Merge pull request pybamm-team#1631 from pybamm-team/develop

Release 21.08

.all-contributorsrc

@@ -4,6 +4,7 @@
   ],
   "imageSize": 100,
   "commit": false,
+  "badgeTemplate": "[![All Contributors](https://img.shields.io/badge/all_contributors-<%= contributors.length %>-orange.svg)](#-contributors)",
   "contributors": [
     {
       "login": "tinosulzer",
@@ -355,6 +356,56 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "alibh95",
+      "name": "Ali Hussain Umar Bhatti",
+      "avatar_url": "https://avatars.githubusercontent.com/u/65511923?v=4",
+      "profile": "https://github.com/alibh95",
+      "contributions": [
+        "code",
+        "test"
+      ]
+    },
+    {
+      "login": "molel-gt",
+      "name": "Leshinka Molel",
+      "avatar_url": "https://avatars.githubusercontent.com/u/81125862?v=4",
+      "profile": "https://github.com/molel-gt",
+      "contributions": [
+        "code",
+        "ideas"
+      ]
+    },
+    {
+      "login": "tobykirk",
+      "name": "tobykirk",
+      "avatar_url": "https://avatars.githubusercontent.com/u/42966045?v=4",
+      "profile": "https://github.com/tobykirk",
+      "contributions": [
+        "ideas",
+        "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/release_checklist.md

@@ -1,4 +1,5 @@
-- Increment version number in `version`	
-- Increment version number in `docs/conf.py`	
-- Update CHANGELOG.md with a summary of the release	
-- Update (and pin) jax and jaxlib to latest version and fix any bugs that arise	
+- Increment version number in `version`
+- Increment version number in `docs/conf.py`
+- Increment version number in `CITATION.cff`
+- Update CHANGELOG.md with a summary of the release
+- Update (and pin) jax and jaxlib to latest version and fix any bugs that arise

.github/workflows/run_benchmarks_over_history.yml

@@ -60,18 +60,21 @@ jobs:
       - name: Checkout pybamm-bench repo
         uses: actions/checkout@v2
         with:
-          repository: tlestang/pybamm-bench
+          repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
       - name: Download results artifact
         uses: actions/download-artifact@v2
         with:
           name: asv_new_results
           path: new_results
       - name: Copy new results and push to pybamm-bench repo
+        env:
+          PUSH_BENCH_EMAIL: ${{ secrets.PUSH_BENCH_EMAIL }}
+          PUSH_BENCH_NAME: ${{ secrets.PUSH_BENCH_NAME }}
         run: |
           cp -vr new_results/* results
-          git config --global user.email "[email protected]"
-          git config --global user.name "Thibault Lestang"
+          git config --global user.email "$PUSH_BENCH_EMAIL"
+          git config --global user.name "$PUSH_BENCH_NAME"
           git add results
           git commit -am "Add new results"
           git push

.github/workflows/test_on_push.yml

@@ -40,11 +40,13 @@ jobs:
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    
+
     - 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
     
     - name: Install MacOS system dependencies
       if: matrix.os == 'macos-latest'

.github/workflows/update_parameter_sets_doc.yml

@@ -5,8 +5,8 @@ on:
     branches:
     - develop
     paths:
-    - 'pybamm/parameters/parameter_sets.py'
-    - 'pybamm/parameters/CITATIONS.txt'
+    - pybamm/parameters/parameter_sets.py
+    - pybamm/CITATIONS.txt
 
 jobs:
   build:

