Usage: mlmm path-opt [OPTIONS]
MEP optimization via the Growing String method or Direct Max Flux.
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... Two endpoint structures in PDB/mmCIF, or XYZ
with a corresponding --ref-pdb for each
endpoint. [required]
-q, --charge INTEGER ML region charge. 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 input or --ref-pdb).
-m, --multiplicity INTEGER Spin multiplicity (2S+1). [default: (1)]
--mep-mode [gsm|dmf] MEP optimizer: Growing String Method (gsm) or
Direct Max Flux (dmf). [default: gsm]
--dmf-backend [cpu|gpu] DMF compute backend (--mep-mode dmf only): gpu
(dmf.torch / CUDA) or cpu (dmf / NumPy). On a
GPU out-of-memory error, retry with cpu.
[default: gpu]
--max-nodes INTEGER Number of movable internal images for GSM or
DMF (total images = max_nodes + 2 endpoints).
[default: 20]
--gsm-param [equi|energy] GSM node parameterization after string growth.
The energy scheme concentrates nodes in high-
energy regions and may be tried when an
equidistant path skips the reaction-coordinate
region near the HEI. [default: (equi)]
--max-cycles-gsm INTEGER RANGE Maximum GSM string-optimizer cycles for the
MEP stage. [default: (300); x>=1]
--max-cycles-dmf INTEGER RANGE Maximum IPOPT iterations for the DMF MEP
stage. This is a solver iteration count, not a
string-optimizer cycle count. [default:
(300); x>=1]
--climb / --no-climb Search for a transition state (climbing image)
after path growth. [default: climb]
--preopt / --no-preopt Pre-optimize the two endpoint structures with
L-BFGS before string growth. [default:
preopt]
--preopt-max-cycles INTEGER RANGE
Maximum L-BFGS cycles for endpoint pre-
optimization. [default: (100000); x>=1]
--fix-ends / --no-fix-ends Fix endpoint structures during path growth.
[default: fix-ends]
--dump / --no-dump Dump optimizer trajectory/restarts during the
run. [default: no-dump]
-o, --out-dir TEXT Output directory. [default:
./result_path_opt/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for endpoint
preoptimization only. The MEP itself keeps
--thresh-gsm / --thresh-dmf. [default: (gau)]
--thresh-gsm [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for the GSM string
optimizer (gau_loose|gau|gau_tight|gau_vtight|
baker|never). [default: (gau_loose)]
--thresh-dmf TEXT IPOPT dual-infeasibility tolerance for the DMF
path optimizer: tight (0.04) | middle (0.10) |
loose (0.20) or a positive float. This is not
a Gaussian preset. [default: (tight)]
--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 path optimization. [default:
no-dry-run]
--parm FILE Amber parm7 topology for the enzyme complex
(MM layers). [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 indices to freeze
(applied to every image).
--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)]
--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)]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--ref-pdb FILE Full-size template PDBs in the same order as
--input. Required when using XYZ inputs to
provide topology and B-factor information.
--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.
-h, --help Show this message and exit.