Usage: pdb2reaction sp [OPTIONS]
Compute a single-point MLIP energy + forces (and optionally Hessian).
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+detailed step logging
and 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 (PDB / mmCIF / XYZ / GJF).
[required]
--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]
-o, --out-dir TEXT Output directory. [default: ./result_sp/]
--hess / --no-hess Also compute a Hessian and save it to
hessian.npy (active block when YAML
geom.freeze_atoms is non-empty). [default:
no-hess]
--hessian-calc-mode [analytical|finitedifference]
Hessian backend when --hess is set.
FiniteDifference is the default for every
backend; UMA, ORB, MACE, and AIMNet2 also
support an explicit Analytical request.
[default: (FiniteDifference)]
--config FILE YAML config file with sections (calc:, geom:,
…).
--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 plan without
running the calculation. [default: no-dry-
run]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
-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).
-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.
-h, --help Show this message and exit.