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, .cif, .mmcif,
.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 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.
-q, --charge INTEGER Net charge of the ML region/model system;
overrides calc.model_charge from YAML.
Required unless --ligand-charge is provided.
-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 Spin multiplicity (2S+1); overrides
calc.model_mult from YAML. [default: (1)]
--max-cycles INTEGER RANGE Maximum number of IRC steps. [default: (125);
x>=1]
--step-size FLOAT Step length in Bohr (unweighted Cartesian
coordinates); overrides irc.step_length from
YAML. [default: (0.10)]
--root INTEGER Imaginary mode index used for the initial
displacement; overrides irc.root from YAML.
[default: (0)]
--forward / --no-forward Run the forward IRC; overrides irc.forward
from YAML. [default: (forward)]
--backward / --no-backward Run the backward IRC; overrides irc.backward
from YAML. [default: (backward)]
--never-stop / --no-never-stop Ignore RMS-gradient, hard-gradient, energy-
rise, and energy-change stops and trace until
max-cycles. Numerical/integration failures and
external interruption still stop the run;
default off. [default: (no-never-stop)]
-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. Runtime and
memory depend on the backend and system;
compare both modes on a representative pilot.
[default: (FiniteDifference)]
--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/mmCIF 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 the experimental, computationally
expensive xTB point-charge delta correction
for MLIP/MM. [default: no-embedcharge]
--embedcharge-cutoff FLOAT Distance cutoff (Å) from the ML region for MM
point charges used by the xTB delta
correction. [default: (12.0)]
--link-atom-method [scaled|fixed]
Link-atom position mode: scaled (g-factor) or
fixed (legacy 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)]
--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 an identified initial Hessian from 'mlmm
freq --dump-hess'. Geometry, atom order,
active-DOF basis, charge, and multiplicity
must match; the file takes priority over
hessian_cache and fresh computation.
[default: (None)]
--allow-unverified-hess-state / --no-allow-unverified-hess-state
Allow a schema-1 Hessian file whose charge and
multiplicity cannot be verified. Use only
after independently checking the electronic
state. [default: no-allow-unverified-hess-
state]
--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
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]
--model-indices-one-based / --model-indices-zero-based
Interpret --model-indices as 1-based or
0-based. [default: model-indices-one-based]
--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)]
--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)]
--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-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.
--irc-pos-def / --no-irc-pos-def
Require pos-def Hessian at IRC convergence
(blocks shoulder false-convergence).
[default: (no-irc-pos-def (rms-only
criterion))]
-h, --help Show this message and exit.