#617 unify mesh generators

docs/source/meshes/meshes.rst

@@ -4,5 +4,8 @@ Meshes
 .. autoclass:: pybamm.Mesh
     :members:
 
+.. autoclass:: pybamm.SubMesh
+    :members:
+
 .. autoclass:: pybamm.MeshGenerator
     :members:

docs/source/meshes/one_dimensional_submeshes.rst

@@ -4,9 +4,6 @@
 .. autoclass:: pybamm.SubMesh1D
     :members:
 
-.. autoclass:: pybamm.MeshGenerator1D
-    :members:
-
 .. autoclass:: pybamm.Uniform1DSubMesh
     :members:
 

docs/source/meshes/two_dimensional_submeshes.rst

@@ -4,9 +4,6 @@
 .. autoclass:: pybamm.ScikitSubMesh2D
     :members:
 
-.. autoclass:: pybamm.MeshGenerator2D
-    :members:
-
 .. autoclass:: pybamm.ScikitUniform2DSubMesh
     :members:
 

docs/source/meshes/zero_dimensional_submeshes.rst

@@ -3,6 +3,3 @@
 
 .. autoclass:: pybamm.SubMesh0D
     :members:
-
-.. autoclass:: pybamm.MeshGenerator0D
-    :members:

examples/notebooks/models/SPM.ipynb

@@ -213,7 +213,7 @@
    "source": [
     "The next step is to mesh the input geometry. We can do this using the [`pybamm.Mesh`](https://pybamm.readthedocs.io/en/latest/source/meshes/meshes.html) class. This class takes in the geometry of the problem, and also two dictionaries containing the type of mesh to use within each domain of the geometry (i.e. within the positive or negative electrode domains), and the number of mesh points. \n",
     "\n",
-    "The default mesh types and the default number of points to use in each variable for the SPH model are:"
+    "The default mesh types and the default number of points to use in each variable for the SPM model are:"
    ]
   },
   {
@@ -227,12 +227,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "negative electrode is of type MeshGenerator1D : Uniform\n",
-      "separator is of type MeshGenerator1D : Uniform\n",
-      "positive electrode is of type MeshGenerator1D : Uniform\n",
-      "negative particle is of type MeshGenerator1D : Uniform\n",
-      "positive particle is of type MeshGenerator1D : Uniform\n",
-      "current collector is of type MeshGenerator0D : Position\n",
+      "negative electrode is of type Generator for Uniform1DSubMesh\n",
+      "separator is of type Generator for Uniform1DSubMesh\n",
+      "positive electrode is of type Generator for Uniform1DSubMesh\n",
+      "negative particle is of type Generator for Uniform1DSubMesh\n",
+      "positive particle is of type Generator for Uniform1DSubMesh\n",
+      "current collector is of type Generator for SubMesh0D\n",
       "x_n has 20 mesh points\n",
       "x_s has 20 mesh points\n",
       "x_p has 20 mesh points\n",
@@ -245,7 +245,7 @@
    ],
    "source": [
     "for k, t in model.default_submesh_types.items():\n",
-    "    print(k,'is of type',t.__class__.__name__,':',t.submesh_type )\n",
+    "    print(k,'is of type',t.__repr__())\n",
     "for var, npts in model.default_var_pts.items():\n",
     "    print(var,'has',npts,'mesh points')"
    ]
@@ -309,7 +309,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.models.full_battery_models.lithium_ion.spm.SPM at 0x7fc1812341d0>"
+       "<pybamm.models.full_battery_models.lithium_ion.spm.SPM at 0x7f75886cf198>"
       ]
      },
      "execution_count": 11,
@@ -760,7 +760,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "19149e76db2642209815a3c6150b8dc7",
+       "model_id": "99e13279bde044ea9cea75d2f873e7c6",
        "version_major": 2,
        "version_minor": 0
       },
@@ -808,7 +808,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "509fb382c8984dc883a10d85dcb2dfbc",
+       "model_id": "5198757616254d11a031a8deee5a51f7",
        "version_major": 2,
        "version_minor": 0
       },

examples/scripts/SPM_compare_particle_grid.py

@@ -32,9 +32,9 @@
 # set mesh
 submesh_types = models[0].default_submesh_types
 particle_meshes = [
-    pybamm.MeshGenerator1D(),
-    pybamm.MeshGenerator1D("Chebyshev"),
-    pybamm.MeshGenerator1D("Exponential", {"side": "right"}),
+    pybamm.MeshGenerator(pybamm.Uniform1DSubMesh),
+    pybamm.MeshGenerator(pybamm.Chebyshev1DSubMesh),
+    pybamm.MeshGenerator(pybamm.Exponential1DSubMesh, submesh_params={"side": "right"}),
 ]
 meshes = [None] * len(models)
 # discretise models

pybamm/__init__.py

@@ -223,19 +223,17 @@ def version(formatted=False):
 # Mesh and Discretisation classes
 #
 from .discretisations.discretisation import Discretisation
-from .meshes.meshes import Mesh, MeshGenerator
-from .meshes.zero_dimensional_submesh import SubMesh0D, MeshGenerator0D
+from .meshes.meshes import Mesh, SubMesh, MeshGenerator
+from .meshes.zero_dimensional_submesh import SubMesh0D
 from .meshes.one_dimensional_submeshes import (
     SubMesh1D,
-    MeshGenerator1D,
     Uniform1DSubMesh,
     Exponential1DSubMesh,
     Chebyshev1DSubMesh,
     UserSupplied1DSubMesh,
 )
 from .meshes.scikit_fem_submeshes import (
     ScikitSubMesh2D,
-    MeshGenerator2D,
     ScikitUniform2DSubMesh,
     ScikitExponential2DSubMesh,
     ScikitChebyshev2DSubMesh,

pybamm/meshes/meshes.py

@@ -31,10 +31,14 @@ def __init__(self, geometry, submesh_types, var_pts):
         # create submesh_pts from var_pts
         submesh_pts = {}
         for domain in geometry:
+            # create mesh generator if just class is passed (will throw an error
+            # later if the mesh needed parameters)
+            if not isinstance(
+                submesh_types[domain], pybamm.MeshGenerator
+            ) and issubclass(submesh_types[domain], pybamm.SubMesh):
+                submesh_types[domain] = pybamm.MeshGenerator(submesh_types[domain])
             # Zero dimensional submesh case (only one point)
-            if submesh_types[domain] == pybamm.SubMesh0D or isinstance(
-                submesh_types[domain], pybamm.MeshGenerator0D
-            ):
+            if issubclass(submesh_types[domain].submesh_type, pybamm.SubMesh0D):
                 submesh_pts[domain] = 1
             # other cases
             else:
@@ -97,24 +101,23 @@ def __init__(self, geometry, submesh_types, var_pts):
 
         # Create submeshes
         for domain in geometry:
-            if domain == "current collector" and not (
-                submesh_types[domain] == pybamm.SubMesh0D
-                or isinstance(submesh_types[domain], pybamm.MeshGenerator0D)
-            ):
+            # repeat mesh if domain has secondary dimension
+            if "secondary" in geometry[domain].keys():
+                repeats = 1
+                for var in geometry[domain]["secondary"].keys():
+                    repeats *= submesh_pts[domain][var.id]  # note (specific to FV)
+            else:
+                repeats = 1
+            # create submesh, passing tab information if provided
+            if "tabs" in geometry[domain].keys():
                 self[domain] = [
                     submesh_types[domain](
                         geometry[domain]["primary"],
                         submesh_pts[domain],
                         geometry[domain]["tabs"],
                     )
-                ]
+                ] * repeats
             else:
-                if "secondary" in geometry[domain].keys():
-                    repeats = 1
-                    for var in geometry[domain]["secondary"].keys():
-                        repeats *= submesh_pts[domain][var.id]  # note (specific to FV)
-                else:
-                    repeats = 1
                 self[domain] = [
                     submesh_types[domain](
                         geometry[domain]["primary"], submesh_pts[domain]
@@ -200,26 +203,38 @@ def add_ghost_meshes(self):
                 )
 
 
+class SubMesh:
+    """
+    Base submesh class.
+    Contains the position of the nodes, the number of mesh points, and
+    (optionally) information about the tab locations.
+    """
+
+    def __init__(self):
+        pass
+
+
 class MeshGenerator:
     """
     Base class for mesh generator objects that are used to generate submeshes.
 
     Parameters
     ----------
 
-    submesh_type: str, optional
-        The type of submeshes to use. Default is "Uniform".
+    submesh_type: :class:`pybamm.SubMesh`
+        The type of submesh to use (e.g. Uniform1DSubMesh).
     submesh_params: dict, optional
         Contains any parameters required by the submesh.
     """
 
-    def __init__(self, submesh_type="Uniform", submesh_params=None):
+    def __init__(self, submesh_type, submesh_params=None):
         self.submesh_type = submesh_type
         self.submesh_params = submesh_params or {}
 
-    def __call__(self):
-        """
-        Each Mesh Generator should implemented a call method which returns
-        an instance of a submesh.
-        """
-        raise NotImplementedError
+    def __call__(self, lims, npts, tabs=None):
+        return self.submesh_type(lims, npts, tabs, **self.submesh_params)
+
+    def __repr__(self):
+        return "Generator for {}".format(
+            self.submesh_type.__name__
+        )

pybamm/meshes/one_dimensional_submeshes.py

@@ -2,16 +2,28 @@
 # One-dimensional submeshes
 #
 import pybamm
-from .meshes import MeshGenerator
+from .meshes import SubMesh
 
 import numpy as np
 
 
-class SubMesh1D:
+class SubMesh1D(SubMesh):
     """
     1D submesh class.
     Contains the position of the nodes, the number of mesh points, and
     (optionally) information about the tab locations.
+
+    Parameters
+    ----------
+    edges : array_like
+        An array containing the points corresponding to the edges of the submesh
+    coord_sys : string
+        The coordinate system of the submesh
+    tabs : dict, optional
+        A dictionary that contains information about the size and location of
+        the tabs
+
+    **Extends:"": :class:`pybamm.SubMesh`
     """
 
     def __init__(self, edges, coord_sys, tabs=None):
@@ -45,50 +57,6 @@ def near(x, point, tol=3e-16):
                     )
 
 
-class MeshGenerator1D(MeshGenerator):
-    """
-    A class to generate a submesh on a 1D domain.
-
-    Parameters
-    ----------
-
-    submesh_type: str, optional
-        The type of submeshes to use. Can be "Uniform", "Exponential", "Chebyshev"
-        or "User". Default is "Uniform".
-    submesh_params: dict, optional
-        Contains any parameters required by the submesh.
-
-    **Extends**: :class:`pybamm.MeshGenerator`
-    """
-
-    def __init__(self, submesh_type="Uniform", submesh_params=None):
-        self.submesh_type = submesh_type
-        self.submesh_params = submesh_params or {}
-
-    def __call__(self, lims, npts, tabs=None):
-
-        if self.submesh_type == "Uniform":
-            return Uniform1DSubMesh(lims, npts, tabs)
-
-        elif self.submesh_type == "Exponential":
-            return Exponential1DSubMesh(lims, npts, tabs, **self.submesh_params)
-
-        elif self.submesh_type == "Chebyshev":
-            return Chebyshev1DSubMesh(lims, npts, tabs)
-
-        elif self.submesh_type == "User":
-            try:
-                edges = self.submesh_params["edges"]
-            except KeyError:
-                raise pybamm.GeometryError("User mesh requires parameter 'edges'")
-            return UserSupplied1DSubMesh(lims, npts, tabs, edges)
-
-        else:
-            raise pybamm.GeometryError(
-                "Submesh {} not recognised.".format(self.submesh_type)
-            )
-
-
 class Uniform1DSubMesh(SubMesh1D):
     """
     A class to generate a uniform submesh on a 1D domain
@@ -104,6 +72,8 @@ class Uniform1DSubMesh(SubMesh1D):
     tabs : dict, optional
         A dictionary that contains information about the size and location of
         the tabs
+
+    **Extends:"": :class:`pybamm.SubMesh1D`
     """
 
     def __init__(self, lims, npts, tabs=None):
@@ -174,6 +144,8 @@ class Exponential1DSubMesh(SubMesh1D):
         The factor (alpha) which appears in the exponential. If side is "symmetric"
         then the default stretch is 1.15. If side is "left" or "right" then the
         default stretch is 2.3.
+
+    **Extends:"": :class:`pybamm.SubMesh1D`
     """
 
     def __init__(self, lims, npts, tabs, side="symmetric", stretch=None):
@@ -257,6 +229,8 @@ class Chebyshev1DSubMesh(SubMesh1D):
     tabs : dict, optional
         A dictionary that contains information about the size and location of
         the tabs
+
+    **Extends:"": :class:`pybamm.SubMesh1D`
     """
 
     def __init__(self, lims, npts, tabs=None):
@@ -302,9 +276,15 @@ class UserSupplied1DSubMesh(SubMesh1D):
         the tabs
     edges : array_like
         The array of points which correspond to the edges of the mesh.
+
+    **Extends:"": :class:`pybamm.SubMesh1D`
     """
 
-    def __init__(self, lims, npts, tabs, edges):
+    def __init__(self, lims, npts, tabs, edges=None):
+
+        # raise error if no edges passed
+        if edges is None:
+            raise pybamm.GeometryError("User mesh requires parameter 'edges'")
 
         # check that only one variable passed in
         if len(lims) != 1: