pybamm-team#1810 allow strings in var_pts and geometry

benchmarks/time_solve_models.py

@@ -14,16 +14,7 @@ def prepare_model(model):
     param.process_geometry(geometry)
 
     # set mesh
-    var = pybamm.standard_spatial_vars
-    var_pts = {
-        var.x_n: 20,
-        var.x_s: 20,
-        var.x_p: 20,
-        var.r_n: 30,
-        var.r_p: 30,
-        var.y: 10,
-        var.z: 10,
-    }
+    var_pts = {"x_n": 20, "x_s": 20, "x_p": 20, "r_n": 30, "r_p": 30, "y": 10, "z": 10}
     mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
 
     # discretise model

examples/notebooks/Getting Started/Tutorial 9 - Changing the mesh.ipynb

@@ -100,11 +100,11 @@
     "\n",
     "# create our dictionary \n",
     "var_pts = {\n",
-    "    var.x_n: 10,  # negative electrode\n",
-    "    var.x_s: 10,  # separator \n",
-    "    var.x_p: 10,  # positive electrode\n",
-    "    var.r_n: 10,  # negative particle\n",
-    "    var.r_p: 10,  # positive particle\n",
+    "    "x_n": 10,  # negative electrode\n",
+    "    "x_s": 10,  # separator \n",
+    "    "x_p": 10,  # positive electrode\n",
+    "    "r_n": 10,  # negative particle\n",
+    "    "r_p": 10,  # positive particle\n",
     "}"
    ]
   },
@@ -210,11 +210,11 @@
     "solutions = []\n",
     "for N in npts:\n",
     "    var_pts = {\n",
-    "        var.x_n: N,  # negative electrode\n",
-    "        var.x_s: N,  # separator \n",
-    "        var.x_p: N,  # positive electrode\n",
-    "        var.r_n: N,  # negative particle\n",
-    "        var.r_p: N,  # positive particle\n",
+    "        "x_n": N,  # negative electrode\n",
+    "        "x_s": N,  # separator \n",
+    "        "x_p": N,  # positive electrode\n",
+    "        "r_n": N,  # negative particle\n",
+    "        "r_p": N,  # positive particle\n",
     "    }    \n",
     "    sim = pybamm.Simulation(\n",
     "        model, solver=solver, parameter_values=parameter_values, var_pts=var_pts\n",

examples/notebooks/expression_tree/broadcasts.ipynb

@@ -44,16 +44,16 @@
    "source": [
     "var = pybamm.standard_spatial_vars\n",
     "geometry = {\n",
-    "    \"negative electrode\": {var.x_n: {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}},\n",
-    "    \"negative particle\": {var.r_n: {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}},\n",
+    "    \"negative electrode\": {"x_n": {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}},\n",
+    "    \"negative particle\": {"r_n": {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}},\n",
     "}\n",
     "\n",
     "submesh_types = {\n",
     "    \"negative electrode\": pybamm.Uniform1DSubMesh,\n",
     "    \"negative particle\": pybamm.Uniform1DSubMesh,\n",
     "}\n",
     "\n",
-    "var_pts = {var.x_n: 5, var.r_n: 3}\n",
+    "var_pts = {"x_n": 5, "r_n": 3}\n",
     "mesh = pybamm.Mesh(geometry, submesh_types, var_pts)\n",
     "\n",
     "spatial_methods = {\n",

examples/notebooks/models/Validating_mechanical_models_Enertech_DFN.ipynb

@@ -87,11 +87,11 @@
     "# update the mesh\n",
     "var = pybamm.standard_spatial_vars\n",
     "var_pts = {\n",
-    "  var.x_n: 50,\n",
-    "  var.x_s: 50,\n",
-    "  var.x_p: 50,\n",
-    "  var.r_n: 21,\n",
-    "  var.r_p: 21,\n",
+    "  "x_n": 50,\n",
+    "  "x_s": 50,\n",
+    "  "x_p": 50,\n",
+    "  "r_n": 21,\n",
+    "  "r_p": 21,\n",
     "}\n",
     "\n",
     "# define the simulation\n",

