ase_notebook.configuration module

A module for creating visualisations of a structure.

class ase_notebook.configuration.MillerPlane(h: float = 0, k: float = 0, l: float = 0, fill_color: str = 'red', stroke_color: str = 'red', stroke_width: float = 1.0, fill_opacity: float = 0.5, stroke_opacity: float = 0.9)

Bases: object

A data class to define a Miller Plane to visualise.

Parameters

• h (float) – Default: 0

• k (float) – Default: 0

• l (float) – Default: 0

• fill_color (str) – Default: “red”

• stroke_color (str) – Default: “red”

• stroke_width (float) – Default: 1.0

• fill_opacity (float) – Default: 0.5

• stroke_opacity (float) – Default: 0.9

_validate_h(attribute, value)

_validate_k(attribute, value)

_validate_l(attribute, value)

fill_color

fill_opacity

h

k

l

stroke_color

stroke_opacity

stroke_width

class ase_notebook.configuration.ViewConfig(*, rotations: str = '', element_colors: str = 'ase', element_radii: str = 'ase', radii_scale: float = 0.89, atom_show_label: bool = True, atom_label_by: str = 'element', atom_label_array: str = '', atom_font_size: int = 14, atom_font_color: str = 'black', atom_stroke_width: float = 1.0, atom_stroke_opacity: float = 0.95, atom_color_by: str = 'element', atom_color_array: str = '', atom_colormap: str = 'jet', atom_colormap_range: Union[list, tuple] = (None, None), atom_lighten_by_depth: float = 0.0, atom_opacity: float = 0.95, force_vector_scale: float = 1.0, velocity_vector_scale: float = 1.0, ghost_stroke_width: float = 0.0, ghost_lighten: float = 0.0, ghost_opacity: float = 0.4, ghost_stroke_opacity: float = 0.4, ghost_show_label: bool = False, ghost_cross_out: bool = False, show_unit_cell: bool = True, show_uc_repeats: Union[bool, list] = False, uc_dash_pattern: Union[None, Tuple[float, float]] = None, uc_color: str = 'black', show_bonds: bool = False, bond_radii_scale: float = 1.5, bond_array_name: Optional[str] = None, bond_pairs_filter: Optional[list] = None, bond_opacity: float = 0.8, bond_color_by: str = 'atoms', bond_colormap: str = 'jet', bond_colormap_range: Union[list, tuple] = (None, None), show_miller_planes: bool = True, miller_planes=(), miller_as_lines: bool = False, show_axes: bool = True, axes_uc: bool = False, axes_length: float = 15, axes_font_size: int = 14, axes_line_color: str = 'black', axes_offset: Tuple[float, float] = (20, 20), canvas_size: Tuple[float, float] = (400, 400), canvas_color_foreground: str = '#000000', canvas_color_background: str = '#ffffff', canvas_background_opacity: float = 0.0, canvas_crop: Union[list, tuple, None] = None, zoom: float = 1.0, camera_fov: float = 10.0, gui_swap_mouse: bool = False)

Bases: object

Configuration settings for initialisation of atom visualisations.

Parameters

• rotations (str) – Initial unit cell rotation in string format, e.g. ‘50x,-10y,120z’ (note: order matters) Default: “”

• element_colors (str) – Element to color mapping to use, if atom_color_by='element'. Default: “ase”

• element_radii (str) – Element to color mapping to use. Default: “ase”

• radii_scale (float) – Scale all radii by this value. Default: 0.89

• atom_show_label (bool) – Add atom labels to visualisation. Default: True

• atom_label_by (str) – Atom property to label atoms by. Default: “element”

• atom_label_array (str) – The array name to use, if array chosen for atom_label_by Default: “”

• atom_font_size (int) – Font size for atom labels. Default: 14

• atom_font_color (str) – Font size for atom labels. Default: “black”

• atom_stroke_width (float) – line width for atom outlines. Default: 1.0

• atom_stroke_opacity (float) – line opacity for atom outlines. Default: 0.95

• atom_color_by (str) – Atom property to color atoms by. Default: “element”

• atom_color_array (str) – The array name to use, if array chosen for atom_color_by Default: “”

• atom_colormap (str) – The matplotlib colormap to use with atom_color_by values Default: “jet”

• atom_colormap_range (list, tuple) – The matplotlib colormap normalisation use with atom_color_by values Default: (None, None)

• atom_lighten_by_depth (float) – Fraction by which to lighten atom colors, based on their fractional distance along the line, from the maximum to minimum z-coordinate of all elements Default: 0.0

• atom_opacity (float) – Default: 0.95

• force_vector_scale (float) – Length of force vector arrows. Default: 1.0

• velocity_vector_scale (float) – Length of velocity vector arrows. Default: 1.0

• ghost_stroke_width (float) – Default: 0.0

• ghost_lighten (float) – Lighten the ghost atom colors by this fraction. Default: 0.0

• ghost_opacity (float) – Default: 0.4

• ghost_stroke_opacity (float) – Default: 0.4

• ghost_show_label (bool) – Default: False

• ghost_cross_out (bool) – Default: False

• show_unit_cell (bool) – Default: True

• show_uc_repeats (bool, list) – If True, and the atoms have been repeated, show each unit cell of the original atoms. Default: False

