Merge branch 'nbmake' of https://github.com/arjxn-py/PyBaMM into nbmake

.all-contributorsrc

@@ -675,6 +675,16 @@
         "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",

.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'

CHANGELOG.md

@@ -8,17 +8,21 @@
 - Implement the MSMR model ([#3116](https://github.com/pybamm-team/PyBaMM/pull/3116))
 
 ## Bug fixes
-
+- 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

@@ -263,6 +263,7 @@ 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></td>
     </tr>
   </tbody>

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>

pybamm/models/submodels/particle_mechanics/base_mechanics.py

@@ -50,12 +50,13 @@ def _get_mechanical_results(self, variables):
         c_0 = domain_param.c_0
         E0 = domain_param.E
         nu = domain_param.nu
+        L0 = domain_param.L
         sto_init = pybamm.r_average(domain_param.prim.c_init / domain_param.prim.c_max)
         v_change = pybamm.x_average(
             eps_s * domain_param.prim.t_change(sto_rav)
         ) - pybamm.x_average(eps_s * domain_param.prim.t_change(sto_init))
 
-        electrode_thickness_change = self.param.n_electrodes_parallel * v_change
+        electrode_thickness_change = self.param.n_electrodes_parallel * v_change * L0
         # Ai2019 eq [10]
         disp_surf = Omega * R0 / 3 * (c_s_rav - c_0)
         # c0 reference concentration for no deformation

pybamm/simulation.py

@@ -648,6 +648,21 @@ def solve(
                     starting_solution.all_first_states.copy()
                 )
 
+            # set simulation initial_start_time
+            if starting_solution is None:
+                initial_start_time = self.experiment.initial_start_time
+            else:
+                initial_start_time = starting_solution.initial_start_time
+
+            if (
+                initial_start_time is None
+                and self.experiment.initial_start_time is not None
+            ):
+                raise ValueError(
+                    "When using experiments with `start_time`, the starting_solution "
+                    "must have a `start_time` too."
+                )
+
             cycle_offset = len(starting_solution_cycles)
             all_cycle_solutions = starting_solution_cycles
             all_summary_variables = starting_solution_summary_variables
@@ -660,6 +675,49 @@ def solve(
             idx = 0
             num_cycles = len(self.experiment.cycle_lengths)
             feasible = True  # simulation will stop if experiment is infeasible
+
+            # Add initial padding rest if current time is earlier than first start time
+            # This could be the case when using a starting solution
+            if starting_solution is not None:
+                op_conds = self.experiment.operating_conditions_steps[0]
+                if op_conds.start_time is not None:
+                    rest_time = (
+                        op_conds.start_time
+                        - (
+                            initial_start_time
+                            + timedelta(seconds=float(current_solution.t[-1]))
+                        )
+                    ).total_seconds()
+                    if rest_time > pybamm.settings.step_start_offset:
+                        # logs["step operating conditions"] = "Initial rest for padding"
+                        # callbacks.on_step_start(logs)
+
+                        kwargs["inputs"] = {
+                            **user_inputs,
+                            "Ambient temperature [K]": (
+                                op_conds.temperature or self._original_temperature
+                            ),
+                            "start time": current_solution.t[-1],
+                        }
+                        steps = current_solution.cycles[-1].steps
+                        step_solution = current_solution.cycles[-1].steps[-1]
+
+                        step_solution_with_rest = self.run_padding_rest(
+                            kwargs, rest_time, step_solution
+                        )
+                        steps[-1] = step_solution + step_solution_with_rest
+
+                        cycle_solution, _, _ = pybamm.make_cycle_solution(
+                            steps, esoh_solver=esoh_solver, save_this_cycle=True
+                        )
+                        old_cycles = current_solution.cycles.copy()
+                        old_cycles[-1] = cycle_solution
+                        current_solution += step_solution_with_rest
+                        current_solution.cycles = old_cycles
+
+                        # Update _solution
+                        self._solution = current_solution
+
             for cycle_num, cycle_length in enumerate(
                 # tqdm is the progress bar.
                 tqdm.tqdm(
@@ -683,6 +741,8 @@ def solve(
                 save_this_cycle = (
                     # always save cycle 1
                     cycle_num == 1
+                    # always save last cycle
+                    or cycle_num == num_cycles
                     # None: save all cycles
                     or save_at_cycles is None
                     # list: save all cycles in the list
@@ -710,7 +770,7 @@ def solve(
                             (
                                 op_conds.end_time
                                 - (
-                                    self.experiment.initial_start_time
+                                    initial_start_time
                                     + timedelta(seconds=float(start_time))
                                 )
                             ).total_seconds(),
@@ -765,41 +825,25 @@ def solve(
                         rest_time = (
                             op_conds.next_start_time
                             - (
-                                self.experiment.initial_start_time
+                                initial_start_time
                                 + timedelta(seconds=float(step_solution.t[-1]))
                             )
                         ).total_seconds()
                         if rest_time > pybamm.settings.step_start_offset:
-                            start_time = step_solution.t[-1]
-                            # Let me know if you have a better name
-                            op_conds_str = "Rest for padding"
-                            model = self.op_conds_to_built_models[op_conds_str]
-                            solver = self.op_conds_to_built_solvers[op_conds_str]
-
                             logs["step number"] = (step_num, cycle_length)
-                            logs["step operating conditions"] = op_conds_str
+                            logs["step operating conditions"] = "Rest for padding"
                             callbacks.on_step_start(logs)
 
