Merge branch 'master' into issue-729-add-ecker-parameters

.gitignore

@@ -5,11 +5,13 @@
 /local/
 *.DS_Store
 *.mat
+*.csv
 
-# don't ignore important .txt files
+# don't ignore important .txt and .csv files
 !requirements*
 !LICENSE.txt
 !CMakeLists.txt
+!input/**/*.csv
 
 # running files
 *.pyc

.travis.yml

@@ -62,6 +62,7 @@ matrix:
           env:
             - PYTHON=3.7.4
             - PYBAMM_UNIT=true
+            - PYBAMM_KLU=true
           if: type != cron
         - python: "3.7"
           addons:
@@ -177,6 +178,8 @@ before_install: |
     brew update;
     # Per the `pyenv homebrew recommendations <https://github.com/yyuu/pyenv/wiki#suggested-build-environment>`_.
     brew install graphviz openssl readline;
+    # Other brew packages
+    brew install gcc cmake openblas suitesparse;
     # See https://docs.travis-ci.com/user/osx-ci-environment/#A-note-on-upgrading-packages.
     brew outdated pyenv || brew upgrade pyenv
     # virtualenv doesn't work without pyenv knowledge. venv in Python 3.3

CHANGELOG.md

@@ -2,9 +2,16 @@
 
 ## Features
 
+-   Added NCA parameter set ([#824](https://github.com/pybamm-team/PyBaMM/pull/824))
+-   Added functionality to `Solution` that automatically gets `t_eval` from the data when simulating drive cycles and performs checks to ensure the output has the required resolution to accurately capture the input current ([#819](https://github.com/pybamm-team/PyBaMM/pull/819))
+-   Added options to export a solution to matlab or csv ([#811](https://github.com/pybamm-team/PyBaMM/pull/811))
+-   Allow porosity to vary in space ([#809](https://github.com/pybamm-team/PyBaMM/pull/809))
+-   Added functionality to solve DAE models with non-smooth current inputs ([#808](https://github.com/pybamm-team/PyBaMM/pull/808))
+-   Added functionality to simulate experiments and testing protocols ([#807](https://github.com/pybamm-team/PyBaMM/pull/807))
 -   Added fuzzy string matching for parameters and variables ([#796](https://github.com/pybamm-team/PyBaMM/pull/796))
 -   Changed ParameterValues to raise an error when a parameter that wasn't previously defined is updated ([#796](https://github.com/pybamm-team/PyBaMM/pull/796))
 -   Added some basic models (BasicSPM and BasicDFN) in order to clearly demonstrate the PyBaMM model structure for battery models ([#795](https://github.com/pybamm-team/PyBaMM/pull/795))
+-   Allow initial conditions in the particle to depend on x ([#786](https://github.com/pybamm-team/PyBaMM/pull/786))
 -   Added the harmonic mean to the Finite Volume method, which is now used when computing fluxes ([#783](https://github.com/pybamm-team/PyBaMM/pull/783))
 -   Refactored `Solution` to make it a dictionary that contains all of the solution variables. This automatically creates `ProcessedVariable` objects when required, so that the solution can be obtained much more easily. ([#781](https://github.com/pybamm-team/PyBaMM/pull/781))
 -   Added notebook to explain broadcasts ([#776](https://github.com/pybamm-team/PyBaMM/pull/776))
@@ -46,6 +53,9 @@
 
 ## Bug fixes
 
+-   Time for solver should now be given in seconds ([#832](https://github.com/pybamm-team/PyBaMM/pull/832))
+-   Fixed a bug where the first line of the data wasn't loaded when parameters are loaded from data ([#819](https://github.com/pybamm-team/PyBaMM/pull/819))
+-   Made `graphviz` an optional dependency ([#810](https://github.com/pybamm-team/PyBaMM/pull/810))
 -   Fixed examples to run with basic pip installation ([#800](https://github.com/pybamm-team/PyBaMM/pull/800))
 -   Added events for CasADi solver when stepping ([#800](https://github.com/pybamm-team/PyBaMM/pull/800))
 -   Improved implementation of broadcasts ([#776](https://github.com/pybamm-team/PyBaMM/pull/776))
@@ -59,10 +69,13 @@
 -   Added missing temperature dependence in electrolyte and interface submodels ([#698](https://github.com/pybamm-team/PyBaMM/pull/698))
 -   Fixed differentiation of functions that have more than one argument ([#687](https://github.com/pybamm-team/PyBaMM/pull/687))
 -   Added warning if `ProcessedVariable` is called outside its interpolation range ([#681](https://github.com/pybamm-team/PyBaMM/pull/681))
+-   Updated installation instructions for Mac OS ([#680](https://github.com/pybamm-team/PyBaMM/pull/680))
 -   Improved the way `ProcessedVariable` objects are created in higher dimensions ([#581](https://github.com/pybamm-team/PyBaMM/pull/581))
 
