From 73ad7fbabe30b5569dcb33bcaf2ce1e7fe627ee8 Mon Sep 17 00:00:00 2001
From: Romain Boman <romain.boman@gmail.com>
Date: Mon, 30 May 2022 17:30:17 +0200
Subject: [PATCH] update README file

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 README.md | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

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 Finite element models of bones loaded by muscle forces.
 
-Collaboration with the [EDDy Lab](https://www.eddylab.uliege.be/) (Prof. Valentin Fisher).
+The FE models (input files) are compatible with the nonlinear FE code [Metafor](http://metafor.ltas.ulg.ac.be/) and with **fossils**, a  free and open-source FE solver whose source code and binaries are provided here. It is written in C++ with the help of the [gmsh](https://gmsh.info/) library for mesh management and pre/postprocessing, [Eigen](https://eigen.tuxfamily.org/) for linear algebra and [MKL Pardiso](https://www.intel.com/content/www/us/en/develop/documentation/onemkl-developer-reference-c/top/sparse-solver-routines/onemkl-pardiso-parallel-direct-sparse-solver-iface.html) (fast parallel linear solver). The code is wrapped in Python thanks to [SWIG](https://www.swig.org/). The small GUI is written in [PyQt](https://www.riverbankcomputing.com/software/pyqt/).
+
+## How to run the models (GUI)?
+
+* The latest Windows installer of **fossils** can be downloaded here: [fossilsetup.exe](https://dox.ulg.ac.be/index.php/s/9SQfoQnQ2vRKUvl).
+* Run the installer and double-click on the link on the desktop. 
+* Choose an input file (see the models folder of this repository).
+* Click the "Run" button.
+* Results are stored in a workspace folder.
+
+## How to run the code (command line)?
+
+```
+fossils.exe [-k nthreads] [--nogui] <path_to_input_file.py>
+```
 
 ## References
 
+This work has been done through a collaboration between the [EDDy Lab](https://www.eddylab.uliege.be/) (Prof. Valentin Fisher) and the [Department of Aerospace and Mechanical Engineering](https://www.am.uliege.be/) (R. Boman, J.-P. Ponthot) at the University of Liège.
+
 * V. Gaudichon - Uncovering the functional disparity of Cretaceous marine reptiles via finite element analysis. Thesis of Master II Paleontology Poitiers-Montpellier 2020-2021.
 * V. Gaudichon et al. [Uncovering the biomechanical disparity of Cretaceous marine reptile feeding via finite element analysis](https://orbi.uliege.be/handle/2268/262672). 69th Symposium on Vertebrate Palaeontology and Comparative Anatomy - September 2021.
 * [Metafor](http://metafor.ltas.ulg.ac.be/).
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