Visualization

The visualization module contains classes for generating three-dimensional visuals.

class CrystalStructure(A, ux, uy, uz, atms, colors, nu=1, nv=1, nw=1)

Draw a crystal structure. Atom can drawn with various radii with occupancy displayed using opacity. Atoms can allso be draw as atomic displacement ellipsoids or be decorated with magnetic moments vectors.

Parameters:

A2d-array

Real-space Cartesian transform.

ux, uy, uz1d-array

Cartesian fractional coordinates.

atms1d-array, str

Atom labels.

colors2d-array

RGB color for each atom.

nu, nv, nwint

Number of cells along each dimension. Default is 1 along each dimension.

Methods

show_figure()
save_figure()
view_direction)
draw_basis_vectors()
draw_cell_edges()
atomic_radii()
atomic_displacement_ellipsoids()
magnetic_vectors()

atomic_displacement_ellipsoids(Uxx, Uyy, Uzz, Uyz, Uxz, Uxy, p=0.99)

Draw atomic displacement ellipsoids

Parameters:

Uxx, Uyy, Uzz, Uyz, Uxz, Uxy1d-array

Atomic displacement parameters in Cartesian coordinates.

pfloat

Probability surface. Default is p=0.99

atomic_radii(radii, occ)

Draw atoms with given radii and displayed with opacity corresponding to site occupancy

Parameters:

radii1d-array

The radii of the atom sites.

occ1d-array

The site occupancy of each atom. The value ranges from 0-1.

draw_basis_vectors()

Draw the baasis vector directions for the crytallographic directions.

draw_cell_edges()

Draw unit cell edges.

magnetic_vectors(sx, sy, sz)

Draw magnetic vectors.

Parameters:

sx, sy, sz1d-array

The magnetic moment vector components in Cartesian coordinates.

save_figure(filename)

Save the figure as a graphic image.

Parameters:

filenamestr

Name of file with extension. Supported extensions are .svg and .pdf.

show_figure()

Display the drawing.

view_direction(u, v, w)

View drawing along a crystallographic direction.

Parameters:

u, v, wfloat

Components of the viewing axis. Units are in fractional coordinates.