#933 merge #546

.requirements-docs.txt

@@ -8,4 +8,3 @@ scikit-fem>=0.2.0
 casadi>=3.5.0
 guzzle-sphinx-theme
 sphinx>=1.5
-python-Levenshtein>=0.12.0

CHANGELOG.md

@@ -13,6 +13,7 @@
 ## Bug fixes
 
 -   Reformatted electrolyte submodels ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+-   Reformatted convection submodels ([#635](https://github.com/pybamm-team/PyBaMM/pull/635))
 
 ## Breaking changes
 

docs/source/spatial_methods/zero_dimensional_method.rst

@@ -1,5 +1,5 @@
 Zero Dimensional Spatial Method
 ===============================
 
-.. autoclass:: pybamm.ZeroDimensionalMethod
+.. autoclass:: pybamm.ZeroDimensionalSpatialMethod
     :members:

examples/notebooks/change-settings.ipynb

@@ -358,7 +358,7 @@
       "macroscale                                                                           FiniteVolume\n",
       "negative particle                                                                    FiniteVolume\n",
       "positive particle                                                                    FiniteVolume\n",
-      "current collector                                                            ZeroDimensionalMethod\n"
+      "current collector                                                            ZeroDimensionalSpatialMethod\n"
      ]
     }
    ],

examples/notebooks/models/SPM.ipynb

@@ -287,7 +287,7 @@
       "macroscale is discretised using FiniteVolume method\n",
       "negative particle is discretised using FiniteVolume method\n",
       "positive particle is discretised using FiniteVolume method\n",
-      "current collector is discretised using ZeroDimensionalMethod method\n"
+      "current collector is discretised using ZeroDimensionalSpatialMethod method\n"
      ]
     }
    ],

examples/scripts/DFN.py

@@ -9,14 +9,13 @@
 
 
 # load model
-model = pybamm.lithium_ion.DFN({"operating mode": "voltage"})
+model = pybamm.lithium_ion.DFN()
 
 # create geometry
 geometry = model.default_geometry
 
 # load parameter values and process model and geometry
 param = model.default_parameter_values
-param.update({"Voltage function [V]": 4.1}, check_already_exists=False)
 param.process_model(model)
 param.process_geometry(geometry)
 

examples/scripts/compare_extrapolations.py

@@ -16,7 +16,7 @@
     "negative particle": pybamm.FiniteVolume(method_options),
     "positive particle": pybamm.FiniteVolume(method_options),
     "macroscale": pybamm.FiniteVolume(method_options),
-    "current collector": pybamm.ZeroDimensionalMethod(),
+    "current collector": pybamm.ZeroDimensionalSpatialMethod(),
 }
 sim_quad = pybamm.Simulation(
     model_quad, spatial_methods=spatial_methods, var_pts=var_pts

pybamm/__init__.py

@@ -193,7 +193,7 @@ def version(formatted=False):
 # Spatial Methods
 #
 from .spatial_methods.spatial_method import SpatialMethod
-from .spatial_methods.zero_dimensional_method import ZeroDimensionalMethod
+from .spatial_methods.zero_dimensional_method import ZeroDimensionalSpatialMethod
 from .spatial_methods.finite_volume import FiniteVolume
 from .spatial_methods.scikit_finite_element import ScikitFiniteElement
 

pybamm/discretisations/discretisation.py

@@ -610,7 +610,7 @@ def create_mass_matrix(self, model):
                 mass_list.append(mass)
                 if isinstance(
                     self.spatial_methods[var.domain[0]],
-                    (pybamm.ZeroDimensionalMethod, pybamm.FiniteVolume),
+                    (pybamm.ZeroDimensionalSpatialMethod, pybamm.FiniteVolume),
                 ):
                     # for 0D methods the mass matrix is just a scalar 1 and for
                     # finite volumes the mass matrix is identity, so no need to

pybamm/input/parameters/lead-acid/electrolytes/sulfuric_acid_Sulzer2019/parameters.csv

