Thank you very much for your reply.
These are the parameters I am using for my projecy. Any guidence on what else needs to be changed would be greatly appreciated thank you. The waveguide is AlAs and I added this in the MODE template file structure group and implemented a relevant Sellmeier equation for this in the runFDEmaterial script. The MODE simulation seems to be working correctly along with good gain curves, it just seems to be the TWLM with issues. Other than the waveguide change, the barrier and well materials are the same as the template with only alloy changes being made as per the documentation with updating of the input file and the MQW template file materials.
One thing I have come accross whilst simulating is that changing the common.centre frequency parameter sometimes causes unstable behaviour in simulations and crashing. If I manually change the spectrum start and end variables in the runTWLM simulation to cover the simulated lasing frequency of 212THz then the simulation seems to run smoothly. However if the simulation is run with the center frequency parameter changed in the input.lsf script to c/1414e-9 i.e. 212THz, as shown in the screenshot, then the simulation is unstable.