Merge pull request #145 from JuliaGeodynamics/bk-joss-paper

JOSS paper

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - 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: docs/paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        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: docs/paper/paper.pdf

.typos.toml

@@ -7,4 +7,4 @@ iy = "iy"
 nin = "nin"
 
 [files]
-extend-exclude = ["tutorials/*.pvsm"]
+extend-exclude = ["tutorials/*.pvsm","docs/paper/paper.bib"]

AUTHORS.md

@@ -14,8 +14,7 @@ provided substantial additions or modifications. Together, these two groups form
 
 
 ## Contributors
-The following people contributed major additions or modifications to `GeophysicalModelGenerator.jl` and
-are listed in alphabetical order:
+The following people contributed major additions or modifications to `GeophysicalModelGenerator.jl` and are listed in alphabetical order:
 
 * Pascal Aellig
 * Albert De Montserrat

Project.toml

@@ -40,8 +40,8 @@ GridapGmsh = "3025c34a-b394-11e9-2a55-3fee550c04c8"
 [extensions]
 Chmy_utils = "Chmy"
 GLMakie_Visualisation = "GLMakie"
-GMT_utils = "GMT"
 Gmsh_utils = "GridapGmsh"
+GMT_utils = "GMT"
 
 [compat]
 Chmy = "0.1.20"
@@ -51,19 +51,19 @@ FFMPEG = "0.4"
 FileIO = "1"
 GDAL_jll = "300.900.0 - 301.901.0"
 GLMakie = "0.8, 0.9, 0.10"
-GMT = "1.0 - 1.14"
 GeoParams = "0.2 - 0.6"
 Geodesy = "1"
 GeometryBasics = "0.1 - 0.4"
 Glob = "1.2 - 1.3"
+GMT = "1"
 GridapGmsh = "0.5 - 0.7"
 ImageIO = "0.1 - 0.6"
 Interpolations = "0.14, 0.15"
 JLD2 = "0.4, 0.5"
 LightXML = "0.8, 0.9"
 MeshIO = "0.1 - 0.4"
-NearestNeighbors = "0.2 - 0.4"
 NCDatasets = "0.14"
+NearestNeighbors = "0.2 - 0.4"
 Parameters = "0.9 - 0.12"
 SpecialFunctions = "1.0, 2"
 StaticArrays = "1"
@@ -74,10 +74,9 @@ julia = "1.9"
 [extras]
 Chmy = "33a72cf0-4690-46d7-b987-06506c2248b9"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
-GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "GMT", "StableRNGs", "GridapGmsh", "Chmy","KernelAbstractions"]
+test = ["Test", "GMT", "StableRNGs", "GridapGmsh", "Chmy", "KernelAbstractions"]

docs/paper/paper.bib

@@ -0,0 +1,109 @@
+@Article{se-10-1785-2019,
+AUTHOR = {Fraters, M. and Thieulot, C. and van den Berg, A. and Spakman, W.},
+TITLE = {The {G}eodynamic {W}orld {B}uilder: 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{Wessel_Luis_Uieda_Scharroo_Wobbe_Smith_Tian_2019, 
+ title={The {G}eneric {M}apping {T}ools {V}ersion 6}, 
+ volume={20}, 
+ ISSN={1525-2027, 1525-2027}, 
+ DOI={10.1029/2019GC008515}, 
+ abstractNote={The {G}eneric {M}apping {T}ools ({GMT}) software is ubiquitous in the Earth and ocean sciences. As a cross‐platform tool producing high‐quality maps and figures, it is used by tens of thousands of scientists around the world. The basic syntax of GMT scripts has evolved very slowly since the 1990s, despite the fact that GMT is generally perceived to have a steep learning curve with many pitfalls for beginners and experienced users alike. Reducing these pitfalls means changing the interface, which would break compatibility with thousands of existing scripts. With the latest GMT version 6, we solve this conundrum by introducing a new “modern mode” to complement the interface used in previous versions, which GMT 6 now calls “classic mode.” GMT 6 defaults to classic mode and thus is a recommended upgrade for all GMT 5 users. Nonetheless, new users should take advantage of modern mode to make shorter scripts, quickly access commonly used global data sets, and take full advantage of the new tools to draw subplots, place insets, and create animations. Plain Language Summary The Generic Mapping Tools software is widely used in Earth and ocean sciences to process data and make maps and illustrations. This new version simplifies usage, adds quick access to key data sets, and provides a tool for making scientific animations.}, 
+ number={11}, 
+ journal={Geochemistry, Geophysics, Geosystems}, 
+ author={Wessel, P. and Luis, J. F. and Uieda, L. and Scharroo, R. and Wobbe, F. and Smith, W. H. F. and Tian, D.}, 
+ year={2019}, month=nov, pages={5556–5564}, language={en} }
+
+ @article{DeLaVarga_Schaaf_Wellmann_2019, title={GemPy 1.0: open-source stochastic geological modeling and inversion}, volume={12}, ISSN={1991-9603}, DOI={10.5194/gmd-12-1-2019}, abstractNote={The representation of subsurface structures is an essential aspect of a wide variety of geoscientific investigations and applications, ranging from geofluid reservoir studies, over raw material investigations, to geosequestration, as well as many branches of geoscientific research and applications in geological surveys. A wide range of methods exist to generate geological models. However, the powerful methods are behind a paywall in expensive commercial packages. We present here a full open-source geomodeling method, based on an implicit potential-field interpolation approach. The interpolation algorithm is comparable to implementations in commercial packages and capable of constructing complex full 3-D geological models, including fault networks, fault–surface interactions, unconformities and dome structures. This algorithm is implemented in the programming language Python, making use of a highly efficient underlying library for efficient code generation (Theano) that enables a direct execution on GPUs. The functionality can be separated into the core aspects required to generate 3-D geological models and additional assets for advanced scientific investigations. These assets provide the full power behind our approach, as they enable the link to machine-learning and Bayesian inference frameworks and thus a path to stochastic geological modeling and inversions. In addition, we provide methods to analyze model topology and to compute gravity fields on the basis of the geological models and assigned density values. In summary, we provide a basis for open scientific research using geological models, with the aim to foster reproducible research in the field of geomodeling.}, number={1}, journal={Geoscientific Model Development}, author={De La Varga, Miguel and Schaaf, Alexander and Wellmann, Florian}, year={2019}, month=jan, pages={1–32}, language={en} }
+
+@article{Paffrath_Friederich_Schmid_Handy_2021, 
+    title={Imaging structure and geometry of slabs in the greater {A}lpine area – a {P}-wave travel-time tomography using {A}lp{A}rray {S}eismic {N}etwork data}, 
+    volume={12}, ISSN={1869-9529}, DOI={10.5194/se-12-2671-2021}, 
+    abstractNote={We perform a teleseismic P-wave travel-time tomography to examine the geometry and structure of subducted lithosphere in the upper mantle beneath the Alpine orogen. The tomography is based on waveforms recorded at over 600 temporary and permanent broadband stations of the dense AlpArray Seismic Network deployed by 24 different European institutions in the greater Alpine region, reaching from the Massif Central to the Pannonian Basin and from the Po Plain to the river Main.}, number={11}, journal={Solid Earth}, author={Paffrath, Marcel and Friederich, Wolfgang and Schmid, Stefan M. and Handy, Mark R. and the AlpArray and AlpArray-Swath D Working Group}, 
