Changelog

PinCFlow.jl follows the interpretation of semantic versioning (semver) used in the Julia ecosystem. Notable changes will be documented in this file for human readability.

Release 2.0.0

The auxiliary states in the wave-packet examples have been parallelized.
The examples now use fewer MPI processes.
In the documentation of the function correct!, the vertical indices of the buoyancy frequency were incorrect. This has been rectified.
Some methods of the functions apply_blocked_layer_scheme!, compute_gw_integrals!, compute_gw_tendencies!, and activate_orographic_source! did not return nothing, due to missing return statements. The latter have been added.
The mind maps in the developer guide have been updated.
Objects involved in PinCFlow.jl's implementation of the BiCGSTAB algorithm have been renamed to respect its correct modern spelling ("BiCGSTAB" instead of "BicGStab"). The documentation has also been adjusted accordingly.
A precompilation block has been added. This block precompiles the model for a one-time-step simulation in its default configuration, thus reducing the compilation time later on.
PinCFlow.jl's implementation of the BiCGSTAB algorithm had a convergence criterion dependent on two different averages of the residual, namely a global RMS and a global RMS of a global vertical mean. The latter prevented convergence in very specific configurations (e.g., a Boussinesq gravity-wave packet), even though it is not actually needed. It has therefore been removed from the criterion. This change has also made the code significantly more efficient.
Experimental features are now being tagged in the documentation.
There were two bugs in the computation of background fields for the following combinations of atmosphere-namelist parameters.
```
background == LapseRates() && (troposphere_lapse_rate != 0 || stratosphere_lapse_rate != 0)
```
The bugs were as follows.
1. The computation of the mass-weighted potential temperature was actually a computation of the pressure.
2. Two different potential temperature profiles were computed for the troposphere and stratosphere, leading to a discontinuity at the tropopause.
Both bugs have been fixed.

Release 1.1.1

A bug has been fixed where uold was not being assigned correctly in update.

Release 1.1.0

Potential-temperature fluxes due to heat conduction are no longer computed in pseudo-incompressible or Boussinesq mode.
Two bugs that prevented MS-GWaM from being run in SingleColumn or SteadyState mode have been fixed.
A bug that prevented the helper function replace_assignments (used in the tests) from properly overwriting variables with strings has been fixed. This function now also issues a warning if an assignment wasn't found.
The writing of attributes to the model output file has been serialized. This fixes a bug that led to occasional HDF5 errors in parallel simulations.
A bug has been fixed in the averaging of orographic wavenumbers in apply_blocked_layer_scheme!.
The developer guide has been extended with information on running and updating tests, and instructions for creating new releases.
The behavior of the default value of the output-namelist parameter iin has been changed, so that it no longer results in an error but in the selection of the last record in the input file.
Several bugs have been fixed in the scripts for the wave-packet examples.
A record of the configured namelists is now included in the model output.

Release 1.0.0

The documentation has been updated, corrected and improved.
The density reconstructions and fluxes have been removed in Boussinesq mode.
The sponges are now configured with functions.
- The following sponge-namelist parameters have been removed.
  - sponge_extent
  - alpharmax
  - betarmax
  - lateral_sponge
  - sponge_type
  - sponge_order
  - cosmo_steps
  - perturbation_period
  - perturbation_amplitude
  - relaxation wind
- The following sponge-namelist parameters have been added.
  - lhs_sponge
  - rhs_sponge
  - relaxed_u
  - relaxed_v
  - relaxed_w
  Each of these must be a function that takes the three spatial coordinates, the time and the time step as arguments and returns a single value. The functions lhs_sponge and rhs_sponge are used to compute the respective Rayleigh-damping coefficients, whereas the other three functions define the wind obtained through the relaxation enforced by the LHS sponge (if the parameter relax_to_mean is set to false).
The internal horizontal-coordinate arrays have been parallelized, making the model slightly more efficient.
A bug has been fixed in the construction of the Realistic atmospheric background.
A bug has been fixed in the re-dimensionalization of the GW tracer fluxes and tracer flux convergence.
Metadata has been added to the output, including long variable names, dimensions and labels in LaTeX format.
A bug has been fixed in the computation of the ray-volume-array size (this only had an impact in configurations with wave_modes > 1).
Type constraints for structure fields have been improved. Namelist parameters that previously had to be of a subtype of AbstractFloat now need to be of a subtype of Real.
The following atmospheric backgrounds (only available in Boussinesq mode) have been renamed.
- UniformBoussinesq $\rightarrow$ NeutralStratification
- StratifiedBoussinesq $\rightarrow$ StableStratification
The function check_rays no longer triggers exit() calls but instead raises errors. The error messages now provide more details.
Fixed a bug that resulted in an incorrect initialization of nonzero density fluctuations in Boussinesq mode.
Fixed a bug in the initialization of the mass-weighted potential temperature in compressible mode. This only had an impact when the model was initialized with nonzero density or potential-temperature fluctuations.
The following atmosphere-namelist parameters have been removed.
- initial_thetap
The initial potential-temperature fluctuations are now always such that $P = \overline{\rho} \overline{\theta}$.
The visualization function plot_contours of PinCFlow.jl's CairoMakie extension has been replaced with the function plot_output, with the following changes.
- It has a simplified call signature.
- It can also visualize ray volumes.
- A bug has been fixed in the setting of colorbar-tick labels.
- The space and time units are configurable.
- Multiple variables can be visualized in one figure.
- The colorbar labels are set automatically.
- The background color of plots in $x$-$z$ or $y$-$z$ plane is black.
The following new examples have been added.
- A 2D cold bubble
- A 2D hot bubble
- A 2D vortex
- A 3D wave packet
- A 3D WKB wave packet
The existing examples have been modified slightly. The run and visualization scripts have been merged.
The default values of the domain-namelist parameters x_size, y_size and z_size have been changed to 1.

Release 0.1.0

First public release of PinCFlow.jl.