#1129 merge develop

.all-contributorsrc

@@ -387,6 +387,25 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "chuckliu1979",
+      "name": "Chuck Liu",
+      "avatar_url": "https://avatars.githubusercontent.com/u/13491954?v=4",
+      "profile": "https://github.com/chuckliu1979",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "partben",
+      "name": "partben",
+      "avatar_url": "https://avatars.githubusercontent.com/u/88316576?v=4",
+      "profile": "https://github.com/partben",
+      "contributions": [
+        "doc"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/codecov.yml

@@ -0,0 +1,3 @@
+ignore:
+  - pybamm/parameters_cli.py
+  - pybamm/install_odes.py

.github/workflows/test_on_push.yml

@@ -50,6 +50,7 @@ jobs:
     - name: Install Linux system dependencies
       if: matrix.os == 'ubuntu-latest'
       run: |
+        sudo apt-get update
         sudo apt install gfortran gcc libopenblas-dev graphviz
         sudo apt install texlive-full
     

CHANGELOG.md

@@ -1,11 +1,23 @@
-# [Unreleased](https://github.com/pybamm-team/PyBaMM)
+# [v21.08](https://github.com/pybamm-team/PyBaMM/tree/v21.08) - 2021-08-26
+
+This release introduces:
+- the switch to calendar versioning: from now on we will use year.month version number
+- sensitivity analysis of solutions with respect to input parameters
+- several new models, including many-particle and state-of-health models
+- improvement on how CasADI solver's handle events, including a new "fast with events" mode
+- several other new features, optimizations, and bug fixes, summarized below
 
 ## Features
 
--   Addes UDDS and WLTC drive cycles  ([#1601](https://github.com/pybamm-team/PyBaMM/pull/1601))
+-   Added submodels and functionality for particle-size distributions in the DFN model, including an
+example notebook ([#1602](https://github.com/pybamm-team/PyBaMM/pull/1602))
+-   Added UDDS and WLTC drive cycles  ([#1601](https://github.com/pybamm-team/PyBaMM/pull/1601))
+-   Added LG M50 (NMC811 and graphite + SiOx) parameter set from O'Regan 2021 ([#1594](https://github.com/pybamm-team/PyBaMM/pull/1594))
+-   `pybamm.base_solver.solve` function can take a list of input parameters to calculate the sensitivities of the solution with respect to. Alternatively, it can be set  to `True` to calculate the sensitivities for all input parameters ([#1552](https://github.com/pybamm-team/PyBaMM/pull/1552))
 -   Added capability for `quaternary` domains (in addition to `primary`, `secondary` and `tertiary`), increasing the maximum number of domains that a `Symbol` can have to 4. ([#1580](https://github.com/pybamm-team/PyBaMM/pull/1580))
 -   Tabs can now be placed at the bottom of the cell in 1+1D thermal models ([#1581](https://github.com/pybamm-team/PyBaMM/pull/1581)) 
 -   Added temperature dependence on electrode electronic conductivity ([#1570](https://github.com/pybamm-team/PyBaMM/pull/1570))
+-   `pybamm.base_solver.solve` function can take a list of input parameters to calculate the sensitivities of the solution with respect to. Alternatively, it can be set  to `True` to calculate the sensitivities for all input parameters ([#1552](https://github.com/pybamm-team/PyBaMM/pull/1552))
 -   Added a new lithium-ion model `MPM` or Many-Particle Model, with a distribution of particle sizes in each electrode. ([#1529](https://github.com/pybamm-team/PyBaMM/pull/1529))
 -   Added 2 new submodels for lithium transport in a size distribution of electrode particles: Fickian diffusion (`FickianSingleSizeDistribution`) and uniform concentration profile (`FastSingleSizeDistribution`). ([#1529](https://github.com/pybamm-team/PyBaMM/pull/1529))
 -   Added a "particle size" domain to the default lithium-ion geometry, including plotting capabilities (`QuickPlot`) and processing of variables (`ProcessedVariable`). ([#1529](https://github.com/pybamm-team/PyBaMM/pull/1529))
@@ -34,14 +46,18 @@
 
