Cell
=======

The cell convention used in OpenFTS is the same as LAMMPS `https://lammps.sandia.gov/doc/Howto_triclinic.html`. Where the cell shape tensor is given by

.. math::

    \pmb{h} = 
  \begin{pmatrix}
  L_x &  xy & xz \\
  0   & L_y & yz \\
  0   &   0 & L_z \\
  \end{pmatrix}

Arguments:

  * `dimension` (int) - Dimension of cell. Options:`1`, `2`, `3`
  * `cell_lengths` (float array) - Diagonals of cell tensor: :math:`L_x`, :math:`L_y`, :math:`L_z`. Length is equal to number of dimensions.
  * `tilt_factors` (float array) - Tilt factors: `xy`, `xz`, `yz`. Length depends on dimsnsion (1d = 0, 2d = 1, 3d = 3).
  * `cell_scale` (float) - Factor to uniformly scale the cell
  * `length_unit` (string) - Length units to perform the simulation in. Options:

    * `Rg` - in units of reference polymer radius of gyration :math:`\sqrt{b_{ref}^2 N_{ref} / 6}` (continuous chains) or :math:`\sqrt{b_{ref}^2 (N_{ref} - 1) / 6}` (discrete chains)
    * `b` - in units of :math:`b_{ref}` 

.. note:: 

  Internally, OpenFTS always stores cell dimensions in units of `Rg`. Unit conversion are performed upon input/output.


Example (python) ::

  import openfts
  fts = openfts.OpenFTS()
  ... 
  fts.cell(cell_scale=1.0,cell_lengths=[4.3],dimension=1,length_unit='Rg')
  ...

Example (json) ::
    
    "cell": {
      "cell_scale": 3.8,
      "cell_lengths": [1.0, 0.866],
      "tilt_factors": [0.57735],
      "dimension": 2,
      "length_unit": "Rg"
    },