+    year={2021}, month=nov, pages={2671–2702}, language={en} }
+
+ @article{Macherel_Räss_Schmalholz_2024, title={3D Stresses and Velocities Caused by Continental Plateaus: Scaling Analysis and Numerical Calculations With Application to the {T}ibetan Plateau}, volume={25}, ISSN={1525-2027, 1525-2027}, DOI={10.1029/2023GC011356}, abstractNote={Understanding stresses is crucial for geodynamics since they govern rock deformation and metamorphic reactions. However, the magnitudes and distribution of crustal stresses are still uncertain. Here, we use a 3D numerical model in spherical coordinates to investigate stresses and velocities that result from lateral crustal thickness variations around continental plateaus like those observed for the Tibetan plateau. We do not consider any far‐field deformation so that the plateau deforms by horizontal dilatation and vertical thinning. We assume viscous creep, a simplified plateau geometry, and simplified viscosity and density distributions to couple the numerical results with a scaling analysis. Specifically, we study the impact of the viscosity ratio between crust and lithospheric mantle, a rectangular plateau corner, a stress‐dependent power‐law flow law and Earth’s double curvature on the crustal stress field and horizontal velocities. Two orders of magnitude variation in crustal and lithospheric mantle viscosities change the maximum crustal differential stress only by a factor of ≈2. We derive simple analytical estimates for the crustal deviatoric stress and horizontal velocity which agree to first order with 3D numerical calculations. We apply these estimates to calculate the average crustal viscosity in the eastern Tibetan plateau as ≈1022 Pa · s. Furthermore, our results show that a corner strongly affects the stress distribution, particularly the shear stresses, while Earth’s curvature has a minor impact on the stresses. We further discuss potential implications of our results to strike‐slip faulting and fast exhumation around the Tibetan plateau’s syntaxes.}, number={3}, journal={Geochemistry, Geophysics, Geosystems}, author={Macherel, Emilie and Räss, Ludovic and Schmalholz, Stefan M.}, year={2024}, month=mar, pages={e2023GC011356}, language={en} }
+
+ @article{Rappisi_VanderBeek_Faccenda_Morelli_Molinari_2022, title={Slab Geometry and Upper Mantle Flow Patterns in the {C}entral {M}editerranean From {3D} Anisotropic {P}‐Wave Tomography}, volume={127}, ISSN={2169-9313, 2169-9356}, DOI={10.1029/2021JB023488}, abstractNote={We present the first three-dimensional (3D) anisotropic teleseismic P-wave tomography model of the upper mantle covering the entire Central Mediterranean. Compared to isotropic tomography, it is found that including the magnitude, azimuth, and, importantly, dip of seismic anisotropy in our inversions simplifies isotropic heterogeneity by reducing the magnitude of slow anomalies while yielding anisotropy patterns that are consistent with regional tectonics. The isotropic component of our preferred tomography model is dominated by numerous fast anomalies associated with retreating, stagnant, and detached slab segments. In contrast, relatively slower mantle structure is related to slab windows and the opening of back-arc basins. To better understand the complexities in slab geometry and their relationship to surface geological phenomenon, we present a 3D reconstruction of the main Central Mediterranean slabs down to 700 km based on our anisotropic model. P-wave seismic anisotropy is widespread in the Central Mediterranean upper mantle and is strongest at 200–300 km depth. The anisotropy patterns are interpreted as the result of asthenospheric material flowing primarily horizontally around the main slabs in response to pressure exerted by their mid-to-late Cenezoic horizontal motion, while sub-vertical anisotropy possibly reflects asthenospheric entrainment by descending lithosphere. Our results highlight the importance of anisotropic P-wave imaging for better constraining regional upper mantle geodynamics.}, number={5}, journal={Journal of Geophysical Research: Solid Earth}, author={Rappisi, F. and VanderBeek, B. P. and Faccenda, M. and Morelli, A. and Molinari, I.}, year={2022}, month=may, pages={e2021JB023488}, language={en} }
+
+ @phdthesis{Schori_2021, type={PhD}, title={The {D}evelopment of the {J}ura {F}old-and-{T}hrust {B}elt: pre-existing {B}asement {S}tructures and the {F}ormation of {R}amps}, url={https://folia.unifr.ch/unifr/documents/313053}, 
+    DOI={10.51363/unifr.sth.2022.001},school={University of Fribourg (Switzerland)}, author={Schori, Marc}, year={2021}, month=oct, language={en} }
+