 ## Breaking changes
 
+-   Model events are now represented as a list of `pybamm.Event` ([#759](https://github.com/pybamm-team/PyBaMM/issues/759)
+-   Removed `ParameterValues.update_model`, whose functionality is now replaced by `InputParameter` ([#801](https://github.com/pybamm-team/PyBaMM/pull/801))
 -   Removed `Outer` and `Kron` nodes as no longer used ([#777](https://github.com/pybamm-team/PyBaMM/pull/777))
 -   Moved `results` to separate repositories ([#761](https://github.com/pybamm-team/PyBaMM/pull/761))
 -   The parameters "Bruggeman coefficient" must now be specified separately as "Bruggeman coefficient (electrolyte)" and "Bruggeman coefficient (electrode)"

INSTALL-LINUX.md → INSTALL-LINUX-MAC.md

@@ -1,6 +1,7 @@
 ## Prerequisites
 
-To use and/or contribute to PyBaMM, you must have Python 3.6 or above installed.
+To use and/or contribute to PyBaMM, you must have Python 3.6 or 3.7 installed (note that 3.8 is not yet supported).
+
 To install Python 3 on Debian-based distribution (Debian, Ubuntu, Linux mint), open a terminal and run
 ```bash
 sudo apt update
@@ -10,6 +11,18 @@ On Fedora or CentOS, you can use DNF or Yum. For example
 ```bash
 sudo dnf install python3
 ```
+On Mac OS distributions, you can use `homebrew`. 
+First [install `brew`](https://docs.python-guide.org/starting/install3/osx/):
+
+```bash
+ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
+```
+
+then follow instructions in link on adding brew to path, and run
+
+```bash
+brew install python3
+```
 
 ## Install PyBaMM
 
@@ -39,38 +52,34 @@ PyBaMM can be installed via pip:
 pip install pybamm
 ```
 
+PyBaMM's dependencies (such as `numpy`, `scipy`, etc) will be installed automatically when you install PyBaMM using `pip`.
 
-PyBaMM has the following python libraries as dependencies: `numpy`, `scipy`, `pandas`,
-`matplotlib`. These will be installed automatically when you install PyBaMM using `pip`,
-following the instructions below. First, make sure you have activated your virtual
-environment as above, and that you have the latest version of pip installed:
+For an introduction to virtual environments, see (https://realpython.com/python-virtual-environments-a-primer/).
+
+### Developer install
 
-Then navigate to the path where you downloaded PyBaMM to (you will already be in the
-correct location if you followed the instructions above), and install both PyBaMM and
-its dependencies by typing:
+If you wish to contribute to PyBaMM, you should get the latest version from the GitHub repository.
+To do so, you must have Git and graphviz installed. For instance run
 
 ```bash
-pip install pybamm
+sudo apt install git graphviz
 ```
-For an introduction to virtual environments, see (https://realpython.com/python-virtual-environments-a-primer/).
 
-### developer install
+on Debian-based distributions, or
 
-If you wish to contribute to PyBaMM, you should get the latest version from the GitHub repository.
-To do so, you must have Git installed.
-For instance run
 ```bash
-sudo apt install git
+brew install git graphviz
 ```
-on Debian-based distributions.
+
+on Mac OS.
 
 To install PyBaMM, the first step is to get the code by cloning this repository
 
 ```bash
 git clone https://github.com/pybamm-team/PyBaMM.git
 cd PyBaMM
 ```
-Then, install PyBaMM as a develop per with [developer](CONTRIBUTING.md), use
+Then, to install PyBaMM as a [developer](CONTRIBUTING.md), type
 
 ```bash
 pip install -e .[dev,docs]
@@ -100,10 +109,10 @@ This can be done using `git`, running
 git clone https://github.com/pybamm-team/PyBaMM.git
 cd PyBaMM
 ```
-Alternatively, you can dowload the source code archive from [the PyBaMM GitHub repo](https://github.com/pybamm-team/PyBaMM.git) and extract it the location of your choice.
+Alternatively, you can download the source code archive from [the PyBaMM GitHub repo](https://github.com/pybamm-team/PyBaMM.git) and extract it to the location of your choice.
 
