mmml normal-mode-sample¶
Sample along vibrational modes.
Usage¶
mmml normal-mode-sample --help
Options¶
usage: mmml normal-mode-sample [-h] -i INPUT [-o OUTPUT] [--amplitude AMPLITUDE]
[--amplitudes AMPLITUDES [AMPLITUDES ...]]
[--freq-min FREQ_MIN] [--include-equilibrium]
[--samples-per-mode {1,2}] [--max-samples N]
Sample geometries along vibrational modes from pyscf-dft harmonic output.
Input & configuration:
-i, --input INPUT Path to pyscf-dft output .h5 (must contain harmonic
group)
Output & artifacts:
-o, --output OUTPUT Output NPZ path (default: sampled.npz)
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--amplitude AMPLITUDE
Displacement amplitude in Angstrom (default: 0.1)
--amplitudes AMPLITUDES [AMPLITUDES ...]
List of amplitudes (overrides --amplitude)
--freq-min FREQ_MIN Minimum frequency (cm^-1) to include (default: 50)
--include-equilibrium
Add equilibrium geometry as first sample
--samples-per-mode {1,2}
2 for +/- amplitude (default), 1 for + only
--max-samples N Maximum number of structures to generate (default: no
limit)
CLI for normal mode sampling from pyscf-dft harmonic output. Samples geometries
along vibrational modes for downstream QM/ML. Input: .h5 from mmml pyscf-dft
--harmonic Output: NPZ with R (n_samples, n_atoms, 3), Z, N Usage: mmml normal-
mode-sample -i out/04_results.h5 -o out/06_sampled.npz --amplitude 0.1 mmml
normal-mode-sample -i out/04_results.h5 -o out/06_sampled.npz --amplitude 0.1
--include-equilibrium