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model_submission's Introduction

Welcome to the Model Atlas of The Earth (M@TE)

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Model submission overview and objectives

  • M@TE models begin their life as github repositories, based on a this repository template
  • New models are spawned using the github issues functionality, within this repository
  • We provide workflows (using github actions) that aim to harvest and reuse as much existing metadata as possible, using persistent identifiers such as ORCiDs and RoRs
  • The result is a model repository that comes with a rich metadata document, based on the RO-Crate project
  • This process also assembles material so we can feature the model on the M@TE website

Model submission workflow:

1) Make a new model request:

  • open a new issue using the New model request
  • fill in as much information as you can and submit the issue
  • a new model New model label will appear on the original issue
  • This will trigger workflows that collect this information and source additional metadata relavant to your model
  • You will see a summary report for your model, including potential missing information or errors (e.g. URLs that didn't resolve)
  • If you have requested the content of your model to be embargoed, you should see an embargo requested label. We can still create a model repository, metadata file, and DOI for this model

2) Editing and review:

  • By editing the first comment in the issue discussion, you will trigger a rebuild of the model information
  • When you are satisfied with the information contained in the report, add a review requested Review requested label to the issue

3) Model repository creation:

  • The model_reviewers team will add an model approved Model approved label to the issue
  • this triggers the creation of a new model repository within the M@TE organization, based on this simple template
  • the model metadata is stored as an RO-Crate (named ro-crate-metadata.json) in the top level of the repository
  • A model created Model created label will appear on your issue
  • The github account holder who submitted the model will have owner privillages.

4) Clone and configure your model repository:

  • Your model repository is now yours to customize and fill with files (payload)
  • We encourage you to use github to add any material that is within github's typical repository limits (files < 100 Mb, total repository size < 5 Gb)
  • You may customize the model repository as you feel fit. This may require editing of the metadata file () to reflect changes in directory structure
  • Push any changes back to the M@TE organization.

5) Upload model to our NCI Server:

  • Add an upload to NCI label to the model submission issue
  • Let us know (via the original issue) if you need to add additional files that exceed Github's limits
    • The model_reviewers team will contact you via email to orchestrate this process

6) Model published:

  • Your model will be published on the NCI GeoNetworkCatalog
  • It will recieve a DOI and this will be automatically added to your model metadata
  • Your model will be featured on the M@TE website
  • a model published Model published label will appear on the original issue

Links

Motivation and further reading

model_submission's People

Contributors

dansand avatar hvidy avatar

Watchers

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Forkers

dansand

model_submission's Issues

M@TE submission request from @dansand

-> submitter ORCID (or name)

0000-0002-2207-6837

-> slug

test_embargo_2024

-> license

CC-BY-4.0

-> model category

other

-> model status

completed

-> associated publication DOI

https://doi.org/10.1029/2023TC007958

-> model creators

0000-0002-2207-6837

-> model contributors

No response

-> title

No response

-> description

No response

-> scientific keywords

foo

-> funder

No response

-> model embargo?

2025-01-01

-> include model code ?

  • yes

-> model code/inputs DOI

No response

-> model code/inputs notes

No response

-> include model output data?

  • yes

-> data creators

No response

-> model output data DOI

No response

-> model output data notes

No response

-> model output data size

No response

-> software framework DOI/URI

No response

-> software framework source repository

No response

-> name of primary software framework (e.g. Underworld, ASPECT, Badlands, OpenFOAM)

No response

-> software framework authors

No response

-> software & algorithm keywords

No response

-> computer URI/DOI

No response

-> add landing page image and caption

No response

-> add an animation (if relevant)

No response

-> add a graphic abstract figure (if relevant)

No response

-> add a model setup figure (if relevant)

No response

-> add a description of your model setup

No response

Please provide any feedback on the model submission process?

