Commit 849bf30f authored by Antoine Jacquey's avatar Antoine Jacquey

Added Readme file and CITATION

parent 5c1100b6
You are welcome to use and modify the LYNX simulator.
See the README.md for details.
If you use LYNX for your research, we would appreciate appropriate citation.
This includes a reference to the repository:
Antoine B. Jacquey, & Mauro Cacace. (2019, July 30). LYNX: Lithosphere dYnamic Numerical toolboX, a MOOSE-based application v1.0.
And also a reference to the publication describing the theory and implementation of the LYNX simulator:
The articles presenting the LYNX simulator are currently under review.
Lynx <h1 align="center">
===== <br>
<a href="https://gitext.gfz-potsdam.de/ajacquey/lynx">LYNX</a>
<br>
Lithosphere dYnamic Numerical toolboX
<br>
A MOOSE-based application
<br>
</h1>
"Fork Lynx" to create a new MOOSE-based application. <h4 align="center">A numerical simulator for modelling deformation of the lithosphere, based on <a href="http://mooseframework.org/" target="blank">MOOSE</a>.</h4>
For more information see: [http://mooseframework.org/create-an-app/](http://mooseframework.org/create-an-app/) <p align="center">
<a href="LICENSE">
<img src="https://img.shields.io/badge/license-GPLv3-blue.svg"
alt="GPL License">
</a>
</p>
## About
LYNX (Lithosphere dYnamic Numerical toolboX) is a numerical simulator for modelling coupled Thermo-Hydro-Mechanical processes of porous rocks.
The simulator is developed by [Antoine Jacquey](http://www.gfz-potsdam.de/en/staff/antoine-jacquey/) <a href="https://orcid.org/0000-0002-6259-4305" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon"></a> and [Mauro Cacace](http://www.gfz-potsdam.de/en/section/basin-modeling/staff/profil/mauro-cacace/) <a href="https://orcid.org/0000-0001-6101-9918" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon"></a> at the [GFZ Potsdam, German Research Centre for Geosciences](http://www.gfz-potsdam.de/en/home/) from the section [Basin Modelling](http://www.gfz-potsdam.de/en/section/basin-modeling/).
LYNX is a MOOSE-based application. Visit the [MOOSE framework](http://mooseframework.org) page for more information.
## Licence
LYNX is distributed under the [GNU GENERAL PUBLIC LICENSE v3](https://gitext.gfz-potsdam.de/ajacquey/lynx/blob/master/LICENSE).
## Getting Started
#### Minimum System Requirements
The following system requirements are from the MOOSE framework (see [Getting Started](http://mooseframework.org/getting-started/) for more information):
* Compiler: C++11 Compliant GCC 4.8.4, Clang 3.4.0, Intel20130607
* Python 2.7+
* Memory: 16 GBs (debug builds)
* Processor: 64-bit x86
* Disk: 30 GBs
* OS: UNIX compatible (OS X, most flavors of Linux)
#### 1. Setting Up a MOOSE Installation
To install LYNX, you need first to have a working and up-to-date installation of the MOOSE framework.
To do so, please visit the [Getting Started](http://mooseframework.org/getting-started/) page of the MOOSE framework and follow the instructions. If you encounter difficulties at this step, you can ask for help on the [MOOSE-users Google group](https://groups.google.com/forum/#!forum/moose-users).
#### 2. Clone LYNX
LYNX can be cloned directly from [GitLab](https://gitext.gfz-potsdam.de/ajacquey/lynx) using [Git](https://git-scm.com/). In the following, we refer to the directory `projects` which you created during the MOOSE installation (by default `~/projects`):
cd ~/projects
git clone https://gitext.gfz-potsdam.de/ajacquey/lynx.git
cd ~/projects/lynx
git checkout master
*Note: the "master" branch of LYNX is the "stable" branch which is updated only if all tests are passing.*
#### 3. Compile LYNX
You can compile LYNX by following these instructions:
cd ~/projects/lynx
make -j4
#### 4. Test LYNX
To make sure that everything was installed properly, you can run the tests suite of LYNX:
cd ~/projects/lynx
./run_tests -j2
If all the tests passed, then your installation is working properly. You can now use the LYNX simulator!
## Usage
To run LYNX from the command line with multiple processors, use the following command:
mpiexec -n <nprocs> ~/projects/lynx/lynx-opt -i <input-file>
Where `<nprocs>` is the number of processors you want to use and `<input-file>` is the path to your input file (extension `.i`).
Information about the structure of the LYNX input files can be found in the documentation (link to follow).
## Cite
If you use LYNX for your work please cite:
* This repository:
Antoine B. Jacquey, & Mauro Cacace. (2019, July 30). LYNX: Lithosphere dYnamic Numerical toolboX, a MOOSE-based application v1.0.
Please read the [CITATION](https://gitext.gfz-potsdam.de/ajacquey/lynx//blob/master/CITATION) file for more information.
## Publications using LYNX
More to come...
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