Building things

Quick links:

See also

  • The ase.lattice module. The module contains functions for creating most common crystal structures with arbitrary orientation. The user can specify the desired Miller index along the three axes of the simulation, and the smallest periodic structure fulfilling this specification is created. Both bulk crystals and surfaces can be created.

  • The ase.cluster module. Useful for creating nanoparticles and clusters.

  • The ase.spacegroup module

  • The ase.geometry module

Molecules

The G2-database of common molecules is available:

ase.build.molecule(name, vacuum=None, **kwargs)[source]

Example:

>>> from ase.build import molecule
>>> atoms = molecule('H2O')

The list of available molecules is those from the ase.collections.g2 database:

>>> from ase.collections import g2
>>> g2.names
['PH3', 'P2', 'CH3CHO', 'H2COH', 'CS', 'OCHCHO', 'C3H9C', 'CH3COF',
 'CH3CH2OCH3', 'HCOOH', 'HCCl3', 'HOCl', 'H2', 'SH2', 'C2H2',
 'C4H4NH', 'CH3SCH3', 'SiH2_s3B1d', 'CH3SH', 'CH3CO', 'CO', 'ClF3',
 'SiH4', 'C2H6CHOH', 'CH2NHCH2', 'isobutene', 'HCO', 'bicyclobutane',
 'LiF', 'Si', 'C2H6', 'CN', 'ClNO', 'S', 'SiF4', 'H3CNH2',
 'methylenecyclopropane', 'CH3CH2OH', 'F', 'NaCl', 'CH3Cl',
 'CH3SiH3', 'AlF3', 'C2H3', 'ClF', 'PF3', 'PH2', 'CH3CN',
 'cyclobutene', 'CH3ONO', 'SiH3', 'C3H6_D3h', 'CO2', 'NO',
 'trans-butane', 'H2CCHCl', 'LiH', 'NH2', 'CH', 'CH2OCH2',
 'C6H6', 'CH3CONH2', 'cyclobutane', 'H2CCHCN', 'butadiene', 'C',
 'H2CO', 'CH3COOH', 'HCF3', 'CH3S', 'CS2', 'SiH2_s1A1d', 'C4H4S',
 'N2H4', 'OH', 'CH3OCH3', 'C5H5N', 'H2O', 'HCl', 'CH2_s1A1d',
 'CH3CH2SH', 'CH3NO2', 'Cl', 'Be', 'BCl3', 'C4H4O', 'Al', 'CH3O',
 'CH3OH', 'C3H7Cl', 'isobutane', 'Na', 'CCl4', 'CH3CH2O', 'H2CCHF',
 'C3H7', 'CH3', 'O3', 'P', 'C2H4', 'NCCN', 'S2', 'AlCl3', 'SiCl4',
 'SiO', 'C3H4_D2d', 'H', 'COF2', '2-butyne', 'C2H5', 'BF3', 'N2O',
 'F2O', 'SO2', 'H2CCl2', 'CF3CN', 'HCN', 'C2H6NH', 'OCS', 'B', 'ClO',
 'C3H8', 'HF', 'O2', 'SO', 'NH', 'C2F4', 'NF3', 'CH2_s3B1d', 'CH3CH2Cl',
 'CH3COCl', 'NH3', 'C3H9N', 'CF4', 'C3H6_Cs', 'Si2H6', 'HCOOCH3', 'O',
 'CCH', 'N', 'Si2', 'C2H6SO', 'C5H8', 'H2CF2', 'Li2', 'CH2SCH2', 'C2Cl4',
 'C3H4_C3v', 'CH3COCH3', 'F2', 'CH4', 'SH', 'H2CCO', 'CH3CH2NH2', 'Li',
 'N2', 'Cl2', 'H2O2', 'Na2', 'BeH', 'C3H4_C2v', 'NO2']

plus Be2, C7NH5, BDA, biphenyl and C60 (for historical reasons).

Common bulk crystals

ase.build.bulk(name, crystalstructure=None, a=None, c=None, covera=None, u=None, orthorhombic=False, cubic=False)[source]

Creating bulk systems.

Crystal structure and lattice constant(s) will be guessed if not provided.

name: str

Chemical symbol or symbols as in ‘MgO’ or ‘NaCl’.

crystalstructure: str

Must be one of sc, fcc, bcc, hcp, diamond, zincblende, rocksalt, cesiumchloride, fluorite or wurtzite.

a: float

Lattice constant.

c: float

Lattice constant.

covera: float

c/a ratio used for hcp. Default is ideal ratio: sqrt(8/3).

u: float

Internal coordinate for Wurtzite structure.

orthorhombic: bool

Construct orthorhombic unit cell instead of primitive cell which is the default.

cubic: bool

Construct cubic unit cell if possible.

examples:

>>> from ase.build import bulk
>>> a1 = bulk('Cu', 'fcc', a=3.6)
>>> a2 = bulk('Cu', 'fcc', a=3.6, orthorhombic=True)
>>> a3 = bulk('Cu', 'fcc', a=3.6, cubic=True)
>>> a1.cell
array([[ 0. ,  1.8,  1.8],
       [ 1.8,  0. ,  1.8],
       [ 1.8,  1.8,  0. ]])
>>> a2.cell
array([[ 2.546,  0.   ,  0.   ],
       [ 0.   ,  2.546,  0.   ],
       [ 0.   ,  0.   ,  3.6  ]])
>>> a3.cell
array([[ 3.6,  0. ,  0. ],
       [ 0. ,  3.6,  0. ],
       [ 0. ,  0. ,  3.6]])

a1 a2 a3

Nanotubes

ase.build.nanotube(n, m, length=1, bond=1.42, symbol='C', verbose=False, vacuum=None)[source]

examples:

>>> from ase.build import nanotube
>>> cnt1 = nanotube(6, 0, length=4)
>>> cnt2 = nanotube(3, 3, length=6, bond=1.4, symbol='Si')

cnt1 cnt2

Graphene nanoribbons

ase.build.graphene_nanoribbon(n, m, type='zigzag', saturated=False, C_H=1.09, C_C=1.42, vacuum=None, magnetic=False, initial_mag=1.12, sheet=False, main_element='C', saturate_element='H')[source]

Create a graphene nanoribbon.

Creates a graphene nanoribbon in the x-z plane, with the nanoribbon running along the z axis.

Parameters:

n: int

The width of the nanoribbon. For armchair nanoribbons, this n may be half-integer to repeat by half a cell.

m: int

The length of the nanoribbon.

type: str

The orientation of the ribbon. Must be either ‘zigzag’ or ‘armchair’.

saturated: bool

If true, hydrogen atoms are placed along the edge.

C_H: float

Carbon-hydrogen bond length. Default: 1.09 Angstrom.

C_C: float

Carbon-carbon bond length. Default: 1.42 Angstrom.

vacuum: None (default) or float

Amount of vacuum added to non-periodic directions, if present.

magnetic: bool

Make the edges magnetic.

initial_mag: float

Magnitude of magnetic moment if magnetic.

sheet: bool

If true, make an infinite sheet instead of a ribbon (default: False)

examples:

>>> from ase.build import graphene_nanoribbon
>>> gnr1 = graphene_nanoribbon(3, 4, type='armchair', saturated=True,
                               vacuum=3.5)
>>> gnr2 = graphene_nanoribbon(2, 6, type='zigzag', saturated=True,
...                            C_H=1.1, C_C=1.4, vacuum=3.0,
...                            magnetic=True, initial_mag=1.12)

gnr1 gnr2

ASE contains a number of modules for setting up atomic structures, mainly molecules, bulk crystals and surfaces. Some of these modules have overlapping functionality, but strike a different balance between flexibility and ease-of-use.