Merge branch 'develop' into issue3051-BPX-diffusivity-activation-ener…

…gies

.all-contributorsrc

@@ -674,6 +674,27 @@
         "ideas",
         "bug"
       ]
+    },
+    {
+      "login": "bobonice",
+      "name": "bobonice",
+      "avatar_url": "https://avatars.githubusercontent.com/u/22030806?v=4",
+      "profile": "https://github.com/bobonice",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "kratman",
+      "name": "Eric G. Kratz",
+      "avatar_url": "https://avatars.githubusercontent.com/u/10170302?v=4",
+      "profile": "https://github.com/kratman",
+      "contributions": [
+        "doc",
+        "infra",
+        "bug"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/lychee_url_checker.yml

@@ -45,6 +45,7 @@ jobs:
             --accept 200,429
             --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py
+            --exclude-path docs/conf.py
             './**/*.rst'
             './**/*.md'
             './**/*.py'

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.0.284"
+    rev: "v0.0.288"
     hooks:
       - id: ruff
         args: [--fix, --ignore=E741, --exclude=__init__.py]
@@ -17,7 +17,7 @@ repos:
         args: ["--fix","--ignore=E501,E402"]
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.15.0"
+    rev: "1.16.0"
     hooks:
        - id: blacken-docs
          additional_dependencies: [black==22.12.0]

CHANGELOG.md

@@ -1,25 +1,29 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
 ## Features
-
 - The parameter "Ambient temperature [K]" can now be given as a function of position `(y,z)` and time `t`. The "edge" and "current collector" heat transfer coefficient parameters can also depend on `(y,z)` ([#3257](https://github.com/pybamm-team/PyBaMM/pull/3257))
 - Spherical and cylindrical shell domains can now be solved with any boundary conditions ([#3237](https://github.com/pybamm-team/PyBaMM/pull/3237))
 - Processed variables now get the spatial variables automatically, allowing plotting of more generic models ([#3234](https://github.com/pybamm-team/PyBaMM/pull/3234))
 - Numpy functions now work with PyBaMM symbols (e.g. `np.exp(pybamm.Symbol("a"))` returns `pybamm.Exp(pybamm.Symbol("a"))`). This means that parameter functions can be specified using numpy functions instead of pybamm functions. Additionally, combining numpy arrays with pybamm objects now works (the numpy array is converted to a pybamm array) ([#3205](https://github.com/pybamm-team/PyBaMM/pull/3205))
+- Implement the MSMR model ([#3116](https://github.com/pybamm-team/PyBaMM/pull/3116))
 
 ## Bug fixes
-
 - Fixed bug causing incorrect activation energies using `create_from_bpx()` ([#3242](https://github.com/pybamm-team/PyBaMM/pull/3242))
+- Fixed a bug that caused incorrect results of “{Domain} electrode thickness change [m]” due to the absence of dimension for the variable `electrode_thickness_change`([#3329](https://github.com/pybamm-team/PyBaMM/pull/3329)).
 - Fixed a bug that occured in `check_ys_are_not_too_large` when trying to reference `y-slice` where the referenced variable was not a `pybamm.StateVector` ([#3313](https://github.com/pybamm-team/PyBaMM/pull/3313)
 - Fixed a bug with `_Heaviside._evaluate_for_shape` which meant some expressions involving heaviside function and subtractions did not work ([#3306](https://github.com/pybamm-team/PyBaMM/pull/3306))
 - The `OneDimensionalX` thermal model has been updated to account for edge/tab cooling and account for the current collector volumetric heat capacity. It now gives the correct behaviour compared with a lumped model with the correct total heat transfer coefficient and surface area for cooling. ([#3042](https://github.com/pybamm-team/PyBaMM/pull/3042))
 - Fixed a bug where the "basic" lithium-ion models gave incorrect results when using nonlinear particle diffusivity ([#3207](https://github.com/pybamm-team/PyBaMM/pull/3207))
 - Particle size distributions now work with SPMe and NewmanTobias models ([#3207](https://github.com/pybamm-team/PyBaMM/pull/3207))
 - Fix to simulate c_rate steps with drive cycles ([#3186](https://github.com/pybamm-team/PyBaMM/pull/3186))
-- Parameters in `Prada2013` have been updated to better match those given in the paper, which is a 2.3 Ah cell, instead of the mix-and-match with the 1.1 Ah cell from Lain2019.
-- Error generated when invalid parameter values are passed. ([#3132](https://github.com/pybamm-team/PyBaMM/pull/3132))
-- Thevenin() model is now constructed with standard variables: `Time [s], Time [min], Time [h]` ([#3143](https://github.com/pybamm-team/PyBaMM/pull/3143))
+- Always save last cycle in experiment, to fix issues with `starting_solution` and `last_state` ([#3177](https://github.com/pybamm-team/PyBaMM/pull/3177))
+- Fix simulations with `starting_solution` to work with `start_time` experiments ([#3177](https://github.com/pybamm-team/PyBaMM/pull/3177))
 - Fix SEI Example Notebook ([#3166](https://github.com/pybamm-team/PyBaMM/pull/3166))
+- Thevenin() model is now constructed with standard variables: `Time [s]`, `Time [min]`, `Time [h]` ([#3143](https://github.com/pybamm-team/PyBaMM/pull/3143))
+- Error generated when invalid parameter values are passed ([#3132](https://github.com/pybamm-team/PyBaMM/pull/3132))
+- Parameters in `Prada2013` have been updated to better match those given in the paper, which is a 2.3 Ah cell, instead of the mix-and-match with the 1.1 Ah cell from Lain2019 ([#3096](https://github.com/pybamm-team/PyBaMM/pull/3096))
+
+
 
