fix nufeb/growth/eps command

Syntax

fix ID group-ID nufeb/growth/eps sub-ID keyword value ...

  • ID = user-assigned name for the fix

  • group-ID = ID of the group atoms to apply the fix to

  • sub-ID = ID for organic substrate

  • zero or more keyword/value pairs may be appended

  • keyword = growth or yield or decay

    decay value = decay rate

Examples

group EPS type 1
grid_style nufeb/chemostat 1 sub

fix f_geps EPS nufeb/growth/eps sub decay 2e-6

Description

Perform EPS (extracellular polymeric substances) decay to the atoms defined in group-ID. The affected atoms are considered as EPS, which have a spherical shape (see atom_style coccus). The model assumes that EPS dissolves into organic substrate in a constant decay rate.

The fix is called at each biological step (see run_style nufeb) to update atom attributes. The value of the organic substrate ID keyword sub-ID must be consistent with the name defined in the grid_style chemostat command. The following forward Euler method is implemented to update the mass (m) of each atom in the group:

\[ \begin{align}\begin{aligned}m' & = m - b_{decay} \cdot \Delta t\\\hfill\end{aligned}\end{align} \]

The new mass is then used to update the diameter.

Restrictions

This fix is not compatible with the following commands: