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‎CHANGELOG.md

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- Add new symbols `VariableDot`, representing the derivative of a variable wrt time,
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and `StateVectorDot`, representing the derivative of a state vector wrt time
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([#858](https://github.com/pybamm-team/PyBaMM/issues/858))
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- Added a helper function for info on function parameters ([#881](https://github.com/pybamm-team/PyBaMM/pull/881))
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- Added additional notebooks showing how to create and compare models ([#877](https://github.com/pybamm-team/PyBaMM/pull/877))
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- Added `Minimum`, `Maximum` and `Sign` operators
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([#876](https://github.com/pybamm-team/PyBaMM/pull/876))
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- Added a search feature to `FuzzyDict` ([#875](https://github.com/pybamm-team/PyBaMM/pull/875))
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- Add ambient temperature as a function of time ([#872](https://github.com/pybamm-team/PyBaMM/pull/872))
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- Added `CasadiAlgebraicSolver` for solving algebraic systems with CasADi ([#868](https://github.com/pybamm-team/PyBaMM/pull/868))
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- Added electrolyte functions from Landesfeind ([#860](https://github.com/pybamm-team/PyBaMM/pull/860))
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- Add new symbols `VariableDot`, representing the derivative of a variable wrt time,
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and `StateVectorDot`, representing the derivative of a state vector wrt time
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([#858](https://github.com/pybamm-team/PyBaMM/issues/858))
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## Bug fixes
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‎INSTALL-WINDOWS-WSL.md

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We recommend the use of Windows Subsystem for Linux (WSL) to install PyBaMM, see the
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instructions below to get PyBaMM working using Windows, WSL and VSCode.
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## Install WSL
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Follow the instructions from Microsoft
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[here](https://docs.microsoft.com/en-us/windows/wsl/install-win10). When given the
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option, choose the Ubuntu 18.04 LTS distribution to install. Don't forget to initialise
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the Ubuntu installation using the instructions given
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[here](https://docs.microsoft.com/en-us/windows/wsl/initialize-distro).
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## Install PyBaMM
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Open a terminal window in your installed Ubuntu distribution by selecting "Ubuntu" from
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the start menu. This should give you a bash prompt in your home directory.
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To download the PyBaMM source code, you first need to install git, which you can do by
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typing
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```bash
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sudo apt install git-core
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```
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For easier integration with WSL, we recommend that you install PyBaMM in your *Windows*
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Documents folder, for example by first navigating to
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```bash
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$ cd /mnt/c/Users/USER_NAME/Documents
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```
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where USER_NAME is your username. Exact path to Windows documents may vary. Now use git to clone the PyBaMM repository:
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```bash
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git clone https://github.com/pybamm-team/PyBaMM.git
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```
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This will create a new directly called `PyBaMM`, you can move to this directory in bash
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using the `cd` command:
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```bash
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cd PyBaMM
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```
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If you are unfamiliar with the linux command line, you might find it useful to work through this
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[tutorial](https://tutorials.ubuntu.com/tutorial/command-line-for-beginners) provided by Ubuntu.
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Now head over and follow the installation instructions for PyBaMM for linux
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[here](INSTALL-LINUX-MAC.md).
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## Use Visual Studio Code to run PyBaMM
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You will probably want to use a native Windows IDE such as Visual Studio Code or the
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full Microsoft Visual Studio IDE. Both of these packages can connect to WSL so that you
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can write python code in a native windows environment, while at the same time using WSL
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to run the code using your installed Ubuntu distribution. The following instructions
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assume that you are using Visual Studio Code.
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First, setup VSCode to run within the `PyBaMM` directory that you created above, using
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the instructions provided [here](https://code.visualstudio.com/docs/remote/wsl).
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Once you have opened the `PyBaMM` folder in vscode, use the `Extensions` panel to
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install the `Python` extension from Microsoft. Note that extensions are either installed
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on the Windows (Local) or on in WSL (WSL:Ubuntu), so even if you have used VSCode
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previously with the Python extension, you probably haven't installed it in WSL. Make
65+
sure to reload after installing the Python extension so that it is available.
66+
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If you have installed PyBaMM into the virtual environment `env` as in the PyBaMM linux
68+
install guide, then VSCode should automatically start using this environment and you
69+
should see something similar to "Python 3.6.8 64-bit ('env': venv)" in the bottom bar.
70+
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To test that vscode can run a PyBaMM script, navigate to the `examples/scripts` folder
72+
and right click on the `create-model.py` script. Select "Run current file in Python
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Interactive Window". This should run the script, which sets up and solves a model of SEI
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thickness using PyBaMM. You should see a plot of SEI thickness versus time pop up in the
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interactive window.
76+
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The Python Interactive Window in VSCode can be used to view plots, but is restricted in
78+
functionality and cannot, for example, launch separate windows to show plot. To setup an
79+
xserver on windows and use this to launch windows for plotting, follow these
80+
instructions:
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1. Install VcXsrv from [here](https://sourceforge.net/projects/vcxsrv/).
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1. Set the display port in the WSL command-line: `echo "export DISPLAY=localhost:0.0" >>
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~/.bashrc`
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1. Install python3-tk in WSL: `sudo apt-get install python3-tk`
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1. Set the matplotlib backend to TKAgg in WSL: `echo "backend : TKAgg" >>
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~/.config/matplotlib/matplotlibrc`
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1. Before running the code, just launch XLaunch (with the default settings) from within
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Windows. Then the code works as usual.

‎INSTALL-WINDOWS.md

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We recommend the use of Windows Subsystem for Linux (WSL) to install PyBaMM, see the
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instructions below to get PyBaMM working using Windows, WSL and VSCode.
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## Prerequisites
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## Install WSL
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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).
54

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Follow the instructions from Microsoft
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[here](https://docs.microsoft.com/en-us/windows/wsl/install-win10). When given the
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option, choose the Ubuntu 18.04 LTS distribution to install. Don't forget to initialise
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the Ubuntu installation using the instructions given
10-
[here](https://docs.microsoft.com/en-us/windows/wsl/initialize-distro).
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To install Python 3 download the installation files from [Python's website](https://www.python.org/downloads/windows/). Make sure
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to tick the box on `Add Python 3.X to PATH`. For more detailed instructions please see the
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[official Python on Windows guide](https://docs.python.org/3.7/using/windows.html).
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## Install PyBaMM
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Open a terminal window in your installed Ubuntu distribution by selecting "Ubuntu" from
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the start menu. This should give you a bash prompt in your home directory.
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### User install
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Launch the Command Prompt and go to the directory where you want to install PyBaMM. You can find a reminder of how to
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navigate the terminal [here](http://www.cs.columbia.edu/~sedwards/classes/2015/1102-fall/Command%20Prompt%20Cheatsheet.pdf).
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To download the PyBaMM source code, you first need to install git, which you can do by
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typing
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We recommend to install PyBaMM within a virtual environment, in order not
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to alter any distribution python files.
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```bash
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sudo apt install git-core
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```
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For easier integration with WSL, we recommend that you install PyBaMM in your *Windows*
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Documents folder, for example by first navigating to
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To create a virtual environment `env` within your current directory type:
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```bash
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$ cd /mnt/c/Users/USER_NAME/Documents
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python -m venv env
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```
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where USER_NAME is your username. Exact path to Windows documents may vary. Now use git to clone the PyBaMM repository:
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You can then "activate" the environment using:
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```bash
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git clone https://github.com/pybamm-team/PyBaMM.git
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env\Scripts\activate.bat
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```
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Now all the calls to pip described below will install PyBaMM and its dependencies into
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the environment `env`. When you are ready to exit the environment and go back to your
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original system, just type:
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This will create a new directly called `PyBaMM`, you can move to this directory in bash
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using the `cd` command:
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```bash
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cd PyBaMM
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```bash
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deactivate
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```
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If you are unfamiliar with the linux command line, you might find it useful to work through this
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[tutorial](https://tutorials.ubuntu.com/tutorial/command-line-for-beginners) provided by Ubuntu.
46-
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Now head over and follow the installation instructions for PyBaMM for linux
48-
[here](INSTALL-LINUX-MAC.md).
49-
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## Use Visual Studio Code to run PyBaMM
51-
52-
You will probably want to use a native Windows IDE such as Visual Studio Code or the
53-
full Microsoft Visual Studio IDE. Both of these packages can connect to WSL so that you
54-
can write python code in a native windows environment, while at the same time using WSL
55-
to run the code using your installed Ubuntu distribution. The following instructions
56-
assume that you are using Visual Studio Code.
57-
58-
First, setup VSCode to run within the `PyBaMM` directory that you created above, using
59-
the instructions provided [here](https://code.visualstudio.com/docs/remote/wsl).
60-
61-
Once you have opened the `PyBaMM` folder in vscode, use the `Extensions` panel to
62-
install the `Python` extension from Microsoft. Note that extensions are either installed
63-
on the Windows (Local) or on in WSL (WSL:Ubuntu), so even if you have used VSCode
64-
previously with the Python extension, you probably haven't installed it in WSL. Make
65-
sure to reload after installing the Python extension so that it is available.
36+
PyBaMM can be installed via pip:
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```bash
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pip install pybamm
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```
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If you have installed PyBaMM into the virtual environment `env` as in the PyBaMM linux
68-
install guide, then VSCode should automatically start using this environment and you
69-
should see something similar to "Python 3.6.8 64-bit ('env': venv)" in the bottom bar.
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PyBaMM's dependencies (such as `numpy`, `scipy`, etc) will be installed automatically when you install PyBaMM using `pip`.
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To test that vscode can run a PyBaMM script, navigate to the `examples/scripts` folder
72-
and right click on the `create-model.py` script. Select "Run current file in Python
73-
Interactive Window". This should run the script, which sets up and solves a model of SEI
74-
thickness using PyBaMM. You should see a plot of SEI thickness versus time pop up in the
75-
interactive window.
43+
For an introduction to virtual environments, see (https://realpython.com/python-virtual-environments-a-primer/).
7644

77-
The Python Interactive Window in VSCode can be used to view plots, but is restricted in
78-
functionality and cannot, for example, launch separate windows to show plot. To setup an
79-
xserver on windows and use this to launch windows for plotting, follow these
80-
instructions:
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## Uninstall PyBaMM
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PyBaMM can be uninstalled by running
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```bash
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pip uninstall pybamm
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```
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in your virtual environment.
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1. Install VcXsrv from [here](https://sourceforge.net/projects/vcxsrv/).
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1. Set the display port in the WSL command-line: `echo "export DISPLAY=localhost:0.0" >>
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~/.bashrc`
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1. Install python3-tk in WSL: `sudo apt-get install python3-tk`
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1. Set the matplotlib backend to TKAgg in WSL: `echo "backend : TKAgg" >>
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~/.config/matplotlib/matplotlibrc`
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1. Before running the code, just launch XLaunch (with the default settings) from within
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Windows. Then the code works as usual.
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## Installation using WSL
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If you want to install the optional PyBaMM solvers, you have to use the Windows Subsystem for Linux (WSL). You can find
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the installation instructions [here](INSTALL-WINDOWS-WSL.md).

‎README.md

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### Linux
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For instructions on installing PyBaMM on Debian-based distributions, please see [here](INSTALL-LINUX-MAC.md)
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For instructions on installing PyBaMM on Debian-based distributions, please see [here](INSTALL-LINUX-MAC.md).
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### Mac OS
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For instructions on installing PyBaMM on Mac OS distributions, please see [here](INSTALL-LINUX-MAC.md)
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For instructions on installing PyBaMM on Mac OS distributions, please see [here](INSTALL-LINUX-MAC.md).
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### Windows
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We recommend using Windows Subsystem for Linux to install PyBaMM on a Windows OS, for
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instructions please see [here](INSTALL-WINDOWS.md)
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For instructions on installing PyBaMM on Windows distributions, please see [here](INSTALL-WINDOWS.md). If you want to install the optional solvers (such as scikits-odes and KLU solvers), install PyBaMM on the Windows Subsystem for Linux following the instructions [here](INSTALL-WINDOWS-WSL.md)
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## Citing PyBaMM
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‎examples/notebooks/Creating Models/1-an-ode-model.ipynb

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.9"
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"version": "3.7.5"
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}
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},
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"nbformat": 4,

‎examples/notebooks/Creating Models/2-a-pde-model.ipynb

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.9"
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"version": "3.7.5"
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}
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},
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"nbformat": 4,

‎examples/notebooks/Creating Models/3-negative-particle-problem.ipynb

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.9"
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"version": "3.7.5"
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}
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},
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"nbformat": 4,

‎examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.9"
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"version": "3.7.5"
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}
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},
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"nbformat": 4,

‎examples/notebooks/Creating Models/5-a-simple-SEI-model.ipynb

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"c_inf_dim = pybamm.Parameter(\"Bulk electrolyte solvent concentration\")\n",
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"\n",
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"def D_dim(cc):\n",
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" return pybamm.FunctionParameter(\"Diffusivity\", cc)\n",
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" return pybamm.FunctionParameter(\"Diffusivity\", {\"Solvent concentration [mol.m-3]\": cc})\n",
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"\n",
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"# dimensionless parameters\n",
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"k = k_dim * L_0_dim / D_dim(c_inf_dim)\n",
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "b2a5f649a3b64685ad9510649f130829",
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"model_id": "efe1fe18458a42d88056baf689f6da80",
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"version_major": 2,
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"version_minor": 0
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.9"
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"version": "3.7.5"
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}
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},
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"nbformat": 4,

‎examples/notebooks/parameter-values.ipynb

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‎examples/scripts/create-model.py

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def D_dim(cc):
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return pybamm.FunctionParameter("Diffusivity", cc)
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return pybamm.FunctionParameter("Diffusivity", {"Concentration [mol.m-3]": cc})
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# dimensionless parameters

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