#617 mesh generator class

.gitignore

@@ -7,6 +7,7 @@
 # don't ignore important .txt files
 !requirements*
 !LICENSE.txt
+!CMakeLists.txt
 
 # running files
 *.pyc
@@ -54,6 +55,7 @@ pyproject.toml
 # virtual enviroment
 venv/
 venv3.5/
+PyBaMM-env/
 bin/
 etc/
 lib/
@@ -64,3 +66,5 @@ pyvenv.cfg
 
 # sundials
 sundials
+sundials4
+SuiteSparse

docs/source/meshes/meshes.rst

@@ -3,3 +3,6 @@ Meshes
 
 .. autoclass:: pybamm.Mesh
     :members:
+
+.. autoclass:: pybamm.MeshGenerator
+    :members:

docs/source/meshes/one_dimensional_submeshes.rst

@@ -10,7 +10,7 @@
 .. autoclass:: pybamm.Exponential1DSubMesh
     :members:
 
-.. autoclass:: pybamm.GetExponential1DSubMesh
+.. autoclass:: pybamm.Exponential1DSubMeshGenerator
     :members:
 
 .. autoclass:: pybamm.Chebyshev1DSubMesh
@@ -19,5 +19,5 @@
 .. autoclass:: pybamm.UserSupplied1DSubMesh
     :members:
 
-.. autoclass:: pybamm.GetUserSupplied1DSubMesh
+.. autoclass:: pybamm.UserSupplied1DSubMeshGenerator
     :members:

docs/source/meshes/two_dimensional_submeshes.rst

@@ -16,5 +16,5 @@
 .. autoclass:: pybamm.UserSupplied2DSubMesh
     :members:
 
-.. autoclass:: pybamm.GetUserSupplied2DSubMesh
+.. autoclass:: pybamm.UserSupplied2DSubMeshGenerator
     :members:

examples/scripts/SPM_compare_particle_grid.py

@@ -34,7 +34,7 @@
 particle_meshes = [
     pybamm.Uniform1DSubMesh,
     pybamm.Chebyshev1DSubMesh,
-    pybamm.GetExponential1DSubMesh(side="right"),
+    pybamm.Exponential1DSubMeshGenerator(side="right"),
 ]
 meshes = [None] * len(models)
 # discretise models

pybamm/__init__.py

@@ -208,24 +208,24 @@ def version(formatted=False):
 # Mesh and Discretisation classes
 #
 from .discretisations.discretisation import Discretisation
-from .meshes.meshes import Mesh
+from .meshes.meshes import Mesh, MeshGenerator
 from .meshes.zero_dimensional_submesh import SubMesh0D
 from .meshes.one_dimensional_submeshes import (
     SubMesh1D,
     Uniform1DSubMesh,
     Exponential1DSubMesh,
-    GetExponential1DSubMesh,
+    Exponential1DSubMeshGenerator,
     Chebyshev1DSubMesh,
     UserSupplied1DSubMesh,
-    GetUserSupplied1DSubMesh,
+    UserSupplied1DSubMeshGenerator,
 )
 from .meshes.scikit_fem_submeshes import (
     ScikitSubMesh2D,
     ScikitUniform2DSubMesh,
     ScikitTopExponential2DSubMesh,
     ScikitChebyshev2DSubMesh,
     UserSupplied2DSubMesh,
-    GetUserSupplied2DSubMesh,
+    UserSupplied2DSubMeshGenerator,
 )
 
 #

pybamm/meshes/meshes.py

@@ -196,3 +196,20 @@ def add_ghost_meshes(self):
                 self[domain + "_right ghost cell"][i] = pybamm.SubMesh1D(
                     rgs_edges, submesh.coord_sys
                 )
+
+
+class MeshGenerator:
+    """
+    Base class for mesh generator objects that are used to generate submeshes
+    that require input paramaters.
+    """
+
+    def __init__(self):
+        pass
+
+    def __call__(self):
+        """
+        Each Mesh Generator should implemented a call method which returns
+        an instance of a submesh.
+        """
+        raise NotImplementedError

pybamm/meshes/one_dimensional_submeshes.py

@@ -2,6 +2,7 @@
 # One-dimensional submeshes
 #
 import pybamm
+from .meshes import MeshGenerator
 
 import numpy as np
 
@@ -82,7 +83,8 @@ 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
-    [a,b]. Note: this mesh should be created using :class:`GetExponential1DSubMesh`.
+    [a,b]. Note: this mesh should be created using
+    :class:`Exponential1DSubMeshGenerator`.
 