No response

Flexural isostatic response of continental-scale deltas to climatically driven sea level changes

-> submitter ORCID (or name)

0000-0002-1270-4377

-> slug

polanco-2024-deltas

-> license

CC-BY-4.0

-> alternative license URL

No response

-> model category

model published in study

-> model status

completed

-> associated publication DOI

10.5194/esurf-12-301-2024

-> model creators

No response

-> title

No response

-> description

Two-thirds of the world's most populated cities are situated close to deltas. We use computer simulations to understand how deltas sink or rise in response to climate-driven sea level changes that operate from thousands to millions of years. Our research shows that because of the interaction between the outer layers of the Earth, sediment transport, and sea level changes deltas develop a self-regulated mechanism that modifies the space they need to gain or lose land.

-> abstract

No response

-> scientific keywords

No response

-> funder

Australian Research Council, IH130200012
Australian–American Fulbright Commission
The University of Melbourne

-> model embargo?

No

-> include model code ?

  • yes

-> model code/inputs DOI

10.5281/zenodo.10553849

-> model code/inputs notes

The input and boundary conditions for the model are structured as follows:
an input XML file where the initial and boundary conditions are set
a data folder containing the initial surface and the boundary conditions, in this case different sea-level scenarios
a series of IPython Notebooks used to run the experiment and perform some pre or post-processing tasks.

-> include model output data?

  • yes

-> data creators

0000-0002-1270-4377

-> model output data DOI

No response

-> model output data notes

The model output data is stored in a hdf5 format. You will see a h5 folder and a series of xdmf files.

  • h5 folder contains the hdf5 data, all the information computed by the model are stored in these files. You will have at least the tin (surface) and flow (stream network) dataset and also the sed (stratigraphy) data if the stratal structure is computed in your simulation.

  • two .xdmf files for the surface (tin_series.xdmf) and the flow network (flow_series.xdmf) that read the xmf files through time.

-> model output data size

No response

-> software framework DOI/URI

doi: 10.5281/zenodo.1069573

-> software framework source repository

https://github.com/badlands-model/badlands

-> name of primary software framework (e.g. Underworld, ASPECT, Badlands, OpenFOAM)

Badlands

-> software framework authors

No response

-> software & algorithm keywords

No response

-> computer URI/DOI

No response

-> add landing page image and caption

fig1
Our simulations produce catchment areas, river lengths, and volumes of deposited sediment that are consistent with the ranges observed in continental-scale deltas such as the Mississippi and Amazon rivers. (a) Example showing the outputs from the numerical simulation showing the elevation and bathymetry (top) and cumulative flexure (bottom). Model dimensions are 4500 km x 2000 km, with a vertical exaggeration of 100x. (b) Scatter plot of river length (top) and 405 shelf width (bottom) versus catchment area from river systems. Data is from Somme et al. (2009), Nyberg et al. (2018), Blum et al. (2013, 2017) and simulations presented in this study. Pal= Paleocene, Oli=Oligocene, PM= Paleo-Mississippi. (c) Example of synthetic stratigraphy from a simulation without (left) and with flexural compensation (right).

-> add an animation (if relevant)

https://github.com/ModelAtlasofTheEarth/model_submission/assets/29790931/b6dae5a4-f5bd-413d-ab7f-14349e1f54a1
The animation shows the surface and stratigraphic evolution of our simulated continental-scale deltas. We let each simulation initialize and run for 2 Myr without any sea-level fluctuations so that the delta can reach dynamic equilibrium without any disturbances in base level, then impose climate-forced sea-level changes.

-> add a graphic abstract figure (if relevant)

egusphere-2023-53_Fig5.pdf

Output of numerical simulations with imposed synthetic sea-level curves with different frequencies (f) showing elevation, bathymetry and discharge of the river mouth at 8 Myr. Note the difference in lateral extent, elevation due to flexural rebound, and river mouth morphology between the flexural (top) and non-flexural (bottom) cases. (b) Change of river mouth location though time for simulations where synthetic and empirical sea-level curves were imposed. Mean river mouth transit distances in the non-flexurally compensated simulations are shown in lighter shades, whereas the flexurally compensated cases are shown in darker shades. (c) Bar plot showing the frequency of the number of times where the de-trended river-mouth trajectory crosses an arbitrary point in the shelf an indicator of how often the river mouth is close to the shelf break. NF = non-flexural, F = flexural, IH = icehouse, and GH = greenhouse.

