Merge branch 'develop' into issue-3115-shell-domains

.all-contributorsrc

@@ -631,7 +631,8 @@
       "profile": "https://www.aboutenergy.io/",
       "contributions": [
         "code",
-        "bug"
+        "bug",
+        "ideas"
       ]
     },
     {

.github/workflows/lychee_url_checker.yml

@@ -41,6 +41,7 @@ jobs:
             --exclude-loopback
             --exclude https://twitter.com/pybamm_
             --exclude "https://doi\.org|www.sciencedirect\.com/*"
+            --exclude https://www.rse.ox.ac.uk
             --accept 200,429
             --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py

.github/workflows/need_reply_remove.yml

@@ -11,7 +11,7 @@ jobs:
     if: |
       github.event.comment.author_association != 'OWNER' &&
       github.event.comment.author_association != 'COLLABORATOR' &&
-      github.repository-owner == 'pybamm-team'
+      github.repository_owner == 'pybamm-team'
     steps:
       - name: Remove needs-reply label
         uses: octokit/[email protected]

.github/workflows/needs_reply.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    if: github.repository-owner == 'pybamm-team'
+    if: github.repository_owner == 'pybamm-team'
     steps:
       - name: Close old issues that need reply
         uses: dwieeb/needs-reply@v2

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.0.281"
+    rev: "v0.0.282"
     hooks:
       - id: ruff
         args: [--fix, --ignore=E741, --exclude=__init__.py]

.readthedocs.yaml

@@ -12,7 +12,6 @@ sphinx:
   fail_on_warning: false
 
 formats:
-  - pdf
   - epub
   - htmlzip
 

README.md

@@ -254,7 +254,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/chenzhao-py"><img src="https://avatars.githubusercontent.com/u/75906533?v=4?s=100" width="100px;" alt="CHEN ZHAO"/><br /><sub><b>CHEN ZHAO</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Achenzhao-py" title="Bug reports">🐛</a></td>
     </tr>
     <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://www.aboutenergy.io/"><img src="https://avatars.githubusercontent.com/u/91731499?v=4?s=100" width="100px;" alt="darryl-ad"/><br /><sub><b>darryl-ad</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=darryl-ad" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Adarryl-ad" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://www.aboutenergy.io/"><img src="https://avatars.githubusercontent.com/u/91731499?v=4?s=100" width="100px;" alt="darryl-ad"/><br /><sub><b>darryl-ad</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=darryl-ad" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Adarryl-ad" title="Bug reports">🐛</a> <a href="#ideas-darryl-ad" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/julian-evers"><img src="https://avatars.githubusercontent.com/u/133691040?v=4?s=100" width="100px;" alt="julian-evers"/><br /><sub><b>julian-evers</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=julian-evers" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://batterycontrolgroup.engin.umich.edu/"><img src="https://avatars.githubusercontent.com/u/633873?v=4?s=100" width="100px;" alt="Jason Siegel"/><br /><sub><b>Jason Siegel</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=js1tr3" title="Code">💻</a> <a href="#ideas-js1tr3" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/tommaull"><img src="https://avatars.githubusercontent.com/u/101814207?v=4?s=100" width="100px;" alt="Tom Maull"/><br /><sub><b>Tom Maull</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=tommaull" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=tommaull" title="Tests">⚠️</a></td>

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

@@ -320,7 +320,7 @@
    "outputs": [],
    "source": [
     "comsol_model = pybamm.BaseModel()\n",
-    "comsol_model.geometry = pybamm.battery_geometry(options={\"dimensionality\": 1})\n",
+    "comsol_model._geometry = pybamm.battery_geometry(options={\"dimensionality\": 1})\n",
     "comsol_model.variables = {\n",
     "    \"Voltage [V]\": comsol_voltage,\n",
     "    \"Negative current collector potential [V]\": comsol_phi_s_cn,\n",