@@ -18,7 +18,6 @@ Electrolyte conductivity [S.m-1],[function]conductivity_Gu1997,,
 Darken thermodynamic factor,[function]darken_thermodynamic_factor_Chapman1968,,
 Electrolyte diffusivity [m2.s-1],[function]diffusivity_Gu1997,,
 Electrolyte viscosity [kg.m-1.s-1],[function]viscosity_Chapman1968,,
-MacInnes t_plus function,[function]macinnes_tplus_function,,
 ,,,
 # Other species properties,,,
 Oxygen diffusivity [m2.s-1],2.1e-9,cussler2009diffusion

pybamm/models/full_battery_models/base_battery_model.py

@@ -124,7 +124,9 @@ def default_spatial_methods(self):
         }
         if self.options["dimensionality"] == 0:
             # 0D submesh - use base spatial method
-            base_spatial_methods["current collector"] = pybamm.ZeroDimensionalMethod()
+            base_spatial_methods[
+                "current collector"
+            ] = pybamm.ZeroDimensionalSpatialMethod()
         elif self.options["dimensionality"] == 1:
             base_spatial_methods["current collector"] = pybamm.FiniteVolume()
         elif self.options["dimensionality"] == 2:
@@ -165,7 +167,7 @@ def options(self, extra_options):
 
         # Options that are incompatible with models
         if isinstance(self, pybamm.lithium_ion.BaseModel):
-            if options["convection"] is True:
+            if options["convection"] is not False:
                 raise pybamm.OptionError(
                     "convection not implemented for lithium-ion models"
                 )
@@ -205,6 +207,14 @@ def options(self, extra_options):
             raise pybamm.OptionError(
                 "surface form '{}' not recognised".format(options["surface form"])
             )
+        if options["convection"] not in [
+            False,
+            "uniform transverse",
+            "full transverse",
+        ]:
+            raise pybamm.OptionError(
+                "convection option '{}' not recognised".format(options["convection"])
+            )
         if options["current collector"] not in [
             "uniform",
             "potential pair",
@@ -234,7 +244,6 @@ def options(self, extra_options):
         if options["dimensionality"] == 0:
             if options["current collector"] not in [
                 "uniform",
-                "potential pair quite conductive averaged",
             ]:
                 raise pybamm.OptionError(
                     "current collector model must be uniform in 0D model"
@@ -243,13 +252,6 @@ def options(self, extra_options):
                 raise pybamm.OptionError(
                     "cannot have transverse convection in 0D model"
                 )
-        if (
-            options["current collector"] == "potential pair quite conductive averaged"
-            and options["dimensionality"] == 2
-        ):
-            raise pybamm.OptionError(
-                "potential pair quite conductive average model not valid in 2D"
-            )
         if options["particle"] not in ["Fickian diffusion", "fast diffusion"]:
             raise pybamm.OptionError(
                 "particle model '{}' not recognised".format(options["particle"])
@@ -555,7 +557,6 @@ def set_current_collector_submodel(self):
 
         if self.options["current collector"] in [
             "uniform",
-            "potential pair quite conductive averaged",
         ]:
             submodel = pybamm.current_collector.Uniform(self.param)
         elif self.options["current collector"] == "potential pair":

pybamm/models/full_battery_models/lead_acid/basic_full.py

@@ -88,13 +88,9 @@ def __init__(self, name="Full model"):
         pressure_n = pybamm.Variable(
             "Negative electrolyte pressure", domain="negative electrode",
         )
-        pressure_s = pybamm.Variable(
-            "Separator electrolyte pressure", domain="separator",
-        )
         pressure_p = pybamm.Variable(
             "Positive electrolyte pressure", domain="positive electrode",
         )
-        pressure = pybamm.Concatenation(pressure_n, pressure_s, pressure_p)
 
         # Constant temperature
         T = param.T_init
@@ -140,32 +136,43 @@ def __init__(self, name="Full model"):
         ######################
         # Convection
         ######################
-        v = -pybamm.grad(pressure)
+        v_n = -pybamm.grad(pressure_n)
+        v_p = -pybamm.grad(pressure_p)
         l_s = pybamm.geometric_parameters.l_s
+        l_n = pybamm.geometric_parameters.l_n
+        x_s = pybamm.SpatialVariable("x_s", domain="separator")
 
