Issue 1029 reformat geometry

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+-   Reformatted `Geometry` and `Mesh` classes ([#1032](https://github.com/pybamm-team/PyBaMM/pull/1032))
 -   Added arbitrary geometry to the lumped thermal model ([#718](https://github.com/pybamm-team/PyBaMM/issues/718))
 -   Allowed `ProcessedVariable` to handle cases where `len(solution.t)=1` ([#1020](https://github.com/pybamm-team/PyBaMM/pull/1020))
 -   Added `BackwardIndefiniteIntegral` symbol ([#1014](https://github.com/pybamm-team/PyBaMM/pull/1014))
@@ -45,6 +46,7 @@
 
 ## Breaking changes
 
+-   Geometry should no longer be given keys 'primary' or 'secondary' ([#1032](https://github.com/pybamm-team/PyBaMM/pull/1032))
 -   Calls to `ProcessedVariable` objects are now made using dimensional time and space ([#1028](https://github.com/pybamm-team/PyBaMM/pull/1028))
 -   For variables discretised using finite elements the result returned by calling `ProcessedVariable` is now transposed ([#1020](https://github.com/pybamm-team/PyBaMM/pull/1020))
 -   Renamed "surface area density" to "surface area to volume ratio" ([#975](https://github.com/pybamm-team/PyBaMM/pull/975))

docs/source/geometry/battery_geometry.rst

@@ -0,0 +1,4 @@
+Battery Geometry
+================
+
+.. autofunction:: pybamm.battery_geometry

docs/source/geometry/geometry.rst

@@ -3,27 +3,3 @@ Geometry
 
 .. autoclass:: pybamm.Geometry
     :members:
-
-.. autoclass:: pybamm.Geometry1DMacro
-    :members:
-
-.. autoclass:: pybamm.Geometry3DMacro
-    :members:
-
-.. autoclass:: pybamm.Geometry1DMicro
-    :members:
-
-.. autoclass:: pybamm.Geometry1p1DMicro
-    :members:
-
-.. autoclass:: pybamm.Geometryxp1DMacro
-    :members:
-
-.. autoclass:: pybamm.Geometryxp0p1DMicro
-    :members:
-
-.. autoclass:: pybamm.Geometryxp1p1DMicro
-    :members:
-
-.. autoclass:: pybamm.Geometry2DCurrentCollector
-    :members:

docs/source/geometry/index.rst

@@ -4,4 +4,5 @@ Geometry
 .. toctree::
 
   geometry
+  battery_geometry
 

docs/tutorials/add-model.rst

@@ -130,7 +130,7 @@ 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
+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 a dictionary of the right format (see :meth:`pybamm.battery_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
 :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/Creating Models/4-comparing-full-and-reduced-order-models.ipynb

@@ -218,7 +218,7 @@
    "source": [
     "# geometry\n",
     "r = pybamm.SpatialVariable(\"r\", domain=[\"negative particle\"], coord_sys=\"spherical polar\")\n",
-    "geometry = {\"negative particle\": {\"primary\": {r: {\"min\": pybamm.Scalar(0), \"max\": R}}}}\n",
+    "geometry = {\"negative particle\": {r: {\"min\": pybamm.Scalar(0), \"max\": R}}}\n",
     "param.process_geometry(geometry)\n",
     "\n",
     "# models\n",
@@ -279,10 +279,18 @@
    "execution_count": 10,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2020-05-30 11:14:09,214 - [WARNING] processed_variable.get_spatial_scale(497): No scale set for spatial variable r_n. Using default of 1 [m].\n",
+      "2020-05-30 11:14:09,244 - [WARNING] processed_variable.get_spatial_scale(497): No scale set for spatial variable r_n. Using default of 1 [m].\n"
+     ]
+    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a020dc7cd8574e698ef0e06d4392e689",
+       "model_id": "c043c0f27ffc46f88fe69b0cbdf14d46",
        "version_major": 2,
        "version_minor": 0
       },
@@ -312,7 +320,7 @@
     "c_av_reduced = solutions[1][\"Average concentration [mol.m-3]\"]\n",
     "\n",
     "# plot\n",
-    "r = mesh[\"negative particle\"][0].nodes # radial position\n",
+    "r = mesh[\"negative particle\"].nodes # radial position\n",
     "\n",
     "def plot(t):\n",
     "    fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(13, 4))\n",
@@ -382,7 +390,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.7.7"
   }
  },
  "nbformat": 4,

examples/notebooks/Creating Models/5-a-simple-SEI-model.ipynb

@@ -532,11 +532,20 @@
    "cell_type": "code",
    "execution_count": 14,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2020-05-30 11:30:30,931 - [WARNING] processed_variable.get_spatial_scale(497): No scale set for spatial variable x. Using default of 1 [m].\n"
+     ]
+    }
+   ],
    "source": [
     "# define geometry\n",
-    "geometry = pybamm.Geometry()\n",
-    "geometry.add_domain(\"SEI layer\", {\"primary\": {x: {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}}})\n",
+    "geometry = pybamm.Geometry(\n",
+    "    {\"SEI layer\": {x: {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}}}\n",
+    ")\n",
     "\n",
     "def Diffusivity(cc):\n",
     "    return cc * 10**(-5)\n",
@@ -591,7 +600,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8d9c98b030934135908c6ddd5c92699b",
+       "model_id": "03d0d8fd63324d16858941bfcbe513be",
        "version_major": 2,
        "version_minor": 0
       },
@@ -660,7 +669,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.7.7"
   }
  },
  "nbformat": 4,

examples/notebooks/expression_tree/broadcasts.ipynb

@@ -35,9 +35,8 @@
    "source": [
     "var = pybamm.standard_spatial_vars\n",
     "geometry = {\n",
-    "    \"negative electrode\": {\"primary\": {var.x_n: {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}}},\n",
-    "    \"negative particle\": {\"primary\": {var.r_n: {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}}},\n",
-    "\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",
     "}\n",
     "\n",
     "submesh_types = {\n",
@@ -261,7 +260,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.7.7"
   }
  },
  "nbformat": 4,

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

@@ -248,7 +248,7 @@
     "# set up space\n",
     "mesh = simulations[\"1+1D DFN\"].mesh\n",
     "L_z = param.evaluate(pybamm.standard_parameters_lithium_ion.L_z)\n",
-    "pybamm_z = mesh[\"current collector\"][0].nodes\n",
+    "pybamm_z = mesh[\"current collector\"].nodes\n",
     "z_interp = pybamm_z * L_z\n",
     "\n",
     "    \n",