Juan Carlos Graciosa

Introduction and benchmarking

The convection of the Earth’s mantle is usually modelled as an incompressible process, referred to as the Boussinesq approximation. However, in the Earth’s mantle, the pressure increase associated with depth also increases the density due to self-compression (King et al. 2010). In some applications, this compressibility may be non-negligible and modelling it may be desirable.

Compressible convection in cartesian coordinates with Underworld3

Romain Beucher

Conda packages are now available for most of the underworldcode suite of software


 (Underworld, UWGeodynamics, Lavavu, Stripy) from the geo-down-under conda channel.

Let’s face it. Users don’t want to spend time compiling code on their machine. It is time consuming, requires some specific skills and creates unnecessary hurdles in a workflow.

Here comes Conda...

Haibin Yang

A Lagrangian integration point finite element method for large deformation modeling of viscoelastic geomaterials

Abstract   Numerical models have become an indispensable tool for understanding and predicting the flow of ice sheets and glaciers. Here we present the full-Stokes software package Underworld to the glaciological community. The code is already well established in simulating complex geodynamic systems. Advantages for glaciology are that it provides a full-Stokes solution for elastic–viscous–plastic materials and includes mechanical anisotropy.

ISMIP-HOM benchmark experiments using Underworld

Louis Moresi

Meghan S Miller, Louis Moresi, Research School of Earth Sciences, Australian National University


 A new study by an international team of scientists has found lockdown measures to stop the spread of COVID-19 led to a 50 per cent reduction in seismic noise observed around the world.

It is the largest reduction in human-generated noise ever observed globally.

COVID-19 lockdown leads to seismic noise “quiet period”

Meghan S. Miller,

 Australian National University

and Louis Moresi,

 Australian National University


 
 How we built a simple dashboard using Github actions with open source software and openly available (FAIR) data.
 

We recently wrote an article in The Conversation that shows how the Australian Seismometers in schools network registers the pulse of Australian life through changes in the seismic noise

Australian Seismometers in Schools - Noise monitoring dashboard

Julian Giordani

The Underworld team would like to congratulate Bénédicte Cenki-Tok and co-authors at the University of Sydney and the University of Montpellier on their recent publication,  B. Cenki-Tok, P.F. Rey, D. Arcay;

Underworld publication news: Crustal thickness anomalies in stable continents.

Meghan S. Miller,

 Australian National University

and Louis Moresi,

 Australian National University

Our responses to the COVID-19 pandemic have dramatically changed human activity all over the world. People are working from home, schools are closed in many places, travel is restricted, and in some cases only essential shops and businesses are open. Scientists see signs of these changes wherever they look.

Australian cities are quiet during lockdown. Earthquake scientists are making the most of it

John Mansour

A new paper by John Mansour and others has just been published in the Journal of Open Source Software. Mansour, J., Giordani, J., Moresi, L., Beucher, R., Kaluza, O.,  Velic,  M., Farrington, R., Quenette, S., Beall, A., 2020, Underworld2:  Python  Geodynamics Modelling for Desktop, HPC and Cloud, Journal of Open

JOSS publication - Underworld 2

Rohan Byrne

As the old truism states, the best way to learn is by doing. This is terribly unhelpful since, really, you can't 'do' anything

 until

you learn. This is a Catch-22 that every grad student encounters; doubly so when it comes to anything involving code, where daily life provides very little in the way of intuition. Unlike other geodynamic modelling software,

 Underworld

is designed to be approached with code.

Getting started: 60 seconds to Underworld

Rebecca Farrington

Viscoelastic materials exhibit the properies of both solids and liquids, with deformation rates dependent on both the viscous stress and elastic stress rate.

Viscoelasticity in Underworld2

Making your research reproducible means that you provide the entire workflow from data, through software and post-processing freely available. Not only can somebody repeat your experiments and verify them, they can build upon them. In lab-based disciplines, there are many further challenges, but in research that is predominantly based on data processing, this ought to be an achievable goal.

Alaska Moho Model (Reproducible research with containers)

Zenodo is a repository for immutable versions of software that are provided with a persistent DOI for the purposes of citation and reproducibility.   Underworld can be cited via a zenodo DOI. There is a master DOI for all releases (10.5281/zenodo.1436039) and releases after 2.6.0 are automatically given a DOI _under the master_.

Cite Underworld from Zenodo

(they don't make them like they used to ... )

Cratons are anomalously-strong regions of the continents that have largely resisted tectonic forces for billions of years. How such strong zones could be forged in a hot, low-viscosity, low stress,  early-Earth has been a long-standing puzzle for geologists.

Craton Formation and the Onset of Plate Tectonics

Using physical units and how to appropriately scale a model is a top question users ask when beginning with Underworld. The equations Underworld solves are stated in a physically correct form, they remain valid as long as every material constant, geometry, time, etc., are expressed in the same system.  There is no explicit concept of units no scaling in Underworld, the choice is entirely left to the user.

Using physical units in Underworld

(aka the Underworld renovation project)

Underworld is our parallel, particle-in-cell, finite element geodynamics code [1]. For the past year or so, the Underworld team has been working on a refurbished user interface. We've known for a long time that it needed to be done but we finally bit the bullet.

Underworld 2

In a recent paper [1], we used Underworld models to examine subduction congestion associated with the ingestion of a continental ribbon. The SE Australian geological record turned out to be a wonderful place to study this process. Here is a short summary of the work for a relatively non-technical audience that we put together and some additional figures which I prepared.

The Dynamics of Continental Accretion

The Underworld Community has been supporting usage of Docker containers for developing and running Underworld powered scientific models.

Developing Underworld using Python Virtual Environments

The new generation of Apple Mac comes with the new Apple Silicon (M1) chip which has an Arm architecture (as opposed to the older generation that had i386 Intel processor). This brings all manner of troubles and requirements for the development of codes. Here I detail how to install Underworld on Mac OSX Big Sur 11.5.2 (Apple Silicon) using Python 3.9  Important Note: The following guide uses the CMake branch of Underworld.

How to install Underworld on Mac OSX (Apple Silicon M1)

How we added an auto-updating set of citations to underworld in our publications webpage.

We need to curate all the publications that we can find that use the underworld geodynamics code and provide this information on our website. To avoid needless repetition, we take advantage of the fact that nearly all the information we require is online and automatically construct the bibliography from an online public zotero library.

An automated (zotero) bibliography in a webpage

By the way, before you read this post, catch up with how we use docker by reading part 1  Docker allows us to distribute pre-built applications which are hosted in a virtual machine and are therefore platform independent.

Underworld and Docker (part 2)

How does Underworld scale on a HPC? In this post we showcase how Underworld 2.11 scales across two of Australia's premiere HPC systems. Gadi - https://nci.org.au/our-systems/hpc-systems Magnus - https://pawsey.org.au/systems/magnus/  The reference model chosen for this scaling showcase is a extended 3D stokes flow: Analytic Solution SolDB3D . Q1P0 elements were used and a fixed solver iteration count for solving the saddle point problem.

Underworld 2.11 Scaling

One of the most popular cloud services for python / jupyter - based codes is binder (www.mybinder.org) which can transform an online repository into a running instance in the cloud with little effort on the part of the owner of that repository to set it up and no effort at all for the end user.

Underworld's  lightweight cloud for online classrooms.

Modelling the relative time-scales of the Rayleigh-Taylor Instability and delamination, using Underworld

With Adam Beall, Cardiff University. Why model sub-continental gravitational instabilities? Within the plate tectonics framework, continents are generally considered to have a much lower density than the asthenosphere below and therefore avoid the kind of recycling that the oceanic crust and lithosphere undergoes.

Modelling Drips and Delamination with Underworld

In honour of Hans Mühlhaus' 70th birthday this month, here are some shear band simulations made with Underworld. We are investigating the role of dilatancy in the geometry of the shear bands for a box of material when a small trapdoor is opened. The extent to which large-scale deformation is needed to release material through the trapdoor depends on how much the material dilates when shear bands form.

