.. hash=d9c35f7c887b713be2df5f60058f5b9fd86823db .. Generated: 21/09/22 18:48 .. Do not edit! ============== ``symmetrise`` ============== By **Pierre Beaujean** (`pierre.beaujean@unamur.be `_). **Version 0.1** (Development). Synopsis ++++++++ ``symmetrise`` - Detect point group, symmetrise molecule and outputs it as XYZ .. program:: symmetrise .. code-block:: console usage: symmetrise [-h] [-v] [-t TOLERANCE] [-s] [-u] [-S] [infile] Positional arguments: .. option:: infile source of the derivatives Optional arguments: .. option:: -h, --help show this help message and exit .. option:: -v, --version show program's version number and exit .. option:: -t, --tolerance Tolerance threshold .. option:: -s, --symmetrise Fully symmetrise the molecule (involve small displacements and the full generation of the group) .. option:: -u, --uniques Get unique atoms (implies `-s`) .. option:: -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 :math:`\#\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!!