Output

All results are written under the directory specified by -o (default: ./output).

Directory structure

output/
  Monomer/<smiles_slug>/
    rdkit/
      conformers.sdf              # all MMFF conformers
      xtb/rdkit/results.csv       # xTB H, S, G for each conformer
    crest_confgen/
      crest_best.xyz              # lowest-energy CREST conformer
      crest_conformers.xyz        # full CREST ensemble
    censo/
      censo.txt                   # raw CENSO output
      results.json                # parsed H, S, G for each sub-stage
      3_REFINEMENT.xyz            # refined conformer ensemble
    crest_entropy/
      crest.txt                   # raw CREST entropy output
      results.json                # S_conf, S_rrho, S_total
    results.json                  # merged results across all sections
    summary/
      rdkit.csv                   # ΔH, ΔS, ΔG vs polymer length (RDKit level)
      crest.csv                   # ΔH, ΔS, ΔG vs polymer length (CREST level)
      censo_refinement.csv        # ΔH, ΔS, ΔG vs polymer length (DFT level)
      censo_corrected.csv         # ΔH, ΔS, ΔG with CREST entropy correction

  Polymer/<smiles_slug>_<length>/
    ...                           # same structure as Monomer/

  Initiator/<smiles_slug>/
    ...                           # same structure as Monomer/

  larest.log                      # full pipeline log

Summary CSVs

The summary/ CSVs are the primary output. Each file corresponds to one pipeline section and contains one row per polymer length with the following columns:

Column	Description
polymer_length	Chain length n
monomer_H/S/G	Monomer thermodynamic parameters (J/mol)
initiator_H/S/G	Initiator parameters (J/mol); zero for RER
polymer_H/S/G	Polymer parameters (J/mol)
delta_H	ΔH of ring-opening (J/mol)
delta_S	ΔS of ring-opening (J/mol/K)
delta_G	ΔG of ring-opening (J/mol)

Delta values are computed as:

delta_param = (polymer_param - n * monomer_param - initiator_param) / n

Sections

Section	Description
rdkit	RDKit + xTB level
crest	CREST + xTB level
censo_prescreening	CENSO prescreening sub-stage
censo_screening	CENSO screening sub-stage
censo_optimization	CENSO optimisation sub-stage
censo_refinement	CENSO refinement sub-stage (highest accuracy)
censo_corrected	censo_refinement + CREST conformational entropy

Log file

larest.log is written to the output directory and contains the full pipeline log at DEBUG level. Console output respects the --verbose flag.