Merge pull request #513 from MFraters/add_draft_JOSS_paper

Add draft JOSS paper

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push,pull_request]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: doc/JOSS/1.0/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: doc/JOSS/1.0/paper.pdf

.typos.toml

@@ -13,6 +13,7 @@ ba = "ba"
 
 # Don't correct some other abbreviations
 FOT = "FOT"
+OCE = "OCE"
 GWB = "GWB"
 NWO = "NWO"
 SEH = "SEH"

doc/JOSS/1.0/paper.bib

@@ -0,0 +1,205 @@
+@Article{Fraters_Thieulot_etal_2019,
+AUTHOR = {Fraters, M. and Thieulot, C. and van den Berg, A. and Spakman, W.},
+TITLE = {The Geodynamic World Builder: a solution for complex initial conditions in numerical modeling},
+JOURNAL = {Solid Earth},
+VOLUME = {10},
+YEAR = {2019},
+NUMBER = {5},
+PAGES = {1785--1807},
+URL = {https://se.copernicus.org/articles/10/1785/2019/},
+DOI = {10.5194/se-10-1785-2019}
+}
+
+@article{Bauville_Baumann_2019,
+author = {Bauville, A. and Baumann, T. S.},
+title = {geomIO: An Open-Source MATLAB Toolbox to Create the Initial Configuration of 2-D/3-D Thermo-Mechanical Simulations From 2-D Vector Drawings},
+journal = {Geochemistry, Geophysics, Geosystems},
+volume = {20},
+number = {3},
+pages = {1665-1675},
+keywords = {3-D modeling, numerical simulation, MATLAB toolbox, 3-D temperature distribution},
+doi = {https://doi.org/10.1029/2018GC008057},
+url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018GC008057},
+eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2018GC008057},
+abstract = {Abstract Creating the initial geometry and temperature configuration of 3-D numerical simulations is a challenging task. Professional tools are expensive. They often have a steep learning curve and do mostly not interface with the numerical simulation software used by the geodynamics and tectonics academic community. There, we developed geometry Input/Output (geomIO), a MATLAB toolbox to create the initial configuration of geological models regarding model geometry and temperature structure. geomIO allows users to create a geo-referenced 3-D volume by drawing multiple 2-D cross sections in a standard vector graphics editor. The volume is then used to assign material properties and set up initial temperature distribution on a set of vertices. In 2-D mode, polygons can also be used to create a triangular mesh. In addition to the standard functionality, the gravity anomaly of any geometry created with geomIO can be calculated. In this paper, we give an overview of the basic functionalities of geomIO. We illustrate the strength of our software with advanced tectonic and geodynamic applications that could not have been performed with currently available free software. Applications include the Himalayan orogen, the Japanese subduction zones, present-day salt diapirs, and small-scale tectonic structures. We describe algorithms and file formats in the supporting information. The toolbox is user-friendly and flexible. Users can use custom pipelines or preset data processing pipelines, so most applications require only a few lines of code. geomIO is distributed under the GNU General Public License and includes an online wiki with tutorials and additional examples.},
+year = {2019}
+}
+
+@article{Spang_Baumann_2022,
+author = {Spang, A. and Baumann, T. S. and Kaus, B. J. P.},
+title = {Geodynamic Modeling With Uncertain Initial Geometries},
+journal = {Geochemistry, Geophysics, Geosystems},
+volume = {23},
+number = {6},
+pages = {e2021GC010265},
+keywords = {geometry parameterization, variable geometry, salt tectonics, subduction velocity, inversion, subduction angle},
+doi = {https://doi.org/10.1029/2021GC010265},
+url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021GC010265},
+eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021GC010265},
+note = {e2021GC010265 2021GC010265},
+abstract = {Abstract Geodynamic codes have become fast and efficient enough to facilitate sensitivity analysis of rheological parameters. With sufficient data, they can even be inverted for. Yet, the geodynamic inverse problem is often regularized by assuming a constant geometry of the geological setting (e.g., shape, location and size of salt diapirs or magma bodies) or approximating irregular bodies with simple shapes like boxes, spheres or ellipsoids to reduce the parameter space. Here, we present a simple and intuitive method to parameterize complex 3D bodies and incorporate them into geodynamic inverse problems. The approach can automatically create an entire ensemble of initial geometries, enabling us to account for uncertainties in imaging data. Furthermore, it allows us to investigate the sensitivity of the model results to geometrical properties and facilitates inverting for them. We demonstrate the method with two examples. A salt diapir in an extending regime and free subduction of an oceanic plate under a continent. In both cases, small differences in the model's initial geometry lead to vastly different results. Be it the formation of faults or the velocity of plates. Using the salt diapir example, we demonstrate that, given an additional geophysical observation, we are able to invert for uncertain geometric properties. This highlights that geodynamic studies should investigate the sensitivity of their models to the initial geometry and include it in their inversion framework. We make our method available as part of the open-source software geomIO.},
