Usage: pdb2reaction tsopt [OPTIONS]
Transition state optimization (Dimer or RS-P-RFO).
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 Single-geometry input (.pdb, .cif, .mmcif,
.xyz, or .gjf). Extract a trajectory frame to
.xyz before use. [required]
--ref-mode FILE Advanced/internal Cartesian reference
direction(s) for Hessian TS root selection and
overlap tracking. Accepts .npz path-mode
caches, .npy arrays, or whitespace text
containing one 3N vector or a 2-D candidate
table. This guides mode identity; it does not
replace the Hessian and is not supported by
Dimer. The all workflow supplies it from the
MEP; standalone tsopt users normally leave it
unset.
--workers INTEGER MLIP predictor workers; >1 spawns a parallel
predictor. NOTE: with UMA, workers>1 plus an
explicit Analytical Hessian request is an
error; use workers=1 or FiniteDifference.
[default: 1]
--workers-per-node INTEGER Workers per node when using a parallel MLIP
predictor (workers>1). [default: 1]
--freeze-links / --no-freeze-links
Freeze parent atoms of cap hydrogens
(PDB/mmCIF input or XYZ/GJF with --ref-pdb).
[default: freeze-links]
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., '1,3,5').
--convert-files / --no-convert-files
Convert XYZ/TRJ outputs into PDB/CIF/GJF
companions based on the input format.
[default: convert-files]
--ref-pdb FILE Reference PDB/mmCIF topology to use when the
input is XYZ/GJF (keeps XYZ coordinates).
--max-cycles INTEGER RANGE Maximum number of optimization cycles.
[default: (100000); x>=1]
--flatten / --no-flatten Enable the extra-imaginary-mode flattening
loop (grad: dimer loop, hess: post-RS-P-RFO).
[default: no-flatten]
--opt-mode [grad|hess|dimer|rsirfo|trim|rsprfo]
TS optimizer: 'grad'/'dimer' → Hessian Guided
Dimer; 'hess'/'rsprfo' → RS-P-RFO (Banerjee,
default); 'trim' → TRIM (Helgaker); 'rsirfo' →
RS-I-RFO. [default: hess]
--dump / --no-dump Write the per-cycle trajectory
('optimization_trj.xyz' for RS-P-RFO/RS-I-
RFO/TRIM, 'optimization_all_trj.xyz' for
Dimer). [default: no-dump]
-o, --out-dir TEXT Output directory. [default: ./result_tsopt/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for the active optimizer (g
au_loose|gau|gau_tight|gau_vtight|baker|never)
. [default: (baker)]
--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 TS optimization. [default:
no-dry-run]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--hessian-calc-mode [finitedifference|analytical]
Choose MLIP Hessian evaluation mode. YAML
supplies the value when this option is
omitted; explicit CLI wins. [default:
(FiniteDifference)]
-b, --backend [uma|orb|mace|aimnet2]
MLIP backend. [default: uma]
--solvent TEXT Experimental, computationally expensive xTB
solvent delta correction. Examples: water,
methanol, acetonitrile, dmso, thf, toluene.
'none' disables it. [default: none]
--solvent-model [alpb|cpcmx] xTB solvent model. [default: alpb]
-q, --charge INTEGER Total charge. Required for non-.gjf inputs
unless --ligand-charge is provided (.gjf
templates inherit the charge automatically).
-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/mmCIF input or --ref-
pdb).
-m, --multiplicity INTEGER RANGE
Spin multiplicity (2S+1). [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)]
--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 energy/gradient
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 strict same-stack PyTorch determinism
(deterministic algorithms + index_reduce_
shim). Slower; raises for detected unsupported
ops; custom calculators are outside its scope.
[default: no-deterministic]
--allow-charge-mult-mismatch Skip the cluster charge/multiplicity electron-
parity check (logs that it was skipped). Open-
shell clusters need a matching multiplicity
instead; use this only for an intentionally
nonstandard electron count.
--coord-type [cart|redund|dlc|tric]
Optimization coordinate system
(cart|redund|dlc|tric). [default: (cart)]
--print-every INTEGER RANGE Print optimizer status every N cycles.
[default: (100); x>=1]
--stop-plateau / --no-stop-plateau
Stop when the energy stops changing while the
convergence criteria are still unmet, and
report the run as stalled. It never signals
convergence; --max-cycles remains the real
bound. [default: no-stop-plateau]
--stop-plateau-thresh FLOAT Energy range (hartree) below which --stop-
plateau treats the window as flat. [default:
(1e-4)]
--stop-plateau-window INTEGER Number of consecutive cycles --stop-plateau
inspects. [default: (50)]
-h, --help Show this message and exit.