-> add a model setup figure (if relevant)

fig_setup

-> add a description of your model setup

Planview of model setup (top) and cross-section in the middle of the modeling domain. The initial configuration of the modeling domain resembles the topography of a natural source-to-sink system with 3400 m elevation in the headwaters, a length of 4500 km, a downstream-decreasing fluvial channel slope, and successive inflections in gradient associated with the coastal-plain to continental shelf and shelf to slope transitions. To ensure that our simulated drainage basin produces a point-source for sediment input to the marine domain we imposed a longitudinal topographic low in the middle of the model.

Please provide any feedback on the model submission process?

Thanks Dan, great job!

M@TE submission request from [@dansand]

-> submitter ORCID (or name)

0000-0002-2207-6837

-> slug

mather-2022-groundwater

-> license

CC-BY-4.0

-> alternative license URL

No response

-> model category

model published in study, inverse model

-> model status

completed

-> associated publication DOI

http://dx.doi.org/10.1038/s41598-022-08384-w

-> model creators

0000-0003-3566-1557
0000-0002-3334-5764
0000-0002-6034-1881
0000-0002-7182-1864
0000-0002-6557-0237
0000-0003-3685-174X

-> title

No response

-> description

This model was developed in order to study groundwater flow on a continental scale, focusing on the Sydney–Gunnedah–Bowen Basin in Australia. Using data such as hydraulic head measurements and borehole temperatures, it predicts how water moves through deep aquifers to the surface. Coastal aquifers show fast water flow, while inland aquifers have much slower flow. The study shows that increased water extraction from inland areas could permanently change water flow patterns. This open-source model can be used for other regions and aims to support sustainable groundwater management policies

-> abstract

Numerical models of groundwater flow play a critical role for water management scenarios under climate extremes. Large-scale models play a key role in determining long range flow pathways from continental interiors to the oceans, yet struggle to simulate the local flow patterns offered by small-scale models. We have developed a highly scalable numerical framework to model continental groundwater flow which capture the intricate flow pathways between deep aquifers and the near-surface. The coupled thermal-hydraulic basin structure is inferred from hydraulic head measurements, recharge estimates from geochemical proxies, and borehole temperature data using a Bayesian framework. We use it to model the deep groundwater flow beneath the Sydney–Gunnedah–Bowen Basin, part of Australia’s largest aquifer system. Coastal aquifers have flow rates of up to 0.3 m/day, and a corresponding groundwater residence time of just 2,000 years. In contrast, our model predicts slow flow rates of 0.005 m/day for inland aquifers, resulting in a groundwater residence time of 400,000 years. Perturbing the model to account for a drop in borehole water levels since 2000, we find that lengthened inland flow pathways depart significantly from pre-2000 streamlines as groundwater is drawn further from recharge zones in a drying climate. Our results illustrate that progressively increasing water extraction from inland aquifers may permanently alter long-range flow pathways. Our open-source modelling approach can be extended to any basin and may help inform policies on the sustainable management of groundwater.

-> scientific keywords

groundwater, thermal-hydraulic, Bayesian, water-management

-> funder

NSW Department of Industry
https://ror.org/04s1m4564

-> model embargo?

No response

-> include model code ?

  • yes

-> model code/inputs DOI

https://github.com/brmather/Sydney_Basin/tree/master

-> model code/inputs notes

In the Scripts folder, HL05 was used to run the optimisation problem and HL06 was used to take the maximum a posteriori model and run it at high resolution.

-> include model output data?

  • yes

-> data creators

No response

-> model output data DOI

No response

-> model output data notes

model_output_data contains the following file types:

.h5 - Underworld2 data files
.xdmf- Underworld2 xdmf header files
.csv - Various data in csv format
.npz - data on numpy binary format
.png - image files
.pvsm - Paraview state files
.txt - data in .txt format

-> model output data size

15 Gb

-> software framework DOI/URI

https://doi.org/10.5281/zenodo.7455999

-> software framework source repository

https://github.com/underworldcode/underworld2

-> name of primary software framework (e.g. Underworld, ASPECT, Badlands, OpenFOAM)

