6. Commands

This section lists all NUFEB commands and extended LAMMPS commands (with asterisk *) that can be used for modelling microbial systems. Some commands are part of NUFEB or LAMMPS optional packages, which means they cannot be used unless the packages were included when building NUFEB.

Note

The section only lists the LAMMPS commands which have been modified or extended for microbial modelling. Many of the commands not listed here are also compatible with NUFEB package and their descriptions are available in LAMMPS user manual.

Microbes and substrates
Biological processes
Physical processes
Post-physical processes
Chemical processes
Reactor processes
Computes
Outputs
Run

6.1. Microbes and substrates 

atom_style coccus: spherical microbe
atom_style bacillus: rod-shaped microbe
fix nufeb/property/cycletime: microbe attribute: cell cycle time
fix nufeb/property/generation: microbe attribute: cell generation
grid_modify: modify grid attributes
grid_style chemostat: grid style for chemostat coupling
read_data*: read external data file
set*: set one or more properties of atoms

6.2. Biological processes 

fix nufeb/growth/anammox: growth model for Anammox bacteria
fix nufeb/growth/aob: growth model for Ammonia-Oxidizing Bacteria
fix nufeb/growth/cyano: growth model for cyanobacteria
fix nufeb/growth/ecoli: growth model for E.coli
fix nufeb/growth/energy: energy-based growth model
fix nufeb/growth/eps: growth model for Extracellular Polymeric Substances
fix nufeb/growth/het: growth model for heterotroph
fix nufeb/growth/monod: simple Monod-based growth model
fix nufeb/growth/nob: growth model for Nitrite-Oxidizing Bacteria
fix nufeb/growth/simple: exponential growth model
fix nufeb/division/coccus: division for coccus
fix nufeb/division/bacillus: division for bacillus
fix nufeb/eps_secretion: EPS secretion from heterotroph
fix nufeb/death/diameter: microbe death (critical diameter)

6.3. Physical processes 

pair_style bacillus: pairwise interaction for bacillus
pair_style gran/hooke: pairwise interaction for coccus
fix nufeb/adhesion: adhesion force
fix nufeb/adhesion/eps: EPS adhesion force
fix nufeb/adhesion/bacillus: adhesion force for bacillus
fix nve/bacillus/limit: constant NVE update for bacillus
fix nufeb/shear: shear force
fix nufeb/wall_adhesion: wall-microbe adhesion force
fix wall/gran: wall-microbe frictional force

6.4. Post-physical processes 

fix nufeb/diffusion_coeff: dynamic diffusion coefficient

6.5. Chemical processes 

fix nufeb/diffusion_reaction: substrate diffusion and reaction
fix nufeb/gas_liquid: gas liquid transfer
fix nufeb/reactor/gas_balance: mass balance in gas phase
fix nufeb/reactor/solute_balance: mass balance in solute phase

6.6. Reactor processes 

fix nufeb/boundary_layer: dynamic diffusion boundary layer

6.7. Computes 

compute nufeb/ave_conc: average substrate concentration
compute nufeb/ave_length: average microbe length
compute nufeb/density: biomass density
compute nufeb/volume: total microbe volume

6.8. Outputs 

dump image: dump JPEG, PNG or PPM image files
dump movie: dump movie file
dump modify: modify parameters of dump command
dump vtk: dump microbe data in VTK format
dump vtk/grid: dump grid data in VTK format
dump hdf5: dump data in hdf5 format

6.9. Run 

run_style nufeb: time integrator for NUFEB simulation