mmml umbrella-sample¶
Batched distance umbrella NVT sampling (PhysNet/SpookyNet).
Usage¶
mmml umbrella-sample --help
Options¶
usage: mmml umbrella-sample [-h] [--config CONFIG] [--checkpoint CHECKPOINT]
[--structure STRUCTURE] [--output-dir OUTPUT_DIR]
[--atoms ATOMS] [--targets TARGETS]
[--xi-min XI_MIN] [--xi-max XI_MAX]
[--n-windows N_WINDOWS] [--k K_EV_A2]
[--temperature TEMPERATURE_K]
[--timestep TIMESTEP_FS] [--nsteps NSTEPS]
[--printfreq PRINTFREQ] [--savefreq SAVEFREQ]
[--seed SEED] [--no-ema] [--overwrite]
Batched distance umbrella sampling with a PhysNet / SpookyNet checkpoint via
JAX-MD NVT Nose-Hoover.
Input & configuration:
--config CONFIG YAML/JSON UmbrellaConfig; CLI flags override file values
when set
--checkpoint CHECKPOINT
PhysNet / SpookyNet checkpoint
--structure STRUCTURE
Input XYZ / structure file
Scientific model:
--temperature TEMPERATURE_K
NVT temperature in K (default: 300)
Execution:
--nsteps NSTEPS NVT steps (default: 1000)
--seed SEED PRNG seed (default: 42)
Output & artifacts:
--output-dir, -o OUTPUT_DIR
Directory for snapshots, trajectories, and summary
--savefreq SAVEFREQ Snapshot save interval (default: same as printfreq)
--overwrite Allow writing into a non-empty output directory
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--atoms ATOMS 0-based atom indices for the distance CV (I,J)
--targets TARGETS Comma-separated umbrella centers ξ₀ (Å)
--xi-min XI_MIN Grid start (Å) if --targets omitted
--xi-max XI_MAX Grid end (Å) if --targets omitted
--n-windows N_WINDOWS
Number of windows on [xi-min, xi-max]
--k K_EV_A2 Harmonic force constant (eV/Ų); shared across windows
(default: 10)
--timestep TIMESTEP_FS
Timestep in fs (default: 0.5)
--printfreq PRINTFREQ
Print interval in steps (default: 100)
--no-ema Prefer non-EMA checkpoint params
CLI for batched umbrella NVT sampling with PhysNet / SpookyNet. Usage: mmml
umbrella-sample \ --checkpoint out/ckpts/model \ --structure molecule.xyz \
--atoms 0,1 \ --xi-min 1.5 --xi-max 3.5 --n-windows 11 \ --k 20 --temperature
300 --nsteps 5000 -o out/umbrella