-                            ambient_temp = (
-                                op_conds.temperature or self._original_temperature
-                            )
                             kwargs["inputs"] = {
                                 **user_inputs,
-                                "Ambient temperature [K]": ambient_temp,
-                                "start time": start_time,
+                                "Ambient temperature [K]": (
+                                    op_conds.temperature or self._original_temperature
+                                ),
+                                "start time": step_solution.t[-1],
                             }
-                            # Make sure we take at least 2 timesteps
-                            # The period is hardcoded to 10 minutes, the user can
-                            # always override it by adding a rest step
-                            npts = max(int(round(rest_time / 600)) + 1, 2)
-
-                            step_solution_with_rest = solver.step(
-                                step_solution,
-                                model,
-                                rest_time,
-                                npts=npts,
-                                save=False,
-                                **kwargs,
+
+                            step_solution_with_rest = self.run_padding_rest(
+                                kwargs, rest_time, step_solution
                             )
                             step_solution += step_solution_with_rest
 
@@ -903,8 +947,30 @@ def solve(
 
             callbacks.on_experiment_end(logs)
 
+            # record initial_start_time of the solution
+            self.solution.initial_start_time = initial_start_time
+
         return self.solution
 
+    def run_padding_rest(self, kwargs, rest_time, step_solution):
+        model = self.op_conds_to_built_models["Rest for padding"]
+        solver = self.op_conds_to_built_solvers["Rest for padding"]
+
+        # Make sure we take at least 2 timesteps. The period is hardcoded to 10
+        # minutes,the user can always override it by adding a rest step
+        npts = max(int(round(rest_time / 600)) + 1, 2)
+
+        step_solution_with_rest = solver.step(
+            step_solution,
+            model,
+            rest_time,
+            npts=npts,
+            save=False,
+            **kwargs,
+        )
+
+        return step_solution_with_rest
+
     def step(
         self, dt, solver=None, npts=2, save=True, starting_solution=None, **kwargs
     ):

pybamm/solvers/solution.py

@@ -131,6 +131,9 @@ def __init__(
         # Initialize empty summary variables
         self._summary_variables = None
 
+        # Initialise initial start time
+        self.initial_start_time = None
+
         # Solution now uses CasADi
         pybamm.citations.register("Andersson2019")
 
@@ -434,6 +437,15 @@ def cycles(self, cycles):
     def summary_variables(self):
         return self._summary_variables
 
+    @property
+    def initial_start_time(self):
+        return self._initial_start_time
+
+    @initial_start_time.setter
+    def initial_start_time(self, value):
+        """Updates the reason for termination"""
+        self._initial_start_time = value
+
     def set_summary_variables(self, all_summary_variables):
         summary_variables = {var: [] for var in all_summary_variables[0]}
         for sum_vars in all_summary_variables: