CHANGES.md

CHANGES: Underworld2

Release 2.15.0 [2023-04-19]

New:

• Move to Petsc-3.19.4
• New 3D free surface implementation. (Not fully tested).
• new install guides for Gadi and setonix.

Changes:

Fixes:

• UWGeodynamics - add dynamic heating back into the advection diffusion solver, #669
• Using updated Badlands-2.2.3 without license issue.

Release 2.14 [2022-11-29]

New:

• New Dockerfile configuration resulting in smaller docker images.
• Move to Petsc-3.18.1.

Changes:

• Multiple mpi implementation images for HPC usage (Gadi and Setonix).

Fixes:

• Revert to HDF5 1.10. Fix for Checkpointing issues.

Release 2.13.1 [2022-08-15]

Fixes:

• Improved CMAKE workflow.
• Fixes to failing unit tests.
• Dockerfile updates - revert MPICH version to 3.4.3.

Release 2.13.0 [2022-05-25]

New:

• Merge UWGeodynamics into Underworld (from underworld import UWGeodynamics as GEO)
• Compatibility with petsc 3.17.
• Update Docker images: Ubuntu 22.04LTS and mpich 4.0.2, python 3.10, petsc 3.17.1
• Update install_docs/nci gadi

Release 2.12.0 [2022-01-31]

New:

• CMake based builder instead of Scons.
• Added M1 (arm64) based docker. Upcoming release Changes:
• GitHub actions for CI and docker publications.
• Compatibility with petsc 3.16.
• Update Docker images: Ubuntu 21.10 and mpich 3.4.2, python 3.9.2, petsc 3.16
• Update install_docs/nci gadi

Fixes:

• Unit fix for temperature saved in celcius.

Release 2.11.0 []

Changes:

• Enabled user defined Gauss integration swarms for all systems.
• Update docker base images: switch to ubuntu(20.04), update petsc(3.14) & mpich(3.3.2), other tweaks.
• Cleaner Python compile time configuration.
• Add runtime check for solver availability (for example, 'mumps'). Also add test for check.

Docker image changes:

• Update base image.
• Updated to PETSc 3.15.1
• Updated to MPICH 3.4.2
• Removed petsc4py.
• Switched /opt to ugo+rwx to allow users to install Python packages.

New:

• Model for EBA convection, based on King et al. (2010) benchmarks. See docs/test/14_Convection_EBA.ipynb
• Mesh/MeshVariable/Swarm/SwarmVariable objects now support loading and saving of units information, as well as additional attributes. For usage examples, see docs/test/mesh_aux.py and docs/test/swarm_aux.py.
• Added underworld.function.count() method, which counts function calls.
• Conda binaries available via underworldcode conda channel conda install -c underworldcode underworld2
• Added underworld.function.count() method, which counts function calls.
• Added GADI install/run scripts @ ./docs/install_guides/nci_gadi/
• Updated pull request related documentation and added template.

Fixes:

• Updates for SCons4.1.
• Fix bug where multiple solvers added multiple preconditioners.
• H5py v3 is more strict in allowed indexing array shapes. Updated our structures to accomodate.
• Tester uses jupyter-nbconvert which no longer defaults to Python. Update to explicitly select Python.
• Switched h5 file save to mode "w" instead of "a" as append mode resulted in data from previous datasets (with identical name) not being removed from file, and file sizes therefore growing unnecessarily.

Release 2.10.1 [2020-08-28]

Changes:

• Updating Dockerfile to include UWGeodynamics new docs structure.

Release 2.10.0 [2020-08-07]

Fixes:

• SWIG4 compatibility changes.
• libxml2 ubuntu20.04 changes.
• Numpy 1.19 compatability changes.
• Fix LGPLv3.txt contents. File incorrect contained GPLv3 text.

Changes:

• Check for compressibility/penalty clash.
• Update example models for parallel usage.

New:

• Add Dockerfile for Deepnote.
• Add test_long.sh long test runner.

Release 2.9.5 [2020-07-27]

Changes:

• Fix LGPLv3.txt contents. File incorrect contained GPLv3 text.

Release 2.9.4 [2020-03-26]

Changes:

• Updating Dockerfile to include UWGeodynamics-2.9.4.

Release 2.9.3 [2020-03-09]

Changes:

• Update citation information in README.md.

Release 2.9.2 [2020-02-26]

Changes:

• Update Zenodo title.

Release 2.9.1 [2020-02-18]

Enhancements:

• Update base docker image & implement permission fixes.
• Other docker tweaks and corrections.
• Fixes for image tests

Release 2.9.0 [2020-01-20]

New:

• Experimental pip install functionality.
• Installation instructions for NCI Gadi.
• Singularity usage instruction Pawsey Magnus.
• UW_VIS_PORT environment variable flag added to set vis port.

Docker:

• Images now use Python 3.7 (previously Python 3.5).
• Multi-stage builds used improved image creation.
• Images minimised with unnecessary items removed.
• XVFB no longer required for image generation within container.

API changes:

• glucifer module moved inside underworld and renamed visualisation. Access as import underworld.visualisation
• GLUCIFER_USE_XVFB -> UW_USE_XVFB.
• --prefix=/SOME/DIR now installs to /SOME/DIR/underworld
• test_basic.py no longer sets PYTHONPATH
• underworld.matplotlib_inline() -> underworld.utils.matplotlib_inline().

Enhancements:

• By default, UW was creating significant filesystem chatter in generating debug messages for functions. This has been significantly reduced through judicious usage of Python inspection tool. Also, as default, only root proc now generates messages. Users can set the UW_WORLD_FUNC_MESSAGES (export UW_WORLD_FUNC_MESSAGES=1) environment variable to have all procs report, or can set UW_NO_FUNC_MESSAGES (export UW_NO_FUNC_MESSAGES=1) to disable these messages altogether for minimal filesystem noise.
• Complete long type SwarmVariable implementation. Specifically, evaluate() methods now work for this data type.

Deprecations:

• Raijin install instructions removed.

Release 2.8.3b [2019-10-29]

Docker:

• Revert to a compatible version of lavavu (v1.4.3).
• Revert to a stable version of UWGeodynamics.

Documentation:

• Update README.md to with new Jenkins url.

Release 2.8.2b [2019-10-28]

Docker:

• Enable token authentication for Jupyter.

Documentation:

• Update README.md to inform users of Jupter Authentication requirements.
• Update "Getting Started" page with info on how to use Authentication.
• Minor tweaks to documentation generator to handle static images.

Release 2.8.1b [2019-09-02]

Documentation:

• Fix broken live documentation generator.
• Fix broken and incomplete docstrings.
• Update advection-diffusion test, see ./docs/test/2DCosineHillAdvection.ipynb.
• Update README.md to mention pip.

Release 2.8.0b [2019-07-18]

New:

• MOVE TO PYTHON3. PYTHON2 NO LONGER SUPPORTED.
• New Examples & tests.
• New Semi-Lagrangian Crank Nicolson advection diffusion scheme.
• Collective H5 read/write for faster parallel IO operations.
• Arbitrary coordinate evaluate() for swarm data using nearest neighbouring (kdtree) algorithm. See function section of user guide.
• XDMF for subMesh element types.
• Async test runner.

Enhancements:

• Move all mpi functionality into uw.mpi submodule.
• Non-parallel h5py is now sufficient for UW, although parallel h5py is recommended for larger parallel simulations.
• Integral returns numpy array results (as opposed to Py natives).
• GlobalSpaceFillerLayout deprecated.
• Other tweaks & bug fixes.

Documentation:

• Many class docstrings updates.
• Function user guide section updated.
• Improved error messaging in parallel.
• Stampede2 build & usage instructions.
• Update for NCI/Raijin build instructions.

Release 2.7.1b [2019-02-19]

Documentation:

• Dockerfile for TACC/Stampede2
• New build instructions for NCI/Raijin.
• Add dev Binder to README.md

Release 2.7.0b [2019-02-06]

New functionality:

• Timing module for high level profiling.
• Scaling module for numerical value scaling.
• Index set objects can now directly index numpy arrays.
• show_grid() image rendering.

Changes:

• glucifer Surface defaults to use onMesh=True.
• added data handle to swarm as shortcut to particle coordinates data.
• Adding aliases for mesh vertex sets (left,right,etc)
• Removed unsupported subrepo.
• Docker images switch to MPICH for Shifter compatibility at magnus.

Documentation:

• Examples reorganised.
• All examples now include quantitative tests.
• Moved many examples to models library repo. https://github.com/underworldcode/model_library
• Added new example, 08_Uplift_TractionBCs.ipynb.
• Moved benchmarks and tutorials to models library repo.
• Relocated defunct models: https://github.com/underworldcode/model_graveyard
• Big overhaul of user guide.
• User guide rendered to html for Readthedocs page.
• Updates for docstrings and doctests.
• Improved error messaging.

Fixes:

• Fix incorrect particle outside domain issue #335
• Other stability improvements.

Release 2.6.1b [2018-10-31]

• Remove warning module visibility from top level underworld module.

Release 2.6.0b [2018-09-27]

Enhancements:

• Removed submodules in favour of direct access.
• Petsc-3.9.x compatible.
• Support for nested SafeMaths operations.
• Improved function error messaging.

Release 2.5.1b [2018-04-13]

Documentation:

• Fixes for Sphinx API documentation generation.

Release 2.5.0b [2018-04-10]

New features:

• New 'long' type swarm variable.
• User provided post-solve callback functionality added.

Enhancements:

• Speed up (minimum 5x) for SwarmVariable reload.
• Petsc-3.8 compatible.
• Non root dockerfile now.

