fix nufeb/eps_secretion command

Syntax

fix ID group-ID nufeb/eps_secretion type-eps group-eps ratio eps_den seed

  • ID = user-assigned name for the fix

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

  • eps-type = numeric type of EPS

  • group-eps = ID of the EPS group

  • ratio = extraction threshold ratio

  • eps_den = density of EPS

  • seed = random # seed (positive integer)

Examples

#--- examples/biofilm-heterotroph ---#

group HET type 1
group EPS type 2

fix eps_ext HET nufeb/eps_secretion 2 EPS 1.3 30 1234

Description

Perform EPS secretion to the atoms defined in group-ID. The fix requires fix nufeb/growth/het to accomplish as the command updates the outer_mass and outer_diameter of the atoms. Atoms using other growth models do not form an EPS shell.

The keywords eps-type and group-eps are the pre-defined numeric type and group ID that are utilised to associate EPS. EPS secretion occurs when the ratio between outer_diameter and (inner) diameter of an atom exceeds the threshold value (ratio). Upon secretion, 40% - 60% of the outer_mass becomes a separate EPS particle and is randomly placed next the to the parent.

The random seed is used for the stochastic operation, and the random numbers generated by each processor are different. This means the coordinates of individual atoms will be different when running on different numbers of processors.

Restrictions

This fix is only compatible with the following commands: