mxl-meep

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UpdatedFebruary 7, 2026 at 01:19

This skill should be used when users need MaxwellLink + Meep FDTD workflows, including embedded vs socket coupling, MPI considerations, and recommended templates.

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TaoELi

TaoELi/MaxwellLink

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SKILL.md

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name	mxl-meep
description	This skill should be used when users need MaxwellLink + Meep FDTD workflows, including embedded vs socket coupling, MPI considerations, and recommended templates.

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.

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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.