In general, the harness script is called by the FRESHS client with command line arguments, which are constructed by the client from the server message and can contain user-defined elements (see the configuration files for more details). For calculating trajectory fragments, the harness script should include the following elements:
equilibration/initial_configroutine to set up the system
save_snapshotroutine for saving the complete system state
load_snapshotroutine for loading a full system snapshot
calculate_rcroutine for calculating the reaction coordinate
Here is an example for an ESPResSo harness script using FFS, written in TCL.
Here is an example for a FFS LAMMPS harness script using the pythonlib of LAMMPS. This script can analogously be converted to a compiled C++ simulation script, if LAMMPS is not used as python library.