StructureMap¶

class StructureMap(data, sites, hoppings, boundaries=())¶

A subclass of SpatialMap that also includes hoppings between sites

Attributes

`boundaries`	Boundary hoppings between different translation units (only for infinite systems)
`data`	1D array of values for each site, i.e.
`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
`clipped`(v_min, v_max)	Clip (limit) the values in the `data` array, see `clip()`
`cropped`(**limits)	Return a copy which retains only the sites within the given limits
`plot`([cmap, site_radius, num_periods])	Plot the spatial structure with a colormap of `data` at the lattice sites
`plot_contour`(**kwargs)	Contour plot of the xy plane
`plot_contourf`([num_levels])	Filled contour plot of the xy plane
`plot_pcolor`(**kwargs)	Color plot of the xy plane
`with_data`(data)	Return a copy of this object with different data mapped to the sites

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

cropped(**limits)¶

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

Parameters:	**limits Attribute names and corresponding limits. See example.

Examples

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

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

plot(cmap='YlGnBu', site_radius=(0.03, 0.05), num_periods=1, **kwargs)¶

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:	cmap : str Matplotlib colormap to be used for the data. site_radius : Tuple[float, float] Min and max radius of lattice sites. This range will be used to visually represent the magnitude of the data. num_periods : int Number of times to repeat periodic boundaries. **kwargs Additional plot arguments as specified in `structure_plot_properties()`.

plot_contour(**kwargs)¶

Contour plot of the xy plane

Parameters:	**kwargs Forwarded to `tricontour()`.

plot_contourf(num_levels=50, **kwargs)¶

Filled contour plot of the xy plane

Parameters:	num_levels : int Number of contour levels. **kwargs Forwarded to `tricontourf()`.

plot_pcolor(**kwargs)¶

Color plot of the xy plane

Parameters:	**kwargs Forwarded to `tripcolor()`.

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

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

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

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

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