mmml physnet-md¶
PhysNet MD sampling.
Usage¶
mmml physnet-md --help
Options¶
usage: mmml physnet-md [-h] --checkpoint CHECKPOINT (--structure STRUCTURE |
--data DATA) [-o OUTPUT_DIR] [--temperature TEMPERATURE]
[--timestep TIMESTEP] [--nsteps-ase NSTEPS_ASE]
[--nsteps-jaxmd NSTEPS_JAXMD] [--printfreq PRINTFREQ]
[--skip-jaxmd] [--n-replicas B]
[--use-ema | --no-use-ema]
PhysNet MD sampling with ASE and JAX-MD.
Input & configuration:
--checkpoint CHECKPOINT
Path to PhysNet checkpoint directory (e.g.
out/ckpts/cybz_physnet)
--structure STRUCTURE
Initial structure (XYZ, PDB, etc.)
--data DATA NPZ with R, Z (e.g.
splits/energies_forces_dipoles_train.npz)
Scientific model:
--temperature TEMPERATURE
Temperature in K (default: 300)
Execution:
--nsteps-ase NSTEPS_ASE
ASE Langevin steps (default: 100)
--nsteps-jaxmd NSTEPS_JAXMD
JAX-MD Nose-Hoover steps (default: 200)
Output & artifacts:
-o, --output-dir OUTPUT_DIR
Output directory (default: .)
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--timestep TIMESTEP Timestep in fs (default: 0.5)
--printfreq PRINTFREQ
Print/save interval (default: 25)
--skip-jaxmd Skip JAX-MD (ASE only)
--n-replicas B Number of independent replicas to run in parallel. ASE:
ProcessPoolExecutor; JAX-MD: batched GPU. With --data,
uses first B structures as initial geometries if
available. (default: 1)
--use-ema, --no-use-ema
Deploy the checkpoint's EMA params (default: on). Use
--no-use-ema for the live training weights.
CLI for PhysNet molecular dynamics sampling with ASE and JAX-MD. Runs NVT
Langevin (ASE) and NVT Nose-Hoover (JAX-MD) using a trained PhysNet checkpoint
as the energy/force calculator. Usage: mmml physnet-md --checkpoint
out/ckpts/cybz_physnet --structure molecule.xyz -o out/ mmml physnet-md
--checkpoint out/ckpts/cybz_physnet --data
splits/energies_forces_dipoles_train.npz -o out/ mmml physnet-md --checkpoint
out/ckpts/cybz_physnet --data splits/train.npz -o out/ --n-replicas 4