+year = {2022}
+}
+
+@article{Beucher_Moresi_etal_2019, 
+doi = {10.21105/joss.01136}, 
+url = {https://doi.org/10.21105/joss.01136}, 
+year = {2019}, 
+publisher = {The Open Journal}, 
+volume = {4}, 
+number = {36}, 
+pages = {1136}, 
+author = {Romain Beucher and Louis Moresi and Julian Giordani and John Mansour and Dan Sandiford and Rebecca Farrington and Luke Mondy and Claire Mallard and Patrice Rey and Guillaume Duclaux and Owen Kaluza and Arijit Laik and Sara Morón}, 
+title = {UWGeodynamics: A teaching and research tool for numerical geodynamic modelling}, 
+journal = {Journal of Open Source Software} 
+} 
+
+@article{Moresi_Dufour_2002,
+authors = {Moresi, L. and Dufour, F. and Mühlhaus, HB. },
+title = {Mantle Convection Modeling with Viscoelastic/Brittle Lithosphere: Numerical Methodology and Plate Tectonic Modeling.},
+journal = {Pure appl. geophys.},
+volume = {159},
+pages = {2335–2356},
+year = {2002},
+url = {https://doi.org/10.1007/s00024-002-8738-3}
+}
+
+@article{Varga_Schaaf_2019,
+AUTHOR = {de la Varga, M. and Schaaf, A. and Wellmann, F.},
+TITLE = {GemPy 1.0: open-source stochastic geological modeling and inversion},
+JOURNAL = {Geoscientific Model Development},
+VOLUME = {12},
+YEAR = {2019},
+NUMBER = {1},
+PAGES = {1--32},
+URL = {https://gmd.copernicus.org/articles/12/1/2019/},
+DOI = {10.5194/gmd-12-1-2019}
+}
+
+@article{Schaaf_Varga_2021,
+AUTHOR = {Schaaf, A. and de la Varga, M. and Wellmann, F. and Bond, C. E.},
+TITLE = {Constraining stochastic 3-D structural geological models with topology information using approximate Bayesian computation in GemPy 2.1},
+JOURNAL = {Geoscientific Model Development},
+VOLUME = {14},
+YEAR = {2021},
+NUMBER = {6},
+PAGES = {3899--3913},
+URL = {https://gmd.copernicus.org/articles/14/3899/2021/},
+DOI = {10.5194/gmd-14-3899-2021}
+}
+
+@article{McKenzie_1970,
+  title = "Temperature and potential temperature beneath island arcs",
+  journal = "Tectonophysics",
+  volume = "10",
+  number = "1",
+  pages = "357 - 366",
+  year = "1970",
+  note = "Geothermal Problems",
+  issn = "0040-1951",
+  doi = "https://doi.org/10.1016/0040-1951(70)90115-0",
+  url = "http://www.sciencedirect.com/science/article/pii/0040195170901150",
+  author = "D.P. McKenzie"
+}
+@software{sebastien_jourdain_2024,
+  author       = {Sebastien Jourdain (Kitware) and
+                  Forrest Li and
+                  Julien Finet and
+                  Sankhesh Jhaveri and
+                  Laurenn Lam and
+                  Adnane Belmadiaf and
+                  Matt McCormick and
+                  Scott Wittenburg and
+                  Alireza and
+                  Thibault Bruyère and
+                  Tom Birdsong and
+                  Lucie Macron and
+                  Shreeraj Jadhav and
+                  JiayiXuu and
+                  Patrick Avery and
+                  rodrigobasilio2022 and
+                  Jules BOURDAIS and
+                  gandis and
+                  Erik Ziegler and
+                  RemiCecchinato and
+                  Anne Haley and
+                  Tom Suchel and
+                  TristanWright and
+                  David Thompson and
+                  Mayeul Chassagnard and
+                  Madison Dickson and
+                  Aron Helser and
+                  Paul Elliott and
+                  ocrossi},
+  title        = {Kitware/vtk-js: v29.7.2},
+  month        = feb,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v29.7.2},
+  doi          = {10.5281/zenodo.10680530},
+  url          = {https://doi.org/10.5281/zenodo.10680530}
+}
+
+@article{Billen_Fraters_AGU_2023,
+  title={A New Method for Assigning Thermal Structure to 2D and 3D Present-day Geodynamic and Seismological Models of Subduction Zones},
+  author={Billen, Magali I and Fraters, Menno},
+  journal={AGU23},
+  year={2023},
+  publisher={AGU}
+}
+
+@article{vanderWiel_Hinsbergen_etal_2024,
+  title = {Linking rates of slab sinking to long-term lower mantle flow and mixing},
+  journal = {Earth and Planetary Science Letters},
+  volume = {625},
+  pages = {118471},
+  year = {2024},
+  issn = {0012-821X},
+  doi = {https://doi.org/10.1016/j.epsl.2023.118471},
+  url = {https://www.sciencedirect.com/science/article/pii/S0012821X23004843},
+  author = {Erik {van der Wiel} and Douwe J.J. {van Hinsbergen} and Cedric Thieulot and Wim Spakman},
+  keywords = {Mantle convection, Slab sinking rates, Mantle mixing, Modelling constraints},
+}
+
+@article{Sandiford_Craig_timothy_2023,
+  author = {Sandiford, Dan and Craig, Timothy J},
+  title = "{Plate bending earthquakes and the strength distribution of the lithosphere}",
+  journal = {Geophysical Journal International},
