Devito Edition #98
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Devito Edition #98
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Phase 0 and 0.5 of the Devito book refactoring: - src/symbols.py: Common SymPy symbols for variables, parameters - src/operators.py: Finite difference operators with Taylor series analysis - src/display.py: LaTeX rendering utilities for Quarto documents - src/verification.py: Tools for verifying mathematical derivations - src/plotting.py: Reproducible plotting with fixed seed (42) - src/wave/wave1D_devito.py: 1D wave equation solver using Devito DSL Testing infrastructure: - tests/test_operators.py: 37 tests for FD operators - tests/test_derivations.py: 22 tests for heat, wave, advection equations - tests/test_wave_devito.py: 13 tests for Devito wave solver - tests/conftest.py: Shared pytest fixtures CI/CD: - .github/workflows/ci.yml: GitHub Actions workflow - codecov.yml: Coverage reporting configuration - pytest.ini: Pytest configuration Dependencies: - Add optional devito and devito-petsc dependencies from GitHub
- Add progress summary table to devito-plan.md with phase status - Document recent completions (Phase 0, 0.5, 7) - Update README for Quarto-based build system - Add CI and Codecov badges to README - Add Devito installation instructions (pip install -e ".[devito]") - Update directory structure to reflect new src/ package layout - Add pre-commit hooks and code style documentation
- Add ignores to .markdownlint-cli2.yaml for devito_repo/, venv/, etc. - Disable MD018 (shebang false positives) and MD036 (exercise labels)
Phase 2 Wave Equations progress: - src/wave/wave2D_devito.py: 2D wave solver using Devito .laplace - src/wave/sources.py: Ricker wavelet, Gaussian pulse, spectrum analysis - Updated src/wave/__init__.py with new exports - Added 16 new tests (29 total wave tests, 88 total) Also includes typo fixes in legacy files from pre-commit hooks.
Phase 2 chapter content for wave equations using Devito DSL: - wave1D_devito.qmd: Core 1D solver with Grid, TimeFunction, Operator - Symbolic derivatives (.dt2, .dx2) - Boundary conditions using Eq - Verification with standing wave solution - wave1D_features.qmd: Source terms and variable coefficients - Ricker and Gaussian source wavelets - Point sources with SparseTimeFunction - Variable velocity fields - Absorbing boundary conditions - wave2D_devito.qmd: 2D extension using .laplace - Dimension-agnostic Laplacian - 2D CFL stability condition - Visualization with surface/contour plots - wave_exercises.qmd: 10 Devito-based exercises with solutions - Standing waves, convergence rates, guitar string - Source wavelets, 2D propagation, interface reflections - Manufactured solutions, energy conservation, dispersion Updated index.qmd to include new sections.
Python Solvers: - src/diffu/diffu1D_devito.py: 1D diffusion solver (Forward Euler explicit) with DiffusionResult dataclass, exact solution, convergence testing - src/diffu/diffu2D_devito.py: 2D diffusion solver using .laplace - src/diffu/__init__.py: Module exports for new Devito solvers Quarto Chapters: - chapters/diffu/diffu1D_devito.qmd: Forward Euler with Devito covering time_order=1, .dt derivative, Fourier number F <= 0.5 stability - chapters/diffu/diffu2D_devito.qmd: 2D extension with .laplace and F <= 0.25 stability for equal spacing - chapters/diffu/diffu_devito_exercises.qmd: 10 exercises with solutions covering stability, convergence, Gaussian/plug initial conditions, 2D heat diffusion, variable coefficients, manufactured solutions Tests: - tests/test_diffu_devito.py: 23 tests covering 1D/2D solvers, exact solutions, convergence rates, boundary conditions, initial conditions All 111 tests pass.
