update paper and readme

Author: CyprienBosserelle

README.md

@@ -1,5 +1,5 @@
 # BG Flood
-Numerical model for simulating shallow water hydrodynamics on the GPU using an Adaptive Mesh Refinement type grid. The model was designed with the goal of simulating inundation (River, Storm surge or tsunami). The model uses a Block Uniform Quadtree approach that runs on the GPU but the adaptive/multi-resolution/AMR is being implemented and not yet operational.
+Numerical model for simulating shallow water hydrodynamics on the GPU using an Adaptive Mesh Refinement type grid. The model was designed with the goal of simulating inundation (Rain, river, storm-surge or tsunami). The model uses a Block Uniform Quadtree approach that runs on the GPU using variable resolution grid.Developent of .
 
 The core SWE engine and adaptivity has been inspired and taken from St Venant solver from [Basilisk](http://basilisk.fr/) and the CUDA GPU memory model has been inspired by the work from [Vacondio _et al._2017](https://dl.acm.org/citation.cfm?id=3031292))
 
@@ -8,12 +8,41 @@ The adaptive version of the model is currently under heavy development. Makefile
 
 
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://www.gnu.org/licenses/gpl-3.0)
+
+
+
+## Documentation and manual
+
 [![DocumentationNNN](https://img.shields.io/badge/Documentation-MkDocs-blue?logo=materialformkdocs)](https://cyprienbosserelle.github.io/BG_Flood/)
 
+
+
+## Installation & Compiling
+For Windows users we make binaries/executable available for download in the [release](https://github.com/CyprienBosserelle/BG_Flood/releases/tag/v1.0) section.
+
+MacOS and Linux users need to compile the code. Find compile guide [here.](https://cyprienbosserelle.github.io/BG_Flood/Install/#linux)
+
+
+## Basic usage
+The simplest usage of BG_Flood is to move the executable (an accompanying DLLs for Windows users) to a working folder (e.g. BG_Flood\Examples\SimpleRain) and either launch from CLI:
+```
+./BG_FLood BG_param.txt
+```
+
+or by double clicking the excecutable (BG_Flood will automatically look for ```BG_param.txt```)
+
+Refer to [Manual](https://cyprienbosserelle.github.io/BG_Flood/) and examples to understand how to use the param file and  parameters.
 ## Reference
 
 Bosserelle C., Lane E., Harang A., (2021) BG-Flood: A GPU adaptive, open-source, general inundation hazard model. Proceedings of the Australasian Coasts & Ports 2021 Conference. [PDF](docs/150_bosserelle_finalpaper.pdf)
 
 
-## Testing
-CI test (development branch):![Test](https://github.com/CyprienBosserelle/BG_Flood/actions/workflows//main.yml/badge.svg?branch=development)
+## Testing and validation
+
+BG_Flood has 12+ internal tests to make sure the hydrodynamics engine and input work as expected. 
+
+Below is the result of all the tests (development branch):
+
+![Test](https://github.com/CyprienBosserelle/BG_Flood/actions/workflows//main.yml/badge.svg?branch=development)
+
+To run the test yourself add ```test = xx``` where xx is the test number (1 to 14) to your param file. 

docs/BG_Flood_Paper_fig1.png

@@ -32,10 +32,13 @@ @Article{jmse11050945
 }
 
 @Article{Coast_ports2022,
-AUTHOR = {Bosserelle, Cyprien and Lane, Emily and Harang, Alice},
-TITLE = {Coastal Flooding and Port Infrastructure: A Case Study of Apia, Samoa},
-JOURNAL = {Coasts and Ports}, 
-YEAR = {2022},
+author    = {Bosserelle, Cyprien and Lane, Emily M. and Harang, Alice},
+  title     = {{BG-Flood}: {A} {GPU} adaptive, open-source, general inundation hazard model},
+  booktitle = {Proceedings of the Australasian Coasts \& Ports 2021 Conference},
+  year      = {2021},
+  pages     = {112--118},
+  address   = {Christchurch, New Zealand},
+  url       = {https://coastsandports2021.com.au/}
 }
 
