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LICENCES. first draft of start.ipynb and README.md
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2 changes: 1 addition & 1 deletion LICENSE
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MIT License
MIT License - apply to all except ./data/

Copyright (c) 2021 tth030

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86 changes: 72 additions & 14 deletions README.md
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# SM_ESR_isostasy
# my-first-binder
my-first-binder

This repository contains a collection of Jupyter notebooks that contains the display and the analysis of data presented in the following research paper:
This repository contains a collection of [Jupyter notebooks](#jupyter-notebooks) and [datasets](#datasets) as supplement of the following research paper:

Theunissen, T., Huismans, R. S., Gang L. and Riel N. Relative continent/mid-ocean ridge elevation: a reference case for isostasy in geodynamics. Submitted to Earth Science Reviews, October 2021
- Theunissen, T., Huismans, R.S., Lu, G. and Riel, N. Relative continent/mid-ocean ridge elevation: a reference case for isostasy in geodynamics. Earth-Science Reviews (Under preparation, submission december 2021)

SM: Supplementary Material
ESR: Earth Science Reviews
***Please cite the source when using these data.***

This Repository allows:

- Displaying data and computing statistics on elevation of continents and mid-ocean ridges
- Displaying and downloading thermodynamic solutions including input files, raw data and grids of density, melt fraction,...
- Computing basic 1-D isostatic balance for a reference case

## Content

- [How to run the notebooks?](#how-to-run-the-notebooks)
- [Run in the cloud (Binder)](#run-in-the-cloud-binder)
- [Install and run locally (Conda)](#install-and-run-locally-conda)
- [How to contribute?](#how-to-contribute)
- [Jupyter notebooks](#jupyter-notebooks)
- [Datasets](#datasets)

## How to run the notebooks?

### Run in the cloud (Binder)

You can run the notebooks in your browser without installing anything thanks to
[binder](https://mybinder.org/). Just follow the link below or click on the
"launch binder" badge above and it will launch remotely a new notebook server
for you:
[binder](https://mybinder.org/). Just follow the link below and it will launch
remotely a new notebook server for you:

- [Run on binder](https://mybinder.org/v2/gh/tth030/SM_ESR_isostasy/main?urlpath=lab)
- [Run on binder](https://mybinder.org/v2/gh/tth030/my-first-binder/main?labpath=start.ipynb)

### Install and run locally (Conda)

Expand All @@ -30,10 +38,10 @@ installed, you can install all the packages required to run the notebooks in a
new conda environment using the following commands:

```bash
$ git clone https://github.com/fastscape-lem/fastscape-demo
$ cd fastscape-demo
$ git clone https://github.com/tth030/my-first-binder.git
$ cd my-first-binder
$ conda env create -f environment.yml
$ conda activate SM_ESR_isostasy
$ conda activate my-first-binder
```

You also need to install a few Jupyterlab extensions with the following command
Expand All @@ -51,5 +59,55 @@ Finally run the command below to start the Jupyterlab application. It should
open a new tab in your browser.

```bash
$ jupyter lab
$ jupyter-lab start.ipynb
```

## Jupyter notebooks

- `start.ipynb`: general introduction and disclaimers
- `topography.ipynb`: data display and download, computation of statistics of Earth Topography
- `thermodyn.ipynb`: data display and download, results from thermodynamic calculations

## Datasets

### Disclaimer:

Some files provided here (data/) comes from a preliminary filtering using a command that is described in each binary header (can be read using `ncinfo` or `gmt gmtinfo`). Links provided here will give you access directly to the raw data or to a contact email.

***Please cite each specific source when using these data.***

### ETOPO1

- [https://www.ngdc.noaa.gov/mgg/global/](https://www.ngdc.noaa.gov/mgg/global/)
- NOAA National Geophysical Data Center. 2009: ETOPO1 1 Arc-Minute Global Relief Model. NOAA National Centers for Environmental Information. Accessed [date]\
- Amante, C. and B.W. Eakins, 2009. ETOPO1 1 Arc-Minute Global Relief Model: Procedures, Data Sources and Analysis. NOAA Technical Memorandum NESDIS NGDC-24. National Geophysical Data Center, NOAA. [doi:10.7289/V5C8276M](http://dx.doi.org/10.7289/V5C8276M) [access date]

