Merge pull request #1503 from pybamm-team/issue-1501-different-submodels

Issue 1501 different submodels

pybamm/models/full_battery_models/base_battery_model.py

@@ -44,9 +44,10 @@ class BatteryModelOptions(pybamm.FuzzyDict):
                 variable for instead of solving in PyBaMM. The entries of the lists
                 are strings that correspond to the submodel names in the keys
                 of `self.submodels`.
-            * "interfacial surface area" : str
-                Sets the model for the interfacial surface area. Can be "constant"
-                (default) or "varying". Not currently implemented in any of the models.
+            * "hydrolysis" : str
+                Whether to include hydrolysis in the model. Only implemented for
+                lead-acid models. Can be "false" (default) or "true". If "true", then
+                "surface form" cannot be 'false'.
             * "lithium plating" : str, optional
                 Sets the model for lithium plating. Can be "none" (default),
                 "reversible" or "irreversible".
@@ -120,10 +121,6 @@ class BatteryModelOptions(pybamm.FuzzyDict):
             * "SEI porosity change" : str
                 Whether to include porosity change due to SEI formation, can be "false"
                 (default) or "true".
-            * "side reactions" : list
-                Contains a list of any side reactions to include. Default is []. If this
-                list is not empty (i.e. side reactions are included in the model), then
-                "surface form" cannot be 'false'.
             * "surface form" : str
                 Whether to use the surface formulation of the problem. Can be "false"
                 (default), "differential" or "algebraic".
@@ -141,77 +138,72 @@ class BatteryModelOptions(pybamm.FuzzyDict):
 
     def __init__(self, extra_options):
         self.possible_options = {
-            "surface form": ["false", "differential", "algebraic"],
+            "cell geometry": ["arbitrary", "pouch"],
             "convection": ["none", "uniform transverse", "full transverse"],
             "current collector": [
                 "uniform",
                 "potential pair",
                 "potential pair quite conductive",
             ],
             "dimensionality": [0, 1, 2],
-            "interfacial surface area": ["constant", "varying"],
-            "thermal": ["isothermal", "lumped", "x-lumped", "x-full"],
-            "cell geometry": ["arbitrary", "pouch"],
-            "SEI": [
-                "none",
-                "constant",
-                "reaction limited",
-                "solvent-diffusion limited",
-                "electron-migration limited",
-                "interstitial-diffusion limited",
-                "ec reaction limited",
+            "electrolyte conductivity": [
+                "default",
+                "full",
+                "leading order",
+                "composite",
+                "integrated",
             ],
-            "SEI film resistance": ["none", "distributed", "average"],
-            "SEI porosity change": ["true", "false"],
+            "hydrolysis": ["true", "false"],
             "lithium plating": ["none", "reversible", "irreversible"],
+            "lithium plating porosity change": ["true", "false"],
             "loss of active material": ["none", "stress-driven", "reaction-driven"],
             "operating mode": ["current", "voltage", "power"],
-            "particle mechanics": [
-                "none",
-                "swelling only",
-                "swelling and cracking",
-            ],
-            "lithium plating porosity change": ["true", "false"],
             "particle": [
                 "Fickian diffusion",
                 "fast diffusion",
                 "uniform profile",
                 "quadratic profile",
                 "quartic profile",
             ],
+            "particle mechanics": ["none", "swelling only", "swelling and cracking"],
             "particle shape": ["spherical", "user", "no particles"],
-            "electrolyte conductivity": [
-                "default",
-                "full",
-                "leading order",
-                "composite",
-                "integrated",
+            "SEI": [
+                "none",
+                "constant",
+                "reaction limited",
+                "solvent-diffusion limited",
+                "electron-migration limited",
+                "interstitial-diffusion limited",
+                "ec reaction limited",
             ],
+            "SEI film resistance": ["none", "distributed", "average"],
+            "SEI porosity change": ["true", "false"],
+            "surface form": ["false", "differential", "algebraic"],
+            "thermal": ["isothermal", "lumped", "x-lumped", "x-full"],
             "total interfacial current density as a state": ["true", "false"],
         }
 
         default_options = {
-            "operating mode": "current",
-            "dimensionality": 0,
-            "surface form": "false",
+            "cell geometry": "none",
             "convection": "none",
-            "side reactions": [],
-            "interfacial surface area": "constant",
             "current collector": "uniform",
-            "particle": "Fickian diffusion",
-            "particle shape": "spherical",
+            "dimensionality": 0,
             "electrolyte conductivity": "default",
-            "thermal": "isothermal",
-            "cell geometry": "none",
             "external submodels": [],
-            "SEI": "none",
+            "hydrolysis": "false",
             "lithium plating": "none",
-            "SEI porosity change": "false",
             "lithium plating porosity change": "false",
             "loss of active material": "none",
-            "working electrode": "none",
+            "operating mode": "current",
+            "particle": "Fickian diffusion",
             "particle mechanics": "none",
+            "particle shape": "spherical",
+            "SEI": "none",
+            "SEI porosity change": "false",
+            "surface form": "false",
+            "thermal": "isothermal",
             "total interfacial current density as a state": "false",
+            "working electrode": "none",
         }
 
