ipyatom

a package primarily fpr interfacing ase/pymatgen with ipyvolume/matplotlib ipyatom

Installation

pip install ipyatom

That's it! (preferably in a fresh Anaconda environment)

Example

from ase.build import bulk
from jsonextended import edict
from ipyatom import repeat_cell
from ipyatom import render_ivol
from ipyatom import bonds
from ipyatom import plot_mpl

atoms = bulk("Fe").repeat((2,1,1))
atoms

Atoms(symbols='Fe2', pbc=True, cell=[[-2.87, 2.87, 2.87], [1.435, -1.435, 1.435], [1.435, 1.435, -1.435]])

vstruct = repeat_cell.atoms_to_dict(atoms)
vstruct["elements"][0]["sites"][0]["label"] = "S"
vstruct = repeat_cell.change_site_variable(
    vstruct, {"color_fill": "green"}, {"label": "S"})
edict.pprint(vstruct)

elements:
  - bonds:    []
    cell_vectors:
      a: [-2.87, 2.87, 2.87]
      b: [1.435, -1.435, 1.435]
      c: [1.435, 1.435, -1.435]
    centre:   [0.0, 1.435, 1.4349999999999998]
    color_bbox: black
    name:
    sites:
      - anum:        26
        ccoord:      [0.0, 0.0, 0.0]
        cell:        [0, 0, 0]
        color_fill:  green
        color_outline: None
        label:       S
        radius:      1.32
        transparency: 1
      - anum:        26
        ccoord:      [-1.435, 1.435, 1.435]
        cell:        [0, 0, 0]
        color_fill:  #e06633
        color_outline: None
        label:       Fe
        radius:      1.32
        transparency: 1
    transforms: []
    type:     repeat_cell
transforms: []

new_struct, fig, controls = render_ivol.create_ivol(vstruct)
render_ivol.ipy_style(fig)

vstruct2 = bonds.add_bonds(vstruct, "Fe", "S", 2.5)
edict.pprint(vstruct2)

elements:
  - bonds:
      - cmap_name:      jet
        color_by_dist:  False
        coord_label:    S
        drange:         (0, 10)
        include_periodic: True
        label:          Fe
        max_dist:       2.5
        radius:         0.1
    cell_vectors:
      a: [-2.87, 2.87, 2.87]
      b: [1.435, -1.435, 1.435]
      c: [1.435, 1.435, -1.435]
    centre:   [0.0, 1.435, 1.4349999999999998]
    color_bbox: black
    name:
    sites:
      - anum:        26
        ccoord:      [0.0, 0.0, 0.0]
        cell:        [0, 0, 0]
        color_fill:  green
        color_outline: None
        label:       S
        radius:      1.32
        transparency: 1
      - anum:        26
        ccoord:      [-1.435, 1.435, 1.435]
        cell:        [0, 0, 0]
        color_fill:  #e06633
        color_outline: None
        label:       Fe
        radius:      1.32
        transparency: 1
    transforms: []
    type:     repeat_cell
transforms: []

new_struct, fig, controls = render_ivol.create_ivol(vstruct2)
render_ivol.ipy_style(fig)

vstruct3 = bonds.add_bonds(vstruct, "Fe", "S", 2.5, color_by_dist=True, drange=(2,4))
edict.pprint(vstruct3)

elements:
  - bonds:
      - cmap_name:      jet
        color_by_dist:  True
        coord_label:    S
        drange:         (2, 4)
        include_periodic: True
        label:          Fe
        max_dist:       2.5
        radius:         0.1
    cell_vectors:
      a: [-2.87, 2.87, 2.87]
      b: [1.435, -1.435, 1.435]
      c: [1.435, 1.435, -1.435]
    centre:   [0.0, 1.435, 1.4349999999999998]
    color_bbox: black
    name:
    sites:
      - anum:        26
        ccoord:      [0.0, 0.0, 0.0]
        cell:        [0, 0, 0]
        color_fill:  green
        color_outline: None
        label:       S
        radius:      1.32
        transparency: 1
      - anum:        26
        ccoord:      [-1.435, 1.435, 1.435]
        cell:        [0, 0, 0]
        color_fill:  #e06633
        color_outline: None
        label:       Fe
        radius:      1.32
        transparency: 1
    transforms: []
    type:     repeat_cell
transforms: []

new_struct, fig, controls = render_ivol.create_ivol(vstruct3)
render_ivol.ipy_style(fig)

%matplotlib inline
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1)
plot_mpl.create_colorbar(ax, (2, 4), "jet", "Bond Length")
fig.set_size_inches((5,1))

plot_mpl.plot_atoms_top(vstruct)

(<matplotlib.axes._subplots.AxesSubplot at 0x118a279e8>,
 {'Fe': <matplotlib.lines.Line2D at 0x118c465c0>,
  'S': <matplotlib.lines.Line2D at 0x118c37a90>})