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CHANGES: Underworld2

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

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.