         # Change the default for cell geometry based on which thermal option is provided
@@ -309,11 +301,7 @@ def __init__(self, extra_options):
             )
 
         for option, value in options.items():
-            if (
-                option == "side reactions"
-                or option == "external submodels"
-                or option == "working electrode"
-            ):
+            if option == "external submodels" or option == "working electrode":
                 pass
             else:
                 if isinstance(value, str) or option in [
@@ -328,6 +316,7 @@ def __init__(self, extra_options):
                             in [
                                 "loss of active material",
                                 "particle mechanics",
+                                "particle",
                             ]
                             and isinstance(value, tuple)
                             and len(value) == 2
@@ -483,14 +472,14 @@ def options(self, extra_options):
         if (
             isinstance(self, (pybamm.lead_acid.LOQS, pybamm.lead_acid.Composite))
             and options["surface form"] == "false"
+            and options["hydrolysis"] == "true"
         ):
-            if len(options["side reactions"]) > 0:
-                raise pybamm.OptionError(
-                    """must use surface formulation to solve {!s} with side reactions
+            raise pybamm.OptionError(
+                """must use surface formulation to solve {!s} with hydrolysis
                     """.format(
-                        self
-                    )
+                    self
                 )
+            )
 
         self._options = options
 

pybamm/models/full_battery_models/lead_acid/full.py

@@ -122,7 +122,7 @@ def set_electrolyte_submodel(self):
                 ] = surf_form.FullAlgebraic(self.param, domain)
 
     def set_side_reaction_submodels(self):
-        if "oxygen" in self.options["side reactions"]:
+        if self.options["hydrolysis"] == "true":
             self.submodels["oxygen diffusion"] = pybamm.oxygen_diffusion.Full(
                 self.param
             )

pybamm/models/full_battery_models/lead_acid/higher_order.py

@@ -167,7 +167,7 @@ def set_full_interface_submodel(self):
         )
 
         # Oxygen
-        if "oxygen" in self.options["side reactions"]:
+        if self.options["hydrolysis"] == "true":
             self.submodels[
                 "positive oxygen interface"
             ] = pybamm.interface.FirstOrderKinetics(
@@ -231,7 +231,7 @@ def set_electrolyte_diffusion_submodel(self):
         ] = pybamm.electrolyte_diffusion.FirstOrder(self.param)
 
     def set_other_species_diffusion_submodels(self):
-        if "oxygen" in self.options["side reactions"]:
+        if self.options["hydrolysis"] == "true":
             self.submodels["oxygen diffusion"] = pybamm.oxygen_diffusion.FirstOrder(
                 self.param
             )
@@ -261,7 +261,7 @@ def set_electrolyte_diffusion_submodel(self):
         ] = pybamm.electrolyte_diffusion.Composite(self.param)
 
     def set_other_species_diffusion_submodels(self):
-        if "oxygen" in self.options["side reactions"]:
+        if self.options["hydrolysis"] == "true":
             self.submodels["oxygen diffusion"] = pybamm.oxygen_diffusion.Composite(
                 self.param
             )
@@ -307,7 +307,7 @@ def set_electrolyte_diffusion_submodel(self):
         ] = pybamm.electrolyte_diffusion.Composite(self.param, extended="distributed")
 
     def set_other_species_diffusion_submodels(self):
-        if "oxygen" in self.options["side reactions"]:
+        if self.options["hydrolysis"] == "true":
             self.submodels["oxygen diffusion"] = pybamm.oxygen_diffusion.Composite(
                 self.param, extended="distributed"
             )
@@ -329,7 +329,7 @@ def set_electrolyte_diffusion_submodel(self):
         ] = pybamm.electrolyte_diffusion.Composite(self.param, extended="average")
 
     def set_other_species_diffusion_submodels(self):
-        if "oxygen" in self.options["side reactions"]:
+        if self.options["hydrolysis"] == "true":
             self.submodels["oxygen diffusion"] = pybamm.oxygen_diffusion.Composite(
                 self.param, extended="average"
             )

pybamm/models/full_battery_models/lead_acid/loqs.py

@@ -214,7 +214,7 @@ def set_electrolyte_submodel(self):
         ] = pybamm.electrolyte_diffusion.LeadingOrder(self.param)
 
     def set_side_reaction_submodels(self):
-        if "oxygen" in self.options["side reactions"]:
+        if self.options["hydrolysis"] == "true":
             self.submodels[
                 "leading-order oxygen diffusion"
             ] = pybamm.oxygen_diffusion.LeadingOrder(self.param)

pybamm/models/full_battery_models/lithium_ion/dfn.py

@@ -76,28 +76,29 @@ def set_interfacial_submodel(self):
 
     def set_particle_submodel(self):
 