No response

-> software framework authors

No response

-> software & algorithm keywords

Python, C, finite element, heat equation, advection-diffusion

-> computer URI/DOI

https://ror.org/04yx6dh41

-> add landing page image and caption

No response

-> add an animation (if relevant)

No response

-> add a graphic abstract figure (if relevant)

Coupled heat-groundwater flow model of the Sydney–Gunnedah–Bowen Basin based on the MAP estimate of material properties and boundary conditions. (A) Groundwater velocity field with coal seams outlined in grey overlain with temperature gradients measured in boreholes. This visualisation of the velocity field obtained from our model was rendered in 3D using Paraview 5.9 (https://www.paraview.org/). (B) temperature field overlain with heat flux vectors. The 2D slice was generated from our models using Matplotlib 3.4 (https://matplotlib.org/).

fig1

-> add a model setup figure (if relevant)

3D stratigraphy of the Sydney–Gunnedah–Bowen Basin. The vertical spacing of layers has been exaggerated for visual clarity. The model of the basin was rendered in 3D using Underworld.
figure_2

-> add a description of your model setup

In this paper, we apply our numerical framework to the Sydney–Gunnedah–Bowen (SGB) Basin in eastern Australia. The SGB Basin covers about 1.5 million square kilometers, and we model it in high-resolution 3D, using over 10 million cells (or 6 x 6 x 0.6 km, in the x, y, z directions, respectively) to detail flow patterns down to 12 km beneath the crust. By adjusting the model to match real-world data, it provides accurate insights into water and heat movement through deep aquifers in large areas. Temperature advection due to groundwater flow is described by the advection-diffusion equation. Darcy flux is calculated from the groundwater flow equation. Groundwater recharge and discharge are driven by changes in hydraulic head, which is set to the height of the water table at the top boundary surface. The thermal boundary conditions include a constant temperature set to the top boundary, which corresponds to the annual mean surface temperature. The side walls are assigned zero flux, and the bottom temperature boundary is an unknown variable that we invert from borehole temperature data within our Bayesian optimization scheme.

Please provide any feedback on the model submission process?

No response

M@TE submission request from @dansand

-> submitter ORCID (or name)

0000-0002-2207-6837

-> slug

sandiford-2021-detachment

-> license

CC-BY-4.0

-> model category

model published in study, forward model

-> associated publication DOI

http://dx.doi.org/10.1029/2021gc009681

-> model creators

-> model contributors

No response

-> title

No response

-> description

This model was developed in order to study the rotation of footwall rocks beneath oceanic detachment faults (ODFs). It showed that solid-block rotation dominates beneath a concave-down fault, while significant flexural stresses form later during "apparent unbending," causing both compression and extension-related brittle strain within oceanic core complexes (OCCs).

-> abstract

No response

-> scientific keywords

tectonics, faulting, detachment faults

-> funder

https://ror.org/05mmh0f86, DP180102280
https://www.helmholtz.de/, VH-NG-1132

-> include model code ?

  • yes

-> model code/inputs DOI

https://github.com/dansand/odf_paper

-> model code/inputs notes

ASPECT Input files for model. Input file has been updated for compatibility with more recent ASPECT versions. Input file tested on ASPECT version 2.6.0-pre (fix_stresses_elasticity, 621dd61f2), using deal.II 9.4.2.

-> include model output data?

  • yes

-> data creators

0000-0002-2207-6837

-> model output data DOI

No response

-> model output data notes

Data directory contains output data for 2 simulations stored in the following directories: ref_model_hires, alt_model_hires. Top level contains typical ASPECT output files, including log.txt and restart files. Topography and mesh variables were output at 100 Kyr intervals. Model end time is 5 Myr. Main output data consists of of plain text files representing model topography (e.g. topography.00000), vtu files (in the ./solution sub-directory) representing model output fields (e.g. solution-00000.0000.vtu). At each output step, there are 16 vtu files written. These can be opened with Paraview using the solution.pvd file in the top level.

-> model output data size

Model output data total about 11Gb

-> software framework DOI/URI

https://doi.org/10.5281/zenodo.8200213

-> software framework source repository

No response

-> name of primary software framework (e.g. Underworld, ASPECT, Badlands, OpenFOAM)

No response

-> software framework authors

No response

-> software & algorithm keywords

C++, finite-element, mesh-refinement

-> computer URI/DOI

https://dx.doi.org/10.25914/608bfd1838db2

-> add landing page image and caption

fig1
Deviatoric stresses and vorticity in reference model.

