#617 fix examples

docs/source/meshes/index.rst

@@ -4,6 +4,6 @@ Meshes
 .. toctree::
 
   meshes
-  one_dimensional_submeshes
-  scikits_fem_submeshes
   zero_dimensional_submeshes
+  one_dimensional_submeshes
+  two_dimensional_submeshes

docs/source/meshes/one_dimensional_submeshes.rst

@@ -1,17 +1,23 @@
 1D Sub Meshes
 =============
 
-.. autoclass:: pybamm.SubMesh1D
+.. autoclass:: pybamm.one_dimensional_meshes.SubMesh1D
     :members:
 
-.. autoclass:: pybamm.Uniform1DSubMesh
+.. autoclass:: pybamm.one_dimensional_meshes.Uniform1DSubMesh
     :members:
 
-.. autoclass:: pybamm.Chebyshev1DSubMesh
+.. autoclass:: pybamm.one_dimensional_meshes.Chebyshev1DSubMesh
     :members:
 
-.. autoclass:: pybamm.GetExponential1DSubMesh
+.. autoclass:: pybamm.one_dimensional_meshes.GetExponential1DSubMesh
     :members:
 
-.. autoclass:: pybamm.Exponential1DSubMesh
+.. autoclass:: pybamm.one_dimensional_meshes.Exponential1DSubMesh
+    :members:
+
+.. autoclass:: pybamm.one_dimensional_meshes.GetUserSupplied1DSubMesh
+    :members:
+
+.. autoclass:: pybamm.one_dimensional_meshes.UserSupplied1DSubMesh
     :members:

docs/source/meshes/two_dimensional_submeshes.rst

@@ -0,0 +1,14 @@
+2D Sub Meshes
+=============
+
+.. autoclass:: pybamm.two_dimensional_meshes.ScikitSubMesh2D
+    :members:
+
+.. autoclass:: pybamm.two_dimensional_meshes.ScikitUniform2DSubMesh
+    :members:
+
+.. autoclass:: pybamm.two_dimensional_meshes.ScikitChebyshev2DSubMesh
+    :members:
+
+.. autoclass:: pybamm.two_dimensional_meshes.ScikitTopExponential2DSubMesh
+    :members:

docs/source/meshes/zero_dimensional_submeshes.rst

@@ -1,5 +1,5 @@
 0D Sub Mesh
 ===========
 
-.. autoclass:: pybamm.SubMesh0D
+.. autoclass:: pybamm.zero_dimensional_meshes.SubMesh0D
     :members:

docs/tutorials/add-model.rst

@@ -131,7 +131,7 @@ Events will stop the solver whenever they return 0.
 Setting defaults
 ~~~~~~~~~~~~~~~~
 It can be useful for testing, and quickly running a model to have a default setup. Each of the defaults listed above should adhere to the API requirements but in short, we require ``self.default_geometry`` to be an instance of :class:`pybamm.Geometry`, ``self.default_solver`` to be an instance of :class:`pybamm.BaseSolver`, and
-``self.default_parameter_values`` to be an instance of :class:`pybamm.ParameterValues`. We also require that ``self.default_submesh_types`` is a dictionary with keys which are strings corresponding to the regions of the battery (e.g. "negative electrode") and values which are an instance of :class:`pybamm.SubMesh1D`. The ``self.default_spatial_methods`` attribute is also required to be a dictionary with keys corresponding to the regions of the battery but with values which are an instance of
+``self.default_parameter_values`` to be an instance of :class:`pybamm.ParameterValues`. We also require that ``self.default_submesh_types`` is a dictionary with keys which are strings corresponding to the regions of the battery (e.g. "negative electrode") and values which are an instance of :class:`pybamm.one_dimensional_meshes.SubMesh1D`. The ``self.default_spatial_methods`` attribute is also required to be a dictionary with keys corresponding to the regions of the battery but with values which are an instance of
 :class:`pybamm.SpatialMethod`. Finally, ``self.default_var_pts`` is required to be a dictionary with keys which are an instance of :class:`pybamm.SpatialVariable` and values which are integers.
 
 

examples/notebooks/create-model.ipynb

@@ -596,7 +596,7 @@
    ],
    "source": [
     "# mesh and discretise\n",
-    "submesh_types = {\"SEI layer\": pybamm.Uniform1DSubMesh}\n",
+    "submesh_types = {\"SEI layer\": pybamm.one_dimensional_meshes.Uniform1DSubMesh}\n",
     "var_pts = {x: 100}\n",
     "mesh = pybamm.Mesh(geometry, submesh_types, var_pts)\n",
     "                   \n",

examples/notebooks/spatial_methods/finite-volumes.ipynb

@@ -97,12 +97,12 @@
    "outputs": [],
    "source": [
     "submesh_types = {\n",
-    "    \"negative electrode\": pybamm.Uniform1DSubMesh,\n",
-    "    \"separator\": pybamm.Uniform1DSubMesh,\n",
-    "    \"positive electrode\": pybamm.Uniform1DSubMesh,\n",
-    "    \"negative particle\": pybamm.Uniform1DSubMesh,\n",
-    "    \"positive particle\": pybamm.Uniform1DSubMesh,\n",
-    "    \"current collector\": pybamm.SubMesh0D,\n",
+    "    \"negative electrode\": pybamm.one_dimensional_meshes.Uniform1DSubMesh,\n",
+    "    \"separator\": pybamm.one_dimensional_meshes.Uniform1DSubMesh,\n",
+    "    \"positive electrode\": pybamm.one_dimensional_meshes.Uniform1DSubMesh,\n",
+    "    \"negative particle\": pybamm.one_dimensional_meshes.Uniform1DSubMesh,\n",
+    "    \"positive particle\": pybamm.one_dimensional_meshes.Uniform1DSubMesh,\n",
+    "    \"current collector\": pybamm.zero_dimensional_meshes.SubMesh0D,\n",
     "}\n",
     "\n",
     "var = pybamm.standard_spatial_vars\n",

examples/notebooks/unsteady_heat_equation.ipynb

@@ -211,7 +211,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "submesh_types = {\"rod\": pybamm.Uniform1DSubMesh}\n",
+    "submesh_types = {\"rod\": pybamm.one_dimensional_meshes.Uniform1DSubMesh}\n",
     "var_pts = {x: 30}\n",
     "mesh = pybamm.Mesh(geometry, submesh_types, var_pts)\n",
     "spatial_methods = {\"rod\": pybamm.FiniteVolume}\n",

examples/scripts/SPM_compare_particle_grid.py

@@ -32,9 +32,9 @@
 # set mesh
 submesh_types = models[0].default_submesh_types
 particle_meshes = [
-    pybamm.Uniform1DSubMesh,
-    pybamm.Chebyshev1DSubMesh,
-    pybamm.GetExponential1DSubMesh(side="right"),
+    pybamm.one_dimensional_meshes.Uniform1DSubMesh,
+    pybamm.one_dimensional_meshes.Chebyshev1DSubMesh,
+    pybamm.one_dimensional_meshes.GetExponential1DSubMesh(side="right"),
 ]
 meshes = [None] * len(models)
 # discretise models

examples/scripts/create-model.py

@@ -101,7 +101,7 @@ def Diffusivity(cc):
 param.process_geometry(geometry)
 
 # mesh and discretise
-submesh_types = {"SEI layer": pybamm.Uniform1DSubMesh}
+submesh_types = {"SEI layer": pybamm.one_dimensional_meshes.Uniform1DSubMesh}
 var_pts = {x: 50}
 mesh = pybamm.Mesh(geometry, submesh_types, var_pts)
 

examples/scripts/heat_equation.py