-        if self.options["particle"] == "Fickian diffusion":
-            self.submodels["negative particle"] = pybamm.particle.FickianManyParticles(
-                self.param, "Negative"
-            )
-            self.submodels["positive particle"] = pybamm.particle.FickianManyParticles(
-                self.param, "Positive"
-            )
-        elif self.options["particle"] in [
-            "uniform profile",
-            "quadratic profile",
-            "quartic profile",
+        if isinstance(self.options["particle"], str):
+            particle_left = self.options["particle"]
+            particle_right = self.options["particle"]
+        else:
+            particle_left, particle_right = self.options["particle"]
+        for particle_side, domain in [
+            [particle_left, "Negative"],
+            [particle_right, "Positive"],
         ]:
-            self.submodels[
-                "negative particle"
-            ] = pybamm.particle.PolynomialManyParticles(
-                self.param, "Negative", self.options["particle"]
-            )
-            self.submodels[
-                "positive particle"
-            ] = pybamm.particle.PolynomialManyParticles(
-                self.param, "Positive", self.options["particle"]
-            )
+            if particle_side == "Fickian diffusion":
+                self.submodels[
+                    domain.lower() + " particle"
+                ] = pybamm.particle.FickianManyParticles(self.param, domain)
+            elif particle_side in [
+                "uniform profile",
+                "quadratic profile",
+                "quartic profile",
+            ]:
+                self.submodels[
+                    domain.lower() + " particle"
+                ] = pybamm.particle.PolynomialManyParticles(
+                    self.param, domain, particle_side
+                )
 
     def set_solid_submodel(self):
 

pybamm/models/full_battery_models/lithium_ion/spm.py

@@ -96,29 +96,29 @@ def set_interfacial_submodel(self):
             )
 
     def set_particle_submodel(self):
-
-        if self.options["particle"] == "Fickian diffusion":
-            self.submodels["negative particle"] = pybamm.particle.FickianSingleParticle(
-                self.param, "Negative"
-            )
-            self.submodels["positive particle"] = pybamm.particle.FickianSingleParticle(
-                self.param, "Positive"
-            )
-        elif self.options["particle"] in [
-            "uniform profile",
-            "quadratic profile",
-            "quartic profile",
+        if isinstance(self.options["particle"], str):
+            particle_left = self.options["particle"]
+            particle_right = self.options["particle"]
+        else:
+            particle_left, particle_right = self.options["particle"]
+        for particle_side, domain in [
+            [particle_left, "Negative"],
+            [particle_right, "Positive"],
         ]:
-            self.submodels[
-                "negative particle"
-            ] = pybamm.particle.PolynomialSingleParticle(
-                self.param, "Negative", self.options["particle"]
-            )
-            self.submodels[
-                "positive particle"
-            ] = pybamm.particle.PolynomialSingleParticle(
-                self.param, "Positive", self.options["particle"]
-            )
+            if particle_side == "Fickian diffusion":
+                self.submodels[
+                    domain.lower() + " particle"
+                ] = pybamm.particle.FickianSingleParticle(self.param, domain)
+            elif particle_side in [
+                "uniform profile",
+                "quadratic profile",
+                "quartic profile",
+            ]:
+                self.submodels[
+                    domain.lower() + " particle"
+                ] = pybamm.particle.PolynomialSingleParticle(
+                    self.param, domain, particle_side
+                )
 
     def set_negative_electrode_submodel(self):
 

pybamm/models/full_battery_models/lithium_ion/spme.py

@@ -107,28 +107,29 @@ def set_interfacial_submodel(self):
 
     def set_particle_submodel(self):
 
-        if self.options["particle"] == "Fickian diffusion":
-            self.submodels["negative particle"] = pybamm.particle.FickianSingleParticle(
-                self.param, "Negative"
-            )
-            self.submodels["positive particle"] = pybamm.particle.FickianSingleParticle(
-                self.param, "Positive"
-            )
-        elif self.options["particle"] in [
-            "uniform profile",
-            "quadratic profile",
-            "quartic profile",
+        if isinstance(self.options["particle"], str):
+            particle_left = self.options["particle"]
+            particle_right = self.options["particle"]
+        else:
+            particle_left, particle_right = self.options["particle"]
+        for particle_side, domain in [
+            [particle_left, "Negative"],
+            [particle_right, "Positive"],
         ]:
-            self.submodels[
-                "negative particle"
-            ] = pybamm.particle.PolynomialSingleParticle(
-                self.param, "Negative", self.options["particle"]
-            )
-            self.submodels[
-                "positive particle"
-            ] = pybamm.particle.PolynomialSingleParticle(
-                self.param, "Positive", self.options["particle"]
-            )
+            if particle_side == "Fickian diffusion":
+                self.submodels[
+                    domain.lower() + " particle"
+                ] = pybamm.particle.FickianSingleParticle(self.param, domain)
+            elif particle_side in [
+                "uniform profile",
+                "quadratic profile",
+                "quartic profile",
+            ]:
+                self.submodels[
+                    domain.lower() + " particle"
+                ] = pybamm.particle.PolynomialSingleParticle(
+                    self.param, domain, particle_side
+                )
 
     def set_negative_electrode_submodel(self):