Usage: mlmm freq [OPTIONS]
ML/MM vibrational frequency analysis (PHVA-compatible).
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+detailed step logging
and deliverable paths; 3=everything (full
config blocks, per-file paths, DEBUG logging).
[0<=x<=3]
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Enzyme complex PDB/mmCIF, or XYZ with --ref-
pdb, used by geom_loader and the ML/MM
calculator. [required]
--parm7, --parm FILE Amber parm7 topology for the full enzyme
complex. [required]
--model-pdb FILE ML-only, link-H-free PDB subset; atom
identity/order must match the full PDB/parm7.
When provided, it defines ML membership;
--detect-layer still reads valid
movable/frozen MM B-factors.
--model-indices TEXT Comma-separated atom indices for the ML region
(ranges allowed like 1-5). Used when --model-
pdb is omitted.
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., '1,3,5').
--hessian-cutoff, --hess-cutoff FLOAT
Distance cutoff (Å) from ML region for MM
atoms to include in Hessian calculation.
Applied to movable MM atoms and can be
combined with --detect-layer. [default: (all
movable MM atoms)]
--movable-cutoff FLOAT Distance cutoff (Å) from ML region for movable
MM atoms. MM atoms beyond this are frozen.
Providing --movable-cutoff disables --detect-
layer. [default: (use freeze_atoms)]
--hessian-calc-mode [analytical|finitedifference]
How the ML backend builds the Hessian
(Analytical or FiniteDifference); overrides
calc.hessian_calc_mode from YAML. Runtime and
memory depend on the backend and system;
compare both modes on a representative pilot.
[default: (FiniteDifference)]
--max-write INTEGER Maximum number of modes to export. [default:
10]
--amplitude-ang FLOAT Mode-trajectory amplitude (Å). [default: 0.8]
--n-frames INTEGER Frames per vibrational mode trajectory.
[default: 20]
--sort [value|abs] Sort modes by signed value or absolute value.
[default: value]
--temperature FLOAT Temperature (K) for thermochemistry summary.
[default: 298.15]
--pressure FLOAT Pressure (atm) for thermochemistry summary.
[default: 1.0]
--dump / --no-dump Write 'thermoanalysis.yaml' alongside the
console summary. [default: no-dump]
-o, --out-dir TEXT Output directory. [default: ./result_freq/]
--active-dof-mode [all|ml-only|partial|unfrozen]
Active DOF selection for frequency analysis:
all (all atoms), ml-only (ML only), partial
(ML + MovableMM, default), unfrozen (all non-
frozen atoms). [default: partial]
--config FILE Base YAML configuration file applied before
explicit CLI options.
--show-config / --no-show-config
Print the loaded YAML file and its top-level
keys, then continue. [default: no-show-
config]
--dry-run / --no-dry-run Validate options and inputs without running
frequency analysis. [default: no-dry-run]
--ref-pdb FILE Reference PDB topology to use when --input is
XYZ (keeps XYZ coordinates).
--convert-files / --no-convert-files
Convert XYZ/TRJ outputs into PDB companions
based on the input format. [default: convert-
files]
--hess-device [auto|cuda|cpu] Device for post-evaluation Hessian placement
and diagonalization (auto/cuda/cpu). Use 'cpu'
to move the evaluated Hessian off GPU before
diagonalization. ML model inference always
uses ml_device (typically GPU). [default:
auto]
-b, --backend [uma|orb|mace|aimnet2|dft]
High-level backend for the ONIOM model region.
[default: (uma)]
--embedcharge / --no-embedcharge
Enable electrostatic embedding. MLIP backends
use the computationally expensive xTB point-
charge delta correction; dft uses native PySCF
MM point charges. [default: no-embedcharge]
--embedcharge-cutoff FLOAT Distance cutoff (Å) from the ML region for MM
point charges used by embedding. [default:
(12.0)]
--link-atom-method [scaled|fixed]
Link-atom position mode: scaled (g-factor) or
fixed (1.09/1.01 Å). [default: (scaled)]
--mm-backend [hessian_ff|openmm]
MM backend. MM Hessians use finite differences
by default; set calc.mm_fd: false for the
hessian_ff analytical path. [default:
(hessian_ff)]
--cmap / --no-cmap Preserve CMAP terms in both real and model MM
layers when present in parm7. [default:
(cmap)]
--read-hess FILE Use the Hessian in this .npy file (e.g. from
freq or tsopt --dump-hess) instead of
computing it: the Cartesian Hessian of the
input geometry in Hartree/bohr^2, for all
atoms, only the atoms selected by --active-
dof-mode, or only the atoms in the Hessian
calculation. [default: (None)]
--dump-hess FILE Save the Hessian as a NumPy .npy array
(Cartesian, Hartree/bohr^2; the atoms selected
by --active-dof-mode) for '--read-hess' in
freq, tsopt, or irc, or for other programs.
[default: (None)]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--detect-layer / --no-detect-layer
Automatically detect ML/MM layers from input
PDB B-factors (ML=0, MovableMM=10,
FrozenMM=20) when explicit ML membership is
absent. With explicit membership, retain valid
movable/frozen MM B-factor layers. [default:
detect-layer]
-q, --charge INTEGER ML region charge. Required unless --ligand-
charge or YAML calc.model_charge gives it.
-l, --ligand-charge TEXT Total charge for unknown ligand residues or a
per-resname mapping (e.g., GPP:-3,SAM:1), used
to derive the ML-region charge when -q is
omitted (requires PDB/mmCIF input or --ref-
pdb).
-m, --multiplicity INTEGER RANGE
Spin multiplicity (2S+1) for the ML region.
[default: (1); x>=1]
--precision [fp32|fp64] MLIP backend precision: fp32 or fp64. Unset
defaults per backend (uma: fp32; orb, mace:
fp64). Routed to backend-specific kwargs (UMA
precision / ORB precision / MACE
default_dtype). aimnet2: fp32 no-op; fp64
rejected. [default: (per backend: uma fp32;
orb, mace fp64)]
--uma-workers, --workers INTEGER
MLIP predictor workers (UMA). >1 uses a
parallel predictor (fairchem-core[extras]);
combining it with an analytical Hessian is an
error. Default 1. [default: (1)]
--uma-workers-per-node, --workers-per-node INTEGER
Workers per node when the parallel MLIP
predictor is used (--workers > 1). [default:
(1)]
--backend-model TEXT Model variant for the selected --backend (e.g.
uma-s-1p2 / uma-m-1p1 for uma,
orb_v3_conservative_omol for orb, MACE-OMOL-0
/ off:small for mace). [default: (the
selected backend's own model)]
--calc-file FILE Python file exposing get_calculator(...) -> an
ASE Calculator used as the ML-region backend
(overrides --backend). Couples GFN-xTB / DFTB+
/ any ASE engine. See --calc-file-func-name.
--calc-factory, --calc-file-func-name TEXT
Name of the callable in --calc-file that
returns an ASE Calculator (or a module-level
Calculator instance). CLI overrides config
YAML; otherwise defaults to get_calculator.
[default: (get_calculator)]
--deterministic / --no-deterministic
Request deterministic algorithms for
controlled operations; verify exact
reproducibility on the complete target stack.
[default: no-deterministic]
--allow-charge-mult-mismatch Skip the ML-region charge/multiplicity
electron-parity check (logs that it was
skipped). An open-shell ML region needs a
matching multiplicity; use this only for an
intentional nonstandard input such as a
covalently-cut region.
--func-basis TEXT High-level method as FUNCTIONAL/BASIS;
HF/BASIS is accepted. [default:
(wb97m-v/def2-svp)]
--dft-engine, --engine [gpu|cpu]
PySCF execution engine used by --backend dft.
[default: (gpu)]
--save-scf-checkpoint / --no-save-scf-checkpoint
Persist a structure-bound PySCF checkpoint.
[default: (disabled)]
--scf-checkpoint FILE Load/save the optional structure-bound PySCF
checkpoint at PATH.
--dft-low-memory, --lowmem / --no-dft-low-memory, --no-lowmem
Use GPU4PySCF rks_lowmem for closed-shell GPU
DFT; open-shell GPU and CPU use standard
direct JK. --no-lowmem enables density
fitting. [default: (lowmem)]
--scf-stepwise-grid / --no-scf-stepwise-grid
Converge the first SCF on a coarse grid, then
on the final grid (later SCFs reuse the
previous density as usual). [default:
(enabled)]
--dft-nprocs INTEGER RANGE PySCF/OpenMP CPU threads; GPU count is
unaffected. [default: (auto); x>=1]
--dft-memory, --dft-mem TEXT PySCF host RAM limit (for example 64GB or
120000MB). [default: (auto)]
-h, --help Show this message and exit.
