Implementing bulk creep dynamics requires application of a constant shear stress.
Shear can be done using the SLLOD equations of motion, however these impose a homogeneous flow profile to the sample. It would be better to control the shear by modifying the shear rate based on a feedback loop which measures the stress at each timestep. We then need to add DPD dynamics to adsorb some of the energy created by the shear and prevent velocity drift.
The gel_setup folder contains a Python script to initialise a configuration of a polydisperse gel described by a Morse potential. It is easier to create a LAMMPS dump file and read this in than define this potential entirely using a LAMMPS script.
The lammps_scripts folder contains example scripts for equilibrating and shearing a gel configuration at constant stress. This is the method used in https://doi.org/10.1039/C8SM01432A
The strain_wrapping folder contains a script for unwrapping the measured strain from LAMMPS output files for analysis.