Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[2.3.0]

Changed

  • Improve docs

  • Improve Utils/benchmark_c scripts and visualization

  • Move Maths and Physics subclasses outside of the Grid class

  • Move ETD4RK from Examples to Utils

Fixed

  • Error on a,b not integers in l_params

  • Fix a potential error where plastic was not supplied in l_params

  • Fix compiler warnings on convolver.c

  • Fix signature of interactive functions in plotLib

  • Improve stability of windows installation

Removed

  • Remove obsolete Examples/2D_basilisk/

[2.2.1]

Changed

  • Publish to pypi.org (used to be test.pypi.org)

Fixed

  • Fix Gitlab CI to only publish on new master tags

  • Fix docs

  • Fix poetry install when compiled files already exist

[2.2.0]

Added

  • Add A11 - 3D rotation to archive

  • Add proper packaging to release on pypi. Update the documentation accordingly

  • Add support for MSVC in convolver.c (MSVC isn’t supported in the installation yet though)

Changed

  • Change license

  • Change doc to Sphinx, and improve many docs

  • Rename plotLib.pad_array_2D to plotLib.rightpad_array_2D

  • Rename LogGrid.convolver to LogGrid.compute_convolution_kernel for clarity

  • Update requirements

  • Improve installation documentation

Fixed

  • Fix pyyaml version

  • Fix normalization of datasci.randcomplex (was square instead of circular)

  • Fix the documentation build for newer Sphinx versions

  • Fix files not being cleaned by makefiles

  • Fix docs in .gitignore

[2.1.0]

Added

  • Auto-lint with pre-commit

  • Add optional fill arg to datasci.ragged_array_to_array

  • Add HRB v7 edgevisc to archive

Changed

  • Tests use pyling fixtures

  • Return axes in interactive_spectrum

  • Auto-rescale interactive_3D_logplot_positive axes for each step

  • Rename fields_to_linear to fields_to_1D and linear_to_fields to D1_to_fields to avoid a confusion with the linear equation part

Fixed

  • Fix TimeTracker output when time<1ms

  • Fix RLIMIT_STACK setting error

[2.0.0]

Added

  • Add test coverage

  • Add timers to evaluate the time spend reading/writing to disk, and convolving. Also measure time spent in DataExplorer.

  • Add a TimeTracker class to Libs.misc to help with time-tracking

  • Add loading initial conditions from a step in a hdf5 file using initial_conditions=["file.h5", step]

  • Add a tool in Utils to find the fastest compiler flags for the convolver

  • Add a script in Utils to install gcc-12 from source

  • Add utests

  • Add deploy stage to CI to view latest benchmark result, + artifact

  • Add a generated doc page, replaces the wiki

  • Add Grid.to_new_size and Grid.to_new_size_empty

Changed

  • Change the way spectra are normalized, now divided by the number of pts in each shell. This should straighten spectra.

  • Change the saving format to hdf5.

  • Rename update_parameters to update_json_settings in Libs.IOLib

  • Change the repo’s name from Log Grid to PyLogGrid

  • Move the initial_conditions argument from Solver() to solver.solve and merge it with loadfromsave: the loadfromsaveargument is removed, to resume the simulation set initial_conditions="loadfromsave".

  • Improve the convolution, now compiled from C instead of Cython, and with several major improvements. Should now be >2x faster.

  • Improve the convolution’s multithreading. As part of this effort, the way convolutions are distributed changes. One can still call convolve as before, but a new function convolve_batch that takes a several (f,g) and computes their convolution in parallel now can be used.

  • When initial_conditions="loadfromsave", automatically load dt from the latest timestep.

  • Rename equation_update to equation_l and viscosity_update to equation_nl in all its implementations.

  • Remove N_points from Solver() args, pass it with initial_conditions instead.

  • Change Solver(fields_name=) to Solver.fields_names to align with Grid.

  • Move several attributes shared between Solver and Grid to be only owned by Grid.

  • Remove fields from the arguments of equation_l and equation_nl. They should now be accessed via grid.field(...).

  • Only recompute the missing fields in DataExplorer if loadfromsave=True instead of recomputing all the fields.

  • Hardcode a (better) default size for plotshowm(full=True) when the backend is non-interactive.

  • initial_conditions="loadfromsave" now updates end_simulation, solver_params, simu_params rather than loading them from the existing simulation

  • Move Libs and LogGrid into the pyloggrid package

  • Change docstrings from REST to google style for improved lisibility

  • Switch dependency management from requirements.txt to poetry

Fixed

  • Increase the max recursion depth to avoid crashing simulations with a lot of grid size changes

  • Fix the save directory of a few tests

  • Fix a crash in windows related to the resource library

  • Ending a simulation no longer shows a stack trace of InterruptedError if the grid size is adaptive.

Removed

  • Remove the save_data arg from DataExplorer.display (now always True)

[1.8.0]

Added

  • Add default MR template

  • Add LittlewoodP code in Examples

  • Add support in DataExplorer for varying grid sizes in outputs

  • Add support for “u” fields in grid.physics.enstrophy

  • Add HRB v5 to archive

  • Add a new solver based on https://github.com/whalenpt/rkstiff and made it default

  • Add an ax argument to plotLib.scatter, if None defaults to plt

  • Add plotLib.interactive_spectrum

  • Add datasci.logmean, datasci.fit

  • Add grid parameter to DataExplorer.load_step

  • Add new optional solver parameter to Solver.solve to chose among the different solvers

  • Add Examples/ETD4RK

  • Add interactive_grid_imshow, interactive_grid_3Dslice, interactive_3D_logplot_positive in plotLib

  • Add optional ax argument to plotLib.legends

  • Add PlotFun custom type in DataExplorer

  • Add HRBv6 to archive

  • Add new generic bencharking util

  • Add a save argument to plot_interactive_XX in plotLib to save the interactive graphs as videos

Changed

  • Change the default solver (see above)

  • In DataExplorer, a field t is automatically stored when perstep=True

  • Fix singlethread_np import in DataExplorer

  • Grid.field now returns a single array when called with a single argument

  • Move atol, rtol, exact_viscous_splitting to a dict solver_params which may take additional parameters

  • The very first and last steps of the simulation are now always saved

  • Rename interactive_3D_logplot to interactive_3D_logplot_by_z

  • Update the structure of save files, in which the order the fields is no longer relevant. This is not backwards-compatible, but legacy support has been added to read old save files.

  • end_simulation no longer defaults to t=1 in solver.solve

  • datasci.mean now returns the mean and the variance

  • add sliders to Examples/LittlewoodPaley/proto_gamma.py and update some plots

  • datasci.mean now returns the mean and the std

  • default ̀end_simulationparameters no longer include{“t”: 1}`

Fixed

  • Fix plotLib.scatter when supplying linestyle

  • Fix interactive_3D_logplot_by_z not updating properly

  • Fix saving duplicate steps on grid size update

[1.7.1]

Added

  • Add a -s flag to the automatic installation scripts to skip the installation of the python executable

  • Add an option exact_viscous_splitting: bool in the solver. If enabled, we solve the equation via “exact” viscous splitting, by multiplying dydt by exp(-visc * t). If the viscous term is big, this requires much smaller time steps, and is significantly less stable. Not recommended for use in everyday simulations, but more as a baseline for comparison.

  • Add a function in treat_3D.py to plot the “theoretical” injection and dissipation of energy. Note that those formulas are only local derivatives, and therefore are expected to slightly differ from the RK estimates. In particuler, there might be a time shift of the order of dt. /!\ The injection and viscosity need to be hardcoded in the treatment.

  • Add0 grid.maths.div2d

  • Add utests for NS3D evolution of energy and div2d

  • Add interactive_3D_logplot_by_z to PlotLib to plot 2D/3D data in 3D with interactive visualisation (z slice / time)

Changed

  • Remove a hard to see marker from the default cycler in PlotLib

  • Update requirements

  • Change behavior of drawables argument passed by DataExplorer: was dict, is now a function that can be called as drawables(key1, key2, ...)̀

Fixed

  • Fix the new default method for calculating the viscous term (was not on by default)

  • Remove bad markers from default plotting cycle

  • Fix a sign error in NS3D.py

[1.7.0]

Added

  • Add launch_treat_batch.sh as a template to launch/treat many simulations at once

  • Add QG 1&2layer(s) to Archive

  • Add HRBv3 to the archive

  • Add missing HRBv2 .ods data and pdfs to the archive

  • Add Draft folder in Example

  • Add spectrum investigation code in Draft

  • Add benchmark_rust to Draft

  • Add sys.path.insert to NS3D.py for compatibility when launched directly from python

  • Add options to select which steps to treat, the number of threads, and whether to save treatment results in DataExplorer

  • Add functions cumulative_k, compute_by_shell to Grid.Physics

  • Add enforce_grid_symmetry, used after each ode step to make sure there’s no drift

  • Add simu_params to solver initial_conditions

  • Add complete_array_with_nans in Libs/datasci

  • Add automated setup scripts for linux & windows. Those scripts install python, create a venv, install the requirements, and compile the convolver. They can be run on already existing installations to update them.

  • Add tight option to pltshowm

  • Add a scatter function to PlotLib

  • Add a field(name) method to Grid

Changed

  • Bump pyparsing to >=3 since the Cython bug seems to have been fixed in newer versions

  • Update README to use python3.11

  • Update convolving utests to be faster (probe smaller grids in 3D)

  • Change the handling of absolute tolerance. Now, atol is relative to the max possible value of y.

  • Change ujson to orjson. This de-facto removes the support for serializing np.nan, np.inf as strings (now serialized as null), but afaik it was not of any use.

  • Cleanup requirements

  • Update the way custom colormaps are handled (was broken by this matplotlib commit)

  • Change default plot style (more article-like, automatic linestyle and marker, colorblind-friendly, perceptually uniform colormap)

  • Refactor the ViscDopri solver:

    • Change the signature of the visc_update, which is now expected to return only the value of the viscous term for each field

    • Change the computation of the viscous term, which should be significantly more precise as long as the timestep is not too big

    • Minor fixes

    • Split visc_update_lin using the new save_step method

Fixed

  • Fix the way RK updated the derivative after the viscosity step. It is now recomputed every step. This changes the signature of the viscosity update, so update your code accordingly (doesn’t require/return the derivative anymore)

  • Fix spectrum calculation crash with k0=True

  • Fix Basilisk test missing fonts

  • Fix some edge cases in the ViscDopri solver

[1.6.0]

Added

  • Decorators to simply run tests on many parameters (N, D, l_params, k0)

  • Support for k=0 mode (set grid.k0=True)

  • Test for convolutions

  • Test for 3D Euler, which checks that the divergence is zero and the energy is conserved over 100 ode steps.

  • Added timings (instead of just speed) to benchmarking

  • Add rainbow desaturated colormap as default

  • Add min and max solver step size

  • Add “compact” option to pltshowm

  • The latest convolution kernel is automatically cached, ensuring that if the grid doesn’t change it’s only computed once.

  • Added cumulative_k function in Grid.Physics

  • Added utests for k0 and many more parameter combinations

Changed

  • drastically changed the way convolutions are computed. We compute a convolution kernel on grid initialisation (which computes all the triads), then we simply iterate over this kernel. This results in a faster convolution (and it makes handling the k=0 mode easier).

  • update typing to py3.9 (typing.Dict -> dict, …)

  • solver.ode_step no longer resets on a resumed run. It can now be used to set the end of the simulation.

