# A software workflow for fingerprinting and visualizing defects in damaged crystal structures
---
#### Udo von Toussaint, F. J. Domı́nguez-Gutiérrez, Markus Rampp, Michele Compostella
###### Max-Planck-Institut für Plasmaphysik, Boltzmannstrasse 2, 85748 Garching, Germany
###### Max-Planck Computing and Data Facility, Giessenbachstrasse 2, 85748 Garching, Germany
---
## Introduction
This repository contains the recipe to create a Docker container where users can test the workflow for fingerprinting and visualizing defects in damaged crystal structures.
Together with the required software, data for the analysis of point defects in a bcc Fe sample are provided. This dataset was obtained by performing MD simulations to emulate neutron bombardment at a primary-knock on-atom of 10 keV.
## Requirements
In order to build the Docker image, the following software is required on the local machine:
* tar
* curl
* wget
* git
* docker
#### Important:
The workflow presented in this repository uses the GAP library for the software QUIP. When installing this software, you are accepting the [GAP license agreement](http://www.libatoms.org/gap/gap_download.html).
## Installation
After cloning this repository, run the following command to create the Docker image
```shell
./build.sh /root/software/
```
The parameter for the build.sh script is the installation path of the software stack inside the Docker image.
Additional optional parameters can be provided to automatically accept the GAP license agreement:
```shell
./build.sh /root/software/ "I accept""FULL NAME""EMAIL ADDRESS""ORGANIZATION"
```
If these optional parameters are not specified, the build process will ask for them during runtime.
## How to run the Docker image
Once the Docker image has been created, use the following command to shell into the container:
```shell
docker run -t-i--volume /local_folder/:/root/sample/output/ favad /bin/bash
```
The ouput files generated inside the Docker container will be stored in the specified /local_folder/.
Please note that the content of this folder will be overwritten, if the folder is not empty.
At this point you can run the workflow for fingerprinting and visualizing defects on the sample dataset inside the Docker container:
```shell
cd /root/sample/
python3 FaVaD.py -p /root/sample/parameters.txt
```
---
## Local Installation
In the 'assets' folder we provide a script for the installation of the entire software stack on a local machine (instead of inside a Docker container) running Ubuntu 18.04 LTS.