EPWpy.structure.lattice

Functions

get_supercell(atom_pos2, natoms, mat, ...)	Builds supercell of a certain size
get_supercell_pl(atom_pos2, natoms, mat, ...)	Builds supercell of a certain size for the polarization vector

Classes

Lattice(data)

A class representing a crystal lattice and its associated data.

class EPWpy.structure.lattice.Lattice(data)

Bases: object

A class representing a crystal lattice and its associated data.

This class provides a basic interface for storing and managing lattice-related information. It can serve as the foundational class for structural manipulation, symmetry analysis, or visualization routines in materials simulations.

Parameters:

data (dict or object) -- Input data structure containing lattice information. Typically includes lattice vectors, atomic positions, and element types, but may be any user-defined format compatible with downstream methods.

data

The input lattice data, stored for use by other methods.

Type:

dict or object

home

The working directory path at the time of object initialization.

Type:

str

Examples

>>> lattice_data = {
...     'lattice_vectors': [[1.0, 0.0, 0.0],
...                         [0.0, 1.0, 0.0],
...                         [0.0, 0.0, 1.0]],
...     'atomic_positions': [[0.0, 0.0, 0.0]],
...     'elements': ['Si']
... }
>>> lat = Lattice(lattice_data)
>>> lat.home
'/home/user/project'

atom_cart()

Gets atomic positions in cartesian co-ordinate

display_lattice(supercell=None, view=None, bond_length=3.5, type_view='mayavi')

Visualize the atomic lattice of the system.

This method displays the atomic structure of the simulated material using either Mayavi (for interactive 3D visualization) or Matplotlib (for static plotting). It supports supercell expansion and customizable view parameters.

Parameters:

• supercell (list or None, optional) -- Supercell expansion factors along each lattice direction, e.g., [2, 2, 1] for a 2×2×1 supercell. If None, uses the primitive cell.

• view (dict or None, optional) -- Dictionary specifying visualization options such as rotation, zoom, or color scheme. Example: {'azimuth': 45, 'elevation': 30, 'wrap': False} If None, defaults are used.

• bond_length (float, optional) -- Maximum interatomic distance (in Å) for drawing bonds (default: 3.5).

• type_view (str, optional) -- Visualization backend: - 'mayavi' → interactive 3D visualization (default) - 'matplotlib' → static 3D plotting for environments without Mayavi

Returns:

Visualization object returned by the selected backend: - Mayavi scene if available and selected. - Matplotlib figure otherwise.

Return type:

object

Notes

• Requires Mayavi to be installed for full 3D interactive visualization.

• If Mayavi is not available, falls back automatically to Matplotlib rendering.

• The visualization includes lattice vectors and atomic species.

Example

>>> epw = EPWProperties(file='epw2.out', system='MoS2')
>>> epw.display_lattice(supercell=[2,2,1], type_view='matplotlib')

display_lattice_legacy(supercell=None, view=None)

display_phonons(pl_vec, supercell=None, view=None, bond_length=3.5, type_view='mayavi')

Display the phonon displacement modes of the crystal structure.

This method visualizes phonon modes (atomic vibrations) using the provided phonon displacement vectors (pl_vec). The visualization can be generated using either Mayavi or Matplotlib, depending on availability and the type_view argument.

Parameters:

• pl_vec (array-like) -- Phonon displacement vectors for each atom in the structure. Typically obtained from a phonon calculation or interpolation step. Must have shape (N_atoms, 3).

• supercell (list[int], optional) -- Supercell expansion factors in each lattice direction [nx, ny, nz]. If not provided, the primitive cell is used.

• view (dict, optional) -- Visualization parameters, such as camera orientation or zoom level. Default is an empty dictionary.

• bond_length (float, optional) -- Maximum bond distance (in Ångströms) used to determine which atoms are connected by bonds in the visualization. Default is 3.5 Å.

• type_view (str, optional) --

  Visualization backend to use. Options are:

  • 'mayavi': use Mayavi for 3D interactive rendering (default)

  • 'matplotlib': use Matplotlib for static rendering

Returns:

A visualization object or figure handle created by the selected visualization backend.

Return type:

object

Notes

This method constructs the full crystal structure (including optional supercell expansion) and overlays atomic displacement vectors representing phonon modes. The resulting data is passed to an external visualization routine (display_crystal_phonon).

Examples

>>> pl_vec = np.random.randn(4, 3)  # Example displacement vectors
>>> model.display_phonons(pl_vec, supercell=[2, 2, 1], type_view='matplotlib')

gen_supercell(supercell=None)

returns the co-ordinates for supercell

get_Data(pl_vec, supercell=None, view=None, bond_length=3.5, type_view='mayavi')

Display phonon modes

get_QE_structure()

Gets structure from a QE input

get_atom()

Gets atomic attributes from a poscar structure file

get_ecutwfc()

Gets standard ecutwfc

get_mass()

get mass

get_poscar()

Gets the structure file from materials project

get_pseudo(name='pseudo')

Automatically download pseudopotential from pseudodojo

get_response(atoms)

get_supercell(supercell=None, pl_vec=None)

returns the co-ordinates for supercell

get_xyz(supercell=None)

property structure_params

Returns structure parameters as a dictionary Units are Angstrom for variables in Cartesian

property structure_params_summary

Print structure as a formatted string

EPWpy.structure.lattice.get_supercell(atom_pos2, natoms, mat, lattice_vec, a, supercell)

Builds supercell of a certain size

EPWpy.structure.lattice.get_supercell_pl(atom_pos2, natoms, mat, lattice_vec, a, supercell, pl_vec)

Builds supercell of a certain size for the polarization vector