Documentation:

• Viscoelastic tutorial, see ./docs/tutorials/
• Update raijin and magnus build instructions.

API Changes:

• New interface for a MeshVariable, mesh.add_variable().
• New interface to Integrate, mesh.integrate().

Release 2.4.1b [2017-10-24]

• Updating release to the correct version of lavavu

Release 2.4.0b [2017-10-23]

Documentation:

• Darcy flow models.
• New NCI Raijin build recipe.
• Many new models and tutorials.
• Cheatsheet added.

Enhancements:

• Docker usage no longer requires tokens.
• KSP convergence status now captured in python interface.
• solve() method now displays warnings for floating point over/underruns.
• Many general enhancements to visualisation.

New Features:

• New features for min_max function.
• solHA added.

API Changes:

• min_max function no longer accepts vector functions by default, with instead a fn_norm function having to
  be provided by the user.

• Neumann condition now takes indexSetsPerDof parameter instead of nodeIndexSet.

  Bug fixes:

  • Catch out fortran ordered numpy arrays when using evaluate() method.
  • Parallel isosurface visualisation fixed.
  • Corrected sampling for FieldSampler visualisation object.

Release 2.3.0b [2017-07-07]

Enhancements:

• Improved swarm reload times for parallel simulations.
• Efficiency improvements for large proc count (>128) parallel simulations.
• Faster algorithms for swarms with deformed mesh.
• Many updates to visualisation routines.
• Compressible Stokes general improvements.
• New example models and analytic tests.
• Addressed numerous memory leaks (some minor ones still exist).
• Improved error handling, documentation & testing.

New features:

• User provided pre-solve callback function.
• Updated or new vis objects: Isosurfaces, contours, discrete colourmap.

API Changes:

• Neumann condition change in user provided stress function.

Release 2.2.2b [2017-03-08]

Bug fixes:

• Critical bug fixed where retrieving symmetric tensor in 3d returned 2d result.

Release 2.2.1b [2017-02-14]

Documentation

• Updates to make api documentation available via read the docs: http://underworld2.readthedocs.io/

Release 2.2.0b [2017-02-11]

Enhancements:

• Improved function evaluation efficiency.
• Handle numpy int types in index sets correctly.
• Webgl figure saving.
• General visualisation enhancements.
• Better testing for visualisation.
• petsc 3.7 compatibility

New Features:

• ParticleFound function. Allows for 'sparse' swarm operations.
• Figure copying functionality
• SurfaceOnMesh visualisation object

Documentation:

• HTML api documentation.
• Big docstring updates.

Deprecated:

• 'swarm' parameter now removed in favour of 'voronoi_swarm' parameter.

Release 2.1.2b [2016-10-31]

• Bug fix for the stokes system's psuedo incompressibility

Release 2.1.1b [2016-10-13]

• Improvements for docker usage.

Release 2.1.0b [2016-10-11]

New Features:

• Shadow particles sync added.
• Finer solver execution control.
• Added XOR function.
• Can now describe functions using python tuples: fn = (fn1, fn2, fn3)
• Inline interactive visualisation.
• Better handling of systems without rendering capabilities.
• gLucufer Surface renderer resolution setting.
• Parallel and recursive test runner.

Bug Fixes:

• General improvements to stability and error handling.
• MeshVariables can not be used with multiple SLE systems.
• glucifer deadlock when deleting from db in parallel.
• glucifer DB situation where zero compression results in abort().
• glucifer valueRange fix.
• Fn.MinMax parallel fix.
• Issue saving swarms in parallel.

Documentation:

• Big update for User Guide.
• New examples added.
• Examples updated for better usage patterns.
• Updates for docstrings & doctests.
• New & updated build recipes.

Interface changes:

• SLE 'swarm' option renamed to 'voronoi_swarm'
• Conditions can be passed in directly now instead of in lists.
• underworld.help function removed.

Release 2.0.3b2 [2016-06-08]

• Pseudo Compressibility python wrapped.
• Neumann boundary conditions for Stokes & SSHeat & AdvectionDiffusion (SUPG!)
• Exposed population control mechanisms. Zero population control now occurs without using the uw.swarm.PopulationControl object.
• Bug: Potentially critical bug in the integration to material swarm mapping fixed.
• Glucifer/LavaVu graphics 'Store' workflows introduced.
• Dockers upgraded to use ipyparallel where possible.
• Global evaluation for functions (experimental!)
• Exposed non-linear tolerance.
• Deprecated various old interface options.
• PICIntegrationSwarm -> VoronoiIntegrationSwarm
• Viscoelasticity implementation and example.
• 'deform_swarm' context manager for particle relocations.
• Auto-repopulate now occurs for voronoi swarms (except for the uw.utils.Integral class)
• SUPG source terms.
• MeshVariable_Projection method introduced.
• Various bug fixes.
• Various documentation improvements.
• Various testing improvements.
• Various other minor impementations.