docs/source/examples/notebooks/models/thermal-models.ipynb

@@ -519,7 +519,7 @@
   ],
   "metadata": {
     "kernelspec": {
-      "display_name": "Python 3 (ipykernel)",
+      "display_name": "dev",
       "language": "python",
       "name": "python3"
     },
@@ -533,7 +533,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.0"
+      "version": "3.9.16"
     },
     "toc": {
       "base_numbering": 1,
@@ -547,6 +547,11 @@
       "toc_position": {},
       "toc_section_display": true,
       "toc_window_display": true
+    },
+    "vscode": {
+      "interpreter": {
+        "hash": "bca2b99bfac80e18288b793d52fa0653ab9b5fe5d22e7b211c44eb982a41c00c"
+      }
     }
   },
   "nbformat": 4,

examples/scripts/compare_comsol/compare_comsol_DFN.py

@@ -102,7 +102,7 @@ def get_interp_fun(variable_name, domain):
 
 # Create comsol model with dictionary of Matrix variables
 comsol_model = pybamm.lithium_ion.BaseModel()
-comsol_model.geometry = pybamm_model.default_geometry
+comsol_model._geometry = pybamm_model.default_geometry
 comsol_model.variables = {
     "Negative particle surface concentration [mol.m-3]": comsol_c_n_surf,
     "Electrolyte concentration [mol.m-3]": comsol_c_e,

examples/scripts/thermal_lithium_ion.py

@@ -3,58 +3,35 @@
 #
 
 import pybamm
-import numpy as np
 
-# load model
 pybamm.set_logging_level("INFO")
 
-options = {"thermal": "x-full"}
-full_thermal_model = pybamm.lithium_ion.SPMe(options)
-
-options = {"thermal": "x-lumped"}
-lumped_thermal_model = pybamm.lithium_ion.SPMe(options)
-
-models = [full_thermal_model, lumped_thermal_model]
-
-# load parameter values and process models and geometry
-param = models[0].default_parameter_values
+# load models
+models = [
+    pybamm.lithium_ion.SPMe({"thermal": "x-full"}),
+    pybamm.lithium_ion.SPMe({"thermal": "x-lumped"}),
+]
 
-# for x-full, cooling is only implemented on the surfaces
-# so set other forms of cooling to zero for comparison.
-param.update(
+# load parameter values and update cooling coefficients
+parameter_values = pybamm.ParameterValues("Marquis2019")
+parameter_values.update(
     {
-        "Negative current collector"
-        + " surface heat transfer coefficient [W.m-2.K-1]": 5,
-        "Positive current collector"
-        + " surface heat transfer coefficient [W.m-2.K-1]": 5,
-        "Negative tab heat transfer coefficient [W.m-2.K-1]": 0,
-        "Positive tab heat transfer coefficient [W.m-2.K-1]": 0,
-        "Edge heat transfer coefficient [W.m-2.K-1]": 0,
+        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]"
+        "": 5,
+        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]"
+        "": 5,
+        "Negative tab heat transfer coefficient [W.m-2.K-1]": 10,
+        "Positive tab heat transfer coefficient [W.m-2.K-1]": 10,
+        "Edge heat transfer coefficient [W.m-2.K-1]": 5,
     }
 )
 
+# create and solve simulations
+sols = []
 for model in models:
-    param.process_model(model)
-
-# set mesh
-var_pts = {"x_n": 10, "x_s": 10, "x_p": 10, "r_n": 10, "r_p": 10}
-
-# discretise models
-for model in models:
-    # create geometry
-    geometry = model.default_geometry
-    param.process_geometry(geometry)
-    mesh = pybamm.Mesh(geometry, models[-1].default_submesh_types, var_pts)
-    disc = pybamm.Discretisation(mesh, model.default_spatial_methods)
-    disc.process_model(model)
-
-# solve model
-solutions = [None] * len(models)
-t_eval = np.linspace(0, 3600, 100)
-for i, model in enumerate(models):
-    solver = pybamm.ScipySolver(atol=1e-8, rtol=1e-8)
-    solution = solver.solve(model, t_eval)
-    solutions[i] = solution
+    sim = pybamm.Simulation(model, parameter_values=parameter_values)
+    sol = sim.solve([0, 3600])
+    sols.append(sol)
 
