Atomic displacement DoF

Simple cubic with atomic displacement DoF

This example constructs the prim for simple cubic crystal system with atomic displacement degrees of freedom (DoF).

To construct this prim, the following must be specified:

• the lattice vectors

• basis site coordinates

• occupant DoF

• atomic displacement DoF

This example uses a fixed “A” sublattice for occ_dof, which by default are created as isotropic atoms.

import numpy as np
import libcasm.xtal as xtal

# Lattice vectors
lattice_column_vector_matrix = np.array([
    [1., 0., 0.],  # a
    [0., 1., 0.],  # a
    [0., 0., 1.],  # a
]).transpose()  # <--- note transpose
lattice = xtal.Lattice(lattice_column_vector_matrix)

# Basis sites positions, as columns of a matrix,
# in fractional coordinates with respect to the lattice vectors
coordinate_frac = np.array([
    [0., 0., 0.],  # coordinates of basis site, b=0
]).transpose()

# Occupation degrees of freedom (DoF)
occ_dof = [
    ["A"],  # occupants allowed on basis site, b=0
]

# Local continuous degrees of freedom (DoF)
disp_dof = xtal.DoFSetBasis("disp")  # Atomic displacement
local_dof = [
    [disp_dof],  # allow displacements on basis site b=0
]

# Construct the prim
prim = xtal.Prim(lattice=lattice,
                 coordinate_frac=coordinate_frac,
                 occ_dof=occ_dof,
                 local_dof=local_dof,
                 title="simple_cubic_disp")

This prim as JSON: simple_cubic_disp.json