add temperature dependence to MSMR model

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+- MSMR open-circuit voltage model now depends on the temperature ([#3832](https://github.com/pybamm-team/PyBaMM/pull/3832))
 - Added support for macOS arm64 (M-series) platforms. ([#3789](https://github.com/pybamm-team/PyBaMM/pull/3789))
 - Renamed "electrode diffusivity" to "particle diffusivity" as a non-breaking change with a deprecation warning ([#3624](https://github.com/pybamm-team/PyBaMM/pull/3624))
 - Add support for BPX version 0.4.0 which allows for blended electrodes and user-defined parameters in BPX([#3414](https://github.com/pybamm-team/PyBaMM/pull/3414))
@@ -33,14 +34,15 @@
 - Added a method, `insert_reference_electrode`, to `pybamm.lithium_ion.BaseModel` that insert a reference electrode to measure the electrolyte potential at a given position in space and adds new variables that mimic a 3E cell setup. ([#3573](https://github.com/pybamm-team/PyBaMM/pull/3573))
 - Serialisation added so models can be written to/read from JSON ([#3397](https://github.com/pybamm-team/PyBaMM/pull/3397))
 - Added a `get_parameter_info` method for models and modified "print_parameter_info" functionality to extract all parameters and their type in a tabular and readable format ([#3584](https://github.com/pybamm-team/PyBaMM/pull/3584))
-- Mechanical parameters are now a function of stoichiometry and temperature ([#3576](https://github.com/pybamm-team/PyBaMM/pull/3576))
-
 
 ## Bug fixes
 
 - Fixed a bug that lead to a `ShapeError` when specifying "Ambient temperature [K]" as an `Interpolant` with an isothermal model ([#3761](https://github.com/pybamm-team/PyBaMM/pull/3761))
 - Fixed a bug where if the first step(s) in a cycle are skipped then the cycle solution started from the model's initial conditions instead of from the last state of the previous cycle ([#3708](https://github.com/pybamm-team/PyBaMM/pull/3708))
-- Fixed a bug where the lumped thermal model conflates cell volume with electrode volume  ([#3707](https://github.com/pybamm-team/PyBaMM/pull/3707))
+  <<<<<<< HEAD
+- # Fixed a bug where the lumped thermal model conflates cell volume with electrode volume ([#3707](https://github.com/pybamm-team/PyBaMM/pull/3707))
+- Fixed a bug where the lumped thermal model conflates cell volume with electrode volume ([#3707](https://github.com/pybamm-team/PyBaMM/pull/3707))
+  > > > > > > > develop
 - Reverted a change to the coupled degradation example notebook that caused it to be unstable for large numbers of cycles ([#3691](https://github.com/pybamm-team/PyBaMM/pull/3691))
 - Fixed a bug where simulations using the CasADi-based solvers would fail randomly with the half-cell model ([#3494](https://github.com/pybamm-team/PyBaMM/pull/3494))
 - Fixed bug that made identical Experiment steps with different end times crash ([#3516](https://github.com/pybamm-team/PyBaMM/pull/3516))

docs/source/api/models/submodels/particle/msmr_diffusion.rst

@@ -4,4 +4,7 @@ MSMR Diffusion
 .. autoclass:: pybamm.particle.MSMRDiffusion
     :members:
 
+.. autoclass:: pybamm.particle.MSMRStoichiometryVariables
+    :members:
+
 .. footbibliography::

pybamm/__init__.py

@@ -54,7 +54,6 @@
 from .logger import logger, set_logging_level, get_new_logger
 from .settings import settings
 from .citations import Citations, citations, print_citations
-
 #
 # Classes for the Expression Tree
 #

pybamm/models/full_battery_models/lithium_ion/dfn.py

@@ -69,6 +69,17 @@ def set_particle_submodel(self):
                     submod = pybamm.particle.MSMRDiffusion(
                         self.param, domain, self.options, phase=phase, x_average=False
                     )
+                    # also set the submodel for calculating stoichiometry from
+                    # potential
+                    self.submodels[
+                        f"{domain} {phase} stoichiometry"
+                    ] = pybamm.particle.MSMRStoichiometryVariables(
+                        self.param,
+                        domain,
+                        self.options,
+                        phase=phase,
+                        x_average=False,
+                    )
                 self.submodels[f"{domain} {phase} particle"] = submod
                 self.submodels[
                     f"{domain} {phase} total particle concentration"

pybamm/models/full_battery_models/lithium_ion/electrode_soh.py

@@ -199,6 +199,7 @@ def __init__(
         x_n = param.n.prim.x
         x_p = param.p.prim.x
 
+        T = param.T_ref
         V_max = param.voltage_high_cut
         V_min = param.voltage_low_cut
         Q_n = pybamm.InputParameter("Q_n")
@@ -214,21 +215,21 @@ def __init__(
         if "Un_0" in solve_for:
             Un_0 = pybamm.Variable("Un(x_0)")
             Up_0 = V_min + Un_0
-            x_0 = x_n(Un_0)
-            y_0 = x_p(Up_0)
+            x_0 = x_n(Un_0, T)
+            y_0 = x_p(Up_0, T)
 
