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Waiwera releases

1.5.0

Date: 14 October 2024

Changes:

  • significantly improved non-linear solver convergence and time-stepping behaviour when using source networks (from modifications to the Jacobian matrix)
  • improved handling of deliverability thresholds
  • new option for reading simulation start time (time.start) from initial conditions HDF5 file
  • new option for setting negative initial.index, e.g. -1 to start from last set of results in initial conditions HDF5 file (note: this is now the default)
  • initial conditions filename added to YAML logfile summary info
  • new option for flushing of output HDF5 file
  • added piecewise cubic Hermite (PCHIP) option for interpolation tables
  • allow selection of mesh partitioner type
  • an error is now raised if progressive scaling is used with a source network group separator
  • new option for pressure-dependent cutoff pressure in deliverability source control -- for simulating e.g. pumps
  • Docker image updated to use a Debian 12 base image and Python 3
  • PETSc update - PETSc version 3.22.0 or later is now required, and PETSc 3.22.0 will be downloaded and built if PETSc is not found on the system (some changes to the Waiwera code were required to accommodate changes made to PETSc since version 3.15)
  • revamped user guide based on the Shibuya Sphinx theme
  • updated PyWaiwera Python packaging using pyproject.toml configuration file

1.4.0

Date: 30 June 2023

Changes:

  • source networks, representing interacting networks of sources and sinks, for modelling e.g. multi-feed wells, borefields with grouped production wells (and optional limits or targets imposed on the group), or reinjection
  • salt equation of state modules - Waiwera now includes three new EOS modules for modelling mixtures of non-isothermal water, salt (sodium chloride) and non-condensible gases (currently carbon dioxide or air). These new EOS modules are wse (water, salt, energy), wsae (water, salt, air, energy) and wsce (water, salt, carbon dioxide, energy).
  • allowing sources with no associated cell (e.g. for reinjection outside the model)
  • allowing unlimited number of time steps (by setting time.step.maximum.number to null)
  • various minor code modifications to allow building Waiwera using newer versions (10, 11) of gfortran

1.3.1

Date: 29 June 2022

Changes:

  • time-dependent rock properties - rock permeabilities and porosities can now be assigned prescribed time-dependent values.
  • modified handling of Dirichlet boundary conditions - equations for boundary ghost cells are no longer included in the Jacobian matrix (used to solve the non-linear flow equations at each time step). This makes the Jacobian significantly less ill-conditioned and slightly smaller.
  • Jacobian output - Jacobian matrices can now be optionally output to a binary file. These may be used e.g. for inverse modelling or uncertainty quantification.
  • added ability to set Jacobian differencing parameters in input (rather than as PETSc arguments).
  • Modified time stepping behaviour around checkpoints - the pre-checkpoint time step size is now restored after hitting a checkpoint.
  • PETSc update - PETSc version 3.15.5 will be downloaded and built if PETSc is not found on the system.

1.3.0

Date: 8 September 2021

Changes:

  • tracers - Waiwera can now simulate passive tracers. Any number of tracers can be simulated, in conjunction with any equation of state. Tracers may be either liquid-phase or vapour-phase, and the effects of diffusion and decay can be included. Decay can be constant or temperature-dependent. The tracer equations are solved independently of the flow equations, with only one additional linear solve needed per time step.
  • output at faces - Waiwera can now optionally output results on mesh faces, e.g. component or phase mass or energy fluxes, and also face geometry (areas etc.) to the output HDF5 file. Face output is fully configurable by the user. It is also now possible to control (e.g. omit) the output of cell geometry data.
  • PETSc update - PETSc version 3.15.2 or later is now required, and PETSc 3.15.4 will be downloaded and built if PETSc is not found on the system.
  • new output datasets in the HDF5 file to simplify post-processing MINC simulations - these contain the MINC level and parent cell index for each cell in the output
  • the Waiwera Docker images should now run on older CPUs. Previously the Docker images contained a PETSc library built using compiler settings which prevented it from running on older CPUs. This is now built using more generic settings so it should run on any x86 CPU capable of running Docker.
  • a fix for a minor issue which prevented native Linux builds on distributions which no longer have Python 2 installed by default (e.g. Ubuntu 20.04)
  • the user guide has new material on using the recently-released Layermesh library to create meshes for Waiwera models, and use them for pre- and post-processing
  • the Waiwera continuous integration (CI) pipeline has been transferred from Travis CI to Github Actions