examples/notebooks/models/compare-comsol-discharge-curve.ipynb

@@ -93,7 +93,7 @@
     "\n",
     "# create mesh\n",
     "var = pybamm.standard_spatial_vars\n",
-    "var_pts = {var.x_n: 31, var.x_s: 11, var.x_p: 31, var.r_n: 11, var.r_p: 11}\n",
+    "var_pts = {"x_n": 31, "x_s": 11, "x_p": 31, "r_n": 11, "r_p": 11}\n",
     "mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)\n",
     "\n",
     "# discretise model\n",

examples/notebooks/models/compare-ecker-data.ipynb

@@ -100,11 +100,11 @@
    "source": [
     "var = pybamm.standard_spatial_vars\n",
     "var_pts = {\n",
-    "    var.x_n: int(parameter_values.evaluate(model.param.L_n / 1e-6)),\n",
-    "    var.x_s: int(parameter_values.evaluate(model.param.L_s / 1e-6)),\n",
-    "    var.x_p: int(parameter_values.evaluate(model.param.L_p / 1e-6)),\n",
-    "    var.r_n: int(parameter_values.evaluate(model.param.R_n_typ / 1e-7)),\n",
-    "    var.r_p: int(parameter_values.evaluate(model.param.R_p_typ / 1e-7)),\n",
+    "    "x_n": int(parameter_values.evaluate(model.param.L_n / 1e-6)),\n",
+    "    "x_s": int(parameter_values.evaluate(model.param.L_s / 1e-6)),\n",
+    "    "x_p": int(parameter_values.evaluate(model.param.L_p / 1e-6)),\n",
+    "    "r_n": int(parameter_values.evaluate(model.param.R_n_typ / 1e-7)),\n",
+    "    "r_p": int(parameter_values.evaluate(model.param.R_p_typ / 1e-7)),\n",
     "}"
    ]
   },

examples/notebooks/models/pouch-cell-model.ipynb

@@ -157,12 +157,12 @@
     "var = pybamm.standard_spatial_vars\n",
     "npts = 16\n",
     "var_pts = {\n",
-    "    var.x_n: npts,\n",
-    "    var.x_s: npts,\n",
-    "    var.x_p: npts,\n",
-    "    var.r_n: npts,\n",
-    "    var.r_p: npts,\n",
-    "    var.z: npts,\n",
+    "    "x_n": npts,\n",
+    "    "x_s": npts,\n",
+    "    "x_p": npts,\n",
+    "    "r_n": npts,\n",
+    "    "r_p": npts,\n",
+    "    "z": npts,\n",
     "}"
    ]
   },

examples/notebooks/models/simulating-ORegan-2021-parameter-set.ipynb

@@ -71,7 +71,7 @@
    "outputs": [],
    "source": [
     "var = pybamm.standard_spatial_vars\n",
-    "var_pts = {var.x_n: 30, var.x_s: 30, var.x_p: 30, var.r_n: 40, var.r_p: 40}\n",
+    "var_pts = {"x_n": 30, "x_s": 30, "x_p": 30, "r_n": 40, "r_p": 40}\n",
     "\n",
     "submesh_types = model.default_submesh_types\n",
     "submesh_types[\"negative particle\"] = pybamm.MeshGenerator(\n",

examples/notebooks/spatial_methods/finite-volumes.ipynb

@@ -119,7 +119,7 @@
     "}\n",
     "\n",
     "var = pybamm.standard_spatial_vars\n",
-    "var_pts = {var.x_n: 15, var.x_s: 10, var.x_p: 15, var.r_n: 10, var.r_p: 10}\n",
+    "var_pts = {"x_n": 15, "x_s": 10, "x_p": 15, "r_n": 10, "r_p": 10}\n",
     "mesh = pybamm.Mesh(geometry, submesh_types, var_pts)"
    ]
   },

examples/scripts/DFN_ambient_temperature.py

@@ -30,8 +30,7 @@ def ambient_temperature(t):
 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 = {"x_n": 30, "x_s": 30, "x_p": 30, "r_n": 10, "r_p": 10}
 mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
 