### Seafloor ages and spreading rate

- [https://www.earthbyte.org/age-spreading-rates-and-spreading-asymmetry-of-the-worlds-ocean-crust/](https://www.earthbyte.org/age-spreading-rates-and-spreading-asymmetry-of-the-worlds-ocean-crust/)
- Müller, R.D., M. Sdrolias, C. Gaina, and W.R. Roest 2008. Age, spreading rates and spreading symmetry of the world's ocean crust, Geochem. Geophys. Geosyst., 9, Q04006, [doi:10.1029/2007GC001743](https://doi.org/10.1029/2007GC001743)

### Horizontal strain rate

- [https://gsrm2.unavco.org/intro/intro.html](https://gsrm2.unavco.org/intro/intro.html)
- Kreemer, C., G. Blewitt, E.C. Klein, 2014, A geodetic plate motion and Global Strain Rate Model, Geochemistry, Geophysics, Geosystems, 15, 3849-3889, [https://doi.org/10.1002/2014GC005407](https://doi.org/10.1002/2014GC005407)

### High resolution bathymetry data

- [https://www.gmrt.org/about/](https://www.gmrt.org/about/)
- Ryan, W. B. F., et al. (2009), Global Multi-Resolution Topography synthesis, Geochem. Geophys. Geosyst., 10, Q03014, [doi:10.1029/2008GC002332](https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2008GC002332)

### Lithospheric thickness (average based on several seismological estimates)

- Steinberger, B. and Becker, T.W. A comparison of lithospheric thickness models, Tectonophysics, 746 (2018), pp. 325-338, [doi.org/10.1016/j.tecto.2016.08.001](https://www.sciencedirect.com/science/article/pii/S004019511630316X?via%3Dihub)

### Age of the lithosphere from seismological analysis

- Poupinet, G., Shapiro, N.M. Worldwide distribution of ages of the continental lithosphere derived from a global seismic tomographic model, Lithos, 109 (2009), pp. 125-130, [doi.org/10.1016/j.lithos.2008.10.023](https://www.sciencedirect.com/science/article/pii/S0024493708002582?via%3Dihub)

### Hot spots list

- [http://www.mantleplumes.org/P%5E4/P%5e4Chapters/MorganP4ElectronicSupp1.pdf](http://www.mantleplumes.org/P%5E4/P%5e4Chapters/MorganP4ElectronicSupp1.pdf)
- Morgan, W.J. and Morgan, J.P. Plate velocities in the hotspot reference frame, Plates, Plumes and Planetary Processes, Gillian R. Foulger, Donna M. Jurdy, (2007), [doi.org/10.1130/2007.2430(04)](https://pubs.geoscienceworld.org/gsa/books/book/618/chapter/3805271/Plate-velocities-in-the-hotspot-reference-frame)


