SimEx

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Start-to-end photon experiment simulation platform

// repository documentation

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SimEx
==================

Software platform for **Sim**ulation of advanced photon **Ex**periments.

[![Build Status master](https://travis-ci.org/PaNOSC-ViNYL/SimEx.svg?branch=master)](https://travis-ci.org/github/panosc-vinyl/simex/branches)
[![Build Status develop](https://travis-ci.org/PaNOSC-ViNYL/SimEx.svg?branch=develop)](https://travis-ci.org/github/panosc-vinyl/simex/branches)

## Purpose of SimEx

SimEx is a python library to facilitate setup, execution, and analysis of
simulations of experiments at advanced laser light sources.
As an example, consider a molecule radiated by highly brilliant,
ultrashort x-ray pulses such as delivered by an X-Ray Free Electron Laser (X-FEL).
The simulation platform allows to combine tools and codes for the
simulation of each step of the experiment: Generation of radiation in the
photon source, propagation through optics and waveguides to the interaction
point, photon-matter interaction, scattering of the radiation into the far
field and detection of the latter. The platform provides slots and
interfaces for the various simulation steps.

## User manual

For more details (user manual, installation instructions, examples, etc.),
please visit the project's readthedocs page at https://simex.readthedocs.io/

## Install
Get source code:
```
git clone --depth 1 -b master https://github.com/PaNOSC-ViNYL/SimEx.git
```

### CENTOS 8
```
yum install -y hdf5 hdf5-devel fftw-devel flex bison
```

#### Conda (preferred)
```
wget -c -O /tmp/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh /tmp/miniconda.sh
```

* Select a directory XX where to install miniconda, consider 5GB of free disk space.
 * Add the XX/miniconda/bin/ directory to your path

```
./install.sh conda-env
conda init $SHELL
```
restart your shell
```
conda activate simex
./install.sh conda
```

## Docker image
https://github.com/PaNOSC-ViNYL/SimEx/tree/master/Docker

To run the docker image, edit `run_docker.sh` and run the script.

```
./run_docker.sh
```

## Tutorial notebooks
https://github.com/PaNOSC-ViNYL/SimEx-notebooks

## Development
The size of this Github repository of SimEx is huge due to the historical TestFiles.

This command can clone only the newest develop branch to reduce the dowloading size:
```
git clone --depth 1 -b develop https://github.com/PaNOSC-ViNYL/SimEx.git
```
Now the TestFiles are hosted at [Zenodo](https://zenodo.org/record/3750541#.X2R9DZMzZE5).
The files can be downloaded with [this script](get_testdata.sh).

## Acknowledgements
This project has received funding from the European Union’s Horizon 2020 research
and innovation programme under grant agreement No 654220 and No 823852.

SimEx

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