Shear Bands with Dilatancy modelled with Underworld

Underworld2 is a python-friendly version of the Underworld geodynamics code which provides a programmable and flexible front end to all the functionality of the code running in a parallel HPC environment. This gives signficant advantages to the user, with access to the power of python libraries for setup of complex problems, analysis at runtime, problem steering, and coupling of multiple problems.

Underworld2 Workshop at CIG 2016 Meeting

While huge improvements in usability have been achieved in Underworld2, the installation process is still unfortunately as painful as ever. This difficulty is in large part due to Underworld's numerous dependencies, and also the multiple platforms we try to support. Compounding this, the legacy of a individual user's machine often conspires against success, rarely in obvious ways. Simply, compiling is not fun. Enter docker.

Underworld and Docker (part 1)

https://doi.org/10.59350/t7ghx-8f823 The following is compatible with Ubuntu 20.04 under

 
 Windows
 

10/11 WSL 2 (

 
 Windows
 

Subsystem for Linux). PETSc, the Portable, Extensible Toolkit for Scientific Computation is the main dependency required for building Underworld. In the following, I will describe my current workflow for configuring and installing PETSc on Linux.

Configuring and Installing PETSc for Underworld

Version control systems and online-communities such as Github have made contributing to the development of opensource software incredibly easy. That is assuming that people get over their initial fear of sharing their code!  In this short blog post I go through how to submit a pull request to one of our repository. Do not fear and join us for some fun!

Getting started with Pull requests

Version 2.8 of Underworld has been released recently. As with all major releases, this release brings numerous new features, enhancements and bug fixes. A summary of changes may be found within the usual CHANGES.md file. As is also usually the case, numerous API changes have been necessary or warranted.

Underworld Release&nbsp;2.8

Computational approaches to studying non-linear dynamics of the crust and mantle

Numerical investigation of 2D convection with extremely large viscosity variations

The accuracy of finite element solutions of Stokes's flow with strongly varying viscosity

Role of temperature‐dependent viscosity and surface plates in spherical shell models of mantle convection

We mark January 17, 1994 (the day better known for the Northridge Earthquake) as the birthday of the CITCOM family of codes. I was shaken awake early in the morning, and spent the rest of the day nervously waiting for the next aftershock while I checked that the code was really solving all the test problems quickly and accurately.

30 Years of Citcom, Ellipsis and Underworld

Yeah, one repo, one vision! In an effort to simplify maintenance and compatibility between Underworld and UWGeodynamics, we have decided to merge the codes into a single  repository. Starting with version 2.13, UWGeodynamics will now live under Underworld. All UWGeodynamics functionalities and workflows will remain available to the users.

Folding UWGeodynamics into Underworld

Neng Lu

Free surface in geodynamics simulations

Geodynamic simulations increasingly rely on models with a true free surface to investigate questions of tectonic deformation, mantle convection, and coupling of surface processes and lithosphere dynamics. Historically, most mantle convection simulations have been performed with free-slip boundary conditions at the surface.

Free surface in Underworld

To date

 weak scaling

tests have been run on two of the largest computers in Australia:

 Gadi

(NCI) and

 Magnus

(Pawsey). Here we present the results of those tests and discuss:

 Gadi: Weak scaling - SolDB3D Q1


 Gadi: Weak scaling - SolDB3D Q2


 Magnus: Weak scaling - SolDB3D Q2 - v2.10 vs v2.9

Underworld's

 Gadi

installation is setup as a

Scaling in Underworld

Issues with intra-element discontinuities in PIC-FEM   The classical finite element method (FEM) has been widely used to simulate diverse problems in engineering. Unlike most engineering problems, geological simulations are dominated by emergence of geometrical structures due to the non-linear processes involved.

Stress recovery in Underworld

As mentioned, packages can be installed directly from our conda channel. You may however want to build your own package at some point in the future or you may want to fix some of ours by submitting a Pull Request on github (You are more welcome to do so...)  The following goes through the steps of building a conda package for Badlands which contains Python and Fortran code. This is relatively advanced but not really difficult.

How to build Conda packages?

Underworld 2.10 has been released! Available via

 docker

(recommended),

 pip

and

 source code

. See here for more information on each install process. For a

 quick

taste of Underworld try our binder cloud resource, a temporary "virtual sandbox" to explore the release and example models. Click the button below. This new release includes the following: Enhancements Using UWGeodynamics-2.10.1, see here.

Underworld 2.10

Ben Mather

We've been busy creating the next major release of Stripy. To refresh your memory, Stripy is a Python tool for triangulating scattered points either in Cartesian coordinates or on the sphere. It wraps a bunch of Fortran codes in a neat, object-oriented Python interface that can be used for many geographical applications. What's new?

 Spline tension

- a lot of data transformations in Stripy are underpinned by cubic splines (e.g.

Stripy 2.0 released

The Underworld 2.9 release is available from Github, as a docker container and via zenodo (doi:10.5281/zenodo.3964957) it is also available through pip install for the first time (see below). Underworld paper in the Journal of Open Source Software   The paper of record for underworld 2 has been published. It does tie to the Underworld 2.9 release but is sufficiently broad to cite for all 2.x releases.

Underworld 2.9

Underworld Geodynamics Community

> CITCOM is a geodynamics modelling code based on the finite element
> method that is designed for planetary evolution modelling where large
> spatial variations and strong non-linearities occur in the material
> properties. CITCOM was originally conceived by Louis Moresi working at
> Caltech with Professor David Stevenson but quickly developed into an
> open-source community software effort with the work of Shijie Zhong,
> Slava Solomatov, Mike Gurnis and many others. CITCOM spun off many
> novel software tools including CITCOM-S, CITCOM-SVE, Ellipsis and
> Underworld. In this article, Louis Moresi reflects on a 30 year
> community-software development journey.

We mark January 17, 1994 (the day better known for the [Northridge
Earthquake](https://en.wikipedia.org/wiki/1994_Northridge_earthquake?ref=underworldcode.org){rel="noreferrer"})
as the birthday of the CITCOM family of codes. I was shaken awake early
in the morning, and spent the rest of the day nervously waiting for the
next aftershock while I checked that the code was really solving all the
test problems quickly and accurately. CITCOM took more than a year to
get right and many deadlines went by un-met as a result including the
pre-Christmas deadline of the 1993 AGU Fall Meeting.

There were two notable papers that eventually came out of this early
version of CITCOM: 1) Moresi and Solomatov (1995) where we were able to
model fully-stagnant lid convection for the first time and demonstrate
how all the theoretical scalings really worked; and 2) Moresi, Zhong &
Gurnis (1996) where we proved that the method itself was accurate using
analytical solutions. In the following two years we expanded on these
topics in numerous other papers, Shijie Zhong developed a parallel
version of the code, and we declared the code to be formally open source
and encouraged the community to use it.

When Shijie Zhong and his team developed CITCOM-S (Zhong et al, 2000),
the parallel, spherical code that inherited all the robust solvers from
the Cartesian version, the community embraced the code and it became one
of the most widely used software tools in the geodynamics community and
continues to be used today.

The other branch of this family tree took a different path: the Ellipsis
code was developed to study history-dependent fluid-dynamics problems
(e.g. materials with damage, anisotropic flow, viscoelastic convection)
using Lagrangian particles embedded in the finite element mesh (Moresi
et al, 2003). Ellipsis became Underworld when we adopted the
[PETSc](www.petsc.org){rel="noreferrer"} parallel computing framework
and received funding from
[AuScope](www.auscope.org.au){rel="noreferrer"} to develop a community
of users and support their research needs.

As the CITCOM codes celebrate 30 years, and active development of
Underworld passes the 20 year mark, we will be unveiling our next
generation of software, **Underworld3**.