 # discretise model

examples/scripts/SPMe_SOC.py

@@ -58,14 +58,7 @@
         )
         param.process_model(model)
         param.process_geometry(geometry)
-        s_var = pybamm.standard_spatial_vars
-        var_pts = {
-            s_var.x_n: 5,
-            s_var.x_s: 5,
-            s_var.x_p: 5,
-            s_var.r_n: 5,
-            s_var.r_p: 10,
-        }
+        var_pts = {"x_n": 5, "x_s": 5, "x_p": 5, "r_n": 5, "r_p": 10}
         # set mesh
         mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
         # discretise model

examples/scripts/compare_comsol/compare_comsol_DFN.py

@@ -45,8 +45,7 @@
 param.process_geometry(geometry)
 
 # create mesh
-var = pybamm.standard_spatial_vars
-var_pts = {var.x_n: 31, var.x_s: 11, var.x_p: 31, var.r_n: 11, var.r_p: 11}
+var_pts = {"x_n": 31, "x_s": 11, "x_p": 31, "r_n": 11, "r_p": 11}
 mesh = pybamm.Mesh(geometry, pybamm_model.default_submesh_types, var_pts)
 
 # discretise model

examples/scripts/compare_comsol/discharge_curve.py

@@ -30,8 +30,7 @@
 param.process_geometry(geometry)
 
 # create mesh
-var = pybamm.standard_spatial_vars
-var_pts = {var.x_n: 31, var.x_s: 11, var.x_p: 31, var.r_n: 11, var.r_p: 11}
+var_pts = {"x_n": 31, "x_s": 11, "x_p": 31, "r_n": 11, "r_p": 11}
 mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
 
 # discretise model

examples/scripts/compare_dae_solver.py

@@ -15,8 +15,7 @@
 param.process_geometry(geometry)
 
 # set mesh
-var = pybamm.standard_spatial_vars
-var_pts = {var.x_n: 50, var.x_s: 50, var.x_p: 50, var.r_n: 20, var.r_p: 20}
+var_pts = {"x_n": 50, "x_s": 50, "x_p": 50, "r_n": 20, "r_p": 20}
 mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
 
 # discretise model

examples/scripts/compare_lithium_ion_2D.py

@@ -34,16 +34,7 @@
 for model in models:
     geometry = model.default_geometry
     param.process_geometry(geometry)
-    var = pybamm.standard_spatial_vars
-    var_pts = {
-        var.x_n: 10,
-        var.x_s: 10,
-        var.x_p: 10,
-        var.r_n: 10,
-        var.r_p: 10,
-        var.y: 10,
-        var.z: 10,
-    }
+    var_pts = {"x_n": 10, "x_s": 10, "x_p": 10, "r_n": 10, "r_p": 10, "y": 10, "z": 10}
     mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
     disc = pybamm.Discretisation(mesh, model.default_spatial_methods)
     disc.process_model(model)

examples/scripts/compare_spectral_volume.py

@@ -23,8 +23,7 @@
     p.process_geometry(g)
 
 # set mesh
-var = pybamm.standard_spatial_vars
-var_pts = {var.x_n: 1, var.x_s: 1, var.x_p: 1, var.r_n: 1, var.r_p: 1}
+var_pts = {"x_n": 1, "x_s": 1, "x_p": 1, "r_n": 1, "r_p": 1}
 # the Finite Volume method also works on spectral meshes
 meshes = [
     pybamm.Mesh(

examples/scripts/thermal_lithium_ion.py

@@ -37,8 +37,7 @@
     param.process_model(model)
 
 # set mesh
-var = pybamm.standard_spatial_vars
-var_pts = {var.x_n: 10, var.x_s: 10, var.x_p: 10, var.r_n: 10, var.r_p: 10}
+var_pts = {"x_n": 10, "x_s": 10, "x_p": 10, "r_n": 10, "r_p": 10}
 
 # discretise models
 for model in models:

pybamm/geometry/battery_geometry.py

@@ -28,7 +28,6 @@ def battery_geometry(
         A geometry class for the battery
 
