Wrap FFT for specific array structures in Exponax #4
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Ceyron
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* Also run pre-commit on dev * Update docs requirements * Remove old requirements * Remove no longer needed setup.py * No longer target incompatible Python versions * Add credits and improve settings * Wrap FFT for specific array structures in Exponax (#4) * Add custom wrapped FFT calls * Rewrite derivative routines to use wrapped FFT calls * Make number of spatial dims optional * Run black * Correctly declare as optional * Use wrapped routines * Use wrapped routines * Use wrapped routines * Use wrapped routines * Use wrapped routines * Use wrapped routines * Export the spectral submodule * Add more details on usage * Start documentation of spectral module * Stepper restructure (#21) * Move reaction into stepper * Adapt imports in tests * Move linear timesteppers into separete files * Move generic physical stepper into submodule * Rename to nonlinear * Correctly export in submodule * Move utilities * Export generic utilities * Fully translate linear generic stepper * Fully translate convection stepper * Fully translate generic nonlinear stepper * Fully translate generic Gradient norm stepper * Correctly forward dealiasing fraction * No need to set dealiasing fraction * Fully translate generic polynomial stepper * Don't translate vorticity convection * Remove normalized submodule * Remove no longer relevant exports * Export generic stepper * Fix issues with dealiasing_fraction arguments * Adapt tests * Remove commented sections * Adapt cross-references * New docs layout to better reflect the API * Add a boilerplate for the overview * Consistent docs (#26) * Add documentation to base * Add documentation to etdrk core * Adapt to Equinox style * Change to Equinox style * Change to Equinox style * Change to Equinox style * Fix typo * Consistent documentation * Improve nonlin fun base documentation * Change to Equinox style * Improve docs for convection * Improve docs for gradient norm * Improve docs for combined general nonlinearity * Fix docstring * Improve and fix documentation * Fix broken link * Adapt to Equinox style * Improve documentation * Add clarification * better wording * Fix convection difficulty computation * Improve doc of generic gradient norm stepper * Add docstring * Add documentation * Add documentation * Add documentation * Use correct tuple typing (#27) * Add type hints (#28) * Fourier repeated stepper (#29) * Implement logic of fourier substepping * Forward .step() to call signature with shape check * Add hints from Base Stepper * Add hints on cost-saving * Also add hint to constructor * Add a test for the new repeated stepper * Add CI for running a test on PRs * Fix repeated Python versions * Fourier Interpolation and Up/Downsampling (#33) * Add simple Fourier interpolator * Add 1D tests * Add tests in 2d * Loosen tests * Fix the generalization to 2d * Add tests in 3d * Forward indexing convention * Correctly use ellipsis * Add documentation * Add documentation * Add utility to get modes slices * Add test for mode slice generation * Return tuples * Utility to move between resolutions * Add tests for mapping between resolutions * Fix issue with oddball sanity * Add new utilities to documentation * Add documentation * Add return type hint * Simple showcase of new functions * Properly rerun notebook * Add PyTest dependency * Fix tests to use tuples * Loosen requirements on (decaying) Burgers problem * Add requirement on 3d volume renderer * Use quotes to correctly get 3.10 * Ignore test requiring GPU * Remove vape dependency because we no longer test for it * Spectral updates (#35) * Preliminary function to compute the spectrum * Potential improvement to spectrum computation * Add hint on enstrophy * Fix on wavenumber norm computation * Rename to better reflect its effect on oddball mode * Add tests on filter mask * Improve first half of spectral documentation * Merge common subexpressions * Extend and fix documentation * Add experimental convinience function to extract the Fourier coefficients * Unify the creation of scaling arrays * Test scaling array for norm_compensation * Add tests for coefficient extraction in 1D * Test for coefficient extration in 2D * Enhance docstring * Remove experimental function * Fix spectrum function * Export get_spectrum instead of make_incompressible * Adapt docs * Use proper links * Enhance docstring * Enhance docstring * Test the spectrum creation * Restructure docstring * Tests helper utilities for fft setup * Hyperviscous kdv [BREAKING] (#36) * Have the dispersion operator being created seperately * Make KdV hyper-viscous by default * Remove unnecessary copy * Requires new coefficients to work with changed defaults in KdV * Fourier Coefficient Extractor (#38) * Add function * Enhance docstring * Change rounding default * Add coefficient extractor to docs * Quicker spectrum in 1D * More validation (#39) * Add note * Add 2d and 3d advection * Add diffusion analytical solution in 2D * Add diffusion test in 3D * Ensure all presets are working * Employ a fix for single facets * Use Exponax viz routines * Also employ fix for faceted animations * Fix defaults for Kolmogorov * Change to exponax viz routines * Add 3D dynamics * Add hint on where to find the reference qualitative rollouts * Re-Execute Notebook * Re-Execute Notebook * Re-Execute notebook * Start with a validation notebook for KdV * Test if KdV without convection is purely linear * Finished KdV soliton comparison * Faster way to compute the spectrum binning in higher dimensions * Improved version of kolmogorov comparison * Improved Metrics System (#40) * Start implementing metrics tests * Starting a notebook on validating the metrics * [WIP] Start generalizing the fourier nRMSE to allow for derivative based losses * Set up a new structure for metrics * New export structure * Overwrite the existing metrics submodule * Adapt tests because domain_extent is now considered correctly * Test against analytical solution * Fix parameterization of test * Start set up with a new fourier metrics implementation * Ensure correct shape * Add first test on Fourier aggregation * Add basic abolute metrics, more TODO * Port the correlation metric * New API in docs * Port new spatial metrics to API docs * Rework correlation documentation * Add drafts on an advanced background notebook on metrics and their relation to functional norms * Fix the scaling in the Fourier aggregation * Use pytest approx * Fix scaling * Add equivalence test of Fourier and spatial aggregation * Rework implementations * Remove mean correlation * Add soboleb based metrics * Add helper function to apply metric functions on batched states * Test with non-unit domain * Start with a low-level introduction to metrics * Add basics notebook * Adapt API docs * Add to API docs * Add documentation to spatial metrics * Reference does not be zero in normalized metrics * Add documentation * Fix documentation * Test Sobolev against manual adding of derivatives with fourier-base metrics * Fix typo * Add documentation * Add tests on Filtering * Add notes on preliminary notebook * Fix broken links * Also add warning to advanced metrics notebook * Continue with the metric convergence notebook, still WIP * Add example on Sobolev usage * Finish validation notebook * Add temporal convergence notebook (#41) * Add warning for KS conservative in higher dimensions * Symmetric Metrics & Metrics improvements (#44) * Extend docstring for symmetric metrics * Improve aggregator docstring * Fix that identity is only guaranteed for L^p norm * Fix docstring * Implement symmetric mode * Fix missing sqrt * Add symmetric versions for MAE, MSE, and RMSE * Add new symmetric metrics to documentation * Add test for symmetric metrics * Ensure mean is only taken over axis zero in case there are additional axes * Add details * Add non-conservative convection term (#46) * add non-conservative convection term * fix errors in docstring * update docstring * use the dealiased value for non-conservative convection * Fix non-forwarded conservative flag * Small Improvements to Gaussian Random Field (#48) * Retain mean mode from white noise * Add comment on why there is a 2.0 in denominator * Polynomial Stepper Fix (#49) * Have general diffusion coefficient consisten with norm/diff * Use correct sign on quadratic nonlinearity * Conservative KS should use conservative convection (#50) * Conservative KS should use conservative convection * Adapt tests * Consistent Generic Steppers (#52) * Use consistent attribute names * Forward API changes to tests * Forward changes to qualitative rollout * Ensure single-channel convection nonlin is conservative (#53) * Rework KS Attributes (#54) * Remove name of diffusivities from combustion KS * Remove name of diffusivities from conservative KS * Foward changes to tests * Fix missing factor of 0.5 * Rework 1D example notebook * Docs tweak (#55) * Change to proper markdown * Add KS conservative docstring * Re-Execute IC notebook * Rerun general and normalized notebookt * Rerun subclassing example * Rerun showcase 2D * Add solver overview in 3D * Add 3D Solver overview to docs * Automatically deduce version number --------- Co-authored-by: Qiang <[email protected]>
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