Merge branch 'pybamm-team:develop' into casadi-windows-wheels

.all-contributorsrc

@@ -773,6 +773,16 @@
       "contributions": [
         "infra"
       ]
+    },
+    {
+      "login": "XuboGU",
+      "name": "XuboGU",
+      "avatar_url": "https://avatars.githubusercontent.com/u/53944452?v=4",
+      "profile": "https://github.com/XuboGU",
+      "contributions": [
+        "code",
+        "bug"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/periodic_benchmarks.yml

@@ -48,9 +48,9 @@ jobs:
           LD_LIBRARY_PATH: $HOME/.local/lib
 
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: asv_new_results
+          name: asv_periodic_results
           path: results
 
   publish-results:
@@ -73,9 +73,9 @@ jobs:
           token: ${{ secrets.BENCH_PAT }}
 
       - name: Download results artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: asv_new_results
+          name: asv_periodic_results
           path: new_results
 
       - name: Copy new results and push to pybamm-bench repo

.github/workflows/publish_pypi.yml

@@ -57,7 +57,7 @@ jobs:
           CIBW_ARCHS: "AMD64"
 
       - name: Upload Windows wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: windows_wheels
           path: ./wheelhouse/*.whl
@@ -110,7 +110,7 @@ jobs:
           CIBW_SKIP: "pp* *musllinux*"
 
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: wheels
           path: ./wheelhouse/*.whl
@@ -133,7 +133,7 @@ jobs:
         run: pipx run build --sdist
 
       - name: Upload SDist
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: sdist
           path: ./dist/*.tar.gz
@@ -146,7 +146,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download all artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
 
       - name: Move all package files to files/
         run: |

.github/workflows/run_benchmarks_over_history.yml

@@ -42,9 +42,9 @@ jobs:
           asv run -m "GitHubRunner" -s ${{ github.event.inputs.ncommits }} \
           ${{ github.event.inputs.commit_start }}..${{ github.event.inputs.commit_end }}
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: asv_new_results
+          name: asv_over_history_results
           path: results
 
   publish-results:
@@ -65,9 +65,9 @@ jobs:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
       - name: Download results artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: asv_new_results
+          name: asv_over_history_results
           path: new_results
       - name: Copy new results and push to pybamm-bench repo
         env:

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-71-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-72-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -277,6 +277,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/prady0t"><img src="https://avatars.githubusercontent.com/u/99216956?v=4?s=100" width="100px;" alt="Pradyot Ranjan"/><br /><sub><b>Pradyot Ranjan</b></sub></a><br /><a href="#infra-prady0t" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/XuboGU"><img src="https://avatars.githubusercontent.com/u/53944452?v=4?s=100" width="100px;" alt="XuboGU"/><br /><sub><b>XuboGU</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=XuboGU" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3AXuboGU" title="Bug reports">🐛</a></td>
     </tr>
   </tbody>
 </table>

noxfile.py

@@ -60,6 +60,10 @@ def run_coverage(session):
     """Run the coverage tests and generate an XML report."""
     set_environment_variables(PYBAMM_ENV, session=session)
     session.install("coverage", silent=False)
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.install("setuptools", silent=False)
     if sys.platform != "win32":
         if sys.version_info > (3, 12):
             session.install("-e", ".[all,jax]", silent=False)
@@ -79,6 +83,10 @@ def run_coverage(session):
 def run_integration(session):
     """Run the integration tests."""
     set_environment_variables(PYBAMM_ENV, session=session)
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.install("setuptools", silent=False)
     if sys.platform != "win32":
         if sys.version_info > (3, 12):
             session.install("-e", ".[all,jax]", silent=False)
@@ -95,6 +103,10 @@ def run_integration(session):
 @nox.session(name="doctests")
 def run_doctests(session):
     """Run the doctests and generate the output(s) in the docs/build/ directory."""
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.install("setuptools", silent=False)
     session.install("-e", ".[all,docs]", silent=False)
     session.run("python", "run-tests.py", "--doctest")
 