-> add an animation (if relevant)

https://github.com/ModelAtlasofTheEarth/Model_Submission/assets/10967872/1f89632e-53ee-4b34-8eaf-2f8a8ce351a4
Animation for alternative model showing vorticity.

-> add a graphic abstract figure (if relevant)

fig4
Schematic showing the stress state that would be generated assuming elastic constitutive response of the ODF footwall (top). Bottom shows the strain-rate due to "advective" component of the curvature rate.

-> add a model setup figure (if relevant)

initialconds
Initial conditions, showing mesh refinement.

-> add a description of your model setup

The domain is $400 ; \mathrm{km}$ wide and $100 ; \mathrm{km}$ deep, and includes five levels of mesh refinement, as shown in the figure. The model is initialised with a symmetric temperature structure, defined by a transient 1-D cooling profile, with an age of $0.5 ; \mathrm{Myr}$ in the center of the domain. The thermal profile ages outwardly in proportion to the applied spreading rate of $2 ; \mathrm{cm,{yr}^{-1}}$ (full rate), which is representative for slow spreading ridges. Uniform inflow at the bottom boundary balances the outward flux of material at the side boundaries. The model has a true free surface, and a diffusion process is applied to the surface topography in order to counteract strong mesh deformation. A simplification here is that the effect of the water column is ignored, i.e. the detachment system is modeled as sub-aerial. There is no compositional differentiation in the model (i.e. no crust/mantle) and all parts of the domain are subject to the same constitutive model. The constitutive model incorporates viscous (dislocation creep), elastic and plastic (pseudo-brittle) deformation mechanisms, hereafter referred to as visco-elastic plastic (VEP) rheology, following the approach of Moresi et al. (2003). The advection-diffusion equation included an anomalously- high diffusivity $(3 \times {10}^{-6} ; \mathrm{m^2 , s^{-1}})$ which is intended to model the near axis cooling effect of hydrothermal circulation (cf. Lavier and Buck, 2002). As implemented here, the higher diffusivity applies throughout the domain, rather than being localized at the ridge (as in Lavier and Buck, 2002). The parameters chosen here result in $\sim 10 ; \mathrm{km}$ lithosphere at the ridge axis, which is in the range identified for ODF development. Due to the difference in diffusivity values in the initial conditions $({10}^{-6} ; \mathrm{m^2 , s^{-1}})$, and temperature evolution equation $(3 \times {10}^{-6})$, the thermal structure is not in steady state and some cooling of the off-axis lithosphere occurs.

M@TE submission request from @hvidy

-> submitter ORCID (or name)

0000-0003-3566-1557

-> slug

mather-2022-newerslug

-> license

GPL-3.0

-> model category

model published in study

-> associated publication DOI

10.1038/s41598-022-08384-w

-> model creators

No response

-> model contributors

No response

-> title

No response

-> description

No response

-> scientific keywords

test keyword, science

-> funder

https://ror.org/05mmh0f86

-> include model code ?

  • yes

-> model code/inputs DOI

No response

-> model code/inputs notes

No response

-> include model output data?

  • yes

-> data creators

No response

-> model output data DOI

https://zenodo.org/doi/10.5281/zenodo.5831990

-> model output data notes

No response

-> model output data size

No response

-> software framework DOI/URI

https://zenodo.org/doi/10.5281/zenodo.7455999

-> software framework source repository

https://github.com/underworldcode/underworld2

-> name of primary software framework (e.g. Underworld, ASPECT, Badlands, OpenFOAM)

No response

-> software framework authors

No response

-> software & algorithm keywords

Python, C, finite element

-> computer URI/DOI

https://ror.org/04yx6dh41

-> add landing page image and caption

image
Here is a caption

-> add an animation (if relevant)

No response

-> add a graphic abstract figure (if relevant)

new-image
Graphic abstract caption

-> add a model setup figure (if relevant)

No response

-> add a description of your model setup

No response

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