fmo_oct

Code for optimization of FMO complex transport

Prerequisites

• qdyn library (Koch group, University of Kassel)

Overview

compile with make.

Available programs:

• fmo_oct: Starting from the pulse defined in the config file, run a Krotov optimization.

• fmo_prop: Propagate the optimized pulse for analysis purpose. You may also propagate the guess pulse by specifying 'propagate_guess' in the config file

How to run

• Create a runfolder (e.g. mkdir r001) and change to it
• Create a config file using the python script ../scripts/generate_config.py (and review it)
• Create the dissipator using the python script ../scripts/generate_dissipator.py
• Go back to the parent folder and run the optimal control (./fmo_oct r001)
• After the optimization finishes, you can run the program for the propagation (./fmo_prop r001)