 Ideally you should have the python package `wget` installed.
-This allows for the automatic download of some of the dependencies has part of the installation process.
+This allows for the automatic download of some of the dependencies that are part of the installation process.
 You can install it using (within your virtual environment)
 ```bash
 pip install wget
@@ -113,7 +122,6 @@ pip install wget
 Users can install [scikits.odes](https://github.com/bmcage/odes) in order to use the
 wrapped SUNDIALS ODE and DAE
 [solvers](https://pybamm.readthedocs.io/en/latest/source/solvers/scikits_solvers.html).
-The Sundials DAE solver is required to solve the DFN battery model in PyBaMM.
 
 Before installing scikits.odes, you need to have installed:
 
@@ -139,15 +147,15 @@ Alternatively, you can specify a directory containing the source code of the Sun
 ```bash
 python setup.py install_odes --sundials-src=<path/to/sundials/source>
 ```
-By default, the sundials are installed in a `sundials` directory located at the root of the PyBaMM package.
+By default, sundials is installed in a `sundials` directory located at the root of the PyBaMM package.
 You can provide another location by using the `--sundials-inst=<path/to/other/location>` option.
 
 If you are installing `scikits.odes` within a virtual environment, the `activate` script will be automatically
 updated to add the sundials installation directory to your `LD_LIBRARY_PATH`.
 This is required in order to use `scikits.odes`.
 As a consequence, after installation you should restart your virtual environment.
 
-If you wish to install the scikits.odes outside of a virtual environment, your `.bashrc` will be modified instead.
+If you wish to install `scikits.odes` outside of a virtual environment, your `.bashrc` will be modified instead.
 After installation you should therefore run
 ```bash
 source ~/.bashrc
@@ -166,7 +174,7 @@ sparse solver.
 PyBaMM currently offers a direct interface to the sparse KLU solver within Sundials.
 
 #### Prerequisites
-The requirements are the same than for the installation of `scikits.odes` (see previous section).
+The requirements are the same as for the installation of `scikits.odes` (see previous section).
 Additionally, the [pybind11 GitHub repository](https://github.com/pybind/pybind11.git) should be located in `PyBaMM/third-party/`.
 First create a directory `third-party` and clone the repository:
 ```bash
@@ -198,14 +206,13 @@ python -c "import pybamm; print(pybamm.have_idaklu())
 ```
 
 ### Install everything
-It is possible to install both `scikits.odes` and KLU solver using the command
+It is possible to install both `scikits.odes` and the KLU solver using the command
 ```bash
 python setup.py install_all
 ```
 Note that options `--sundials-src`, `--sundials-inst` and  `suitesparse-src` are still usable
 here.
 
-You can make sure the install was successful by runing
 Finally, you can check your install by running
 ```bash
 python -c "import pybamm; print(pybamm.have_scikits_odes())

INSTALL-WINDOWS.md

@@ -18,7 +18,7 @@ To download the PyBaMM source code, you first need to install git, which you can
 typing
 
 ```bash 
-$ sudo apt install git-core
+sudo apt install git-core
 ```
 
 For easier integration with WSL, we recommend that you install PyBaMM in your *Windows* 
@@ -31,21 +31,21 @@ $ cd /mnt/c/Users/USER_NAME/Documents
 where USER_NAME is your username. Exact path to Windows documents may vary. Now use git to clone the PyBaMM repository:
 
 ```bash
-$ git clone https://github.com/pybamm-team/PyBaMM.git
+git clone https://github.com/pybamm-team/PyBaMM.git
 ```
 
 This will create a new directly called `PyBaMM`, you can move to this directory in bash
 using the `cd` command:
 
 ```bash 
-$ cd PyBaMM 
+cd PyBaMM 
 ```
 
 If you are unfamiliar with the linux command line, you might find it useful to work through this
 [tutorial](https://tutorials.ubuntu.com/tutorial/command-line-for-beginners) provided by Ubuntu.
 
 Now head over and follow the installation instructions for PyBaMM for linux
-[here](INSTALL-LINUX.md).
+[here](INSTALL-LINUX-MAC.md).
 
 ## Use Visual Studio Code to run PyBaMM 
 

README.md

@@ -35,7 +35,11 @@ For further examples, see the list of repositories that use PyBaMM [here](https:
 
 ### Linux
 
-For instructions on installing PyBaMM on Debian-based distributions, please see [here](INSTALL-LINUX.md)
+For instructions on installing PyBaMM on Debian-based distributions, please see [here](INSTALL-LINUX-MAC.md)
+
+### Mac OS
+
+For instructions on installing PyBaMM on Mac OS distributions, please see [here](INSTALL-LINUX-MAC.md)
 
 ### Windows
 

docs/index.rst

@@ -30,6 +30,7 @@ Contents
     source/meshes/index
     source/spatial_methods/index
     source/solvers/index
+    source/experiments/index
     source/processed_variable
     source/util
     source/simulation

docs/source/experiments/experiment.rst

@@ -0,0 +1,5 @@
+Base Experiment Class
+=====================
+
+.. autoclass:: pybamm.Experiment
+  :members:

docs/source/experiments/index.rst

@@ -0,0 +1,8 @@
+Experiments
+===========
+
+Classes to help set operating conditions for some standard battery modelling experiments
+
+.. toctree::
+
+  experiment

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

@@ -3,7 +3,6 @@ Fickian
 
 .. toctree::
 
-  base_fickian_particle
   fickian_many_particles
   fickian_single_particle
 

docs/source/solvers/solution.rst

@@ -1,5 +1,8 @@
 Solution
 ========
 
+.. autoclass:: pybamm._BaseSolution
+  :members:
+
 .. autoclass:: pybamm.Solution
   :members: