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Updated README to include instructions for systems without root #2

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Updated README to include instructions for systems without root #2

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27 changes: 26 additions & 1 deletion README.md
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Expand Up @@ -2,7 +2,7 @@

This code uses a Kinetic Monte Carlo simulation to estimate the behaviour of variable range hopping in Dopant Networks. More information can be found [here](https://www.researchsquare.com/article/rs-757616/latest.pdf).

## Installation
## Installation (with root)
This installation guide has been written using Ubuntu on WSL2 (Windows Subsystem for Linux), but should be usable on a range of linux operating systems.

Install the dependencies through apt (for Ubuntu/Debian):
Expand All @@ -28,6 +28,31 @@ conda create --name mcnetwork numpy scipy matplotlib h5py
conda activate mcnetwork
```

## Installation (without root)
On systems without libhdf5 and no root one has to manually include libhdf5.

Note: Replace the HDF download link by the appropriate CMake version, which can be found [here](https://portal.hdfgroup.org/display/support/Downloads).
```bash
git clone https://github.com/MUTUEL/MCNetwork.git
git clone https://github.com/mfem/mfem.git
mkdir mfem-build && cd mfem-build
cmake ../mfem
make ../mfem

wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.N/hdf5-1.N.N/src/<distribution>.tar.gz
gzip -cd <distribution>.tar.gz | tar xvf -
cd CMake-hdf5-<version>
./build-unix.sh
cp HDF5-<version>-Linux.tar.gz ..
cd ..
tar -xvf HDF5-<version>-Linux.tar.gz

mkdir MCNetwork/build && cd MCNetwork/build
env MFEM_DIR=../../mfem-build HDF5_DIR=../../HDF5-<version>-Linux/HDF_Group/HDF5/<version>/share/cmake/hdf5 cmake ..
make
```
These install instruction have been adapted from the [HDF5 Building with CMake manual](https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake).

## Usage
Define the device parameters you want to use in `data/in.txt`. To make a new device with Monte Carlo optimization and random voltages go to the `data` folder in your shell and enter the following command:
```bash
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