 ## Breaking changes
 

README.md

@@ -14,7 +14,7 @@
 [![code style](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-61-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-63-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -54,6 +54,7 @@ The easiest way to use PyBaMM is to run a 1C constant-current discharge with a m
 
 ```python3
 import pybamm
+
 model = pybamm.lithium_ion.DFN()  # Doyle-Fuller-Newman model
 sim = pybamm.Simulation(model)
 sim.solve([0, 3600])  # solve for 1 hour
@@ -64,13 +65,16 @@ or simulate an experiment such as a constant-current discharge followed by a con
 
 ```python3
 import pybamm
+
 experiment = pybamm.Experiment(
     [
-        ("Discharge at C/10 for 10 hours or until 3.3 V",
-        "Rest for 1 hour",
-        "Charge at 1 A until 4.1 V",
-        "Hold at 4.1 V until 50 mA",
-        "Rest for 1 hour")
+        (
+            "Discharge at C/10 for 10 hours or until 3.3 V",
+            "Rest for 1 hour",
+            "Charge at 1 A until 4.1 V",
+            "Hold at 4.1 V until 50 mA",
+            "Rest for 1 hour",
+        )
     ]
     * 3,
 )
@@ -259,6 +263,8 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <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>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/ejfdickinson"><img src="https://avatars.githubusercontent.com/u/116663050?v=4?s=100" width="100px;" alt="ejfdickinson"/><br /><sub><b>ejfdickinson</b></sub></a><br /><a href="#ideas-ejfdickinson" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Aejfdickinson" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/bobonice"><img src="https://avatars.githubusercontent.com/u/22030806?v=4?s=100" width="100px;" alt="bobonice"/><br /><sub><b>bobonice</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Abobonice" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=bobonice" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/kratman"><img src="https://avatars.githubusercontent.com/u/10170302?v=4?s=100" width="100px;" alt="Eric G. Kratz"/><br /><sub><b>Eric G. Kratz</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=kratman" title="Documentation">📖</a> <a href="#infra-kratman" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Akratman" title="Bug reports">🐛</a></td>
     </tr>
   </tbody>
 </table>

benchmarks/README.md

@@ -63,8 +63,8 @@ Note that benchmark functions _must_ start with the prefix `time_`, for instance
 
 ```python3
 def time_solve_SPM_ScipySolver(self):
-        solver = pb.ScipySolver()
-        solver.solve(self.model, [0, 3600])
+    solver = pb.ScipySolver()
+    solver.solve(self.model, [0, 3600])
 ```
 