+  volume = {235},
+  number = {1},
+  pages = {488-508},
+  year = {2023},
+  month = {06},
+  issn = {0956-540X},
+  doi = {10.1093/gji/ggad230},
+  url = {https://doi.org/10.1093/gji/ggad230},
+  eprint = {https://academic.oup.com/gji/article-pdf/235/1/488/50659012/ggad230.pdf},
+}
+
+@ARTICLE{Gea_Negredo_etal_2023,
+  AUTHOR={Gea, Pedro J. and Negredo, Ana M. and Mancilla, Flor de Lis},
+  TITLE={The Gibraltar slab dynamics and its influence on past and present-day Alboran domain deformation: Insights from thermo-mechanical numerical modelling},
+  JOURNAL={Frontiers in Earth Science},
+  VOLUME={11},
+  YEAR={2023},
+  URL={https://www.frontiersin.org/articles/10.3389/feart.2023.995041},
+  DOI={10.3389/feart.2023.995041},
+  ISSN={2296-6463},
+  ABSTRACT={The origin and tectonic evolution of the Gibraltar Arc system is the result of a complex geodynamic evolution involving the convergence of the Eurasian and African plates and the dynamic impact of the Gibraltar slab. Although geologic and geophysical data collected in the last few years have increased our knowledge of the Gibraltar Arc region, it is still unclear which are the mechanical links between the Gibraltar slab and the past deformation of the overriding Alboran lithosphere, as well as to which degree this subduction system is presently active. In this study, we use 2D numerical modelling to investigate the impact of the Gibraltar slab dynamics on the deformation of the overriding Alboran lithosphere. Our model simulates a WE generic vertical section at an approximate latitude of 36°N and considers an initial setup at about Burdigalian times (∼20 Ma), when the subduction front position is relatively well constrained by recent tectonic reconstructions. Our modelling shows a switch in the overriding plate (OP) stress state from extensional stresses during the slab rollback to compressional stresses near the trench when the rollback velocity decreases, caused by the change in slab-induced mantle flow. We also find that much of the crustal and lithospheric deformation occur during fast slab rollback and OP extension in the first 10 Myr of evolution, while after that only moderate deformation associated with subduction is predicted. Finally, we find that despite the subduction rollback ceases, the ongoing motion of the deeper portion of the slab induces a mantle flow that causes some amount of west-directed basal drag of the Alboran lithosphere. This basal drag generates interplate compresional stresses compatible with the distribution of intermediate-depth earthquakes in western Alboran.}
+}
+
+@article{Saxena_Dannberg_etal_2023,
+  author = {Saxena, Arushi and Dannberg, Juliane and Gassmöller, Rene and Fraters, Menno and Heister, Timo and Styron, Richard},
+  title = {High-Resolution Mantle Flow Models Reveal Importance of Plate Boundary Geometry and Slab Pull Forces on Generating Tectonic Plate Motions},
+  journal = {Journal of Geophysical Research: Solid Earth},
+  volume = {128},
+  number = {8},
+  pages = {e2022JB025877},
+  keywords = {global mantle flow models, plate driving forces, plate tectonics},
+  doi = {https://doi.org/10.1029/2022JB025877},
+  url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2022JB025877},
+  eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2022JB025877},
+  note = {e2022JB025877 2022JB025877},
+  abstract = {Abstract Mantle convection models based on geophysical constraints have provided us with a basic understanding of the forces driving and resisting plate motions on Earth. However, existing studies computing the balance of underlying forces are contradicting, and the impact of plate boundary geometry on surface deformation remains unknown. We address these issues by developing global instantaneous 3-D mantle convection models with a heterogeneous density and viscosity distribution and weak plate boundaries prescribed using different geometries. We find that the plate boundary geometry of the Global Earthquake Model (GEM, Pagani et al., 2018, https://doi.org/10.1177/8755293020931866), featuring open plate boundaries with discrete lithospheric-depth weak zones in the oceans and distributed crustal faults within continents, achieves the best fit to the observed GPS data with a directional correlation of 95.1\% and a global point-wise velocity residual of 1.87 cm/year. A good fit also requires plate boundaries being 3 to 4 orders of magnitude weaker than the surrounding lithosphere and low asthenospheric viscosities between 5 × 1017 and 5 × 1018 Pa s. Models without asthenospheric and lower mantle heterogeneities retain on average 30\% and 70\% of the plate speeds, respectively. Our results show that Earth's plate boundaries are not uniform and better described by more discrete plate boundaries within the oceans and distributed faults within continents. Furthermore, they emphasize the impact of plate boundary geometry on the direction and speed of plate motions and reaffirm the importance of slab pull in the uppermost mantle as a major plate driving force.},
+  year = {2023}
+}