     If side is "left", the gridpoints are given by
 
@@ -125,7 +127,7 @@ class Exponential1DSubMesh(SubMesh1D):
         A dictionary that contains information about the size and location of
         the tabs
     stretch : float
-        The factor which appears in the exponential.
+        The factor (alpha) which appears in the exponential.
     """
 
     def __init__(self, lims, npts, tabs, side, stretch):
@@ -176,7 +178,7 @@ def __init__(self, lims, npts, tabs, side, stretch):
         super().__init__(edges, coord_sys=coord_sys, tabs=tabs)
 
 
-class GetExponential1DSubMesh:
+class Exponential1DSubMeshGenerator(MeshGenerator):
     """
     A class to generate a submesh on a 1D domain in which the points are clustered
     close to one or both boundaries using an exponential formula on the interval [a,b].
@@ -188,8 +190,8 @@ class GetExponential1DSubMesh:
         or both boundaries. Can be "left", "right" or "symmetric". Defualt is
         "symmetric".
     stretch : float, optional
-        The factor which appears in the exponential, defualt is 1.15 is side is
-        "symmetric" and 2.3 is side is "left" or "right".
+        The factor (alpha) which appears in the exponential, defualt is 1.15 is
+        side is "symmetric" and 2.3 is side is "left" or "right".
 
     """
 
@@ -261,7 +263,7 @@ def __init__(self, lims, npts, tabs=None):
 class UserSupplied1DSubMesh(SubMesh1D):
     """
     A class to generate a submesh on a 1D domain from a user supplied array of
-    Note: this mesh should be created using :class:`GetUserSupplied1DSubMesh`.
+    Note: this mesh should be created using :class:`UserSupplied1DSubMeshGenerator`.
     edges.
 
     Parameters
@@ -319,7 +321,7 @@ def __init__(self, lims, npts, tabs, edges):
         super().__init__(edges, coord_sys=coord_sys, tabs=tabs)
 
 
-class GetUserSupplied1DSubMesh:
+class UserSupplied1DSubMeshGenerator(MeshGenerator):
     """
     A class to generate a submesh on a 1D domain using a user supplied vector of
     edges.

pybamm/meshes/scikit_fem_submeshes.py

@@ -2,6 +2,7 @@
 # scikit-fem meshes for use in PyBaMM
 #
 import pybamm
+from .meshes import MeshGenerator
 
 import skfem
 import numpy as np
@@ -325,7 +326,7 @@ class UserSupplied2DSubMesh(ScikitSubMesh2D):
     """
     A class to generate a tensor product submesh on a 2D domain by using two user
     supplied vectors of edges: one for the y-direction and one for the z-direction.
-    Note: this mesh should be created using :class:`GetUserSupplied2DSubMesh`.
+    Note: this mesh should be created using :class:`UserSupplied2DSubMeshGenerator`.
 
     Parameters
     ----------
@@ -401,7 +402,7 @@ def __init__(self, lims, npts, tabs, y_edges, z_edges):
         super().__init__(edges, coord_sys=coord_sys, tabs=tabs)
 
 
-class GetUserSupplied2DSubMesh:
+class UserSupplied2DSubMeshGenerator(MeshGenerator):
     """
     A class to generate a tensor product submesh on a 2D domain by using two user
     supplied vectors of edges: one for the y-direction and one for the z-direction.

results/2plus1D/user_mesh_spm_1plus1D.py

@@ -37,7 +37,7 @@
 # set mesh using user-supplied edges in z
 z_edges = np.array([0, 0.03, 0.1, 0.3, 0.47, 0.5, 0.73, 0.8, 0.911, 1])
 submesh_types = model.default_submesh_types
-submesh_types["current collector"] = pybamm.GetUserSupplied1DSubMesh(z_edges)
+submesh_types["current collector"] = pybamm.UserSupplied1DSubMeshGenerator(z_edges)
 # Need to make sure var_pts for z is one less than number of edges (variables are
 # evaluated at cell centres)
 npts_z = len(z_edges) - 1

tests/unit/test_meshes/test_meshes.py

@@ -453,6 +453,13 @@ def test_1plus1D_tabs_right_left(self):
         self.assertEqual(mesh["current collector"][0].tabs["positive tab"], "left")
 
