Meep FDTD workflows (MaxwellLink)

Confirm prerequisites

• Ensure pymeep is installed and importable before generating Meep-based inputs.
• Use mxl.MeepSimulation (not raw meep.Simulation) when using the unified mxl.Molecule API.

Build a Meep-coupled run

• Set time_units_fs explicitly and keep it consistent across analysis.
• Create molecules with either:
  • Embedded driver: Molecule(driver=..., driver_kwargs=...)
  • Socket driver: SocketHub(...) + Molecule(hub=hub, ...)
• For "baseline" EM-only runs (no molecules), use raw mp.Simulation(...); switch to mxl.MeepSimulation(...) only when MaxwellLink molecules are present (common when generating reference spectra/fields first, then enabling coupling).
• Use boundary_layers=[mp.PML(...)], set resolution, and keep Courant=0.5 (Meep default).

Prefer templates

• Start from the copy-ready templates:
  • skills/mxl-project-scaffold/assets/templates/meep-tls-embedded
  • skills/mxl-project-scaffold/assets/templates/meep-tls-socket-unix
  • skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp (3D plasmonic structure + RT-Ehrenfest molecular lattice)
• Use SLURM/HPC patterns from skills/mxl-hpc-slurm/SKILL.md for multi-node socket runs.

References

• Recipes: skills/mxl-meep/references/meep_run_recipes.md
• Docs: docs/source/em_solvers/meep.rst

MPI/libfabric init tips (macOS/local single-rank)

• Sandbox note: sandboxed runs often block the libfabric endpoint; if MPI_Init_thread fails with ep_enable/socket errors, rerun unsandboxed (sandbox_permissions=require_escalated).
• When Matplotlib is imported, set MPLCONFIGDIR=/tmp/mplconfig to avoid cache permission errors.

Other common bugs

• The dimensions=... input can only be assigned in mxl.Molecule() not mxl.MeepSimulation(). For example, assigning dimensions=1 in both mxl.Molecule() and mxl.MeepSimulation() will lead to runtime error: meep: cannot require a ez component in a 1D grid.
• In 1D and 2D simulations, mxl.Molecule (or molecular drivers) should have a transition dipole moment along z-direction, because mxl.MeepSimulation() sets the mxl.Molecule to emit only along z-direction in 1D and 2D.
• Cylindrical cells additionally support an on-axis x/y dipole with polarization_type="analytical" and m=+1 or m=-1 passed to mxl.MeepSimulation(). Unlike the x/y/z^2-weighted Cartesian analytical kernels, the cylindrical x/y dipole uses an isotropic Gaussian polarization density, which is exactly representable in a single |m|=1 sector.