Merge pull request #103 from devitocodes/devito-em

Devito em

Author: ggorman

.gitignore

@@ -53,6 +53,24 @@ doc/pub/
 /_book/
 **/*.quarto_ipynb
 
+# Root-level TeX artifacts (Quarto/Pandoc intermediates)
+/*.tex
+
+# Quarto HTML render artifacts
+**/*_files/
+
+# Review and planning documents
+book-review.md
+codex-review.md
+codex-reviewer.md
+review.md
+review-2.md
+review-3.md
+review-4.md
+ianmgdev_review.txt
+*.docx
+Proposed Extension Roadmap*.md
+
 # Coverage
 .coverage
 coverage.xml

.typos.toml

@@ -6,3 +6,7 @@ ue = "ue"
 # Strang splitting (named after mathematician Gilbert Strang)
 strang = "strang"
 Strang = "Strang"
+# Variable name for "p at iteration n" in Jacobi iteration
+pn = "pn"
+# Journal abbreviation: "J. Comput. Phys."
+Comput = "Comput"

Makefile

@@ -0,0 +1,70 @@
+# Makefile for Finite Difference Computing with PDEs book
+
+.PHONY: pdf html all preview clean test test-devito test-no-devito lint format check help
+
+# Default target
+all: pdf html
+
+# Build targets
+pdf:
+	quarto render --to pdf
+
+html:
+	quarto render --to html
+
+# Build both PDF and HTML
+book:
+	quarto render
+
+# Live preview with hot reload
+preview:
+	quarto preview
+
+# Clean build artifacts
+clean:
+	rm -rf _book/
+	rm -rf .quarto/
+	find . -name "*.aux" -delete
+	find . -name "*.log" -delete
+	find . -name "*.out" -delete
+
+# Test targets
+test:
+	pytest tests/ -v
+
+test-devito:
+	pytest tests/ -v -m devito
+
+test-no-devito:
+	pytest tests/ -v -m "not devito"
+
+test-phase1:
+	pytest tests/test_elliptic_devito.py tests/test_burgers_devito.py tests/test_swe_devito.py -v
+
+# Linting and formatting
+lint:
+	ruff check src/
+
+format:
+	ruff check --fix src/
+	isort src/
+
+check:
+	pre-commit run --all-files
+
+# Help
+help:
+	@echo "Available targets:"
+	@echo "  pdf          - Build PDF (default)"
+	@echo "  html         - Build HTML"
+	@echo "  book         - Build all formats (PDF + HTML)"
+	@echo "  preview      - Live preview with hot reload"
+	@echo "  clean        - Remove build artifacts"
+	@echo "  test         - Run all tests"
+	@echo "  test-devito  - Run only Devito tests"
+	@echo "  test-no-devito - Run tests without Devito"
+	@echo "  test-phase1  - Run Phase 1 tests (elliptic, burgers, swe)"
+	@echo "  lint         - Check code with ruff"
+	@echo "  format       - Auto-format code with ruff and isort"
+	@echo "  check        - Run all pre-commit hooks"
+	@echo "  help         - Show this help message"

README.md

@@ -16,20 +16,30 @@ Based on *Finite Difference Computing with Partial Differential Equations* by Ha
 Devito is a domain-specific language (DSL) embedded in Python for solving PDEs using finite differences. Instead of manually implementing stencil operations, you write mathematical expressions symbolically and Devito generates optimized C code:
 
 ```python
-from devito import Grid, TimeFunction, Eq, Operator
+import numpy as np
+from devito import Constant, Eq, Grid, Operator, TimeFunction, solve
 
 # Define computational grid
 grid = Grid(shape=(101,), extent=(1.0,))
 
 # Create field with time derivative capability
 u = TimeFunction(name='u', grid=grid, time_order=2, space_order=2)
 
-# Write the wave equation symbolically
-eq = Eq(u.dt2, c**2 * u.dx2)
+# Wave speed parameter (passed at runtime)
+c = Constant(name="c")
+
+# Set an initial condition (Gaussian pulse)
+x = np.linspace(0.0, 1.0, 101)
+u.data[0, :] = np.exp(-((x - 0.5) ** 2) / (2 * 0.1**2))
+u.data[1, :] = u.data[0, :]  # zero initial velocity (demo)
+
+# Write the wave equation symbolically and derive an explicit update stencil
+pde = Eq(u.dt2, c**2 * u.dx2)
+update = Eq(u.forward, solve(pde, u.forward))
 
 # Devito generates optimized C code automatically
-op = Operator([eq])
-op.apply(time_M=100, dt=0.001)
+op = Operator([update])
+op.apply(time_M=100, dt=0.001, c=1.0)
 ```
 
