StructureMap¶

A subclass of SpatialMap that also includes hoppings between sites

Attributes

`boundaries`	Boundary hoppings between different translation units (only for infinite systems)
`callsig`
`data`	1D array of values for each site, i.e. maps directly to x, y, z site coordinates.
`hoppings`	Sparse matrix of hopping IDs
`num_sites`	Total number of lattice sites
`positions`	Lattice site positions.
`spatial_map`	Just the `SpatialMap` subset without hoppings
`sub`	1D array of sublattices IDs, short for `.sublattices`
`sublattices`	1D array of sublattices IDs
`x`	1D array of coordinates, short for `.positions.x`
`xyz`	Return a new array with shape=(N, 3).
`y`	1D array of coordinates, short for `.positions.y`
`z`	1D array of coordinates, short for `.positions.z`

Methods

`__getitem__`(idx)	Same rules as numpy indexing
`_decorate_plot`([ax])
`_make_crop_indices`(limits)	Return the indices into `obj` which retain only the data within the given limits
`clipped`(v_min, v_max)	Clip (limit) the values in the `data` array, see `clip()`
`convolve`([sigma])	Convolve the data with a Gaussian kernel of the given standard deviation
`cropped`(**limits)	Return a copy which retains only the sites within the given limits
`plot`([cmap, site_radius, num_periods, ax])	Plot the spatial structure with a colormap of `data` at the lattice sites
`plot_contour`([ax])	Contour plot of the xy plane
`plot_contourf`([num_levels, ax])	Filled contour plot of the xy plane
`plot_pcolor`([ax])	Color plot of the xy plane
`save_txt`(filename)
`with_data`(data)	Return a copy of this object with different data mapped to the sites

__getitem__(idx: int | List[int]) → StructureMap¶: Same rules as numpy indexing

clipped(v_min: int, v_max: int) → SpatialMap¶: Clip (limit) the values in the data array, see clip()

convolve(sigma: float = 0.25)¶

Convolve the data with a Gaussian kernel of the given standard deviation

Parameters:

cropped(**limits) → SpatialMap¶

Return a copy which retains only the sites within the given limits

Parameters:

Examples

Leave only the data where -10 <= x < 10 and 2 <= y < 4:

new = original.cropped(x=[-10, 10], y=[2, 4])

plot(cmap: str = 'YlGnBu', site_radius: List[float] | float | Tuple[float, float] = (0.03, 0.05), num_periods: int = 1, ax: Axes | None = None, **kwargs) → CircleCollection | None¶

Plot the spatial structure with a colormap of data at the lattice sites

Both the site size and color are used to display the data.

Parameters:

cmapstr: Matplotlib colormap to be used for the data.
site_radiusUnion[List[float], float, Tuple[float, float]]: Min and max radius of lattice sites. This range will be used to visually represent the magnitude of the data.
num_periodsint: Number of times to repeat periodic boundaries.
axOptional[plt.Axes]: The axis to plot on.
**kwargs: Additional plot arguments as specified in structure_plot_properties().

plot_contour(ax: Axes | None = None, **kwargs) → TriContourSet¶

Contour plot of the xy plane

Parameters:

plot_contourf(num_levels: int = 50, ax: Axes | None = None, **kwargs) → TriContourSet¶

Filled contour plot of the xy plane

Parameters:

plot_pcolor(ax: Axes | None = None, **kwargs) → TriMesh | PolyCollection¶

Color plot of the xy plane

Parameters:

with_data(data) → StructureMap¶: Return a copy of this object with different data mapped to the sites

property boundaries: list¶: Boundary hoppings between different translation units (only for infinite systems)

property data: ndarray¶: 1D array of values for each site, i.e. maps directly to x, y, z site coordinates

property positions: Positions¶: Lattice site positions. Named tuple with x, y, z fields, each a 1D array.

property spatial_map: SpatialMap¶: Just the SpatialMap subset without hoppings

property sub: ndarray¶: 1D array of sublattices IDs, short for .sublattices

property xyz: ndarray¶: Return a new array with shape=(N, 3). Convenient, but slow for big systems.