 
+class TestMeshGenerator(unittest.TestCase):
+    def test_not_implemented(self):
+        generator = pybamm.MeshGenerator()
+        with self.assertRaises(NotImplementedError):
+            generator()
+
+
 if __name__ == "__main__":
     print("Add -v for more debug output")
     import sys

tests/unit/test_meshes/test_one_dimensional_submesh.py

@@ -28,7 +28,7 @@ def test_exceptions(self):
 class TestExponential1DSubMesh(unittest.TestCase):
     def test_exceptions(self):
         lims = [[0, 1], [0, 1]]
-        mesh = pybamm.GetExponential1DSubMesh()
+        mesh = pybamm.Exponential1DSubMeshGenerator()
         with self.assertRaises(pybamm.GeometryError):
             mesh(lims, None)
 
@@ -44,7 +44,7 @@ def test_symmetric_mesh_creation_no_parameters(self):
         }
 
         submesh_types = {
-            "negative particle": pybamm.GetExponential1DSubMesh(
+            "negative particle": pybamm.Exponential1DSubMeshGenerator(
                 side="symmetric", stretch=1.5
             )
         }
@@ -77,7 +77,7 @@ def test_left_mesh_creation_no_parameters(self):
         }
 
         submesh_types = {
-            "negative particle": pybamm.GetExponential1DSubMesh(side="left")
+            "negative particle": pybamm.Exponential1DSubMeshGenerator(side="left")
         }
         var_pts = {r: 21}
         mesh = pybamm.Mesh(geometry, submesh_types, var_pts)
@@ -108,7 +108,7 @@ def test_right_mesh_creation_no_parameters(self):
         }
 
         submesh_types = {
-            "negative particle": pybamm.GetExponential1DSubMesh(side="right")
+            "negative particle": pybamm.Exponential1DSubMeshGenerator(side="right")
         }
         var_pts = {r: 20}
         mesh = pybamm.Mesh(geometry, submesh_types, var_pts)
@@ -168,7 +168,7 @@ class TestUser1DSubMesh(unittest.TestCase):
     def test_exceptions(self):
         lims = [[0, 1], [0, 1]]
         edges = np.array([0, 0.3, 1])
-        mesh = pybamm.GetUserSupplied1DSubMesh(edges)
+        mesh = pybamm.UserSupplied1DSubMeshGenerator(edges)
         # test too many lims
         with self.assertRaises(pybamm.GeometryError):
             mesh(lims, None)
@@ -205,7 +205,9 @@ def test_mesh_creation_no_parameters(self):
         }
 
         edges = np.array([0, 0.3, 1])
-        submesh_types = {"negative particle": pybamm.GetUserSupplied1DSubMesh(edges)}
+        submesh_types = {
+            "negative particle": pybamm.UserSupplied1DSubMeshGenerator(edges)
+        }
         var_pts = {r: len(edges) - 1}
         mesh = pybamm.Mesh(geometry, submesh_types, var_pts)
 

tests/unit/test_meshes/test_scikit_fem_submesh.py

@@ -370,7 +370,9 @@ def test_mesh_creation(self):
             "negative electrode": pybamm.Uniform1DSubMesh,
             "separator": pybamm.Uniform1DSubMesh,
             "positive electrode": pybamm.Uniform1DSubMesh,
-            "current collector": pybamm.GetUserSupplied2DSubMesh(y_edges, z_edges),
+            "current collector": pybamm.UserSupplied2DSubMeshGenerator(
+                y_edges, z_edges
+            ),
         }
 
         mesh_type = pybamm.Mesh
@@ -404,7 +406,7 @@ def test_exceptions(self):
         lims = {var.y: {"min": 0, "max": 1}}
         y_edges = np.array([0, 0.3, 1])
         z_edges = np.array([0, 0.3, 1])
-        mesh = pybamm.GetUserSupplied2DSubMesh(y_edges, z_edges)
+        mesh = pybamm.UserSupplied2DSubMeshGenerator(y_edges, z_edges)
         # test not enough lims
         with self.assertRaises(pybamm.GeometryError):
             mesh(lims, None)