         # Define variables for 100% state of charge
         # TODO: thermal effects (include dU/dT)
         if "Un_100" in solve_for:
             Un_100 = pybamm.Variable("Un(x_100)")
             Up_100 = V_max + Un_100
-            x_100 = x_n(Un_100)
-            y_100 = x_p(Up_100)
+            x_100 = x_n(Un_100, T)
+            y_100 = x_p(Up_100, T)
         else:
             Un_100 = pybamm.InputParameter("Un(x_100)")
             Up_100 = pybamm.InputParameter("Up(y_100)")
-            x_100 = x_n(Un_100)
-            y_100 = x_p(Up_100)
+            x_100 = x_n(Un_100, T)
+            y_100 = x_p(Up_100, T)
 
         # Define equations for 100% state of charge
         if "Un_100" in solve_for:
@@ -678,20 +679,20 @@ def get_initial_stoichiometries(self, initial_value, tol=1e-6):
             soc = pybamm.Variable("soc")
             x = x_0 + soc * (x_100 - x_0)
             y = y_0 - soc * (y_0 - y_100)
+            T_ref = parameter_values["Reference temperature [K]"]
             if self.options["open-circuit potential"] == "MSMR":
                 xn = param.n.prim.x
                 xp = param.p.prim.x
                 Up = pybamm.Variable("Up")
                 Un = pybamm.Variable("Un")
-                soc_model.algebraic[Up] = x - xn(Un)
-                soc_model.algebraic[Un] = y - xp(Up)
+                soc_model.algebraic[Up] = x - xn(Un, T_ref)
+                soc_model.algebraic[Un] = y - xp(Up, T_ref)
                 soc_model.initial_conditions[Un] = 0
                 soc_model.initial_conditions[Up] = V_max
                 soc_model.algebraic[soc] = Up - Un - V_init
             else:
                 Up = param.p.prim.U
                 Un = param.n.prim.U
-                T_ref = parameter_values["Reference temperature [K]"]
                 soc_model.algebraic[soc] = Up(y, T_ref) - Un(x, T_ref) - V_init
             # initial guess for soc linearly interpolates between 0 and 1
             # based on V linearly interpolating between V_max and V_min
@@ -1043,14 +1044,15 @@ def _get_msmr_potential_model(parameter_values, param):
     V_min = param.voltage_low_cut
     x_n = param.n.prim.x
     x_p = param.p.prim.x
+    T = param.T_ref
     model = pybamm.BaseModel()
     Un = pybamm.Variable("Un")
     Up = pybamm.Variable("Up")
     x = pybamm.InputParameter("x")
     y = pybamm.InputParameter("y")
     model.algebraic = {
-        Un: x_n(Un) - x,
-        Up: x_p(Up) - y,
+        Un: x_n(Un, T) - x,
+        Up: x_p(Up, T) - y,
     }
     model.initial_conditions = {
         Un: 1 - x,

pybamm/models/full_battery_models/lithium_ion/newman_tobias.py

@@ -52,6 +52,17 @@ def set_particle_submodel(self):
                     submod = pybamm.particle.MSMRDiffusion(
                         self.param, domain, self.options, phase=phase, x_average=True
                     )
+                    # also set the submodel for calculating stoichiometry from
+                    # potential
+                    self.submodels[
+                        f"{domain} {phase} stoichiometry"
+                    ] = pybamm.particle.MSMRStoichiometryVariables(
+                        self.param,
+                        domain,
+                        self.options,
+                        phase=phase,
+                        x_average=True,
+                    )
                 self.submodels[f"{domain} {phase} particle"] = submod
                 self.submodels[
                     f"{domain} {phase} total particle concentration"

pybamm/models/full_battery_models/lithium_ion/spm.py

@@ -108,6 +108,17 @@ def set_particle_submodel(self):
                     submod = pybamm.particle.MSMRDiffusion(
                         self.param, domain, self.options, phase=phase, x_average=True
                     )
+                    # also set the submodel for calculating stoichiometry from
+                    # potential
+                    self.submodels[
+                        f"{domain} {phase} stoichiometry"
+                    ] = pybamm.particle.MSMRStoichiometryVariables(
+                        self.param,
+                        domain,
+                        self.options,
+                        phase=phase,
+                        x_average=True,
+                    )
                 self.submodels[f"{domain} {phase} particle"] = submod
                 self.submodels[
                     f"{domain} {phase} total particle concentration"

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

@@ -117,7 +117,7 @@ def _get_standard_exchange_current_by_reaction_variables(self, j0, index):
         return variables
 
     def _get_kinetics_by_reaction(self, j0, ne, eta_r, T, u, index):
-        alpha = self.phase_param.alpha_bv_j(index)
+        alpha = self.phase_param.alpha_bv_j(T, index)
         Feta_RT = self.param.F * eta_r / (self.param.R * T)
         return (
             u

pybamm/models/submodels/particle/__init__.py

@@ -3,4 +3,4 @@
 from .polynomial_profile import PolynomialProfile
 from .x_averaged_polynomial_profile import XAveragedPolynomialProfile
 from .total_particle_concentration import TotalConcentration
-from .msmr_diffusion import MSMRDiffusion
+from .msmr_diffusion import MSMRDiffusion, MSMRStoichiometryVariables