Phase 4 implements 1D advection solvers using Devito DSL: Solvers (src/advec/advec1D_devito.py): - Upwind scheme: first-order, uses .subs() for shifted indexing - Lax-Wendroff scheme: second-order accurate - Lax-Friedrichs scheme: first-order, very stable - Helper functions for exact solutions and convergence testing Chapter content: - chapters/advec/advec1D_devito.qmd: scheme comparison and implementation - chapters/advec/advec_devito_exercises.qmd: 10 exercises with solutions - Updated chapters/advec/index.qmd with new includes Testing: - 25 tests for advection solvers (convergence, boundary conditions, accuracy)
Python Solvers (src/nonlin/nonlin1D_devito.py): - solve_nonlinear_diffusion_explicit: Explicit scheme with lagged coefficient - solve_reaction_diffusion_splitting: Lie and Strang operator splitting - solve_burgers_equation: Viscous Burgers' equation with conservative form - solve_nonlinear_diffusion_picard: Picard iteration for implicit schemes - Helper functions: constant_diffusion, linear_diffusion, porous_medium_diffusion - Reaction terms: logistic_reaction, fisher_reaction, allen_cahn_reaction Quarto Chapters: - chapters/nonlin/nonlin1D_devito.qmd: Nonlinear diffusion, reaction-diffusion splitting, Burgers' equation implementation with Devito - chapters/nonlin/nonlin_devito_exercises.qmd: 10 exercises with solutions Tests: - tests/test_nonlin_devito.py: 29 tests for all nonlinear solvers Also added "Strang" to typos exclusion (mathematician Gilbert Strang).
- Add "Devito and Truncation Errors" section to truncation appendix covering space_order parameter, stencil viewing, and accuracy tradeoffs - Add "Software Engineering with Devito" section to softeng appendix covering project structure, pytest fixtures, convergence testing, and performance profiling - Fix Strang splitting typo in tests (strange -> strang) - Update devito-plan.md to mark Phase 6 complete
- Add ipython to test-derivations dependencies (required by src/display.py) - Ignore E741/E743 in ruff check (I is standard notation for initial condition)
- Limit ruff check to new Devito code paths (skip legacy code with pre-existing issues) - Ignore F841 (unused variables), E722 (bare except), E731 (lambda), E402 (import order)
- Create chapters/devito_intro/ with five QMD files covering: - What is Devito (motivation, traditional vs DSL approach) - First PDE (1D wave equation complete example) - Core abstractions (Grid, Function, TimeFunction, Eq, Operator) - Boundary conditions (Dirichlet, Neumann, absorbing, periodic) - Verification (convergence testing, MMS) - Update _quarto.yml to use devito_intro as first main chapter - Update devito-plan.md to mark Phase 1 complete
- Add Devito references to bibliography (4 entries) - Fix Unicode characters causing pdflatex errors (lambda, pi, nu, approx) - Replace box-drawing characters with ASCII in directory tree - Update cross-references from removed vib chapter to devito_intro - Add section label for absorbing boundary conditions - Fix preface chapter reference from @sec-ch-vib to @sec-ch-devito-intro - Remove obsolete vib animation references from wave chapter - PDF builds cleanly (4.9MB), all 165 tests pass
- Delete all .do.txt files and conversion scripts - Remove doconce, mako, and related dependencies from pyproject.toml and requirements.txt - Replace doconce combine_images with ImageMagick montage in source files - Clean up .gitignore, config files, and documentation references - Remove legacy doc/ build directory
- Rewrite README.md to highlight Devito DSL and modern tooling - Update index.qmd with Devito introduction and code example - Update CLAUDE.md with Devito patterns and project structure - Update _quarto.yml source URLs to point to devitocodes repo - Remove devito-plan.md (completed development roadmap) - Remove issues.md (conversion tracking no longer needed)
- Change subtitle from "A Modern Software Approach" to "A Devito Approach" - Add "About This Adaptation" section to preface with CC BY 4.0 attribution - Fix license from CC BY-NC 4.0 to CC BY 4.0 (matching original work) - Add adapter credit (Gerard J. Gorman, Imperial College London) - Create LICENSE file with full attribution requirements - Add license badge and DOI link to README and index
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