@@ -103,6 +115,10 @@ def run_doctests(session):
 def run_unit(session):
     """Run the unit tests."""
     set_environment_variables(PYBAMM_ENV, session=session)
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.install("setuptools", silent=False)
     if sys.platform != "win32":
         if sys.version_info > (3, 12):
             session.install("-e", ".[all,jax]", silent=False)
@@ -120,6 +136,10 @@ def run_unit(session):
 def run_examples(session):
     """Run the examples tests for Jupyter notebooks."""
     set_environment_variables(PYBAMM_ENV, session=session)
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev]", silent=False)
     notebooks_to_test = session.posargs if session.posargs else []
     session.run("pytest", "--nbmake", *notebooks_to_test, external=True)
@@ -129,6 +149,10 @@ def run_examples(session):
 def run_scripts(session):
     """Run the scripts tests for Python scripts."""
     set_environment_variables(PYBAMM_ENV, session=session)
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.install("setuptools", silent=False)
     session.install("-e", ".[all]", silent=False)
     session.run("python", "run-tests.py", "--scripts")
 
@@ -140,6 +164,10 @@ def set_dev(session):
     session.install("virtualenv", "cmake")
     session.run("virtualenv", os.fsdecode(VENV_DIR), silent=True)
     python = os.fsdecode(VENV_DIR.joinpath("bin/python"))
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.run(python, "-m", "pip", "install", "setuptools", external=True)
     if sys.platform == "linux":
         if sys.version_info > (3, 12):
             session.run(
@@ -188,6 +216,10 @@ def set_dev(session):
 def run_tests(session):
     """Run the unit tests and integration tests sequentially."""
     set_environment_variables(PYBAMM_ENV, session=session)
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.install("setuptools", silent=False)
     if sys.platform != "win32":
         if sys.version_info > (3, 12):
             session.install("-e", ".[all,jax]", silent=False)
@@ -206,6 +238,10 @@ def build_docs(session):
     """Build the documentation and load it in a browser tab, rebuilding on changes."""
     envbindir = session.bin
     session.install("-e", ".[all,docs]", silent=False)
+    # Temporary fix for Python 3.12 CI. TODO: remove after
+    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+    # is fixed
+    session.install("setuptools", silent=False)
     session.chdir("docs")
     # Local development
     if session.interactive:

pybamm/expression_tree/binary_operators.py

@@ -1239,11 +1239,14 @@ def minimum(left, right):
     if out is not None:
         return out
 
-    k = pybamm.settings.min_smoothing
+    mode = pybamm.settings.min_max_mode
+    k = pybamm.settings.min_max_smoothing
     # Return exact approximation if that is the setting or the outcome is a constant
     # (i.e. no need for smoothing)
-    if k == "exact" or (left.is_constant() and right.is_constant()):
+    if mode == "exact" or (left.is_constant() and right.is_constant()):
         out = Minimum(left, right)
+    elif mode == "smooth":
+        out = pybamm.smooth_min(left, right, k)
     else:
         out = pybamm.softminus(left, right, k)
     return pybamm.simplify_if_constant(out)
@@ -1260,11 +1263,14 @@ def maximum(left, right):
     if out is not None:
         return out
 
-    k = pybamm.settings.max_smoothing
+    mode = pybamm.settings.min_max_mode
+    k = pybamm.settings.min_max_smoothing
     # Return exact approximation if that is the setting or the outcome is a constant
     # (i.e. no need for smoothing)
-    if k == "exact" or (left.is_constant() and right.is_constant()):
+    if mode == "exact" or (left.is_constant() and right.is_constant()):
         out = Maximum(left, right)
+    elif mode == "smooth":
+        out = pybamm.smooth_max(left, right, k)
     else:
         out = pybamm.softplus(left, right, k)
     return pybamm.simplify_if_constant(out)
@@ -1311,20 +1317,38 @@ def _heaviside(left, right, equal):
 
 def softminus(left, right, k):
     """
-    Softplus approximation to the minimum function. k is the smoothing parameter,
-    set by `pybamm.settings.min_smoothing`. The recommended value is k=10.
+    Softminus approximation to the minimum function. k is the smoothing parameter,
+    set by `pybamm.settings.min_max_smoothing`. The recommended value is k=10.
     """
     return pybamm.log(pybamm.exp(-k * left) + pybamm.exp(-k * right)) / -k
 
 
 def softplus(left, right, k):
     """
     Softplus approximation to the maximum function. k is the smoothing parameter,
-    set by `pybamm.settings.max_smoothing`. The recommended value is k=10.
+    set by `pybamm.settings.min_max_smoothing`. The recommended value is k=10.
     """
     return pybamm.log(pybamm.exp(k * left) + pybamm.exp(k * right)) / k
 
