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One of our products, OptiSPICE, allows for the complete design and analysis of electrical and optical components. This software is based on the SPICE nodal simulation model (for electrical circuits) and has been extended to include optical components using the same concept (with the exception we model the phase and magnitude of the optical signal thus giving a full picture of the optical signal behavior within the system; including reflections, phase shifts, interference, etc.). Once a design is set, you can then run a time-domain transient analysis on the project to assess system performance and behavior. All our components are modelled using industry standard Netlists, making it straightforward to incorporate commercially available components.
Based on the requirements described above, it should be possible to model the majority of the system (if not all), from the laser source (with input signals and driving circuitry) to the photo-detector and associated electrical circuitry (such as TIAs). We also have a free space optics component which could be used to model the signal path between the laser and receiver. As there are many types of models for atmospheric propagation, it is possible that we may not have an exact match for your Lidar system. If this is the case, we can use an interface with Matlab to allow you to model atmospheric effects.
One of our other products, OptiSystem, could fit your needs for simulating the optical system level design. I have attached an example OptiSystem file of a FMCW Lidar System with Direct Detection. I have also included a Matlab file that OptiSystem calls to simulate the free space channel model.
To your final question, yes we do have specific offers for academic institutions.
Reference for simulation: Ahmed H. Elghandour and Chen D. Ren, ” Modeling and comparative study of various detection techniques for FMCW LIDAR using optisystem “, Proc. SPIE 8905, International Symposium on Photoelectronic