 ## Bug fixes
 
+-   Updated documentation to include some previously missing functions, such as `erf` and `tanh` ([#1628](https://github.com/pybamm-team/PyBaMM/pull/1628))
+-   Fixed reading citation file without closing ([#1620](https://github.com/pybamm-team/PyBaMM/pull/1620))
+-   Porosity variation for SEI and plating models is calculated from the film thickness rather than from a separate ODE ([#1617](https://github.com/pybamm-team/PyBaMM/pull/1617))
 -   Fixed a bug where the order of the indexing for the entries of variables discretised using FEM was incorrect ([#1556](https://github.com/pybamm-team/PyBaMM/pull/1556))
 -   Fix broken module import for spyder when running a script twice ([#1555](https://github.com/pybamm-team/PyBaMM/pull/1555))
 -   Fixed ElectrodeSOH model for multi-dimensional simulations ([#1548](https://github.com/pybamm-team/PyBaMM/pull/1548))
 -   Removed the overly-restrictive check "each variable in the algebraic eqn keys must appear in the eqn" ([#1510](https://github.com/pybamm-team/PyBaMM/pull/1510))
 -   Made parameters importable through pybamm ([#1475](https://github.com/pybamm-team/PyBaMM/pull/1475))
 
 ## Breaking changes
-
+-   Refactored the `particle` submodel module, with the models having no size distribution now found in `particle.no_distribution`, and those with a size distribution in `particle.size_distribution`. Renamed submodels to indicate the transport model (Fickian diffusion, polynomial profile) and if they are "x-averaged". E.g., `FickianManyParticles` and `FickianSingleParticle` are now `no_distribution.FickianDiffusion` and `no_distribution.XAveragedFickianDiffusion` ([#1602](https://github.com/pybamm-team/PyBaMM/pull/1602))
+-   Changed sensitivity API. Removed `ProcessedSymbolicVariable`, all sensitivity now handled within the solvers and `ProcessedVariable` ()  ([#1552](https://github.com/pybamm-team/PyBaMM/pull/1552))
 -   The `Yang2017` parameter set has been removed as the complete parameter set is not publicly available in the literature ([#1577](https://github.com/pybamm-team/PyBaMM/pull/1577))
 -   Changed how options are specified for the "loss of active material" and "particle cracking" submodels. "loss of active material" can now be one of "none", "stress-driven", or "reaction-driven", or a 2-tuple for different options in negative and positive electrode. Similarly "particle cracking" (now called "particle mechanics") can now be "none", "swelling only", "swelling and cracking", or a 2-tuple ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
 -   Changed the variable in the full diffusion model from "Electrolyte concentration" to "Porosity times concentration" ([#1476](https://github.com/pybamm-team/PyBaMM/pull/1476))
@@ -189,7 +205,6 @@ This release adds new operators for more complex models, some basic sensitivity
 (e.g. `standard_parameters_lithium_ion` is now `LithiumIonParameters`) ([#1120](https://github.com/pybamm-team/PyBaMM/pull/1120))
 -   Renamed `quick_plot_vars` to `output_variables` in `Simulation` to be consistent with `QuickPlot`. Passing `quick_plot_vars` to `Simulation.plot()` has been deprecated and `output_variables` should be passed instead ([#1099](https://github.com/pybamm-team/PyBaMM/pull/1099))
 
-
 # [v0.2.3](https://github.com/pybamm-team/PyBaMM/tree/v0.2.3) - 2020-07-01
 
 This release enables the use of [Google Colab](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/main/) for running example notebooks, and adds some small new features and bug fixes.
@@ -338,7 +353,7 @@ This release introduces many new features and optimizations. All models can now
 
 ## Features
 
--   Added LG M50 parameter set ([#854](https://github.com/pybamm-team/PyBaMM/pull/854))
+-   Added LG M50 parameter set from Chen 2020 ([#854](https://github.com/pybamm-team/PyBaMM/pull/854))
 -   Changed rootfinding algorithm to CasADi, scipy.optimize.root still accessible as an option ([#844](https://github.com/pybamm-team/PyBaMM/pull/844))
 -   Added capacitance effects to lithium-ion models ([#842](https://github.com/pybamm-team/PyBaMM/pull/842))
 -   Added NCA parameter set ([#824](https://github.com/pybamm-team/PyBaMM/pull/824))

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: 0.4.0
+version: 21.08
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

CONTRIBUTING.md

@@ -21,7 +21,7 @@ We use [GIT](https://en.wikipedia.org/wiki/Git) and [GitHub](https://en.wikipedi
 1. Create an [issue](https://guides.github.com/features/issues/) where new proposals can be discussed before any coding is done.
 2. Create a [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/) of this repo (ideally on your own [fork](https://help.github.com/articles/fork-a-repo/)), where all changes will be made
 3. Download the source code onto your local system, by [cloning](https://help.github.com/articles/cloning-a-repository/) the repository (or your fork of the repository).
-4. [Install](#installation) PyBaMM with the developer options.
+4. [Install](https://pybamm.readthedocs.io/en/latest/install/install-from-source.html) PyBaMM with the developer options.
 5. [Test](#testing) if your installation worked, using the test script: `$ python run-tests.py --unit`.
 