1.2.1

Date: 20 July 2020

The main change in this version is that the installation process will now install MPICH instead of OpenMPI, if it does not detect any existing MPI on the system.

This change was prompted by an apparent memory leak (possibly this one) in some versions of OpenMPI, including version 3.1.3 which was used in the Waiwera 1.2 Docker image.

That version of OpenMPI also has another bug which causes error messages when running in Docker containers. Waiwera 1.2 introduced a workaround for this bug in the waiwera-dkr script, but with the change to MPICH this is no longer needed, and has now been removed.

1.2.0

Date: 8 June 2020

Changes:

  • PETSc update: PETSc version 3.13.2 or later is now required, and PETSc 3.13.2 will be downloaded and built if PETSc is not found on the system.
  • this new version of PETSc includes substantial modifications to the DMPlex class, including the ability to handle hybrid meshes with arbitrary mixes of cell types (8-node hexahedron, 6-node wedge, etc.). This means Waiwera is also now able to handle these meshes.
  • a modification to the behaviour of the deliverability source control when a threshold pressure is specified. The deliverability control will now deactivate if the computed flow rate is larger in magnitude than the specified production rate (which can happen for time-dependent specified flow rates).
  • the Waiwera executable now has --version and --help command line arguments. Running with no arguments now gives the more common behaviour of printing the help information, rather than prompting for a filename.
  • the Travis continuous integration (CI) pipeline now includes the full suite of benchmark tests as well as just the unit tests.
  • users can now run the benchmark tests via Docker, by passing the --docker argument to the benchmark test script.
  • Waiwera Docker images are now based on a Debian 10 base image (was Debian 9 in previous versions).
  • the waiwera-dkr utility now has --version and revised --help arguments, and its default number of parallel processes is now 1 (rather than the maximum available).

1.1.0

Date: 31 January 2020

Changes:

  • MINC mesh rebalancing: after MINC processing, the mesh is redistributed to regain optimal load balancing, and hence better scaling behaviour for large parallel MINC problems. This entailed a substantial rewrite of parts of the Waiwera MINC code.
  • PETSc update: PETSc version 3.12 or later is now required (some of its new features and bugfixes are needed for the MINC mesh rebalancing). If PETSc is not found on the system, version 3.12.3 will be downloaded and built.
  • PyWaiwera: this is a new Python library for working with Waiwera simulations. Its source is in the main Waiwera source tree under /utils/pywaiwera, and it can be installed from PyPI using pip. For now, it contains only code related to running Waiwera via Docker, either from Python scripts or from the command line, for which it installs an executable waiwera-dkr script (which replaces the previous waiwera-dkr.py script). In future it is invisaged that other modules will be added to PyWaiwera, for assisting with pre- and post-processing.
  • the new waiwera-dkr script includes many improvements and some new features, for example downloading example model input files using the --examples option.
  • continuous integration (CI) using Travis for automated building/testing of Waiwera.
  • additional log file messages for reporting simulation degrees of freedom and imbalance statistics, as well as linear solver iteration counts

1.0.0

Date: 24 November 2019

Waiwera version 1.0 has just been released, after five years of development and testing.

The Waiwera team would like to thank everyone who contributed to making this possible, including MBIE and Contact Energy for financial support; Matt Knepley and others on the PETSc team, for invaluable advice and support; and Joseph Levin for developing the FSON library.