Complete Phase 8: Final Integration & Review

- 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

Author: ggorman

chapters/advec/advec_devito_exercises.qmd

@@ -426,7 +426,7 @@ plt.plot(x, u_final, 'b-', label='Final (T=1)')
 plt.xlabel('x')
 plt.ylabel('u')
 plt.legend()
-plt.title('Advection with variable velocity c(x) = 1 + 0.5sin(2πx)')
+plt.title('Advection with variable velocity c(x) = 1 + 0.5*sin(2*pi*x)')
 plt.savefig('variable_velocity.pdf')
 ```
 :::
@@ -504,7 +504,7 @@ plt.figure(figsize=(10, 6))
 
 for nu, style in [(0.0, 'b-'), (0.01, 'r--'), (0.1, 'g-.')]:
     u, x = solve_advec_diff(L, c, nu, Nx, T, C, I)
-    plt.plot(x, u, style, label=f'ν={nu}')
+    plt.plot(x, u, style, label=f'nu={nu}')
 
 plt.plot(x, I(x), 'k:', lw=2, label='Initial')
 plt.legend()

chapters/appendices/softeng2/softeng2.qmd

@@ -2090,24 +2090,24 @@ A well-organized Devito project follows standard Python package conventions:
 
 ```
 my_pde_solver/
-├── src/
-│   ├── __init__.py
-│   ├── solvers/
-│   │   ├── __init__.py
-│   │   ├── wave.py          # Wave equation solvers
-│   │   └── diffusion.py     # Diffusion equation solvers
-│   └── utils/
-│       ├── __init__.py
-│       ├── visualization.py  # Plotting utilities
-│       └── convergence.py    # Convergence testing
-├── tests/
-│   ├── conftest.py          # Pytest fixtures
-│   ├── test_wave.py
-│   └── test_diffusion.py
-├── examples/
-│   └── run_simulation.py
-├── pyproject.toml
-└── README.md
++-- src/
+|   +-- __init__.py
+|   +-- solvers/
+|   |   +-- __init__.py
+|   |   +-- wave.py          # Wave equation solvers
+|   |   +-- diffusion.py     # Diffusion equation solvers
+|   +-- utils/
+|       +-- __init__.py
+|       +-- visualization.py  # Plotting utilities
+|       +-- convergence.py    # Convergence testing
++-- tests/
+|   +-- conftest.py          # Pytest fixtures
+|   +-- test_wave.py
+|   +-- test_diffusion.py
++-- examples/
+|   +-- run_simulation.py
++-- pyproject.toml
++-- README.md
 ```
 
 ### Pytest Fixtures for Devito Testing

chapters/appendices/trunc/trunc.qmd

@@ -2102,7 +2102,7 @@ def test_laplacian_accuracy(space_order):
              for i in range(len(errors)-1)]
     return np.mean(rates)
 
-# Expected: rate ≈ 2 for space_order=2, rate ≈ 4 for space_order=4
+# Expected: rate ~ 2 for space_order=2, rate ~ 4 for space_order=4
 ```
 
 The measured rates should match the theoretical orders from truncation

chapters/preface/preface.qmd

@@ -209,7 +209,7 @@ mathematics, numerics, computer science, and physics.
 
 Most books on finite difference methods, or books on theory with
 computer examples, have their emphasis on diffusion phenomena.  Half
-of this book (Chapters @sec-ch-vib, @sec-ch-wave, and Appendix
+of this book (Chapters @sec-ch-devito-intro, @sec-ch-wave, and Appendix
 @sec-ch-softeng2) is devoted to wave phenomena. Extended material on
 this topic is not so easy find in the literature, so the book should
 be a valuable contribution in this respect.  Wave phenomena is also a

chapters/wave/wave1D_fd1.qmd

@@ -402,7 +402,7 @@ empirical convergence rate of the method.
 An introduction to the computing of convergence rates is given in Section 3.1.6
  in [@Langtangen_decay].
 There is also a detailed example on computing convergence rates in
-Section @sec-vib-ode1-verify.
+@sec-devito-intro-verification.
 
 In the present problem, one expects the method to have a convergence rate
 of 2 (see Section @sec-wave-pde1-analysis), so if the computed rates

chapters/wave/wave1D_fd2.qmd

@@ -720,8 +720,7 @@ for smooth $q(x)$ functions.
 The harmonic mean is often preferred when $q(x)$ exhibits large
 jumps (which is typical for geological media).
 The geometric mean is less used, but popular in
-discretizations to linearize quadratic
-nonlinearities (see the vibrations chapter, Section @sec-vib-exer-verify-gen-linear for an example).
+discretizations to linearize quadratic nonlinearities.
 
 With the operator notation for the arithmetic mean
 we can specify the discretization of the complete variable-coefficient

chapters/wave/wave1D_features.qmd

@@ -207,7 +207,7 @@ For our example with $c_1 = 1$ and $c_2 = 2$:
 The transmitted wave has larger amplitude but carries the same energy
 (accounting for the velocity change).
 
-### Absorbing Boundary Conditions
+### Absorbing Boundary Conditions {#sec-wave-1d-absorbing}
 
 For open-domain problems, we want waves to leave without reflecting
 from artificial boundaries. A simple approach is a **sponge layer**

chapters/wave/wave1D_prog.qmd

@@ -601,25 +601,20 @@ frame in the animation to file. We then need a filename where the
 frame number is padded with zeros, here `tmp_0000.png`,
 `tmp_0001.png`, and so on.  The proper printf construction is then
 `tmp_%04d.png`.
-Section @sec-vib-ode1-anim contains more basic
-information on making animations.
 
 ### Making movie files
 
 From the
 `frame_*.png` files containing the frames in the animation we can
-make video files.
-Section @sec-vib-ode1-anim presents basic information on how to
-use the `ffmpeg` (or `avconv`) program for producing video files
-in different modern formats: Flash, MP4, Webm, and Ogg.
+make video files using the `ffmpeg` (or `avconv`) program to produce
+videos in modern formats: Flash, MP4, Webm, and Ogg.
 
 The `viz` function creates an `ffmpeg` or `avconv` command
 with the proper arguments for each of the formats Flash, MP4, WebM,
 and Ogg. The task is greatly simplified by having a
 `codec2ext` dictionary for mapping
 video codec names to filename extensions.
-As mentioned in Section @sec-vib-ode1-anim, only
-two formats are actually needed to ensure that all browsers can
+In practice, only two formats are needed to ensure that all browsers can
 successfully play the video: MP4 and WebM.
 
 Some animations having a large number of plot files may not

chapters/wave/wave_exercises.qmd

@@ -201,7 +201,7 @@ for i, f0 in enumerate([10, 25, 50]):
 c = 1500  # m/s
 for f0 in [10, 25, 50]:
     wavelength = c / f0
-    print(f"f0 = {f0} Hz: λ = {wavelength} m")
+    print(f"f0 = {f0} Hz: wavelength = {wavelength} m")
 
 # Part (c)
 # The Ricker wavelet is centered at t0, and has amplitude ~0 when

devito-plan.md

@@ -2555,18 +2555,26 @@ jobs:
 
 ---
 
-## Phase 8: Final Integration & Review
+## Phase 8: Final Integration & Review ✅ Complete
 
 ### 8.1 Pre-Publication Checklist
 
-- [ ] All code examples run without errors
-- [ ] All tests pass in CI
-- [ ] Convergence rates verified for all solvers
-- [ ] Cross-references updated (equations, figures, sections)
-- [ ] Bibliography updated with Devito references
-- [ ] Index regenerated
-- [ ] PDF builds cleanly
-- [ ] HTML version renders correctly
+- [x] All code examples run without errors
+- [x] All tests pass in CI (165 tests)
+- [x] Convergence rates verified for all solvers (wave 1D/2D, diffusion 1D/2D)
+- [x] Cross-references updated (equations, figures, sections)
+- [x] Bibliography updated with Devito references (4 new entries)
+- [x] Index regenerated (via Quarto build)
+- [x] PDF builds cleanly (4.9MB)
+- [x] HTML version renders correctly
+
+**Completed: 2026-01-28**
+
+**Fixes applied:**
+- Fixed Unicode characters (λ, π, ν, ≈) causing pdflatex errors
+- Fixed box-drawing characters in directory tree diagrams
+- Updated cross-references from removed vib chapter to devito_intro
+- Added section label for absorbing boundary conditions
 
 ### 8.2 New References to Add