NUFEB-manual
0.0.1
User Guide
1. Introduction
2. Install NUFEB on Linux & Mac
3. Install NUFEB on Windows
4. Run NUFEB
5. Input Script
6. Commands
7. Optional packages
Tutorial
1. Workshop: modelling microbial dynamics in soil
2. Extend NUFEB with new growth model
3. Managing Multiple Simulations with Snakemake
4. Editing NUFEB code
5. Adding Type VI Secretion System Interactions
Cookbook
1. Stopping simulations at a consistent percent biomass
2. Creating a file to indicate the run completed successfully
3. Altering the dimensions of the simulation box
4. Saving simulation output to a CSV file
5. Computing species relative abundances
Command Reference
Microbes and substrates
Biological processes
Physical processes
Post-physical processes
Chemical processes
Reactor processes
Computes
Outputs
Run
NUFEB-manual
Index
Index
A
|
C
|
D
|
F
|
G
|
N
|
P
|
R
|
S
A
atom_style bacillus
atom_style coccus
C
compute nufeb/ave_conc
compute nufeb/ave_length
compute nufeb/density
compute nufeb/volume
D
dump hdf5
dump image
dump modify
dump movie
dump vtk
dump vtk/grid
F
fix nufeb/adhesion
fix nufeb/adhesion/bacillus
fix nufeb/adhesion/eps
fix nufeb/boundary_layer
fix nufeb/death/diameter
fix nufeb/diffusion_coeff
fix nufeb/diffusion_reaction
fix nufeb/division/bacillus
fix nufeb/division/coccus
fix nufeb/eps_secretion
fix nufeb/gas_liquid
fix nufeb/growth/aob
fix nufeb/growth/cyano
fix nufeb/growth/ecoli
fix nufeb/growth/energy
fix nufeb/growth/eps
fix nufeb/growth/het
fix nufeb/growth/monod
fix nufeb/growth/nob
fix nufeb/growth/simple
fix nufeb/property/cycletime
fix nufeb/property/generation
fix nufeb/property/plasmid
fix nufeb/reactor/gas_balance
fix nufeb/reactor/solute_balance
fix nufeb/shear
fix nufeb/T6SS/contact
fix nufeb/T6SS/lysis
fix nufeb/wall_adhesion
fix nve/bacillus/limit
fix wall/gran
G
grid_modify
grid_style chemostat
N
nufeb/growth/anammox
P
pair_style bacillus
pair_style gran/hooke
R
read_data
run_style nufeb
S
set