 In the case where some setup is necessary, but should not be timed, a `setup` function
@@ -76,7 +76,7 @@ class TimeSPM:
         model = pb.lithium_ion.SPM()
         geometry = model.default_geometry
 
-	    # ...
+        # ...
 
         self.model = model
 

docs/conf.py

@@ -303,14 +303,52 @@
 # a conflict with the sphinx-docsearch extension for Algolia search
 
 nbsphinx_requirejs_path = ""
+
+# For notebook downloads (23.5 onwards), we get the version from the environment
+# variable READTHEDOCS_VERSION and set it accordingly.
+
+# If the version is set to "latest", then we are on the develop branch, and we
+# point to the notebook in the develop blob
+# If we are on "stable", we point to the notebook in the relevant release tree
+# for the PyBaMM version
+# On a PR build, we use READTHEDOCS_GIT_COMMIT_HASH which will always point to changes
+# made to a notebook, if any.
+# On local builds, the version is not set, so we use "latest".
+
+if (os.environ.get("READTHEDOCS_VERSION") == "latest") or (
+    os.environ.get("READTHEDOCS_VERSION") is None
+):
+    notebooks_version = "develop"
+    append_to_url = f"blob/{notebooks_version}"
+
+if os.environ.get("READTHEDOCS_VERSION") == "stable":
+    notebooks_version = version
+    append_to_url = f"tree/v{notebooks_version}"
+
+if os.environ.get("READTHEDOCS_VERSION_TYPE") == "external":
+    notebooks_version = os.environ.get("READTHEDOCS_GIT_COMMIT_HASH")
+    append_to_url = f"blob/{notebooks_version}"
+
+github_download_url = f"https://github.com/pybamm-team/PyBaMM/{append_to_url}"
+google_colab_url = github_download_url.replace("github.com", "githubtocolab.com")
+
+html_context.update(
+    {
+        "notebooks_version": notebooks_version,
+        "github_download_url": github_download_url,
+        "google_colab_url": google_colab_url,
+    }
+)
+
 nbsphinx_prolog = r"""
 
 {% set github_docname =
 'github/pybamm-team/pybamm/blob/develop/docs/' +
 env.doc2path(env.docname, base=None) %}
 
-{% set readthedocs_download_url =
-'https://docs.pybamm.org/en/latest/' %}
+{% set notebooks_version = env.config.html_context.notebooks_version %}
+{% set github_download_url = env.config.html_context.github_download_url %}
+{% set google_colab_url = env.config.html_context.google_colab_url %}
 
 {% set doc_path = env.doc2path(env.docname, base=None) %}
 
@@ -323,15 +361,15 @@
         <p>
             An interactive online version of this notebook is available, which can be
             accessed via
-            <a href="https://colab.research.google.com/{{ github_docname | e }}"
+            <a href="{{ google_colab_url | e }}/docs/{{ doc_path | e }}"
             target="_blank">
             <img src="https://colab.research.google.com/assets/colab-badge.svg"
             alt="Open this notebook in Google Colab"/></a>
         </p>
             <hr>
         <p>
             Alternatively, you may
-            <a href="{{ readthedocs_download_url | e }}{{ doc_path | e }}"
+            <a href="{{ github_download_url | e }}/docs/{{ doc_path | e }}"
             target="_blank" download>
             download this notebook</a> and run it offline.
         </p>

docs/source/api/models/lithium_ion/electrode_soh.rst

@@ -8,4 +8,8 @@ Electrode SOH models
 
 .. autofunction:: pybamm.lithium_ion.get_min_max_stoichiometries
 
+.. autofunction:: pybamm.lithium_ion.get_initial_ocps
+
+.. autofunction:: pybamm.lithium_ion.get_min_max_ocps
+
 .. footbibliography::

docs/source/api/models/lithium_ion/index.rst

@@ -9,5 +9,6 @@ Lithium-ion Models
   mpm
   dfn
   newman_tobias
+  msmr
   yang2017
   electrode_soh

docs/source/api/models/lithium_ion/msmr.rst

@@ -0,0 +1,7 @@
+Multi-Species Multi-Reaction (MSMR) Model
+=========================================
+
+.. autoclass:: pybamm.lithium_ion.MSMR
+    :members:
+
+.. footbibliography::