@@ -48,7 +48,7 @@
 param.process_geometry(geometry)
 
 # Pick mesh, spatial method, and discretise
-submesh_types = {"rod": pybamm.Uniform1DSubMesh}
+submesh_types = {"rod": pybamm.one_dimensional_meshes.Uniform1DSubMesh}
 var_pts = {x: 30}
 mesh = pybamm.Mesh(geometry, submesh_types, var_pts)
 spatial_methods = {"rod": pybamm.FiniteVolume}

pybamm/__init__.py

@@ -212,20 +212,24 @@ def version(formatted=False):
 #
 from .discretisations.discretisation import Discretisation
 from .meshes.meshes import Mesh
-from .meshes.zero_dimensional_submesh import SubMesh0D
-from .meshes.one_dimensional_submeshes import (
-    SubMesh1D,
-    Uniform1DSubMesh,
-    Chebyshev1DSubMesh,
-    GetExponential1DSubMesh,
-    Exponential1DSubMesh,
-)
-from .meshes.scikit_fem_submeshes import (
-    ScikitSubMesh2D,
-    ScikitUniform2DSubMesh,
-    ScikitChebyshev2DSubMesh,
-    ScikitTopExponential2DSubMesh,
-)
+from .meshes import zero_dimensional_meshes
+from .meshes import one_dimensional_meshes
+from .meshes import two_dimensional_meshes
+
+#from .meshes.zero_dimensional_submesh import SubMesh0D
+#from .meshes.one_dimensional_submeshes import (
+#    SubMesh1D,
+#    Uniform1DSubMesh,
+#    Chebyshev1DSubMesh,
+#    GetExponential1DSubMesh,
+#    Exponential1DSubMesh,
+#)
+#from .meshes.scikit_fem_submeshes import (
+#    ScikitSubMesh2D,
+#    ScikitUniform2DSubMesh,
+#    ScikitChebyshev2DSubMesh,
+#    ScikitTopExponential2DSubMesh,
+#)
 
 #
 # Spatial Methods

pybamm/discretisations/discretisation.py

@@ -374,7 +374,7 @@ def check_tab_conditions(self, symbol, bcs):
             )
 
         # Replace keys with "left" and "right" as appropriate for 1D meshes
-        if isinstance(mesh, pybamm.SubMesh1D):
+        if isinstance(mesh, pybamm.one_dimensional_meshes.SubMesh1D):
             # replace negative and/or positive tab
             for tab in ["negative tab", "positive tab"]:
                 if any(tab in side for side in list(bcs.keys())):
@@ -633,7 +633,7 @@ def _process_symbol(self, symbol):
                 # "left" or "right" as appropriate
                 if symbol.side in ["negative tab", "positive tab"]:
                     mesh = self.mesh[symbol.children[0].domain[0]][0]
-                    if isinstance(mesh, pybamm.SubMesh1D):
+                    if isinstance(mesh, pybamm.one_dimensional_meshes.SubMesh1D):
                         symbol.side = mesh.tabs[symbol.side]
                 return child_spatial_method.boundary_value_or_flux(symbol, disc_child)
 

pybamm/meshes/meshes.py

@@ -32,7 +32,7 @@ def __init__(self, geometry, submesh_types, var_pts):
         submesh_pts = {}
         for domain in geometry:
             # Zero dimensional submesh case (only one point)
-            if submesh_types[domain] == pybamm.SubMesh0D:
+            if submesh_types[domain] == pybamm.zero_dimensional_meshes.SubMesh0D:
                 submesh_pts[domain] = 1
             # other cases
             else:
@@ -97,7 +97,7 @@ def __init__(self, geometry, submesh_types, var_pts):
         for domain in geometry:
             if (
                 domain == "current collector"
-                and submesh_types[domain] != pybamm.SubMesh0D
+                and submesh_types[domain] != pybamm.zero_dimensional_meshes.SubMesh0D
             ):
                 self[domain] = [
                     submesh_types[domain](
@@ -160,7 +160,9 @@ def combine_submeshes(self, *submeshnames):
                 + [self[submeshname][i].edges[1:] for submeshname in submeshnames[1:]]
             )
             coord_sys = self[submeshnames[0]][i].coord_sys
-            submeshes[i] = pybamm.SubMesh1D(combined_submesh_edges, coord_sys)
+            submeshes[i] = pybamm.one_dimensional_meshes.SubMesh1D(
+                combined_submesh_edges, coord_sys
+            )
         return submeshes
 
     def add_ghost_meshes(self):
@@ -174,7 +176,11 @@ def add_ghost_meshes(self):
             (domain, submesh_list)
             for domain, submesh_list in self.items()
             if not isinstance(
-                submesh_list[0], (pybamm.SubMesh0D, pybamm.ScikitSubMesh2D)
+                submesh_list[0],
+                (
+                    pybamm.zero_dimensional_meshes.SubMesh0D,
+                    pybamm.two_dimensional_meshes.ScikitSubMesh2D,
+                ),
             )
         ]
         for domain, submesh_list in submeshes:
@@ -186,13 +192,17 @@ def add_ghost_meshes(self):
 
                 # left ghost cell: two edges, one node, to the left of existing submesh
                 lgs_edges = np.array([2 * edges[0] - edges[1], edges[0]])
-                self[domain + "_left ghost cell"][i] = pybamm.SubMesh1D(
+                self[domain + "_left ghost cell"][
+                    i
+                ] = pybamm.one_dimensional_meshes.SubMesh1D(
                     lgs_edges, submesh.coord_sys
                 )
 
                 # right ghost cell: two edges, one node, to the right of
                 # existing submesh
                 rgs_edges = np.array([edges[-1], 2 * edges[-1] - edges[-2]])
-                self[domain + "_right ghost cell"][i] = pybamm.SubMesh1D(
+                self[domain + "_right ghost cell"][
+                    i
+                ] = pybamm.one_dimensional_meshes.SubMesh1D(
                     rgs_edges, submesh.coord_sys
                 )

pybamm/meshes/one_dimensional_meshes/__init__.py

@@ -0,0 +1,6 @@
+from .base_submesh import SubMesh1D
+
+from .chebyshev_submesh import Chebyshev1DSubMesh
+from .exponential_submesh import GetExponential1DSubMesh, Exponential1DSubMesh
+from .uniform_submesh import Uniform1DSubMesh
+from .user_supplied_submesh import GetUserSupplied1DSubMesh, UserSupplied1DSubMesh

pybamm/meshes/one_dimensional_submeshes/base_one_dimensional_submesh.py → pybamm/meshes/one_dimensional_meshes/base_submesh.py

@@ -30,7 +30,15 @@ def near(x, point, tol=3e-16):
                 return abs(x - point) < tol
 
             for tab in ["negative", "positive"]:
-                if near(tabs[tab]["z_centre"], 0):
+                tab_location = tabs[tab]["z_centre"]
+                if near(tab_location, 0):
                     self.tabs[tab + " tab"] = "left"
-                elif near(tabs[tab]["z_centre"], l_z):
+                elif near(tab_location, l_z):
                     self.tabs[tab + " tab"] = "right"
+                else:
+                    raise pybamm.GeometryError(
+                        """{} tab located at {}, but must be at either 0 or {}
+                        (in dimensionless coordinates).""".format(
+                            tab, tab_location, l_z
+                        )
+                    )

pybamm/meshes/one_dimensional_submeshes/chebyshev_submesh.py → pybamm/meshes/one_dimensional_meshes/chebyshev_submesh.py

@@ -2,11 +2,12 @@
 # Chebyshev one-dimensional submesh
 #
 import pybamm
+from .base_submesh import SubMesh1D
 
 import numpy as np
 
 
-class Chebyshev1DSubMesh(pybamm.SubMesh1D):
+class Chebyshev1DSubMesh(SubMesh1D):
     """
     A class to generate a submesh on a 1D domain using Chebyshev nodes on the
     interval (a, b), given by

pybamm/meshes/one_dimensional_submeshes/exponential_submesh.py → pybamm/meshes/one_dimensional_meshes/exponential_submesh.py

@@ -2,6 +2,7 @@
 # Exponential formula for one-dimensional submesh
 #
 import pybamm
+from .base_submesh import SubMesh1D
 
 import numpy as np
 
@@ -36,7 +37,7 @@ def __call__(self, lims, npts, tabs=None):
         return Exponential1DSubMesh(lims, npts, tabs, self.side, self.stretch)
 
 
-class Exponential1DSubMesh(pybamm.SubMesh1D):
+class Exponential1DSubMesh(SubMesh1D):
     """
     A class to generate a submesh on a 1D domain in which the points are clustered
     close to one or both of boundaries using an exponential formula on the interval

pybamm/meshes/one_dimensional_submeshes/uniform_submesh.py → pybamm/meshes/one_dimensional_meshes/uniform_submesh.py

@@ -2,11 +2,12 @@
 # Uniform one-dimensional submesh
 #
 import pybamm
+from .base_submesh import SubMesh1D
 
 import numpy as np
 
 
-class Uniform1DSubMesh(pybamm.SubMesh1D):
+class Uniform1DSubMesh(SubMesh1D):
     """
     A class to generate a uniform submesh on a 1D domain
 

pybamm/meshes/one_dimensional_submeshes/user_supplied_submesh.py → pybamm/meshes/one_dimensional_meshes/user_supplied_submesh.py

@@ -2,6 +2,7 @@
 # User supplied one-dimensional submesh
 #
 import pybamm
+from .base_submesh import SubMesh1D
 
 
 class GetUserSupplied1DSubMesh:
@@ -21,7 +22,7 @@ def __call__(self, lims, npts, tabs=None):
         return UserSupplied1DSubMesh(lims, npts, tabs, self.nodes)
 
 
-class UserSupplied1DSubMesh(pybamm.SubMesh1D):
+class UserSupplied1DSubMesh(SubMesh1D):
     """
     A class to generate a submesh on a 1D domain from a user supplied array of
     nodes.