atom_style coccus command

Syntax

atom_style coccus

Description

Define the coccus 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/coccus.png

For the coccus style, atoms are represented as spheres that model spherical-shaped microbes. Each microbe stores a set per-atom attributes, including: including mass, biomass, outer_mass, diameter, outer_diameter, coordinate, as well as mechanical attributes used in physical (DEM) processes (e.g, force, velocity, etc):

The diameter and outer_diameter attributes specify the inner and outer sizes of a spherical microbe, respectively. Some microorganism excrete extracellular polymeric substances (EPS) which is initially accumulated as an extra shell beyond the microbes. The outer_diameter is defined as the sum of EPS shell depth and the inner diameter, while the outer_mass represents the weight of EPS shell. The mass and biomass attributes correspond to 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.