docs/source/api/models/submodels/interface/kinetics/butler_volmer.rst

@@ -1,5 +1,5 @@
-Butler Volumer
-==============
+Butler Volmer
+=============
 
 .. autoclass:: pybamm.kinetics.SymmetricButlerVolmer
     :members:

docs/source/api/models/submodels/interface/kinetics/index.rst

@@ -10,5 +10,6 @@ Kinetics
   marcus
   no_reaction
   tafel
+  msmr_butler_volmer
   total_main_kinetics
   inverse_kinetics/index

docs/source/api/models/submodels/interface/kinetics/msmr_butler_volmer.rst

@@ -0,0 +1,5 @@
+MSMR Butler Volmer
+==================
+
+.. autoclass:: pybamm.kinetics.MSMRButlerVolmer
+    :members:

docs/source/api/models/submodels/interface/open_circuit_potential/index.rst

@@ -6,3 +6,4 @@ Open-circuit potential models
   base_ocp
   current_sigmoid_ocp
   single_ocp
+  msmr_ocp

docs/source/api/models/submodels/interface/open_circuit_potential/msmr_ocp.rst

@@ -0,0 +1,8 @@
+MSMR Open Circuit Potential
+===========================
+
+
+.. autoclass:: pybamm.open_circuit_potential.MSMROpenCircuitPotential
+    :members:
+
+.. footbibliography::

docs/source/api/models/submodels/particle/index.rst

@@ -8,3 +8,4 @@ Particle
   fickian_diffusion
   polynomial_profile
   x_averaged_polynomial_profile
+  msmr_diffusion

docs/source/api/models/submodels/particle/msmr_diffusion.rst

@@ -0,0 +1,7 @@
+MSMR Diffusion
+==============
+
+.. autoclass:: pybamm.particle.MSMRDiffusion
+    :members:
+
+.. footbibliography::

docs/source/examples/index.rst

@@ -59,6 +59,7 @@ The notebooks are organised into subfolders, and can be viewed in the galleries
     notebooks/models/lead-acid.ipynb
     notebooks/models/lithium-plating.ipynb
     notebooks/models/MPM.ipynb
+    notebooks/models/MSMR.ipynb
     notebooks/models/pouch-cell-model.ipynb
     notebooks/models/rate-capability.ipynb
     notebooks/models/SEI-on-cracks.ipynb

docs/source/examples/notebooks/creating_models/6-a-simple-SEI-model.ipynb

@@ -199,6 +199,7 @@
     "V_hat = pybamm.Parameter(\"Partial molar volume [m3.mol-1]\")\n",
     "c_inf = pybamm.Parameter(\"Bulk electrolyte solvent concentration [mol.m-3]\")\n",
     "\n",
+    "\n",
     "def D(cc):\n",
     "    return pybamm.FunctionParameter(\"Diffusivity [m2.s-1]\", {\"Solvent concentration [mol.m-3]\": cc})"
    ]
@@ -485,9 +486,11 @@
     "    {\"SEI layer\": {xi: {\"min\": pybamm.Scalar(0), \"max\": pybamm.Scalar(1)}}}\n",
     ")\n",
     "\n",
+    "\n",
     "def Diffusivity(cc):\n",
     "    return cc * 10**(-12)\n",
     "\n",
+    "\n",
     "# parameter values (not physically based, for example only!)\n",
     "param = pybamm.ParameterValues(\n",
     "    {\n",
@@ -565,6 +568,7 @@
     "L_0_eval = param.evaluate(L_0)\n",
     "xi = np.linspace(0, 1, 100) # dimensionless space\n",
     "\n",
+    "\n",
     "def plot(t):\n",
     "    _, (ax1, ax2) = plt.subplots(1, 2 ,figsize=(10,5))\n",
     "    ax1.plot(solution.t, L_out(solution.t) * 1e6)\n",
@@ -581,6 +585,7 @@
     "    plt.tight_layout()\n",
     "    plt.show()\n",
     "    \n",
+    "\n",
     "import ipywidgets as widgets\n",
     "widgets.interact(plot, t=widgets.FloatSlider(min=0,max=solution.t[-1],step=0.1,value=0));"
    ]