+ @article{McKenzie_1969, title={Speculations on the Consequences and Causes of Plate Motions}, volume={18}, ISSN={0956-540X, 1365-246X}, DOI={10.1111/j.1365-246X.1969.tb00259.x}, abstractNote={Plate theory has successfully related sea floor spreading to the focal mechanisms of earthquakes and the deep structure of island arcs. It is used here to calculate the temperature distribution in the lithosphere thrust beneath island arcs, and to determine the flow and the stress elsewhere in the mantle. Comparison with observations demonstrates that earthquakes are restricted to those regions of the mantle which are colder than a definite temperature. The flow and the stress heating in the mantle can maintain the high heat flow anomaly observed behind island arcs.}, number={1}, journal={Geophysical Journal International}, author={McKenzie, D. P.}, year={1969}, month=sep, pages={1–32}, language={en} }
+
+@article{bezanson2017julia,
+  title={Julia: {A} Fresh Approach to Numerical Computing},
+  author={Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and
+          Shah, Viral B},
+  journal={SIAM Review},
+  volume={59},
+  number={1},
+  pages={65--98},
+  year={2017},
+  publisher={SIAM},
+  eprint={1411.1607},
+  eprinttype={arxiv},
+  eprintclass={cs.MS},
+  doi={10.1137/141000671}
+}
+
+ @article{desiena2024geophysical,
+  title={Geophysical responses to an environmentally-boosted volcanic unrest},
+  author={De Siena, L and Amoruso, A and Petrosino, S and Crescentini, L},
+  journal={Geophysical Research Letters},
+  volume={51},
+  number={5},
+  pages={e2023GL104895},
+  year={2024},
+  doi={10.1029/2023GL104895},
+  publisher={Wiley Online Library}
+}
+
+@article{gabrielli2023scattering,
+  title={Scattering attenuation images of the control of thrusts and fluid overpressure on the 2016--2017 Central Italy seismic sequence},
+  author={Gabrielli, Simona and Akinci, Aybige and De Siena, Luca and Del Pezzo, Edoardo and Buttinelli, Mauro and Maesano, Francesco Emanuele and Maffucci, Roberta},
+  journal={Geophysical Research Letters},
+  volume={50},
+  number={8},
+  pages={e2023GL103132},
+  year={2023},
+  doi={10.1029/2023GL103132},
+  publisher={Wiley Online Library}
+}
+
+ @inproceedings{Kaus_Popov_Baumann_Pusok_Bauville_Fernandez_Collignon_2016, 
+ title={Forward and inverse modelling of lithospheric deformation on geological timescales}, 
+ volume={48}, 
+ rights={All rights reserved}, 
+ ISBN={978-3-95806-109-5}, 
+ url={https://juser.fz-juelich.de/record/507751/files/nic_2016_kaus.pdf}, 
+ booktitle={NIC Series}, 
+ author={Kaus, Boris JP and Popov, Anton A. and Baumann, T. and Püsök, A. and Bauville, Arthur and Fernandez, Naiara and Collignon, Marine}, 
+ year={2016}, 
+ pages={299-306}
+}
+@article{napolitano2023imaging,
+  title={Imaging overpressurised fracture networks and geological barriers hindering fluid migrations across a slow-deformation seismic gap},
+  author={Napolitano, Ferdinando and Gabrielli, Simona and De Siena, Luca and Amoroso, Ortensia and Capuano, Paolo},
+  journal={Scientific Reports},
+  volume={13},
+  number={1},
+  pages={19680},
+  year={2023},
+  doi={10.1038/s41598-023-47104-w},
+  publisher={Nature Publishing Group UK London}
+}
+
+ @article{Bauville_Baumann_2019, 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}, volume={20}, ISSN={1525-2027, 1525-2027}, DOI={10.1029/2018GC008057}, number={3}, journal={Geochemistry, Geophysics, Geosystems}, author={Bauville, A. and Baumann, T. S.}, year={2019}, month=mar, pages={1665–1675}, language={en} }
+
+ @article{Shephard_Matthews_Hosseini_Domeier_2017, title={On the consistency of seismically imaged lower mantle slabs}, volume={7}, ISSN={2045-2322}, DOI={10.1038/s41598-017-11039-w}, abstractNote={Abstract
+            The geoscience community is increasingly utilizing seismic tomography to interpret mantle heterogeneity and its links to past tectonic and geodynamic processes. To assess the robustness and distribution of positive seismic anomalies, inferred as subducted slabs, we create a set of vote maps for the lower mantle with 14 global P-wave or S-wave tomography models. Based on a depth-dependent threshold metric, an average of 20% of any given tomography model depth is identified as a potential slab. However, upon combining the 14 models, the most consistent positive wavespeed features are identified by an increasing vote count. An overall peak in the most robust anomalies is found between 1000–1400 km depth, followed by a decline to a minimum around 2000 km. While this trend could reflect reduced tomographic resolution in the middle mantle, we show that it may alternatively relate to real changes in the time-dependent subduction flux and/or a mid-lower mantle viscosity increase. An apparent secondary peak in agreement below 2500 km depth may reflect the degree-two lower mantle slow seismic structures. Vote maps illustrate the potential shortcomings of using a limited number or type of tomography models and slab threshold criteria.}, number={1}, journal={Scientific Reports}, author={Shephard, G. E. and Matthews, K. J. and Hosseini, K. and Domeier, M.}, year={2017}, month=sep, pages={10976}, language={en} }
+