 You now have everything you need to start making changes!
@@ -44,62 +44,6 @@ You now have everything you need to start making changes!
 Finally, if you really, really, _really_ love developing PyBaMM, have a look at the current [project infrastructure](#infrastructure).
 
 
-## Installation
-
-To install PyBaMM with all developer options follow the steps below:
-
-
-1. Install tox using the commands below:
-```bash
-pip install tox # (Using this, you will need to additionally install tox in your virtual environment as decribed below)
-# or
-pip install pipx # (For installing pipx)
-pipx install tox # (Using this, tox can automatically be accessed in your virtual environment)
-```
-You can also explore and install pipx from their [GitHub repository](https://github.com/pipxproject/pipx)
-
-2. Install sundials using the command below:
-```bash
-# (Skip this step for Windows installation)
-brew install sundials # (MacOS)
-#
-tox -e pybamm-requires # (GNU/Linux)
-```
-3. Installing PyBaMM
-
-This can be achieved by forking the repository and cloning it in your machine.
-
-4. Navigate to the cloned repository and create a virtual environment using the commands below:
-```bash
-tox -e dev # (GNU/Linux and MacOS)
-#
-python -m tox -e windows-dev # (Windows)
-```
-
-This will
-
-a. Create a virtual environment located at `.tox/dev`.
-
-b. Install all the dependencies for PyBaMM, including the ones for documentation and development.
-
-c. Tell Python to use your local pybamm files when you use `import pybamm` anywhere on your system.
-
-5. Finally, activate your environment.
-
-
-```bash
-source .tox/dev/bin/activate # (GNU/Linux and MacOS)
-#
-.tox\windows-dev\Scripts\activate.bat # (Windows)
-```
-6. Inside the virtual environment, type:
-```bash
-pip install tox # (Skip this step if you used pipx above)
-```
-
-
-Full documentation with an installation guide can be found [here](https://pybamm.readthedocs.io/en/latest/install/install-from-source.html)
-
 ## Coding style guidelines
 
 PyBaMM follows the [PEP8 recommendations](https://www.python.org/dev/peps/pep-0008/) for coding style. These are very common guidelines, and community tools have been developed to check how well projects implement them.

FindSUNDIALS.cmake

@@ -27,7 +27,7 @@
 # find the SUNDIALS include directories
 find_path(SUNDIALS_INCLUDE_DIR
   NAMES
-    ida/ida.h
+    idas/idas.h
     sundials/sundials_math.h
     sundials/sundials_types.h
     sunlinsol/sunlinsol_klu.h
@@ -39,7 +39,7 @@ find_path(SUNDIALS_INCLUDE_DIR
   )
 
 set(SUNDIALS_WANT_COMPONENTS
-  sundials_ida
+  sundials_idas
   sundials_sunlinsolklu
   sundials_sunmatrixsparse
   sundials_nvecserial

README.md

@@ -11,7 +11,7 @@
 [![release](https://img.shields.io/github/v/release/pybamm-team/PyBaMM?color=yellow)](https://github.com/pybamm-team/PyBaMM/releases)
 [![black code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-33-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-35-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -175,6 +175,8 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <td align="center"><a href="https://github.com/alibh95"><img src="https://avatars.githubusercontent.com/u/65511923?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Ali Hussain Umar Bhatti</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=alibh95" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=alibh95" title="Tests">⚠️</a></td>
     <td align="center"><a href="https://github.com/molel-gt"><img src="https://avatars.githubusercontent.com/u/81125862?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Leshinka Molel</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=molel-gt" title="Code">💻</a> <a href="#ideas-molel-gt" title="Ideas, Planning, & Feedback">🤔</a></td>
     <td align="center"><a href="https://github.com/tobykirk"><img src="https://avatars.githubusercontent.com/u/42966045?v=4?s=100" width="100px;" alt=""/><br /><sub><b>tobykirk</b></sub></a><br /><a href="#ideas-tobykirk" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=tobykirk" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=tobykirk" title="Tests">⚠️</a></td>
+    <td align="center"><a href="https://github.com/chuckliu1979"><img src="https://avatars.githubusercontent.com/u/13491954?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Chuck Liu</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Achuckliu1979" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=chuckliu1979" title="Code">💻</a></td>
+    <td align="center"><a href="https://github.com/partben"><img src="https://avatars.githubusercontent.com/u/88316576?v=4?s=100" width="100px;" alt=""/><br /><sub><b>partben</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=partben" title="Documentation">📖</a></td>
   </tr>
 </table>
 

docs/conf.py

@@ -26,9 +26,9 @@
 author = "The PyBaMM Team"
 