 
+def smooth_min(left, right, k):
+    """
+    Smooth_min approximation to the minimum function. k is the smoothing parameter,
+    set by `pybamm.settings.min_max_smoothing`. The recommended value is k=100.
+    """
+    sigma = (1.0 / k)**2
+    return ((left + right) - (pybamm.sqrt((left - right)**2 + sigma))) / 2
+
+
+def smooth_max(left, right, k):
+    """
+    Smooth_max approximation to the maximum function. k is the smoothing parameter,
+    set by `pybamm.settings.min_max_smoothing`. The recommended value is k=100.
+    """
+    sigma = (1.0 / k) ** 2
+    return (pybamm.sqrt((left - right)**2 + sigma) + (left + right)) / 2
+
+
 def sigmoid(left, right, k):
     """
     Sigmoidal approximation to the heaviside function. k is the smoothing parameter,

pybamm/input/parameters/lithium_ion/Ai2020.py

@@ -451,7 +451,7 @@ def electrolyte_diffusivity_Ai2020(c_e, T):
         Solid diffusivity
     """
 
-    D_c_e = 10 ** (-8.43 - 54 / (T - 229 - 5e-3 * c_e) - 0.22e-3 * c_e)
+    D_c_e = 10 ** (-4.43 - 54 / (T - 229 - 5e-3 * c_e) - 0.22e-3 * c_e)
 
     return D_c_e
 

pybamm/settings.py

@@ -6,8 +6,8 @@
 class Settings:
     _debug_mode = False
     _simplify = True
-    _min_smoothing = "exact"
-    _max_smoothing = "exact"
+    _min_max_mode = "exact"
+    _min_max_smoothing = 10
     _heaviside_smoothing = "exact"
     _abs_smoothing = "exact"
     max_words_in_line = 4
@@ -43,35 +43,49 @@ def simplify(self, value):
         self._simplify = value
 
     def set_smoothing_parameters(self, k):
-        "Helper function to set all smoothing parameters"
-        self.min_smoothing = k
-        self.max_smoothing = k
+        """Helper function to set all smoothing parameters"""
+        if k == "exact":
+            self.min_max_mode = "exact"
+        else:
+            self.min_max_smoothing = k
+            self.min_max_mode = "soft"
         self.heaviside_smoothing = k
         self.abs_smoothing = k
 
-    def check_k(self, k):
+    @staticmethod
+    def check_k(k):
         if k != "exact" and k <= 0:
             raise ValueError(
-                "smoothing parameter must be 'exact' or a strictly positive number"
+                "Smoothing parameter must be 'exact' or a strictly positive number"
             )
 
     @property
-    def min_smoothing(self):
-        return self._min_smoothing
+    def min_max_mode(self):
+        return self._min_max_mode
 
-    @min_smoothing.setter
-    def min_smoothing(self, k):
-        self.check_k(k)
-        self._min_smoothing = k
+    @min_max_mode.setter
+    def min_max_mode(self, mode):
+        if mode not in ["exact", "soft", "smooth"]:
+            raise ValueError(
+                "Smoothing mode must be 'exact', 'soft', or 'smooth'"
+            )
+        self._min_max_mode = mode
 
     @property
-    def max_smoothing(self):
-        return self._max_smoothing
+    def min_max_smoothing(self):
+        return self._min_max_smoothing
 
-    @max_smoothing.setter
-    def max_smoothing(self, k):
-        self.check_k(k)
-        self._max_smoothing = k
+    @min_max_smoothing.setter
+    def min_max_smoothing(self, k):
+        if self._min_max_mode == "soft" and k <= 0:
+            raise ValueError(
+                "Smoothing parameter must be a strictly positive number"
+            )
+        if self._min_max_mode == "smooth" and k < 1:
+            raise ValueError(
+                "Smoothing parameter must be greater than 1"
+            )
+        self._min_max_smoothing = k
 
     @property
     def heaviside_smoothing(self):