Usage: mlmm path-search [OPTIONS]
Multistep MEP search via recursive GSM/DMF segmentation.
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 or more PDB/mmCIF structures, or XYZ files
with corresponding --ref-pdb entries, in
reaction order. Either repeat '-i' (e.g., '-i
A -i B -i C') or use a single '-i' followed by
multiple space-separated paths (e.g., '-i A B
C'). [required]
--parm7, --parm FILE Amber parm7 topology covering 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.
-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). [default: (1);
x>=1]
--mep-mode [gsm|dmf] MEP method: gsm (Growing String) or dmf
(Direct Max Flux). [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]
--refine-mode [peak|minima] Refinement seed around the highest-energy
image: 'peak' uses HEI±1, 'minima' uses
nearest local minima. Defaults to peak for gsm
and minima for dmf. [default: (peak for gsm,
minima for dmf)]
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., '1,3,5').
--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)]
--max-nodes INTEGER Number of movable internal images per GSM or
DMF segment (total images = max_nodes + 2
endpoints); recursive segments may override it
with YAML search.max_nodes_segment. [default:
20]
--max-depth INTEGER RANGE Maximum recursive subdivision levels. 0
disables subdivision. Intervals retained at a
positive cap use seg_NNN_maxdepth and may
contain multiple steps. When omitted, YAML
search.max_depth applies. [default: (10);
x>=0]
--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]
--dmf-max-iterations, --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:
(3000); x>=1]
--climb / --no-climb Enable transition-state search after path
growth. [default: climb]
--opt-mode [grad|hess] Single-structure optimizer: grad (=LBFGS) or
hess (=RFO). [default: grad]
--dump / --no-dump Dump GSM/single-optimization trajectories
during the run. [default: no-dump]
-o, --out-dir TEXT Output directory. [default:
./result_path_search/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for single-structure
optimizations only. The MEP itself keeps
--thresh-gsm / --dmf-tol. [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)]
--dmf-tol, --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 the resolved configuration blocks and
the loaded YAML file, then continue.
[default: no-show-config]
--dry-run / --no-dry-run Validate options and inputs without running
path search. [default: no-dry-run]
--preopt / --no-preopt If True, run initial single-structure
optimizations of inputs. [default: preopt]
--align / --no-align After optional preoptimization, align adjacent
inputs in sequence and match frozen-atom
positions while relaxing the remaining atoms.
[default: align]
--ref-pdb FILE Full-size template PDBs in the same reaction
order as --input. Required when using XYZ
inputs to provide topology and B-factor
information.
--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|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)]
--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]
--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.