.gitignore

@@ -44,6 +44,7 @@ out/
 config.py
 matplotlibrc
 *.pickle
+*.sav
 
 # ideas
 ideas/
@@ -103,11 +104,14 @@ KLU_module_deps
 # setup
 setup.log
 
+# test
+test.c
+
 # tox
 .tox/
 
 # julia
 Manifest.toml
 
 # vcpkg
-vcpkg_installed/
+vcpkg_installed/

CHANGELOG.md

@@ -1,3 +1,68 @@
+# [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
+
+-   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))
+-   Added fitted expressions for OCPs for the Chen2020 parameter set ([#1526](https://github.com/pybamm-team/PyBaMM/pull/1497))
+-   Added `initial_soc` argument to `Simualtion.solve` for specifying the initial SOC when solving a model ([#1512](https://github.com/pybamm-team/PyBaMM/pull/1512))
+-   Added `print_name` to some symbols ([#1495](https://github.com/pybamm-team/PyBaMM/pull/1495), [#1497](https://github.com/pybamm-team/PyBaMM/pull/1497))
+-   Added Base Parameters class and SymPy in dependencies ([#1495](https://github.com/pybamm-team/PyBaMM/pull/1495))
+-   Added a new "reaction-driven" model for LAM from Reniers et al (2019) ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
+-   Some features ("loss of active material" and "particle mechanics") can now be specified separately for the negative electrode and positive electrode by passing a 2-tuple ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
+-   `plot` and `plot2D` now take and return a matplotlib Axis to allow for easier customization ([#1472](https://github.com/pybamm-team/PyBaMM/pull/1472))
+-   `ParameterValues.evaluate` can now return arrays to allow function parameters to be easily evaluated ([#1472](https://github.com/pybamm-team/PyBaMM/pull/1472))
+-   Added option to save only specific cycle numbers when simulating an `Experiment` ([#1459](https://github.com/pybamm-team/PyBaMM/pull/1459))
+-   Added capacity-based termination conditions when simulating an `Experiment` ([#1459](https://github.com/pybamm-team/PyBaMM/pull/1459))
+-   Added "summary variables" to track degradation over several cycles ([#1459](https://github.com/pybamm-team/PyBaMM/pull/1459))
+-   Added `ElectrodeSOH` model for calculating capacities and stoichiometric limits ([#1459](https://github.com/pybamm-team/PyBaMM/pull/1459))
+-   Added Batch Study class ([#1455](https://github.com/pybamm-team/PyBaMM/pull/1455))
+-   Added `ConcatenationVariable`, which is automatically created when variables are concatenated ([#1453](https://github.com/pybamm-team/PyBaMM/pull/1453))
+-   Added "fast with events" mode for the CasADi solver, which solves a model and finds events more efficiently than "safe" mode. As of PR #1450 this feature is still being tested and "safe" mode remains the default ([#1450](https://github.com/pybamm-team/PyBaMM/pull/1450))
+
+## Optimizations
+
+-   Models that mostly use x-averaged quantities (SPM and SPMe) now use x-averaged degradation models ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
+-   Improved how the CasADi solver's "safe" mode finds events ([#1450](https://github.com/pybamm-team/PyBaMM/pull/1450))
+-   Perform more automatic simplifications of the expression tree ([#1449](https://github.com/pybamm-team/PyBaMM/pull/1449))
+-   Reduce time taken to hash a sparse `Matrix` object ([#1449](https://github.com/pybamm-team/PyBaMM/pull/1449))
+
+## 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))
+-   Renamed `lithium-ion` folder to `lithium_ion` and `lead-acid` folder to `lead_acid` in parameters ([#1464](https://github.com/pybamm-team/PyBaMM/pull/1464))
+
 # [v0.4.0](https://github.com/pybamm-team/PyBaMM/tree/v0.4.0) - 2021-03-28
 
 This release introduces:
@@ -69,11 +134,11 @@ This release introduces:
 
 # [v0.3.0](https://github.com/pybamm-team/PyBaMM/tree/v0.3.0) - 2020-12-01
 
-This release introduces a new aging model for particle swelling and cracking, a new reduced-order model (TSPMe), and a parameter set for A123 LFP cells. Additionally, there have been several backend optimizations to speed up model creation and solving, and other minor features and bug fixes.
+This release introduces a new aging model for particle mechanics, a new reduced-order model (TSPMe), and a parameter set for A123 LFP cells. Additionally, there have been several backend optimizations to speed up model creation and solving, and other minor features and bug fixes.
 
 ## Features
 
--   Added a submodel for particle swelling and cracking ([#1232](https://github.com/pybamm-team/PyBaMM/pull/1232))
+-   Added a submodel for particle mechanics ([#1232](https://github.com/pybamm-team/PyBaMM/pull/1232))
 -   Added a notebook on how to speed up the solver and handle instabilities ([#1223](https://github.com/pybamm-team/PyBaMM/pull/1223))
 -   Improve string printing of `BinaryOperator`, `Function`, and `Concatenation` objects ([#1223](https://github.com/pybamm-team/PyBaMM/pull/1223))
 -   Added `Solution.integration_time`, which is the time taken just by the integration subroutine, without extra setups ([#1223](https://github.com/pybamm-team/PyBaMM/pull/1223))
@@ -140,7 +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.
@@ -289,7 +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

@@ -0,0 +1,29 @@
+cff-version: 1.1.0
+message: "If you use PyBaMM, please cite it as below."
+authors: 
+- family-names: Sulzer
+  given-names: Valentin
+  orcid: "https://orcid.org/0000-0002-8687-327X"
+- family-names: Marquis
+  given-names: Scott G.
+  orcid: "https://orcid.org/0000-0002-6895-990X"
+- family-names: Timms
+  given-names: Robert
+  orcid: "https://orcid.org/0000-0002-8858-4818"
+- family-names: Robinson
+  given-names: Martin
+  orcid: "https://orcid.org/0000-0002-1572-6782"
+- family-names: Chapman
+  given-names: S. Jon
+  orcid: "https://orcid.org/0000-0003-3347-6024"
+journal: "Journal of Open Research Software"
+date-released: 2021-06-08
+doi: 10.5334/jors.309
+keywords: 
+  - "battery modelling"
+  - "expression tree"
+  - "python"
+  - "symbolic differentiation"
+version: 21.08
+repository-code: "https://github.com/pybamm-team/PyBaMM"
+title: "Python Battery Mathematical Modelling (PyBaMM)"