 # The short X.Y version
-version = "0.4"
+version = "21.08"
 # The full version, including alpha/beta/rc tags
-release = "0.4.0"
+release = "21.08"
 
 
 # -- General configuration ---------------------------------------------------

docs/source/expression_tree/functions.rst

@@ -7,6 +7,16 @@ Functions
 .. autoclass:: pybamm.SpecificFunction
   :members:
 
+.. autoclass:: pybamm.Arcsinh
+  :members:
+
+.. autofunction:: pybamm.arcsinh
+
+.. autoclass:: pybamm.Arctan
+  :members:
+
+.. autofunction:: pybamm.arctan
+
 .. autoclass:: pybamm.Cos
   :members:
 
@@ -17,6 +27,13 @@ Functions
 
 .. autofunction:: pybamm.cosh
 
+.. autoclass:: pybamm.Erf
+  :members:
+
+.. autofunction:: pybamm.erf
+
+.. autofunction:: pybamm.erfc
+
 .. autoclass:: pybamm.Exponential
   :members:
 
@@ -27,10 +44,20 @@ Functions
 
 .. autofunction:: pybamm.log
 
+.. autofunction:: pybamm.log10
+
+.. autoclass:: pybamm.Max
+  :members:
+
 .. autofunction:: pybamm.max
 
+.. autoclass:: pybamm.Min
+  :members:
+
 .. autofunction:: pybamm.min
 
+.. autofunction:: pybamm.sech
+
 .. autoclass:: pybamm.Sin
   :members:
 
@@ -40,3 +67,13 @@ Functions
   :members:
 
 .. autofunction:: pybamm.sinh
+
+.. autoclass:: pybamm.Sqrt
+  :members:
+
+.. autofunction:: pybamm.sqrt
+
+.. autoclass:: pybamm.Tanh
+  :members:
+
+.. autofunction:: pybamm.tanh

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

@@ -5,8 +5,5 @@ Particle
   :maxdepth: 1
 
   base_particle
-  fickian_single_particle
-  fickian_many_particles
-  polynomial_single_particle
-  polynomial_many_particles
+  no_distribution/index
   size_distribution/index

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

@@ -0,0 +1,7 @@
+Fickian Diffusion
+=================
+
+.. autoclass:: pybamm.particle.no_distribution.FickianDiffusion
+    :members:
+
+

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

@@ -0,0 +1,10 @@
+No Particle-Size Distribution
+=============================
+
+.. toctree::
+  :maxdepth: 1
+
+  fickian_diffusion
+  x_averaged_fickian_diffusion
+  polynomial_profile
+  x_averaged_polynomial_profile

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

@@ -0,0 +1,5 @@
+Polynomial Profile
+==================
+
+.. autoclass:: pybamm.particle.no_distribution.PolynomialProfile
+    :members:

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

@@ -0,0 +1,6 @@
+X-averaged Fickian Diffusion
+============================
+
+.. autoclass:: pybamm.particle.no_distribution.XAveragedFickianDiffusion
+    :members:
+

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

@@ -0,0 +1,5 @@
+X-averaged Polynomial Profile
+=============================
+
+.. autoclass:: pybamm.particle.no_distribution.XAveragedPolynomialProfile
+    :members:

docs/source/models/submodels/particle/size_distribution/base_distribution.rst

@@ -1,6 +1,6 @@
 Particle Size Distribution Base Model
 =====================================
 
-.. autoclass:: pybamm.particle.BaseSizeDistribution
+.. autoclass:: pybamm.particle.size_distribution.BaseSizeDistribution
     :members:
 

docs/source/models/submodels/particle/size_distribution/fickian_diffusion.rst

@@ -0,0 +1,7 @@
+Fickian Diffusion
+=================
+
+.. autoclass:: pybamm.particle.size_distribution.FickianDiffusion
+    :members:
+
+