Getting Started¶

This page introduces the core simulation workflow and the command-line tools that ship with MQED-QD. Make sure you have completed Installation before proceeding.

Simulation workflow¶

A typical MQED-QD study follows a three-stage pipeline:

Each stage reads its configuration from a YAML file under configs/ and writes results into a timestamped Hydra output directory under outputs/.

CLI commands¶

Installing the package registers the following entry points:

Command	Description
`mqed_GF_Sommerfeld`	Compute the dyadic Green’s function for a planar layered system (Sommerfeld integration).
`mqed_RET`	Resonance energy transfer analysis.
`mqed_FE`	Field-enhancement analysis.
`mqed_lindblad`	Time evolution with Lindblad master equation.
`mqed_nhse`	Time evolution with the non-Hermitian Schrödinger equation (faster for large systems).
`mqed_nhse_disorder`	Disorder-averaged NHSE sweep.
`mqed_plot_msd`	Plot mean-squared displacement.
`mqed_plot_sqrt_msd`	Plot root-mean-squared displacement.
`mqed_plot_IPR`	Plot inverse participation ratio.
`mqed_plot_PR`	Plot participation ratio.
`mqed_BEM_compute_peff`	Compute effective dipole-moment intensity (BEM).
`mqed_BEM_reconstruct_GF`	Reconstruct dyadic Green’s function from BEM simulation.

Quick first run¶

The fastest way to verify everything works is to run the Green’s function simulation with default settings:

mqed_GF_Sommerfeld

This computes the dyadic Green’s function for a silver half-space at 1.0 eV with donor and acceptor 5 nm above the surface. When it finishes you will see a log line like:

Simulation complete. Output saved to: /…/outputs/Dyadic_GF_Sommerfeld/…/result_Ag_5_nm.hdf5

To override a parameter from the command line:

mqed_GF_Sommerfeld simulation.energy_eV=1.864

Use a different YAML in the same config directory (Recommended)

mqed_GF_Sommerfeld --config-name=my_GF

This loads configs/Dyadic_GF/my_GF.yaml instead of the default GF_Sommerfeld.yaml. Your custom file must live in the same configs/Dyadic_GF/ directory. Users are recommended to copy the default YAML to a new file and edit the copy to explore different settings while keeping the original intact. This approach also applies to all other commands and their respective config directories.

Use a YAML from an arbitrary directory

mqed_GF_Sommerfeld --config-dir=/path/to/my/configs --config-name=my_GF

This tells Hydra to look for my_GF.yaml in /path/to/my/configs/ instead of the default config directory. If users wish to store their custom YAML files in a separate directory, they can use this approach to keep them organized and avoid cluttering the default.

See the Dyadic Green’s Function via Sommerfeld Integrals tutorial for a full walkthrough including multi-energy runs and downstream usage.

Hydra configuration¶

Every command reads a YAML config from the configs/ directory. You can inspect the active configuration for any command with the --cfg job flag:

mqed_GF_Sommerfeld --cfg job

Override any key on the command line using dot-notation:

mqed_lindblad simulation.Nmol=50 simulation.d_nm=5.0

Hydra automatically:

writes all outputs to a timestamped directory under outputs/,
saves a copy of the resolved config alongside the results, and
supports multi-run sweeps via the -m flag.

See the Hydra documentation for details on overrides, config groups, and sweeps.

What’s next?¶

Dyadic Green’s Function via Sommerfeld Integrals	Compute Green’s functions for a planar two-layer system.
Field Enhancement	Analyse field enhancement from cached Green’s functions.
Quantum Dynamics	Run Lindblad or NHSE time evolution.
Plotting & Analysis	Plot MSD, RMSD, and participation ratios.