Cell

class openfts.Cell(cell_scale=None, cell_lengths=None, tilt_factors=None, dimension=None, length_unit=None)

TODO Simple one-sentence explanation of Cell object

Parameters:

  • dimension (int) – Dimension of cell. Options:1, 2, 3

  • cell_lengths (float array) – Diagonals of cell tensor: \(L_x\), \(L_y\), \(L_z\). Length is equal to number of dimensions.

  • tilt_factors (float array) – Tilt factors: xy, xz, yz. Length depends on dimension (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, b. See note below for explanation.

Note

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

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

  • b - in units of \(b_{ref}\)

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

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

Example (python)

import openfts
fts = openfts.OpenFTS()
...
fts.cell = openfts.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"
},