  • Changed laplacian3D_inv and laplacian3D to laplacian_inv and laplacian in Grid.Math since the formula is generic

  • Change all Grid.Math linear operators to properties: M.dx(arr) becomes M.dx * arr. This allows to easily invert them, ex: M.laplacian_inv * arr = M.inv(M.laplacian) * arr

  • Set default plot behavior to initFormat

Fixed

  • Fixed the formula of P_projector

  • Added rough support for k0 mode in spectrum (not calculated for k=0, but won’t error anymore)

[1.5.0]

Added

  • Add P_projector in Grid (faster to use than going through the rotational)

  • Add a save and legend option in pltshowm

  • Add the propertygrid.ks_1D_mid to represent k values of data averaged over ks_1D intervals (ex spectras)

  • Add initFormat function to plotLib.py to easily make plots that are formatted for scientific publications

  • Add an Examples folder that showcases the following features from the past months (none of which are polished): 2D basilisk code, JP Laval’s Fortran code and the visualisation of its .nc outputs, the new initFormat function.

  • Add random_cmap in Utils to generate a random colormap with N items (from SO)

Changed

  • Set default number of CPUs used to max//2 instead of max (which hogs all the resources and slows down a lot). We still recommend setting the numbr of threads manually for best performances.

  • Updated several libs in requirements.txt

  • Moved old files to the Archive, restructured the Archive for a clearer chronological browsing

  • Benchmarking now also tests running several convolutions at once using Joblib. The final graph has also been reworked.

Fixed

  • The end_simulation parameters now have proper default values

  • Grid fields get updated earlier in visc_update_lin (was done later, could result in incorrect results)

  • Fixed a sign in P_projector

  • Fix singlethreading import in NS3D.py

[1.4.0]

Added

  • Unit tests for datasci.py, custom_logger.py, IOLib.py, misc.py, Grid.py except for Grid.Maths.convolve

  • Requirements: deepdiff->5.2.3

  • function randcomplex in datasci.py to generate normal-random complex arrays from a shape

Changed

  • Requirements: numpy 1.20.1->1.20.2

  • Renamed rot_inv_3D_divfree to rot3D_inv, rot_inv_3D to rot3D_inv (same 2D), laplacian_inv to laplacian3D_inv

  • powerlaw_fit can take an additional argument a to fit with a determined power law

  • much faster spectrum method. Spectrum’s callback now takes a bool mask of points as its secondary arg.

Fixed

  • powerlaw_fit’s mask argument now defaults to None

  • laplacian3D_inv now has the correct sign

  • spectrum was divided by a spurrious factor 2

Removed

  • Removed legacy support for .npy save files

  • Removed energyspectrum now that we have the more general spectrum

  • Removed wkmax (lack of utility)

[1.3.0]

Added

  • Log means in treat_3D.py for Re and “epsilon” dissipation rates

  • Install instructions in README

  • grid real-space length and volume are accessible via properties of the Grid() object

  • new function plot2axesX in plotlib to get a figure with two X axis

Changed

  • pltshowm now plots with a grid (alpha=0.3)

Fixed

  • HRB Scalings in Reynolds and dissipation rates (epsilons)

[1.2.0]

Added

  • changelog

Fixed

  • Saved source now correctly saved as .py

  • .gitignore now properly ignores pycache

  • reflected previous namechanges in launch_batch.sh

  • Libraries path added to simulation env. SImulation files can be run out-of-the-box without fiddling with the source dir

  • datasci.py now properly singlethreads (was broken by a previous import of scipy)

  • Python no longer errors if plotting on a backend that doesn’t support fullscreen

  • Missing rescaling time in several treat_?D functions

[1.1.0] - 2021-03-25

Added

  • Simulation source files (the “topmost” file ran) is saved as source.py in the save dir

[1.0.3_release] - 2021-03-25

Warning: this release is NOT backwards-compatible in any way.

Since it’s the first one of the changelog, I will not bother listing all the changes from the previous (undocumented) release.

Added

  • Proper gitlab CI (only lint for now)

  • Licence CC BY-NC-SA 4.0

Changed

  • Whole project linted, inline-documented, refactored (also structure-wise)

  • Numpy threads capped to 1

  • Prints replaced by logging

Fixed

  • Corrupted JSON files on a brutal stoppage are now backed up. Writing process is more robust.

  • Fix last step > max step in DataExplorer

  • Too many fixes to list here. Later changelog entries will be more precise.