atomli.build
Generated from the public Python surface of Atomli 0.1.4.
molecule(name, vacuum=None, **kwargs)
Section titled “molecule(name, vacuum=None, **kwargs)”Build a named molecule, with ASE’s names and geometries.
Covers the G2/97 set plus ASE’s extras (Be2, C7NH5, BDA, biphenyl, C60),
so molecule("H2O") is the same structure ASE returns. Common aliases
("water", "ethanol", …) resolve to the matching G2 entry.
name: Molecule name or alias (e.g. "H2O").
vacuum: Vacuum padding in angstrom added around the molecule.
Returns: A new Atoms object.
bulk(name, crystalstructure=None, a=None, b=None, c=None, *, alpha=None, covera=None, u=None, orthorhombic=False, cubic=False, basis=None, **kwargs)
Section titled “bulk(name, crystalstructure=None, a=None, b=None, c=None, *, alpha=None, covera=None, u=None, orthorhombic=False, cubic=False, basis=None, **kwargs)”Build a bulk crystal, following ase.build.bulk.
Returns the primitive cell by default, exactly as ASE does; pass
cubic=True for the conventional cubic cell or orthorhombic=True for
the orthorhombic one.
name: Element symbol or formula ("Cu", "NaCl", "CaF2").
crystalstructure: Crystal name (fcc, bcc, hcp, diamond, …).
Defaults to the element’s reference phase.
a: Lattice constant in angstrom. Defaults to the reference value.
b: Not implemented; only used by ASE structures atomli cannot build.
c: Lattice constant along z; for hcp and wurtzite this sets c/a.
alpha: Not implemented (rhombohedral only).
covera: c/a ratio for hcp and wurtzite.
u: Internal wurtzite coordinate.
orthorhombic: Build the orthorhombic cell.
cubic: Build the conventional cubic cell.
basis: Not implemented (bct and rhombohedral only).
Returns: A new bulk Atoms.
fcc111(symbol, size, a=None, vacuum=None, **kwargs)
Section titled “fcc111(symbol, size, a=None, vacuum=None, **kwargs)”Build an FCC (111) surface slab.
symbol: Element symbol.
size: (nx, ny, nlayers).
a: Lattice constant in angstrom.
vacuum: Vacuum in angstrom added on EACH side of the slab, ASE’s
convention: the z cell is the slab thickness plus 2 * vacuum.
Returns: A new slab Atoms.
add_adsorbate(slab, adsorbate, height, position=(0.0, 0.0), **kwargs)
Section titled “add_adsorbate(slab, adsorbate, height, position=(0.0, 0.0), **kwargs)”Place an adsorbate above a slab. Mutates slab.
slab: Surface Atoms.
adsorbate: Adsorbate Atoms.
height: Height in angstrom.
position: (x, y) of the first adsorbate atom.