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docs(notebooks): wire optimise_cubic_lattice_parameter into dynaphopy_grace_example_long (#71)

Section A is now a pyiron_workflow.Workflow("dynaphopy_grace_ase") with three
nodes: optimise_cubic_lattice_parameter -> get_bulk (rebuild 2-atom primitive
at a0, since the macro returns the conventional cubic cell) -> phonon-MD macro.
A second ASEEngine ("engine_min", CalcInputMinimize, tol=0.05, max_iter=100)
drives the EOS scan; the existing ase_engine (CalcInputStatic) drives FC2 +
Langevin NVT MD as before. Both engines use with_working_directory("...") to
keep on-disk artefacts separated under ./_dynaphopy_grace_long_runs.

Section B rebuilds si_supercell from the GRACE-optimised primitive before the
LAMMPS run, so the ASE and LAMMPS halves now share the same equilibrated
geometry (apples-to-apples) rather than both being pinned to a=5.43 A.

MD parameters (production_steps=50000, time_step=0.7 fs, temperature=300 K,
thermostat_time_constant=100, seed=42, etc.) and the LAMMPS-driven Section B
logic are unchanged otherwise.

Edits validated statically: nbformat round-trip ok, nbconvert --to script
produces a 641-line python script with no syntax errors. End-to-end execution
was not attempted in this worktree because tensorpotential/GRACE is not
installed in /home/liger/miniforge3 (lives in env "calphy" per project memory
[[project_calphy_grace_lammps]]); the notebook will need to be re-executed in
that env or the dedicated GRACE env to refresh recorded outputs.

Co-authored-by: Han Mai <ligerzerof@gmail.com>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

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