 # plot
 output_variables = [
@@ -63,5 +40,4 @@
     "Cell temperature [K]",
 ]
 labels = ["Full thermal model", "Lumped thermal model"]
-plot = pybamm.QuickPlot(solutions, output_variables, labels)
-plot.dynamic_plot()
+pybamm.dynamic_plot(sols, output_variables, labels=labels)

pybamm/discretisations/discretisation.py

@@ -243,7 +243,7 @@ def process_model(
 
         # Save geometry
         pybamm.logger.verbose("Save geometry for {}".format(model.name))
-        model_disc.geometry = getattr(self.mesh, "_geometry", None)
+        model_disc._geometry = getattr(self.mesh, "_geometry", None)
 
         # Check that resulting model makes sense
         if check_model:

pybamm/models/base_model.py

@@ -317,10 +317,6 @@ def length_scales(self, values):
     def geometry(self):
         return self._geometry
 
-    @geometry.setter
-    def geometry(self, geometry):
-        self._geometry = geometry
-
     @property
     def default_var_pts(self):
         return {}

pybamm/models/full_battery_models/base_battery_model.py

@@ -26,8 +26,8 @@ class BatteryModelOptions(pybamm.FuzzyDict):
                 "true" or "false". "false" is the default, since calculating discharge
                 energy can be computationally expensive for simple models like SPM.
             * "cell geometry" : str
-                Sets the geometry of the cell. Can be "pouch" (default) or
-                "arbitrary". The arbitrary geometry option solves a 1D electrochemical
+                Sets the geometry of the cell. Can be "arbitrary" (default) or
+                "pouch". The arbitrary geometry option solves a 1D electrochemical
                 model with prescribed cell volume and cross-sectional area, and
                 (if thermal effects are included) solves a lumped thermal model
                 with prescribed surface area for cooling.
@@ -283,9 +283,9 @@ def __init__(self, extra_options):
         default_options = {
             name: options[0] for name, options in self.possible_options.items()
         }
+        extra_options = extra_options or {}
 
         # Change the default for cell geometry based on which thermal option is provided
-        extra_options = extra_options or {}
         # return "none" if option not given
         thermal_option = extra_options.get("thermal", "none")
         if thermal_option in ["none", "isothermal", "lumped"]:

pybamm/models/submodels/thermal/base_thermal.py

@@ -175,6 +175,8 @@ def _get_standard_coupled_variables(self, variables):
                 "Total heating [W.m-3]": Q,
                 "X-averaged total heating [W.m-3]": Q_av,
                 "Volume-averaged total heating [W.m-3]": Q_vol_av,
+                "Negative current collector Ohmic heating [W.m-3]": Q_ohm_s_cn,
+                "Positive current collector Ohmic heating [W.m-3]": Q_ohm_s_cp,
             }
         )
         return variables

pybamm/models/submodels/thermal/lumped.py

@@ -54,7 +54,6 @@ def set_rhs(self, variables):
         T_amb = variables["Ambient temperature [K]"]
 
         # Account for surface area to volume ratio in cooling coefficient
-        # The factor 1/delta^2 comes from the choice of non-dimensionalisation.
         if self.options["cell geometry"] == "pouch":
             cell_volume = self.param.L * self.param.L_y * self.param.L_z
 

pybamm/models/submodels/thermal/pouch_cell/pouch_cell_2D_current_collectors.py

@@ -57,8 +57,7 @@ def set_rhs(self, variables):
         T_amb = variables["Ambient temperature [K]"]
 
         # Account for surface area to volume ratio of pouch cell in cooling
-        # coefficient. Note: the factor 1/delta^2 comes from the choice of
-        # non-dimensionalisation
+        # coefficient.
         yz_surface_area = self.param.L_y * self.param.L_z
         cell_volume = self.param.L * self.param.L_y * self.param.L_z
         yz_surface_cooling_coefficient = (