Critical bug fix for Model.dt Critical bug fix for passive tracer tracked fields during checkpoint restart()

Critical bug fix for Model.dt

Version 2.12

• 2D surface processes implementation. Update to surface processes file to include erosion & sedimentation rate or diffusive surface in 2D.
• Tutorials that outline how to use the different surface processes.
• Free Surface examples.

Bug Fixes:

• Drucker Prager Yield Criterion in 3D. A sign error resulted in a lower Yield Stress which resulted in more diffuse weakening when using plasticity with a DP criterion. This has likely impacted all 3D models since early versions of UWGeodynamics. We recommend updating asap.
• Fix some typos in the Rheology references (Asthenospheric type rheology from Watremez et al was referred as Lithospheric)
• Fix Free surface implementation.

What's Changed

• Change Passive Tracers Interface. The Model.add_passive_tracers method now return None. Tracers can be accessed via the Model object. - This is to avoid orphans and usage errors when doing a restart.
• Add option to pass UW function (or mesh variable) to the density material properties.
• Model.init_model() excepts arguments to optional to initiliase temperature and pressure fields with an UW function or a mesh variable.
• Various bug fixes and example notebook updates.

Full Changelog: https://github.com/underworldcode/UWGeodynamics/compare/v2.10.2...v2.11.0

Fix issue #203

User related changes:

• Require boundary condition definitions to contain wall keys. d9e30eeb74fb57e0cf87f9b9002901e04124c127

Enhancements:

• Passive tracers can now track swarm variables. 7cfbb4a363d41233a6eab91d005eb2dd4ca4916f
• Added testing via pytest and Github Actions.

Bug Fixes:

• Fix for 1_08_ViscoElasticHalfSpace.ipynb model. f9d4fe90e99d53245d551bbbbc7e14b5e49f05c0
• Fix for passive tracer reloading in parallel. bcce1832677044104a8f5670eaab79e4fea6ec7c
• Fix for yielding when elasticity is included. 863b5cc48d2ea2b6ac14c40981a6d26b55a9f92a

Version 2.9

User related changes:

• The 'visualisation' python module replaces the 'glucifer' python module (as per UW 2.9) To update in your model, replace the line import glucifer with from UWGeodynamics import visualisation as vis 'vis' can be used as 'glucifer' was.

• Compatible with UW 2.9

• New Numpy Pressure Smoother

Enhancements:

• Upgrade to Dockerfile configuration, using "muli-stage" builds.

Bug Fixes:

• Passive tracer initialisation in 3D.
• Restarting with track fields and swarm global indices.

This version includes the change needed to support Badlands 2.0 pyBadlands has been deprecated, the module is now simply called badlands. Please refer to Badlands documentation.

• Update dockerfile: badlands and its dependencies are now installed using pip.
• The Docker Image >=v2.8.5 works with Singularity on Pawsey Magnus

• Compatible with UW 2.8 (Python 3 only)
• Fix bugs reported on Github
• Update documentation on ReadTheDocs
• Support for SLCN (Semi Lagrangian Crank Nicholson method for Advection Diffusion) The default advection-diffusion remains SUPG but the user can switch to SLCN by setting: GEO.rcParams["advection.diffusion.method"] = "SLCN" I have added a simple example that illustrate the advection of the isotherm when a column of materials is extended (Thanks to P.Lovely).
• Add option to use pre-defined initial viscosities of the materials for the first solve. myMaterial.initial_viscosity = 1e22 * u.Pa * u.s
• Add option to pass the Lithostatic field as an initial stress condition. Note that the value used at the boundary is not updated as the conditions evolve during a simulation.
• Simplified Dockerfile / Docker Image
• UWGeodynamics Shape now behave as normal UW function. This means that classic UW function can be used to define a shape.
• IMPORTANT Shape Combination: The & operator now define the intersection of shapes, combining shapes is done using |. This is to be consistent with the previous point. The use of the + and - operator have also been removed as it was causing confusions.
• Passive Tracers now directly inherit from Swarm. There is no swarm method on the PassiveTracer object anymore. User can use it as a normal swarm.