paper-tutorial-plasmon-heating

name	paper_tutorial_plasmon_heating
description	Dual-purpose tutorial to reproduce manuscript Figure 5b, 5d, and 5e plasmonic flux and HCN heating maps (EM-only, TLS, and ASE/BOMD), and to transfer the workflow to related plasmon-molecule systems by adjusting geometry, molecular model, and run procedures.

Paper Tutorial: Plasmonic Flux and HCN Heating (Figure 5b, 5d, 5e)

Use this skill to reproduce the scoped Pt/Si plasmonic manuscript results for:

• Figure 5b: EM-only flux/absorption spectrum.
• Figure 5d: MaxwellLink + TLS heating map (nmol=256).
• Figure 5e: MaxwellLink + ASE/Psi4 BOMD heating map (nmol=256) plus TLS-vs-BOMD consistency.

Core Simulation Strategy

• Run all simulations and postprocessing in one dated runtime folder under projects/YYYY-MM-DD-<scope>/.
• Recommended scope slug: plasmon-heating.
• Copy assets/implementation_2025/ into the runtime folder, then run three branches with fixed paper anchors:
  • aa=2.79, rr=1.11, nmol=256, y-polarized excitation, coupled propagation t=60.
  • EM-only branch (meep_plasmon_empty) for Figure 5b.
  • TLS branch (meep_plasmon_HCN_excitation_tls_strong) for Figure 5d.
  • BOMD branch (meep_plasmon_HCN_excitation_bomd_strong) for Figure 5e.
• Use trend-level agreement targets (peak positions and anisotropy structure), not bitwise trajectory identity.
• Figure 5f (RT-Ehrenfest) is intentionally out of scope.

Minimal Execution Recipes

Run commands from repository root.

1. Create runtime workspace and stage assets:

RUN_DATE="${RUN_DATE:-$(date +%F)}"
RUN_SCOPE="${RUN_SCOPE:-plasmon-heating}"
RUN_DIR="projects/${RUN_DATE}-${RUN_SCOPE}"
mkdir -p "$RUN_DIR"
cp -R skills/paper_tutorial_plasmon_heating/assets/implementation_2025 "$RUN_DIR/"

2. Figure 5b (EM-only spectrum):

cd "$RUN_DIR/implementation_2025/meep_plasmon_empty"
mkdir -p vac no_mol_with_dielectric
cp template/* vac/
cp template/* no_mol_with_dielectric/

cd vac
mpirun -np 128 python -u emitter.py -empty -aa 2.79 > flux0_a2.79.out
grep flux1: flux0_a2.79.out | cut -d , -f2- > flux0_a2.79.dat

cd ../no_mol_with_dielectric
mpirun -np 128 python -u emitter.py -dielectric -aa 2.79 -rr 1.11 -nmol 1 > flux_a2.79_r1.11.out
grep flux1: flux_a2.79_r1.11.out | cut -d , -f2- > flux_a2.79_r1.11.dat

3. Figure 5d (TLS coupled map via Slurm templates):

cd "$RUN_DIR/implementation_2025/meep_plasmon_HCN_excitation_tls_strong"
mkdir -p nmol_256_with_dielectric
cp -R template/* nmol_256_with_dielectric/
cd nmol_256_with_dielectric
sbatch submit_all.sh

4. Figure 5e (BOMD coupled map via Slurm templates):

cd "$RUN_DIR/implementation_2025/meep_plasmon_HCN_excitation_bomd_strong"
mkdir -p nmol_256_with_dielectric
cp -R template/* nmol_256_with_dielectric/
cd nmol_256_with_dielectric
sbatch submit_all.sh

5. Build scoped figures and enforce acceptance checks:

cd "$RUN_DIR/implementation_2025/plotting"
python fig5bde_postprocess.py \
  --mode all \
  --base-dir .. \
  --nmol 256 \
  --figure-out fig5bde_scope.pdf \
  --report-out fig5bde_metrics.json \
  --strict

6. Runtime guardrails:

• Do not run simulations inside skills/paper_tutorial_plasmon_heating/.
• Do not write runtime output under skills/.

Figure Routing

• fig_001 (Figure 5b): EM-only Pt/Si plasmonic baseline from vacuum-normalized flux, reproducing a strong absorption peak near 3492 cm^-1 and high absorption around HCN stretch; playbook: skills/paper_tutorial_plasmon_heating/playbooks/fig_001_plasmon_flux_spectrum.md.
• fig_002 (Figure 5d): MaxwellLink+TLS 16x16 molecular-lattice heating map with y-gap-dominant anisotropy and y-edge hotspot structure under the same EM geometry; playbook: skills/paper_tutorial_plasmon_heating/playbooks/fig_002_tls_heating_map.md.
• fig_003 (Figure 5e): MaxwellLink+ASE/Psi4 BOMD heating map with stronger y-gap anisotropy and BOMD mean gain exceeding TLS under matched settings; playbook: skills/paper_tutorial_plasmon_heating/playbooks/fig_003_bomd_heating_map.md.

Beyond Manuscript Exploration

• Sweep rr around 1.11 (for example 1.00-1.20) at fixed aa=2.79 to quantify peak shifts.
• Sweep perfect-square molecular grids (nmol=64, 100, 144, 256) while preserving lattice placement.
• Sweep TLS dipole strength mu12 around 0.15 and track anisotropy ratio sensitivity.
• Benchmark BOMD settings (basis, memory, num_threads) only after baseline reproduction passes strict checks.
• Keep EM geometry and source window fixed when comparing TLS vs BOMD to preserve interpretability.