 @article{Kurganov2002,

docs/References.bib

@@ -0,0 +1,78 @@
+@inproceedings{bosserelle2021bgflood,
+  author    = {Bosserelle, Cyprien and Lane, Emily M. and Harang, Alice},
+  title     = {{BG-Flood}: {A} {GPU} adaptive, open-source, general inundation hazard model},
+  booktitle = {Proceedings of the Australasian Coasts \& Ports 2021 Conference},
+  year      = {2021},
+  pages     = {112--118},
+  address   = {Christchurch, New Zealand},
+  url       = {https://coastsandports2021.com.au/}
+}
+
+@article{bosserelle2020effects,
+  author    = {Bosserelle, Cyprien and Williams, Shaun and Cheung, Kwok Fai and Lay, Thorne and Yamazaki, Yoshiki and Simi, Titimanu and Gilleland, C. and Lane, Emily M.},
+  title     = {Effects of source faulting and fringing reefs on the 2009 South Pacific Tsunami inundation in southeast Upolu, Samoa},
+  journal   = {Journal of Geophysical Research: Oceans},
+  year      = {2020},
+  volume    = {125},
+  number    = {12},
+  pages     = {e2020JC016537},
+  doi       = {10.1029/2020JC016537},
+  url       = {https://doi.org/10.1029/2020JC016537}
+}
+
+@unpublished{harang2026,
+  author    = {Harang, A. and Lane, Emily M. and Bosserelle, Cyprien and Dean, S. and Catto{\"e}n, C. and Pearson, R. and Carey-Smith, T. and Srinivasan, R. and Shiona, H. and Wilkins, M. and Smart, G.},
+  title     = {Flood Hazard in {Aotearoa New Zealand} under Current and Future Climates},
+  year      = {2026},
+  note      = {To be submitted to {Geoscience Data Journal}},
+  address   = {New Zealand}
+}
+
+@article{pelmard2026regional,
+  author    = {Pelmard, Jo{\"e} and Lane, Emily Margaret and Harang, Alice and Bosserelle, Cyprien and Xu, Zhonghou and Pearson, Rose and Carey-Smith, Trevor and Smart, Graeme and Bind, Jochen and Kumar, Raghunathan Senthil and Cheng, Elvira and Bui, Giang and Paulik, Ryan and Zorn, Conrad and Wotherspoon, Liam},
+  title     = {Regional flood hazard mapping for {February 2023 Ex-Tropical Cyclone Gabrielle}, {New Zealand}},
+  journal   = {Earth System Science Data Discussions},
+  year      = {2026},
+  volume    = {2026},
+  pages     = {1--32},
+  doi       = {10.5194/essd-2026-56},
+  url       = {https://essd.copernicus.org/preprints/essd-2026-56/},
+  note      = {Preprint under review}
+}
+
+@article{popinet2011quadtree,
+  author    = {Popinet, St{\'e}phane},
+  title     = {Quadtree-adaptive hydrological modelling of sub-grid-scale features in variable-density shallow-water flows},
+  journal   = {Environmental Modelling \& Software},
+  year      = {2011},
+  volume    = {26},
+  number    = {9},
+  pages     = {1170--1182},
+  doi       = {10.1016/j.envsoft.2011.03.010},
+  url       = {https://doi.org/10.1016/j.envsoft.2011.03.010},
+  publisher = {Elsevier}
+}
+
+@article{pozo2026,
+  author    = {Pozo Estivariz, Andrea and M{\'e}ndez, Fernando and Bosserelle, Cyprien and Wilson, Matthew and Katurji, Marwan and Lane, Emily M.},
+  title     = {Hybrid Hydrodynamic--Machine Learning Modelling for Rapid Flood Scenario Assessment: {A} Case Study in {Aotearoa New Zealand}},
+  journal   = {Earth's Future},
+  year      = {2026},
+  volume    = {14},
+  number    = {3},
+  pages     = {e2023EF004123},
+  doi       = {10.1029/2023EF004123},
+  url       = {https://doi.org/10.1029/2023EF004123}
+}
+
+@article{vacondio2017,
+  author    = {Vacondio, Renato and Dal Palu, Alessandro and Rogers, Benedict D.},
+  title     = {{GPU}-Enhanced {Hierarchical Quadtree-Block Shallow Water 2D Solver}},
+  journal   = {Environmental Modelling \& Software},
+  year      = {2017},
+  volume    = {98},
+  pages     = {116--135},
+  doi       = {10.1016/j.envsoft.2017.09.007},
+  url       = {https://doi.org/10.1016/j.envsoft.2017.09.007},
+  publisher = {Elsevier}
+}