Bond length
===========

The bond length between two atoms is one of the easiest CVs to be used in a metadynamics \
simulation. It is simply defined by the length of the vector between to atoms :math:`i` and \
:math:`j`

.. math::
    d_{ij} = \left| r_{j}-r_{i} \right|.

The use of the bond length is invoked by the following block in the `meta-config.json` file::

    "collective variables": [
      {
        "type": "bond",
        "name": "bond length between two atoms",
        "atoms": [i, j]
      },
      ...
    ]

Apart from type and name, only the indices of the contributing ``"atoms"`` are needed.