11_butane_conformers_on_cu.toml

# Example 11 — Butane conformers on Cu(111): gauche vs. anti landscape
#
# WHY THIS EXAMPLE EXISTS
# -----------------------
# Butane (CCCC) is the textbook conformer example:
#   anti   (C-C-C-C dihedral ~180°) — global minimum in gas phase
#   gauche (C-C-C-C dihedral ~60°)  — ~3.8 kJ/mol higher in gas phase
# On a metal surface the energy ordering can flip depending on the
# adsorbate–surface interaction.  Raman spectra of the two conformers
# differ substantially in the 800–1100 cm⁻¹ region (C-C stretch region).
#
# This example pairs a larger MC run (more steps, more conformer moves)
# with surface_packing to start from multiple butane molecules so that
# the final dataset contains a mix of coverages and conformers.
#
# TWO-STAGE WORKFLOW
# ------------------
# The 'surface_packing' builder (Packmol) places 3 butane molecules above
# the slab in random orientations.  The MC sampler then explores each
# molecule's conformational freedom independently (each is a separate
# fragment: 0, 1, 2).  At every conformer move, an independent fresh ETKDG
# conformer is drawn for the target fragment — the other two molecules are
# unaffected.
#
# MONITORING CONFORMERS IN THE OUTPUT
# ------------------------------------
# Load the dataset and inspect the C-C-C-C dihedral per frame:
#
#   from traincraft.datasets.io import read_frames
#   from ase.geometry.analysis import Analysis
#   frames = read_frames("runs/11_butane.../dataset.extxyz")
#   for f in frames:
#       an = Analysis(f.atoms)
#       print(an.get_dihedrals("C", "C", "C", "C"))
#
# Requires the science environment (rdkit + packmol):
#   pixi install -e science
#   pixi run -e science example-11

[run]
name   = "11_butane_conformers_cu111"
outdir = "runs"
seed   = 99

[geometry.builder]
type          = "surface_packing"
element       = "Cu"
facet         = "fcc111"
size          = [4, 4, 4]
vacuum        = 20.0
smiles        = "CCCC"       # butane — SMILES required for conformer moves
n_molecules   = 3
tolerance     = 2.0
region_height = 8.0
gap           = 2.0
seed          = 5

[calculator]
type = "emt"                 # swap for tblite or mace for real energetics

[sampling]
type          = "monte_carlo"
steps         = 300
interval      = 30           # 10 recorded frames
temperature   = 500.0        # K — higher T to overcome conformer barriers
p_translate   = 0.25
p_rotate      = 0.25
p_conformer   = 0.50         # 50% conformer moves — this is the point of the example
max_translate = 0.5          # Å
max_rotate    = 30.0         # degrees
seed          = 7

[selection]
steps  = ["physicality", "dedup", "diversity"]
budget = 6

[dataset]
path = "dataset"