From 849bf30f9f4aa89ef7730b80931359a49babd6d1 Mon Sep 17 00:00:00 2001 From: Antoine Jacquey Date: Tue, 30 Jul 2019 14:03:48 +0200 Subject: [PATCH] Added Readme file and CITATION --- CITATION | 10 ++++++ README.md | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++++--- 2 files changed, 98 insertions(+), 4 deletions(-) create mode 100644 CITATION diff --git a/CITATION b/CITATION new file mode 100644 index 0000000..d118c42 --- /dev/null +++ b/CITATION @@ -0,0 +1,10 @@ +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. diff --git a/README.md b/README.md index 2f7ea01..f9e03ae 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,90 @@ -Lynx -===== +

+
+ LYNX +
+ Lithosphere dYnamic Numerical toolboX +
+ A MOOSE-based application +
+

-"Fork Lynx" to create a new MOOSE-based application. +

A numerical simulator for modelling deformation of the lithosphere, based on MOOSE.

-For more information see: [http://mooseframework.org/create-an-app/](http://mooseframework.org/create-an-app/) +

+ + GPL License + +

+ +## 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/) ORCID iD icon and [Mauro Cacace](http://www.gfz-potsdam.de/en/section/basin-modeling/staff/profil/mauro-cacace/) ORCID iD icon 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 ~/projects/lynx/lynx-opt -i + +Where `` is the number of processors you want to use and `` 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... -- GitLab