molsysmt.pbc.get_volume_from_lengths_and_angles#

molsysmt.pbc.get_volume_from_lengths_and_angles(box_lengths, box_angles)[source]#

Computing box volume from lengths and angles.

Parameters:

  • box_lengths (quantity) – Edge lengths (a, b, c).

  • box_angles (quantity) – Angles (alpha, beta, gamma).

Returns:

Volume in cubic nanometers.

Return type:

quantity

Notes

The volume is evaluated directly as

abc * sqrt(1 + 2 cos(alpha) cos(beta) cos(gamma) - cos(alpha)**2 - cos(beta)**2 - cos(gamma)**2).

This avoids propagating the six-decimal matrix rounding performed by molsysmt.pbc.get_box_from_lengths_and_angles().

See also

molsysmt.pbc.get_volume_from_box()

Computing the volume from a box matrix.

Examples

Computing the volume of a triclinic box with a 60-degree gamma angle:

>>> import numpy as np
>>> import molsysmt as msm
>>> 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)
>>> value = msm.pyunitwizard.get_value(volume, to_unit='nm**3')
>>> np.testing.assert_allclose(value, [6.0 * np.sqrt(3.0)], atol=1.0e-12)

User guide

See the User Guide tutorial for a worked example: molsysmt.pbc.get_volume_from_lengths_and_angles().

Added in version 1.0.0.