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
pair_style bacillus command
pair_style gran/hooke command
fix nufeb/adhesion command
fix nufeb/adhesion/bacillus command
fix nufeb/adhesion/eps command
fix nve/bacillus/limit command
fix nufeb/shear command
fix nufeb/wall_adhesion command
fix wall/gran command
Post-physical processes
Chemical processes
Reactor processes
Computes
Outputs
Run
NUFEB-manual
Physical processes
fix nve/bacillus/limit command
View page source
fix nve/bacillus/limit command