from ase.build import molecule, fcc111, add_adsorbate
from ase.constraints import FixAtoms
from ase.visualize import view
from ase.optimize import BFGS
from gpaw import GPAW, PW

# Build Cu(111) surface
slab = fcc111("Cu", size=(4, 4, 3), vacuum=10.0)
slab.center(axis=2)  # Center in z

# Fix bottom layer of Cu atoms
mask = [atom.tag == 1 for atom in slab]
slab.set_constraint(FixAtoms(mask=mask))

# Load glycine molecule (neutral form, gas phase)
gly = molecule("glycine")

# Optional: adjust conformation if needed here
gly.center()

# Add glycine 3 Å above the surface
add_adsorbate(slab, gly, height=3.0, position="ontop")

# Set calculator
slab.calc = GPAW(
    mode=PW(500), xc="PBE", kpts=(4, 4, 1), txt="glycine_cu_adsorption.log"
)

# Relaxation
dyn = BFGS(slab, trajectory="adsorption.traj")
dyn.run(fmax=0.05)

# Optional: View result
view(slab)