atom_style bacillus command

Syntax

atom_style bacillus

Description

Define the bacillus style of atoms in a simulation. This command must be used before a simulation is setup via a read_data*, read_restart*, or create_box* command.

_images/rod.png

For the bacillus style, atoms are represented as rods that model rod-shaped microbes. Each microbe stores a set per-atom attributes, including length, diameter, mass, biomass, coordinate, as well as the mechanical attributes used in physical (DEM) processes (e.g, force, velocity, inertia, angular momentum, etc).

The shape is implemented as cylinder with hemispherical caps. Therefore, cell length is the height of the cylinder (i.e, distance between the two hemispherical caps), and cell width is the diameter of the cap. The mass and biomass are the wet and dry weights of microbes, respectively.

Initial microbes and their attributes can be specified in 3 ways:

  • use read_data* command to explicitly create each individual microbe with the initial attributes from a data file;

  • use create_atom* and set commands to create microbes on a lattice, or a single microbe, or a random collection of microbes;

  • use read_restart* command to read previously saved system configuration from a restart file.