         # Difference in negative and positive electrode velocities determines the
         # velocity in the separator
-        v_box_n_right = param.beta_n * i_cell
-        v_box_p_left = param.beta_p * i_cell
-        d_vbox_s__dx = (v_box_p_left - v_box_n_right) / l_s
+        v_n_right = param.beta_n * i_cell
+        v_p_left = param.beta_p * i_cell
+        d_v_s__dx = (v_p_left - v_n_right) / l_s
 
         # Simple formula for velocity in the separator
-        dVbox_dz = pybamm.Concatenation(
+        div_V_s = -d_v_s__dx
+        v_s = d_v_s__dx * (x_s - l_n) + v_n_right
+
+        # v is the velocity in the x-direction
+        # div_V is the divergence of the velocity in the yz-directions
+        v = pybamm.Concatenation(v_n, v_s, v_p)
+        div_V = pybamm.Concatenation(
             pybamm.PrimaryBroadcast(0, "negative electrode"),
-            pybamm.PrimaryBroadcast(-d_vbox_s__dx, "separator"),
+            pybamm.PrimaryBroadcast(div_V_s, "separator"),
             pybamm.PrimaryBroadcast(0, "positive electrode"),
         )
-        beta = pybamm.Concatenation(
-            pybamm.PrimaryBroadcast(param.beta_n, "negative electrode"),
-            pybamm.PrimaryBroadcast(0, "separator"),
-            pybamm.PrimaryBroadcast(param.beta_p, "positive electrode"),
-        )
-        self.algebraic[pressure] = pybamm.div(v) + dVbox_dz - beta * j
-        self.boundary_conditions[pressure] = {
+        # Simple formula for velocity in the separator
+        self.algebraic[pressure_n] = pybamm.div(v_n) - param.beta_n * j_n
+        self.algebraic[pressure_p] = pybamm.div(v_p) - param.beta_p * j_p
+        self.boundary_conditions[pressure_n] = {
+            "left": (pybamm.Scalar(0), "Neumann"),
+            "right": (pybamm.Scalar(0), "Dirichlet"),
+        }
+        self.boundary_conditions[pressure_p] = {
             "left": (pybamm.Scalar(0), "Dirichlet"),
             "right": (pybamm.Scalar(0), "Neumann"),
         }
-        self.initial_conditions[pressure] = pybamm.Scalar(0)
+        self.initial_conditions[pressure_n] = pybamm.Scalar(0)
+        self.initial_conditions[pressure_p] = pybamm.Scalar(0)
 
         ######################
         # Current in the electrolyte
@@ -237,7 +244,7 @@ def __init__(self, name="Full model"):
         ######################
         # Electrolyte concentration
         ######################
-        N_e = -tor * param.D_e(c_e, T) * pybamm.grad(c_e) + c_e * v
+        N_e = -tor * param.D_e(c_e, T) * pybamm.grad(c_e) + param.C_e * c_e * v
         s = pybamm.Concatenation(
             -pybamm.PrimaryBroadcast(param.s_plus_n_S, "negative electrode"),
             pybamm.PrimaryBroadcast(0, "separator"),
@@ -247,6 +254,7 @@ def __init__(self, name="Full model"):
             -pybamm.div(N_e) / param.C_e
             + (s - param.t_plus(c_e)) * j / param.gamma_e
             - c_e * deps_dt
+            - c_e * div_V
         )
         self.boundary_conditions[c_e] = {
             "left": (pybamm.Scalar(0), "Neumann"),
@@ -276,6 +284,10 @@ def __init__(self, name="Full model"):
             - param.U_n_ref
             + pot * phi_s_p,
             "Terminal voltage [V]": param.U_p_ref - param.U_n_ref + pot * voltage,
+            "x [m]": pybamm.standard_spatial_vars.x * param.L_x,
+            "x": pybamm.standard_spatial_vars.x,
+            "Volume-averaged velocity": v,
+            "X-averaged separator transverse volume-averaged velocity": div_V_s,
         }
         self.events.extend(
             [

pybamm/models/full_battery_models/lead_acid/higher_order.py

@@ -63,7 +63,6 @@ def set_current_collector_submodel(self):
 
