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.. 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
|