 ## Quick Start

_quarto.yml

@@ -6,19 +6,28 @@ book:
   title: "Finite Difference Computing with PDEs"
   subtitle: "A Devito Approach"
   author:
-    - name: Hans Petter Langtangen
-    - name: Svein Linge
+    - name: Gerard J. Gorman
+      affiliation: Imperial College London
   date: today
   chapters:
     - index.qmd
     - chapters/preface/index.qmd
+    # Note: chapters/vib/ exists on disk but is excluded from the build.
+    # The vibration ODE content from the original Langtangen & Linge text
+    # has not yet been ported to the Devito approach. Readers interested
+    # in vibration ODEs can refer to Langtangen_deqbook_vib in the bibliography.
     - part: "Main Chapters"
       chapters:
         - chapters/devito_intro/index.qmd
         - chapters/wave/index.qmd
         - chapters/diffu/index.qmd
         - chapters/advec/index.qmd
         - chapters/nonlin/index.qmd
+        - chapters/elliptic/index.qmd
+        - chapters/systems/index.qmd
+    - part: "Applications"
+      chapters:
+        - chapters/applications/electromagnetics/index.qmd
     - part: "Appendices"
       chapters:
         - chapters/appendices/formulas/index.qmd
@@ -39,6 +48,86 @@ format:
     number-depth: 3
     crossref:
       chapters: true
+    include-in-header:
+      text: |
+        <script>
+        MathJax = {
+          tex: {
+            macros: {
+              half: "\\frac{1}{2}",
+              halfi: "{1/2}",
+              tp: "\\thinspace .",
+              Ddt: ["\\frac{D #1}{dt}", 1],
+              E: ["\\text{E}\\lbrack #1 \\rbrack", 1],
+              Var: ["\\text{Var}\\lbrack #1 \\rbrack", 1],
+              Std: ["\\text{Std}\\lbrack #1 \\rbrack", 1],
+              xpoint: "\\boldsymbol{x}",
+              normalvec: "\\boldsymbol{n}",
+              Oof: ["\\mathcal{O}(#1)", 1],
+              x: "\\boldsymbol{x}",
+              X: "\\boldsymbol{X}",
+              uu: "\\boldsymbol{u}",
+              vv: "\\boldsymbol{v}",
+              w: "\\boldsymbol{w}",
+              acc: "\\boldsymbol{a}",
+              rpos: "\\boldsymbol{r}",
+              V: "\\boldsymbol{V}",
+              e: "\\boldsymbol{e}",
+              f: "\\boldsymbol{f}",
+              F: "\\boldsymbol{F}",
+              stress: "\\boldsymbol{\\sigma}",
+              strain: "\\boldsymbol{\\varepsilon}",
+              stressc: "{\\sigma}",
+              strainc: "{\\varepsilon}",
+              I: "\\boldsymbol{I}",
+              T: "\\boldsymbol{T}",
+              U: "\\boldsymbol{U}",
+              q: "\\boldsymbol{q}",
+              g: "\\boldsymbol{g}",
+              dfc: "\\alpha",
+              ii: "\\boldsymbol{i}",
+              jj: "\\boldsymbol{j}",
+              kk: "\\boldsymbol{k}",
+              ir: "\\boldsymbol{i}_r",
+              ith: "\\boldsymbol{i}_{\\theta}",
+              iz: "\\boldsymbol{i}_z",
+              Ix: "\\mathcal{I}_x",
+              It: "\\mathcal{I}_y",
+              Iz: "\\mathcal{I}_z",
+              It: "\\mathcal{I}_t",
+              If: "\\mathcal{I}_s",
+              Ifd: "{I_d}",
+              Ifb: "{I_b}",
+              setb: ["#1^0", 1],
+              sete: ["#1^{-1}", 1],
+              setl: ["#1^-", 1],
+              setr: ["#1^+", 1],
+              seti: ["#1^i", 1],
+              sequencei: ["\\left\\{ {#1}_i \\right\\}_{i\\in\\If}", 1],
+              sequencej: ["\\left\\{ {#1}_j \\right\\}_{j\\in\\If}", 1],
+              stepzero: "*",
+              stephalf: "***",
+              stepone: "**",
+              basphi: "\\varphi",
+              baspsi: "\\psi",
+              refphi: "\\tilde\\basphi",
+              psib: "\\boldsymbol{\\psi}",
+              sinL: ["\\sin\\left((#1+1)\\pi\\frac{x}{L}\\right)", 1],
+              xno: ["x_{#1}", 1],
+              Xno: ["X_{(#1)}", 1],
+              yno: ["y_{#1}", 1],
+              Yno: ["Y_{(#1)}", 1],
+              xdno: ["\\boldsymbol{x}_{#1}", 1],
+              dX: "\\, \\mathrm{d}X",
+              dx: "\\, \\mathrm{d}x",
+              ds: "\\, \\mathrm{d}s",
+              Real: "\\mathbb{R}",
+              Integerp: "\\mathbb{N}",
+              Integer: "\\mathbb{Z}"
+            }
+          }
+        };
+        </script>
   pdf:
     documentclass: scrbook
     classoption:
@@ -63,26 +152,20 @@ format:
         \SetWatermarkColor[gray]{0.9}
 
         % Required packages
+        \usepackage[T1]{fontenc}  % Proper glyph support for accents and symbols
+        \usepackage{textcomp}     % Additional text symbols
         \usepackage{bm}  % For bold math symbols
 
         % Custom LaTeX macros from the book
         \newcommand{\half}{\frac{1}{2}}
         \newcommand{\halfi}{{1/2}}
         \newcommand{\tp}{\thinspace .}
 
-        \newcommand{\uex}{u_{\mbox{\footnotesize e}}}
-        \newcommand{\uexd}[1]{u_{\mbox{\footnotesize e}, #1}}
-        \newcommand{\vex}{v_{\mbox{\footnotesize e}}}
-        \newcommand{\Vex}{V_{\mbox{\footnotesize e}}}
-        \newcommand{\vexd}[1]{v_{\mbox{\footnotesize e}, #1}}
-        \newcommand{\Aex}{A_{\mbox{\footnotesize e}}}
-        \newcommand{\wex}{w_{\mbox{\footnotesize e}}}
-
         % Operators
         \newcommand{\Ddt}[1]{\frac{D #1}{dt}}
-        \newcommand{\E}[1]{\hbox{E}\lbrack #1 \rbrack}
-        \newcommand{\Var}[1]{\hbox{Var}\lbrack #1 \rbrack}
-        \newcommand{\Std}[1]{\hbox{Std}\lbrack #1 \rbrack}
+        \newcommand{\E}[1]{\text{E}\lbrack #1 \rbrack}
+        \newcommand{\Var}[1]{\text{Var}\lbrack #1 \rbrack}
+        \newcommand{\Std}[1]{\text{Std}\lbrack #1 \rbrack}
 
         \newcommand{\xpoint}{\bm{x}}
         \newcommand{\normalvec}{\bm{n}}
@@ -169,8 +252,11 @@ src_diffu: "https://github.com/devitocodes/devito_book/tree/devito/src/diffu"
 src_nonlin: "https://github.com/devitocodes/devito_book/tree/devito/src/nonlin"
 src_trunc: "https://github.com/devitocodes/devito_book/tree/devito/src/trunc"
 src_advec: "https://github.com/devitocodes/devito_book/tree/devito/src/advec"
+src_elliptic: "https://github.com/devitocodes/devito_book/tree/devito/src/elliptic"
+src_systems: "https://github.com/devitocodes/devito_book/tree/devito/src/systems"
 src_formulas: "https://github.com/devitocodes/devito_book/tree/devito/src/formulas"
 src_softeng2: "https://github.com/devitocodes/devito_book/tree/devito/src/softeng2"
+src_em: "https://github.com/devitocodes/devito_book/tree/devito/src/em"
 
 crossref:
   eq-prefix: ""