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1 change: 1 addition & 0 deletions scripts/__init__.py
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from .hello import *
3 changes: 3 additions & 0 deletions scripts/hello.py
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print("Hello world!!!")
177 changes: 177 additions & 0 deletions start.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<img src=\"./assets/illustration.png\" style=\"width: 1000px;\"/>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<script>\n",
" // AUTORUN ALL CELLS ON NOTEBOOK-LOAD!\n",
" require(\n",
" ['base/js/namespace', 'jquery'], \n",
" function(jupyter, $) {\n",
" $(jupyter.events).on(\"kernel_ready.Kernel\", function () {\n",
" console.log(\"Auto-running all cells-below...\");\n",
" jupyter.actions.call('jupyter-notebook:run-all-cells-below');\n",
" jupyter.actions.call('jupyter-notebook:save-notebook');\n",
" });\n",
" }\n",
" );\n",
"</script>"
]
},
{
"cell_type": "markdown",
"metadata": {
"tags": []
},
"source": [
"## Supplementary material\n",
"\n",
"<p style=\"color:rgb(255,0,0);\">Please cite the source when using these data:</p>\n",
"Theunissen, T., Huismans, R.S., Lu, G. and Riel, N. Relative continent/mid-ocean ridge elevation: a reference case for isostasy in geodynamics. Earth-Science Reviews (Under preparation, submission december 2021)<br><br>\n",
"\n",
"\n",
"This Repository allows:\n",
"- Displaying data and computing statistics on elevation of continents and mid-ocean ridges\n",
"\n",
"- Displaying and downloading thermodynamic solutions (raw data and grids of density, melt fraction,...)\n",
"\n",
"- Computing a basic 1-D isostatic balance for a reference case\n",
"\n",
"## What are the data used to analyse Earth topography?\n",
"\n",
"<strong>Disclaimer</strong>: Some files provided here (data/) comes from a preliminary filtering using a command that is described in each binary header (can be read using `ncinfo` or `gmt gmtinfo`). Links provided here will give you access directly to the raw data or to a contact email. <p style=\"color:rgb(255,0,0);\">Please cite each specific source when using these data.</p>\n",
"\n",
"\n",
"- ETOPO1\n",
" - https://www.ngdc.noaa.gov/mgg/global/\n",
" - NOAA National Geophysical Data Center. 2009: ETOPO1 1 Arc-Minute Global Relief Model. NOAA National Centers for Environmental Information. Accessed [date]\n",
" - Amante, C. and B.W. Eakins, 2009. ETOPO1 1 Arc-Minute Global Relief Model: Procedures, Data Sources and Analysis. NOAA Technical Memorandum NESDIS NGDC-24. National Geophysical Data Center, NOAA. doi:10.7289/V5C8276M [access date]\n",
"\n",
"\n",
"- Seafloor ages and spreading rate\n",
" - https://www.earthbyte.org/age-spreading-rates-and-spreading-asymmetry-of-the-worlds-ocean-crust/\n",
" - Müller, R.D., M. Sdrolias, C. Gaina, and W.R. Roest 2008. Age, spreading rates and spreading symmetry of the world's ocean crust, Geochem. Geophys. Geosyst., 9, Q04006, <a href=\"https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2007GC001743\">doi:10.1029/2007GC001743</a>\n",
"\n",
"\n",
"- Horizontal strain rate\n",
" - https://gsrm2.unavco.org/intro/intro.html\n",
" - Kreemer, C., G. Blewitt, E.C. Klein, 2014, A geodetic plate motion and Global Strain Rate Model, Geochemistry, Geophysics, Geosystems, 15, 3849-3889, <a href=\"https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2014GC005407\">https://doi.org/10.1002/2014GC005407</a>\n",
"\n",
"\n",
"- High resolution bathymetry data\n",
" - https://www.gmrt.org/about/\n",
" - Ryan, W. B. F., et al. (2009), Global Multi-Resolution Topography synthesis, Geochem. Geophys. Geosyst., 10, Q03014, <a href=\"https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2008GC002332\">doi:10.1029/2008GC002332</a>\n",
"\n",
"\n",
"- Lithospheric thickness (average based on several seismological estimates)\n",
" - Steinberger, B. and Becker, T.W. A comparison of lithospheric thickness models, Tectonophysics, 746 (2018), pp. 325-338, <a href=\"https://www.sciencedirect.com/science/article/pii/S004019511630316X?via%3Dihub\">doi.org/10.1016/j.tecto.2016.08.001</a>\n",
"\n",
"\n",
"- Age of the lithosphere from seismological analysis\n",
" - Poupinet, G., Shapiro, N.M. Worldwide distribution of ages of the continental lithosphere derived from a global seismic tomographic model, Lithos, 109 (2009), pp. 125-130, <a href=\"https://www.sciencedirect.com/science/article/pii/S0024493708002582\">doi.org/10.1016/j.lithos.2008.10.023</a>\n",
"\n",
"\n",
"- Hot spots list\n",
" - http://www.mantleplumes.org/P%5E4/P%5e4Chapters/MorganP4ElectronicSupp1.pdf\n",
" - Morgan, W.J. and Morgan, J.P. Plate velocities in the hotspot reference frame, Plates, Plumes and Planetary Processes, Gillian R. Foulger, Donna M. Jurdy, (2007), <a href=\"https://pubs.geoscienceworld.org/gsa/books/book/618/chapter/3805271/Plate-velocities-in-the-hotspot-reference-frame\">doi.org/10.1130/2007.2430(04)</a>\n",
"\n",
"\n",
"## PerpleX | Thermodynamic calculations\n",
"\n",
"- PerpleX\n",
"\n",
"\n",
"- What are inputfiles and output files?\n",
"\n",
"\n",
"- P-T grids (density,melting,)\n",
"\n",
"\n",
"Link to [Thermodyn](thermo.ipynb)\n"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from os import listdir ; from os.path import isfile, join"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"######### input files ########\n",
"illustration.png\n"
]
}
],
"source": [
"onlyfiles = [f for f in listdir('./assets') if isfile(join('./assets', f))]\n",
"print(\"######### input files ########\")\n",
"for file in onlyfiles:\n",
" print('{}'.format(file))"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Hello world!!!\n"
]
}
],
"source": [
"from scripts.hello import *"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
48 changes: 48 additions & 0 deletions thermo.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"[Back to the starting page](start.ipynb)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
}
},
"nbformat": 4,
"nbformat_minor": 4
}

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