From bedc15494ff8e8af43f35548d62d157c870e7bec Mon Sep 17 00:00:00 2001 From: Menno Fraters Date: Tue, 20 Aug 2024 21:06:43 +0200 Subject: [PATCH 1/3] Adress comment from Juliane Dannberg on JOSS paper. --- doc/JOSS/1.0/paper.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/JOSS/1.0/paper.md b/doc/JOSS/1.0/paper.md index d9f927a78..753f7a0cd 100644 --- a/doc/JOSS/1.0/paper.md +++ b/doc/JOSS/1.0/paper.md @@ -73,11 +73,11 @@ Today's computational resources, infrastructure, and numerical methods allow for 3. The model setup is not portable to other computing systems or reproducible in other software frameworks. 4. The model setup is not shareable with other users. -These issues lead to a number of problems with the reproducibility and reliability of modeling studies, which threaten to undermine the predictive power and usefulness of modeling results, and highlighting the need for a way to describe model setups that is easy, efficient, and robust. The GWB has been designed to address these challenges, by creating human readable, parameterized, portable, reproducible, and shareable geodynamic model setups. Critically, the GWB comes with its own programs to visualize the constructed model through applications like Paraview. Creating the models requires no programming knowledge. Therefore, the GWB can be easily used to visualize tectonic and geodynamic settings for publications, teaching, and public outreach. +These issues lead to a number of problems with the reproducibility and reliability of modeling studies, which threaten to undermine the predictive power and usefulness of modeling results, and highlight the need for an easy, efficient, and robust way to describe model setups. The GWB has been designed to address these challenges, by creating human readable, parameterized, portable, reproducible, and shareable geodynamic model setups. Critically, the GWB comes with its own programs to visualize the constructed model through applications like Paraview. Creating the models requires no programming knowledge. Therefore, the GWB can be easily used to visualize tectonic and geodynamic settings for publications, teaching, and public outreach. ![A workflow diagram for how a world builder file can be used to create and visualize a geodynamic model.](workflow_diagram.png) -The GWB has been used in several published studies to model global fault patterns, plume, and plate dynamics [@Saxena_Dannberg_etal_2023; @Gea_Negredo_etal_2023; @Sandiford_Craig_timothy_2023; and @vanderWiel_Hinsbergen_etal_2024]. Other tools to solve this problem have emerged at around the same time as the first GWB release [@Fraters_Thieulot_etal_2019]. Examples include GeomIO [@Bauville_Baumann_2019; @Spang_Baumann_2022], which uses an approach based on vector graphics; Easy (https://easyinit.readthedocs.io/), which uses a more generic function-based approach; UWGeodynamics [@Beucher_Moresi_etal_2019], which is specifically designed for Underworld [@Moresi_Dufour_2002]; and GemPy [@Varga_Schaaf_2019; @Schaaf_Varga_2021], which is designed for structural modeling. The GWB was designed to be a more general planetary structure creator, using the methods shown below. +The GWB has been used in several published studies to model global fault patterns, plumes, and plate dynamics [@Saxena_Dannberg_etal_2023; @Gea_Negredo_etal_2023; @Sandiford_Craig_timothy_2023; and @vanderWiel_Hinsbergen_etal_2024]. Other tools to solve this problem have emerged at around the same time as the first GWB release [@Fraters_Thieulot_etal_2019]. Examples include GeomIO [@Bauville_Baumann_2019; @Spang_Baumann_2022], which uses an approach based on vector graphics; Easy (https://easyinit.readthedocs.io/), which uses a more generic function-based approach; UWGeodynamics [@Beucher_Moresi_etal_2019], which is specifically designed for Underworld [@Moresi_Dufour_2002]; and GemPy [@Varga_Schaaf_2019; @Schaaf_Varga_2021], which is designed for structural modeling. The GWB was designed to be a more general planetary structure creator, using the methods shown below. # Methods @@ -121,9 +121,9 @@ Below we show an example input file for a Cartesian model that contains a single } ``` -A more complicated example (only requiring 85 lines, and can be found [here](https://github.com/GeodynamicWorldBuilder/WorldBuilder/blob/GWB-v1.0.0/doc/sphinx/_static/gwb_input_files/BST_19_spherical_models.wb)) features a spherical geometry, a spatially variable subducting plate, continental plate, oceanic plate and plume can be seen in Fig 2. +A more complicated example (only requiring 85 lines, and can be found [here](https://github.com/GeodynamicWorldBuilder/WorldBuilder/blob/GWB-v1.0.0/doc/sphinx/_static/gwb_input_files/BST_19_spherical_models.wb)) featuring a spherical geometry, a spatially variable subducting plate, continental plate, oceanic plate and plume can be seen in Fig 2. -![A schematic example of what can be built with 85 lines of a GWB input file formatted in the same way as in the example input file shown above. This includes a slab with variable dip and thickness along strike and down dip, subducting under an oceanic plate on the right side of the ridge, as well as a passive continental margin with layers of variable on the left side of the ridge, and a mantle plume beneath the ridge. The temperature of the continent is linear, the oceanic plates are defined by a half-space cooling model, the slab temperature is defined by a mass conserving temperature model and the plume adds heat based on a Gaussian around the center.\label{fig:example}](../../sphinx/_static/images/user_manual/basic_starter_tutorial/BST_19.png) +![A schematic example of what can be built with 85 lines of a GWB input file formatted in the same way as in the example input file shown above. This includes a slab with variable dip and thickness along strike and down dip, subducting under an oceanic plate on the right side of the ridge, as well as a passive continental margin with variable thickness, and a mantle plume beneath the ridge. The temperature profile of the continent is linear, the oceanic plates are defined by a half-space cooling model, the slab temperature is defined by a mass conserving temperature model and the plume adds heat based on a Gaussian around the center.\label{fig:example}](../../sphinx/_static/images/user_manual/basic_starter_tutorial/BST_19.png) # Acknowledgements From 40e5773a281d205aaf43e472cd11a354beb6218f Mon Sep 17 00:00:00 2001 From: Menno Fraters Date: Tue, 20 Aug 2024 21:12:40 +0200 Subject: [PATCH 2/3] update affiliations for authors. --- doc/JOSS/1.0/paper.md | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/doc/JOSS/1.0/paper.md b/doc/JOSS/1.0/paper.md index 753f7a0cd..ccefe06c9 100644 --- a/doc/JOSS/1.0/paper.md +++ b/doc/JOSS/1.0/paper.md @@ -19,41 +19,45 @@ authors: affiliation: "2" - name: Rene Gassmöller orcid: 0000-0001-7098-8198 - affiliation: "1" + affiliation: "3,4" - name: Arushi Saxena orcid: 0000-0003-2930-3497 - affiliation: "3" + affiliation: "2,5" - name: Timo Heister orcid: 0000-0002-8137-3903 - affiliation: "3" + affiliation: "5" - name: Haoyuan Li orcid: 0000-0003-0676-9884 affiliation: "2" - name: Daniel Douglas orcid: 0000-0002-7871-018X - affiliation: "4" + affiliation: "6" - name: Juliane Dannberg orcid: 0000-0003-0357-7115 - affiliation: "1" + affiliation: "3,4" - name: Wolfgang Bangerth orcid: 0000-0003-2311-9402 - affiliation: "5" + affiliation: "7" - name: Yijun Wang orcid: 0000-0002-7637-3239 - affiliation: "6" + affiliation: "8" affiliations: - - name: Universiy of Florida, USA + - name: GFZ German Research Centre for Geosciences, Potsdam, Germany index: 1 - name: UC Davis, USA index: 2 - - name: Clemson University, USA + - name: GEOMAR Helmholtz-Zentrum für Ozeanforschung, Kiel, Germany index: 3 - - name: New Mexico Tech, USA + - name: Universiy of Florida, USA index: 4 - - name: Colorado State University, USA + - name: Clemson University, USA index: 5 - - name: University of Oslo, Norway + - name: New Mexico Tech, USA index: 6 + - name: Colorado State University, USA + index: 7 + - name: University of Oslo, Norway + index: 8 date: 11 March 2024 bibliography: paper.bib --- From c992693ba4e8d1ea9782fc000c76aee6d0467668 Mon Sep 17 00:00:00 2001 From: Menno Fraters Date: Tue, 20 Aug 2024 21:15:40 +0200 Subject: [PATCH 3/3] Add acknoledgmnt of UC Davis and UF where most of the work was done. --- doc/JOSS/1.0/paper.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/JOSS/1.0/paper.md b/doc/JOSS/1.0/paper.md index ccefe06c9..a534605dc 100644 --- a/doc/JOSS/1.0/paper.md +++ b/doc/JOSS/1.0/paper.md @@ -134,6 +134,8 @@ A more complicated example (only requiring 85 lines, and can be found [here](htt We would like to acknowledge all other contributors to the project, especially Lorraine Hwang, Rebecca Fildes, and John Naliboff for their advice and support for this project throughout the years. We would also like to acknowledge NSF for their funding and support through grants EAR-1620618, OCE-1948902, EAR-0949446, EAR-1550901, EAR-1925677, and EAR-2149126. +M. Fraters also acknowledges the support of the Department of Earth and Planetary Sciences at UC Davis and the Department of Geological Sciences at the University of Florida, where much of the research presented was completed while he was a postdoctoral scholar. + # References