Issue 1253 reformat dfn half cell

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+-   Reformatted the `BasicDFNHalfCell` to be consistent with the other models ([#1282](https://github.com/pybamm-team/PyBaMM/pull/1282))
 -   Added option to make the total interfacial current density a state ([#1280](https://github.com/pybamm-team/PyBaMM/pull/1280))
 -   Added functionality to initialize a model using the solution from another model ([#1278](https://github.com/pybamm-team/PyBaMM/pull/1278))
 -   Added submodels for active material ([#1262](https://github.com/pybamm-team/PyBaMM/pull/1262))
@@ -14,6 +15,7 @@
 ## Bug fixes
 
 -   Fixed `Simulation` and `model.new_copy` to fix a bug where changes to the model were overwritten ([#1278](https://github.com/pybamm-team/PyBaMM/pull/1278))
+
 ## Breaking changes
 
 -   Boolean model options ('sei porosity change', 'convection') must now be given in string format ('true' or 'false' instead of True or False) ([#1280](https://github.com/pybamm-team/PyBaMM/pull/1280))

examples/scripts/DFN_half_cell.py

@@ -28,36 +28,39 @@
     check_already_exists=False,
 )
 
+param["Initial concentration in negative electrode [mol.m-3]"] = 1000
+param["Current function [A]"] = 2.5
+
 # process model and geometry
 param.process_model(model)
 param.process_geometry(geometry)
 
 # set mesh
-var = pybamm.standard_spatial_vars
-var_pts = {var.x_n: 30, var.x_s: 30, var.x_p: 30, var.r_n: 10, var.r_p: 10}
+var_pts = model.default_var_pts
 mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
 
 # discretise model
 disc = pybamm.Discretisation(mesh, model.default_spatial_methods)
 disc.process_model(model)
 
 # solve model
-t_eval = np.linspace(0, 3800, 1000)
-solver = pybamm.CasadiSolver(mode="fast", atol=1e-6, rtol=1e-3)
+t_eval = np.linspace(0, 7200, 1000)
+solver = pybamm.CasadiSolver(mode="safe", atol=1e-6, rtol=1e-3)
 solution = solver.solve(model, t_eval)
 
 # plot
 plot = pybamm.QuickPlot(
     solution,
     [
-        "Negative particle surface concentration [mol.m-3]",
+        "Working particle concentration [mol.m-3]",
         "Electrolyte concentration [mol.m-3]",
-        "Positive particle surface concentration [mol.m-3]",
         "Current [A]",
-        "Negative electrode potential [V]",
+        "Working electrode potential [V]",
         "Electrolyte potential [V]",
-        "Positive electrode potential [V]",
-        "Terminal voltage [V]",
+        "Total electrolyte concentration",
+        "Total lithium in working electrode [mol]",
+        "Working electrode open circuit potential [V]",
+        ["Terminal voltage [V]", "Voltage drop in the cell [V]"],
     ],
     time_unit="seconds",
     spatial_unit="um",

pybamm/expression_tree/symbol.py

@@ -27,6 +27,8 @@ def domain_size(domain):
         "negative electrode": 11,
         "separator": 13,
         "positive electrode": 17,
+        "working electrode": 19,
+        "working particle": 23,
     }
     if isinstance(domain, str):
         domain = [domain]

pybamm/expression_tree/unary_operators.py

@@ -1286,22 +1286,27 @@ def r_average(symbol):
         raise ValueError("Can't take the r-average of a symbol that evaluates on edges")
     # Otherwise, if symbol doesn't have a particle domain,
     # its r-averaged value is itself
-    elif symbol.domain not in [["positive particle"], ["negative particle"]]:
+    elif symbol.domain not in [
+        ["positive particle"],
+        ["negative particle"],
+        ["working particle"],
+    ]:
         new_symbol = symbol.new_copy()
         new_symbol.parent = None
         return new_symbol
     # If symbol is a secondary broadcast onto "negative electrode" or
     # "positive electrode", take the r-average of the child then broadcast back
     elif isinstance(symbol, pybamm.SecondaryBroadcast) and symbol.domains[
         "secondary"
-    ] in [["positive electrode"], ["negative electrode"]]:
+    ] in [["positive electrode"], ["negative electrode"], ["working electrode"]]:
         child = symbol.orphans[0]
         child_av = pybamm.r_average(child)
         return pybamm.PrimaryBroadcast(child_av, symbol.domains["secondary"])
     # If symbol is a Broadcast onto a particle domain, its average value is its child
     elif isinstance(symbol, pybamm.PrimaryBroadcast) and symbol.domain in [
         ["positive particle"],
         ["negative particle"],
+        ["working particle"],
     ]:
         return symbol.orphans[0]
     else:

pybamm/geometry/half_cell_geometry.py

@@ -0,0 +1,88 @@
+#
+# Function to create battery geometries
+#
+import pybamm
+from pybamm.geometry import half_cell_spatial_vars
+
+
+def half_cell_geometry(
+    include_particles=True, current_collector_dimension=0, working_electrode="positive"
+):
+    """
+    A convenience function to create battery geometries.
+
+    Parameters
+    ----------
+    include_particles : bool
+        Whether to include particle domains
+    current_collector_dimensions : int, default
+        The dimensions of the current collector. Should be 0 (default), 1 or 2
+    current_collector_dimensions : string
+        The electrode taking as working electrode. Should be "positive" or "negative"
+
+    Returns
+    -------
+    :class:`pybamm.Geometry`
+        A geometry class for the battery
+
+    """
+    var = half_cell_spatial_vars
+    geo = pybamm.geometric_parameters
+    if working_electrode == "positive":
+        l_w = geo.l_p
+    elif working_electrode == "negative":
+        l_w = geo.l_n
+    else:
+        raise ValueError(
+            "The option 'working_electrode' should be either 'positive'"
+            " or 'negative'"
+        )
+    l_Li = geo.l_Li
+    l_s = geo.l_s
+
+    geometry = {
+        "lithium counter electrode": {var.x_Li: {"min": 0, "max": l_Li}},
+        "separator": {var.x_s: {"min": l_Li, "max": l_Li + l_s}},
+        "working electrode": {var.x_w: {"min": l_Li + l_s, "max": l_Li + l_s + l_w}},
+    }
+    # Add particle domains
+    if include_particles is True:
+        geometry.update(
+            {"working particle": {var.r_w: {"min": 0, "max": 1}}}
+        )
+
+    if current_collector_dimension == 0:
+        geometry["current collector"] = {var.z: {"position": 1}}
+    elif current_collector_dimension == 1:
+        geometry["current collector"] = {
+            var.z: {"min": 0, "max": 1},
+            "tabs": {
+                "negative": {"z_centre": geo.centre_z_tab_n},
+                "positive": {"z_centre": geo.centre_z_tab_p},
+            },
+        }
+    elif current_collector_dimension == 2:
+        geometry["current collector"] = {
+            var.y: {"min": 0, "max": geo.l_y},
+            var.z: {"min": 0, "max": geo.l_z},
+            "tabs": {
+                "negative": {
+                    "y_centre": geo.centre_y_tab_n,
+                    "z_centre": geo.centre_z_tab_n,
+                    "width": geo.l_tab_n,
+                },
+                "positive": {
+                    "y_centre": geo.centre_y_tab_p,
+                    "z_centre": geo.centre_z_tab_p,
+                    "width": geo.l_tab_p,
+                },
+            },
+        }
+    else:
+        raise pybamm.GeometryError(
+            "Invalid current collector dimension '{}' (should be 0, 1 or 2)".format(
+                current_collector_dimension
+            )
+        )
+
+    return pybamm.Geometry(geometry)

pybamm/geometry/half_cell_spatial_vars.py

@@ -0,0 +1,85 @@
+import pybamm
+
+whole_cell = ["separator", "working electrode"]
+
+# Domains at cell centres
+x_Li = pybamm.SpatialVariable(
+    "x_Li",
+    domain=["lithium counter electrode"],
+    auxiliary_domains={"secondary": "current collector"},
+    coord_sys="cartesian",
+)
+x_s = pybamm.SpatialVariable(
+    "x_s",
+    domain=["separator"],
+    auxiliary_domains={"secondary": "current collector"},
+    coord_sys="cartesian",
+)
+x_w = pybamm.SpatialVariable(
+    "x_w",
+    domain=["working electrode"],
+    auxiliary_domains={"secondary": "current collector"},
+    coord_sys="cartesian",
+)
+x = pybamm.SpatialVariable(
+    "x",
+    domain=whole_cell,
+    auxiliary_domains={"secondary": "current collector"},
+    coord_sys="cartesian",
+)
+
+y = pybamm.SpatialVariable("y", domain="current collector", coord_sys="cartesian")
+z = pybamm.SpatialVariable("z", domain="current collector", coord_sys="cartesian")
+
+r_w = pybamm.SpatialVariable(
+    "r_w",
+    domain=["working particle"],
+    auxiliary_domains={
+        "secondary": "working electrode",
+        "tertiary": "current collector",
+    },
+    coord_sys="spherical polar",
+)
+
+# Domains at cell edges
+x_Li_edge = pybamm.SpatialVariableEdge(
+    "x_Li",
+    domain=["lithium counter electrode"],
+    auxiliary_domains={"secondary": "current collector"},
+    coord_sys="cartesian",
+)
+x_s_edge = pybamm.SpatialVariableEdge(
+    "x_s",
+    domain=["separator"],
+    auxiliary_domains={"secondary": "current collector"},
+    coord_sys="cartesian",
+)
+x_w_edge = pybamm.SpatialVariableEdge(
+    "x_w",
+    domain=["working electrode"],
+    auxiliary_domains={"secondary": "current collector"},
+    coord_sys="cartesian",
+)
+x_edge = pybamm.SpatialVariableEdge(
+    "x",
+    domain=whole_cell,
+    auxiliary_domains={"secondary": "current collector"},
+    coord_sys="cartesian",
+)
+
+y_edge = pybamm.SpatialVariableEdge(
+    "y", domain="current collector", coord_sys="cartesian"
+)
+z_edge = pybamm.SpatialVariableEdge(
+    "z", domain="current collector", coord_sys="cartesian"
+)
+
+r_w_edge = pybamm.SpatialVariableEdge(
+    "r_w",
+    domain=["working particle"],
+    auxiliary_domains={
+        "secondary": "working electrode",
+        "tertiary": "current collector",
+    },
+    coord_sys="spherical polar",
+)