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docs(notebooks): run dynaphopy GRACE/EMT examples at 788 K (#74)

* docs(notebooks): switch dynaphopy GRACE/EMT examples to 788 K + restore mass-weighted Boltzmann

Three changes to align both example notebooks with the dynaphopy upstream
Si Tersoff page (https://abelcarreras.github.io/DynaPhoPy/examples.html)
so the velocity histograms and dispersion plots can be eyeballed
side-by-side with the docs.

1. Bump MD target T from 300 K → 788 K everywhere (`temperature=`, LAMMPS
   `velocity create` / `langevin`, plot titles, print f-strings).
2. Restore the mass-weighted Boltzmann analysis lost in a previous
   worktree-cleanup: histogram v · √m_amu in √u·Å/ps and back-derive
   T from the Maxwell scale parameter via T = a² / kB with
   kB = 0.831446 u·Å²/(ps²·K), matching dynaphopy/analysis/energy.py.
   Predicted ⟨|v|⟩_mw at 788 K ≈ 40.86 √u·Å/ps, matches the upstream
   page's 40.7 figure.
3. Replace the straight-lines-between-4-commensurate-points dispersion
   plots with phonopy-sampled smooth Γ→X→K/W→L band paths
   (`_fine_band_path`, ~50 pts/segment). Renormalised MD-projected
   values stay as markers at the commensurate q's only — that's where
   dynaphopy's mode projection is well-defined.

Outputs cleared; re-execution follows in a separate commit.

* fix(notebooks): seed dynaphopy_grace_example_long lat_opt with conventional Si

PR #71 wired optimise_cubic_lattice_parameter into the dynaphopy GRACE
example using the *primitive* 2-atom diamond Si seed. That trips the
known optimise-cubic-lattice-param quirk (function computes
a0 = v0**(1/3) which is only correct when v0 is the conventional cell
volume), so a0 silently comes out at ~3.45 Å instead of ~5.43 Å.
Downstream MD then runs on a squashed cell and the optical mode shifts
from ~16 THz up to ~33 THz — the dispersion plot becomes unphysical.

Add a separate `si_conv_seed` (8-atom conventional) for the EOS scan,
keep `si_prim_initial` for the cheap GRACE smoke-test. Mirrors the
fix the EMT... (continued)

3305 of 3675 relevant lines covered (89.93%)

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Coverage Regressions

Lines Coverage ∆ File
6
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 -16.67% physics/phonons/_compat.py
4
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 -0.12% physics/free_energy/anharmonic_dynaphopy.py
Jobs
ID Job ID Ran Files Coverage
1 26024424108.1 55
89.93
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