symmetrise

By Pierre Beaujean (pierre.beaujean@unamur.be).

Version 0.1 (Development).

Synopsis

symmetrise - Detect point group, symmetrise molecule and outputs it as XYZ

usage: symmetrise [-h] [-v] [-t TOLERANCE] [-s] [-u] [-S] [infile]

Positional arguments:

infile

source of the derivatives

Optional arguments:

-h, --help

show this help message and exit

-v, --version

show program’s version number and exit

-t, --tolerance

Tolerance threshold

-s, --symmetrise

Fully symmetrise the molecule (involve small displacements and the full generation of the group)

-u, --uniques

Get unique atoms (implies -s)

-S, --same-output

Output in the same format as the input

More information

Detect point group and symmetrise molecule.

The tolerance option (--tolerance) depends of the quality of an eventual optimisation: 1e-3 (the default) is ok in most cases, but may results in a larger group than it should in a few cases, so lower this threshold if any.

By default, the script only orient the molecule w.r.t. symmetry elements, so that it matches its group. But --symmetrise and/or --uniques implies to generate the whole group, which may take time for large ones (thus very symmetrical molecules, with \(\#\mathcal{G} \geq 60\)). Then, it generates uniques atoms, and eventually the whole molecule back (if only --symmetrise is set).

Warning

--symmetrise and --uniques do not work for icosahedral molecules!!