Sound in Matter: scripts and outputs (companion to Sound_in_Matter_Calibration.md, draft 0.2, 1 November 2026)

Lennard-Jones fluids
  ljmd.py            numba molecular dynamics (cell lists, velocity Verlet); pulse_run (travelling pulse) and wave_run (one wavelength in the box)
  run_fluids.py      the cases (argon gas, helium gas, liquid argon); usage: python3 run_fluids.py <case> <seed>
  analyse_fluids.py  pulse speeds -> fluids_pulse.txt
  analyse_waves.py   standing-wave speeds with thermal-noise error bars -> waves.txt
Rock salt
  nacl.py -> nacl.txt  Born-Mayer + Ewald elastic constants and wave speeds
Sodium
  lattice.py, stage0_chain.py   Ewald lattice dynamics and plane chains (shared with the Model L work)
  sodium.py -> sodium.txt       Bohm-Staver; Thomas-Fermi (Yukawa) lattice; rigid background; chain pulses (sodium.pkl)
  sodium_ladder.py -> sodium_ladder.txt   the energy-route ladder, steps 1-4, sensitivities
  liquid_na.py                  liquid sodium MD; usage: test | run <r_c> <density factor> <T> <seed> [N] | analyse <r_c> [<r_c for T runs>]
  liquid_na_A.txt, liquid_na_B.txt   analyses at r_c = 1.971 and 1.986 bohr (with the cut-off pressure term)
  na_final.py -> na_final.txt   correction to 371 K and zero pressure
  sodium_crystal2.py -> sodium_crystal2.txt   crystal by the force (long-wave) route; sodium2.pkl
  shear_check.py -> shear_check.txt           shear stiffnesses by the energy route (must match the force route)
  sodium_anim.py                the animation (sodium-push.mp4)
Figures
  fig_sound.py (Figures 1, 2), fig_models.py (Figures 3, 4), law.py -> law.txt
Logs: log_*.txt
