Configuration

Pipeline behaviour is controlled by a config.toml file. User settings are deep-merged on top of the built-in defaults in src/larest/defaults.toml, so you only need to set values that differ from defaults.

A minimal starting point is config/example.config. The full reference is config/reference.toml.

[reaction]

The most important section — defines what to compute.

[reaction]
type = "RER"                         # "RER" (no initiator) or "ROR" (with initiator)
monomers = ["O=C1OCC1"]             # list of monomer SMILES
lengths = [2, 3, 4]                  # polymer chain lengths to evaluate
initiator = "C1=CC=C(C=C1)CO"       # initiator SMILES (required for ROR only)

• RER (Ring Equilibrium Reaction) requires lengths >= 2.

• ROR (Ring-Opening polymerization Reaction) requires lengths >= 1 and an initiator SMILES.

[parallelisation]

Set the core count once; it propagates to every stage automatically.

[parallelisation]
n_cores = 16

Stage	Config key set	CLI flag
RDKit	[rdkit].n_cores	(internal)
xTB	[xtb].parallel	--parallel N
CREST confgen	[crest.confgen].T	--T N
CREST entropy	[crest.entropy].T	--T N
CENSO	[censo.cli].maxcores	--maxcores N

Override a specific stage by setting its key directly:

[parallelisation]
n_cores = 16

[censo.cli]
maxcores = 8    # CENSO uses fewer cores (e.g. limited by ORCA memory)

[steps]

Toggle individual pipeline stages on or off.

[steps]
rdkit = true          # RDKit conformer generation + xTB ranking
crest_confgen = true  # CREST conformer ensemble
censo = true          # CENSO DFT refinement
crest_entropy = true  # CREST conformational entropy correction
xtb = true            # xTB re-ranking after rdkit and crest_confgen

[rdkit]

Controls MMFF conformer generation.

Key	Default	Description
n_conformers	50	Number of conformers to generate
n_cores	1	CPU cores for parallel embedding
mmff	"MMFF94"	MMFF variant: "MMFF94" or "MMFF94s"
random_seed	42	Seed for reproducibility

[xtb]

All keys (except etemp) are passed directly as CLI flags to the xtb binary.

Key	Default	Description
etemp	298.15	Electronic temperature (K); used to derive S = (H − G) / T
gfn	2	GFN-xTB method level (0, 1, 2)
alpb	"toluene"	ALPB implicit solvent
ohess	"vtight"	Hessian level after optimisation
parallel	1	Number of CPU threads

[crest.confgen] and [crest.entropy]

All keys are passed directly as CLI flags to the crest binary. Separate sections control conformer generation and entropy calculation.

Key	Default	Description
T	1	Number of CPU threads
gfn2 / gfnff		Level of theory
alpb	"toluene"	ALPB implicit solvent
ewin	6.0	Energy window for ensemble (kcal/mol)
rthr	0.125	RMSD threshold for deduplication (Å)

[censo.*]

Controls the four CENSO DFT sub-stages. Each sub-stage (prescreening, screening, optimization, refinement) has its own section.

Key	Description
func	DFT functional
basis	Basis set
sm	Solvation model ("smd", "cpcm", "cosmo")
threshold	Energy window for ensemble pruning (kcal/mol)

The [censo.general] section sets global CENSO settings:

Key	Default	Description
temperature	298.15	Temperature (K)
solvent	"toluene"	Solvent for implicit solvation

Boolean flags

For [xtb] and [crest.*] sections, boolean values are translated to CLI flags:

• true → --flag

• false → flag is omitted entirely

• scalar → --key value