Getting volume from box lengths and angles#

Computing periodic-cell volume directly from edge lengths and crystallographic angles.

API documentation

molsysmt.pbc.get_volume_from_lengths_and_angles()

Added in version 1.0.0.

import numpy as np
import molsysmt as msm

MolSysMT uses lengths (a, b, c) and angles (alpha, beta, gamma), where alpha is between b and c, beta is between a and c, and gamma is between a and b. The function evaluates the closed-form triclinic-cell expression directly, avoiding precision loss from constructing an intermediate rounded box matrix.

lengths = [[2.0, 2.0, 3.0]] * msm.pyunitwizard.unit('nm')
angles = [[90.0, 90.0, 60.0]] * msm.pyunitwizard.unit('degrees')
volume = msm.pbc.get_volume_from_lengths_and_angles(lengths, angles)

expected = 6.0 * np.sqrt(3.0)
np.testing.assert_allclose(
    msm.pyunitwizard.get_value(volume, to_unit='nm**3'),
    [expected],
    rtol=0.0,
    atol=1.0e-12,
)
volume

The analytic result is 6*sqrt(3) nm^3. This example is part of MolSysMT’s Scientific Truth Suite rather than a cross-implementation parity check.