     """
-    var = pybamm.standard_spatial_vars
     geo = pybamm.geometric_parameters
     l_n = geo.l_n
     l_s = geo.l_s
@@ -38,52 +37,45 @@ def battery_geometry(
     l_n_l_s.print_name = "l_n + l_s"
 
     geometry = {
-        "negative electrode": {var.x_n: {"min": 0, "max": l_n}},
-        "separator": {var.x_s: {"min": l_n, "max": l_n_l_s}},
-        "positive electrode": {var.x_p: {"min": l_n_l_s, "max": 1}},
+        "negative electrode": {"x_n": {"min": 0, "max": l_n}},
+        "separator": {"x_s": {"min": l_n, "max": l_n_l_s}},
+        "positive electrode": {"x_p": {"min": l_n_l_s, "max": 1}},
     }
     # Add particle domains
     if include_particles is True:
         geometry.update(
             {
-                "negative particle": {var.r_n: {"min": 0, "max": 1}},
-                "positive particle": {var.r_p: {"min": 0, "max": 1}},
+                "negative particle": {"r_n": {"min": 0, "max": 1}},
+                "positive particle": {"r_p": {"min": 0, "max": 1}},
             }
         )
     # Add particle size domains
-    if (
-        options is not None and
-        options["particle size"] == "distribution"
-    ):
+    if options is not None and options["particle size"] == "distribution":
         R_min_n = geo.R_min_n
         R_min_p = geo.R_min_p
         R_max_n = geo.R_max_n
         R_max_p = geo.R_max_p
         geometry.update(
             {
-                "negative particle size": {
-                    var.R_n: {"min": R_min_n, "max": R_max_n}
-                },
-                "positive particle size": {
-                    var.R_p: {"min": R_min_p, "max": R_max_p}
-                },
+                "negative particle size": {"R_n": {"min": R_min_n, "max": R_max_n}},
+                "positive particle size": {"R_p": {"min": R_min_p, "max": R_max_p}},
             }
         )
 
     if current_collector_dimension == 0:
-        geometry["current collector"] = {var.z: {"position": 1}}
+        geometry["current collector"] = {"z": {"position": 1}}
     elif current_collector_dimension == 1:
         geometry["current collector"] = {
-            var.z: {"min": 0, "max": 1},
+            "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},
+            "y": {"min": 0, "max": geo.l_y},
+            "z": {"min": 0, "max": geo.l_z},
             "tabs": {
                 "negative": {
                     "y_centre": geo.centre_y_tab_n,

pybamm/meshes/meshes.py

@@ -26,8 +26,17 @@ class Mesh(dict):
 
     def __init__(self, geometry, submesh_types, var_pts):
         super().__init__()
+
+        # Preprocess var_pts
+        var_pts_input = var_pts
+        var_pts = {}
+        for key, value in var_pts_input.items():
+            if isinstance(key, str):
+                key = getattr(pybamm.standard_spatial_vars, key)
+            var_pts[key] = value
+
         # convert var_pts to an id dict
-        var_id_pts = {var.id: pts for var, pts in var_pts.items()}
+        var_name_pts = {var.name: pts for var, pts in var_pts.items()}
 
         # create submesh_pts from var_pts
         submesh_pts = {}
@@ -54,11 +63,13 @@ def __init__(self, geometry, submesh_types, var_pts):
                         )
                     # skip over tabs key
                     if var != "tabs":
+                        if isinstance(var, str):
+                            var = getattr(pybamm.standard_spatial_vars, var)
                         # Raise error if the number of points for a particular
                         # variable haven't been provided, unless that variable
                         # doesn't appear in the geometry
                         if (
-                            var.id not in var_id_pts.keys()
+                            var.name not in var_name_pts.keys()
                             and var.domain[0] in geometry.keys()
                         ):
                             raise KeyError(
@@ -67,7 +78,7 @@ def __init__(self, geometry, submesh_types, var_pts):
                                 )
                             )
                         # Otherwise add to the dictionary of submesh points
-                        submesh_pts[domain][var.id] = var_id_pts[var.id]
+                        submesh_pts[domain][var.name] = var_name_pts[var.name]
         self.submesh_pts = submesh_pts
 
         # Input domain order manually

pybamm/meshes/one_dimensional_submeshes.py

@@ -90,7 +90,9 @@ class Uniform1DSubMesh(SubMesh1D):
     def __init__(self, lims, npts):
 
         spatial_var, spatial_lims, tabs = self.read_lims(lims)
-        npts = npts[spatial_var.id]
+        if isinstance(spatial_var, str):
+            spatial_var = getattr(pybamm.standard_spatial_vars, spatial_var)
+        npts = npts[spatial_var.name]
 
         edges = np.linspace(spatial_lims["min"], spatial_lims["max"], npts + 1)