• uc_dash_pattern (NoneType, Tuple[float, float]) – A (length, gap) dash pattern for unit cell lines. Default: None

• uc_color (str) – Unit cell line color. Default: “black”

• show_bonds (bool) – Show atomic bonds. Default: False

• bond_radii_scale (float) – Factor to scale atomic radii by, when computing bonds (via overlapping radii) Default: 1.5

• bond_array_name (str, NoneType) – The name of a boolean array on the Atoms, specifying which atoms that bonds should be drawn for (if None, then all bonds are drawn). Default: None

• bond_pairs_filter (list, NoneType) – A list of bond element pairs to filter by, e.g. [(‘Fe’, ‘O’), (‘Fe’, ‘Fe’)]. Default: None

• bond_opacity (float) – Opacity of atomic bond lines. Default: 0.8

• bond_color_by (str) – How to color bond: ‘atoms’ (same as connecting atoms) or ‘length’. Default: “atoms”

• bond_colormap (str) – The matplotlib colormap to use with bond_color_by='length' Default: “jet”

• bond_colormap_range (list, tuple) – The matplotlib colormap normalisation to use with bond_color_by='length' Default: (None, None)

• show_miller_planes (bool) – Default: True

• miller_planes (Tuple[dict]) – List of dictionaries, describing miller index planes to create. Default: ()

• miller_as_lines (bool) – If True, the miller planes will be created as lines, rather than polygons. Default: False

• show_axes (bool) – Show the ‘world’ axes, at a corner of the visualisation. Default: True

• axes_uc (bool) – Show the ‘unit cell’ axes (abc), instead of the ‘world’ axes (XYZ) Default: False

• axes_length (float) – Length of axes lines. Default: 15

• axes_font_size (int) – Default: 14

• axes_line_color (str) – Default: “black”

• axes_offset (Tuple[float, float]) – Offset of axis origin from the bottom left of the canvas Default: (20, 20)

• canvas_size (Tuple[float, float]) – Default: (400, 400)

• canvas_color_foreground (str) – Default: “#000000”

• canvas_color_background (str) – Default: “#ffffff”

• canvas_background_opacity (float) – Default: 0.0

• canvas_crop (list, tuple, NoneType) – Crop canvas: (left, right, top, bottom) Default: None

• zoom (float) – 3D camera zoom. Default: 1.0

• camera_fov (float) – 3D camera field-of-view. Default: 10.0

• gui_swap_mouse (bool) – Used with make_gui only. Default: False

_bond_pairs_filter(attribute, value)

Validate bond_pairs_filter attribute.

_validate_canvas_crop(attribute, value)

Validate crop is of form (left, right, top, bottom).

_validate_uc_dash_pattern(attribute, value)

Validate uc_dash_pattern is of form (solid, gap).

atom_color_array: str = None

atom_color_by: str = None

atom_colormap: str = None

atom_colormap_range: Union[list, tuple] = None

atom_font_color: str = None

atom_font_size: int = None

atom_label_array: str = None

atom_label_by: str = None

atom_lighten_by_depth: float = None

atom_opacity: float = None

atom_show_label: bool = None

atom_stroke_opacity: float = None

atom_stroke_width: float = None

axes_font_size: int = None

axes_length: float = None

axes_line_color: str = None

axes_offset: Tuple[float, float] = None

axes_uc: bool = None

bond_array_name: Optional[str] = None

bond_color_by: str = None

bond_colormap: str = None

bond_colormap_range: Union[list, tuple] = None

bond_opacity: float = None

bond_pairs_filter: Optional[list] = None

bond_radii_scale: float = None

camera_fov: float = None

canvas_background_opacity: float = None

canvas_color_background: str = None

canvas_color_foreground: str = None

canvas_crop: Union[list, tuple, None] = None

canvas_size: Tuple[float, float] = None

element_colors: str = None

element_radii: str = None

force_vector_scale: float = None

ghost_cross_out: bool = None

ghost_lighten: float = None

ghost_opacity: float = None

ghost_show_label: bool = None

ghost_stroke_opacity: float = None

ghost_stroke_width: float = None

gui_swap_mouse: bool = None

miller_as_lines: bool = None

miller_planes: Tuple[dict] = None

radii_scale: float = None

rotations: str = None

show_axes: bool = None

show_bonds: bool = None

show_miller_planes: bool = None

show_uc_repeats: Union[bool, list] = None

show_unit_cell: bool = None

uc_color: str = None

uc_dash_pattern: Union[None, Tuple[float, float]] = None

velocity_vector_scale: float = None

zoom: float = None

ase_notebook.configuration.convert_to_miller_dicts(iterable)

Convert items in a list to MillerPlane validated dictionaries.

ase_notebook.configuration.in_range(minimum=None, maximum=None, inclusive_min=True)

Validate that an attribute value is a number >= 0.

ase_notebook.configuration.is_html_color(self, attribute, value)

Validate that an attribute value is a valid HTML color.

ase_notebook.configuration.iterable_length(length)

Validate that an attribute is an iterable of a certain length.