NUFEB (Newcastle University Frontier in Engineering Biology) is an open source tool for 3D individual-based simulation of microbial communities. The tool is built on top of the molecular dynamic simulator LAMMPS, and extended with features for microbial modelling. For more details about NUFEB software and model look at our paper.
NUFEB is distributed under the terms of the GNU Public License. The development has been funded by the UK’s EPSRC EP/K039083/1 Frontiers in Engineering Biology project.
Installation guide, tutorial, example videos, and more details can be found in NUFEB Wiki page and User Manual
The NUFEB distribution includes the following files and directories:
README this file LICENSE the GNU General Public License (GPL) install.sh script for building NUFEB uninstall.sh script for uninstalling NUFEB doc user manual and other documentation examples test problems and cases used in publications lib libraries NUFEB can be linked with lammps LAMMPS source code post-processing Povray visualisation routine src source files thirdparty thirdparty tools
Get NUFEB source code and submodules for its thirdparty libraries:
git clone https://github.com/nufeb/NUFEB --recursive
NUFEB requires gcc/g++ and openmpi for a successful build.
Build NUFEB:
./install.sh
Run a case in /examples after building NUFEB, for example:
cd examples/simple-growth mpirun -np 4 lmp_mpi -in Inputscript.lammps
Developers:
Bowen Li: [email protected]
Denis Taniguchi: [email protected]