Merge pull request #1797 from pybamm-team/issue-1748-stress-induced-d…

…iffusion

Issue 1748 stress induced diffusion

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+-   Stress-induced diffusion is now a separate model option instead of being automatically included when using the particle mechanics submodels ([#1797](https://github.com/pybamm-team/PyBaMM/pull/1797))
 -   `Experiment`s with drive cycles can be solved ([#1793](https://github.com/pybamm-team/PyBaMM/pull/1793))
 -   Added surface area to volume ratio as a factor to the SEI equations ([#1790](https://github.com/pybamm-team/PyBaMM/pull/1790))
 -   Half-cell SPM and SPMe have been implemented ([#1731](https://github.com/pybamm-team/PyBaMM/pull/1731))

docs/source/models/submodels/particle/no_distribution/base_fickian.rst

@@ -0,0 +1,5 @@
+Base Fickian Diffusion
+======================
+
+.. autoclass:: pybamm.particle.no_distribution.BaseFickian
+    :members:

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

@@ -4,6 +4,7 @@ No Particle-Size Distribution
 .. toctree::
   :maxdepth: 1
 
+  base_fickian
   fickian_diffusion
   x_averaged_fickian_diffusion
   polynomial_profile

examples/notebooks/models/submodel_cracking_DFN_or_SPM.ipynb

@@ -14,11 +14,9 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "stream",
      "name": "stdout",
+     "output_type": "stream",
      "text": [
-      "\u001b[33mWARNING: You are using pip version 21.0.1; however, version 21.1.2 is available.\n",
-      "You should consider upgrading via the '/Users/vsulzer/Documents/Energy_storage/PyBaMM/.tox/dev/bin/python -m pip install --upgrade pip' command.\u001b[0m\n",
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
     }
@@ -88,16 +86,18 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "display_data",
      "data": {
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       "application/vnd.jupyter.widget-view+json": {
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-       "model_id": "653353cedea84635a916a217d9826e3c"
-      }
+       "version_minor": 0
+      },
+      "text/plain": [
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…"
+      ]
      },
-     "metadata": {}
+     "metadata": {},
+     "output_type": "display_data"
     }
    ],
    "source": [
@@ -125,16 +125,18 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "display_data",
      "data": {
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       "application/vnd.jupyter.widget-view+json": {
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-       "model_id": "a5ed452d11ce494d83f30efec6b6abb4"
-      }
+       "version_minor": 0
+      },
+      "text/plain": [
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=3600.0, step=10.0), Output()), _dom_classes=…"
+      ]
      },
-     "metadata": {}
+     "metadata": {},
+     "output_type": "display_data"
     }
    ],
    "source": [
@@ -190,16 +192,18 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "display_data",
      "data": {
-      "text/plain": "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…",
       "application/vnd.jupyter.widget-view+json": {
+       "model_id": "70f30cf8e80d4a7a9c671844decddcdb",
        "version_major": 2,
-       "version_minor": 0,
-       "model_id": "dbe2842d65ad4cbd9d0efcaf97a50b57"
-      }
+       "version_minor": 0
+      },
+      "text/plain": [
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+      ]
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-     "metadata": {}
+     "metadata": {},
+     "output_type": "display_data"
     }
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@@ -229,16 +233,29 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "stream",
      "name": "stdout",
+     "output_type": "stream",
      "text": [
-      "[1] Weilong Ai, Ludwig Kraft, Johannes Sturm, Andreas Jossen, and Billy Wu. Electrochemical thermal-mechanical modelling of stress inhomogeneity in lithium-ion pouch cells. Journal of The Electrochemical Society, 167(1):013512, 2019. doi:10.1149/2.0122001JES.\n[2] Joel A. E. Andersson, Joris Gillis, Greg Horn, James B. Rawlings, and Moritz Diehl. CasADi – A software framework for nonlinear optimization and optimal control. Mathematical Programming Computation, 11(1):1–36, 2019. doi:10.1007/s12532-018-0139-4.\n[3] Rutooj Deshpande, Mark Verbrugge, Yang-Tse Cheng, John Wang, and Ping Liu. Battery cycle life prediction with coupled chemical degradation and fatigue mechanics. Journal of the Electrochemical Society, 159(10):A1730, 2012. doi:10.1149/2.049210jes.\n[4] Marc Doyle, Thomas F. Fuller, and John Newman. Modeling of galvanostatic charge and discharge of the lithium/polymer/insertion cell. Journal of the Electrochemical society, 140(6):1526–1533, 1993. doi:10.1149/1.2221597.\n[5] Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, and others. Array programming with NumPy. Nature, 585(7825):357–362, 2020. doi:10.1038/s41586-020-2649-2.\n[6] Valentin Sulzer, Scott G. Marquis, Robert Timms, Martin Robinson, and S. Jon Chapman. Python Battery Mathematical Modelling (PyBaMM). ECSarXiv. February, 2020. doi:10.1149/osf.io/67ckj.\n\n"
+      "[1] Weilong Ai, Ludwig Kraft, Johannes Sturm, Andreas Jossen, and Billy Wu. Electrochemical thermal-mechanical modelling of stress inhomogeneity in lithium-ion pouch cells. Journal of The Electrochemical Society, 167(1):013512, 2019. doi:10.1149/2.0122001JES.\n",
+      "[2] Joel A. E. Andersson, Joris Gillis, Greg Horn, James B. Rawlings, and Moritz Diehl. CasADi – A software framework for nonlinear optimization and optimal control. Mathematical Programming Computation, 11(1):1–36, 2019. doi:10.1007/s12532-018-0139-4.\n",
+      "[3] Rutooj Deshpande, Mark Verbrugge, Yang-Tse Cheng, John Wang, and Ping Liu. Battery cycle life prediction with coupled chemical degradation and fatigue mechanics. Journal of the Electrochemical Society, 159(10):A1730, 2012. doi:10.1149/2.049210jes.\n",
+      "[4] Marc Doyle, Thomas F. Fuller, and John Newman. Modeling of galvanostatic charge and discharge of the lithium/polymer/insertion cell. Journal of the Electrochemical society, 140(6):1526–1533, 1993. doi:10.1149/1.2221597.\n",
+      "[5] Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, and others. Array programming with NumPy. Nature, 585(7825):357–362, 2020. doi:10.1038/s41586-020-2649-2.\n",
+      "[6] Valentin Sulzer, Scott G. Marquis, Robert Timms, Martin Robinson, and S. Jon Chapman. Python Battery Mathematical Modelling (PyBaMM). Journal of Open Research Software, 9(1):14, 2021. doi:10.5334/jors.309.\n",
+      "\n"
      ]
     }
    ],
    "source": [
     "pybamm.print_citations()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -257,7 +274,7 @@
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@@ -275,4 +292,4 @@
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+}