The files "ElastoHydro.edp" and "ElastoCapillaryHydro.edp" are FreeFem++ scripts for the simulation of bacterial gliding on soft substrates. While the first script only account for viscous and elastic forces, the second one also accounts for capillarity effects.
Note that the scripts correspond to a dimensionless formulation of the problem with the main parameters being the softness parameters (eta) and capillary numbers (Ca, Cas), the lubrication parameter (eps), the interface thickness (a), the surface tension ratio (tref).
For each script:
1- Create the mesh
2- Choose a certain number of parameters: bacterial membrane length (L) and amplitude (amp), softness parameter (eta), Ca, eps, ...
3- Choose carefully the increment step for Newton's iteration. These iterations can be made over a loop of various parameters (eta, Ca, etc.)
4- Run the code with freefem++ (https://freefem.org/)
5- There are several output files, but the user can add or suppress as needed. For now, there are 3 files, respectively for instantaneous variables (position, velocity, etc), for time-averaged scalar (position, velocity, etc) and time-averages fields (pressure, substrate deformations, stresses, etc.).