param, domain, reaction, options, phase="primary"):
         }
         super().__init__(param, domain, reaction, options, phase)
 
-    def set_phase(self, phase):
-        """
-        Bypass the phase checks from BaseSubmodel
-        """
-        super().set_phase(phase, check_phases=False)
-
     def get_fundamental_variables(self):
         zero = pybamm.Scalar(0)
         variables = self._get_standard_interfacial_current_variables(zero)