The Bond object

The Bond object is used to draw bond for Batoms. It has a settings attribute (BondSettings object), which stores and sets all parameters related to bonds. Possible keywords for settings are: symbol1, symbol2, min, max, search, polyhedra, color1, color2, bondlinewidth, style, material_style.

>>> from ase.build import molecule
>>> from batoms import Batoms
>>> ch4 = Batoms('ch4', from_ase = molecule('CH4'))
>>> ch4.model_style = 2
../_images/bondsetting_ch4_0.png

You can print the default bond.settings by:

>>> ch4.bond.settings
../_images/bondsetting_ch4_1.png

By defaut, we use default radius (ase.data.covalent_radii) for every atoms, and the maximum bondlength is the sum of two radius and then scaled by a default cutoff (1.3). The minimum bondlength is 0.5.

Style

One set the bond style for a bond pair by:

>>> ch4.bond.settings[('C', 'H')].style = '3'
../_images/bond_style_setting_0.png

One set the bond style for a bond by (Here is the first bond):

>>> ch4.bonds[0].style = '3'
../_images/bond_style_setting_1.png

Here, four bond models are supported.

0

1

2

3
../_images/bondsetting_style_0.png ../_images/bondsetting_style_1.png ../_images/bondsetting_style_2.png ../_images/bondsetting_style_3.png

Polyhedra

One can change setting for a bond pair. For example, to build up coordination polyhedra, the value for polyhedra should be set to True:

>>> ch4.bond.settings[('C', 'H')].polyhedra = True
>>> ch4.model_style = 2
../_images/bondsetting_ch4_2.png

Search bond mode

  • 0 Do not search atoms beyond the boundary

  • 1 Search additional atoms if species1 is included in the boundary

  • 2 Search bonded atoms of species1 or species2 recursively. This mode is the used for searching molecules.

To change setting for search by:

>>> tio2.bond.settings[('Ti', 'O')].search = 0
>>> tio2.update_boundary()
>>> tio2.model_style = 2
../_images/bondsetting_tio2_2.png

Color

One can print the default color by:

>>> ch4.bond.settings[('C', 'H')].color1[:]

One can change color for a bond pair.

>>> ch4.bond.settings[('C', 'H')].color1 = [0.8, 0.1, 0.3, 0.5]
>>> ch4.bond.settings[('C', 'H')].color2 = [0.1, 0.3, 0.2, 1.0]
>>> ch4.model_style = 1
../_images/bondsetting_ch4_3.png

High order bond

One can set bond order for each bond:

>>> from ase.build import molecule
>>> from batoms import Batoms
>>> c6h6 = Batoms("c6h6", from_ase = molecule("C6H6"))
>>> c6h6.model_style = 1
>>> c6h6.bonds[0].order = 2
>>> c6h6.bonds[5].order = 2
>>> c6h6.bonds[9].order = 2
../_images/bondsetting_order.png

Or one can set the bond order automaticaly based on pybel:

>>> c6h6.bonds.bond_order_auto_set()