pyextal.densityMap

This module provides functions for generating and visualizing 3D electron density maps.

It includes capabilities for Fourier synthesis from structure factors, plotting 3D isosurfaces and 2D slices of the density map, and writing the volumetric data to a Gaussian cube file for visualization in other software like VESTA.

Functions

fourierSynthesis(→ numpy.ndarray)

Performs Fourier synthesis to generate a 3D density map.

plotDensityMapIsosurface(→ None)

Plots a 3D isosurface of the density map.

plotDensityMap_2D(→ None)

Plots 2D slices of the density map.

write_cube(→ None)

Writes volumetric data to a Gaussian cube file.

Module Contents

pyextal.densityMap.fourierSynthesis(getSF: callable, order: int, sampling: int) → numpy.ndarray

Performs Fourier synthesis to generate a 3D density map.

This function constructs a 3D electron density map by summing crystallographic structure factors over a specified range of Miller indices.

Parameters:

  • getSF (callable) – A function that takes a Miller index tuple (h, k, l) and returns its complex structure factor.

  • order (int) – The maximum Miller index (h, k, l) to include in the synthesis. The range will be from -order to +order for each index.

  • sampling (int) – The number of grid points along each dimension of the output density map.

Returns:

A 3D real-valued density map, normalized by the unit cell volume.

Return type:

np.ndarray

pyextal.densityMap.plotDensityMapIsosurface(density_map: numpy.ndarray, threshold: float = 10) → None

Plots a 3D isosurface of the density map.

Uses the marching cubes algorithm to extract and display a surface at a given density threshold. Note: The orientation of X, Y, Z axes might need to be verified with software like VESTA.

Parameters:

  • density_map (np.ndarray) – The 3D density map to be visualized.

  • threshold (float, optional) – The density value at which to draw the isosurface. Defaults to 10.

pyextal.densityMap.plotDensityMap_2D(density_map: numpy.ndarray, clim: tuple, cmap: str) → None

Plots 2D slices of the density map.

Displays four 2D slices taken from the 3D density map along one axis.

Parameters:

  • density_map (np.ndarray) – The 3D density map.

  • clim (tuple) – A tuple (min, max) to set the color limits.

  • cmap (str) – The colormap to use for the plot.

pyextal.densityMap.write_cube(filename: str, data: numpy.ndarray) → None

Writes volumetric data to a Gaussian cube file.

This function creates a .cube file, which is a standard format for volumetric data like electron density, readable by visualization software (e.g., VESTA). The atom and cell information is read from the global cryst object.

Parameters:

  • filename (str) – The path to the output .cube file.

  • data (np.ndarray) – A 3D NumPy array containing the charge density values.