         if self.options["current collector"] in [
             "uniform",
-            "potential pair quite conductive averaged",
         ]:
             submodel = cc.Uniform(self.param)
         elif self.options["current collector"] == "potential pair quite conductive":
@@ -300,9 +299,7 @@ def __init__(self, options=None, name="Extended composite model (average)"):
     def set_electrolyte_diffusion_submodel(self):
         self.submodels[
             "electrolyte diffusion"
-        ] = pybamm.electrolyte.stefan_maxwell.diffusion.Composite(
-            self.param, extended="average"
-        )
+        ] = pybamm.electrolyte_diffusion.Composite(self.param, extended="average")
 
     def set_other_species_diffusion_submodels(self):
         if "oxygen" in self.options["side reactions"]:

pybamm/models/full_battery_models/lead_acid/loqs.py

@@ -82,7 +82,6 @@ def set_current_collector_submodel(self):
         if self.options["current collector"] in [
             "uniform",
             "potential pair quite conductive",
-            "potential pair quite conductive averaged",
         ]:
             submodel = pybamm.current_collector.Uniform(self.param)
         elif self.options["current collector"] == "potential pair":

pybamm/models/submodels/convection/base_convection.py

@@ -26,8 +26,8 @@ def _get_standard_whole_cell_velocity_variables(self, variables):
 
         Parameters
         ----------
-        v_box : :class:`pybamm.Symbol`
-            The volume-averaged fluid velocity
+        variables : dict
+            The existing variables in the model
 
         Returns
         -------
@@ -58,8 +58,8 @@ def _get_standard_whole_cell_acceleration_variables(self, variables):
 
         Parameters
         ----------
-        v_box : :class:`pybamm.Symbol`
-            The volume-averaged fluid velocity
+        variables : dict
+            The existing variables in the model
 
         Returns
         -------
@@ -93,8 +93,8 @@ def _get_standard_whole_cell_pressure_variables(self, variables):
 
         Parameters
         ----------
-        p : :class:`pybamm.Symbol`
-            The fluid pressure
+        variables : dict
+            The existing variables in the model
 
         Returns
         -------
@@ -118,6 +118,7 @@ def _separator_velocity(self, variables):
         ----------
         variables : dict
             Dictionary of variables in the whole model.
+
         Returns
         -------
         v_box_s : :class:`pybamm.Symbol`

pybamm/models/submodels/convection/through_cell/base_through_cell_convection.py

@@ -19,41 +19,6 @@ class BaseThroughCellModel(BaseModel):
     def __init__(self, param):
         super().__init__(param)
 
-    def _get_separator_velocity(self, variables):
-        # Set up
-        param = self.param
-        l_n = pybamm.geometric_parameters.l_n
-        x_s = pybamm.standard_spatial_vars.x_s
-
-        # Transverse velocity in the separator determines through-cell velocity
-        div_Vbox_s = variables[
-            "X-averaged separator transverse volume-averaged acceleration"
-        ]
-        i_boundary_cc = variables["Current collector current density"]
-        v_box_n_right = param.beta_n * pybamm.PrimaryBroadcast(
-            i_boundary_cc, "separator"
-        )
-        div_v_box_s_av = -div_Vbox_s
-        div_v_box_s = pybamm.PrimaryBroadcast(div_v_box_s_av, "separator")
-
-        # Simple formula for velocity in the separator
-        v_box_s = div_v_box_s_av * (x_s - l_n) + v_box_n_right
-
-        variables = self._get_standard_sep_velocity_variables(v_box_s, div_v_box_s)
-
-        return variables
-
-    def get_coupled_variables(self, variables):
-
-        variables.update(self._get_separator_velocity(variables))
-        variables.update(self._get_standard_whole_cell_velocity_variables(variables))
-        variables.update(
-            self._get_standard_whole_cell_acceleration_variables(variables)
-        )
-        variables.update(self._get_standard_whole_cell_pressure_variables(variables))
-
-        return variables
-
     def _get_standard_sep_velocity_variables(self, v_box_s, div_v_box_s):
         """Volume-averaged velocity in the separator"""