JuliaClimate/Notebooks

The listed notebooks highlight JuliaClimate packages used within the broader Julia package ecosystem.

Numerical Models

ClimateModels.jl provides a uniform interface to climate models of varying complexity and completeness (up to whole Earth System models). The examples also illustrate cloud computing workflows that replay model output accessed from the web. Common file formats are supported. Version control, using git, is included to allow for workflow documentation and reproducibility.

• Random walk model (0D) ➭ notebook url : two-dimensional random walk

• ShallowWaters.jl model (2D) ➭ notebook url : shallow water equations

• Oceananigans.jl model (3D) ➭ notebook url : non-hydrostatic model

• Hector climate model (global) ➭ notebook url : simple global climate carbon-cycle model

• FaIR climate model (global) ➭ notebook url : simple global climate carbon-cycle model

• SPEEDY atmosphere model (3D) ➭ notebook url : fast, simplified, atmospheric model

• MITgcm general circulation model (3D) ➭ notebook url : general circulation model

IndividualDisplacements.jl supports the modeling of geophysical fluids at moving point locations. It computes single point displacements within a flow field, and follow individual fluid parcels as they move over time.

IndividualDisplacements.jl is geared towards the analysis of Climate, Ocean, etc model output over a gridded domain. It can simulate material transports within the Earth System (e.g., for plastics or planktons in the Ocean; dusts or chemicals in the Atmosphere).

• Simple Two-Dimensional Flow (notebook url) : simulate particle trajectories in 2D

• Simple Three-Dimensional Flow (notebook url) : rotate, converge, and sink in 3D

• Global Ocean Circulation (2D) (notebook url) : monthly flow climatology in 2D

• Global Ocean Circulation (3D) (notebook url) : mean flow climatology in 3D

MITgcmTools.jl is a set of tools for running MITgcm, and analyzing its output.

• MITgcm_configurations.jl (notebook url); explore MITgcm configurations and their parameters.

• MITgcm_scan_output.jl (notebook url) : scan run directory, standard output, read grid files, and visualize.

• MITgcm_run.jl (notebook url) : a detailed look into compiling and running the model.

• MITgcm_worklow.jl (notebook url): build, setup, run, and plot for a chosen standard MITgcm configuration.

The examples run MITgcm interactively via ClimateModels.jl, use MeshArrays.jl for visualizing outputs, and exploit IndividualDisplacements.jl to derive material pathways.

• HS94_animation.jl (notebook url) : run simple Atmosphere configuration, read output, interpolate, and plot maps.

• HS94_particles.jl (notebook url) : compute particle trajectories from model output generated in HS94_animation.jl.

• HS94_Makie.jl (notebook url) : using Makie.jl instead of Plots.jl

The JuliaCon 2021 Workshop on Modeling Marine Ecosystems was based on notebooks listed below. Additional detail is available in this repository.

• AIBECS (notebook url) : global steady-state biogeochemistry and gridded transport models that run fast for long time scales (centuries or even millennia).

• PlanktonIndividuals (notebook url) local to global agent-based model, particularly suited to study microbial communities, plankton physiology, and nutrient cycles.

• MITgcm global biogeo (notebook url) : interface to full-featured, Fortran-based, general circulation model and its output (transports, chemistry, ecology, ocean, sea-ice, atmosphere, and more).

• IndividualDisplacements (notebook url) : local to global particle tracking, for simulating dispersion, connectivity, transports in the ocean or atmosphere, etc.

MeshArrays.jl defines an array type that can contain / organize / distribute collections of inter-connected arrays as generally done in climate models. These data structures can be used to simulate variables of the climate system such as particles and transports.

• Geography (notebook url) tutorial : deals with interpolation, projection, and visualization of gridded fields in geographic coordinates.

• Vector Fields (notebook url) tutorial : covers the computation of global transports, streamfunctions, potentials, gradients, curls, and more.

• Basics (notebook url) tutorial : illustrates how the MeshArrays.jl data structures let us write generic code readily applicable to whole families of grids.

How To

Get in Touch

Please use the repository issue tracker (this one) for feedback, bug reports, queries, new contribution ideas, etc.

Run Notebooks

The Pluto notebook server can be used directly from your familiar Julia environment. Alternatively, you should be able use the computer configuration that we provide on any platform (cloud, laptop, or cluster) as explained below.

To start an interactive version of a notebook, you then launch Pluto and proceed as follows :

• copy notebook url from webpage

• paste notebook url into Pluto

• click open and wait for notebook to boot up

• interact with the reactive notebook

• shut down or restart notebooks as needed

You can specify the notebook URL or file path directly via Pluto.run.

using Pluto, Downloads
path="examples/IPCC.jl"
Pluto.run(notebook=path)

Additionally, the ClimateModels.jl package provides methods to gather and open any of the notebooks found in this page.

using Pluto, ClimateModels

Pluto.run()
pluto_url="http://localhost:1234/"

nbs=notebooks.list()
notebooks.open(pluto_url,notebook_url=nbs.url[1])

Computer Configuration

Anyone should be able to run the provided computer configuration on a commercial cloud, a laptop, or a cluster from the Docker image using this command for example:

docker run -p 8888:8888 gaelforget/notebooks:latest

A bit more explanation is provided here in text and here in video.

We are very grateful to the BinderHub Federation for deploying public BinderHubs to serve the community at no cost to the user.