Usage: mlmm irc [OPTIONS]
Run an IRC calculation with EulerPC. Only the documented CLI options are
accepted; all other settings come from YAML.
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+optimizer cycle tables,
per-stage timing, VRAM, 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 Input structure file (.pdb, .xyz, _trj.xyz,
etc.). [required]
--parm FILE Amber parm7 topology for the whole enzyme (MM
region). If omitted, must be provided in YAML
as calc.real_parm7.
--model-pdb FILE PDB defining atoms belonging to the ML region.
Optional when --detect-layer is enabled.
--model-indices TEXT Comma-separated atom indices for the ML region
(ranges allowed like 1-5). Used when --model-
pdb is omitted.
-q, --charge INTEGER Total charge; overrides calc.charge from YAML.
Required unless --ligand-charge is provided.
-l, --ligand-charge TEXT Total charge or per-resname mapping (e.g.,
GPP:-3,SAM:1) used to derive charge when -q is
omitted (requires PDB input or --ref-pdb).
-m, --multiplicity INTEGER Spin multiplicity (2S+1); overrides calc.spin
from YAML.
--max-cycles INTEGER Maximum number of IRC steps; overrides
irc.max_cycles from YAML.
--step-size FLOAT Step length in Bohr (unweighted Cartesian
coordinates). Default: 0.10 Bohr. Overrides
irc.step_length from YAML.
--root INTEGER Imaginary mode index used for the initial
displacement; overrides irc.root from YAML.
--forward / --no-forward Run the forward IRC; overrides irc.forward
from YAML.
--backward / --no-backward Run the backward IRC; overrides irc.backward
from YAML.
-o, --out-dir TEXT Output directory; overrides irc.out_dir from
YAML. [default: ./result_irc/]
--hessian-calc-mode [analytical|finitedifference]
How the ML backend builds the Hessian
(Analytical or FiniteDifference); overrides
calc.hessian_calc_mode from YAML. Default:
'FiniteDifference'. Use 'Analytical' when VRAM
is sufficient.
--config FILE Base YAML configuration file applied before
explicit CLI options.
--show-config / --no-show-config
Print resolved configuration and continue
execution. [default: no-show-config]
--dry-run / --no-dry-run Validate options and print the execution plan
without running IRC. [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]
-b, --backend [uma|orb|mace|aimnet2]
ML backend for the ONIOM high-level region
(default: uma).
--embedcharge / --no-embedcharge
Enable xTB point-charge embedding correction
for MM→ML environmental effects
(experimental). [default: no-embedcharge]
--embedcharge-cutoff FLOAT Distance cutoff (Å) from ML region for MM
point charges in xTB embedding. Default: 12.0
Å. Only used when --embedcharge is enabled.
--link-atom-method [scaled|fixed]
Link-atom position mode: scaled (g-factor,
default) or fixed (legacy 1.09/1.01 Å).
--mm-backend [hessian_ff|openmm]
MM backend: hessian_ff (analytical Hessian,
default) or openmm (finite-difference Hessian,
slower).
--cmap / --no-cmap Enable CMAP (backbone cross-map) terms in
model parm7. Default: disabled (Gaussian
ONIOM-compatible).
--hess-device [auto|cuda|cpu] Device for initial Hessian storage and IRC
operations (auto/cuda/cpu). Use 'cpu' for
large unfrozen systems to avoid VRAM limits.
[default: auto]
--read-hess FILE Read initial Hessian from a .npz file
(produced by 'mlmm freq --dump-hess'). Takes
priority over the hessian_cache and fresh
computation.
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., '1,3,5').
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--detect-layer / --no-detect-layer
Detect ML/MM layers from input PDB B-factors
(ML=0, MovableMM=10, FrozenMM=20). If
disabled, you must provide --model-pdb or
--model-indices. [default: detect-layer]
--model-indices-one-based / --model-indices-zero-based
Interpret --model-indices as 1-based (default)
or 0-based. [default: model-indices-one-
based]
--precision [fp32|fp64] MLIP backend precision: fp32 (default) or
fp64. Routed to backend-specific kwargs (UMA
precision / ORB precision / MACE
default_dtype). aimnet2: fp32 no-op; fp64
rejected.
--backend-model TEXT Model variant for the selected --backend (e.g.
uma-s-1p1 / uma-m-1p1 for uma,
orb_v3_conservative_omol for orb, MACE-OMOL-0
/ MACE-OFF23_small for mace). Default: the
backend's built-in 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-factory.
--calc-factory TEXT Name of the callable in --calc-file that
returns an ASE Calculator (or a module-level
Calculator instance). [default:
get_calculator]
--deterministic / --no-deterministic
Strict bit-reproducible GPU runs
(deterministic algorithms + index_reduce_
shim). Slower; raises if unsupported. Default
off.
--allow-charge-mult-mismatch Skip the ML-region charge/multiplicity
electron-parity check (logs that it was
skipped). For an intentional open-shell or
covalently-cut ML region.
--irc-pos-def / --no-irc-pos-def
Require pos-def Hessian at IRC convergence
(blocks shoulder false-convergence).
-h, --help Show this message and exit.