Get box from lengths and angles#

Building 3x3 periodic box matrices from lengths and angles.

The function molsysmt.pbc.get_box_from_lengths_and_angles() constructs a standard \(3\times 3\) box matrix (or array of matrices) from edge lengths \((a, b, c)\) and crystallographic angles \((\alpha, \beta, \gamma)\).

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.pbc.get_box_from_lengths_and_angles().

Basic usage#

Let’s construct an orthorhombic periodic box matrix from specified dimensions and 90-degree angles:

import molsysmt as msm
import pyunitwizard as puw

lengths = puw.quantity([[4.0, 5.0, 6.0]], 'nm')
angles = puw.quantity([[90.0, 90.0, 90.0]], 'degrees')
box = msm.pbc.get_box_from_lengths_and_angles(lengths, angles)
print('Constructed box matrix:\n', box)

Constructed box matrix:
 [[[4.0 0.0 0.0]  [0.0 5.0 0.0]  [0.0 0.0 6.0]]] nanometer

Constructing triclinic box matrices#

Non-orthogonal angles generate corresponding triclinic/skewed cell matrices:

lengths_tri = puw.quantity([[3.0, 3.0, 3.0]], 'nm')
angles_tri = puw.quantity([[60.0, 60.0, 90.0]], 'degrees')
box_tri = msm.pbc.get_box_from_lengths_and_angles(lengths_tri, angles_tri)
print('Triclinic box matrix:\n', box_tri)

Triclinic box matrix:
 [[[3.0 0.0 0.0]  [0.0 3.0 0.0]  [1.5 1.5 2.12132]]] nanometer