.. module:: ase.build ================ Building things ================ Quick links: * Simple bulk crystals: :func:`~ase.build.bulk` * Simple molecules: :func:`~ase.build.molecule` * Special surfaces: * fcc: :func:`~ase.build.fcc100`, :func:`~ase.build.fcc110`, :func:`~ase.build.fcc111`, :func:`~ase.build.fcc211`, :func:`~ase.build.fcc111_root` * bcc: :func:`~ase.build.bcc100`, :func:`~ase.build.bcc110`, :func:`~ase.build.bcc111` * - :func:`~ase.build.bcc111_root` * hcp: :func:`~ase.build.hcp0001`, :func:`~ase.build.hcp10m10`, :func:`~ase.build.hcp0001_root` * diamond: :func:`~ase.build.diamond100`, :func:`~ase.build.diamond111` * `MX_2` (2H or 1T): :func:`~ase.build.mx2` * Other surface tools: :func:`~ase.build.surface`, :func:`~ase.build.add_adsorbate`, :func:`~ase.build.add_vacuum`, :func:`~ase.build.root_surface` * 1D: :func:`~ase.build.nanotube`, :func:`~ase.build.graphene_nanoribbon` * Other tools: :func:`~ase.build.cut`, :func:`~ase.build.stack`, :func:`~ase.build.sort`, :func:`~ase.build.minimize_tilt`, :func:`~ase.build.niggli_reduce`, :func:`~ase.build.rotate`, :func:`~ase.build.minimize_rotation_and_translation`, :func:`~ase.build.get_deviation_from_optimal_cell_shape`, :func:`~ase.build.find_optimal_cell_shape`, :func:`~ase.build.make_supercell` * Separation: :func:`~ase.build.connected_indices`, :func:`~ase.build.connected_atoms`, :func:`~ase.build.separate`, :func:`~ase.build.split_bond` .. toctree:: :maxdepth: 2 surface tools connected .. seealso:: * The :mod:`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 :mod:`ase.cluster` module. Useful for creating nanoparticles and clusters. * The :mod:`ase.spacegroup` module * The :mod:`ase.geometry` module Molecules ========= The G2-database of common molecules is available: .. autofunction:: molecule Example:: >>> from ase.build import molecule >>> atoms = molecule('H2O') The list of available molecules is those from the :data:`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). More complicated molecules may be obtained using the PubChem API integration in the :func:`~ase.data.pubchem.pubchem_atoms_search` and :func:`~ase.data.pubchem.pubchem_atoms_conformer_search` functions. You may search based on common name, chemical identification number (cid), smiles string, or conformer identification number. .. _bulk-crystal-section: Common bulk crystals ==================== .. autofunction:: bulk 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| .. |a1| image:: a1.png .. |a2| image:: a2.png .. |a3| image:: a3.png .. _nanotubes-section: Nanotubes ========= .. autofunction:: nanotube 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| .. |cnt1| image:: cnt1.png .. |cnt2| image:: cnt2.png .. _nanoribbons-section: Graphene nanoribbons ==================== .. autofunction:: graphene_nanoribbon 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| .. |gnr1| image:: gnr1.png .. |gnr2| image:: gnr2.png 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. .. _attaching-section: Attaching structures ==================== .. autofunction:: ase.build.attach.attach .. autofunction:: ase.build.attach.attach_randomly .. autofunction:: ase.build.attach.attach_randomly_and_broadcast