<figure class="kg-card kg-image-card kg-card-hascaption">
<img
src="https://www.underworldcode.org/content/images/2024/01/Screenshot-2024-01-16-at-9.27.44-pm.png"
class="kg-image" loading="lazy"
srcset="https://www.underworldcode.org/content/images/size/w600/2024/01/Screenshot-2024-01-16-at-9.27.44-pm.png 600w, https://www.underworldcode.org/content/images/size/w1000/2024/01/Screenshot-2024-01-16-at-9.27.44-pm.png 1000w, https://www.underworldcode.org/content/images/size/w1600/2024/01/Screenshot-2024-01-16-at-9.27.44-pm.png 1600w, https://www.underworldcode.org/content/images/2024/01/Screenshot-2024-01-16-at-9.27.44-pm.png 1606w"
sizes="(min-width: 720px) 720px" width="1606" height="1386" />
<figcaption>Underworld3 is
integrated with Jupyter and with sympy. The development environment is
easy to use, close to the original mathematical formulation and highly
interactive. Once ready for deployment, parallel execution is efficient
and scalable - no modification of the notebooks is needed.
</figcaption>
</figure>

**Underworld3** continues the long collaboration with the ***PETSc***
team. We have completely re-engineered the internal structure of the
code to leverage the ***PETSc*** computational infrastructure while
focusing on ease of use for geophysical fluid dynamics problems. We
introduce a pure symbolic interface to the conservations equations that
builds the python ***sympy*** system --- this provides automatic
differentiation of PDEs (required for non-linear problems and
optimisation for example) but also simplification, code-compilation, and
mathematical verification. This system puts Lagrangian and Eulerian
formulations on a completely equal footing and makes the two
representations inter-operable. Parallel scaling is robust and reliable
thanks to ***PETSc*** and, at the same time, the code is very
straightforward to follow because the built-in documentation is
perfectly integrated with ***Jupyter***.

Stay tuned for a series of posts introducing **Underworld3** and, this
time (fingers crossed) no natural disasters to accompany the release.

### References

Moresi, L., Dufour, F., & Mühlhaus, H.-B. (2003). A Lagrangian
integration point finite element method for large deformation modeling
of viscoelastic geomaterials. *Journal of Computational
Physics*, *184*(2),
476--497. [https://doi.org/10.1016/S0021-9991(02)00031-1](https://doi.org/10.1016/S0021-9991(02)00031-1?ref=underworldcode.org)

Moresi, L., Quenette, S., Lemiale, V., Mériaux, C., Appelbe, B., &
Mühlhaus, H.-B. (2007). Computational approaches to studying non-linear
dynamics of the crust and mantle. *Physics of the Earth and Planetary
Interiors*, *163*(1),
69--82. [https://doi.org/10.1016/j.pepi.2007.06.009](https://doi.org/10.1016/j.pepi.2007.06.009?ref=underworldcode.org)

Moresi, L.-N., & Solomatov, V. S. (1995). Numerical investigation of 2D
convection with extremely large viscosity variations. *Physics of
Fluids*, *7*(9),
2154--2162. [https://doi.org/10.1063/1.868465](https://doi.org/10.1063/1.868465?ref=underworldcode.org)

Moresi, L., Zhong, S., & Gurnis, M. (1996). The accuracy of finite
element solutions of Stokes' flow with strongly varying
viscosity. *Physics of the Earth and Planetary Interiors*, *97*(1--4),
83--94. [https://doi.org/10.1016/0031-9201(96)03163-9](https://doi.org/10.1016/0031-9201(96)03163-9?ref=underworldcode.org)

Zhong, S., Zuber, M. T., Moresi, L., & Gurnis, M. (2000). Role of
temperature-dependent viscosity and surface plates in spherical shell
models of mantle convection. *Journal of Geophysical Research B: Solid
Earth*, *105*(B5),
11063--11082. [https://doi.org/10.1029/2000JB900003](https://doi.org/10.1029/2000JB900003?ref=underworldcode.org)